@article {pmid31116227,
year = {2019},
author = {Hong, JH and Oh, CS and Seo, M and Shin, DH},
title = {Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {114},
number = {},
pages = {e180595},
doi = {10.1590/0074-02760180595},
pmid = {31116227},
issn = {1678-8060},
abstract = {The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.},
}

@article {pmid31113254,
year = {2019},
author = {Ham, E and Underdown, SJ and Houldcroft, CJ},
title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.},
journal = {Annals of human biology},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/03014460.2019.1622038},
pmid = {31113254},
issn = {1464-5033},
abstract = {BACKGROUND: Simoni et al (2016) reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious but can also help prevent blood loss.

AIM: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth.

SUBJECTS AND METHODS: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture.

RESULTS: National census data indicates a positive correlation between presence of rs3917862 and decreased maternal mortality ratios. When maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862.

CONCLUSION: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.},
}

@article {pmid31109769,
year = {2019},
author = {Perry, GH and Makarewicz, CA},
title = {Horse Paleogenomes and Human-Animal Interactions in Prehistory.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2019.04.006},
pmid = {31109769},
issn = {0168-9525},
abstract = {A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities.},
}

@article {pmid31092597,
year = {2019},
author = {Bennett, RJ and Baker, KS},
title = {Looking backwards to move forward: the utility of sequencing historical bacterial genomes.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JCM.00100-19},
pmid = {31092597},
issn = {1098-660X},
abstract = {Many pathogens which caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously-understudied resource. This minireview brings together example studies which have utilised ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing, and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterising genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilising historical isolate collections, such as those from NCTC, ATCC and the Institut Pasteur, offer enhanced insight as they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilising ancient DNA, continued improvement in molecular and sequencing technologies, and the resourcefulness of investigators, mean this area of study will continue to expand and contribute to the understanding of pathogens.},
}

@article {pmid31088861,
year = {2019},
author = {Renaud, G and Hanghøj, K and Korneliussen, TS and Willerslev, E and Orlando, L},
title = {Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1534/genetics.119.302057},
pmid = {31088861},
issn = {1943-2631},
abstract = {Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6X and down to 7-8X for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.},
}

@article {pmid31080507,
year = {2019},
author = {Upadhyay, M and Bortoluzzi, C and Barbato, M and Ajmone-Marsan, P and Colli, L and Ginja, C and Sonstegard, TS and Bosse, M and Lenstra, JA and Groenen, MAM and Crooijmans, RPMA},
title = {Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs.},
journal = {Evolutionary applications},
volume = {12},
number = {5},
pages = {951-963},
doi = {10.1111/eva.12770},
pmid = {31080507},
issn = {1752-4571},
abstract = {The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.},
}

@article {pmid31080083,
year = {2019},
author = {Saag, L and Laneman, M and Varul, L and Malve, M and Valk, H and Razzak, MA and Shirobokov, IG and Khartanovich, VI and Mikhaylova, ER and Kushniarevich, A and Scheib, CL and Solnik, A and Reisberg, T and Parik, J and Saag, L and Metspalu, E and Rootsi, S and Montinaro, F and Remm, M and Mägi, R and D'Atanasio, E and Crema, ER and Díez-Del-Molino, D and Thomas, MG and Kriiska, A and Kivisild, T and Villems, R and Lang, V and Metspalu, M and Tambets, K},
title = {The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2019.04.026},
pmid = {31080083},
issn = {1879-0445},
abstract = {In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.},
}

@article {pmid31075917,
year = {2019},
author = {Merheb, M and Matar, R and Hodeify, R and Siddiqui, SS and Vazhappilly, CG and Marton, J and Azharuddin, S and Al Zouabi, H},
title = {Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.},
journal = {Cells},
volume = {8},
number = {5},
pages = {},
doi = {10.3390/cells8050433},
pmid = {31075917},
issn = {2073-4409},
abstract = {Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.},
}

@article {pmid31074010,
year = {2019},
author = {Maurer-Alcalá, XX and Nowacki, M},
title = {Evolutionary origins and impacts of genome architecture in ciliates.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.14108},
pmid = {31074010},
issn = {1749-6632},
support = {//NCCR RNA & Disease/ ; G-EDIT//H2020 European Research Council/ ; },
abstract = {Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon-rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ-line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ-line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ-line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.},
}

@article {pmid31061125,
year = {2019},
author = {Schroeder, H and Margaryan, A and Szmyt, M and Theulot, B and Włodarczak, P and Rasmussen, S and Gopalakrishnan, S and Szczepanek, A and Konopka, T and Jensen, TZT and Witkowska, B and Wilk, S and Przybyła, MM and Pospieszny, Ł and Sjögren, KG and Belka, Z and Olsen, J and Kristiansen, K and Willerslev, E and Frei, KM and Sikora, M and Johannsen, NN and Allentoft, ME},
title = {Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1820210116},
pmid = {31061125},
issn = {1091-6490},
abstract = {The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.},
}

@article {pmid31056281,
year = {2019},
author = {Fages, A and Hanghøj, K and Khan, N and Gaunitz, C and Seguin-Orlando, A and Leonardi, M and McCrory Constantz, C and Gamba, C and Al-Rasheid, KAS and Albizuri, S and Alfarhan, AH and Allentoft, M and Alquraishi, S and Anthony, D and Baimukhanov, N and Barrett, JH and Bayarsaikhan, J and Benecke, N and Bernáldez-Sánchez, E and Berrocal-Rangel, L and Biglari, F and Boessenkool, S and Boldgiv, B and Brem, G and Brown, D and Burger, J and Crubézy, E and Daugnora, L and Davoudi, H and de Barros Damgaard, P and de Los Ángeles de Chorro Y de Villa-Ceballos, M and Deschler-Erb, S and Detry, C and Dill, N and do Mar Oom, M and Dohr, A and Ellingvåg, S and Erdenebaatar, D and Fathi, H and Felkel, S and Fernández-Rodríguez, C and García-Viñas, E and Germonpré, M and Granado, JD and Hallsson, JH and Hemmer, H and Hofreiter, M and Kasparov, A and Khasanov, M and Khazaeli, R and Kosintsev, P and Kristiansen, K and Kubatbek, T and Kuderna, L and Kuznetsov, P and Laleh, H and Leonard, JA and Lhuillier, J and Liesau von Lettow-Vorbeck, C and Logvin, A and Lõugas, L and Ludwig, A and Luis, C and Arruda, AM and Marques-Bonet, T and Matoso Silva, R and Merz, V and Mijiddorj, E and Miller, BK and Mochlov, O and Mohaseb, FA and Morales, A and Nieto-Espinet, A and Nistelberger, H and Onar, V and Pálsdóttir, AH and Pitulko, V and Pitskhelauri, K and Pruvost, M and Rajic Sikanjic, P and Rapan Papeša, A and Roslyakova, N and Sardari, A and Sauer, E and Schafberg, R and Scheu, A and Schibler, J and Schlumbaum, A and Serrand, N and Serres-Armero, A and Shapiro, B and Sheikhi Seno, S and Shevnina, I and Shidrang, S and Southon, J and Star, B and Sykes, N and Taheri, K and Taylor, W and Teegen, WR and Trbojević Vukičević, T and Trixl, S and Tumen, D and Undrakhbold, S and Usmanova, E and Vahdati, A and Valenzuela-Lamas, S and Viegas, C and Wallner, B and Weinstock, J and Zaibert, V and Clavel, B and Lepetz, S and Mashkour, M and Helgason, A and Stefánsson, K and Barrey, E and Willerslev, E and Outram, AK and Librado, P and Orlando, L},
title = {Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2019.03.049},
pmid = {31056281},
issn = {1097-4172},
abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.},
}

