@article {pmid30545868,
year = {2018},
author = {Gibbons, A},
title = {Why modern humans have round heads.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6420},
pages = {1229},
doi = {10.1126/science.362.6420.1229-a},
pmid = {30545868},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Brain/*anatomy & histology ; *DNA, Ancient ; Head/*anatomy & histology ; Humans ; Neanderthals/*genetics ; },
}

Animals
*Biological Evolution
Brain/*anatomy & histology
*DNA, Ancient
Head/*anatomy & histology
Humans
Neanderthals/*genetics

@article {pmid30633908,
year = {2019},
author = {O'Connor, TD},
title = {Native American Genomic Diversity through Ancient DNA.},
journal = {Cell},
volume = {176},
number = {1-2},
pages = {405-406},
doi = {10.1016/j.cell.2018.12.033},
pmid = {30633908},
issn = {1097-4172},
}

@article {pmid29933384,
year = {2018},
author = {Matsumura, H and Shinoda, KI and Shimanjuntak, T and Oktaviana, AA and Noerwidi, S and Octavianus Sofian, H and Prastiningtyas, D and Nguyen, LC and Kakuda, T and Kanzawa-Kiriyama, H and Adachi, N and Hung, HC and Fan, X and Wu, X and Willis, A and Oxenham, MF},
title = {Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198689},
pmid = {29933384},
issn = {1932-6203},
mesh = {Anthropometry ; Asia, Southeastern ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Datasets as Topic ; *Human Migration ; Humans ; Skull/*anatomy & histology ; },
abstract = {The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712-5591cal BP to 1864-1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin's standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.},
}

Anthropometry
Asia, Southeastern
DNA, Ancient/*analysis
DNA, Mitochondrial/*analysis
Datasets as Topic
*Human Migration
Humans
Skull/*anatomy & histology

@article {pmid30628076,
year = {2019},
author = {Tackney, J and Jensen, AM and Kisielinski, C and O'Rourke, DH},
title = {Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska.},
journal = {American journal of physical anthropology},
volume = {168},
number = {2},
pages = {303-317},
doi = {10.1002/ajpa.23746},
pmid = {30628076},
issn = {1096-8644},
support = {OPP-0732846//Office of Polar Programs/ ; OPP-0732857//Office of Polar Programs/ ; OPP-0637246//Office of Polar Programs/ ; OPP-0535356//Office of Polar Programs/ ; OPP-1460387//Office of Polar Programs/ ; OPP-0820790//Office of Polar Programs/ ; OPP-0726253//Office of Polar Programs/ ; OPP-0820790//National Science Foundation (NSF)/ ; ARC-0726253//National Science Foundation (NSF)/ ; OPP-1460387//National Science Foundation (NSF)/ ; OPP-0535356//National Science Foundation (NSF)/ ; OPP-0637246//National Science Foundation (NSF)/ ; OPP-0732857//International Polar Year grant/ ; OPP-0732846//International Polar Year grant/ ; },
abstract = {OBJECTIVES: The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat.

MATERIALS AND METHODS: We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements.

RESULTS: We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations.

DISCUSSION: The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.},
}

@article {pmid30622634,
year = {2019},
author = {Wales, N and Akman, M and Watson, RHB and Sánchez Barreiro, F and Smith, BD and Gremillion, KJ and Gilbert, MTP and Blackman, BK},
title = {Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement.},
journal = {Evolutionary applications},
volume = {12},
number = {1},
pages = {38-53},
doi = {10.1111/eva.12594},
pmid = {30622634},
issn = {1752-4571},
abstract = {Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.},
}

@article {pmid30615665,
year = {2019},
author = {Harris, AJT and Duggan, AT and Marciniak, S and Marshall, I and Fuller, BT and Southon, J and Poinar, HN and Grimes, V},
title = {Dorset Pre-Inuit and Beothuk foodways in Newfoundland, ca. AD 500-1829.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210187},
doi = {10.1371/journal.pone.0210187},
pmid = {30615665},
issn = {1932-6203},
abstract = {Archaeological research on the Canadian island of Newfoundland increasingly demonstrates that the island's subarctic climate and paucity of terrestrial food resources did not restrict past Pre-Inuit (Dorset) and Native American (Beothuk) hunter-gatherer populations to a single subsistence pattern. This study first sought to characterize hunter-gatherer diets over the past 1500 years; and second, to assess the impact of European colonization on Beothuk lifeways by comparing the bone chemistry of Beothuk skeletal remains before and after the intensification of European settlement in the early 18th century. We employed radiocarbon dating and stable carbon and nitrogen isotope ratio analysis of bulk bone collagen from both Dorset (n = 9) and Beothuk (n = 13) cultures, including a naturally mummified 17th century Beothuk individual. Carbon and nitrogen isotope analysis of 108 faunal samples from Dorset and Beothuk archaeological sites around the island were used as a dietary baseline for the humans. We combined our results with previously published isotope data and radiocarbon dates from Dorset (n = 12) and Beothuk (n = 18) individuals and conducted a palaeodietary analysis using Bayesian modelling, cluster analysis and comparative statistical tests. Dorset diets featured more marine protein than those of the Beothuk, and the diets of Beothuk after the 18th century featured less high trophic level marine protein than those of individuals predating the 18th century. Despite inhabiting the same island, Dorset and Beothuk cultures employed markedly different dietary strategies, consistent with interpretations of other archaeological data. Significantly, European colonization had a profound effect on Beothuk lifeways, as in response to the increasing European presence on the coast, the Beothuk relied more extensively on the limited resources of the island's boreal forests and rivers.},
}

@article {pmid30586168,
year = {2018},
author = {Ziesemer, KA and Ramos-Madrigal, J and Mann, AE and Brandt, BW and Sankaranarayanan, K and Ozga, AT and Hoogland, M and Hofman, CA and Salazar-García, DC and Frohlich, B and Milner, GR and Stone, AC and Aldenderfer, M and Lewis, CM and Hofman, CL and Warinner, C and Schroeder, H},
title = {The efficacy of whole human genome capture on ancient dental calculus and dentin.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23763},
pmid = {30586168},
issn = {1096-8644},
support = {319209//H2020 European Research Council/ ; 649307DK-TAF 5662//Horizon 2020 Framework Programme/ ; BCS 1516633, BCS-1528698//National Science Foundation/ ; },
abstract = {OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.

MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing.

RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction.

DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.},
}

@article {pmid30581455,
year = {2018},
author = {Aguiar, TS and Torrecilha, RBP and Milanesi, M and Utsunomiya, ATH and Trigo, BB and Tijjani, A and Musa, HH and Lopes, FL and Ajmone-Marsan, P and Carvalheiro, R and Neves, HHR and do Carmo, AS and Hanotte, O and Sonstegard, TS and Garcia, JF and Utsunomiya, YT},
title = {Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {627},
doi = {10.3389/fgene.2018.00627},
pmid = {30581455},
issn = {1664-8021},
abstract = {Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.},
}

@article {pmid30558455,
year = {2018},
author = {Varano, S and Gaspari, L and De Angelis, F and Scano, G and Contini, I and Martínez-Labarga, C and Rickards, O},
title = {Mitochondrial characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain).},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/03014460.2018.1559355},
pmid = {30558455},
issn = {1464-5033},
abstract = {This survey reports the mitochondrial data of two Spanish populations living in the Vera and Bejar valleys, on the opposite slopes of the Sierra de Gredos (Central Spain), which crosses Spain east to west. The aim of the study was to characterise the mitochondrial genetic pool of the Vera and Bejar populations to investigate a putative mitogenetic differentiation between them, evidence that would support the role of the Sierra de Gredos as a genetic barrier in their micro-evolutionary histories. Blood samples of 137 people (66 from Vera and 71 from Bejar) were collected and mtDNA hypervariable regions I and II (HVR-I and HVR-II) were dissected along with several mtDNA- coding region SNPs. The main European mitochondrial lineages have been found both in Vera and in Bejar, together with the typical African haplogroups L (in Vera) and U6 (in Bejar). FST value and the 95% credible regions calculated for haplogroup frequencies do not reveal genetic differentiation among the populations. In conclusion, Vera and Bejar contain an expected mitochondrial variability within them, but they do not seem to be genetically different from each other, leading us to conclude that the Sierra de Gredos is not a significant genetic barrier in their maternal genetic history.},
}

@article {pmid30556221,
year = {2018},
author = {Afonso, C and Nociarova, D and Santos, C and Martinez-Labarga, C and Mestres, I and Duran, M and Malgosa, A},
title = {Sex selection in late Iberian infant burials: Integrating evidence from morphological and genetic data.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {},
number = {},
pages = {e23204},
doi = {10.1002/ajhb.23204},
pmid = {30556221},
issn = {1520-6300},
support = {//Tona City Council/ ; //Museu d'Arqueologia de Catalunya/ ; 2017SGR1630//Generalitat de Catalunya/ ; SFRH/BD/76765/2011//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {OBJECTIVE: The aim of this study was to analyze the infant burials found inside Iberian homes in relation to a possible case of sex selection.

METHODS: The study included the remains of 11 infant individuals buried under the 10 houses excavated in the late Iberian village of Camp de les Lloses (Tona, Barcelona, Spain). Sex was determined using genetic analysis.

RESULTS: Our results showed that almost all the burials were females. However, the age interval of death was wide enough to weaken the premise of infanticide, and the burials probably represent cases of natural death.

DISCUSSION: Infanticide in its different forms has long been argued as an explanation for the infant remains found throughout various burial sites. Many authors thought that infanticide, mainly femicide, was the main method of population control in ancient times. However, there is no anthropological evidence (age distribution and sex analyzed genetically) to support the intentional killing of females in this or in other cases. We hypothesized that there was a positive selection for females to be buried inside the houses, probably related to their benefactor roles.},
}

@article {pmid30554877,
year = {2018},
author = {Mohni, KN and Wessel, SR and Zhao, R and Wojciechowski, AC and Luzwick, JW and Layden, H and Eichman, BF and Thompson, PS and Mehta, KPM and Cortez, D},
title = {HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2018.10.055},
pmid = {30554877},
issn = {1097-4172},
abstract = {Abasic sites are one of the most common DNA lesions. All known abasic site repair mechanisms operate only when the damage is in double-stranded DNA. Here, we report the discovery of 5-hydroxymethylcytosine (5hmC) binding, ESC-specific (HMCES) as a sensor of abasic sites in single-stranded DNA. HMCES acts at replication forks, binds PCNA and single-stranded DNA, and generates a DNA-protein crosslink to shield abasic sites from error-prone processing. This unusual HMCES DNA-protein crosslink intermediate is resolved by proteasome-mediated degradation. Acting as a suicide enzyme, HMCES prevents translesion DNA synthesis and the action of endonucleases that would otherwise generate mutations and double-strand breaks. HMCES is evolutionarily conserved in all domains of life, and its biochemical properties are shared with its E. coli ortholog. Thus, HMCES is an ancient DNA lesion recognition protein that preserves genome integrity by promoting error-free repair of abasic sites in single-stranded DNA.},
}

