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Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data
Abstract and Figures
Two important advances: 1) the accumulation of BigY and FGC test data, and 2) the publication of Y-chromosome sequences for three ancient samples (Anzick-1, Ust-Ishim, and K14), have made it possible to estimate the average rate of base-substitutions (SNPs). The authors of this study have developed a new method of selecting true mutations in modern and ancient samples, and have defined with high accuracy the rate constant of SNP mutations: 0.82 • 10 per year per bp (95% CI: (0.70 − 0.94) • 10).
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... The Yakuts-Sakha is represented by samples of 18 men and 7 women. For further studies of the demography NSNP = Σ i N i -the total number of observed mutations formed since the split of the branch until the present, N i -number of mutations in each sample i, B = Σ i B i -the total length of read nucleotide sequences of all samples within the borders of the combBED region [24]. B i -length of read nucleotide sequences in each sample i, μ -SNP mutation rate constant, taken equal 8.2 . ...
... B i -length of read nucleotide sequences in each sample i, μ -SNP mutation rate constant, taken equal 8.2 . 10-9 mutations per year per base pair [24]. ...
... The relative standard deviation was estimated taking into account the calibration error of the mutation rate constant σ µ =7.3%, carried out in [24]: ...
Based on the massive parallel sequencing, phylogenetic tree of the Y-chromosomal haplogroup N-M2016 was built. The branch N-M1982 of Yakut-Sakha men majority is located on the tree. The ages of tree branching nodes are estimated. Time to the most recent common ancestor (TMRCA) 970 ± 210 years BP (“present” defined as AD 1950) of one of the main Yakut male lineages N-M1991 is confirmed by accelerator mass spectrometry dating of a sample of the ancient man Yana Young [1] who died about 766 yBP. A sharp increase in the number of Yakut-Sakha ancestors observed on the Yakut branch N-M1982, began from 1320 ± 100 AD. Age of the population explosion is consistent with the radiocarbon dating of the Kulun-Atakh archaeological culture sites.
... Rasmussen et al. assigned the little boy to Y-chromosome haplogroup QL54*(xM3) and mtDNA haplogroup D4h3a. Based on subsequent clarification of Q haplogroup phylogeny (e.g., Adamov et al. 2015;Kivisild 2017), the infant is now assigned to Q-FGC47595 (YFull 2021), which is a descendant branch of the Q-M1107 clade. "Upstream" clades of the Q-M1107 haplogroup, the legacy of older branching events (mutations), are found in living men in Mexico and Peru. ...
... 11,040 rcbp for the elk-antler rods that were found with him (along with more than 100 Clovis-style chipped stone artifacts). The Anzick genome has provided the necessary ancient calibration point for calculation of the ages of the Q clades (Adamov et al. 2015). ...
The study of the peopling of the Americas has been transformed in the past decade by astonishing progress in paleogenomic research. Ancient genomes now show that Native American ancestors were formed in Siberia or the Amur region by admixture of ca. 15–30% Ancient North Eurasian genes with those of East Asians. The Anzick infant, buried with Clovis bifaces at 12,900 cal BP, belonged to a group that was ancestral to later Native Central and South Americans. Fishtail points, derived from Clovis, mark the arrival and rapid expansion of Clovis-descended Paleoindians across South America, also evident in the sharp increase of radiocarbon dates, continent-wide, at 13,000–12,500 cal BP. In both North and South America, extinction of most genera of megafauna was virtually simultaneous with Paleoindian expansion. Human hunting must have been involved, perhaps in concert with other indirect impacts. Contrary to the alternative bolide impact theory, there is no evidence of a dramatic human population decline after 12,800 cal BP. Ancient genomes show that divergent lithic traditions after 13,000 cal BP need not be attributed to a separate Pacific Rim migration stream. Several recent finds raise the possibility that pre-Clovis people might have reached the Americas before 20,000 cal BP, but these precursors must have either failed to thrive, or were ultimately replaced by proto-Clovis or Clovis people. Consilient paleogenomic and archaeological data indicate that initial colonization by Paleoindian ancestors of living Native Americans occurred after 14,500 cal BP.
... kya), considering that cluster 1 is the founder haplotype, which is higher than that of the SNP-based calculation (4.6 kya, 95% CI: 4.2-5.0 kya) (Adamov et al. 2015; ...
In this study, we delved into the uniparental genetic lineage of Hungarian-speaking minorities residing in rural villages of Baranja and the Zobor region, located in contemporary Croatia and Slovakia, respectively. Our focus was on identifying ancestral patterns by examining genetic markers distributed across the entire mitogenome and on the Y-chromosomes. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations.
Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of Short Tandem Repeat (STR) data and mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities of East-Central Europe.
... The E-M78 haplogroup may have been formed about 13,400 years ago (Adamov et al., 2015). Remains belonging to the E-M78 subgroup, dating from about 7000 years ago, were discovered in Avellaner cave, Spain (Lacan et al., 2011). ...
