@article {pmid35751552,
year = {2022},
author = {Consortium, VG and Nijman, IJ and Rosen, BD and Bardou, P and Faraut, T and Cumer, T and Daly, KG and Zheng, Z and Cai, Y and Asadollahpour, H and Kul, BÇ and Zhang, WY and Guangxin, E and Ayin, A and Baird, H and Bakhtin, M and Bâlteanu, VA and Barfield, D and Berger, B and Blichfeldt, T and Boink, G and Bugiwati, SRA and Cai, Z and Carolan, S and Clark, E and Cubric-Curik, V and Dagong, MIA and Dorji, T and Drew, L and Guo, J and Hallsson, J and Horvat, S and Kantanen, J and Kawaguchi, F and Kazymbet, P and Khayatzadeh, N and Kim, N and Shah, MK and Liao, Y and Martínez, A and Masangkay, JS and Masaoka, M and Mazza, R and McEwan, J and Milanesi, M and Faruque, MO and Nomura, Y and Ouchene-Khelifi, NA and Pereira, F and Sahana, G and Salavati, M and Sasazaki, S and Da Silva, A and Simčič, M and Sölkner, J and Sutherland, A and Tigchelaar, J and Zhang, H and Consortium, E and Ajmone-Marsan, P and Bradley, DG and Colli, L and Drögemüller, C and Jiang, Y and Lei, C and Mannen, H and Pompanon, F and Tosser-Klopp, G and Lenstra, JA},
title = {Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16579},
pmid = {35751552},
issn = {1365-294X},
abstract = {By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.},
}

@article {pmid35749392,
year = {2022},
author = {Toncheva, D and Marinova, M and Borovska, P and Serbezov, D},
title = {Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269628},
doi = {10.1371/journal.pone.0269628},
pmid = {35749392},
issn = {1932-6203},
abstract = {Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP-52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes-PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210-32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread.},
}

@article {pmid35746807,
year = {2022},
author = {Nishimura, L and Fujito, N and Sugimoto, R and Inoue, I},
title = {Detection of Ancient Viruses and Long-Term Viral Evolution.},
journal = {Viruses},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/v14061336},
pmid = {35746807},
issn = {1999-4915},
support = {JP18H05506//Japan Society for the Promotion of Science/ ; JP21J22509//Japan Society for the Promotion of Science/ ; },
abstract = {The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.},
}

@article {pmid35743173,
year = {2022},
author = {Bodner, M and Amory, C and Olivieri, A and Gandini, F and Cardinali, I and Lancioni, H and Huber, G and Xavier, C and Pala, M and Fichera, A and Schnaller, L and Gysi, M and Sarno, S and Pettener, D and Luiselli, D and Richards, MB and Semino, O and Achilli, A and Torroni, A and Parson, W},
title = {Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126725},
pmid = {35743173},
issn = {1422-0067},
support = {PRIN2017 2017CWHLHY//Italian Ministry of Education, University and Research (MIUR)/ ; Dipartimenti di Eccellenza Program (2018-2022)//Department of Biology and Biotechnology "L. Spallanzani" University of Pavia/ ; 2013042025//Intramural funding program of the Medical University of Innsbruck for young scientists MUISTART/ ; //Theodor Körner-Fonds zur Förderung von Wissenschaft und Kunst/ ; DSF 2015-1-1//D. Swarovski Förderungsfonds/ ; UNI-404/1998//Tiroler Wissenschaftsfonds (TWF)/ ; //Leverhulme Trust/ ; },
abstract = {The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.},
}

@article {pmid35734848,
year = {2022},
author = {Saldías, E and Valdebenito, G and Zamora, L and Bastías, B and Flores, C and Vila, B and Vinueza, D and Tornero, C and Malgosa, A and Becker, E},
title = {Multidisciplinary analysis of a mummy from the War of the Pacific.},
journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur},
volume = {},
number = {},
pages = {},
doi = {10.1127/anthranz/2022/1543},
pmid = {35734848},
issn = {0003-5548},
abstract = {The War of the Pacific (1879-1884) was a big scale war between Chile against the alliance of Peru and Bolivia. One of the most important battles, the "Batalla del Campo de la Alianza" was situated in the desert near Tacna, Peru. The conditions of this environment favored the conservation of the dead soldiers after many years. Decades ago, the Natural History Museum of Concepción in Chile, received a naturally mummified individual of a probably Chilean soldier as a donation; its uncertain context was never studied nor confirmed. Considering this, our investigation analyzed this body under exploratory methods, ballistic analysis, archaeological contrast, 14C radiocarbon dating, ancient DNA, and isotopic analysis to reconstruct the biological profile of this mummy. The results indicated that the mummy belongs to an adult man between 33-39 years of age (> 1.50 m) and has a perimortem wound in the left flank of the abdomen. CT scan and X-rays revealed the presence of a bullet (Comblain II or Gras) hosted near the L2 vertebra. It is possible that the individual died of bleeding from a gunshot wound done by a long-distance firearm projectile from an inferior level, whose trajectory was from left to right, with slight inclination towards the top, and without a projectile exit. Other analyses confirmed the historical context and suggests the Chilean origin of the mummy. Despite the passage of time and other factors, it was possible to reconstruct the death of this individual thanks to technology and approaches from different disciplines.},
}

@article {pmid35732180,
year = {2022},
author = {Gelabert, P and Blazyte, A and Chang, Y and Fernandes, DM and Jeon, S and Hong, JG and Yoon, J and Ko, Y and Oberreiter, V and Cheronet, O and Özdoğan, KT and Sawyer, S and Yang, S and Greytak, EM and Choi, H and Kim, J and Kim, JI and Jeong, C and Bae, K and Bhak, J and Pinhasi, R},
title = {Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.06.004},
pmid = {35732180},
issn = {1879-0445},
abstract = {The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.},
}

@article {pmid35731946,
year = {2022},
author = {Översti, S and Palo, JU},
title = {Variation in the substitution rates among the human mitochondrial haplogroup U sublineages.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evac097},
pmid = {35731946},
issn = {1759-6653},
abstract = {Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA by performing tip-calibrated Bayesian phylogenetic analyses. Tip calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17 700 and U5b: 29 700 years), a disparity not reported previously. After ruling out various alternative causes (e.g. selection, sampling and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.},
}

@article {pmid35729698,
year = {2022},
author = {Zheng, ZQ and Fu, QM and Liu, YC},
title = {Exploration of adaptation, evolution and domestication of fermentation microorganisms by applying ancient DNA technology.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {5},
pages = {414-423},
doi = {10.16288/j.yczz.22-057},
pmid = {35729698},
issn = {0253-9772},
abstract = {Fermentation production is the most primitive application of microorganisms by humans, which is of great significance in human history. However, due to the lack of molecular evidence, the history of human fermentation production and the evolution and domestication of fermentation microorganisms remain to be further investigated. Taking wine and fermented dairy, the two most common types of fermented foods as examples, we introduce the archaeology evidence of fermented foods and the evolution and domestication of fermented microorganisms, introduce the research status of paleomicrobiology and fermented paleomicroorganisms, and explore the feasibility and challenges of the research of ancient fermented microorganisms applying microbial ancient DNA technology, as well as the application potential of ancient DNA capture technology in this field.},
}

@article {pmid35729694,
year = {2022},
author = {Ping, WJ and Liu, YC and Fu, QM},
title = {Exploring the evolution of archaic humans through sedimentary ancient DNA.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {5},
pages = {362-369},
doi = {10.16288/j.yczz.22-032},
pmid = {35729694},
issn = {0253-9772},
abstract = {Recent success in the retrieval of nuclear DNA of ancient humans and animals from cave sediments paves the way for genome-wide studies of past populations directly from sediments. In three studies, nuclear genomes of different species were obtained from the sediments of multiple archeological caves and their genetic histories were revealed, including an unknown population replacement of Neanderthals from Estatuas cave in Spain, which was recovered using a new DNA capture approach. By extending sediments as a source of DNA beyond fossils, this breakthrough is of particular significance to the field of ancient human genomics, which brings about more possibilities for exploring the history of past population migration, evolution and adaptation within larger time-scales and geographical areas where no fossil remains exist. Here, we mainly review the significance of the technical advances in retrieving ancient nuclear DNA from sediments and present new insights into the genetic history of Neanderthals revealed by this technique. By combining ancient genomes retrieved from fossils and additional mitochondrial DNA extracted from sediments of archaeological sites, we may begin investigating diverse archaic populations and examine their genetic relationships, movements and replacements in detail.},
}

@article {pmid35715597,
year = {2022},
author = {Graham, F},
title = {Daily briefing: Ancient DNA traces origin of Black Death.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-01703-1},
pmid = {35715597},
issn = {1476-4687},
}

@article {pmid35719876,
year = {2022},
author = {Rodrigues Soares, AE and Boroffka, N and Schröder, O and Sverchkov, L and Benecke, N and Günther, T},
title = {Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.},
journal = {Royal Society open science},
volume = {9},
number = {6},
pages = {220104},
doi = {10.1098/rsos.220104},
pmid = {35719876},
issn = {2054-5703},
abstract = {Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.},
}

@article {pmid35710940,
year = {2022},
author = {Long, GS and Klunk, J and Duggan, AT and Tapson, M and Giuffra, V and Gazzè, L and Fornaciari, A and Duchene, S and Fornaciari, G and Clermont, O and Denamur, E and Golding, GB and Poinar, H},
title = {A 16th century Escherichia coli draft genome associated with an opportunistic bile infection.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {599},
pmid = {35710940},
issn = {2399-3642},
mesh = {Animals ; Bile ; Escherichia coli/genetics ; *Escherichia coli Infections/genetics/microbiology ; Genome, Bacterial ; Mice ; *Opportunistic Infections ; },
abstract = {Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.},
}

Animals
Bile
Escherichia coli/genetics
*Escherichia coli Infections/genetics/microbiology
Genome, Bacterial
Mice
*Opportunistic Infections

@article {pmid35705867,
year = {2022},
author = {Callaway, E},
title = {Ancient DNA traces origin of Black Death.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35705867},
issn = {1476-4687},
}

@article {pmid35705810,
year = {2022},
author = {Spyrou, MA and Musralina, L and Gnecchi Ruscone, GA and Kocher, A and Borbone, PG and Khartanovich, VI and Buzhilova, A and Djansugurova, L and Bos, KI and Kühnert, D and Haak, W and Slavin, P and Krause, J},
title = {The source of the Black Death in fourteenth-century central Eurasia.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35705810},
issn = {1476-4687},
abstract = {The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences1,2. Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan1,3-9. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals9. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.},
}

@article {pmid35709264,
year = {2022},
author = {Gibbons, A},
title = {Ancient DNA reveals Black Death source.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6599},
pages = {1254-1255},
doi = {10.1126/science.add4865},
pmid = {35709264},
issn = {1095-9203},
mesh = {DNA, Ancient ; Europe ; History, Medieval ; Humans ; *Plague/history ; *Yersinia pestis/genetics ; },
abstract = {Graves in Kyrgyzstan hold early victims of plague that swept medieval Europe.},
}

DNA, Ancient
Europe
History, Medieval
Humans
*Plague/history
*Yersinia pestis/genetics

@article {pmid35702131,
year = {2022},
author = {Mohit, and Sharma, I and Sharma, V and Kumar, S and Rastogi, G and Dutt, P and Shrivastava, A and Rai, N and Chand, P},
title = {Empirical assessment of allele frequencies of genome wide association study variants associated with obstructive sleep apnea.},
journal = {American journal of translational research},
volume = {14},
number = {5},
pages = {3464-3471},
pmid = {35702131},
issn = {1943-8141},
abstract = {OBJECTIVE: Obstructive Sleep Apnea (OSA) is a heterogeneous disorder with a complex interplay of genetic and environmental factors. Over the years, with advancement in genotyping and sequencing techniques, various loci have shown an association with OSA. It is pertinent to understand the status of these associated variants in different ethnic groups. The aim of the study was to assess the genetic affinity among different population groups by evaluating the risk allele frequencies of variants associated with OSA.