@article {pmid29884871,
year = {2018},
author = {Spyrou, MA and Tukhbatova, RI and Wang, CC and Valtueña, AA and Lankapalli, AK and Kondrashin, VV and Tsybin, VA and Khokhlov, A and Kühnert, D and Herbig, A and Bos, KI and Krause, J},
title = {Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2234},
pmid = {29884871},
issn = {2041-1723},
mesh = {Animals ; DNA, Ancient/*analysis ; Dental Pulp/microbiology ; Flea Infestations/epidemiology/microbiology/transmission ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Pandemics ; Phylogeny ; Plague/epidemiology/microbiology/*transmission ; Polymorphism, Single Nucleotide ; Russia/epidemiology ; Siphonaptera/microbiology ; Virulence/genetics ; Yersinia pestis/classification/*genetics/pathogenicity ; },
abstract = {The origin of Yersinia pestis and the early stages of its evolution are fundamental subjects of investigation given its high virulence and mortality that resulted from past pandemics. Although the earliest evidence of Y. pestis infections in humans has been identified in Late Neolithic/Bronze Age Eurasia (LNBA 5000-3500y BP), these strains lack key genetic components required for flea adaptation, thus making their mode of transmission and disease presentation in humans unclear. Here, we reconstruct ancient Y. pestis genomes from individuals associated with the Late Bronze Age period (~3800 BP) in the Samara region of modern-day Russia. We show clear distinctions between our new strains and the LNBA lineage, and suggest that the full ability for flea-mediated transmission causing bubonic plague evolved more than 1000 years earlier than previously suggested. Finally, we propose that several Y. pestis lineages were established during the Bronze Age, some of which persist to the present day.},
}

Animals
DNA, Ancient/*analysis
Dental Pulp/microbiology
Flea Infestations/epidemiology/microbiology/transmission
Genome, Bacterial/*genetics
High-Throughput Nucleotide Sequencing
Humans
Pandemics
Phylogeny
Plague/epidemiology/microbiology/*transmission
Polymorphism, Single Nucleotide
Russia/epidemiology
Siphonaptera/microbiology
Virulence/genetics
Yersinia pestis/classification/*genetics/pathogenicity

@article {pmid30550639,
year = {2018},
author = {Winters, M and Monroe, C and Barta, JL and Kemp, BM},
title = {Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.13973},
pmid = {30550639},
issn = {1556-4029},
support = {2011-DN-BX- K549//National Institute of Justice/ ; //Office of Justice Programs/ ; //U.S. Department of Justice/ ; },
abstract = {In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.},
}

@article {pmid30545160,
year = {2018},
author = {Esposito, U and Das, R and Syed, S and Pirooznia, M and Elhaik, E},
title = {Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians.},
journal = {Genes},
volume = {9},
number = {12},
pages = {},
doi = {10.3390/genes9120625},
pmid = {30545160},
issn = {2073-4425},
support = {MC_PC_14115//Medical Research Council/United Kingdom ; MR/R025126/1//Medical Research Council/United Kingdom ; },
abstract = {The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.},
}

@article {pmid30528431,
year = {2018},
author = {Rascovan, N and Sjögren, KG and Kristiansen, K and Nielsen, R and Willerslev, E and Desnues, C and Rasmussen, S},
title = {Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2018.11.005},
pmid = {30528431},
issn = {1097-4172},
abstract = {Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersiniapestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.},
}

@article {pmid30521562,
year = {2018},
author = {Fischer, CE and Lefort, A and Pemonge, MH and Couture-Veschambre, C and Rottier, S and Deguilloux, MF},
title = {The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0207459},
doi = {10.1371/journal.pone.0207459},
pmid = {30521562},
issn = {1932-6203},
abstract = {The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.},
}

@article {pmid30517116,
year = {2018},
author = {Winkel, T and Aguirre, MG and Arizio, CM and Aschero, CA and Babot, MDP and Benoit, L and Burgarella, C and Costa-Tártara, S and Dubois, MP and Gay, L and Hocsman, S and Jullien, M and López-Campeny, SML and Manifesto, MM and Navascués, M and Oliszewski, N and Pintar, E and Zenboudji, S and Bertero, HD and Joffre, R},
title = {Discontinuities in quinoa biodiversity in the dry Andes: An 18-century perspective based on allelic genotyping.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0207519},
doi = {10.1371/journal.pone.0207519},
pmid = {30517116},
issn = {1932-6203},
abstract = {History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.},
}

@article {pmid30514893,
year = {2018},
author = {Zalloua, P and Collins, CJ and Gosling, A and Biagini, SA and Costa, B and Kardailsky, O and Nigro, L and Khalil, W and Calafell, F and Matisoo-Smith, E},
title = {Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17567},
doi = {10.1038/s41598-018-35667-y},
pmid = {30514893},
issn = {2045-2322},
abstract = {Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.},
}

@article {pmid30514813,
year = {2018},
author = {Thompson, TQ and Bellinger, MR and O'Rourke, SM and Prince, DJ and Stevenson, AE and Rodrigues, AT and Sloat, MR and Speller, CF and Yang, DY and Butler, VL and Banks, MA and Miller, MR},
title = {Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1811559115},
pmid = {30514813},
issn = {1091-6490},
abstract = {Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.},
}

@article {pmid30498238,
year = {2018},
author = {Epp, LS and Kruse, S and Kath, NJ and Stoof-Leichsenring, KR and Tiedemann, R and Pestryakova, LA and Herzschuh, U},
title = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17436},
doi = {10.1038/s41598-018-35550-w},
pmid = {30498238},
issn = {2045-2322},
abstract = {Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.},
}

@article {pmid30497919,
year = {2018},
author = {Eisenhofer, R and Minich, JJ and Marotz, C and Cooper, A and Knight, R and Weyrich, LS},
title = {Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.11.003},
pmid = {30497919},
issn = {1878-4380},
abstract = {Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.},
}

@article {pmid30486782,
year = {2018},
author = {Baichoo, S and Souilmi, Y and Panji, S and Botha, G and Meintjes, A and Hazelhurst, S and Bendou, H and Beste, E and Mpangase, PT and Souiai, O and Alghali, M and Yi, L and O'Connor, BD and Crusoe, M and Armstrong, D and Aron, S and Joubert, F and Ahmed, AE and Mbiyavanga, M and Heusden, PV and Magosi, LE and Zermeno, J and Mainzer, LS and Fadlelmola, FM and Jongeneel, CV and Mulder, N},
title = {Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {457},
doi = {10.1186/s12859-018-2446-1},
pmid = {30486782},
issn = {1471-2105},
support = {U41HG006941//National Human Genome Research Institute/ ; },
abstract = {BACKGROUND: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging.

RESULTS: H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community.

CONCLUSION: The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.},
}

@article {pmid30481358,
year = {2018},
author = {Cascini, M and Mitchell, KJ and Cooper, A and Phillips, MJ},
title = {Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syy080},
pmid = {30481358},
issn = {1076-836X},
abstract = {Combined "total evidence" analysis of molecular and morphological data offers the opportunity to objectively merge fossils into the tree of life, and challenges the primacy of solely DNA based phylogenetic and dating inference, even among modern taxa. To investigate the relative utility of DNA, morphology, and total evidence for evolutionary inference, we sequenced the first near-complete mitochondrial genomes from extinct Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak). We analysed the ancient DNA and fossil data alongside comparable data from extant species to infer phylogeny, divergence times, and ancestral body mass among macropods (kangaroos and wallabies). Our results confirm a close relationship between Protemnodon and the iconic kangaroo genus complex "Macropus", and unite the giant Simothenurus with the hare-sized Lagostrophus fasciatus (banded hare-wallaby), suggesting that the latter is the closest living link to the once diverse sthenurine kangaroo radiation. We find that large body size evolved multiple times among kangaroos, coincident with expansion of open woodland habitats beginning in the Late Miocene. In addition, our results suggest that morphological data mislead macropod phylogeny reconstruction and in turn can distort total evidence estimation of divergence dates. However, a novel result with potentially broad application is that the accuracy and precision of reconstructing ancestral body mass was improved by tracing body mass on morphological branch lengths. This is likely due to positive allometric correlation between morphological and body size variation - a relationship that may be masked or even misleadingly inverted with the temporal or molecular branch lengths that typically underpin ancestral body size reconstruction. Our study supports complementary roles for DNA and morphology in evolutionary inference, and opens a new window into the evolution of Australia's unique marsupial fauna.},
}

@article {pmid30479341,
year = {2018},
author = {Lamnidis, TC and Majander, K and Jeong, C and Salmela, E and Wessman, A and Moiseyev, V and Khartanovich, V and Balanovsky, O and Ongyerth, M and Weihmann, A and Sajantila, A and Kelso, J and Pääbo, S and Onkamo, P and Haak, W and Krause, J and Schiffels, S},
title = {Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5018},
doi = {10.1038/s41467-018-07483-5},
pmid = {30479341},
issn = {2041-1723},
abstract = {European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.},
}

@article {pmid30478308,
year = {2018},
author = {Kosintsev, P and Mitchell, KJ and Devièse, T and van der Plicht, J and Kuitems, M and Petrova, E and Tikhonov, A and Higham, T and Comeskey, D and Turney, C and Cooper, A and van Kolfschoten, T and Stuart, AJ and Lister, AM},
title = {Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0722-0},
pmid = {30478308},
issn = {2397-334X},
abstract = {Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.},
}

@article {pmid30478041,
year = {2018},
author = {Namouchi, A and Guellil, M and Kersten, O and Hänsch, S and Ottoni, C and Schmid, BV and Pacciani, E and Quaglia, L and Vermunt, M and Bauer, EL and Derrick, M and Jensen, AØ and Kacki, S and Cohn, SK and Stenseth, NC and Bramanti, B},
title = {Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1812865115},
pmid = {30478041},
issn = {1091-6490},
abstract = {Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.},
}

@article {pmid30471018,
year = {2018},
author = {Santi, R and Rizzolo, P and Pietragalla, M and Valentini, V and Zelli, V and Galassi, FM and Ottini, L and Nesi, G},
title = {The antiquity of hydrocephalus: the first full palaeo-neuropathological description.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10072-018-3643-4},
pmid = {30471018},
issn = {1590-3478},
support = {no grant number//Mäxi Foundation/ ; },
abstract = {The Pathology Museum of the University of Florence houses a rich collection of anatomical specimens and over a hundred waxworks portraying pathological conditions occurring in the nineteenth century, when the museum was established. Clinical and autopsy findings of these cases can still be retrieved from the original museum catalogue, offering a rare opportunity for retrospective palaeo-pathological diagnostics. We present a historical case of severe hydrocephalus backed by modern-day anthropological, radiological and molecular analyses conducted on the skeleton of an 18-month-old male infant deceased in 1831. Luigi Calamai (1796-1851), a wax craftsman of La Specola workshop in Florence, was commissioned to create a life-sized wax model of the child's head, neck and upper thorax. This artwork allows us to appreciate the cranial and facial alterations determined by 30 lb of cerebrospinal fluid (CSF) accumulated within the cerebral ventricular system. Based on the autopsy report, gross malformations of the neural tube, tumours and haemorrhage could be excluded. A molecular approach proved helpful in confirming sex. We present this case as the so-far most compelling case of hydrocephalus in palaeo-pathological research.},
}

