Updated phylogenetic tree of haplogroup Q-M242 points to Palaeolithic expansions


New paper (behind paywall) Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences by Wei et al., Eur. J. Hum. Genet. (2018)

Interesting excerpts (for Eurasian migrations):

Differentiation and diffusion in Palaeolithic Siberia

Based on the phylogenetic analyses and the current distributions of relative sub-lineages, we propose that the prehistoric population differentiation in Siberia after the LGM (post-LGM) provided the genetic basis for the emergence of the Paleo-Indian, American aborigine, population. According to the phylogenetic tree of Y-chromosome haplogroup C2-M217 (Fig. 2 and Figure S1), eight sub-lineages emerged in a short period between 15.3 kya and 14.3 kya (Table S5). Within these sub-lineages, haplogroups C2-M48, C2-F1918, and C2- F1756 are predominant paternal lineages in modern Altaic-speaking populations [46, 51, 52]. Samples of haplogroups C2-F8535 and C2-P53.1 were found in two Turkic- and Mongolic-speaking minorities in China (Table S1). Both archeological and genetic data suggest that Altaic-speaking populations are results of population expansion in the past several thousand years in the Altai Mountain, Mongolia Plateau, and Amur River region [51–54].

By contrast, three other sub-lineages, C2-B79, C2-B77, and C2-P39, appear only in Koryaks and Native Americans [16, 35]. The latitude of the Altai Mountain, the Mongolia Plateau, and Amur River region are much lower than that of Beringia, where the ancestors of Native Americans finally separated from their close relatives in Siberia. Therefore, the phylogeographic patterns of sub-lineages of C2-M217 in this study reveal a major splitting event between populations in a lower latitude region of Siberia and ancestors of Koryaks and Native Americans during the post-LGM period.

The sub-lineages of the Y-chromosome Q-M242 haplogroup were found in populations throughout the Eurasia continent. According to available data, the Q1-L804 lineage is exclusively found in Northwest Europe, while Q1-M120 is primarily restricted to East Asia [48]. Additionally, the lineage Q1-L330 is the predominant paternal lineage in Altai, Tuva, and Kets in South Siberia [34–36, 55]. A number of Q1-M242 samples have also been found in ancient remains from South Siberia and adjacent regions [56, 57]. Other sub-lineages of Q-M242 are scattered widely in different geographic regions of Eurasia, including Q1-L275, Q1-M25, and Q1-Y2659 [14, 35, 37, 58]. Additionally, the Y-chromosome of a 6000–5100 BCE sample (I4550) from Zvejnieki, Latvia has been identified as Q1-L56 [59]. These findings suggest that the sub-lineages of Q-M242 started to diffuse throughout Eurasia in a very ancient period.

Founding paternal lineages of American aborigines and their most closely related lineages among Eurasia populations

Emergence of Paleo-Indian populations

The revised phylogenetic tree of Y-chromosome haplogroup Q-M242 in this study provides clues regarding the origin of Native American lineages Q1-M3 and Q1-Z780 (Fig. 3). According to our estimates, haplogroup Q1-L54 expanded rapidly between 17.2 kya and 15.0 kya and finally gave rise to two major founding paternal lineages of Native American populations, known as Q1-Z780 and Q1-M3. Ancient DNA studies indicate that the early population in South Siberia, represented by MA1 genomes, had a genetic influence on both modern western European and Native American populations [7]. Therefore, we conclude that the accumulated diversity of sub-lineages of Q-M242 before 15.3 kya resulted from the in situ differentiation of Q-M242 in Central Eurasia and South Siberia since the Paleolithic Age, and the appearance of the Paleo-Indian population is part of the great human diffusion throughout the Eurasia after the Last Glacial Maximum.

The Southern Caucasus PIE homeland

Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them.See the original file here.

The origin of Q-M242 in Zvejnieki, like those of Lola (Q1a2-M25) and Steppe Maykop (Q1a2-M25) from Wang et al. (2018) are therefore most likely migrations throughout North Eurasia dated to the Palaeolithic.

As you might remember, the sample of haplogroup Q1a from Khvalynsk was the closest one (in the PCA, see above) to those we now know most likely represent one or more groups of the steppe north of the Caucasus, which were absorbed during the formation and expansion of Khvalynsk.