METHOD: The variants associated with OSA were obtained from the GWAS catalog with a significant p value of <5 × 10-7; 95 variants were obtained (www.ebi.ac.uk/gwas). Further, the variants were narrowed down on the basis of risk allele frequencies (>5%). The fst was calculated to assess the genetic affinity between super population groups and among the sub-population groups present in the 1000 genome project.

RESULT: The fst values observed indicated all super populations were genetically related (SAS, AMR, EAS and EUR) except in the African (AFR) population group. Further, the closely related super population i.e., SAS, AMR, EAS and EUR when bifurcated on the basis of sub-population groups shows population stratification and SAS population groups form separate clusters on the MDS plot.

CONCLUSION: The study highlights genetic heterogeneity among different population groups that gets diluted and results are biased when the samples are pooled irrespective of their endogamous groups. Our results provide insight to researchers to target specific endogamous groups for future studies on OSA.},
}

@article {pmid35698034,
year = {2022},
author = {Kutschera, VE and Kierczak, M and van der Valk, T and von Seth, J and Dussex, N and Lord, E and Dehasque, M and Stanton, DWG and Khoonsari, PE and Nystedt, B and Dalén, L and Díez-Del-Molino, D},
title = {GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {228},
pmid = {35698034},
issn = {1471-2105},
support = {17:109//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 19:257//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 796877//H2020 Marie Skłodowska-Curie Actions/ ; 2017-04647//Vetenskapsrådet/ ; 2018-05973//Vetenskapsrådet/ ; 2015-676//Svenska Forskningsrådet Formas/ ; P2SKP3_165031/SNSF_/Swiss National Science Foundation/Switzerland ; P300PA_177845/SNSF_/Swiss National Science Foundation/Switzerland ; National Bioinformatics Infrastructure Sweden at SciLifeLab//Knut och Alice Wallenbergs Stiftelse/ ; },
abstract = {BACKGROUND: Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.

RESULTS: Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).

CONCLUSIONS: GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.},
}

@article {pmid35695771,
year = {2022},
author = {Huang, Y and Ringbauer, H},
title = {hapCon: Estimating Contamination of Ancient Genomes by Copying from Reference Haplotypes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btac390},
pmid = {35695771},
issn = {1367-4811},
abstract = {MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1x average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1x and below) remains a challenging task for existing approaches.

RESULTS: We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modelled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1x for SNP capture data (1240k) and 0.02x for whole genome sequencing data (WGS), substantially extending the coverage limit of previous male X chromosome based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45,000 and various global ancestries.

AVAILABILITY: We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid35692842,
year = {2022},
author = {Xue, J and Wang, W and Shao, J and Dai, X and Sun, Z and Gardner, JD and Chen, L and Guo, X and Di, N and Pei, X and Wu, X and Zhang, G and Cui, C and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Zhang, L and He, N and Fu, Q},
title = {Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {909267},
doi = {10.3389/fgene.2022.909267},
pmid = {35692842},
issn = {1664-8021},
abstract = {Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin. Our results show that the populations inhabiting Shimao City had close genetic connections with an earlier population in the Middle Neolithic Yangshao period of northern Shaanxi Province, revealing a mostly local origin for the Shimao Society. In addition, among the populations in other regions of the Yellow River basin, the Shimao-related populations had the closest maternal affinity with the contemporaneous Taosi populations from the Longshan period. The Shimao-related populations also shared more affinity with present-day northern Han populations than with the minorities and southern Han in China. Our study provides a new perspective on the genetic origins and structure of the Shimao people and the population dynamics in the Middle Yellow River basin during the Neolithic period.},
}

@article {pmid35687599,
year = {2022},
author = {Poma, A and Cesare, P and Bonfigli, A and Volpe, AR and Colafarina, S and Vecchiotti, G and Forgione, A and Zarivi, O},
title = {A qPCR-duplex assay for sex determination in ancient DNA.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269913},
doi = {10.1371/journal.pone.0269913},
pmid = {35687599},
issn = {1932-6203},
abstract = {Molecular biology techniques are increasingly being used in sex identification of skeletal remains when traditional anthropometric analyzes are not successful in identifying sex of remains that are incomplete, fragmented and /or of immature individuals. In the present work, we investigated the possibility of determining sex by using the qPCR-duplex method for both ancient and modern DNA samples. This method involves the co-amplification of two genes in a single reaction system and the subsequent analysis of the fusion curves; the gene sequences used for the construction of suitable primers are those of steroid sulfatase (STS) and testis specific protein Y-linked 1 (TSPY) genes which turned out to be two sensitive markers as they have a detection limit of 60 pg and 20 pg respectively on modern DNA. The validity of the method was verified on modern DNA in which gender was identified in all the samples with 100% accuracy; thus, allowing for the same results as the classic method with amelogenin, but in a faster and more immediate way, as it allows for sex determination solely by analyzing the denaturation curves without having to perform an electrophoretic run. The proposed molecular technique proves to be sensitive and precise even on degraded DNA, in fact on 9 archaeological finds dating from the VII-XII century in which sex had been identified through anthropometric analysis, it confirmed the sex of 8 out of 9 finds correctly.},
}

@article {pmid35681049,
year = {2022},
author = {Schulte, L and Meucci, S and Stoof-Leichsenring, KR and Heitkam, T and Schmidt, N and von Hippel, B and Andreev, AA and Diekmann, B and Biskaborn, BK and Wagner, B and Melles, M and Pestryakova, LA and Alsos, IG and Clarke, C and Krutovsky, KV and Herzschuh, U},
title = {Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {570},
pmid = {35681049},
issn = {2399-3642},
support = {772852//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.},
}

@article {pmid35671731,
year = {2022},
author = {Choin, J and Quintana-Murci, L},
title = {Paleogenomics: The demographic past of prehistoric Europeans.},
journal = {Current biology : CB},
volume = {32},
number = {11},
pages = {R535-R538},
doi = {10.1016/j.cub.2022.04.081},
pmid = {35671731},
issn = {1879-0445},
abstract = {Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe.},
}

@article {pmid35652762,
year = {2022},
author = {Nagler, M and Podmirseg, SM and Ascher-Jenull, J and Sint, D and Traugott, M},
title = {Why eDNA fractions need consideration in biomonitoring.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13658},
pmid = {35652762},
issn = {1755-0998},
abstract = {The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. We review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.},
}

@article {pmid35635751,
year = {2022},
author = {Chintalapati, M and Patterson, N and Moorjani, P},
title = {The spatiotemporal patterns of major human admixture events during the European Holocene.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.77625},
pmid = {35635751},
issn = {2050-084X},
support = {R35GM142978/NH/NIH HHS/United States ; Career Award at the Scientific Interface//Burroughs Wellcome Fund/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; },
abstract = {Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on ~1,100 ancient genomes, we reconstruct major gene flow events during European Holocene. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9,600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of steppe pastoralism. Using time transect samples across sixteen regions, we provide a fine-scale chronology of the Neolithization of Europe and the rapid spread of Steppe pastoralist ancestry across Europe. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.},
}

@article {pmid35627311,
year = {2022},
author = {Abondio, P and Cilli, E and Luiselli, D},
title = {Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods.},
journal = {Genes},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/genes13050926},
pmid = {35627311},
issn = {2073-4425},
support = {20177PJ9XF_004//Ministry of Education, Universities and Research/ ; },
abstract = {Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework.},
}

@article {pmid35618734,
year = {2022},
author = {Scorrano, G and Viva, S and Pinotti, T and Fabbri, PF and Rickards, O and Macciardi, F},
title = {Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {6468},
pmid = {35618734},
issn = {2045-2322},
support = {prot.2010EL8TXP//National Scientific Coordinator and Principal Investigator OR: Biological and cultural heritage of the central-southern Italian population trough 30 thousand Years EPIC/ ; },
abstract = {The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius' eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian' genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.},
}

@article {pmid35617951,
year = {2022},
author = {Maróti, Z and Neparáczki, E and Schütz, O and Maár, K and Varga, GIB and Kovács, B and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Horváth, C and Varga, S and Költő, L and Raskó, I and Nagy, PL and Balogh, C and Zink, A and Maixner, F and Götherström, A and George, R and Szalontai, C and Szenthe, G and Gáll, E and Kiss, AP and Gulyás, B and Kovacsóczy, BN and Gál, SS and Tomka, P and Török, T},
title = {The genetic origin of Huns, Avars, and conquering Hungarians.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.04.093},
pmid = {35617951},
issn = {1879-0445},
abstract = {Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5th and 9th centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this "immigrant core" of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the "immigrant core" of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common "proto-Ugric" gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring "native European" ancestry.},
}

@article {pmid35609205,
year = {2022},
author = {Demarchi, B and Stiller, J and Grealy, A and Mackie, M and Deng, Y and Gilbert, T and Clarke, J and Legendre, LJ and Boano, R and Sicheritz-Pontén, T and Magee, J and Zhang, G and Bunce, M and Collins, MJ and Miller, G},
title = {Ancient proteins resolve controversy over the identity of Genyornis eggshell.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {e2109326119},
doi = {10.1073/pnas.2109326119},
pmid = {35609205},
issn = {1091-6490},
abstract = {SignificanceThe controversy over the taxonomic identity of the eggs exploited by Australia's first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless "mihirung" Genyornis and a large megapode Progura, had proven impossible using morphological and geochemical methods. Ancient DNA sequencing remains inconclusive because of the age and burial temperature of the eggshell. In contrast, ancient protein sequences recovered from the eggshell enabled estimation of the evolutionary affinity between the egg and a range of extant taxa. The eggs are those of a Galloanseres (a group that includes extinct Dromornithidae, as well as extant landfowl and waterfowl), Genyornis, and not of the megapode (Megapodiidae, crown Galliformes).},
}