@article {pmid30468917,
year = {2018},
author = {Buckley, M and Lawless, C and Rybczynski, N},
title = {Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jprot.2018.11.014},
pmid = {30468917},
issn = {1876-7737},
abstract = {Proteomic analyses of ancient remains are increasing, with great potential to recover phylogenetic information on extinct animals beyond the reach of ancient DNA, but its limitations remain unclear. Here we carry out LC-MS/MS sequence analysis of a ~3.5 million year old specimen along with the younger Pleistocene remains of the Yukon giant camel (c.f. Paracamelus) and the western camel (Camelops hesternus) for comparison with complete sequences to both extant camels (Bactrian and Dromedary) and the alpaca. Although not complete (~75-80% sequence coverage), no amino acid sequence differences were confidently observed between the giant camels and the extant Dromedary, indicative of a closer relationship than that of the extant Bactrian lineage. However, multiple amino acid changes were observed for the western camel (Camelops) collagen sequence, placing it as a sister group to these members of Camelini tribe consistent recent ancient DNA analyses. Although this supports a role for the sequencing of ancient collagen in the understanding of vertebrate evolution, we also highlight the limitations in phylogenetic reconstructions based on partial sequence data retrieved from proteomic analyses, particularly, the impact of omitting even only a single peptide on the resulting tree topology. The presence of other non-collagenous proteins, such as biglycan and PEDF, indicates a further resource for phylogenetic information, but none more promising than the degraded camel albumin observed in the Plio-Pleistocene specimen. SIGNIFICANCE: As proteomics is becoming more frequently used in the study of ancient proteins, an emerging field known as 'palaeoproteomics' (or 'paleoproteomics'), understanding the limitations of the technique is essential. Here, through the study of the oldest undisputed collagen sequences obtained from proteomics, we confirm that some peptides following diagenetic modifications of tryptic sites are no longer matched with standard searches, but can be matched with Error Tolerant searches. We also demonstrate the ability to retrieve phylogenetic information consistent with that of ancient DNA methods, but that with the omission of only one or more key peptides, the inferred evolutionary relationships change. This is a significant finding for the field of palaeoproteomics implying a need for better understanding the particular composition of the partial sequences retrieved from proteomic analyses.},
}

@article {pmid30464240,
year = {2018},
author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA},
title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17208},
doi = {10.1038/s41598-018-35299-2},
pmid = {30464240},
issn = {2045-2322},
support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/ ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/ ; },
abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.},
}

@article {pmid30455210,
year = {2018},
author = {Andrew, C and Diez, J and James, TY and Kauserud, H},
title = {Fungarium specimens: a largely untapped source in global change biology and beyond.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1763},
pages = {},
doi = {10.1098/rstb.2017.0392},
pmid = {30455210},
issn = {1471-2970},
abstract = {For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.},
}

@article {pmid30445034,
year = {2018},
author = {O'Connor, TD},
title = {Native American Genomic Diversity through Ancient DNA.},
journal = {Cell},
volume = {175},
number = {5},
pages = {1173-1174},
doi = {10.1016/j.cell.2018.10.058},
pmid = {30445034},
issn = {1097-4172},
abstract = {Ancient DNA is a powerful tool to understand the evolutionary dynamics of both current and ancestral populations. Posth et al. use ancient DNA to elucidate important questions surrounding the peopling of Central and South America, giving us greater insights into the ancestry of genetically understudied populations.},
}

@article {pmid30420497,
year = {2018},
author = {Woods, R and Turvey, ST and Brace, S and MacPhee, RDE and Barnes, I},
title = {Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1808603115},
pmid = {30420497},
issn = {1091-6490},
abstract = {The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.},
}

@article {pmid30415837,
year = {2018},
author = {Posth, C and Nakatsuka, N and Lazaridis, I and Skoglund, P and Mallick, S and Lamnidis, TC and Rohland, N and Nägele, K and Adamski, N and Bertolini, E and Broomandkhoshbacht, N and Cooper, A and Culleton, BJ and Ferraz, T and Ferry, M and Furtwängler, A and Haak, W and Harkins, K and Harper, TK and Hünemeier, T and Lawson, AM and Llamas, B and Michel, M and Nelson, E and Oppenheimer, J and Patterson, N and Schiffels, S and Sedig, J and Stewardson, K and Talamo, S and Wang, CC and Hublin, JJ and Hubbe, M and Harvati, K and Nuevo Delaunay, A and Beier, J and Francken, M and Kaulicke, P and Reyes-Centeno, H and Rademaker, K and Trask, WR and Robinson, M and Gutierrez, SM and Prufer, KM and Salazar-García, DC and Chim, EN and Müller Plumm Gomes, L and Alves, ML and Liryo, A and Inglez, M and Oliveira, RE and Bernardo, DV and Barioni, A and Wesolowski, V and Scheifler, NA and Rivera, MA and Plens, CR and Messineo, PG and Figuti, L and Corach, D and Scabuzzo, C and Eggers, S and DeBlasis, P and Reindel, M and Méndez, C and Politis, G and Tomasto-Cagigao, E and Kennett, DJ and Strauss, A and Fehren-Schmitz, L and Krause, J and Reich, D},
title = {Reconstructing the Deep Population History of Central and South America.},
journal = {Cell},
volume = {175},
number = {5},
pages = {1185-1197.e22},
doi = {10.1016/j.cell.2018.10.027},
pmid = {30415837},
issn = {1097-4172},
abstract = {We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.},
}

@article {pmid30409866,
year = {2018},
author = {Wade, L},
title = {Ancient DNA tracks migrations around Americas.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6415},
pages = {627-628},
doi = {10.1126/science.362.6415.627},
pmid = {30409866},
issn = {1095-9203},
}

@article {pmid30408154,
year = {2018},
author = {Quillen, EE and Norton, HL and Parra, EJ and Lona-Durazo, F and Ang, KC and Illiescu, FM and Pearson, LN and Shriver, MD and Lasisi, T and Gokcumen, O and Starr, I and Lin, YL and Martin, AR and Jablonski, NG},
title = {Shades of complexity: New perspectives on the evolution and genetic architecture of human skin.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23737},
pmid = {30408154},
issn = {1096-8644},
support = {1714867//National Science Foundation/ ; },
abstract = {Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.},
}

@article {pmid30406142,
year = {2018},
author = {Guedes, L and Dias, O and Neto, J and Ribeiro da Silva, LDP and Mendonça de Souza, SMF and Iñiguez, AM},
title = {First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {8304129},
doi = {10.1155/2018/8304129},
pmid = {30406142},
issn = {2314-6141},
abstract = {Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.},
}

@article {pmid30391623,
year = {2018},
author = {Hefetz, I and Einot, N and Faerman, M and Horowitz, M and Almog, J},
title = {Touch DNA: The effect of the deposition pressure on the quality of latent fingermarks and STR profiles.},
journal = {Forensic science international. Genetics},
volume = {38},
number = {},
pages = {105-112},
doi = {10.1016/j.fsigen.2018.10.016},
pmid = {30391623},
issn = {1878-0326},
abstract = {Latent fingermarks (FMs) present unique, and sometimes the only, evidence found at a crime scene. Several factors affect their quality, including deposition pressure (DP). Its effect on FM size and quality, and on STR amplification success rate, is an emerging area of interest in forensic science. This study examined 540 FM samples, each consisting of index, middle and ring fingers, deposited by 30 donors on glass, polythene (PE) and paper under a range of weights from 0.1 to 10 kg. Both length and width of FMs increased with the increasing DP. FMs deposited under lower (≤0.5 kg) DPs varied in size (p < 0.01), while those deposited at higher (≥3 kg) DPs were more consistent. FM quality on glass and PE, as determined by the AFIS minutiae count and by a fingerprint examiner on a scale from 0 to 4, improved with the increasing DP, but it deteriorated on PE at DP of 10 kg. FM quality on paper continued to improve from DP of 1 kg up to the maximum DP of 10 kg. The effect DP has on the efficacy of DNA profiling from latent FMs was significant as shown by an increase in the DNA amount recovered, the number of amplified loci per FM sample, and the number of forensically useful DNA profiles (defined here as those with ≥8 full STR loci detected) as DP increased. This effect was most pronounced with PE (R = 0.98) and paper (R = 0.96). Altogether, the success rate of DNA profiling varied from 16.3% in FMs deposited on paper to 21.2% and 22.5% of those on PE and glass. The highest number of useful DNA profiles was obtained from glass under DP of 10 kg. Forensically useful FMs obtained at low (≤1 kg) DP from all three substrates significantly outnumbered that of STR profiles, while an opposite, though less pronounced trend, was observed at high (≥3 kg) DP on PE and paper. Application of the simple device for collecting of FMs under controlled pressure designed for this study, and the palm-up mode of FM deposition as described, allowed us to eliminate the undesirable effect of the hand self-weight and to objectively assess the actual effect of increasing DP on FM size and quality, as well as on the efficacy of DNA profiling.},
}

@article {pmid30379865,
year = {2018},
author = {Taylor, W and Shnaider, S and Abdykanova, A and Fages, A and Welker, F and Irmer, F and Seguin-Orlando, A and Khan, N and Douka, K and Kolobova, K and Orlando, L and Krivoshapkin, A and Boivin, N},
title = {Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205646},
doi = {10.1371/journal.pone.0205646},
pmid = {30379865},
issn = {1932-6203},
abstract = {The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan's high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.},
}

@article {pmid30375193,
year = {2018},
author = {Geigl, EM and Grange, T},
title = {Ancient DNA: The quest for the best.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1185-1187},
doi = {10.1111/1755-0998.12931},
pmid = {30375193},
issn = {1755-0998},
abstract = {It is the dream of all researchers working with ancient DNA to identify prior to DNA extraction from bone the specimens or specific zones within them that contain the highest proportion of endogenous DNA. As it impacts the sacrifice of precious ancient specimens and the financial support needed for the analyses, the question is of high importance to the scientific field of palaeogenomics. The "Holy Grail" of palaeogenomics was reached when Cristina Gamba et al. () discovered that it was in the petrosal part of the temporal bone, the densest part of the mammalian skeleton, where DNA is exceptionally well preserved. As a consequence, osteological collections experienced a rush from palaeogenomicists to "harvest" these precious bone parts. In this issue of Molecular Ecology Resources, Alberti et al. () describe the discovery of another promising source of relatively well-preserved endogenous DNA, that they had identified through computed tomography (CT scans), the outermost layer of cortical bone. These bones being larger and more abundant than petrous bones, this discovery increases markedly the source material for high-quality palaeogenomic studies and releases the pressure on osteological collections.},
}

@article {pmid30374172,
year = {2018},
author = {Zarrillo, S and Gaikwad, N and Lanaud, C and Powis, T and Viot, C and Lesur, I and Fouet, O and Argout, X and Guichoux, E and Salin, F and Solorzano, RL and Bouchez, O and Vignes, H and Severts, P and Hurtado, J and Yepez, A and Grivetti, L and Blake, M and Valdez, F},
title = {The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon.},
journal = {Nature ecology & evolution},
volume = {2},
number = {12},
pages = {1879-1888},
doi = {10.1038/s41559-018-0697-x},
pmid = {30374172},
issn = {2397-334X},
abstract = {Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao's greatest diversity is in the upper Amazon region of northwest South America, pointing to this region as its centre of origin. Here, we report cacao use identified by three independent lines of archaeological evidence-cacao starch grains, absorbed theobromine residues and ancient DNA-dating from approximately 5,300 years ago recovered from the Santa Ana-La Florida (SALF) site in southeast Ecuador. To our knowledge, these findings constitute the earliest evidence of T. cacao use in the Americas and the first unequivocal archaeological example of its pre-Columbian use in South America. They also reveal the upper Amazon region as the oldest centre of cacao domestication yet identified.},
}