The Hunyadi family is one of the most influential families in the history of Central Europe in the 14th–16th centuries. The family’s prestige was established by Johannes Hunyadi, a Turk-beater who rose to the position of governor of the Kingdom of Hungary. His second son, Matthias Hunyadi, became the elected ruler of the Kingdom of Hungary in 1458. The Hunyadi family had unknown origin. Moreover, Matthias failed to found a dynasty because of lacking a legitimate heir and his illegitimate son Johannes Corvinus was unable to obtain the crown. His grandson, Christophorus Corvinus, died in childhood, thus the direct male line of the family ended.
In the framework of on interdisciplinary research, we have determined the whole genome sequences of Johannes Corvinus and Christophorus Corvinus by next-generation sequencing technology. Both of them carried the Y-chromosome haplogroup is E1b1b1a1b1a6a1c ∼, which is widespread in Eurasia. The father-son relationship was verified using the classical STR method and whole genome data. Christophorus Corvinus belongs to the rare, sporadically occurring T2c1+146 mitochondrial haplogroup, most frequent around the Mediterranean, while his father belongs to the T2b mitochondrial haplogroup, widespread in Eurasia, both are consistent with the known origin of the mothers. Archaeogenomic analysis indicated that the Corvinus had an ancient European genome composition.
Based on the reported genetic data, it will be possible to identify all the other Hunyadi family member, whose only known grave site is known, but who are resting assorted with several other skeletons.
... Mapping of reads and SNP (single-nucleotide polymorphism) calling were conducted with the human reference genome hg19 using GATK packages and standard procedures for next-generation sequencing (Li et al., 2009;Li & Durbin, 2010). To obtain a confident Y-SNP dataset for reconstruction of phylogenetic tree and age estimation, we applied a series of strict filters on the original variants file, including: (a) restriction to confident 8.4 Mb region (Adamov, Guryanov, Karzhavin, Tagankin, & Urasin, 2015) which is a subset of the studied region of Poznik et al. (2016) and Karmin et al. (2015); (b) restriction to variants that are Y-SNP; (c) removal of all positions with call rate <80% on all samples with sequences; (d) removal of position with heterozygosis call rate >5% on all samples; (e) base coverage ≥3, base quality >20, and distance between SNPs >10 bp; and (f) removal of recurrent or triadic mutations. ...
Objectives:
The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians.
Materials and methods:
We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation.
Results:
We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia.
Conclusion:
Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a “Caucasus-Lower Volga” (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A “Volga Cline” was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A “Dnipro Cline” was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the “Proto-Indo-Anatolian” ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.
Abstract Figure
Summary Figure:
The origin of Indo-Anatolian and Indo-European languages
Genetic reconstruction of the ancestry of Pontic-Caspian steppe and West Asian populations points to the North Caucasus-Lower Volga area as the homeland of Indo-Anatolian languages and to the Serednii Stih archaeological culture of the Dnipro-Don area as the homeland of Indo-European languages. The Caucasus-Lower Volga people had diverse distal roots, estimated using the qpAdm software on the left barplot, as Caucasus hunter-gatherer (purple), Central Asian (red), Eastern hunter-gatherer (pink), and West Asian Neolithic (green). Caucasus-Lower Volga expansions, estimated using qpAdm on the right barplot as disseminated Caucasus Neolithic (blue)-Lower Volga Eneolithic (orange) proximal ancestries, mixing with the inhabitants of the North Pontic region (yellow), Volga region (yellow), and West Asia (green).
По данным массового параллельного секвенирования игрек-хромосомы построено генеалогическое дерево гаплогруппы N-M2016, на котором располагается ветвь большинства мужчин якутов-саха N-M1982. Определены возрасты узлов ветвления дерева. Возраст ближайшего общего предка (TMRCA) 970±210 лет до нашего времени (1950 г.) одной из основных якутских мужских линий N-M1991 подтверждается датировкой методом ускорительной масс-спектрометрии образца древнего человека Yana Young [1], умершего около 766 лет до н.в. Резкий рост численности предков якутов-саха, наблюдаемый на якутской ветви N-M1982 в составе гаплогруппы N-M2016, начался с 1320±100 года нашей эры. Сроки наблюдаемого демографического взрыва согласуются с радиоуглеродной датировкой памятников кулун-атахской археологической культуры.
The subject of the study was the genealogy of the Qajar dynasty, which ruled Iran in 1795-1925. Documentary sources indicate Gara Piri bey Qajar (XV century – 1513), the first beglyarbek of Karabakh with the center in Ganja (now Azerbaijan) as the earliest ancestor of the dynasty. At the end of the XVI century, the great–grandson of Gar Piri bey was appointed Shah Abbas I beglyarbek of Astrabad (now Gorgan, Iran), from whose descendant - Agha Muhammad Khan Qajar (1741-1797), the shah dynasty began. Agha-Mohammed Khan himself traced his family back to a legendary ancestor named Qajar, the son of Sartak-noyon from the Mongolian Jalai tribe, the mentor of Genghisid Argun Khan (1284-1291). According to other sources, the Qajars are a Turkoman tribe that settled in Transcaucasia during the Mongol period. These data on the early history point to the Qajar dynasty as having originally Central Asian origin. In 2007, a study of the Y-DNA of two modern representatives of different lines of the Qajar dynasty was conducted. Tests have shown that both lines really originate from a recent common paternal ancestor and belong to haplogroup J1-M267, widespread in the Middle East. However, apart from the genetic confirmation of the common paternal origin of these two lines and the declaration of the marginality of the ancestral legend, there is virtually no analysis in the work that gives a definitive answer to the question of the origin of the dynasty itself. In the development of this work, a more in-depth study of Y-DNA by new generation sequencing methods was carried out. The paternal origin of the Qajar dynasty from the indigenous population of the northern regions of Azerbaijan has been revealed.