NOTE. In fact, the position of this early Khvalynsk sample in the PCA is near the Steppe Eneolithic cluster, in turn near ANE (with the Lola sample Q1a2-M25, circle in dark blue/violet above), and Steppe Maykop (which includes the other Q1a2-M25 sample).

It is often assumed that these populations absorbed in the Pontic-Caspian steppe were dominated by haplogroup J, due to the oldest representatives of CHG ancestry (Kotias Klde and Satsurblia).

However, it would not be surprising now to find out that (one or more of) these “CHG/ANE-rich” groups from the steppe (possibly the Kairshak culture in the North Caspian region) were in fact dominated by Q1-M25 subclades.

If this is the case, I don’t know where the proponents of the (south of the) Caucasus homeland will retreat to.


Inca and Spanish Empires had a profound impact on Peruvian demography


Open access Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire by Harris et al., PNAS (2018) 201720798 (published ahead of print).

Abstract (emphasis mine):

Native Americans from the Amazon, Andes, and coastal geographic regions of South America have a rich cultural heritage but are genetically understudied, therefore leading to gaps in our knowledge of their genomic architecture and demographic history. In this study, we sequence 150 genomes to high coverage combined with an additional 130 genotype array samples from Native American and mestizo populations in Peru. The majority of our samples possess greater than 90% Native American ancestry, which makes this the most extensive Native American sequencing project to date. Demographic modeling reveals that the peopling of Peru began ∼12,000 y ago, consistent with the hypothesis of the rapid peopling of the Americas and Peruvian archeological data. We find that the Native American populations possess distinct ancestral divisions, whereas the mestizo groups were admixtures of multiple Native American communities that occurred before and during the Inca Empire and Spanish rule. In addition, the mestizo communities also show Spanish introgression largely following Peruvian Independence, nearly 300 y after Spain conquered Peru. Further, we estimate migration events between Peruvian populations from all three geographic regions with the majority of between-region migration moving from the high Andes to the low-altitude Amazon and coast. As such, we present a detailed model of the evolutionary dynamics which impacted the genomes of modern-day Peruvians and a Native American ancestry dataset that will serve as a beneficial resource to addressing the underrepresentation of Native American ancestry in sequencing studies.

Admixture among Peruvian populations. (A) Colors represent contributions from donor populations into the genomes of Peruvian mestizo groups, as estimated by CHROMOPAINTER and GLOBETROTTER. The label within parentheses for each Peruvian Native American source population corresponds to their geographic region where Ama, And, and Coa represent Amazon, Andes, and coast, respectively. (B) Admixture time and proportion for the best fit three-way ancestry (AP, Trujillo and Lima) and two-way ancestry (Iquitos, Cusco, and Puno) TRACT models [European, African, and Native American (NatAm) ancestries] for six mestizo populations. (C) Network of individuals from Peruvian Native American and mestizo groups according to their shared IBD length. Each node is an individual and the length of an edge equals to (1/total shared IBD). IBD segments with different lengths are summed according to different thresholds representing different times in the past (52), with 7.8 cM, 9.3 cM, and 21.8 cM roughly representing the start of the Inca Empire, the Spanish conquest and occupation, and Peruvian independence. IBD networks are generated by Cytoscape (98) and only the major clusters in the network are shown for different cutoffs of segment length. AP, Central Am, and Matsig are short for Afroperuvians, Central American, and Matsiguenka, respectively. The header of each IBD network specifies the length of IBD segments used in each network.

Interesting excerpts

The high frequency of Native American mitochondrial haplotypes suggests that European males were the primary source of European admixture with Native Americans, as previously found (23, 24, 41, 42). The only Peruvian populations that have a proportion of the Central American component are in the Amazon (Fig. 2A). This is supported by Homburger et al. (4), who also found Central American admixture in other Amazonian populations and could represent ancient shared ancestry or a recent migration between Central America and the Amazon.

Following the peopling of Peru, we find a complex history of admixture between Native American populations from multiple geographic regions (Figs. 2B and 3 A and C). This likely began before the Inca Empire due to Native American and mestizo groups sharing IBD segments that correspond to the time before the Inca Empire. However, the Inca Empire likely influenced this pattern due to their policy of forced migrations, known as “mitma” (mitmay in Quechua) (28, 31, 37), which moved large numbers of individuals to incorporate them into the Inca Empire. We can clearly see the influence of the Inca through IBD sharing where the center of dominance in Peru is in the Andes during the Inca Empire (Fig. 3C).