@article {pmid30369466,
year = {2018},
author = {Tian, JY and Li, YC and Kong, QP and Zhang, YP},
title = {[The origin and evolution history of East Asian populations from genetic perspectives].},
journal = {Yi chuan = Hereditas},
volume = {40},
number = {10},
pages = {814-824},
doi = {10.16288/j.yczz.18-202},
pmid = {30369466},
issn = {0253-9772},
abstract = {East Asia is widely concerned as one of the important places for the dispersal and evolution of the Anatomically Modern Human (AMH). How the diverse ethnic groups in East Asia originated and diversified is also widely focused by different disciplines of Anthropology. The adoption of genetic data had provided new clues for reconstructing the genetic history of East Asian populations. Genetic studies supported the hypothesis that the AMHs originated from Africa's Homo sapiens at about 200 kilo years ago (kya) and then migrated out of Africa at ~100 kya, followed by expansions into the whole East Asia since their arrival in Southern East Asia at 5~6 kya along the coastal route. Early Homo Sapiens might have genetic contribution to the non-African AMHs. Early settlement, cultural assimilation, population migration and genetic exchanges are crucial in the origination and evolution of East Asia populations. Previous studies made detailed analysis for the genetic history of East Asian populations, which largely resolved the longstanding divergence between archaeology and history. However, this needs further verification by whole-genome sequencing and ancient DNA studies. Here we briefly reviewed the progresses of genetic studies in exploring the population origin, dispersal and diversification in East Asia, which improved understanding of the evolution of East Asian populations. We also prospected the future of genetic studies in revealing the prehistory of East Asians.},
}

@article {pmid30368203,
year = {2019},
author = {Zilberman, U and Milevski, I and Yegorov, D and Smith, P},
title = {A 3000 year old case of an unusual dental lesion: Pre-eruptive intracoronal resorption.},
journal = {Archives of oral biology},
volume = {97},
number = {},
pages = {97-101},
doi = {10.1016/j.archoralbio.2018.10.015},
pmid = {30368203},
issn = {1879-1506},
abstract = {OBJECTIVE: To determine the cause of a large dental lesion, tentatively identified as a case of pre-eruptive intra-coronal resorption (PEIR), in the permanent second mandibular molar of a young individual from an Iron Age cemetery at Tel Erani (Israel), dated to ca. 3000 years B.P. The provisional diagnosis was based on the massive size of the lesion in a young individual in whom the adjacent teeth were caries-free and showed no visible enamel defects.

DESIGN: The lower molars of Tel Erani on the affected side were radiographed and compared to radiographs of a modern clinical case of PEIR treated by one of us (U.Z) and the internal structure and mineral content of the lesion examined in detail using energy-dispersive X-ray spectroscopy (EDS).

RESULTS: The Tel Erani specimen closely resembled the modern clinical case of PEIR. Moreover, both cases occurred in young individuals in whom the adjacent teeth were caries-free. Examination with SEM revealed absence of dentine in the affected tooth from Tel Erani, together with changes in structure and mineral content characteristic of resorption.

CONCLUSIONS: Our study shows that the changes found in the lower second molar of the 3000 year old mandible from Tel Erani are characteristic of PEIR and demonstrate the antiquity of this condition.},
}

@article {pmid30367976,
year = {2018},
author = {Cole, TL and Rawlence, NJ and Dussex, N and Ellenberg, U and Houston, DM and Mattern, T and Miskelly, CM and Morrison, KW and Scofield, RP and Tennyson, AJD and Thompson, DR and Wood, JR and Waters, JM},
title = {Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade.},
journal = {Molecular phylogenetics and evolution},
volume = {131},
number = {},
pages = {72-79},
doi = {10.1016/j.ympev.2018.10.025},
pmid = {30367976},
issn = {1095-9513},
abstract = {Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as 'Eudyptes spp.', we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.},
}

@article {pmid30359256,
year = {2018},
author = {de Filippo, C and Meyer, M and Prüfer, K},
title = {Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {121},
doi = {10.1186/s12915-018-0581-9},
pmid = {30359256},
issn = {1741-7007},
support = {No. 694707 to Svante Pääbo//European Research Council ()/ ; No. 31-12LMP Pääbo//Max-Planck-Gesellschaft (DE)/ ; },
abstract = {BACKGROUND: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.

RESULTS: Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage.

CONCLUSIONS: Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.},
}

@article {pmid30348080,
year = {2018},
author = {Paijmans, JLA and Barlow, A and Förster, DW and Henneberger, K and Meyer, M and Nickel, B and Nagel, D and Worsøe Havmøller, R and Baryshnikov, GF and Joger, U and Rosendahl, W and Hofreiter, M},
title = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {156},
doi = {10.1186/s12862-018-1268-0},
pmid = {30348080},
issn = {1471-2148},
support = {310763//European Research Council/International ; Academic Hardware Grant//Nvidia/ ; },
abstract = {BACKGROUND: Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?

RESULTS: In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.

CONCLUSIONS: The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.},
}

@article {pmid30344633,
year = {2018},
author = {Silva, NM and Rio, J and Kreutzer, S and Papageorgopoulou, C and Currat, M},
title = {Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations.},
journal = {Evolutionary applications},
volume = {11},
number = {9},
pages = {1642-1655},
doi = {10.1111/eva.12655},
pmid = {30344633},
issn = {1752-4571},
abstract = {The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here, we extended this approach to estimate the proportion of genetic continuity between two populations, using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter-gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter-gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre-Neolithic hunter-gatherers. It provides a useful tool for the analysis of the numerous ancient DNA data sets that are currently being produced for many different species.},
}

@article {pmid30333851,
year = {2018},
author = {Vajana, E and Barbato, M and Colli, L and Milanesi, M and Rochat, E and Fabrizi, E and Mukasa, C and Del Corvo, M and Masembe, C and Muwanika, VB and Kabi, F and Sonstegard, TS and Huson, HJ and Negrini, R and , and Joost, S and Ajmone-Marsan, P},
title = {Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {385},
doi = {10.3389/fgene.2018.00385},
pmid = {30333851},
issn = {1664-8021},
abstract = {East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda. Vector distribution and host infection risk were estimated over the study area and subsequently tested as triggers of local adaptation by means of landscape genomics analysis. We identified 41 and seven candidate adaptive loci for tick resistance and infection tolerance, respectively. Among the genes associated with the candidate adaptive loci are PRKG1 and SLA2. PRKG1 was already described as associated with tick resistance in indigenous South African cattle, due to its role into inflammatory response. SLA2 is part of the regulatory pathways involved into lymphocytes' proliferation. Additionally, local ancestry analysis suggested the zebuine origin of the genomic region candidate for tick resistance.},
}

@article {pmid30333260,
year = {2018},
author = {Ollivier, M and Tresset, A and Frantz, LAF and Bréhard, S and Bălăşescu, A and Mashkour, M and Boroneanţ, A and Pionnier-Capitan, M and Lebrasseur, O and Arbogast, RM and Bartosiewicz, L and Debue, K and Rabinovich, R and Sablin, MV and Larson, G and Hänni, C and Hitte, C and Vigne, JD},
title = {Dogs accompanied humans during the Neolithic expansion into Europe.},
journal = {Biology letters},
volume = {14},
number = {10},
pages = {},
doi = {10.1098/rsbl.2018.0286},
pmid = {30333260},
issn = {1744-957X},
abstract = {Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe.},
}

@article {pmid30314119,
year = {2018},
author = {Thomson, V and Wiewel, A and Chinen, A and Maryanto, I and Sinaga, MH and How, R and Aplin, K and Suzuki, H},
title = {A perspective for resolving the systematics of Rattus, the vertebrates with the most influence on human welfare.},
journal = {Zootaxa},
volume = {4459},
number = {3},
pages = {431-452},
doi = {10.11646/zootaxa.4459.3.2},
pmid = {30314119},
issn = {1175-5334},
abstract = {The murid rodent genus Rattus Fischer 1803 contains several species that are responsible for massive loss of crops and food, extinction of other species and the spread of zoonotic diseases to humans, as well as a laboratory species used to answer important questions in physiology, immunology, pharmacology, toxicology, nutrition, behaviour and learning. Despite the well-known significant impacts of Rattus, a definitive evolutionary based systematic framework for the genus is not yet available. The past 75 years have seen more dramatic changes in membership of Rattus than in almost any other genus of mammals. In fact, the Rattus genus has been a receptacle for any generalised Old World murine that lacked morphological specialisation and at one point, has included more than 560 species and/or subspecies, spread across Eurasia, Africa and the Australo-Papuan region. The dissolution of Rattus is ongoing as many of its constituent species and many genera of Rattini remain unsampled in any molecular study. To address this sampling limitation, we sequenced the mitochondrial cytochrome b (cytb) gene and examined phylogenetic relationships using both Bayesian and Maximum Likelihood algorithms for an expanded set of taxa within Rattus and among closely related genera. Here we place previously unsampled taxa in a phylogenetic context for the first time, including R. burrus, R. hoogerwerfi, R. lugens, and R. mindorensis within the Asian Rattus group, R. facetus within the Australo-Papuan Rattus radiation, and the undescribed 'Bisa Rat' described by Flannery as sister to the recently described genus Halmaheramys. We also present an exploratory foray into the wider topic of Rattus phylogenetics and propose that a reorganisation of the Rattus genus should require that it be a monophyletic group, include at least the type species R. norvegicus and R. rattus (plus their close allies); and exclude the Bandicota/Nesokia clade and other such specialised genera.},
}

@article {pmid30313742,
year = {2018},
author = {Vences, M and Hildenbrand, A and Warmuth, KM and Andreone, F and Glaw, F},
title = {A new riparian Mantidactylus (Brygoomantis) frog from the Tsaratanana and Manongarivo Massifs in northern Madagascar.},
journal = {Zootaxa},
volume = {4486},
number = {4},
pages = {575-588},
doi = {10.11646/zootaxa.4486.4.10},
pmid = {30313742},
issn = {1175-5334},
abstract = {The subgenus Brygoomantis in the Madagascar-endemic genus Mantidactylus contains 12 nominal species but is in urgent need of taxonomic revision as many additional, genetically divergent but undescribed candidate species have been identified. We here take a first step towards a better resolution of this group by describing a new species, Mantidactylus schulzi sp. nov., occurring at the Tsaratanana and Manongarivo Massifs, differentiated in genetic, bioacoustic and sometimes morphological characters from its closest relatives. We show that upon detailed study, most species in Brygoomantis can be delimited by concordant differentiation of mitochondrial and nuclear DNA, and by bioacoustic and morphological differences. We flag this group of morphologically similar frogs as a test case where molecular data on historical type specimens by ancient DNA methods might be needed to reach a satisfying clarification of taxonomy and nomenclature. However, the status of the new species M. schulzi is not in doubt as it is morphologically distinct from most historical type specimens, and microendemic to a region in northern Madagascar from where no earlier names exist.},
}