@article {pmid35446704,
year = {2022},
author = {Lopez-Valdivia, I and Perkins, AC and Schneider, HM and Vallebueno-Estrada, M and Burridge, JD and González-Orozco, E and Montufar, A and Montiel, R and Lynch, JP and Vielle-Calzada, JP},
title = {Gradual domestication of root traits in the earliest maize from Tehuacán.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {17},
pages = {e2110245119},
doi = {10.1073/pnas.2110245119},
pmid = {35446704},
issn = {1091-6490},
mesh = {*Domestication ; Mexico ; Phenotype ; *Zea mays/genetics ; },
abstract = {Efforts to understand the phenotypic transition that gave rise to maize from teosinte have mainly focused on the analysis of aerial organs, with little insights into possible domestication traits affecting the root system. Archeological excavations in San Marcos cave (Tehuacán, Mexico) yielded two well-preserved 5,300 to 4,970 calibrated y B.P. specimens (SM3 and SM11) corresponding to root stalks composed of at least five nodes with multiple nodal roots and, in case, a complete embryonic root system. To characterize in detail their architecture and anatomy, we used laser ablation tomography to reconstruct a three-dimensional segment of their nodal roots and a scutellar node, revealing exquisite preservation of the inner tissue and cell organization and providing reliable morphometric parameters for cellular characteristics of the stele and cortex. Whereas SM3 showed multiple cortical sclerenchyma typical of extant maize, the scutellar node of the SM11 embryonic root system completely lacked seminal roots, an attribute found in extant teosinte and in two specific maize mutants: root with undetectable meristem1 (rum1) and rootless concerning crown and seminal roots (rtcs). Ancient DNA sequences of SM10—a third San Marcos specimen of equivalent age to SM3 and SM11—revealed the presence of mutations in the transcribed sequence of both genes, offering the possibility for some of these mutations to be involved in the lack of seminal roots of the ancient specimens. Our results indicate that the root system of the earliest maize from Tehuacán resembled teosinte in traits important for maize drought adaptation.},
}

*Domestication
Mexico
Phenotype
*Zea mays/genetics

@article {pmid35580179,
year = {2022},
author = {Slavin, P and Sebbane, F},
title = {Emergence and spread of ancestral Yersinia pestis in Late-Neolithic and Bronze-Age Eurasia, ca. 5,000 to 1,500 y B.P.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {21},
pages = {e2204044119},
doi = {10.1073/pnas.2204044119},
pmid = {35580179},
issn = {1091-6490},
mesh = {DNA, Ancient ; Humans ; *Plague/epidemiology ; *Yersinia pestis/genetics ; *Yersinia pseudotuberculosis/genetics ; },
}

DNA, Ancient
Humans
*Plague/epidemiology
*Yersinia pestis/genetics
*Yersinia pseudotuberculosis/genetics

@article {pmid35588742,
year = {2022},
author = {Ariano, B and Mattiangeli, V and Breslin, EM and Parkinson, EW and McLaughlin, TR and Thompson, JE and Power, RK and Stock, JT and Mercieca-Spiteri, B and Stoddart, S and Malone, C and Gopalakrishnan, S and Cassidy, LM and Bradley, DG},
title = {Ancient Maltese genomes and the genetic geography of Neolithic Europe.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.04.069},
pmid = {35588742},
issn = {1879-0445},
abstract = {Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.},
}

@article {pmid35578825,
year = {2022},
author = {Childebayeva, A and Rohrlach, AB and Barquera, R and Rivollat, M and Aron, F and Szolek, A and Kohlbacher, O and Nicklisch, N and Alt, KW and Gronenborn, D and Meller, H and Friederich, S and Prüfer, K and Deguilloux, MF and Krause, J and Haak, W},
title = {Population Genetics and Signatures of Selection in Early Neolithic European Farmers.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac108},
pmid = {35578825},
issn = {1537-1719},
abstract = {Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA (aDNA) research in the last ten years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here we present high quality genome-wide data from the Linear Pottery Culture (LBK) site Derenburg Meerenstieg II (DER) (N=32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the LBK cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called AIMLESS (Admixture-informed Maximum-likelihood Estimation for Selection Scans) that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.},
}

@article {pmid35573598,
year = {2022},
author = {Zhang, X and Yang, L and Zhao, X and Xiang, H},
title = {The complete mitochondrial genome of an ancient cattle (Bos taurus) from Taosi site, China, and its phylogenetic assessment.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {7},
number = {5},
pages = {804-806},
doi = {10.1080/23802359.2022.2073834},
pmid = {35573598},
issn = {2380-2359},
abstract = {The complete mitochondrial genome (mitogenome) of one 4000-years-old cattle from Taosi site was determined by high throughput sequencing. The mitogenome was 16,336 bp in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The protein-coding genes had two types of start codons (ATG and ATA) and three types of stop codons (TAA, TAG, and AGA). The overall base composition of the genome was 33%-A, 27%-T, 26%-C, 14%-G. The matrilineal genealogical analysis based on mitogenome revealed that the 4000-years-old cattle from Taosi site was domestic taurine cattle. In this study, we not only reported a complete mitogenome for a 4000-years-old bovine remain from the middle Yellow River region but also provided the mitogenomic evidence for the close phylogenetic relationship between the early taurine cattle in Northern China and modern domestic cattle.},
}

@article {pmid35571044,
year = {2022},
author = {Sehrawat, JS and Agrawal, S and Sankhyan, D and Singh, M and Kumar, S and Prakash, S and Rajpal, R and Chaubey, G and Thangaraj, K and Rai, N},
title = {Pinpointing the Geographic Origin of 165-Year-Old Human Skeletal Remains Found in Punjab, India: Evidence From Mitochondrial DNA and Stable Isotope Analysis.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {813934},
doi = {10.3389/fgene.2022.813934},
pmid = {35571044},
issn = {1664-8021},
abstract = {In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ18O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ18O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers.},
}

@article {pmid35563041,
year = {2022},
author = {Heraclides, A and Fernández-Domínguez, E},
title = {Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods.},
journal = {International journal of molecular sciences},
volume = {23},
number = {9},
pages = {},
pmid = {35563041},
issn = {1422-0067},
mesh = {DNA, Ancient ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.},
}

DNA, Ancient
*DNA, Mitochondrial/genetics
*Genome, Mitochondrial
High-Throughput Nucleotide Sequencing/methods
Humans
Sequence Analysis, DNA/methods

@article {pmid35559028,
year = {2022},
author = {Ávila-Arcos, MC and de la Fuente Castro, C and Nieves-Colón, MA and Raghavan, M},
title = {Recommendations for Sustainable Ancient DNA Research in the Global South: Voices From a New Generation of Paleogenomicists.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {880170},
pmid = {35559028},
issn = {1664-8021},
abstract = {Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in "high impact" journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against 'helicopter science', such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos.},
}

@article {pmid35557944,
year = {2022},
author = {Buisan, R and Moriano, J and Andirkó, A and Boeckx, C},
title = {A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {824740},
pmid = {35557944},
issn = {2296-634X},
abstract = {Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of "archaic" haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.},
}

@article {pmid35552521,
year = {2022},
author = {Callaway, E},
title = {Ancient DNA maps 'dawn of farming'.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35552521},
issn = {1476-4687},
}

@article {pmid35550934,
year = {2022},
author = {Rath, K and Käßner, A and Melisch, C and Powers, N and Tichomirowa, M and Nagy, M and Friedrich, R and Riege, J and Rothe, J},
title = {Genetic and isotope analysis of a triple burial from medieval St. Peter's cemetery in Cölln/Berlin.},
journal = {Forensic science international. Genetics},
volume = {59},
number = {},
pages = {102718},
doi = {10.1016/j.fsigen.2022.102718},
pmid = {35550934},
issn = {1878-0326},
abstract = {The German capital Berlin originates from the two medieval settlements Berlin and Cölln on either side of the river Spree. Whereas Berlin is world famous, there is very little awareness of former Cölln. From 2007-2009, during excavations of the earliest cemetery of this forgotten medieval town; 3,126 graves were discovered containing the remains of 3,717 individuals. Amongst those graves was an unusual triple burial. This grave was exceptional due to the relative postures of the skeletons and their extensive facial injuries. Here we present genetic and isotope data for this grave. Genetic results confirmed all of them as biological male individuals and ruled out their biological kinship. Combining genetic ancestry information with strontium isotope data we furthermore determined that two of the men most likely originated from the Berlin-Brandenburg region, whereas a more distant origin of the third individual can be debated.},
}

@article {pmid35543411,
year = {2022},
author = {Cai, D and Zhu, S and Gong, M and Zhang, N and Wen, J and Liang, Q and Sun, W and Shao, X and Guo, Y and Cai, Y and Zheng, Z and Zhang, W and Hu, S and Wang, X and Tian, H and Li, Y and Liu, W and Yang, M and Yang, J and Wu, D and Orlando, L and Jiang, Y},
title = {Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.73346},
pmid = {35543411},
issn = {2050-084X},
support = {17ZDA221//Major Program of National Fund of Philosophy and Social Science of China/ ; 681605//H2020 European Research Council/ ; 31822052//National Natural Science Foundation of China/ ; },
abstract = {The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth-of-coverage. Radiocarbon dating demonstrates that this lineage survived until ~3,500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 Million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.},
}

@article {pmid35538842,
year = {2022},
author = {Verry, AJF and Mitchell, KJ and Rawlence, NJ},
title = {Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus).},
journal = {Biology letters},
volume = {18},
number = {5},
pages = {20220013},
doi = {10.1098/rsbl.2022.0013},
pmid = {35538842},
issn = {1744-957X},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; *Genetic Variation ; Haplotypes ; Phylogeny ; Phylogeography ; *Refugium ; },
abstract = {Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.},
}

Animals
DNA, Mitochondrial/genetics
Ecosystem
*Genetic Variation
Haplotypes
Phylogeny
Phylogeography
*Refugium

@article {pmid35537469,
year = {2022},
author = {Fleskes, RE and Bader, AC and Tsosie, KS and Wagner, JK and Claw, KG and Garrison, NA},
title = {Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives.},
journal = {Annual review of genomics and human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genom-120621-090239},
pmid = {35537469},
issn = {1545-293X},
abstract = {Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities, such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid35537455,
year = {2022},
author = {Segawa, T and Yonezawa, T and Mori, H and Kohno, A and Kudo, Y and Akiyoshi, A and Wu, J and Tokanai, F and Sakamoto, M and Kohno, N and Nishihara, H},
title = {Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.04.034},
pmid = {35537455},
issn = {1879-0445},
abstract = {Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.},
}