ASPCA of combined Peruvian Genome Project with the HGDP genotyped on the Human Origins Array. A.) European ancestry. B.) African ancestry. Samples are filtered by their corresponding ancestral proportion: European ≥ 30% (panel A) and African ≥ 10% (panel B). The two plots in each panel are identical except for the color scheme: reference populations are colored on the left and Peruvian populations are colored on the right. Each point is one haplotype. In the African ASPCA we note three outliers among our samples, two from Trujillo and one from Iquitos, that cluster closer to the Luhya and Luo populations, though not directly. It is likely that these individuals share ancestry with other regions of Africa in addition to western Africa, but we cannot test this hypothesis explicitly as we have too few samples.

A similar policy of large-scale consolidation of multiple Native American populations was continued during Spanish rule through their program of reducciones, or reductions (31, 32), which is consistent with the hypothesis that the Inca and Spanish had a profound impact on Peruvian demography (25). The result of these movements of people created early New World cosmopolitan communities with genetic diversity from the Andes, Amazon, and coast regions as is evidenced by mestizo populations’ ancestry proportions (Fig. 3A). Following Peruvian independence, these cosmopolitan populations were those same ones that predominantly admixed with the Spanish (Fig. 3B). Therefore, this supports our model that the Inca Empire and Spanish colonial rule created these diverse populations as a result of admixture between multiple Native American ancestries, which would then go on to become the modern mestizo populations by admixing with the Spanish after Peruvian independence.

Further, it is interesting that this admixture began before the urbanization of Peru (26) because others suspected the urbanization process would greatly impact the ancestry patterns in these urban centers (25). (…)


Male-biased expansions and migrations also observed in Northwestern Amazonia

Open access preprint Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia, by Arias et al., bioRxiv (2018).

Abstract (emphasis mine):

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

MDS plots for mtDNA and NRY. Stress values (within parentheses) are indicated in percentages.

Looking more precisely at the different groups (even with the resampling approach), there are no significant differences between matrilocal and patrilocal groups. At best, as the study proposes, “this is just one of the factors at play in structuring the observed genetic variation”.

Interesting excerpts:

(…) we found evidence that the patterns of genetic differentiation depend on the geographical scale of the study. The magnitude of between-population differentiation in the NRY compared to the mtDNA is smaller when looking at the continental scale than in NWA (Figure 6). This is in agreement with the findings of Wilkins and Marlowe (2006), who showed that the excess of between-population differentiation for the NRY in comparison to the mtDNA decreases when comparing more geographically distant populations. Heyer et al. (2012) and Wilkins and Marlowe (2006) have proposed that at a local scale the patterns of genetic diversity reflect cultural practices over a relatively small number of generations, whereas at a larger geographic scale the genetic diversity reflects old migration and/or old common ancestry patterns(Heyer et al. 2012; Wilkins and Marlowe 2006).

BSPs for the mtDNA and NRY sequences from NWA. The dotted lines indicate the 95% HPD intervals. Ne was corrected for generation time according to (Fenner 2005), using 26 years for mtDNA and 31 years for NRY.

The BSP plots and the diversity statistics indicate that overall the Ne of males has been smaller than that of females. One tentative explanation for this difference is that it reflects larger differences in reproductive success among males than among females. Some support for this explanation comes from the shape of the phylogenies (Supplementary Figures 1 and 6), since differences in reproductive success and the cultural transmission of fertility lead to imbalance phylogenies (Blum et al. 2006; Heyer et al. 2015). We estimated a common index of tree imbalance (Colless index) and calculated whether the mtDNA and NRY trees were more unbalanced than 1000 simulated trees generated under a Yule process (Bortolussi et al. 2006) (i.e. a simple pure birth process that assumes that the birth rate of new lineages is the same along the tree). We found that the NRY tree is more unbalanced than predicted by the Yule model (p-value=0.001), whereas the mtDNA tree is not significantly different from trees generated by the Yule model (p-value=0.628). It has been suggested that highly mobile hunter-gatherer societies, such as those typical of most of human prehistory, were polygynous bands (Dupanloup et al. 2003); similarly, nomadic horticulturalist Amazonian societies exhibit strong differences in reproductive success due to the common practice of polygyny, especially among community chiefs, whose offspring also enjoy a high fertility (Neel 1970; 1980; Neel and Weiss 1975).

Furthermore, a more recent expansion can be observed in the BSP based on the NRY, but not in the mtDNA BSP (Figure 5), indicating an expansion specifically in the paternal line. The reasons behind this recent male-biased population expansion, which starts ~3.5 kya, are as yet unclear. However, similar male-biased expansions have been observed in other studies using high-resolution NRY sequences (Batini et al. 2017; Karmin et al. 2015).


Ancient human parallel lineages within North America contributed to a coastal expansion


New paper (behind paywall), Ancient human parallel lineages within North America contributed to a coastal expansion, by Scheib et al. Science (2018) 360(6392):1024-1027.


Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We present 91 ancient human genomes from California and Southwestern Ontario and demonstrate the existence of two distinct ancestries in North America, which possibly split south of the ice sheets. A contribution from both of these ancestral populations is found in all modern Central and South Americans. The proportions of these two ancestries in ancient and modern populations are consistent with a coastal dispersal and multiple admixture events.

Visual model of ancestry components and distribution of proportions in the Americas. (A) A model with four admixture events that offers a
good fit to the data (Z = 0.888) (15). (B) Scale of ANC-B ancestry from 0% in Anzick-1 to 100% in the ASO and modern Algonquian-speaking populations.

Interesting excerpts:

We modeled the population history of the Americas using qpGraph (15, 21) and found that the ASO and Mexican (Pima) populations were consistently outgroups to sets of clades formed by Anzick-1, SAM(Surui), and ESNpopulations in analyses that did not involve admixture (fig. S4) (15, 21). Fit between the data and the tree could be significantly improvedwhenmodeling ancient Californian, modern Pima, and Surui populations through admixture of two basal ancestries that we call ANC-A and ANC-B.

The clear separation of ANC-A and ANC-B ancestries is further supported by the sharing of unambiguous, derived haplotype segments in modern Surui and Pima populations (27) with both the ASO (CK-13) and Anzick-1 individuals (fig. S5) (15). The results of this analysis are consistent with ancient substructure and a separation of at least a few thousand years between the ANC-A and ANC-B populations prior to merging (fig. S6) (15). The summary of evidence presented here allows us to reject models of a panmictic “first wave” population from which the ASO diverged after the peopling of South America or in which solely the ANC-A population contributed to modern southern branch populations. Because populations vary in ANC-A and ANC-B proportions but do not differ significantly in their affinity to non-American populations (table S7) (15), it is possible that ANC-A and ANC-B split within America as opposed to Beringia where there would have been ongoing gene flow with Siberia.


Latin Americans show widespread Mediterranean and North African ancestry

Recent preprint Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance, by Chacon-Duque et al. bioRxiv (2018).


Historical records and genetic analyses indicate that Latin Americans trace their ancestry mainly to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Using novel haplotype-based methods here we infer the sub-populations involved in admixture for over 6,500 Latin Americans and evaluate the impact of sub-continental ancestry on the physical appearance of these individuals. We find that pre-Columbian Native genetic structure is mirrored in Latin Americans and that sources of non-Native ancestry, and admixture timings, match documented migratory flows. We also detect South/East Mediterranean ancestry across Latin America, probably stemming from the clandestine colonial migration of Christian converts of non-European origin (Conversos). Furthermore, we find that Central Andean ancestry impacts on variation of facial features in Latin Americans, particularly nose morphology, possibly relating to environmental adaptation during the evolution of Native Americans.

Reference population samples, fineSTRUCTURE groups and SOURCEFIND ancestry estimates for the five Latin American countries examined. (A) Colored pies and grey dots indicate the approximate geographic location of the 117 reference population samples studied. These samples have been subdivided on the world map into five major biogeographic regions: Native Americans (38 populations), Europeans (42 populations), East/South Mediterraneans (15 populations), Sub-Saharan Africans (15 populations) and East Asians (7 populations). The coloring of pies represents the proportion of individuals from that sample included in one of the 35 reference groups defined using fineSTRUCTURE (these groups are listed in the color-coded insets for each region; Supplementary Fig. 2). The grey dots indicate reference populations not inferred to contribute ancestry to the CANDELA sample. Panels (B) and (C) show, respectively, the estimated proportion of sub-continental Native American and European ancestry components in individuals with >5% total Native American or European ancestry in each country sampled (the stacked bars are color-coded as for the reference population groups shown in the insets of panel (A)). Panel (D) shows boxplots of the estimated sub-continental ancestry components for individuals with >5% total Sephardic/East/South Mediterranean ancestry. In this panel colors refer to countries as for the colored country labels shown in (A).