@article {pmid30303530,
year = {2018},
author = {Herrando-Pérez, S and Ferri-Yáñez, F and Monasterio, C and Beukema, W and Gomes, V and Belliure, J and Chown, SL and Vieites, DR and Araújo, MB},
title = {Intraspecific variation in lizard heat tolerance alters estimates of climate impact.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.12914},
pmid = {30303530},
issn = {1365-2656},
support = {CGL2011-26852//Spanish Ministry of Economy and Competitiveness/ ; IC&DT 1/SAESCTN/ALENT-07-0224-FEDER-001755//European Union/ ; 4496-5470//British Ecological Society/ ; DP170101046//Australian Research Council/ ; },
abstract = {Research addressing the effects of global warming on the distribution and persistence of species generally assumes that population variation in thermal tolerance is spatially constant or overridden by interspecific variation. Typically, this rationale is implicit in sourcing one critical thermal maximum (CTmax) population estimate per species to model spatiotemporal cross-taxa variation in heat tolerance. Theory suggests that such an approach could result in biased or imprecise estimates and forecasts of impact from climate warming, but limited empirical evidence in support of those expectations exists. We experimentally quantify the magnitude of intraspecific variation in CTmax among lizard populations, and the extent to which incorporating such variability can alter estimates of climate impact through a biophysical model. To do so, we measured CTmax from 59 populations of 15 Iberian lizard species (304 individuals). The overall median CTmax across all individuals from all species was 42.8°C and ranged from 40.5 to 48.3°C, with species medians decreasing through xeric, climate-generalist and mesic taxa. We found strong statistical support for intraspecific differentiation in CTmax by up to a median of 3°C among populations. We show that annual restricted activity (operative temperature > CTmax) over the Iberian distribution of our study species differs by a median of >80 hr per 25-km2 grid cell based on different population-level CTmax estimates. This discrepancy leads to predictions of spatial variation in annual restricted activity to change by more than 20 days for six of the study species. Considering that during restriction periods, reptiles should be unable to feed and reproduce, current projections of climate-change impacts on the fitness of ectotherm fauna could be under- or over-estimated depending on which population is chosen to represent the physiological spectra of the species in question. Mapping heat tolerance over the full geographical ranges of single species is thus critical to address cross-taxa patterns and drivers of heat tolerance in a biologically comprehensive way.},
}

@article {pmid30291256,
year = {2018},
author = {Fernandes, DM and Strapagiel, D and Borówka, P and Marciniak, B and Żądzińska, E and Sirak, K and Siska, V and Grygiel, R and Carlsson, J and Manica, A and Lorkiewicz, W and Pinhasi, R},
title = {A genomic Neolithic time transect of hunter-farmer admixture in central Poland.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14879},
doi = {10.1038/s41598-018-33067-w},
pmid = {30291256},
issn = {2045-2322},
support = {GOIPG/2013/36//Irish Research Council/ ; },
abstract = {Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.},
}

@article {pmid30286387,
year = {2018},
author = {Metspalu, M and Mondal, M and Chaubey, G},
title = {The genetic makings of South Asia.},
journal = {Current opinion in genetics & development},
volume = {53},
number = {},
pages = {128-133},
doi = {10.1016/j.gde.2018.09.003},
pmid = {30286387},
issn = {1879-0380},
abstract = {South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.},
}

@article {pmid30282648,
year = {2018},
author = {Flammer, PG and Dellicour, S and Preston, SG and Rieger, D and Warren, S and Tan, CKW and Nicholson, R and Přichystalová, R and Bleicher, N and Wahl, J and Faria, NR and Pybus, OG and Pollard, M and Smith, AL},
title = {Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1888},
pages = {},
doi = {10.1098/rspb.2018.0991},
pmid = {30282648},
issn = {1471-2954},
abstract = {Throughout history, humans have been afflicted by parasitic worms, and eggs are readily detected in archaeological deposits. This study integrated parasitological and ancient DNA methods with a large sample set dating between Neolithic and Early Modern periods to explore the utility of molecular archaeoparasitology as a new approach to study the past. Molecular analyses provided unequivocal species-level parasite identification and revealed location-specific epidemiological signatures. Faecal-oral transmitted nematodes (Ascaris lumbricoides and Trichuris trichiura) were ubiquitous across time and space. By contrast, high numbers of food-associated cestodes (Diphyllobothrium latum and Taenia saginata) were restricted to medieval Lübeck. The presence of these cestodes and changes in their prevalence at approximately 1300 CE indicate substantial alterations in diet or parasite availability. Trichuris trichiura ITS-1 sequences grouped into two clades; one ubiquitous and one restricted to medieval Lübeck and Bristol. The high sequence diversity of T.tITS-1 detected in Lübeck is consistent with its importance as a Hanseatic trading centre. Collectively, these results introduce molecular archaeoparasitology as an artefact-independent source of historical evidence.},
}

@article {pmid30272210,
year = {2018},
author = {Mathieson, S and Mathieson, I},
title = {FADS1 and the timing of human adaptation to agriculture.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy180},
pmid = {30272210},
issn = {1537-1719},
abstract = {Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced approximately 8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet or efficiency of selection due to increases in effective population size.},
}

@article {pmid30268682,
year = {2018},
author = {Pośpiech, E and Chen, Y and Kukla-Bartoszek, M and Breslin, K and Aliferi, A and Andersen, JD and Ballard, D and Chaitanya, L and Freire-Aradas, A and van der Gaag, KJ and Girón-Santamaría, L and Gross, TE and Gysi, M and Huber, G and Mosquera-Miguel, A and Muralidharan, C and Skowron, M and Carracedo, Á and Haas, C and Morling, N and Parson, W and Phillips, C and Schneider, PM and Sijen, T and Syndercombe-Court, D and Vennemann, M and Wu, S and Xu, S and Jin, L and Wang, S and Zhu, G and Martin, NG and Medland, SE and Branicki, W and Walsh, S and Liu, F and Kayser, M and , },
title = {Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA.},
journal = {Forensic science international. Genetics},
volume = {37},
number = {},
pages = {241-251},
doi = {10.1016/j.fsigen.2018.08.017},
pmid = {30268682},
issn = {1878-0326},
abstract = {Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.},
}

@article {pmid30262781,
year = {2018},
author = {Santiago-Rodriguez, TM and Toranzos, GA},
title = {On Controls in Ancient Microbiome Studies, and Microbial Resilience in Ancient Samples.},
journal = {Genes},
volume = {9},
number = {10},
pages = {},
doi = {10.3390/genes9100471},
pmid = {30262781},
issn = {2073-4425},
abstract = {In the following comment, we reply to Eisenhofer and Weyrich's letter "Proper authentication of ancient DNA is still essential" responding to the article "Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies" by Santiago-Rodriguez et al. One of the concerns raised was the possibility that the patterns noted in the gut microbiome of pre-Inca/Inca and Italian nobility mummies were due to contamination of the blank control. When examining the blank controls and filtering the operational taxonomic units (OTUs) present in the blank controls, and further performing in-silico contamination analyses, we noticed very similar patterns as those previously reported. We also discuss controls in ancient microbiome studies, and aspects of microbial resilience in ancient samples.},
}

@article {pmid30261278,
year = {2018},
author = {Kavlick, MF},
title = {Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2018.09.007},
pmid = {30261278},
issn = {1872-8278},
abstract = {A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice.},
}

@article {pmid30249639,
year = {2018},
author = {Guellil, M and Kersten, O and Namouchi, A and Bauer, EL and Derrick, M and Jensen, AØ and Stenseth, NC and Bramanti, B},
title = {Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {41},
pages = {10422-10427},
doi = {10.1073/pnas.1807266115},
pmid = {30249639},
issn = {1091-6490},
mesh = {Adult ; Animals ; Bacterial Proteins/*genetics ; Borrelia/classification/*genetics/pathogenicity ; Child ; Female ; *Genome, Bacterial ; History, 15th Century ; Humans ; *Metagenomics ; Phylogeny ; Relapsing Fever/*genetics/history/microbiology ; Scandinavian and Nordic Countries ; },
abstract = {Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.},
}

Adult
Animals
Bacterial Proteins/*genetics
Borrelia/classification/*genetics/pathogenicity
Child
Female
*Genome, Bacterial
History, 15th Century
Humans
*Metagenomics
Phylogeny
Relapsing Fever/*genetics/history/microbiology
Scandinavian and Nordic Countries

@article {pmid30237547,
year = {2018},
author = {Harney, É and May, H and Shalem, D and Rohland, N and Mallick, S and Lazaridis, I and Sarig, R and Stewardson, K and Nordenfelt, S and Patterson, N and Hershkovitz, I and Reich, D},
title = {Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3913},
doi = {10.1038/s41467-018-06484-8},
pmid = {30237547},
issn = {2041-1723},
abstract = {In the original version of this Article, references in the format 'First author et al.' were inappropriately deleted. These errors have been corrected in the PDF and HTML versions of the Article.},
}

@article {pmid30232557,
year = {2018},
author = {Kivisild, T},
title = {Correction to: The study of human Y chromosome variation through ancient DNA.},
journal = {Human genetics},
volume = {137},
number = {10},
pages = {863},
doi = {10.1007/s00439-018-1937-5},
pmid = {30232557},
issn = {1432-1203},
abstract = {The following sentence on the 11th page of the article.},
}

@article {pmid30232341,
year = {2018},
author = {Furtwängler, A and Reiter, E and Neumann, GU and Siebke, I and Steuri, N and Hafner, A and Lösch, S and Anthes, N and Schuenemann, VJ and Krause, J},
title = {Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14075},
doi = {10.1038/s41598-018-32083-0},
pmid = {30232341},
issn = {2045-2322},
abstract = {In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.},
}

@article {pmid30225046,
year = {2018},
author = {Miller, EF and Manica, A and Amos, W},
title = {Global demographic history of human populations inferred from whole mitochondrial genomes.},
journal = {Royal Society open science},
volume = {5},
number = {8},
pages = {180543},
doi = {10.1098/rsos.180543},
pmid = {30225046},
issn = {2054-5703},
abstract = {The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.},
}

@article {pmid30224645,
year = {2018},
author = {Chiang, CWK and Marcus, JH and Sidore, C and Biddanda, A and Al-Asadi, H and Zoledziewska, M and Pitzalis, M and Busonero, F and Maschio, A and Pistis, G and Steri, M and Angius, A and Lohmueller, KE and Abecasis, GR and Schlessinger, D and Cucca, F and Novembre, J},
title = {Genomic history of the Sardinian population.},
journal = {Nature genetics},
volume = {50},
number = {10},
pages = {1426-1434},
doi = {10.1038/s41588-018-0215-8},
pmid = {30224645},
issn = {1546-1718},
support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; RC2 HG005552/HG/NHGRI NIH HHS/United States ; U01 HG006513/HG/NHGRI NIH HHS/United States ; T32 NS048004/NS/NINDS NIH HHS/United States ; F32 GM106656/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; HHSN271201100005C/DA/NIDA NIH HHS/United States ; N01 AG012109/AG/NIA NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; R01 HG007022/HG/NHGRI NIH HHS/United States ; U01 HL117626/HL/NHLBI NIH HHS/United States ; R01 HL117626/HL/NHLBI NIH HHS/United States ; RC2 HG005581/HG/NHGRI NIH HHS/United States ; },
abstract = {The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland ancient DNA samples varies subtly across the island. Together, our results indicate that within-island substructure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight into the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.},
}

@article {pmid30215675,
year = {2018},
author = {Kawash, JK and Smith, SD and Karaiskos, S and Grigoriev, A},
title = {ARIADNA: machine learning method for ancient DNA variant discovery.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsy029},
pmid = {30215675},
issn = {1756-1663},
abstract = {Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results. To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality genome variants with fast runtimes, while reducing the false positive rate compared with other approaches.},
}

@article {pmid30200636,
year = {2018},
author = {Pratas, D and Hosseini, M and Grilo, G and Pinho, AJ and Silva, RM and Caetano, T and Carneiro, J and Pereira, F},
title = {Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.},
journal = {Genes},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/genes9090445},
pmid = {30200636},
issn = {2073-4425},
support = {PD/BD/113969/2015//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/111148/2015//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/77900/2011//Fundação para a Ciência e a Tecnologia/ ; SFRH/BPD/100912/2014//Fundação para a Ciência e a Tecnologia/ ; IF/01356/2012//Fundação para a Ciência e a Tecnologia/ ; UID/BIM/04501/2013//Fundação para a Ciência e a Tecnologia/ ; UID/CEC/00127/2013//Fundação para a Ciência e a Tecnologia/ ; UID/AMB/50017//Fundação para a Ciência e a Tecnologia/ ; PTCD/EEI-SII/6608/2014//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.},
}