@article {pmid30425363,
year = {2018},
author = {Callaway, E},
title = {Ancient genomics is recasting the story of the Americas' first residents.},
journal = {Nature},
volume = {563},
number = {7731},
pages = {303-304},
doi = {10.1038/d41586-018-07374-1},
pmid = {30425363},
issn = {1476-4687},
mesh = {Archaeology ; Central America/ethnology ; DNA, Ancient/*analysis ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Indians, North American/genetics ; Infant ; Male ; Montana ; Oceanic Ancestry Group/genetics ; South America/ethnology ; },
}

Archaeology
Central America/ethnology
DNA, Ancient/*analysis
Genome, Human/*genetics
*Genomics
History, Ancient
Human Migration/*history
Humans
Indians, North American/genetics
Infant
Male
Montana
Oceanic Ancestry Group/genetics
South America/ethnology

@article {pmid28747239,
year = {2018},
author = {Côté, NM and Le Bailly, M},
title = {Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites.},
journal = {Parasitology},
volume = {145},
number = {5},
pages = {656-664},
doi = {10.1017/S003118201700141X},
pmid = {28747239},
issn = {1469-8161},
mesh = {Animals ; DNA, Ancient/*isolation & purification ; DNA, Helminth/genetics/isolation & purification ; Evolution, Molecular ; Genomics/methods ; Helminths/classification/*genetics/isolation & purification ; Humans ; Molecular Diagnostic Techniques ; Parasitic Diseases ; Parasitology ; },
abstract = {While some species of parasites can be identified to species level from archaeological remains using microscopy (i.e. Enterobius vermicularis, Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e. Tænia sp. and Echinococcus sp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time. However, biomolecules can be poorly preserved and modern reference DNA is available only for a limited number of species of parasites, leading to the conclusion that classic microscopic observation should be combined with molecular analyses. Here we present a review of the molecular approaches used over the past two decades to identify human pathogenic helminths (Ascaris sp., Trichuris sp., E. vermicularis, Fasciola sp. etc.) or protists (Giardia sp., Trypanosoma sp., Leishmania sp. etc.). We also discuss the prospects for studying the evolution of parasites with genetics and genomics.},
}

Animals
DNA, Ancient/*isolation & purification
DNA, Helminth/genetics/isolation & purification
Evolution, Molecular
Genomics/methods
Helminths/classification/*genetics/isolation & purification
Humans
Molecular Diagnostic Techniques
Parasitic Diseases
Parasitology

@article {pmid31040238,
year = {2019},
author = {Aouizerat, T and Gutman, I and Paz, Y and Maeir, AM and Gadot, Y and Gelman, D and Szitenberg, A and Drori, E and Pinkus, A and Schoemann, M and Kaplan, R and Ben-Gedalya, T and Coppenhagen-Glazer, S and Reich, E and Saragovi, A and Lipschits, O and Klutstein, M and Hazan, R},
title = {Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.},
journal = {mBio},
volume = {10},
number = {2},
pages = {},
doi = {10.1128/mBio.00388-19},
pmid = {31040238},
issn = {2150-7511},
abstract = {Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.},
}

@article {pmid31036834,
year = {2019},
author = {Stahlschmidt, MC and Collin, TC and Fernandes, DM and Bar-Oz, G and Belfer-Cohen, A and Gao, Z and Jakeli, N and Matskevich, Z and Meshveliani, T and Pritchard, JK and McDermott, F and Pinhasi, R},
title = {Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {6628},
doi = {10.1038/s41598-019-43147-0},
pmid = {31036834},
issn = {2045-2322},
support = {GOIPD/775//Irish Research Council (An Chomhairle um Thaighde in Éirinn)/ ; },
abstract = {Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.},
}

@article {pmid31036632,
year = {2019},
author = {Shaw, B and Burrell, CL and Green, D and Navarro-Martinez, A and Scott, D and Daroszewska, A and van 't Hof, R and Smith, L and Hargrave, F and Mistry, S and Bottrill, A and Kessler, BM and Fischer, R and Singh, A and Dalmay, T and Fraser, WD and Henneberger, K and King, T and Gonzalez, S and Layfield, R},
title = {Molecular insights into an ancient form of Paget's disease of bone.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1820556116},
pmid = {31036632},
issn = {1091-6490},
abstract = {Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.},
}

@article {pmid31013797,
year = {2019},
author = {Santiago-Rodriguez, TM and Fornaciari, A and Fornaciari, G and Luciani, S and Marota, I and Vercellotti, G and Toranzos, GA and Giuffra, V and Cano, RJ},
title = {Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
doi = {10.3390/genes10040299},
pmid = {31013797},
issn = {2073-4425},
abstract = {The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.},
}

@article {pmid31007636,
year = {2018},
author = {Barnett, R and Sinding, MS and Vieira, FG and Mendoza, MLZ and Bonnet, M and Araldi, A and Kienast, I and Zambarda, A and Yamaguchi, N and Henschel, P and Gilbert, MTP},
title = {No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon.},
journal = {Conservation genetics (Print)},
volume = {19},
number = {3},
pages = {611-618},
doi = {10.1007/s10592-017-1039-2},
pmid = {31007636},
issn = {1566-0621},
abstract = {Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.},
}

@article {pmid31006515,
year = {2019},
author = {Haber, M and Doumet-Serhal, C and Scheib, CL and Xue, Y and Mikulski, R and Martiniano, R and Fischer-Genz, B and Schutkowski, H and Kivisild, T and Tyler-Smith, C},
title = {A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2019.03.015},
pmid = {31006515},
issn = {1537-6605},
abstract = {During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3rd and 13th centuries CE. These include nine individuals from the "Crusaders' pit" in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13th century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries.},
}

@article {pmid31004175,
year = {2019},
author = {Membrebe, JV and Suchard, MA and Rambaut, A and Baele, G and Lemey, P},
title = {Bayesian inference of evolutionary histories under time-dependent substitution rates.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz094},
pmid = {31004175},
issn = {1537-1719},
abstract = {Many factors complicate the estimation of time-scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well-established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time-scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus co-speciation history and a lentivirus evolutionary history, and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebola virus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.},
}

@article {pmid31004132,
year = {2019},
author = {Hanghøj, K and Renaud, G and Albrechtsen, A and Orlando, L},
title = {DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.},
journal = {GigaScience},
volume = {8},
number = {4},
pages = {},
doi = {10.1093/gigascience/giz025},
pmid = {31004132},
issn = {2047-217X},
abstract = {BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.

FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues.

CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.},
}

@article {pmid30994442,
year = {2019},
author = {Meffray, A and Perrin, M and Richier, A and Schmitt, A and Ardagna, Y and Biagini, P},
title = {Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France.},
journal = {Journal of medical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jmm.0.000978},
pmid = {30994442},
issn = {1473-5644},
abstract = {PURPOSE: Syphilis, caused by Treponema pallidum subspecies pallidum, is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France).

METHODOLOGY: Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9 months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA.

CONCLUSIONS: Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history.},
}

@article {pmid30992585,
year = {2019},
author = {Phillips, N},
title = {Indigenous groups look to ancient DNA to bring their ancestors home.},
journal = {Nature},
volume = {568},
number = {7752},
pages = {294-297},
doi = {10.1038/d41586-019-01167-w},
pmid = {30992585},
issn = {1476-4687},
}

@article {pmid30988490,
year = {2019},
author = {Brace, S and Diekmann, Y and Booth, TJ and van Dorp, L and Faltyskova, Z and Rohland, N and Mallick, S and Olalde, I and Ferry, M and Michel, M and Oppenheimer, J and Broomandkhoshbacht, N and Stewardson, K and Martiniano, R and Walsh, S and Kayser, M and Charlton, S and Hellenthal, G and Armit, I and Schulting, R and Craig, OE and Sheridan, A and Parker Pearson, M and Stringer, C and Reich, D and Thomas, MG and Barnes, I},
title = {Ancient genomes indicate population replacement in Early Neolithic Britain.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-019-0871-9},
pmid = {30988490},
issn = {2397-334X},
abstract = {The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.},
}

@article {pmid30980085,
year = {2019},
author = {Kutanan, W and Kampuansai, J and Srikummool, M and Brunelli, A and Ghirotto, S and Arias, L and Macholdt, E and Hübner, A and Schröder, R and Stoneking, M},
title = {Contrasting paternal and maternal genetic histories of Thai and Lao populations.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz083},
pmid = {30980085},
issn = {1537-1719},
abstract = {The human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 kya), with two later major male-specific expansions during the Neolithic period (∼4-5 kya) and the Bronze/Iron Age (∼2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories.},
}

@article {pmid30977781,
year = {2019},
author = {Oliva, A and Pulicani, S and Lefort, V and Bréhélin, L and Gascuel, O and Guindon, S},
title = {Accounting for ambiguity in ancestral sequence reconstruction.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz249},
pmid = {30977781},
issn = {1367-4811},
abstract = {MOTIVATION: The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference.

RESULTS: The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned.

AVAILABILITY: The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.},
}

@article {pmid30972043,
year = {2019},
author = {Mills, JG and Brookes, JD and Gellie, NJC and Liddicoat, C and Lowe, AJ and Sydnor, HR and Thomas, T and Weinstein, P and Weyrich, LS and Breed, MF},
title = {Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {550},
doi = {10.3389/fmicb.2019.00550},
pmid = {30972043},
issn = {1664-302X},
abstract = {A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.},
}

@article {pmid30964548,
year = {2019},
author = {Klunk, J and Duggan, AT and Redfern, R and Gamble, J and Boldsen, JL and Golding, GB and Walter, BS and Eaton, K and Stangroom, J and Rouillard, JM and Devault, A and DeWitte, SN and Poinar, HN},
title = {Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23820},
pmid = {30964548},
issn = {1096-8644},
support = {APP1065106//National Health and Medical Research Council (NHMRC)/ ; RGPIN-2015-04477//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 430-2017-01193//Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; 435-2018-0465//Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; //Arbor Biosciences/ ; //McMaster University/ ; //Canada Research Chair Program/ ; //University of Toronto/ ; },
abstract = {OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark.

MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis.

RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing.

DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.},
}

@article {pmid30963935,
year = {2019},
author = {Nakagome, S and Hudson, RR and Di Rienzo, A},
title = {Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1896},
pages = {20182541},
doi = {10.1098/rspb.2018.2541},
pmid = {30963935},
issn = {1471-2954},
abstract = {A fundamental question about adaptation in a population is the time of onset of the selective pressure acting on beneficial alleles. Inferring this time, in turn, depends on the selection model. We develop a framework of approximate Bayesian computation (ABC) that enables the use of the full site frequency spectrum and haplotype structure to test the goodness-of-fit of selection models and estimate the timing of selection under varying population size scenarios. We show that our method has sufficient power to distinguish natural selection from neutrality even if relatively old selection increased the frequency of a pre-existing allele from 20% to 50% or from 40% to 80%. Our ABC can accurately estimate the time of onset of selection on a new mutation. However, estimates are prone to bias under the standing variation model, possibly due to the uncertainty in the allele frequency at the onset of selection. We further extend our approach to take advantage of ancient DNA data that provides information on the allele frequency path of the beneficial allele. Applying our ABC, including both modern and ancient human DNA data, to four pigmentation alleles in Europeans, we detected selection on standing variants that occurred after the dispersal from Africa even though models of selection on a new mutation were initially supported for two of these alleles without the ancient data.},
}

@article {pmid30957607,
year = {2019},
author = {Siripan, S and Wonnapinij, P and Auetrakulvit, P and Wangthongchaicharoen, N and Surat, W},
title = {Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/24701394.2019.1597072},
pmid = {30957607},
issn = {2470-1408},
abstract = {Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.},
}

@article {pmid30954285,
year = {2019},
author = {Brunson, K and Reich, D},
title = {The Promise of Paleogenomics Beyond Our Own Species.},
journal = {Trends in genetics : TIG},
volume = {35},
number = {5},
pages = {319-329},
doi = {10.1016/j.tig.2019.02.006},
pmid = {30954285},
issn = {0168-9525},
abstract = {Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.},
}