@article {pmid35526849,
year = {2022},
author = {Malyarchuk, AB and Andreeva, TV and Kuznetsova, IL and Kunizheva, SS and Protasova, MS and Uralsky, LI and Tyazhelova, TV and Gusev, FE and Manakhov, AD and Rogaev, EI},
title = {Genomics of Ancient Pathogens: First Advances and Prospects.},
journal = {Biochemistry. Biokhimiia},
volume = {87},
number = {3},
pages = {242-258},
pmid = {35526849},
issn = {1608-3040},
mesh = {DNA, Ancient ; *Genomics/methods ; History, Ancient ; Humans ; Mycobacterium leprae/genetics ; Paleontology ; *Yersinia pestis/genetics ; },
abstract = {Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.},
}

DNA, Ancient
*Genomics/methods
History, Ancient
Humans
Mycobacterium leprae/genetics
Paleontology
*Yersinia pestis/genetics

@article {pmid35508651,
year = {2022},
author = {Gelabert, P and Schmidt, RW and Fernandes, DM and Karsten, JK and Harper, TK and Madden, GD and Ledogar, SH and Sokhatsky, M and Oota, H and Kennett, DJ and Pinhasi, R},
title = {Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7242},
pmid = {35508651},
issn = {2045-2322},
support = {PACE #70245//European Commission's Marie Skłodowska-Curie/ ; BCS-1725067//National Science Foundation/ ; BCS-1725067//National Science Foundation/ ; },
mesh = {Agriculture ; *DNA, Ancient ; Europe ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Ukraine ; },
abstract = {The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000-3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935-825 cal BCE). Results reveal that the CTCC individuals' ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980-825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.},
}

Agriculture
*DNA, Ancient
Europe
Genome, Human
History, Ancient
*Human Migration
Humans
Ukraine

@article {pmid35506242,
year = {2022},
author = {Martínez-García, L and Ferrari, G and Hufthammer, AK and Jakobsen, KS and Jentoft, S and Barrett, JH and Star, B},
title = {Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene.},
journal = {Biology letters},
volume = {18},
number = {5},
pages = {20220021},
doi = {10.1098/rsbl.2022.0021},
pmid = {35506242},
issn = {1744-957X},
mesh = {Animals ; Climate Change ; *DNA, Ancient ; Fishes ; *Gadus morhua/genetics ; Temperature ; },
abstract = {Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, 14C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.},
}

Animals
Climate Change
*DNA, Ancient
Fishes
*Gadus morhua/genetics
Temperature

@article {pmid35506233,
year = {2022},
author = {Yarlagadda, K and Zachwieja, AJ and de Flamingh, A and Phungviwatnikul, T and Rivera-Colón, AG and Roseman, C and Shackelford, L and Swanson, KS and Malhi, RS},
title = {Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1974},
pages = {20220052},
doi = {10.1098/rspb.2022.0052},
pmid = {35506233},
issn = {1471-2954},
mesh = {Animals ; Diet ; Dogs ; Feces ; India ; *Microbiota ; South Africa ; },
abstract = {Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.},
}

Animals
Diet
Dogs
Feces
India
*Microbiota
South Africa

@article {pmid35494246,
year = {2022},
author = {Yu, H and van de Loosdrecht, MS and Mannino, MA and Talamo, S and Rohrlach, AB and Childebayeva, A and Villalba-Mouco, V and Aron, F and Brandt, G and Burri, M and Freund, C and Radzeviciute, R and Stahl, R and Wissgott, A and Fewlass, H and Tagliacozzo, A and Piperno, M and Tusa, S and Collina, C and Schimmenti, V and Di Salvo, R and Prüfer, K and Posth, C and Hublin, JJ and Gronenborn, D and Binder, D and Jeong, C and Haak, W and Krause, J},
title = {Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily.},
journal = {iScience},
volume = {25},
number = {5},
pages = {104244},
pmid = {35494246},
issn = {2589-0042},
abstract = {Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell'Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.},
}

@article {pmid35482488,
year = {2022},
author = {Ausmees, K and Sanchez-Quinto, F and Jakobsson, M and Nettelblad, C},
title = {An empirical evaluation of genotype imputation of ancient DNA.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkac089},
pmid = {35482488},
issn = {2160-1836},
abstract = {With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle 4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data with respect to accuracy, reference bias and genetic affinities as captured by PCA. We obtained genotype concordance levels of over 99% for data with 1x coverage, and similar levels of accuracy and reference bias at levels as low as 0.75x. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1x. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for post-processing and validation prior to downstream analysis.},
}

@article {pmid35476992,
year = {2022},
author = {Kędzior, M and Garcia, AK and Li, M and Taton, A and Adam, ZR and Young, JN and Kaçar, B},
title = {Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time.},
journal = {Cell reports},
volume = {39},
number = {4},
pages = {110726},
doi = {10.1016/j.celrep.2022.110726},
pmid = {35476992},
issn = {2211-1247},
support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteria/genetics ; Carbon Isotopes ; *Ribulose-Bisphosphate Carboxylase/chemistry/genetics ; },
abstract = {The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.},
}

*Bacteria/genetics
Carbon Isotopes
*Ribulose-Bisphosphate Carboxylase/chemistry/genetics

@article {pmid35456493,
year = {2022},
author = {Dehasque, M and Pečnerová, P and Kempe Lagerholm, V and Ersmark, E and Danilov, GK and Mortensen, P and Vartanyan, S and Dalén, L},
title = {Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.},
journal = {Genes},
volume = {13},
number = {4},
pages = {},
pmid = {35456493},
issn = {2073-4425},
mesh = {Bone and Bones ; DNA/genetics ; *DNA, Ancient ; *Silicon Dioxide ; Uracil ; },
abstract = {Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.},
}

Bone and Bones
DNA/genetics
*DNA, Ancient
*Silicon Dioxide
Uracil

@article {pmid35456371,
year = {2022},
author = {Gînguță, A and Kovács, B and Tihanyi, B and Maár, K and Schütz, O and Maróti, Z and Varga, GIB and Kiss, AP and Stanciu, I and Török, T and Neparáczki, E},
title = {Maternal Lineages of Gepids from Transylvania.},
journal = {Genes},
volume = {13},
number = {4},
pages = {},
pmid = {35456371},
issn = {2073-4425},
mesh = {Archaeology ; Cemeteries ; *Gene Pool ; *Genetics, Population ; Humans ; Whites ; },
abstract = {According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is explored for the first time, providing new insights into the genetic makeup of this archaic group. The retrieved genetic data showed mainly the presence of Northwestern European mitochondrial ancient lineages in the Gepid group and all population genetic analyses reiterated the same genetic structure, showing that early ancient mitogenomes from Europe were the major contributors to the Gepid maternal genetic pool.},
}

Archaeology
Cemeteries
*Gene Pool
*Genetics, Population
Humans
Whites

@article {pmid35446690,
year = {2022},
author = {Rivollat, M and Thomas, A and Ghesquière, E and Rohrlach, AB and Späth, E and Pemonge, MH and Haak, W and Chambon, P and Deguilloux, MF},
title = {Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {18},
pages = {e2120786119},
doi = {10.1073/pnas.2120786119},
pmid = {35446690},
issn = {1091-6490},
support = {2017-2018//Fondation Fyssen (Fyssen Foundation)/ ; ANR-17-FRAL-0010//ANR / DFG/ ; 771234 - PALEoRIDER//European Union''''s Horizon 2020 research and innovation program/ ; },
mesh = {Archaeology ; Burial/history ; *Cemeteries ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; Genomics ; History, Ancient ; Humans ; Male ; },
abstract = {SignificanceBy integrating genomic and archaeological data, we provide new insights into the Neolithic French monumental site of Fleury-sur-Orne in Normandy, where a group of selected individuals was buried in impressively long monuments. The earliest individuals buried at Fleury-sur-Orne match the expected western European Neolithic genetic diversity, while three individuals, designated as genetic outliers, were buried after 4,000 calibrated BCE. We hypothesize that different, unrelated families or clans used the site over several centuries. Thirteen of 14 of the analyzed individuals were male, indicating an overarching patrilineal system. However, one exception, a female buried with a symbolically male artifact, suggests that the embodiment of the male gender in death was required to access burial at the monumental structures.},
}

Archaeology
Burial/history
*Cemeteries
*DNA, Ancient
DNA, Mitochondrial/genetics
Female
Genomics
History, Ancient
Humans
Male

@article {pmid35445261,
year = {2022},
author = {Vallini, L and Marciani, G and Aneli, S and Bortolini, E and Benazzi, S and Pievani, T and Pagani, L},
title = {Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.},
journal = {Genome biology and evolution},
volume = {14},
number = {4},
pages = {},
pmid = {35445261},
issn = {1759-6653},
mesh = {Africa ; Animals ; Anthropology, Cultural ; Europe ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Siberia ; },
abstract = {The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.},
}

Africa
Animals
Anthropology, Cultural
Europe
Genetics, Population
Humans
*Neanderthals/genetics
Siberia

@article {pmid35440148,
year = {2022},
author = {Brand, CM and Colbran, LL and Capra, JA},
title = {Predicting Archaic Hominin Phenotypes from Genomic Data.},
journal = {Annual review of genomics and human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genom-111521-121903},
pmid = {35440148},
issn = {1545-293X},
abstract = {Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid35422088,
year = {2022},
author = {Guiry, EJ and James, M and Cheung, C and Royle, TCA},
title = {Four millennia of long-term individual foraging site fidelity in a highly migratory marine predator.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {368},
pmid = {35422088},
issn = {2399-3642},
mesh = {Animals ; *Birds ; Geography ; },
abstract = {Theory and field studies suggest that long-term individual foraging site fidelity (IFSF) may be an important adaptation to competition from increasing population. However, the driving mechanisms and extent of long-term IFSF in wild populations of long-lived, migratory animals has been logistically difficult to study, with only a few confirmed instances. Temporal isotopic datasets can reveal long-term patterns in geographical foraging behaviour. We investigate the isotopic compositions of endangered short-tailed albatross (Phoebastria albatrus) over four millennia leading up to their near-extinction. Although not exhibited by short-tailed albatross today, we show past sub-populations displayed a high-degree of long-term IFSF, focusing on the same locations for hundreds of generations. This is the first large-scale evidence for the deep antiquity of long-term IFSF and suggests that it's density-driven. Globally, as populations of species like short-tailed albatross continue to recover from overexploitation, potential for resurgence of geographic specialization may increase exposure to localized hazards, requiring closer conservation monitoring.},
}