@article {pmid30200350,
year = {2018},
author = {Ferrari, G and Lischer, HEL and Neukamm, J and Rayo, E and Borel, N and Pospischil, A and Rühli, F and Bouwman, AS and Campana, MG},
title = {Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf.},
journal = {Genes},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/genes9090436},
pmid = {30200350},
issn = {2073-4425},
support = {URPP Evolution in Action: from Genomes to Ecosystems//Universität Zürich/ ; n/a//Mäxi Foundation Zurich/ ; n/a//Smithsonian Institution/ ; },
abstract = {The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.},
}

@article {pmid30192911,
year = {2018},
author = {Al-Asadi, H and Dey, KK and Novembre, J and Stephens, M},
title = {Inference and visualization of DNA damage patterns using a Grade of Membership Model.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty779},
pmid = {30192911},
issn = {1367-4811},
support = {R01 HG002585/HG/NHGRI NIH HHS/United States ; },
abstract = {Motivation: Quality control plays a major role in the analysis of ancient DNA (aDNA). One key step in this quality control is assessment of DNA damage: aDNA contains unique signatures of DNA damage that distinguish it from modern DNA, and so analyses of damage patterns can help confirmthat DNA sequences obtained are from endogenous aDNA rather than from modern contamination. Predominant signatures of DNA damage include a high frequency of cytosine to thymine substitutions (C-to-T) at the ends of fragments, and elevated rates of purines (A & G) before the 5' strand-breaks. Existing QC procedures help assess damage by simply plotting for each sample, the C-to-T mismatch rate along the read and the composition of bases before the 5' strand-breaks. Here we present a more flexible and comprehensive model-based approach to infer and visualize damage patterns in aDNA, implemented in an R package aRchaic. This approach is based on a "grade of membership" model (also known as "admixture" or "topic" model) in which each sample has an estimated grade of membership in each of K damage profiles that are estimated from the data.

Results: We illustrate aRchaic on data from several aDNA studies and modern individuals from 1000 Genomes Project Consortium (2012). Here, aRchaic clearly distinguishes modern from ancient samples irrespective of DNA extraction, lab and sequencing protocols. Additionally, through an in-silico contamination experiment, we show that the aRchaic grades of membership reflect relative levels of exogenous modern contamination. Together, the outputs of aRchaic provide a concise visual summary of DNA damage patterns, as well as other processes generating mismatches in the data.

Availability: aRchaic is available for download from https://www.github.com/kkdey/aRchaic.

Supplementary Information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid30191172,
year = {2018},
author = {O'Sullivan, N and Posth, C and Coia, V and Schuenemann, VJ and Price, TD and Wahl, J and Pinhasi, R and Zink, A and Krause, J and Maixner, F},
title = {Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard.},
journal = {Science advances},
volume = {4},
number = {9},
pages = {eaao1262},
doi = {10.1126/sciadv.aao1262},
pmid = {30191172},
issn = {2375-2548},
abstract = {From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.},
}

@article {pmid30187463,
year = {2018},
author = {Leonardi, M and Sandionigi, A and Conzato, A and Vai, S and Lari, M and Tassi, F and Ghirotto, S and Caramelli, D and Barbujani, G},
title = {The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany.},
journal = {American journal of physical anthropology},
volume = {167},
number = {3},
pages = {497-506},
doi = {10.1002/ajpa.23679},
pmid = {30187463},
issn = {1096-8644},
abstract = {OBJECTIVES: With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

MATERIALS AND METHODS: We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000 years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.

RESULTS: Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes.

CONCLUSIONS: The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation.},
}

@article {pmid30183732,
year = {2018},
author = {Guedes, L and Jaeger, LH and Liryo, A and Rodrigues-Carvalho, C and Mendonça de Souza, S and Iñiguez, AM},
title = {Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202394},
doi = {10.1371/journal.pone.0202394},
pmid = {30183732},
issn = {1932-6203},
abstract = {Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.},
}

@article {pmid30160314,
year = {2019},
author = {Lang, PLM and Willems, FM and Scheepens, JF and Burbano, HA and Bossdorf, O},
title = {Using herbaria to study global environmental change.},
journal = {The New phytologist},
volume = {221},
number = {1},
pages = {110-122},
doi = {10.1111/nph.15401},
pmid = {30160314},
issn = {1469-8137},
support = {BO 3241/7-1//German Research Foundation/ ; BU 3422/1-1//German Research Foundation/ ; //Presidential Innovation Fund of the Max Planck Society/ ; },
abstract = {During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.},
}

@article {pmid30159882,
year = {2018},
author = {Skelly, E and Kapellas, K and Cooper, A and Weyrich, LS},
title = {Consequences of colonialism: A microbial perspective to contemporary Indigenous health.},
journal = {American journal of physical anthropology},
volume = {167},
number = {2},
pages = {423-437},
doi = {10.1002/ajpa.23637},
pmid = {30159882},
issn = {1096-8644},
support = {DE150101574//Australian Research Council/ ; },
abstract = {Nearly all Indigenous populations today suffer from worse health than their non-Indigenous counterparts, and despite interventions against known factors, this health "gap" has not improved. The human microbiome-the beneficial, diverse microbial communities that live on and within the human body-is a crucial component in developing and maintaining normal physiological health. Disrupting this ecosystem has repercussions for microbial functionality, and thus, human health. In this article, we propose that modern-day Indigenous population health may suffer from disrupted microbial ecosystems as a consequence of historical colonialism. Colonialism may have interrupted the established relationships between the environment, traditional lifeways, and microbiomes, altering the Indigenous microbiome with detrimental health consequences.},
}

@article {pmid30158639,
year = {2018},
author = {Eisenmann, S and Bánffy, E and van Dommelen, P and Hofmann, KP and Maran, J and Lazaridis, I and Mittnik, A and McCormick, M and Krause, J and Reich, D and Stockhammer, PW},
title = {Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13003},
doi = {10.1038/s41598-018-31123-z},
pmid = {30158639},
issn = {2045-2322},
abstract = {Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for the investigation of past populations and migrations. An important objective for the coming years is to properly integrate ancient genomics into archaeological research. This article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analysing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of cultures in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems ('numeric system', 'mixed system (a)', 'geographic-temporal system') along with their advantages and challenges.},
}

@article {pmid30154815,
year = {2018},
author = {Bernardi, J and Stagnati, L and Lucini, L and Rocchetti, G and Lanubile, A and Cortellini, C and De Poli, G and Busconi, M and Marocco, A},
title = {Phenolic Profile and Susceptibility to Fusarium Infection of Pigmented Maize Cultivars.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1189},
doi = {10.3389/fpls.2018.01189},
pmid = {30154815},
issn = {1664-462X},
abstract = {Maize is a staple food source in the world, whose ancient varieties or landraces are receiving a growing attention. In this work, two Italian maize cultivars with pigmented kernels and one inbred line were investigated for untargeted phenolic profile, in vitro antioxidant capacity and resistance to Fusariumverticillioides infection. "Rostrato Rosso" was the richest in anthocyanins whilst phenolic acids were the second class in abundance, with comparable values detected between cultivars. Tyrosol equivalents were also the highest in "Rostrato Rosso" (822.4 mg kg-1). Coherently, "Rostrato Rosso" was highly resistant to fungal penetration and diffusion. These preliminary findings might help in breeding programs, aiming to develop maize lines more resistant to infections and with improved nutraceutical value.},
}

@article {pmid30152893,
year = {2018},
author = {Poyntz, HC and Jones, A and Jauregui, R and Young, W and Gestin, A and Mooney, A and Lamiable, O and Altermann, E and Schmidt, A and Gasser, O and Weyrich, L and Jolly, CJ and Linterman, MA and Gros, GL and Hawkins, ED and Forbes-Blom, E},
title = {Genetic regulation of antibody responsiveness to immunization in substrains of BALB/c mice.},
journal = {Immunology and cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imcb.12199},
pmid = {30152893},
issn = {1440-1711},
support = {1067891//National Health and Medical Research Council/ ; 1051820//National Health and Medical Research Council/ ; //Ministry of Business, Industry and Employment/ ; //High-Value Nutrition National Science Challenge/ ; BBS/E/B/000C0407//Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/B/000C0409//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Antibody-mediated immunity is highly protective against disease. The majority of current vaccines confer protection through humoral immunity, but there is high variability in responsiveness across populations. Identifying immune mechanisms that mediate low antibody responsiveness may provide potential strategies to boost vaccine efficacy. Here, we report diverse antibody responsiveness to unadjuvanted as well as adjuvanted immunization in substrains of BALB/c mice, resulting in high and low antibody response phenotypes. Furthermore, these antibody phenotypes were not affected by changes in environmental factors such as the gut microbiota composition. Antigen-specific B cells following immunization had a marked difference in capability to class switch, resulting in perturbed IgG isotype antibody production. In vitro, a B-cell intrinsic defect in the regulation of class-switch recombination was identified in mice with low IgG antibody production. Whole genome sequencing identified polymorphisms associated with the magnitude of antibody produced, and we propose candidate genes that may regulate isotype class-switching capability. This study highlights that mice sourced from different vendors can have significantly altered humoral immune response profiles, and provides a resource to interrogate genetic regulators of antibody responsiveness. Together these results further our understanding of immune heterogeneity and suggest additional research on the genetic influences of adjuvanted vaccine strategies is warranted for enhancing vaccine efficacy.},
}

@article {pmid30146150,
year = {2018},
author = {Krzewińska, M and Kjellström, A and Günther, T and Hedenstierna-Jonson, C and Zachrisson, T and Omrak, A and Yaka, R and Kılınç, GM and Somel, M and Sobrado, V and Evans, J and Knipper, C and Jakobsson, M and Storå, J and Götherström, A},
title = {Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.},
journal = {Current biology : CB},
volume = {28},
number = {17},
pages = {2730-2738.e10},
doi = {10.1016/j.cub.2018.06.053},
pmid = {30146150},
issn = {1879-0445},
abstract = {The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.},
}

@article {pmid30139851,
year = {2018},
author = {Vogel, G},
title = {Ancient DNA reveals tryst between extinct human species.},
journal = {Science (New York, N.Y.)},
volume = {361},
number = {6404},
pages = {737},
doi = {10.1126/science.361.6404.737},
pmid = {30139851},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Bone and Bones ; *DNA, Ancient ; *Extinction, Biological ; Fathers/history ; Female ; History, Ancient ; Humans ; Mothers/history ; Neanderthals/*genetics ; Women/*history ; },
}

Animals
*Biological Evolution
Bone and Bones
*DNA, Ancient
*Extinction, Biological
Fathers/history
Female
History, Ancient
Humans
Mothers/history
Neanderthals/*genetics
Women/*history