@article {pmid30953039,
year = {2019},
author = {Spyrou, MA and Bos, KI and Herbig, A and Krause, J},
title = {Ancient pathogen genomics as an emerging tool for infectious disease research.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41576-019-0119-1},
pmid = {30953039},
issn = {1471-0064},
abstract = {Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.},
}

@article {pmid30952160,
year = {2019},
author = {Yelmen, B and Mondal, M and Marnetto, D and Pathak, AK and Montinaro, F and Gallego Romero, I and Kivisild, T and Metspalu, M and Pagani, L},
title = {Ancestry-specific analyses reveal differential demographic histories and opposite selective pressures in modern South Asian populations.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz037},
pmid = {30952160},
issn = {1537-1719},
abstract = {Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations, and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex inter-population relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.},
}

@article {pmid30944772,
year = {2019},
author = {Ciucani, MM and Palumbo, D and Galaverni, M and Serventi, P and Fabbri, E and Ravegnini, G and Angelini, S and Maini, E and Persico, D and Caniglia, R and Cilli, E},
title = {Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6424},
doi = {10.7717/peerj.6424},
pmid = {30944772},
issn = {2167-8359},
abstract = {Background: The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated.

Methods: In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses.

Results: Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1.

Discussion: In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.},
}

@article {pmid30942856,
year = {2019},
author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD},
title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evz071},
pmid = {30942856},
issn = {1759-6653},
abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (> 20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.},
}

@article {pmid30913508,
year = {2019},
author = {Traversari, M and Serrangeli, MC and Catalano, G and Petrella, E and Piciucchi, S and Feletti, F and Oxilia, G and Cristiani, E and Vazzana, A and Sorrentino, R and De Fanti, S and Luiselli, D and Calcagnile, L and Saragoni, L and Feeney, RNM and Gruppioni, G and Cilli, E and Benazzi, S},
title = {Multi-analytic study of a probable case of fibrous dysplasia (FD) from certosa monumental cemetery (Bologna, Italy).},
journal = {International journal of paleopathology},
volume = {25},
number = {},
pages = {1-8},
doi = {10.1016/j.ijpp.2019.03.003},
pmid = {30913508},
issn = {1879-9825},
abstract = {OBJECTIVE: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition, believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy.

MATERIALS: A skeletonized cranium and mandible recovered from an ossuary in 2014.

METHODS: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses.

RESULT: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of ˜1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD.

CONCLUSIONS: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses.

SIGNIFICANCE: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples.},
}

@article {pmid30893326,
year = {2019},
author = {Di Maida, G and Mannino, MA and Krause-Kyora, B and Jensen, TZT and Talamo, S},
title = {Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213173},
doi = {10.1371/journal.pone.0213173},
pmid = {30893326},
issn = {1932-6203},
abstract = {Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.},
}

@article {pmid30890703,
year = {2019},
author = {Feldman, M and Fernández-Domínguez, E and Reynolds, L and Baird, D and Pearson, J and Hershkovitz, I and May, H and Goring-Morris, N and Benz, M and Gresky, J and Bianco, RA and Fairbairn, A and Mustafaoğlu, G and Stockhammer, PW and Posth, C and Haak, W and Jeong, C and Krause, J},
title = {Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1218},
doi = {10.1038/s41467-019-09209-7},
pmid = {30890703},
issn = {2041-1723},
mesh = {Adult ; Agriculture/*history ; Archaeology ; Bone and Bones ; DNA, Ancient/*analysis/isolation & purification ; Europe ; Farmers/*history ; Female ; Genome, Human/*genetics ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Human Migration/*history ; Humans ; Iran ; Male ; Radiometric Dating ; },
abstract = {Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80-90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.},
}

Adult
Agriculture/*history
Archaeology
Bone and Bones
DNA, Ancient/*analysis/isolation & purification
Europe
Farmers/*history
Female
Genome, Human/*genetics
High-Throughput Nucleotide Sequencing
History, Ancient
Human Migration/*history
Humans
Iran
Male
Radiometric Dating

@article {pmid30887686,
year = {2019},
author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, C and Breen, J and Cooper, A},
title = {Laboratory contamination over time during low-biomass sample analysis.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13011},
pmid = {30887686},
issn = {1755-0998},
abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g. skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study. This article is protected by copyright. All rights reserved.},
}

@article {pmid30886779,
year = {2019},
author = {Eisenhofer, R and Weyrich, LS},
title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6594},
doi = {10.7717/peerj.6594},
pmid = {30886779},
issn = {2167-8359},
abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.},
}

@article {pmid30884759,
year = {2019},
author = {Abondio, P and Sazzini, M and Garagnani, P and Boattini, A and Monti, D and Franceschi, C and Luiselli, D and Giuliani, C},
title = {The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/genes10030222},
pmid = {30884759},
issn = {2073-4425},
abstract = {Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.},
}

@article {pmid30880015,
year = {2019},
author = {Villalba-Mouco, V and van de Loosdrecht, MS and Posth, C and Mora, R and Martínez-Moreno, J and Rojo-Guerra, M and Salazar-García, DC and Royo-Guillén, JI and Kunst, M and Rougier, H and Crevecoeur, I and Arcusa-Magallón, H and Tejedor-Rodríguez, C and García-Martínez de Lagrán, I and Garrido-Pena, R and Alt, KW and Jeong, C and Schiffels, S and Utrilla, P and Krause, J and Haak, W},
title = {Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.},
journal = {Current biology : CB},
volume = {29},
number = {7},
pages = {1169-1177.e7},
doi = {10.1016/j.cub.2019.02.006},
pmid = {30880015},
issn = {1879-0445},
abstract = {The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3-9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000-15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. VIDEO ABSTRACT.},
}

@article {pmid30875055,
year = {2019},
author = {Hahn, C},
title = {Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {195-213},
doi = {10.1007/978-1-4939-9176-1_18},
pmid = {30875055},
issn = {1940-6029},
abstract = {Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome.},
}

@article {pmid30875054,
year = {2019},
author = {Renaud, G and Schubert, M and Sawyer, S and Orlando, L},
title = {Authentication and Assessment of Contamination in Ancient DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {163-194},
doi = {10.1007/978-1-4939-9176-1_17},
pmid = {30875054},
issn = {1940-6029},
abstract = {Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.},
}

@article {pmid30875053,
year = {2019},
author = {Nichols, RV and Curd, E and Heintzman, PD and Shapiro, B},
title = {Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {149-161},
doi = {10.1007/978-1-4939-9176-1_16},
pmid = {30875053},
issn = {1940-6029},
abstract = {All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic "barcode" primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.},
}