Animals
*Birds
Geography

@article {pmid35421701,
year = {2022},
author = {Bonsu, DOM and Afoakwah, CB and Abedi, M and Higgins, D and Austin, JJ},
title = {Ethics reporting in forensic science research publications - A review.},
journal = {Forensic science international},
volume = {335},
number = {},
pages = {111290},
doi = {10.1016/j.forsciint.2022.111290},
pmid = {35421701},
issn = {1872-6283},
abstract = {An essential element of compliance with ethical standards in scientific research is the reporting of a verifiable declaration of ethical approval and, when human subjects are involved - informed consent, in published works. The level of reporting of ethical permission for research published in forensic and investigative sciences journals has not been explored to date. Hence, we examined the reporting of ethical approval and informed consent in original research utilising human or animal subjects published in six forensic science journals from 2010 to 2019. We identified 10,192 articles and retained 3010 that satisfied the inclusion criteria of utilising human (91.2%), or animal (7.0%) or both (1.8%) subjects or tissues in experiments. Just over a third (1079/3010) of all studies declared obtaining ethical approval, with 927 (85.9%) of those indicating the name of the ethical committee, but only 392 (36%) provided an approval code. Furthermore, while consent was said to have been sought in 527 (17.5%) of studies, only 155 of those reported that written informed consent was obtained, eleven stated oral (verbal) consent, while the remaining 357 studies (67.7%) did not report the process used to gain consent. Ethical approval reporting rates differed between different research types, availability of financial support and whether authors were affiliated to academia or industry. The results demonstrate a low level of declaration of ethical approval and informed consent in forensic science research and publication, requiring urgent rectification. We support the adoption of the model proposed by Forensic Science International: Genetics as baseline recommendations to facilitate consistent nomenclature, transparency, and standard of ethical reporting in forensic science.},
}

@article {pmid35413261,
year = {2022},
author = {Schlebusch, CM},
title = {Genomics: Testing the limits of de-extinction.},
journal = {Current biology : CB},
volume = {32},
number = {7},
pages = {R324-R327},
doi = {10.1016/j.cub.2022.03.023},
pmid = {35413261},
issn = {1879-0445},
mesh = {DNA, Ancient ; *Extinction, Biological ; Genome ; *Genomics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Resurrecting extinct species through de-extinction by genome editing requires full and unbiased information from the extinct species' genome. A new study establishes a framework to assess how much of an extinct species genome can be recovered by ancient DNA sequencing and which factors influence recovery.},
}

DNA, Ancient
*Extinction, Biological
Genome
*Genomics
Phylogeny
Sequence Analysis, DNA

@article {pmid35412864,
year = {2022},
author = {Andrades Valtueña, A and Neumann, GU and Spyrou, MA and Musralina, L and Aron, F and Beisenov, A and Belinskiy, AB and Bos, KI and Buzhilova, A and Conrad, M and Djansugurova, LB and Dobeš, M and Ernée, M and Fernández-Eraso, J and Frohlich, B and Furmanek, M and Hałuszko, A and Hansen, S and Harney, É and Hiss, AN and Hübner, A and Key, FM and Khussainova, E and Kitov, E and Kitova, AO and Knipper, C and Kühnert, D and Lalueza-Fox, C and Littleton, J and Massy, K and Mittnik, A and Mujika-Alustiza, JA and Olalde, I and Papac, L and Penske, S and Peška, J and Pinhasi, R and Reich, D and Reinhold, S and Stahl, R and Stäuble, H and Tukhbatova, RI and Vasilyev, S and Veselovskaya, E and Warinner, C and Stockhammer, PW and Haak, W and Krause, J and Herbig, A},
title = {Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {17},
pages = {e2116722119},
doi = {10.1073/pnas.2116722119},
pmid = {35412864},
issn = {1091-6490},
support = {NA//Max-Planck-Gesellschaft (MPG)/ ; 771234//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; 856453//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; 834616//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; WIN Kolleg//Heidelberger Akademie der Wissenschaften (Heidelberg Academy of Sciences and Humanities)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; AP08856654//Ministry of Education and Science of the Republic of Kazakhstan (Ministry of Education and Science, Republic of Kazakhstan)/ ; },
mesh = {Animal Husbandry/history ; Animals ; DNA, Ancient ; Genetic Variation ; *Genome, Bacterial ; History, Ancient ; Human Migration/history ; Humans ; Phylogeny ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/classification/genetics/isolation & purification ; },
abstract = {SignificanceThe bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen's genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry.},
}

Animal Husbandry/history
Animals
DNA, Ancient
Genetic Variation
*Genome, Bacterial
History, Ancient
Human Migration/history
Humans
Phylogeny
*Plague/epidemiology/history/microbiology
*Yersinia pestis/classification/genetics/isolation & purification

@article {pmid35402880,
year = {2022},
author = {Fischer, CE and Pemonge, MH and Ducoussau, I and Arzelier, A and Rivollat, M and Santos, F and Barrand Emam, H and Bertaud, A and Beylier, A and Ciesielski, E and Dedet, B and Desenne, S and Duday, H and Chenal, F and Gailledrat, E and Goepfert, S and Gorgé, O and Gorgues, A and Kuhnle, G and Lambach, F and Lefort, A and Mauduit, A and Maziere, F and Oudry, S and Paresys, C and Pinard, E and Plouin, S and Richard, I and Roth-Zehner, M and Roure, R and Thevenet, C and Thomas, Y and Rottier, S and Deguilloux, MF and Pruvost, M},
title = {Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics.},
journal = {iScience},
volume = {25},
number = {4},
pages = {104094},
pmid = {35402880},
issn = {2589-0042},
abstract = {The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.},
}

@article {pmid35398984,
year = {2022},
author = {Suchan, T and Chauvey, L and Poullet, M and Tonasso-Calvière, L and Schiavinato, S and Clavel, P and Clavel, B and Lepetz, S and Seguin-Orlando, A and Orlando, L},
title = {Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13619},
pmid = {35398984},
issn = {1755-0998},
support = {//University Paul Sabatier IDEX Chaire d'Excellence (OURASI)/ ; //CNRS Programme de Recherche Conjoint (PRC)/ ; //CNRS International Research Project (IRP AMADEUS)/ ; 681605//European Union's Horizon 2020 Research and Innovation Programme/ ; 797449//Marie Skłodowska-Curie/ ; //European Research Council (ERC)/ ; },
abstract = {Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.},
}

@article {pmid35389750,
year = {2022},
author = {Marciniak, S and Bergey, CM and Silva, AM and Hałuszko, A and Furmanek, M and Veselka, B and Velemínský, P and Vercellotti, G and Wahl, J and Zariņa, G and Longhi, C and Kolář, J and Garrido-Pena, R and Flores-Fernández, R and Herrero-Corral, AM and Simalcsik, A and Müller, W and Sheridan, A and Miliauskienė, Ž and Jankauskas, R and Moiseyev, V and Köhler, K and Király, Á and Gamarra, B and Cheronet, O and Szeverényi, V and Kiss, V and Szeniczey, T and Kiss, K and Zoffmann, ZK and Koós, J and Hellebrandt, M and Maier, RM and Domboróczki, L and Virag, C and Novak, M and Reich, D and Hajdu, T and von Cramon-Taubadel, N and Pinhasi, R and Perry, GH},
title = {An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {15},
pages = {e2106743119},
doi = {10.1073/pnas.2106743119},
pmid = {35389750},
issn = {1091-6490},
support = {222377//Wenner-Gren Foundation/ ; R01-GM115656//HHS | National Institutes of Health (NIH)/ ; 19-20970Y//Czech Science Foundation/ ; HRZZ IP-2016-06-1450//Croatian Science Fund/ ; DKRVO/2019-2023/7.I.d//Ministry of Culture of the Czech Republic/ ; FK128013//Hungarian Research, Development and Innovation Office/ ; H2020-MSCA-IF-2015 -703373//EC | H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (MSCA)/ ; },
mesh = {Adult ; *Agriculture/history ; *Body Height/genetics ; Child ; DNA, Ancient ; Europe ; *Farmers/history ; Genetic Variation ; Genomics ; *Health/history ; History, Ancient ; Humans ; Paleopathology ; *Skeleton/anatomy & histology ; },
abstract = {SignificanceSubsistence shifts from hunting and gathering to agriculture over the last 12,000 y have impacted human culture, biology, and health. Although past human health cannot be assessed directly, adult stature variation and skeletal indicators of nonspecific stress can serve as proxies for health during growth and development. By integrating paleogenomic genotype and osteological stature data on a per-individual basis for 167 prehistoric Europeans, we observe relatively shorter than expected statures among early farmers after correcting for individual genetic contributions to stature. Poorer nutrition and/or increased disease burdens for early agriculturalists may partly underscore this result. Our integrated osteological-genetic model has exciting potential for studies of past human health and expansion into various other contexts.},
}

Adult
*Agriculture/history
*Body Height/genetics
Child
DNA, Ancient
Europe
*Farmers/history
Genetic Variation
Genomics
*Health/history
History, Ancient
Humans
Paleopathology
*Skeleton/anatomy & histology

@article {pmid35383854,
year = {2022},
author = {Di, D and Simon Thomas, J and Currat, M and Nunes, JM and Sanchez-Mazas, A},
title = {Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35383854},
issn = {1537-1719},
support = {/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {DNA ; DNA, Ancient ; Europe ; *Genetic Predisposition to Disease ; *HLA Antigens/genetics ; Histocompatibility Antigens Class II ; Humans ; *Plague/genetics ; Yersinia pestis ; },
abstract = {In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059-4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.},
}

DNA
DNA, Ancient
Europe
*Genetic Predisposition to Disease
*HLA Antigens/genetics
Histocompatibility Antigens Class II
Humans
*Plague/genetics
Yersinia pestis

@article {pmid35382600,
year = {2022},
author = {Barrett, JH and Khamaiko, N and Ferrari, G and Cuevas, A and Kneale, C and Hufthammer, AK and Pálsdóttir, AH and Star, B},
title = {Walruses on the Dnieper: new evidence for the intercontinental trade of Greenlandic ivory in the Middle Ages.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1972},
pages = {20212773},
pmid = {35382600},
issn = {1471-2954},
mesh = {Animals ; Archaeology ; *DNA, Ancient ; Geography ; Russia ; *Walruses/genetics ; },
abstract = {Mediaeval walrus hunting in Iceland and Greenland-driven by Western European demand for ivory and walrus hide ropes-has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine-combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.},
}

