Deep population history of North, Central and South America


Open access Reconstructing the Deep Population History of Central and South America, by Posth et al. Cell (2018).


We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Interesting excerpts:

The D4h3a mtDNA haplogroup has been hypothesized to be a marker for an early expansion into the Americas along the Pacific coast (Perego et al., 2009). However, its presence in two Lapa do Santo individuals and Anzick-1 (Rasmussen et al., 2014) makes this hypothesis unlikely.

The patterns we observe on the Y chromosome also force us to revise our understanding of the origins of present-day variation. Our ancient DNA analysis shows that the Q1a2a1b-CTS1780 haplogroup, which is currently rare, was present in a third of the ancient South Americas. In addition, our observation of the currently extremely rare C2b haplogroup at Lapa do Santo disproves the suggestion that it was introduced after 6,000 BP (Roewer et al., 2013).

(…) Our discovery that the Clovis-associated Anzick-1 genome at ∼12,800 BP shares distinctive ancestry with the oldest Chilean, Brazilian, and Belizean individuals supports the hypothesis that an expansion of people who spread the Clovis culture in North America also affected Central and South America, as expected if the spread of the Fishtail Complex in Central and South America and the Clovis Complex in North America were part of the same phenomenon (direct confirmation would require ancient DNA from a Fishtail-context) (Pearson, 2017). However, the fact that the great majority of ancestry of later South Americans lacks specific affinity to Anzick-1 rules out the hypothesis of a homogeneous founding population. Thus, if Clovis-related expansions were responsible for the peopling of South America, it must have been a complex scenario involving arrival in the Americas of sub-structured lineages with and without specific Anzick-1 affinity, with the one with Anzick-1 affinity making a minimal long-term contribution. While we cannot at present determine when the non-Anzick-1 associated lineages first arrived in South America, we can place an upper bound on the date of the spread to South America of all the lineages represented in our sampled ancient genomes as all are ANC-A and thus must have diversified after the ANC-A/ANC-B split estimated to have occurred ∼17,500–14,600 BP (Moreno-Mayar et al., 2018a).


New paper (behind paywall) Early human dispersals within the Americas, by Moreno-Mayar et al. Science (2018).


Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including an Ancient Beringian individual, and two morphologically distinct “Paleoamericans.” We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Interesting excerpts:

The Australasian signal is not present in USR1 or Spirit Cave, but only appears in Lagoa Santa. None of these individuals has UPopA/Mesoamerican-related admixture, which ap-parently dampened the Australasian signature in South American groups, such as the Karitiana. These findings suggest the Australasian signal, possibly present in a structured ancestral NA population, was absent in NA prior to the Spirit Cave/Lagoa Santa split. Groups carrying this signal were either already present in South America when the ancestors of Lagoa Santa reached the region, or Australasian-related groups arrived later but before 10.4 ka (the Lagoa Santa 14C age). That this signal has not been previously documented in North America implies that an earlier group possessing it had disappeared, or a later-arriving group passed through North America without leaving any genetic trace. If such a signal is ultimately detected in North America it could help determine when groups bear-ing Australasian ancestry arrived, relative to the divergence of SNA groups.

Although we detect the Australasian signal in one of the Lagoa Santa individuals identified as a “Paleoamerican,” it is absent in other “Paleoamericans” (2, 10), including Spirit Cave with its strong genetic affinities to Lagoa Santa. This indicates the “Paleoamerican” cranial form is not associated with the Australasian genetic signal, as previously suggested (6), or any other specific NA clade (2). The cause of this cranial form, if it is representative of broader population pat-terns, evidently did not result from separate ancestry, but likely multiple factors, including isolation and drift and non-stochastic mechanisms.

f-statistics–based tests show a rapid dispersal into South America, followed by Mesoamerican-related admixture. Schematic representation of a model for SNA formation. This model represents a reasonable fit to most present-day populations.

Open access The genetic prehistory of the Andean highlands 7000 years BP though European contact, by Lindo et al. Science Advances (2018).


The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.


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). (…)


Native American genetic continuity and oldest mtDNA hg A2ah in the Andean region

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies by Criollo-Rayo et al., Forensic Sci Int Genet (2018), in press, corrected proof.

Abstract (emphasis mine):

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers. Nasa and Pijao had a predominant Native American ancestry at the autosomal (92%), maternal (97%) and paternal (70%) level. The admixed groups had a predominant Native American mtDNA ancestry (90%), a substantial frequency of European NRY haplotypes (72%) and similar autosomal contributions from Europeans (51%) and Amerindians (45%). Pijao and nearby Ortega were indistinguishable at the mtDNA and autosomal level, suggesting a genetic continuity between them. Comparisons with multiple Native American populations throughout the Americas revealed that Pijao, had close similarities with Carib-speakers from distant parts of the continent, suggesting an ancient correlation between language and genes. In summary, our study aimed to understand Hispanic patterns of migration, settlement and admixture, supporting an extensive contribution of local Amerindian women to the gene pool of admixed groups and consistent with previous reports of European-male driven admixture in Colombia.

Ancestral uniparental haplogroups and diversity in Tolima. Geography of sampling locations. The
top and middle sections show the frequency of Native American mtDNA haplogroups and NRY lineages for all
populations. Gene diversity is shown below their respective pie chart. The lower part depicts the geography of the
region where the sampling sites of Ortega and Pijao are closely located in Tolima’s Magdalena river valley and
Ibague, Planadas and Nasa located in the Andes cordilleras (additional geographic details are shown in SF1).

Highlights from the paper:

  • MtDNA suggest a pre/post Columbian genetic continuity in the Colombian Andes.
  • Y-chromosome diversity follows a clinal gradient in the studied region.
  • Sex-biased/male-driven admixture process, involving Pijao women with European men.
  • Admixed closer to Indigenous resguardos have a higher Native American ancestry.

Also interesting is the recent paper Mitochondrial lineage A2ah found in a pre‐Hispanic individual from the Andean region, by Russo et al., in American Journal of Human Biology (2018), with an interesting sample from the Regional Developments II period (540 ± 60 BP).

Phylogeny of the A2ah mitochondrial lineage based on HVR I sequences. Both MaximumParsimony andMaximumLikelihood reconstructions led to the same typology. The tree was rooted with the RSRS. Sample ID: Cueva: Pukara de La Cueva, STACRUZ: Santa Cruz, BNI: Beni, BR: South-eastern Brazil, TobaChA: TobaGranChaco


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: