Genetic Genealogy & Ancient DNA in the News (TITLES/ABSTRACTS ONLY)

[pmokeefe]

Pushing the limits with million-year-old DNA
Sequencing ancient DNA more than one million years old opens a new era of research, where we can study the process of speciation in real time. This is a personal account of how we broke this boundary.

Patrícia Pečnerová
Postdoc, University of Copenhagen
Published Feb 18, 2021

[pmokeefe]

Circumpolar peoples and their languages: lexical and genomic data suggest ancient Chukotko-Kamchatkan–Nivkh and Yukaghir-Samoyedic connections
George Starostin, N. Ezgi Altınışık, Mikhail Zhivlov, Piya Changmai, Olga Flegontova, Sergey A. Spirin, Andrei Zavgorodnii, Pavel Flegontov,Alexei S. Kassian

Abstract
Relationships between universally recognized language families represent a hotly debated topic in historical linguistics, and the same is true for correlation between signals of genetic and linguistic relatedness. We developed a weighted permutation test and applied it on basic vocabularies for 31 pairs of languages and reconstructed proto-languages to show that three groups of circumpolar language families in the Northern Hemisphere show evidence of relationship though borrowing in the basic vocabulary or common descent: [Chukotko-Kamchatkan and Nivkh]; [Yukaghir and Samoyedic]; [Yeniseian, Na-Dene, and Burushaski]. The former two pairs showed the most significant signals of language relationship, and the same pairs demonstrated parallel signals of genetic relationship implying common descent or substantial gene flows. For finding the genetic signals we used genome-wide genetic data for present-day groups and a bootstrapping model comparison approach for admixture graphs or, alternatively, haplotype sharing statistics. Our findings further support some hypotheses on long-distance language relationship put forward based on the linguistic methods but lacking universal acceptance.

[pmokeefe]

New insights into the fine-scale history of western–eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy
Hongbin Yao, Mengge Wang, Xing Zou, Yingxiang Li, Xiaomin Yang, Ailin Li, Hui-Yuan Yeh, Peixin Wang, Zheng Wang, Jingya Bai, Jianxin Guo, Jinwen Chen, Xiao Ding, Yan Zhang, Baoquan Lin, Chuan-Chao Wang & Guanglin He

Abstract
Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.

[pmokeefe]

Exploring the effects of migration and admixture on human populations through time, using ancient DNA
Dissertation
Thiseas Christos Lamnidis
Affiliation: Max Planck Institute for the Science of Human History, Jena
Date:09/02/2021

Summary
The field of archaeogenetics began in 1984, with the first studies of ancient DNA
analysing the genetic material of ancient Egyptian mummified remains of humans, and an
extinct equine species respectively. A number of technological and technical advances have
been instrumental in expanding this field, which is currently experiencing much interest from
both researchers and the public. The analysis of ancient DNA from archaeological material has
been used to gain insights into disease pandemics in the past, the population dynamics of
human and animal populations, the oral microbiome of ancient populations, and more. In this
thesis I focus on the insights that can be gained about human population history through
archaeogenetic analysis of human ancient DNA.

Manuscript A presents the results from analysis of 14 ancient genomes from
Fennoscandia and a present-day genome from a Saami individual (for whom sequencing data
had previously been released), spanning a temporal range of 3,500 years. This includes the
earliest sampled ancient population that carries Siberian ancestry in northeastern Europe as
well as the first ancient nuclear genomes from Finland. We use a modelling approach to
quantify the proportion of Siberian ancestry in present-day and ancient populations from the
region. The results of this analysis suggest that Siberian ancestry entered the region between
5,000 and 3,500 yBP, although an earlier entry is possible if this ancestry remained
geographically restricted to northern Fennoscandia. In the present-day, the presence of Siberian
ancestry is most pronounced in populations speaking Uralic languages. However, while Siberian
ancestry is present in the region already 3,500 yBP, that time predates most linguistic estimates
for the spread of Uralic languages into Europe. Manuscript A therefore concludes that if Uralic
languages spread into Europe alongside Siberian ancestry, then the extent of Siberian ancestry
observed in present-day populations is the result of multiple waves of this ancestry in the area.
Additionally, comparative analysis of genetic data retrieved from an Iron Age population in
southern Finland revealed that this population was more closely related to the present-day
Saami than to the Finnish population. This result confirms that the ancestors of the Saami
inhabited a larger geographic range than the Saami population does today.