Animals
Archaeology
*DNA, Ancient
Geography
Russia
*Walruses/genetics

@article {pmid35366416,
year = {2022},
author = {Gnecchi-Ruscone, GA and Szécsényi-Nagy, A and Koncz, I and Csiky, G and Rácz, Z and Rohrlach, AB and Brandt, G and Rohland, N and Csáky, V and Cheronet, O and Szeifert, B and Rácz, TÁ and Benedek, A and Bernert, Z and Berta, N and Czifra, S and Dani, J and Farkas, Z and Hága, T and Hajdu, T and Jászberényi, M and Kisjuhász, V and Kolozsi, B and Major, P and Marcsik, A and Kovacsóczy, BN and Balogh, C and Lezsák, GM and Ódor, JG and Szelekovszky, M and Szeniczey, T and Tárnoki, J and Tóth, Z and Tutkovics, EK and Mende, BG and Geary, P and Pohl, W and Vida, T and Pinhasi, R and Reich, D and Hofmanová, Z and Jeong, C and Krause, J},
title = {Ancient genomes reveal origin and rapid trans-Eurasian migration of 7th century Avar elites.},
journal = {Cell},
volume = {185},
number = {8},
pages = {1402-1413.e21},
doi = {10.1016/j.cell.2022.03.007},
pmid = {35366416},
issn = {1097-4172},
mesh = {*Asians/genetics ; *DNA, Ancient ; *Genetics, Population ; Genome ; History, Ancient ; Human Migration/history ; Humans ; Sulfur ; },
abstract = {The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.},
}

*Asians/genetics
*DNA, Ancient
*Genetics, Population
Genome
History, Ancient
Human Migration/history
Humans
Sulfur

@article {pmid35359699,
year = {2022},
author = {Molodtseva, AS and Makunin, AI and Salomashkina, VV and Kichigin, IG and Vorobieva, NV and Vasiliev, SK and Shunkov, MV and Tishkin, AA and Grushin, SP and Anijalg, P and Tammeleht, E and Keis, M and Boeskorov, GG and Mamaev, N and Okhlopkov, IM and Kryukov, AP and Lyapunova, EA and Kholodova, MV and Seryodkin, IV and Saarma, U and Trifonov, VA and Graphodatsky, AS},
title = {Phylogeography of ancient and modern brown bears from eastern Eurasia.},
journal = {Biological journal of the Linnean Society. Linnean Society of London},
volume = {135},
number = {4},
pages = {722-733},
pmid = {35359699},
issn = {0024-4066},
abstract = {The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.},
}

@article {pmid35356467,
year = {2022},
author = {Arizmendi Cárdenas, YO and Neuenschwander, S and Malaspinas, AS},
title = {Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12784},
pmid = {35356467},
issn = {2167-8359},
abstract = {Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.},
}

@article {pmid35356424,
year = {2022},
author = {Xiong, J and Du, P and Chen, G and Tao, Y and Zhou, B and Yang, Y and Wang, H and Yu, Y and Chang, X and Allen, E and Sun, C and Zhou, J and Zou, Y and Xu, Y and Meng, H and Tan, J and Li, H and Wen, S},
title = {Sex-Biased Population Admixture Mediated Subsistence Strategy Transition of Heishuiguo People in Han Dynasty Hexi Corridor.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {827277},
pmid = {35356424},
issn = {1664-8021},
abstract = {The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE-220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oβ-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.},
}

@article {pmid35342764,
year = {2022},
author = {Kim, K and Kim, DH and Kim, KY},
title = {Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {5344418},
pmid = {35342764},
issn = {2314-6141},
mesh = {*DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; },
abstract = {Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.},
}

*DNA, Ancient
DNA, Mitochondrial/genetics
*Genome, Mitochondrial/genetics
Haplotypes/genetics
Humans
Mitochondria/genetics

@article {pmid35336803,
year = {2022},
author = {Horsburgh, KA and Beckett, DB and Gosling, AL},
title = {Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups.},
journal = {Biology},
volume = {11},
number = {3},
pages = {},
pmid = {35336803},
issn = {2079-7737},
support = {N/A//Fry Undergraduate Award, Southern Methodist University/ ; N/A//University of Otago Research Grant/ ; },
abstract = {We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.},
}

@article {pmid35324275,
year = {2022},
author = {Gibbons, A},
title = {Southern roots for the Maya-and the maize that fed them.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6587},
pages = {1325},
doi = {10.1126/science.abq1704},
pmid = {35324275},
issn = {1095-9203},
abstract = {Migrants from the south may have helped spread early farming in Central America, ancient DNA suggests.},
}

@article {pmid35318319,
year = {2022},
author = {Kennett, DJ and Lipson, M and Prufer, KM and Mora-Marín, D and George, RJ and Rohland, N and Robinson, M and Trask, WR and Edgar, HHJ and Hill, EC and Ray, EE and Lynch, P and Moes, E and O'Donnell, L and Harper, TK and Kate, EJ and Ramos, J and Morris, J and Gutierrez, SM and Ryan, TM and Culleton, BJ and Awe, JJ and Reich, D},
title = {South-to-north migration preceded the advent of intensive farming in the Maya region.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1530},
pmid = {35318319},
issn = {2041-1723},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Agriculture ; Central America ; Colombia ; *DNA, Ancient ; Forests ; Humans ; },
abstract = {The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.},
}

*Agriculture
Central America
Colombia
*DNA, Ancient
Forests
Humans

@article {pmid35312358,
year = {2022},
author = {Severson, AL and Byrd, BF and Mallott, EK and Owings, AC and DeGiorgio, M and de Flamingh, A and Nijmeh, C and Arellano, MV and Leventhal, A and Rosenberg, NA and Malhi, RS},
title = {Ancient and modern genomics of the Ohlone Indigenous population of California.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {13},
pages = {e2111533119},
pmid = {35312358},
issn = {1091-6490},
mesh = {Archaeology ; DNA, Ancient ; Genetics, Population ; *Genomics ; History, Ancient ; Humans ; *Indigenous Peoples ; Linguistics ; San Francisco ; },
abstract = {SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.},
}

Archaeology
DNA, Ancient
Genetics, Population
*Genomics
History, Ancient
Humans
*Indigenous Peoples
Linguistics
San Francisco

@article {pmid35307645,
year = {2022},
author = {Fu, M and Li, Y},
title = {The origin and domestication history of domestic horses and the domestication characteristics of breeds.},
journal = {Yi chuan = Hereditas},
volume = {44},
number = {3},
pages = {216-229},
doi = {10.16288/j.yczz.21-260},
pmid = {35307645},
issn = {0253-9772},
mesh = {Animals ; Animals, Domestic/genetics ; *Breeding ; DNA, Mitochondrial/genetics ; *Domestication ; *Horses/genetics ; Phylogeny ; },
abstract = {The horse (Equus caballus) was domesticated thousands of years after dog, cattle, pig, sheep, and goat. Importantly, it represents the domestic animal that mostly impacted the development of human civilization. Its excellent loading and moving ability prompted the changes from fixed farming mode into mobile sharing mode. Accordingly, its domestication history deserves considerable attention. So far, many issues have long been controversial, due to the extinction of the closest wild relatives and the dramatic reduction of genetic diversity. With the continuous development of sequencing technology and the utilization of ancient samples, we got more clues to the origin and domestication process. In this review, we summarize 1) current progresses on the domestication history revealed by nuclear genes, mtDNA, Y chromosome, and ancient DNA, 2) the characteristics of population structure and diversification among modern breeds, 3) the genetic basis of important phenotypes, such as coat color, speed, and body size. The overall aim of the review is to provide in-depth insights into the studies of horse domestication, the preservation and utilization of genetic resources, the direction of breeding improvement, and the development of modern horse industry in future.},
}

Animals
Animals, Domestic/genetics
*Breeding
DNA, Mitochondrial/genetics
*Domestication
*Horses/genetics
Phylogeny

@article {pmid35306727,
year = {2022},
author = {Scarsbrook, L and Verry, AJF and Walton, K and Hitchmough, RA and Rawlence, NJ},
title = {Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16434},
pmid = {35306727},
issn = {1365-294X},
support = {//University of Otago/ ; 16-UOO-096//Royal Society Te Apārangi/ ; },
abstract = {Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898-2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-computed tomography reconstructions. All "large gecko" specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue-derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.},
}

@article {pmid35306671,
year = {2022},
author = {Schwörer, C and Leunda, M and Alvarez, N and Gugerli, F and Sperisen, C},
title = {The untapped potential of macrofossils in ancient plant DNA research.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18108},
pmid = {35306671},
issn = {1469-8137},
support = {SNF- 200021_188472//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; SFL-19 P4//SwissForestLab/ ; },
abstract = {The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.},
}

@article {pmid35294015,
year = {2022},
author = {Biddanda, A and Steinrücken, M and Novembre, J},
title = {Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.},
journal = {Genetics},
volume = {221},
number = {1},
pages = {},
doi = {10.1093/genetics/iyac038},
pmid = {35294015},
issn = {1943-2631},
support = {R01 HG007089/HG/NHGRI NIH HHS/United States ; //University of Chicago's Research Computing Center/ ; T32 GM07197/GF/NIH HHS/United States ; },
mesh = {Archaeology/*methods ; Genetics, Population/*methods ; Genotype ; Haplotypes ; Humans ; Linkage Disequilibrium ; Population Density ; },
abstract = {Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.},
}

Archaeology/*methods
Genetics, Population/*methods
Genotype
Haplotypes
Humans
Linkage Disequilibrium
Population Density

@article {pmid35288946,
year = {2022},
author = {Her, C and Rezaei, HR and Hughes, S and Naderi, S and Duffraisse, M and Mashkour, M and Naghash, HR and Bălășescu, A and Luikart, G and Jordan, S and Özüt, D and Kence, A and Bruford, MW and Tresset, A and Vigne, JD and Taberlet, P and Hänni, C and Pompanon, F},
title = {Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros.},
journal = {Animal genetics},
volume = {53},
number = {3},
pages = {452-459},
doi = {10.1111/age.13191},
pmid = {35288946},
issn = {1365-2052},
support = {ANR 05-GANI-004-02//Project Chronobos/ ; },
mesh = {Animals ; Cytochromes b/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Phylogeny ; Sheep/genetics ; *Sheep, Domestic/genetics ; Turkey ; },
abstract = {We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).},
}

Animals
Cytochromes b/genetics
*DNA, Mitochondrial/genetics
Genetic Variation
Haplotypes
Phylogeny
Sheep/genetics
*Sheep, Domestic/genetics
Turkey

@article {pmid35288565,
year = {2022},
author = {Zhou, BF and Yuan, S and Crowl, AA and Liang, YY and Shi, Y and Chen, XY and An, QQ and Kang, M and Manos, PS and Wang, B},
title = {Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1320},
pmid = {35288565},
issn = {2041-1723},
mesh = {Ecosystem ; Forests ; *Genome, Plastid/genetics ; Phylogeny ; *Quercus ; },
abstract = {Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia.},
}