One hundred and six Rétköz and 48 Váh valley samples were collected from the contact zones of Hungarian-Slovakian territories and were genotyped for Y-chromosomal haplotypes and haplogroups. The results were compared with contemporary and archaic data from published sources. The genetic composition of the Rétköz population from Hungary and the Váh valley population from Slovakia indicates different histories. In the Rétköz population, the paternal lineages that were also found in the Hungarian Conquerors, such as R1a-Z93, N-M46, Q-M242, and R1b-L23, were better preserved. These haplogroups occurred in 10% of the population. The population of the Váh valley, however, is characterized by the complete absence of these haplogroups. Our study did not detect a genetic link between the Váh valley population and the Hungarian Conquerors; the genetic composition of the Váh valley population is similar to that of the surrounding Indo-European populations. The Hungarian Rétköz males shared common haplotypes with ancient Xiongnu, ancient Avar, Caucasian Avar, Abkhazian, Balkarian, and Circassian males within haplogroups R1a-Z93, N1c-M46, and R1b-L23, indicating a common genetic footprint. Another difference between the two studied Hungarian populations can be concluded from the Fst-based MDS plot. The Váh valley, in the western part of the Hungarian-Slovakian contact zone, is genetically closer to the Western Europeans. In contrast, Rétköz is in the eastern part of that zone and therefore closer to the Eastern Europeans.
Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.
Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51 ×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes.
The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia
dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that
Kostenki 14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers,
some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows
evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers.
We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings
reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic
structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe
to central Asia.
We present the high-quality genome sequence of a 45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 3 10 29 to 0.6 3 10 29 per site per year, a Y chromosomal mutation rate of 0.7 3 10 29 to 0.9 3 10 29 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 3 10 28 to 3.2 3 10 28 per site per year based on the age of the bone.
Human impacts have left and are leaving distinctive imprints in the geological record. Here we show that in North America, the human-caused changes evident in the mammalian fossil record since c. 14,000 years ago are as pronounced as earlier faunal changes that subdivide Cenozoic epochs into the North American Land Mammal Ages (NALMAs). Accordingly, we define two new North American Land Mammal Ages, the Santarosean and the Saintagustinean, which subdivide Holocene time and complete a biochronologic system that has proven extremely useful in dating terrestrial deposits and in revealing major features of faunal change through the past 66 million years. The new NALMAs highlight human-induced changes to the Earth system, and inform the debate on whether or not defining an Anthropocene epoch is justified, and if so, when it began.
Y chromosome is a superb tool for inferring human evolution and recent demographic history from a paternal perspective. However, Y chromosomal substitution rates obtained using different modes of calibration vary considerably, and have produced disparate reconstructions of human history. Here, we discuss how substitution rate and date estimates are affected by the choice of different calibration points. We argue that most Y chromosomal substitution rates calculated to date have shortcomings, including a reliance on the ambiguous human-chimpanzee divergence time, insufficient sampling of deep-rooting pedigrees, and using inappropriate founding migrations, although the rates obtained from a single pedigree or calibrated with the peopling of the Americas seem plausible. We highlight the need for using more deep-rooting pedigrees and ancient genomes with reliable dates to improve the rate estimation.
Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 (14)C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.
Demographic change of human populations is one of the central questions for
delving into the past of human beings. To identify major population expansions
related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp
of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified
many new clades. The relative divergence dates can be estimated much more
precisely using molecular clock. We found that all the Paleolithic divergences
were binary; however, three strong star-like Neolithic expansions at ~6 kya
(thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year)
indicates that ~40% of modern Chinese are patrilineal descendants of only three
super-grandfathers at that time. This observation suggests that the main
patrilineal expansion in China occurred in the Neolithic Era and might be
related to the development of agriculture.
Examining Y
The evolution of human populations has long been studied with unique sequences from the nonrecombining, male-specific Y chromosome (see the Perspective by Cann ). Poznik et al. (p. 562 ) examined 9.9 Mb of the Y chromosome from 69 men from nine globally divergent populations—identifying population and individual specific sequence variants that elucidate the evolution of the Y chromosome. Sequencing of maternally inherited mitochondrial DNA allowed comparison between the relative rates of evolution, which suggested that the coalescence, or origin, of the human Y chromosome and mitochondria both occurred approximately 120 thousand years ago. Francalacci et al. (p. 565 ) investigated the sequence divergence of 1204 Y chromosomes that were sampled within the isolated and genetically informative Sardinian population. The sequence analyses, along with archaeological records, were used to calibrate and increase the resolution of the human phylogenetic tree.