@article {pmid30875052,
year = {2019},
author = {Wutke, S and Ludwig, A},
title = {Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {141-147},
doi = {10.1007/978-1-4939-9176-1_15},
pmid = {30875052},
issn = {1940-6029},
abstract = {The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.},
}

@article {pmid30875051,
year = {2019},
author = {Paijmans, JLA and González Fortes, G and Förster, DW},
title = {Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {129-139},
doi = {10.1007/978-1-4939-9176-1_14},
pmid = {30875051},
issn = {1940-6029},
abstract = {Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted "contaminant" DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.},
}

@article {pmid30875050,
year = {2019},
author = {Soares, AER},
title = {Hybridization Capture of Ancient DNA Using RNA Baits.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {121-128},
doi = {10.1007/978-1-4939-9176-1_13},
pmid = {30875050},
issn = {1940-6029},
abstract = {The majority of DNA recovered from ancient remains is derived from organisms that colonize the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from living humans. Additionally, some ancient DNA research projects aim to target specific genomic regions, such as mitochondrial genomes or variable single nucleotide polymorphisms (SNPs). To overcome the challenge of targeting specific fragments of DNA from within a complex DNA extract, methods have been developed to enrich ancient DNA extracts for target DNA relative to nontarget DNA. This chapter describes a method for target DNA enrichment that uses hybridization to biotinylated RNA baits to capture and amplify specific ancient DNA fragments from within the pool of extracted fragments.},
}

@article {pmid30875049,
year = {2019},
author = {Snyder-Mackler, N and Voyles, T and Tung, J},
title = {Generating RNA Baits for Capture-Based Enrichment.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {107-120},
doi = {10.1007/978-1-4939-9176-1_12},
pmid = {30875049},
issn = {1940-6029},
abstract = {Capture-based enrichment techniques have revolutionized genomic analysis of species and populations for which only low-quality or contaminated DNA samples (e.g., ancient DNA, noninvasively collected DNA, environmental DNA) are available. This chapter outlines an optimized laboratory protocol for generating RNA "baits" for genome-wide capture of target DNA from a larger pool of DNA. This method relies on the in vitro transcription of biotinylated RNA baits, which has the dual benefit of eliminating the high cost of synthesizing custom baits and producing a bait set that targets the majority of regions genome-wide. We provide a detailed protocol for the three main steps involved in bait library construction: (1) making a DNA library from a high-quality DNA sample for the organism of interest or a closely related species; (2) using duplex-specific nuclease digestion to reduce the representation of repetitive regions in the DNA library; and (3) performing in vitro transcription of the repetitive region-depleted DNA library to generate biotinylated RNA baits. Where applicable, we include notes and recommendations based on our own experiences.},
}

@article {pmid30875048,
year = {2019},
author = {González Fortes, G and Paijmans, JLA},
title = {Whole-Genome Capture of Ancient DNA Using Homemade Baits.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {93-105},
doi = {10.1007/978-1-4939-9176-1_11},
pmid = {30875048},
issn = {1940-6029},
abstract = {For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency.},
}

@article {pmid30875046,
year = {2019},
author = {Gansauge, MT and Meyer, M},
title = {A Method for Single-Stranded Ancient DNA Library Preparation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {75-83},
doi = {10.1007/978-1-4939-9176-1_9},
pmid = {30875046},
issn = {1940-6029},
abstract = {Genomic library preparation from highly degraded DNA is more efficient when library molecules are prepared separately from the complementary strands of DNA fragments. We describe a protocol in which libraries are constructed from single DNA strands in a three-step procedure: single-stranded ligation of the first adapter with T4 DNA ligase in the presence of a splinter oligonucleotide, copying of the DNA strand with a proofreading polymerase, and blunt-end ligation of the second double-stranded adapter with T4 DNA ligase.},
}

@article {pmid30875045,
year = {2019},
author = {Henneberger, K and Barlow, A and Paijmans, JLA},
title = {Double-Stranded Library Preparation for Ancient and Other Degraded Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {65-73},
doi = {10.1007/978-1-4939-9176-1_8},
pmid = {30875045},
issn = {1940-6029},
abstract = {High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations. Our results show that the protocol performs at a high efficiency.},
}

@article {pmid30875044,
year = {2019},
author = {Campos, PF and Gilbert, MTP},
title = {DNA Extraction from Keratin and Chitin.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {57-63},
doi = {10.1007/978-1-4939-9176-1_7},
pmid = {30875044},
issn = {1940-6029},
abstract = {DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using either silica column or organic methods.},
}

@article {pmid30875043,
year = {2019},
author = {Wales, N and Kistler, L},
title = {Extraction of Ancient DNA from Plant Remains.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {45-55},
doi = {10.1007/978-1-4939-9176-1_6},
pmid = {30875043},
issn = {1940-6029},
abstract = {Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of aDNA. Plant tissues are anatomically and chemically diverse and therefore require optimized DNA extraction approaches. Here, we describe a plant DNA isolation protocol that performs well in most contexts. We include recommendations for optimization to retain the very short DNA fragments that are expected to be preserved in degraded tissues.},
}

@article {pmid30875042,
year = {2019},
author = {Epp, LS and Zimmermann, HH and Stoof-Leichsenring, KR},
title = {Sampling and Extraction of Ancient DNA from Sediments.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {31-44},
doi = {10.1007/978-1-4939-9176-1_5},
pmid = {30875042},
issn = {1940-6029},
abstract = {Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.},
}

@article {pmid30875041,
year = {2019},
author = {Dabney, J and Meyer, M},
title = {Extraction of Highly Degraded DNA from Ancient Bones and Teeth.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {25-29},
doi = {10.1007/978-1-4939-9176-1_4},
pmid = {30875041},
issn = {1940-6029},
abstract = {We provide a DNA extraction protocol optimized for the recovery of highly fragmented molecules preserved within bones and teeth. In this method, the hard tissue matrix is degraded using an EDTA/Proteinase K lysis buffer, and the DNA is purified using spin columns with silica membranes. This method efficiently recovers molecules as short as 35 base-pairs long.},
}

@article {pmid30875040,
year = {2019},
author = {Schroeder, H and de Barros Damgaard, P and Allentoft, ME},
title = {Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {21-24},
doi = {10.1007/978-1-4939-9176-1_3},
pmid = {30875040},
issn = {1940-6029},
abstract = {Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.},
}