Ecosystem
Forests
*Genome, Plastid/genetics
Phylogeny
*Quercus

@article {pmid35279516,
year = {2022},
author = {Lorentz, KO and Kamel, G and Lemmers, SAM and Miyauchi, Y and Çubukçu, E and Alpagut, A and Büyükkarakaya, AM},
title = {Synchrotron Radiation Fourier Transform Infrared (SR-FTIR) spectroscopy in exploring ancient human hair from Roman period Juliopolis: Preservation status and alterations of organic compounds.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {274},
number = {},
pages = {121026},
doi = {10.1016/j.saa.2022.121026},
pmid = {35279516},
issn = {1873-3557},
mesh = {Archaeology/methods ; *Body Remains ; Fourier Analysis ; Hair/chemistry ; Humans ; Organic Chemicals ; Spectroscopy, Fourier Transform Infrared/methods ; *Synchrotrons ; },
abstract = {We explore the preservation status and alterations of organic compounds in Roman period human hairstrandsfrom a specific individual (M196) excavated at Juliopolis (JP). How do these organic compounds present in this c. 2000-year-old human hair compare to those present in modern hair? Alterations to organic compounds in archaeological human hair are caused by biological degradative processes dependent on multifactorial processes acting on the hair since the deposition of a body in a mortuary context. We investigate the type of organic compounds present using Synchrotron Radiation Fourier Transform Infrared (SR-FTIR). Juliopolis (Iuliopolis) is an ancient multiperiod city, located in the Çayırhan district of Nallıhan, northwest of Ankara. The Juliopolis necropolis from which M196 was recovered was in use throughout the Hellenistic, Roman, and Byzantine periods, and yielded over 700 tombs with numerous human remains. One tomb (M196) contained human remains of exceptional preservation status, including substantial amounts of hair. Human hair from archaeological contexts is not only extremely rare, but importantly, has high analytical value, with potential for analysis of diet, geographical origins, ancient DNA, metal exposure, and other aspects of life in a time-resolved manner. These data make significant contributions to the life history of the individual (osteobiography), as well as contribute towards key archaeological questions. As these analyses are in their majority destructive, prior evaluation of the preservation of sufficient amounts of the organic compounds on which many such analyses rely upon is crucial, to avoid unnecessary loss of precious ancient samples. The results of our SR-FTIR analyses at SESAME synchrotron show that keratin in the JP M196 is more degraded in comparison to the modern reference sample. However, the results also point to clear potential for further analyses with techniques relying on organic compound preservation, such as C and N isotopic analyses for diet, and aDNA.},
}

Archaeology/methods
*Body Remains
Fourier Analysis
Hair/chemistry
Humans
Organic Chemicals
Spectroscopy, Fourier Transform Infrared/methods
*Synchrotrons

@article {pmid35273713,
year = {2022},
author = {Singh, H and Shipra, and Sharma, V and Sharma, I and Sharma, A and Modeel, S and Gupta, N and Gupta, G and Pandita, AK and Butt, MF and Sharma, R and Pandita, S and Singh, V and Rai, E and Ikegawa, S and Sharma, S},
title = {The first study of epidemiology of adolescent idiopathic scoliosis shows lower prevalence in females of Jammu and Kashmir, India.},
journal = {American journal of translational research},
volume = {14},
number = {2},
pages = {1100-1106},
pmid = {35273713},
issn = {1943-8141},
abstract = {AIS is a heterogeneous 3D spinal deformity with Cobb angle ≥10°. It affects children in the age group of 10-16 years globally with 2-3% prevalence and significant female predominance. The exact etiology of AIS is not known however, it is supposed to be associated with factors such as anthropometric, metabolic, neuromuscular abnormalities and genetics.

OBJECTIVES: To determine the prevalence of AIS and association of anthropometric factors with AIS in the studied population group.

METHODOLOGY: Scoliosis screening of 9,500 individuals was carried out at different educational institutions of Jammu region in Jammu and Kashmir, India using a scoliosis-meter. The subjects were later examined radiologically.

RESULTS: In population of the region, AIS was most prevalent among all types of scoliosis with overall prevalence of 0.61%. The prevalence was observed to be lower in females (0.31%) than males (0.88%). Based on angle of trunk rotation (ATR), lumbar curves were more prevalent than thoracic curves. Average Cobb angle in males and females were 24.9° and 22.6°, respectively. BMI showed significant association with AIS in the age group of 12-16 years (P value =0.028). Furthermore, height was significantly associated with AIS in the overall screened population (P-value =0.029).

CONCLUSIONS: The AIS patients in the Jammu region of India have unique clinical features. In contrast to the global prevalence data, the prevalence of AIS in females in the region was less in comparison to males. Based on epidemiological literature and our findings, we hypothesized that genetic factors might be a major contributor in the AIS pathogenesis along with other confounding factors such as height, BMI, ethnicity, etc.},
}

@article {pmid35271794,
year = {2022},
author = {Lin, J and Duchêne, D and Carøe, C and Smith, O and Ciucani, MM and Niemann, J and Richmond, D and Greenwood, AD and MacPhee, R and Zhang, G and Gopalakrishnan, S and Gilbert, MTP},
title = {Probing the genomic limits of de-extinction in the Christmas Island rat.},
journal = {Current biology : CB},
volume = {32},
number = {7},
pages = {1650-1656.e3},
doi = {10.1016/j.cub.2022.02.027},
pmid = {35271794},
issn = {1879-0445},
mesh = {Animals ; Australia ; Biological Evolution ; Extinction, Biological ; *Genome ; *Genomics ; Norway ; Phylogeny ; Rats ; },
abstract = {Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3-5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.},
}

Animals
Australia
Biological Evolution
Extinction, Biological
*Genome
*Genomics
Norway
Phylogeny
Rats

@article {pmid35263821,
year = {2022},
author = {Zavala, EI and Aximu-Petri, A and Richter, J and Nickel, B and Vernot, B and Meyer, M},
title = {Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13607},
pmid = {35263821},
issn = {1755-0998},
support = {//Max-Planck-Gesellschaft/ ; },
abstract = {The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains or sediments in single studies. Nevertheless, demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here, we explored the possibility of improving the economics of sample preparation via multiplex capture, that is, the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the reamplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination.},
}

@article {pmid35256608,
year = {2022},
author = {Vågene, ÅJ and Honap, TP and Harkins, KM and Rosenberg, MS and Giffin, K and Cárdenas-Arroyo, F and Leguizamón, LP and Arnett, J and Buikstra, JE and Herbig, A and Krause, J and Stone, AC and Bos, KI},
title = {Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {1195},
pmid = {35256608},
issn = {2041-1723},
mesh = {Animals ; *Caniformia/genetics ; DNA, Ancient ; Humans ; *Mycobacterium/genetics ; *Mycobacterium tuberculosis/genetics ; Racial Groups ; South America/epidemiology ; *Tuberculosis/epidemiology/microbiology ; },
abstract = {Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.},
}

Animals
*Caniformia/genetics
DNA, Ancient
Humans
*Mycobacterium/genetics
*Mycobacterium tuberculosis/genetics
Racial Groups
South America/epidemiology
*Tuberculosis/epidemiology/microbiology

@article {pmid35240033,
year = {2022},
author = {Hong, JH and Oh, CS and Kim, S and Kang, IU and Shin, DH},
title = {Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.21.0500},
pmid = {35240033},
issn = {2765-0189},
abstract = {OBJECTIVE: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea.

METHODS: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by PCR. Cloning and sequencing was conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software.

RESULTS: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

CONCLUSION: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia.},
}

@article {pmid35238427,
year = {2022},
author = {Nores, R and Tavella, MP and Fabra, M and Demarchi, DA},
title = {Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {},
number = {},
pages = {e23733},
doi = {10.1002/ajhb.23733},
pmid = {35238427},
issn = {1520-6300},
support = {//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; //Ministerio de Ciencia y Tecnología, Gobierno de la Provincia de Córdoba/ ; //Secretaria de Ciencia y Tecnología - Universidad Nacional de Córdoba/ ; },
abstract = {OBJECTIVES: The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene.

METHODS: We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes.

RESULTS: Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly.

CONCLUSIONS: The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.},
}

@article {pmid35210171,
year = {2022},
author = {Jäger, HY and Maixner, F and Pap, I and Szikossy, I and Pálfi, G and Zink, AR},
title = {Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {},
number = {},
pages = {102181},
doi = {10.1016/j.tube.2022.102181},
pmid = {35210171},
issn = {1873-281X},
abstract = {The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors.},
}

@article {pmid35208912,
year = {2022},
author = {Reynoso-García, J and Narganes-Storde, Y and Santiago-Rodriguez, TM and Toranzos, GA},
title = {Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations.},
journal = {Microorganisms},
volume = {10},
number = {2},
pages = {},
pmid = {35208912},
issn = {2076-2607},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; 5R25GM061151-20/NH/NIH HHS/United States ; },
abstract = {Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman's large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.},
}

@article {pmid35205259,
year = {2022},
author = {Messelodi, D and Giuliani, C and Cipriani, F and Armuzzi, S and di Palmo, E and Garagnani, P and Bertelli, L and Astolfi, A and Luiselli, D and Ricci, G and Pession, A},
title = {C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205259},
issn = {2073-4425},
mesh = {*Asthma/epidemiology/genetics ; Child ; Gene Frequency ; *Genetic Predisposition to Disease ; Genotype ; Humans ; Polymorphism, Single Nucleotide ; },
abstract = {Asthma is a complex and heterogeneous disease, caused by the interaction between genetic and environmental factors with a predominant allergic background in children. The role of specific genes in asthmatic bronchial reactivity is still not clear, probably because of the many common pathways shared with other allergic disorders. This study is focused on 11 SNPs possibly related to asthma that were previously identified in a GWAS study. The genetic variability of these SNPs has been analysed in a population of 773 Italian healthy controls, and the presence of an association between the polymorphisms and the asthma onset was evaluated performing genotyping analysis on 108 children affected with asthma compared with the controls. Moreover, a pool of 171 patients with only allergic rhinoconjunctivitis has been included in the case-control analysis. The comparison of allele frequencies in asthmatic patients versus healthy controls identified two SNPs-rs1162394 (p = 0.019) and rs25681 (p = 0.044)-associated with the asthmatic condition, which were not differentially distributed in the rhinoconjunctivitis group. The rs25681 SNP, together with three other SNPs, also resulted in not being homogenously distributed in the Italian population. The significantly higher frequency of the rs25681 and rs1162394 SNPs (located, respectively, in the C5 and SRGAP3 genes) in the asthmatic population suggests an involvement of these genes in the asthmatic context, playing a role in increasing the inflammatory condition that may influence asthma onset and clinical course.},
}