Manuscript B presents genomic data from 15 ancient Fuego-Patagonian individuals,
covering a temporal range between 5,000 and 300 yBP. We reveal that ancient Fuego-
Patagonians derive the majority of their ancestry from a lineage that was thought to have been
replaced in the rest of the continent. Between 5,000 and 1,100 yBP, a genetic shift is observed
in the Kaweskar population, with the arrival of a minor ancestry component that is maximised in
a population that inhabited the California Channel Islands 5,200 yBP. Following the arrival of
this component, genetic continuity is detected within Fuego-Patagonian populations. When
compared to present-day Native American populations, the ancient Fuego-Patagonians show
similar affinity to both Andean and Amazonian populations, with groups with discernable
ancestry related to the Channel Islands appearing more closely related to Amazonian
populations. We constructed a demographic model of Native American populations based on
rare variation. We then inferred the most likely branching point for different ancient Native
American individuals on this demographic model, based on the sharing of rare alleles between
the ancient individuals and the populations in the model. We observe the inferred branching
point of ancient Fuego-Patagonians to be closer to the split time between the different present
day Native American populations, while the confidence interval around each placement included
multiple Native American branches in most cases. These findings confirmed the broader Native
American affinity exhibited by the ancient Fuego-Patagonians. We argue that this broad affinity
is the result of population history events within South America. Finally, the most recent sampled
individuals (~300 yBP) show no signs of admixture with European or African populations, a
result that suggests Fuego-Patagonian populations remained isolated from European-contact
for longer than native populations in the rest of the continent.

Manuscript C presents the interdisciplinary study of three individuals who were
discovered in a mass burial at a colonial-time hospital in Mexico City, and who exhibited dental
modifications consistent with certain African populations. Previously, this hospital was thought to
have been exclusively for the treatment of indigenous people. Immunogenetic and uniparental
markers confirmed the African origin of these individuals, while analysis of nuclear DNA from
these individuals identified that all individuals were most closely related to present-day West
African populations. However, each individual was most closely related to a different presentday
population. Strontium ratios obtained from the molars of these individuals revealed that they
arrived in Mexico after the 8th year of their lives, the time when these molars develop. Together
the archaeogenetic and strontium analysis results point to these individuals being firstgeneration
Africans, brought over to Mexico during colonial times. Osteological analyses found
signatures of malnutrition, poor hygiene, hardship, and conflict on the remains of the individuals.
A complete genome of Treponema pallidum sub. pertenue (causative agent of yaws) was
recovered from one individual. Phylogenetic analysis of this genome revealed it is most closely
related to treponemal genomes from present-day Ghana and colonial Mexico. Finally, the
complete genome of a Hepatitis B Virus (HBV) was recovered from another individual. The
recovered HBV genome was most closely related to HBV genotypes isolated in West Africa in
the present. In concert, these results let us reconstruct the life history of these three individuals,
and gain insights into the role of the trans-atlantic slave trade in the dissemination of disease.
This thesis explores the effects of admixture and migration on human population history,
and the breadth of information that archaeogenetic approaches make available to researchers
of human history.