@article {pmid30875039,
year = {2019},
author = {Korlević, P and Meyer, M},
title = {Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {15-19},
doi = {10.1007/978-1-4939-9176-1_2},
pmid = {30875039},
issn = {1940-6029},
abstract = {DNA isolated from ancient bones and teeth comprises a mixture of microbial contamination and DNA from the organism under study. In addition, analyses of ancient human remains are often complicated by contamination with present-day human DNA, which can be introduced during excavation and subsequent handling of the specimens. In most cases, the relative abundance of contaminant DNA is much greater than that of the target organism. Here we present two techniques for reducing the proportion of contaminant DNA in bones and teeth. The first and most efficient technique uses a sodium hypochlorite (bleach) pretreatment to destroy contaminant DNA that may be bound or otherwise attached to the surface of bone/tooth powder. The second, less destructive pretreatment uses a phosphate buffer to release surface-bound DNA.},
}

@article {pmid30875038,
year = {2019},
author = {Fulton, TL and Shapiro, B},
title = {Setting Up an Ancient DNA Laboratory.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1963},
number = {},
pages = {1-13},
doi = {10.1007/978-1-4939-9176-1_1},
pmid = {30875038},
issn = {1940-6029},
abstract = {Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.},
}

@article {pmid30872771,
year = {2019},
author = {Rey-Iglesia, A and García-Vázquez, A and Treadaway, EC and van der Plicht, J and Baryshnikov, GF and Szpak, P and Bocherens, H and Boeskorov, GG and Lorenzen, ED},
title = {Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4462},
doi = {10.1038/s41598-019-40168-7},
pmid = {30872771},
issn = {2045-2322},
support = {13151//Villum Fonden (Villum Foundation)/ ; },
abstract = {Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ13C) and nitrogen (δ15N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ15N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.},
}

@article {pmid30862131,
year = {2019},
author = {Chyleński, M and Ehler, E and Somel, M and Yaka, R and Krzewińska, M and Dabert, M and Juras, A and Marciniak, A},
title = {Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/genes10030207},
pmid = {30862131},
issn = {2073-4425},
support = {UMO-2017/24/T/HS3/00511//Narodowym Centrum Nauki/ ; UMO-2017/24/T/HS3/00511//Narodowe Centrum Nauki/ ; Progress Q17 and Mobility Fund//Univerzita Karlova v Praze/ ; wbuam//Infrastruktura PL-Grid/ ; },
abstract = {Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.},
}

@article {pmid30848092,
year = {2019},
author = {van der Valk, T and Vezzi, F and Ormestad, M and Dalén, L and Guschanski, K},
title = {Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13009},
pmid = {30848092},
issn = {1755-0998},
abstract = {The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged a wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low quantity and quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material. This article is protected by copyright. All rights reserved.},
}

@article {pmid30842617,
year = {2019},
author = {Pinhasi, R and Fernandes, DM and Sirak, K and Cheronet, O},
title = {Isolating the human cochlea to generate bone powder for ancient DNA analysis.},
journal = {Nature protocols},
volume = {14},
number = {4},
pages = {1194-1205},
doi = {10.1038/s41596-019-0137-7},
pmid = {30842617},
issn = {1750-2799},
mesh = {Cochlea/anatomy & histology/*chemistry ; DNA, Ancient/*analysis/isolation & purification ; Gene Library ; History, Ancient ; Humans ; Liquid-Liquid Extraction/*methods ; Petrous Bone/anatomy & histology/*chemistry ; Powders ; Sequence Analysis, DNA/methods ; },
abstract = {The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.},
}

Cochlea/anatomy & histology/*chemistry
DNA, Ancient/*analysis/isolation & purification
Gene Library
History, Ancient
Humans
Liquid-Liquid Extraction/*methods
Petrous Bone/anatomy & histology/*chemistry
Powders
Sequence Analysis, DNA/methods

@article {pmid30828717,
year = {2019},
author = {Signore, AV and Paijmans, JLA and Hofreiter, M and Fago, A and Weber, RE and Springer, MS and Campbell, KL},
title = {Emergence of a chimeric globin pseudogene and increased hemoglobin oxygen affinity underlie the evolution of aquatic specializations in Sirenia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz044},
pmid = {30828717},
issn = {1537-1719},
abstract = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of non-synonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. By contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.},
}

@article {pmid30805020,
year = {2019},
author = {Ballard, JWO and Wilson, LAB},
title = {The Australian dingo: untamed or feral?.},
journal = {Frontiers in zoology},
volume = {16},
number = {},
pages = {2},
doi = {10.1186/s12983-019-0300-6},
pmid = {30805020},
issn = {1742-9994},
abstract = {Background: The Australian dingo continues to cause debate amongst Aboriginal people, pastoralists, scientists and the government in Australia. A lingering controversy is whether the dingo has been tamed and has now reverted to its ancestral wild state or whether its ancestors were domesticated and it now resides on the continent as a feral dog. The goal of this article is to place the discussion onto a theoretical framework, highlight what is currently known about dingo origins and taxonomy and then make a series of experimentally testable organismal, cellular and biochemical predictions that we propose can focus future research.

Discussion: We consider a canid that has been unconsciously selected as a tamed animal and the endpoint of methodical or what we now call artificial selection as a domesticated animal. We consider wild animals that were formerly tamed as untamed and those wild animals that were formerly domesticated as feralized. Untamed canids are predicted to be marked by a signature of unconscious selection whereas feral animals are hypothesized to be marked by signatures of both unconscious and artificial selection. First, we review the movement of dingo ancestors into Australia. We then discuss how differences between taming and domestication may influence the organismal traits of skull morphometrics, brain and size, seasonal breeding, and sociability. Finally, we consider cellular and molecular level traits including hypotheses concerning the phylogenetic position of dingoes, metabolic genes that appear to be under positive selection and the potential for micronutrient compensation by the gut microbiome.

Conclusions: Western Australian Government policy is currently being revised to allow the widespread killing of the Australian dingo. These policies are based on an incomplete understanding of the evolutionary history of the canid and assume the dingo is feralized. However, accumulated evidence does not definitively show that the dingo was ever domesticated and additional focused research is required. We suggest that incorporating ancient DNA data into the debate concerning dingo origins will be pivotal to understanding the evolutionary history of the canid. Further, we advocate that future morphological, behavioural and genetic studies should focus on including genetically pure Alpine and Desert dingoes and not dingo-dog hybrids. Finally, we propose that future studies critically examine genes under selection in the dingo and employ the genome from a wild canid for comparison.},
}

@article {pmid30804909,
year = {2019},
author = {Dick, JM and Yu, M and Tan, J and Lu, A},
title = {Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {120},
doi = {10.3389/fmicb.2019.00120},
pmid = {30804909},
issn = {1664-302X},
abstract = {There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.},
}

@article {pmid30798090,
year = {2019},
author = {Mao, Y and Satoh, N},
title = {A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora.},
journal = {iScience},
volume = {13},
number = {},
pages = {20-32},
doi = {10.1016/j.isci.2019.02.001},
pmid = {30798090},
issn = {2589-0042},
abstract = {Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora, concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora.},
}