*Asthma/epidemiology/genetics
Child
Gene Frequency
*Genetic Predisposition to Disease
Genotype
Humans
Polymorphism, Single Nucleotide

@article {pmid35205247,
year = {2022},
author = {Loreille, O and Tillmar, A and Brandhagen, MD and Otterstatter, L and Irwin, JA},
title = {Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205247},
issn = {2073-4425},
mesh = {Aged ; DNA, Mitochondrial/analysis/genetics ; Female ; *Genome, Mitochondrial ; Hair/chemistry ; Heteroplasmy ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; },
abstract = {This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina's lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas' maternal lineage, including the well-known point heteroplasmy at position 16169.},
}

Aged
DNA, Mitochondrial/analysis/genetics
Female
*Genome, Mitochondrial
Hair/chemistry
Heteroplasmy
*High-Throughput Nucleotide Sequencing/methods
Humans

@article {pmid35205223,
year = {2022},
author = {Niiranen, L and Leciej, D and Edlund, H and Bernhardsson, C and Fraser, M and Quinto, FS and Herzig, KH and Jakobsson, M and Walkowiak, J and Thalmann, O},
title = {Epigenomic Modifications in Modern and Ancient Genomes.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205223},
issn = {2073-4425},
mesh = {Animals ; DNA Methylation/genetics ; *DNA, Ancient ; Epigenesis, Genetic/genetics ; *Epigenomics ; Genome/genetics ; },
abstract = {Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.},
}

Animals
DNA Methylation/genetics
*DNA, Ancient
Epigenesis, Genetic/genetics
*Epigenomics
Genome/genetics

@article {pmid35201891,
year = {2022},
author = {Wohns, AW and Wong, Y and Jeffery, B and Akbari, A and Mallick, S and Pinhasi, R and Patterson, N and Reich, D and Kelleher, J and McVean, G},
title = {A unified genealogy of modern and ancient genomes.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6583},
pages = {eabi8264},
doi = {10.1126/science.abi8264},
pmid = {35201891},
issn = {1095-9203},
support = {/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; },
mesh = {Africa ; Chromosomes, Human, Pair 20/genetics ; Computer Simulation ; *DNA, Ancient ; Databases, Nucleic Acid ; Datasets as Topic ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; *Genome, Human ; *Genomics ; Geography ; Haplotypes ; Human Migration ; Humans ; Mutation ; *Pedigree ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Statistics, Nonparametric ; },
abstract = {The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.},
}

Africa
Chromosomes, Human, Pair 20/genetics
Computer Simulation
*DNA, Ancient
Databases, Nucleic Acid
Datasets as Topic
Evolution, Molecular
Genetic Variation
Genetics, Population
*Genome, Human
*Genomics
Geography
Haplotypes
Human Migration
Humans
Mutation
*Pedigree
Sequence Analysis, DNA
Spatio-Temporal Analysis
Statistics, Nonparametric

@article {pmid35197631,
year = {2022},
author = {Lipson, M and Sawchuk, EA and Thompson, JC and Oppenheimer, J and Tryon, CA and Ranhorn, KL and de Luna, KM and Sirak, KA and Olalde, I and Ambrose, SH and Arthur, JW and Arthur, KJW and Ayodo, G and Bertacchi, A and Cerezo-Román, JI and Culleton, BJ and Curtis, MC and Davis, J and Gidna, AO and Hanson, A and Kaliba, P and Katongo, M and Kwekason, A and Laird, MF and Lewis, J and Mabulla, AZP and Mapemba, F and Morris, A and Mudenda, G and Mwafulirwa, R and Mwangomba, D and Ndiema, E and Ogola, C and Schilt, F and Willoughby, PR and Wright, DK and Zipkin, A and Pinhasi, R and Kennett, DJ and Manthi, FK and Rohland, N and Patterson, N and Reich, D and Prendergast, ME},
title = {Ancient DNA and deep population structure in sub-Saharan African foragers.},
journal = {Nature},
volume = {603},
number = {7900},
pages = {290-296},
pmid = {35197631},
issn = {1476-4687},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Blacks/genetics ; *DNA, Ancient ; Gene Flow/genetics ; Genetics, Population ; History, Ancient ; Humans ; South Africa ; },
abstract = {Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.},
}

*Blacks/genetics
*DNA, Ancient
Gene Flow/genetics
Genetics, Population
History, Ancient
Humans
South Africa

@article {pmid35197586,
year = {2022},
author = {},
title = {Ancient DNA illuminates how humans travelled and interacted in Stone Age Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35197586},
issn = {1476-4687},
}

@article {pmid35183376,
year = {2022},
author = {Cuenca-Cambronero, M and Courtney-Mustaphi, CJ and Greenway, R and Heiri, O and Hudson, CM and King, L and Lemmen, KD and Moosmann, M and Muschick, M and Ngoepe, N and Seehausen, O and Matthews, B},
title = {An integrative paleolimnological approach for studying evolutionary processes.},
journal = {Trends in ecology & evolution},
volume = {37},
number = {6},
pages = {488-496},
doi = {10.1016/j.tree.2022.01.007},
pmid = {35183376},
issn = {1872-8383},
mesh = {*Biological Evolution ; *Ecosystem ; },
abstract = {The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evolutionary perspective, such analyses provide important insights into the chronology of past environmental conditions, the dynamics of phenotypic evolution, and species diversification. Here, we review recent advances in paleolimnological, paleogenetic, and molecular approaches and highlight how their integrative use can help us better understand the ecological and evolutionary responses of species and communities to environmental change.},
}

*Biological Evolution
*Ecosystem

@article {pmid35178874,
year = {2022},
author = {Jiménez-Mena, B and Flávio, H and Henriques, R and Manuzzi, A and Ramos, M and Meldrup, D and Edson, J and Pálsson, S and Ásta Ólafsdóttir, G and Ovenden, JR and Nielsen, EE},
title = {Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13598},
pmid = {35178874},
issn = {1755-0998},
support = {"CODSTORY"//The Icelandic Research Fund/ ; "SDPAS//Innovationsfonden: Udvikling af den danske laksebestand - større populationer, genetiske ressourcer og rekreativt fiskeri"/ ; 6108-00583//The Danish Council for Independent Research Grant DFF/ ; DP170102043//Australian Research Grant/ ; },
abstract = {Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.},
}

@article {pmid35176104,
year = {2022},
author = {Rauf, S and Austin, JJ and Higgins, D and Khan, MR},
title = {Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel.},
journal = {PloS one},
volume = {17},
number = {2},
pages = {e0264125},
pmid = {35176104},
issn = {1932-6203},
mesh = {Chromosomes, Human, Y/*genetics ; DNA Fingerprinting/*methods ; Ethnicity/*genetics ; Female ; *Forensic Genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Pakistan ; *Phenotype ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Sex Determination Processes ; },
abstract = {Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.},
}

Chromosomes, Human, Y/*genetics
DNA Fingerprinting/*methods
Ethnicity/*genetics
Female
*Forensic Genetics
Geography
High-Throughput Nucleotide Sequencing
Humans
Male
Pakistan
*Phenotype
*Polymorphism, Single Nucleotide
Sequence Analysis, DNA
*Sex Determination Processes

@article {pmid35175801,
year = {2022},
author = {Stone, AC},
title = {Genomes in motionOrigin: A Genetic History of the Americas Jennifer Raff Twelve, 2022. 368 pp.},
journal = {Science (New York, N.Y.)},
volume = {375},
number = {6582},
pages = {727},
doi = {10.1126/science.abn7262},
pmid = {35175801},
issn = {1095-9203},
abstract = {Ancient DNA sheds light on the peopling of the Americas.},
}

@article {pmid35171192,
year = {2022},
author = {Antkowiak, PL and Koch, J and Rzepka, P and Nguyen, BH and Strauss, K and Stark, WJ and Grass, RN},
title = {Anhydrous calcium phosphate crystals stabilize DNA for dry storage.},
journal = {Chemical communications (Cambridge, England)},
volume = {58},
number = {19},
pages = {3174-3177},
doi = {10.1039/d2cc00414c},
pmid = {35171192},
issn = {1364-548X},
mesh = {Biocompatible Materials/*chemistry ; Calcium Phosphates/*chemistry ; DNA/*chemistry ; Materials Testing ; },
abstract = {The resilience of ancient DNA (aDNA) in bone gives rise to the preservation of synthetic DNA with bioinorganic materials such as calcium phosphate (CaP). Accelerated aging experiments at elevated temperature and humidity displayed a positive effect of co-precipitated, crystalline dicalcium phosphate on the stability of synthetic DNA in contrast to amorphous CaP. Quantitative PXRD in combination with SEM and EDX measurements revealed distinct CaP phase transformations of calcium phosphate dihydrate (brushite) to anhydrous dicalcium phosphate (monetite) influencing DNA stability.},
}

Biocompatible Materials/*chemistry
Calcium Phosphates/*chemistry
DNA/*chemistry
Materials Testing

@article {pmid35167699,
year = {2022},
author = {Oh, CS and Seo, M and Lee, HJ and Kim, MJ and Lim, DS and Shin, DH},
title = {GENETIC ANALYSIS OF ANCIENT CLONORCHIS SINENSIS EGGS ATTAINED FROM GORYEONG MUMMY OF JOSEON DYNASTY PERIOD.},
journal = {The Journal of parasitology},
volume = {108},
number = {1},
pages = {70-78},
doi = {10.1645/21-49},
pmid = {35167699},
issn = {1937-2345},
mesh = {Animals ; Clonorchiasis/*history/parasitology ; Clonorchis sinensis/classification/*genetics ; DNA, Helminth/chemistry/genetics ; History, Ancient ; Mummies/*parasitology ; Ovum ; Phylogeny ; Republic of Korea ; },
abstract = {Although Clonorchis sinensis is a parasite that still infects many people in East Asia, its genetics remain largely unknown. We conducted ancient DNA analysis of C. sinensis eggs obtained from a Joseon period mummy newly discovered in South Korea. Clonorchis sinensis DNA was amplified for internal transcribed spacer 1, cytochrome c oxidase subunit 1, and NADH dehydrogenase subunit 2 and 5 genes. The results of BLAST/NCBI showed that the consensus sequences were 98.24 to 100% identical to the modern and ancient C. sinensis sequences reported from Korea, China, Japan, and other Asian countries. Our report helps to fill in the genetic profile of ancient C. sinensis strains that infected East Asian people hundreds of years ago.},
}

Animals
Clonorchiasis/*history/parasitology
Clonorchis sinensis/classification/*genetics
DNA, Helminth/chemistry/genetics
History, Ancient
Mummies/*parasitology
Ovum
Phylogeny
Republic of Korea