@article {pmid30130765,
year = {2018},
author = {Senti, S and Habicht, ME and Rayo, E and Eppenberger, PE and Rühli, FJ and Galassi, FM},
title = {Egyptian Canopic Jars at the Crossroad of Medicine and Archaeology: Overview of 100 Years of Research and Future Scientific Expectations.},
journal = {Pathobiology : journal of immunopathology, molecular and cellular biology},
volume = {85},
number = {5-6},
pages = {267-275},
doi = {10.1159/000490797},
pmid = {30130765},
issn = {1423-0291},
abstract = {Ancient Egyptian human remains have been of interest in the fields of both medical and Egyptological research for decades. However, canopic jar holders for internal organs (liver, lungs, stomach, intestines) of Egyptian mummies appear to be but a very occasional source of data for such investigations. The few medical approaches focusing on the content of these jars are summarized and listed according to pathogens and diseases to give a structured overview of this field of study. An extensive search of the literature has been conducted from different bibliographic databases with a total of n = 26 studies found. The majority of diseases found consisted of infectious diseases and internal medicine conditions such as schistosomiasis or emphysema. These are just 2 examples of many that, instead of primarily affecting bone, muscle or skin, specifically target internal organs. Hence, a better understanding of the evolution of diseases that still affect mankind could be gained. In conclusion, this reassessment shows that canopic jars represent a highly underestimated source for histological, radiological and ancient DNA examination of Ancient Egyptian remains and should, thus, be more and more brought back into the focus of retrospective medical research.},
}

@article {pmid30127404,
year = {2018},
author = {Harney, É and May, H and Shalem, D and Rohland, N and Mallick, S and Lazaridis, I and Sarig, R and Stewardson, K and Nordenfelt, S and Patterson, N and Hershkovitz, I and Reich, D},
title = {Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3336},
doi = {10.1038/s41467-018-05649-9},
pmid = {30127404},
issn = {2041-1723},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; },
abstract = {The material culture of the Late Chalcolithic period in the southern Levant (4500-3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi'in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi'in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi'in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.},
}

@article {pmid30127280,
year = {2018},
author = {Sereno, D and Dorkeld, F and Akhoundi, M and Perrin, P},
title = {Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools.},
journal = {Genes},
volume = {9},
number = {8},
pages = {},
doi = {10.3390/genes9080418},
pmid = {30127280},
issn = {2073-4425},
abstract = {Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect's gut, and Lotmaria.},
}

@article {pmid30125802,
year = {2018},
author = {Hoef-Emden, K},
title = {Revision of the Genus Chroomonas HANSGIRG: The Benefits of DNA-containing Specimens.},
journal = {Protist},
volume = {169},
number = {5},
pages = {662-681},
doi = {10.1016/j.protis.2018.04.005},
pmid = {30125802},
issn = {1618-0941},
abstract = {For years the genus Chroomonas was defined as being a cryptophyte with rectangular periplast plates, with a gullet and with biliprotein types PC 630 or 645. In phylogenetic trees the genus proved to be paraphyletic. Moreover, cells with hexagonal periplast plates were found in an SEM preparation from material of the type species C. nordstedtii. In this study, material of Hansgirg's C. nordstedtii was subjected to PCR and to sequencing of two short DNA tags. These tags allowed for an unambiguous identification of the real C. nordstedtii in the phylogeny of the blue-green cryptophytes. The genus Chroomonas corresponds to subclade 1, whereas subclades 3 and 4 do not belong to Chroomonas, if Hemiselmis is maintained. Additional examination by light and scanning electron microscopy and by spectrophotometry demonstrate that subclade 1 comprises only cells with hexagonal periplast plates and PC 630, whereas rectangular periplast plates are found only in subclades 3 and 4. Consequently the genus Chroomonas and its type species, C. nordstedtii, are revised and two novel species, C. debatzensis and C. gentoftensis sp. nov., are described.},
}

@article {pmid30122150,
year = {2018},
author = {Mallard, F and Nolte, V and Tobler, R and Kapun, M and Schlötterer, C},
title = {A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila.},
journal = {Genome biology},
volume = {19},
number = {1},
pages = {119},
doi = {10.1186/s13059-018-1503-4},
pmid = {30122150},
issn = {1474-760X},
support = {W 1225//Austrian Science Fund FWF/Austria ; 294485//European Research Council/International ; H2020-MSCA-IF-661149//H2020 Marie Skłodowska-Curie Actions/International ; ArchAdapt//FP7 Ideas: European Research Council/International ; W1225//Austrian Science Fund/International ; },
abstract = {BACKGROUND: Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation.

RESULTS: To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements reveal extensive metabolic rewiring after only approximately 60 generations in a hot environment. Analysis of genome-wide polymorphisms identifies two interacting selection targets, Sestrin and SNF4Aγ, pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation.

CONCLUSIONS: Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. Because SNF4Aγ also exhibits clinal variation in various Drosophila species, we suggest that this large-effect polymorphism is maintained by temporal and spatial temperature variation in natural environments.},
}

@article {pmid30121342,
year = {2018},
author = {Bover, P and Llamas, B and Thomson, VA and Pons, J and Cooper, A and Mitchell, KJ},
title = {Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.},
journal = {Molecular phylogenetics and evolution},
volume = {129},
number = {},
pages = {70-76},
doi = {10.1016/j.ympev.2018.08.008},
pmid = {30121342},
issn = {1095-9513},
abstract = {The musk ox (Ovibos moschatus) is the only surviving member of a group of Pleistocene North American musk ox genera (Praeovibos, Ovibos, Bootherium, Euceratherium, and Soergelia) whose taxonomy is uncertain. The helmeted musk ox (Bootherium bombifrons) and the woodland musk ox (Symbos cavifrons) have been synonymised as male and female forms of a single Nearctic species found from Alaska, in the north, to Texas, in the south. However, this reclassification has not been tested using molecular data, despite the potential to use ancient DNA to examine these late Pleistocene taxa. In the present study, we sequenced mitochondrial genomes from seven subfossil musk ox specimens (originally identified as Bootherium and/or Symbos), allowing us to evaluate the identity of these muskoxen, explore their phylogeography, and estimate the timeline for their evolution. We also used nuclear genomic data to determine the sex of six of our seven samples. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.},
}

@article {pmid30108597,
year = {2018},
author = {Zhu, B and Li, H and Wen, J and Mysore, KS and Wang, X and Pei, Y and Niu, L and Lin, H},
title = {Functional Specialization of Duplicated AGAMOUS Homologs in Regulating Floral Organ Development of Medicago truncatula.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {854},
doi = {10.3389/fpls.2018.00854},
pmid = {30108597},
issn = {1664-462X},
abstract = {The C function gene AGAMOUS (AG) encodes for a MADS-box transcription factor required for floral organ identity and floral meristem (FM) determinacy in angiosperms. Unlike Arabidopsis, most legume plants possess two AG homologs arose by an ancient genome duplication event. Recently, two euAGAMOUS genes, MtAGa and MtAGb, were characterized and shown to fulfill the C function activity in the model legume Medicago truncatula. Here, we reported the isolation and characterization of a new mtaga allele by screening the Medicago Tnt1 insertion mutant collection. We found that MtAGa was not only required for controlling the stamen and carpel identity but also affected pod and seed development. Genetic analysis indicated that MtAGa and MtAGb redundantly control Medicago floral organ identity, but have minimal distinct functions in regulating stamen and carpel development in a dose-dependent manner. Interestingly, the stamens and carpels are mostly converted to numerous vexillum-like petals in the double mutant of mtaga mtagb, which is distinguished from Arabidopsis ag. Further qRT-PCR analysis in different mtag mutants revealed that MtAGa and MtAGb can repress the expression of putative A and B function genes as well as MtWUS, but promote putative D function genes expression in M. truncatula. In addition, we found that the abnormal dorsal petal phenotype observed in the mtaga mtagb double mutant is associated with the upregulation of CYCLOIDEA (CYC)-like TCP genes. Taken together, our data suggest that the redundant MtAGa and MtAGb genes of M. truncatula employ a conserved mechanism of action similar to Arabidopsis in determining floral organ identity and FM determinacy but may have evolved distinct function in regulating floral symmetry by coordinating with specific floral dorsoventral identity factors.},
}

@article {pmid30107783,
year = {2018},
author = {Cruz-Dávalos, DI and Nieves-Colón, MA and Sockell, A and Poznik, GD and Schroeder, H and Stone, AC and Bustamante, CD and Malaspinas, AS and Ávila-Arcos, MC},
title = {In-solution Y-chromosome capture-enrichment on ancient DNA libraries.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {608},
doi = {10.1186/s12864-018-4945-x},
pmid = {30107783},
issn = {1471-2164},
support = {IA206817//Universidad Nacional Autónoma de México/ ; FP7/2007-2013, grant no. 290344, EUROTAST//European Research Council/International ; },
mesh = {*Chromosomes, Human, Y ; DNA, Ancient/*analysis/*isolation & purification ; *Gene Library ; Genomics ; History, Ancient ; Humans ; Sequence Analysis, DNA/*methods ; Whole Genome Sequencing/*methods ; },
abstract = {BACKGROUND: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries.

RESULTS: The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC + YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.

CONCLUSIONS: We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round.},
}

*Chromosomes, Human, Y
DNA, Ancient/*analysis/*isolation & purification
*Gene Library
Genomics
History, Ancient
Humans
Sequence Analysis, DNA/*methods
Whole Genome Sequencing/*methods

@article {pmid30104352,
year = {2018},
author = {George, RJ and Plog, S and Watson, AS and Schmidt, KL and Culleton, BJ and Harper, TK and Gilman, PA and LeBlanc, SA and Amato, G and Whiteley, P and Kistler, L and Kennett, DJ},
title = {Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {35},
pages = {8740-8745},
doi = {10.1073/pnas.1805856115},
pmid = {30104352},
issn = {1091-6490},
mesh = {Animals ; *Breeding ; *Fossils ; *Models, Biological ; Parrots/*physiology ; Phylogeography ; Southwestern United States ; },
abstract = {Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.},
}

Animals
*Breeding
*Fossils
*Models, Biological
Parrots/*physiology
Phylogeography
Southwestern United States

@article {pmid30101195,
year = {2018},
author = {Potter, BA and Baichtal, JF and Beaudoin, AB and Fehren-Schmitz, L and Haynes, CV and Holliday, VT and Holmes, CE and Ives, JW and Kelly, RL and Llamas, B and Malhi, RS and Miller, DS and Reich, D and Reuther, JD and Schiffels, S and Surovell, TA},
title = {Current evidence allows multiple models for the peopling of the Americas.},
journal = {Science advances},
volume = {4},
number = {8},
pages = {eaat5473},
doi = {10.1126/sciadv.aat5473},
pmid = {30101195},
issn = {2375-2548},
abstract = {Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.},
}

@article {pmid30099804,
year = {2018},
author = {Iliescu, FM and Chaplin, G and Rai, N and Jacobs, GS and Basu Mallick, C and Mishra, A and Thangaraj, K and Jablonski, NG},
title = {The influences of genes, the environment, and social factors on the evolution of skin color diversity in India.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {30},
number = {5},
pages = {e23170},
doi = {10.1002/ajhb.23170},
pmid = {30099804},
issn = {1520-6300},
support = {//Darwin Trust of Edinburgh/ ; //Department of Biotechnology, Ministry of Science and Technology/ ; //Marie Sklodowska-Curie Actions Individual Fellowship/ ; RG47772//UK-India Education Research Initiative/ ; },
abstract = {OBJECTIVES: Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India.

METHODS: Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data.

RESULTS: We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research.