@article {pmid30793442,
year = {2019},
author = {Shaw, JLA and Weyrich, LS and Hallegraeff, G and Cooper, A},
title = {Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15055},
pmid = {30793442},
issn = {1365-294X},
abstract = {Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment samples. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public-health problems caused by harmful algal blooms. This article is protected by copyright. All rights reserved.},
}

@article {pmid30773819,
year = {2019},
author = {Grealy, A and Bunce, M and Holleley, C},
title = {Avian mitochondrial genomes retrieved from museum eggshell.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13007},
pmid = {30773819},
issn = {1755-0998},
abstract = {Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historic populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60 year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterise the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intractrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow-hole can allow sufficient material to be collected for DNA extraction while minimising damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near-complete mitochondrial genomes at a coverage of 40-83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world-wide, genetic data from eggshell could provide a rapid and cost-effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome-wide evolutionary processes. This article is protected by copyright. All rights reserved.},
}

@article {pmid30753886,
year = {2019},
author = {Knapp, M and Thomas, JE and Haile, J and Prost, S and Ho, SYW and Dussex, N and Cameron-Christie, S and Kardailsky, O and Barnett, R and Bunce, M and Gilbert, MTP and Scofield, RP},
title = {Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa.},
journal = {Molecular phylogenetics and evolution},
volume = {134},
number = {},
pages = {122-128},
doi = {10.1016/j.ympev.2019.01.026},
pmid = {30753886},
issn = {1095-9513},
abstract = {Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.},
}

@article {pmid30744646,
year = {2019},
author = {Pont, C and Wagner, S and Kremer, A and Orlando, L and Plomion, C and Salse, J},
title = {Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.},
journal = {Genome biology},
volume = {20},
number = {1},
pages = {29},
doi = {10.1186/s13059-019-1627-1},
pmid = {30744646},
issn = {1474-760X},
mesh = {DNA, Ancient/*analysis ; DNA, Plant/analysis ; *Evolution, Molecular ; *Genome, Plant ; Genomics/*methods ; Paleontology ; },
abstract = {How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.},
}

DNA, Ancient/*analysis
DNA, Plant/analysis
*Evolution, Molecular
*Genome, Plant
Genomics/*methods
Paleontology

@article {pmid30742038,
year = {2019},
author = {Tennant, RK and Lux, TM and Sambles, CM and Kuhn, NJ and Petticrew, EL and Oldfield, R and Parker, DA and Hatton, J and Moore, KA and Lee, R and Turney, CSM and Jones, RT and Love, J},
title = {Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {1776},
doi = {10.1038/s41598-018-38236-5},
pmid = {30742038},
issn = {2045-2322},
abstract = {Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.},
}

@article {pmid30723959,
year = {2019},
author = {Gomez Cabrera, MDC and Young, JM and Roff, G and Staples, T and Ortiz, JC and Pandolfi, JM and Cooper, A},
title = {Broadening the taxonomic scope of coral reef paleoecological studies using ancient DNA.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15038},
pmid = {30723959},
issn = {1365-294X},
abstract = {Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), paleoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here we apply DNA metabarcoding and High-Throughput Sequencing of the 18S rDNA gene on paleoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance paleoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the 3 macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial time-scales. This article is protected by copyright. All rights reserved.},
}

@article {pmid30722030,
year = {2019},
author = {Cole, TL and Ksepka, DT and Mitchell, KJ and Tennyson, AJD and Thomas, DB and Pan, H and Zhang, G and Rawlence, NJ and Wood, JR and Bover, P and Bouzat, JL and Cooper, A and Fiddaman, SR and Hart, T and Miller, G and Ryan, PG and Shepherd, LD and Wilmshurst, JM and Waters, JM},
title = {Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation.},
journal = {Molecular biology and evolution},
volume = {36},
number = {4},
pages = {784-797},
doi = {10.1093/molbev/msz017},
pmid = {30722030},
issn = {1537-1719},
abstract = {The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.},
}

@article {pmid30716066,
year = {2019},
author = {Richards, SM and Hovhannisyan, N and Gilliham, M and Ingram, J and Skadhauge, B and Heiniger, H and Llamas, B and Mitchell, KJ and Meachen, J and Fincher, GB and Austin, JJ and Cooper, A},
title = {Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes.},
journal = {PloS one},
volume = {14},
number = {2},
pages = {e0209499},
doi = {10.1371/journal.pone.0209499},
pmid = {30716066},
issn = {1932-6203},
abstract = {Hybridization capture with in-solution oligonucleotide probes has quickly become the preferred method for enriching specific DNA loci from degraded or ancient samples prior to high-throughput sequencing (HTS). Several companies synthesize sets of probes for in-solution hybridization capture, but these commercial reagents are usually expensive. Methods for economical in-house probe synthesis have been described, but they do not directly address one of the major advantages of commercially synthesised probes: that probe sequences matching many species can be synthesised in parallel and pooled. The ability to make "phylogenetically diverse" probes increases the cost-effectiveness of commercial probe sets, as they can be used across multiple projects (or for projects involving multiple species). However, it is labour-intensive to replicate this with in-house methods, as template molecules must first be generated for each species of interest. While it has been observed that probes can be used to enrich for phylogenetically distant targets, the ability of this effect to compensate for the lack of phylogenetically diverse probes in in-house synthesised probe sets has not been tested. In this study, we present a refined protocol for in-house RNA probe synthesis and evaluated the ability of probes generated using this method from a single species to successfully enrich for the target locus in phylogenetically distant species. We demonstrated that probes synthesized using long-range PCR products from a placental mammal mitochondrion (Bison spp.) could be used to enrich for mitochondrial DNA in birds and marsupials (but not plants). Importantly, our results were obtained for approximately a third of the cost of similar commercially available reagents.},
}

@article {pmid30712776,
year = {2019},
author = {Costedoat, C and Adalian, P and Bouzaid, E and Martinet, A and Vanrell, L and von Gartzen, L and Castellano, P and Signoli, M and Tzortzis, S and Stevanovitch, A},
title = {When a lost "Petit Prince" meets Antoine de Saint Exupéry: An anthropological case report.},
journal = {Forensic science international},
volume = {296},
number = {},
pages = {145-152},
doi = {10.1016/j.forsciint.2019.01.015},
pmid = {30712776},
issn = {1872-6283},
mesh = {Age Determination by Skeleton/methods ; Age Determination by Teeth/methods ; Bone and Bones/*chemistry/*pathology ; DNA/isolation & purification ; *DNA Fingerprinting ; DNA, Mitochondrial/genetics ; *Forensic Anthropology ; France ; History, 20th Century ; Humans ; Male ; Microsatellite Repeats ; Military Personnel ; *Pilots ; Polymerase Chain Reaction ; Radiometric Dating ; Sex Determination by Skeleton/methods ; World War II ; },
abstract = {This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on "The Fountain of the Greeks" square on Riou Island occurred in the 1960's and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was "closed" and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis fürst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.},
}