[pmokeefe]

Population dynamics in the Japanese Archipelago since the Pleistocene
Fuzuki Mizuno, Jun Gojobori, Masahiko Kumagai, Hisao Baba, Yasuhiro Taniguchi, Osamu Kondo, Masami Matsushita, Takayuki Matsushita, Fumihiko Matsuda, Koichiro Higasa, Michiko Hayashi, Li Wang, Kunihiko Kurosaki, Shintaroh Ueda
Abstract
The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which
is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic
sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor.
Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome sequence
from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the
farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is
potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day
Japanese but also present-day East Asians. There were no changes in the gene pool from the huntinggathering
(Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was
no genetic continuity between hunter-gatherers and farmers. We also found that a vast increase of
population size happened and has continued since the Yayoi period, characterized with paddy rice
farming. It means that the cultural transition, i.e. rice agriculture, had signi􀂦cant impact on the
demographic history of Japanese population.

[David Bush]

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France

Summary

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4, 5, 6, 7, 8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400–2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400–1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.

[pmokeefe]

Reevaluating the timing of Neanderthal disappearance in Northwest Europe


Thibaut Devièse, Grégory Abrams, Mateja Hajdinjak, Stéphane Pirson, Isabelle De Groote, Kévin Di Modica, Michel Toussaint, Valentin Fischer, Dan Comeskey, Luke Spindler, Matthias Meyer, Patrick Semal, and Tom Higham

Significance
Understanding when Neanderthals disappeared is a hotly debated topic. When radiocarbon dating placed the Spy Neanderthals amongst the latest surviving in Northwest Europe, questions were raised regarding the reliability of the dates. Using a procedure more efficient in removing contamination and ancient genomic analysis, we show that previous dates produced on Neanderthal specimens from Spy are too young by up to 10,000 y. Our direct radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt show a reduction of the uncertainty for the time window corresponding to Neanderthal disappearance in Northwest Europe. This population disappeared at 44,200 to 40,600 cal B.P. (at 95.4% probability). This is also earlier than previous suggestions based on dates on bulk collagen.

Abstract
Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.

...

Moreover, we reconstructed a complete mtDNA genome from the Fonds-de-Forêt femur based on 135-fold coverage in deaminated DNA fragments. This genome falls within the variation of late Neanderthals (SI Appendix, Fig. S3) and differs by only a single base pair (bp) from the mitochondrial genomes of Goyet Q57-1, Feldhofer 1, and Vindija 33.25.

[Milkyway]

Comprehensive analysis of Japanese archipelago population history by detecting ancestry-marker polymorphisms without using ancient DNA data

Yusuke Watanabe, Jun Ohashi

Abstract

Modern Japanese have two major ancestral populations: the indigenous Jomon people and immigrants from continental East Asia. To figure out the population history in Japanese archipelago, we developed a reference-free detection method of genetic components from ancestral populations using a summary statistic, the ancestry-marker index (AMI). We applied the AMI to modern Japanese samples and identified 208,648 SNPs that were likely derived from the Jomon people (Jomon-derived SNPs). The analysis of Jomon-derived SNPs in 10,842 modern Japanese individuals recruited from all the 47 prefectures of Japan showed that the genetic differences among the prefectures were mainly caused by differences in the admixture proportion of the Jomon people and the population size of immigrants varied between regions in mainland Japan. We also estimated the migration route of the ancestral Jomon population to the Japanese archipelago and their phenotype frequencies based on the haplotype structures of modern Japanese composed of Jomon-derived SNPs.

[pmokeefe]

Genome-wide analysis of nearly all the victims of a 6200 year old massacre
Mario Novak, Iñigo Olalde ,Harald Ringbauer ,Nadin Rohland,James Ahern,Jacqueline Balen,Ivor Janković,Hrvoje Potrebica,Ron Pinhasi ,David Reich
Published: March 10, 2021
Abstract
Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.

...

We generated genome-wide data from almost all individuals retrieved from the Potočani mass burial (n = 38). The genotypes have been deposited for public access to the Reich lab website (https://reich.hms.harvard.edu/datasets) and the aligned sequences to the EMBL Nucleotide Sequence Database (ENA) with the accession number PRJEB42243.

Discussion thread: https://anthrogenica.com/showthread....r-old-massacre

[pmokeefe]

Human genetic admixture
Katharine L. Korunes, Amy Goldberg
Published: March 11, 2021

Abstract
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.