CONCLUSIONS: India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.},
}

@article {pmid30089624,
year = {2018},
author = {Star, B and Barrett, JH and Gondek, AT and Boessenkool, S},
title = {Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1884},
pages = {},
doi = {10.1098/rspb.2018.0978},
pmid = {30089624},
issn = {1471-2954},
abstract = {The importance of the Atlantic walrus ivory trade for the colonization, peak, and collapse of the medieval Norse colonies on Greenland has been extensively debated. Nevertheless, no studies have directly traced medieval European ivory back to distinct Arctic populations of walrus. Analysing the entire mitogenomes of 37 archaeological specimens from Europe, Svalbard, and Greenland, we here discover that Atlantic walrus comprises two monophyletic mitochondrial (MT) clades, which diverged between 23 400 and 251 120 years ago. Our improved genomic resolution allows us to reinterpret the geographical distribution of partial MT data from 306 modern and nineteenth-century specimens, finding that one of these clades was exclusively accessible to Greenlanders. With this discovery, we ascertain the biological origin of 23 archaeological specimens from Europe (most dated between 900 and 1400 CE). These results reveal a significant shift in trade from an early, predominantly eastern source towards a near exclusive representation of Greenland ivory. Our study provides empirical evidence for how this remote Arctic resource was progressively integrated into a medieval pan-European trade network, contributing to both the resilience and vulnerability of Norse Greenland society.},
}

@article {pmid30082377,
year = {2018},
author = {O'Connell, JF and Allen, J and Williams, MAJ and Williams, AN and Turney, CSM and Spooner, NA and Kamminga, J and Brown, G and Cooper, A},
title = {When did Homo sapiens first reach Southeast Asia and Sahul?.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {34},
pages = {8482-8490},
doi = {10.1073/pnas.1808385115},
pmid = {30082377},
issn = {1091-6490},
mesh = {Africa ; Archaeology ; Asia ; History, Ancient ; Human Migration/*history ; Humans ; },
abstract = {Anatomically modern humans (Homo sapiens, AMH) began spreading across Eurasia from Africa and adjacent Southwest Asia about 50,000-55,000 years ago (ca 50-55 ka). Some have argued that human genetic, fossil, and archaeological data indicate one or more prior dispersals, possibly as early as 120 ka. A recently reported age estimate of 65 ka for Madjedbebe, an archaeological site in northern Sahul (Pleistocene Australia-New Guinea), if correct, offers what might be the strongest support yet presented for a pre-55-ka African AMH exodus. We review evidence for AMH arrival on an arc spanning South China through Sahul and then evaluate data from Madjedbebe. We find that an age estimate of >50 ka for this site is unlikely to be valid. While AMH may have moved far beyond Africa well before 50-55 ka, data from the region of interest offered in support of this idea are not compelling.},
}

Africa
Archaeology
Asia
History, Ancient
Human Migration/*history
Humans

@article {pmid30079081,
year = {2018},
author = {Shriner, D},
title = {Re-analysis of Whole Genome Sequence Data From 279 Ancient Eurasians Reveals Substantial Ancestral Heterogeneity.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {268},
doi = {10.3389/fgene.2018.00268},
pmid = {30079081},
issn = {1664-8021},
support = {ZIA HG200362/HG/NHGRI NIH HHS/United States ; },
abstract = {Supervised clustering or projection analysis is a staple technique in population genetic analysis. The utility of this technique depends critically on the reference panel. The most commonly used reference panel in the analysis of ancient DNA to date is based on the Human Origins array. We previously described a larger reference panel that captures more ancestries on the global level. Here, I reanalyzed DNA data from 279 ancient Eurasians using our reference panel. I found substantially more ancestral heterogeneity than has been reported. Reanalysis provides evidence against a resurgence of Western hunter-gatherer ancestry in the Middle to Late Neolithic and evidence for a common ancestor of farmers characterized by Western Asian ancestry, a transition of the spread of agriculture from demic to cultural diffusion, at least two migrations between the Pontic-Caspian steppes and Bronze Age Europe, and a sub-Saharan African component in Natufians that localizes to present-day southern Ethiopia.},
}

@article {pmid30076235,
year = {2018},
author = {Park, SW and Dushoff, J and Earn, DJD and Poinar, H and Bolker, BM},
title = {Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {34},
pages = {E7892-E7893},
doi = {10.1073/pnas.1809775115},
pmid = {30076235},
issn = {1091-6490},
mesh = {Disease Outbreaks ; Humans ; Models, Theoretical ; *Pandemics ; Plague/*epidemiology ; Yersinia pestis ; },
}

Disease Outbreaks
Humans
Models, Theoretical
*Pandemics
Plague/*epidemiology
Yersinia pestis

@article {pmid30065103,
year = {2018},
author = {Larmuseau, MHD and Bodner, M},
title = {The biological relevance of a medieval king's DNA.},
journal = {Biochemical Society transactions},
volume = {46},
number = {4},
pages = {1013-1020},
doi = {10.1042/BST20170173},
pmid = {30065103},
issn = {1470-8752},
abstract = {The discovery of the presumably lost grave of the controversial English king Richard III in Leicester (U.K.) was one of the most important archaeological achievements of the last decennium. The skeleton was identified beyond reasonable doubt, mainly by the match of mitochondrial DNA to that of living maternal relatives, along with the specific archaeological context. Since the genetic genealogical analysis only involved the DNA sequences of a single 15th century individual and a few reference persons, biologists might consider this investigation a mere curiosity. This mini-review shows that the unique context of a historical king's DNA also has relevance for biological research per se - in addition to the more obvious historical, societal and educational value. In the first place, the historical identification appeared to be a renewed forensic case realising a conservative statement with statistical power based on genetic and non-genetic data, including discordant elements. Secondly, the observation of historical non-paternity events within Richard III's patrilineage has given rise to new research questions about potential factors influencing the extra-pair paternity rate in humans and the importance of biological relatedness for the legal recognition of a child in the past. Thirdly, the identification of a named and dated skeleton with the known historical context serves as a reference for bioarchaeological investigations and studies on the spatio-temporal distribution of particular genetic variance. Finally, the Richard III case revealed privacy issues for living relatives which appear to be inherent to any publication of genetic genealogical data.},
}

@article {pmid30053542,
year = {2018},
author = {Leles, D and Cascardo, P and Pucu, E and Brener, B and Sudré, A and Alves, E and Uchoa, F and Fajardo, P and Millar, P and Mattos, D and Chame, M and Cartelle, C},
title = {Methodological innovations for the study of irreplaceable samples reveal giardiasis in extinct animals (Nothrotherium maquinense and Palaeolama maior).},
journal = {Parasitology international},
volume = {67},
number = {6},
pages = {776-780},
doi = {10.1016/j.parint.2018.07.011},
pmid = {30053542},
issn = {1873-0329},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Brazil ; *Camelids, New World ; Cytoskeletal Proteins/analysis ; DNA, Ancient/*analysis ; Giardia lamblia/isolation & purification ; Giardiasis/parasitology/*veterinary ; Immunologic Tests/methods/veterinary ; Paleontology/*methods ; Parasitology/*methods ; Protozoan Proteins/analysis ; *Xenarthra ; },
abstract = {The use of diagnostic methods that prevent irreplaceable samples (from museum collections, archaeological and paleontological samples) of being consumed or that increase their yield is relevant. For museum collections, archaeological and paleontological samples it is essential to conserve samples, subsamples or portions for future research. We are addressing methods for conservation of irreplaceable samples that could be fully consumed. Innovations in methodologies that are used in studies of Paleoparasitology and Paleomicrobiology will contribute to the preservation of collections. Therefore, to the development of archaeology and paleontology in the future, we evaluated whether the discarded material of the immunochromatography test could be used for molecular diagnosis and vice versa. We used a genotyped experimental coprolite positive for Giardia duodenalis. The diagnosis was positive for giardiasis in both cases. This methodology can be corroborated with the coprolite of a Paleolama maior (extinct llama) previously diagnosed for G. duodenalis with an immunoenzymatic test. The residue of the pre-digestion step of the DNA extraction before adding Proteinase K was confirmed positive with the immunochromatographic test. Also, the DNA extraction residue from a coprolite of Nothrotherium maquinense (ground sloth) was tested positive with immunochromatographic test for G. duodenalis. These are the oldest findings for G. duodenalis confirming that this intestinal parasite occurred among Northeastern Brazilian Megafauna animals from the late Pleistocene period, correlated to human occupation. The relevance of these results will allow the study by different methodological approaches from a small amount of material, reusing discarded materials.},
}

Amino Acid Sequence
Animals
Base Sequence
Brazil
*Camelids, New World
Cytoskeletal Proteins/analysis
DNA, Ancient/*analysis
Giardia lamblia/isolation & purification
Giardiasis/parasitology/*veterinary
Immunologic Tests/methods/veterinary
Paleontology/*methods
Parasitology/*methods
Protozoan Proteins/analysis
*Xenarthra

@article {pmid30051821,
year = {2018},
author = {Rodrigues, ASL and Charpentier, A and Bernal-Casasola, D and Gardeisen, A and Nores, C and Pis Millán, JA and McGrath, K and Speller, CF},
title = {Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1882},
pages = {},
doi = {10.1098/rspb.2018.0961},
pmid = {30051821},
issn = {1471-2954},
abstract = {Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.},
}

@article {pmid30047322,
year = {2017},
author = {Long, J},
title = {Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, by David Reich.},
journal = {Human biology},
volume = {89},
number = {4},
pages = {303-304},
pmid = {30047322},
issn = {1534-6617},
}

@article {pmid30037043,
year = {2018},
author = {Honka, J and Heino, MT and Kvist, L and Askeyev, IV and Shaymuratova, DN and Askeyev, OV and Askeyev, AO and Heikkinen, ME and Searle, JB and Aspi, J},
title = {Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA.},
journal = {Genes},
volume = {9},
number = {7},
pages = {},
doi = {10.3390/genes9070367},
pmid = {30037043},
issn = {2073-4425},
abstract = {The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th⁻18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.},
}

@article {pmid30035382,
year = {2018},
author = {Kisand, V and Talas, L and Kisand, A and Stivrins, N and Reitalu, T and Alliksaar, T and Vassiljev, J and Liiv, M and Heinsalu, A and Seppä, H and Veski, S},
title = {From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years.},
journal = {Geobiology},
volume = {16},
number = {6},
pages = {628-639},
doi = {10.1111/gbi.12307},
pmid = {30035382},
issn = {1472-4669},
support = {//European Regional Development Fund through the Centre of Excellence in Chemical Biology/International ; //Biotieteiden ja Ympäristön Tutkimuksen Toimikunta/International ; IUT1-8//Eesti Teadusagentuur/International ; IUT21-2//Eesti Teadusagentuur/International ; PUT134//Eesti Teadusagentuur/International ; PUT1389//Eesti Teadusagentuur/International ; //EBOR project, Academy of Finland/International ; },
abstract = {Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.},
}

@article {pmid30035235,
year = {2018},
author = {Velsko, IM and Frantz, LAF and Herbig, A and Larson, G and Warinner, C},
title = {Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research.},
journal = {mSystems},
volume = {3},
number = {4},
pages = {},
doi = {10.1128/mSystems.00080-18},
pmid = {30035235},
issn = {2379-5077},
support = {//Wellcome Trust/United Kingdom ; 337574//European Research Council/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage characteristic of ancient samples (e.g., reduction in fragment size and cytosine deamination) may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT. In silico-generated data sets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha diversity, beta diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 reconstructed the most accurate community structure. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; false-positive rates were highest by CLARK-S and QIIME/UCLUST. Filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. The addition of ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern data sets for most programs. Overall, taxonomic profiling biases are program specific rather than damage dependent, and the choice of taxonomic classification program should be tailored to specific research questions. IMPORTANCE Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately reconstruct community assemblages. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated data sets with and without aDNA damage. Damage patterns had minimal impact on the taxonomic profiles produced by each program, while false-positive rates and biases were intrinsic to each program. Therefore, the most appropriate classification program is one that minimizes the biases related to the questions being addressed.},
}