Age Determination by Skeleton/methods
Age Determination by Teeth/methods
Bone and Bones/*chemistry/*pathology
DNA/isolation & purification
*DNA Fingerprinting
DNA, Mitochondrial/genetics
*Forensic Anthropology
France
History, 20th Century
Humans
Male
Microsatellite Repeats
Military Personnel
*Pilots
Polymerase Chain Reaction
Radiometric Dating
Sex Determination by Skeleton/methods
World War II

@article {pmid30706600,
year = {2019},
author = {Díaz, FP and Latorre, C and Carrasco-Puga, G and Wood, JR and Wilmshurst, JM and Soto, DC and Cole, TL and Gutiérrez, RA},
title = {Multiscale climate change impacts on plant diversity in the Atacama Desert.},
journal = {Global change biology},
volume = {25},
number = {5},
pages = {1733-1745},
doi = {10.1111/gcb.14583},
pmid = {30706600},
issn = {1365-2486},
abstract = {Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.},
}

@article {pmid30700787,
year = {2019},
author = {Rusu, I and Modi, A and Radu, C and Mircea, C and Vulpoi, A and Dobrinescu, C and Bodolică, V and Potârniche, T and Popescu, O and Caramelli, D and Kelemen, B},
title = {Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {961},
doi = {10.1038/s41598-018-37760-8},
pmid = {30700787},
issn = {2045-2322},
abstract = {The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.},
}

@article {pmid30693949,
year = {2019},
author = {Cilli, E and Sarno, S and Gnecchi Ruscone, GA and Serventi, P and De Fanti, S and Delaini, P and Ognibene, P and Basello, GP and Ravegnini, G and Angelini, S and Ferri, G and Gentilini, D and Di Blasio, AM and Pelotti, S and Pettener, D and Sazzini, M and Panaino, A and Luiselli, D and Gruppioni, G},
title = {The genetic legacy of the Yaghnobis: A witness of an ancient Eurasian ancestry in the historically reshuffled central Asian gene pool.},
journal = {American journal of physical anthropology},
volume = {168},
number = {4},
pages = {717-728},
doi = {10.1002/ajpa.23789},
pmid = {30693949},
issn = {1096-8644},
support = {FdM/1200//Fondazione del Monte di Bologna e Ravenna/ ; ERC-2011-AdG295733//FP7 Ideas: European Research Council/ ; RFO//Università di Bologna/ ; },
abstract = {OBJECTIVES: The Yaghnobis are an ethno-linguistic minority historically settled along the Yaghnob River in the Upper-Zarafshan Valley in Tajikistan. They speak a language of Old Sogdian origin, which is the only present-day witness of the Lingua Franca used along the Silk Road in Late Antiquity. The aim of this study was to reconstruct the genetic history of this community in order to shed light on its isolation and genetic ancestry within the Euro-Asiatic context.

MATERIALS AND METHODS: A total of 100 DNA samples were collected in the Yaghnob and Matcha Valleys during several expeditions and their mitochondrial, Y-chromosome and autosomal genome-wide variation were compared with that from a large set of modern and ancient Euro-Asiatic samples.

RESULTS: Findings from uniparental markers highlighted the long-term isolation of the Yaghnobis. Mitochondrial DNA ancestry traced an ancient link with Middle Eastern populations, whereas Y-chromosome legacy showed more tight relationships with Central Asians. Admixture, outgroup-f3, and D-statistics computed on autosomal variation corroborated Y-chromosome evidence, pointing respectively to low Anatolian Neolithic and high Steppe ancestry proportions in Yaghnobis, and to their closer affinity with Tajiks than to Iranians.

DISCUSSION: Although the Yaghnobis do not show evident signs of recent admixture, they could be considered a modern proxy for the source of gene flow for many Central Asian and Middle Eastern groups. Accordingly, they seem to retain a peculiar genomic ancestry probably ascribable to an ancient gene pool originally wide spread across a vast area and subsequently reshuffled by distinct demographic events occurred in Middle East and Central Asia.},
}

@article {pmid30682121,
year = {2019},
author = {Slepchenko, SM and Gusev, AV and Svyatova, EO and Hong, JH and Oh, CS and Lim, DS and Shin, DH},
title = {Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210718},
doi = {10.1371/journal.pone.0210718},
pmid = {30682121},
issn = {1932-6203},
abstract = {Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.},
}

@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 {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 = {2019},
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 = {168},
number = {3},
pages = {496-509},
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 = {45},
number = {6-8},
pages = {531-539},
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. 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 = {2019},
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 = {31},
number = {1},
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 = {2019},
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 = {176},
number = {1-2},
pages = {144-153.e13},
doi = {10.1016/j.cell.2018.10.055},
pmid = {30554877},
issn = {1097-4172},
support = {T32 CA009582/CA/NCI NIH HHS/United States ; F30 CA228242/CA/NCI NIH HHS/United States ; R01 GM116616/GM/NIGMS NIH HHS/United States ; P01 CA092584/CA/NCI NIH HHS/United States ; F32 GM126646/GM/NIGMS NIH HHS/United States ; },
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 {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 {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 {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 = {2019},
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 = {176},
number = {1-2},
pages = {295-305.e10},
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 Yersinia pestis, 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},
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 = {2019},
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 = {116},
number = {1},
pages = {177-186},
doi = {10.1073/pnas.1811559115},
pmid = {30514813},
issn = {1091-6490},
mesh = {*Adaptation, Physiological/genetics ; Alleles ; Animal Migration ; Animals ; *Ecosystem ; Genetic Loci/genetics ; Genetic Variation/genetics ; Oregon ; *Salmon/genetics ; },
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.},
}

*Adaptation, Physiological/genetics
Alleles
Animal Migration
Animals
*Ecosystem
Genetic Loci/genetics
Genetic Variation/genetics
Oregon
*Salmon/genetics

@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},
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 = {2019},
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 = {27},
number = {2},
pages = {105-117},
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},
pmid = {30486782},
issn = {1471-2105},
support = {U41 HG006941/HG/NHGRI NIH HHS/United States ; U41HG006941//National Human Genome Research Institute/ ; },
mesh = {Africa ; Computational Biology/*methods ; Genomics/*methods ; Humans ; Reproducibility of Results ; },
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.},
}

Africa
Computational Biology/*methods
Genomics/*methods
Humans
Reproducibility of Results