I don’t know how I missed this. It is probably the biggest sample of Latin American populations used for genetic analysis, and it seems it is due for publication soon.

One of its most interesting finds is the eastern Mediterranean and North African ancestry found in almost a quarter of the individuals sampled all over Latin America, which the authors attribute to Sephardic Jews or Conversos.

Although these Conversos were forbidden from migrating to the colonies, historical records document that some individuals made the journey, in an attempt to avoid persecution14. Since this was a clandestine process, the extent of Converso migration to Latin America is poorly documented. Genetic studies have provided suggestive evidence that certain Latin American populations, arguably with a peculiar history, could have substantial Converso ancestry1,18. Our findings indicate that the genetic signature of Converso migration to Latin America is substantially more prevalent than suggested by these special cases, or by historical records.

However, strictly speaking, Converso refers to a recent convert, while this ancestry could have also been part of older Sephardic (and obviously other North African) admixture found in Iberian populations during the Reconquista.

Geographic variation of Native American (A), European (B), and East/South Mediterranean (C) ancestry sub-components in Latin American individuals. Each pie represents an individual with pie location corresponding to birthplace. Since many individuals share birthplace, jittering has been performed based on pie size and how crowded an area is. Pie size is proportional to total continental ancestry and only individuals with >5% of each continental ancestry are shown. Coloring of pies represents the proportion of each sub-continental component estimated for each individual (color-coded as in Fig. 1; Chaco2 does not contribute >5% to any individual and was excluded). Pies in panel (C) have been enlarged to facilitate visualization.

Discovered via Lizzie Wade’s article Latin America’s lost histories revealed in modern DNA, Science (2018).


Ancient Patagonian genomes suggest origin and diversification of late maritime hunter-gatherers


Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia, by de la Fuente et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine):

Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000–20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.

PCA of ancient and present-day South American populations. All of the ancient individuals were projected onto the first two PCs by using the lsq option from smartpca.


Ancient DNA reveals temporal population structure of pre-Incan and Incan periods in South‐Central Andes area

Ancient DNA reveals temporal population structure within the South‐Central Andes area, by Russo et al. Am. J. Phys. Anthropol. (2018).

Abstract (emphasis mine):

The main aim of this work was to contribute to the knowledge of pre‐Hispanic genetic variation and population structure among the South‐central Andes Area by studying individuals from Quebrada de Humahuaca, North‐western (NW) Argentina.

Materials and methods
We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900–1430 AD). Compiling autosomal, mitochondrial, and Y‐chromosome data, we evaluated population structure and differentiation among eight South‐central Andean groups from the current territories of NW Argentina and Peru.

Location of the archaeological sites analyzed in this study (stars) and the South-central Andean populations used for comparisons (triangles). The punctuated line indicates the north-south subdivision of Quebrada de Humahuaca.1: Pe~nas Blancas, 2: San José, 3: Huacalera, 4: Banda de Perchel, 5: Juella, 6: Sarahuaico, 7: Tilcara, 8: Muyuna, 9: Los Amarillos, 10: Las Pirguas, 11: Tompullo 2, 12: Puca, 13: Acchaymarca, 14: Lauricocha. Map constructed from the obtained with the R package ggmap (Kahle & Wickham, 2013)

Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre‐Hispanic history: pre‐Inca and Inca. All pre‐Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y‐chromosome analyses. We mainly found a clearly different haplotype composition between clusters.

Population structure in South America has been mostly studied on current native groups, mainly showing a west‐to‐east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South‐central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio‐political changes occurred in the evermore complex pre‐Hispanic Andean societies.

Principal coordinates analysis (PCoA) based on individual genetic distances obtained with autosomal STRs data. Percentage of variance explained by each coordinate is shown in parenthesis. Colors were assigned according to the two clusters discovered with structure

See also: