Predictions of native American population structure using linguistic covariates in a hidden regression framework

Background

The mainland of the Americas is home to a remarkable diversity of languages, and the relationships between genes and languages have attracted considerable attention in the past. Here we investigate to which extent geography and languages can predict the genetic structure of Native American populations.

Methodology/Principal Findings

Our approach is based on a Bayesian latent cluster regression model in which cluster membership is explained by geographic and linguistic covariates. After correcting for geographic effects, we find that the inclusion of linguistic information improves the prediction of individual membership to genetic clusters. We further compare the predictive power of Greenberg''s and The Ethnologue classifications of Amerindian languages. We report that The Ethnologue classification provides a better genetic proxy than Greenberg''s classification at the stock and at the group levels. Although high predictive values can be achieved from The Ethnologue classification, we nevertheless emphasize that Choco, Chibchan and Tupi linguistic families do not exhibit a univocal correspondence with genetic clusters.

Conclusions/Significance

The Bayesian latent class regression model described here is efficient at predicting population genetic structure using geographic and linguistic information in Native American populations.     

Ethnohistory, intertribal relationships, and genetic diversity among Amazonian Indians

The influence of recent ethnohistorical factors on the microevolution of South American Indians has not been adequately evaluated by population geneticists. This makes difficult a reasonable interpretation of the present genetic structure of these groups. In this article the genetic diversity of 18 tribes of the Amazon and neighboring areas belonging to 3 linguistic groups (Tupi, Carib, and Gê) is analyzed in light of documentary sources about historical events, such as demographic changes, geographic movements, intertribal relationships, and marriage practices, that have taken place since the end of the eighteenth century. The high depopulation rate suffered by the Tupi groups (61.4% on average) is a probable factor conditioning the large intergroup genetic distances in this linguistic stock, for depopulation is a phenomenon associated with random genetic drift caused by a bottleneck effect. On the other hand, the relatively high similarity of the Gê and the Carib shows an association with two main factors: (1) reduced spatial dispersion of the Gê in the recent past, providing adequate conditions for within-stock gene flow, and (2) strong tradition of intergroup contacts among the Carib, frequently followed by genetic admixture and even fusion of groups, as verified for the Wayana and the Aparaí. The patterns of biologic variation of some Tupi tribes (Wai?pi, Emerillon, Parakan?, and Assurini) are better explained by historical and regional contingencies than by linguistic classification.     

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.     

Cultural phylogenetics of the Tupi language family in lowland South America

Background

Recent advances in automated assessment of basic vocabulary lists allow the construction of linguistic phylogenies useful for tracing dynamics of human population expansions, reconstructing ancestral cultures, and modeling transition rates of cultural traits over time.

Methods

Here we investigate the Tupi expansion, a widely-dispersed language family in lowland South America, with a distance-based phylogeny based on 40-word vocabulary lists from 48 languages. We coded 11 cultural traits across the diverse Tupi family including traditional warfare patterns, post-marital residence, corporate structure, community size, paternity beliefs, sibling terminology, presence of canoes, tattooing, shamanism, men''s houses, and lip plugs.

Results/Discussion

The linguistic phylogeny supports a Tupi homeland in west-central Brazil with subsequent major expansions across much of lowland South America. Consistently, ancestral reconstructions of cultural traits over the linguistic phylogeny suggest that social complexity has tended to decline through time, most notably in the independent emergence of several nomadic hunter-gatherer societies. Estimated rates of cultural change across the Tupi expansion are on the order of only a few changes per 10,000 years, in accord with previous cultural phylogenetic results in other language families around the world, and indicate a conservative nature to much of human culture.     

A multi‐perspective view of genetic variation in Cameroon

In this study, we report the genetic variation of autosomal and Y‐chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within‐ and among‐group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y‐chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y‐chromosomal data and obtain a female‐to‐male migration Nν ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter‐populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y‐chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Genetic divergence disclosing a rapid prehistorical dispersion of native americans in central and South america

An accurate estimate of the divergence time between Native Americans is important for understanding the initial entry and early dispersion of human beings in the New World. Current methods for estimating the genetic divergence time of populations could seriously depart from a linear relationship with the true divergence for multiple populations of a different population size and significant population expansion. Here, to address this problem, we propose a novel measure to estimate the genetic divergence time of populations. Computer simulation revealed that the new measure maintained an excellent linear correlation with the population divergence time in complicated multi-population scenarios with population expansion. Utilizing the new measure and microsatellite data of 21 Native American populations, we investigated the genetic divergences of the Native American populations. The results indicated that genetic divergences between North American populations are greater than that between Central and South American populations. None of the divergences, however, were large enough to constitute convincing evidence supporting the two-wave or multi-wave migration model for the initial entry of human beings into America. The genetic affinity of the Native American populations was further explored using Neighbor-Net and the genetic divergences suggested that these populations could be categorized into four genetic groups living in four different ecologic zones. The divergence of the population groups suggests that the early dispersion of human beings in America was a multi-step procedure. Further, the divergences suggest the rapid dispersion of Native Americans in Central and South Americas after a long standstill period in North America.     

Unexpected patterns of mitochondrial DNA variation among Native Americans from the southeastern United States

Mitochondrial DNA (mtDNA) haplogroups were determined by restriction fragment length polymorphism-typing for 66 individuals from four southeastern North American populations, and the HVS I portion of the mtDNA control region was sequenced in 48 of these individuals. Although populations from the same geographic region usually exhibit similar haplogroup frequency distributions (Lorenz and Smith [1996] Am. J. Phys. Anthropol. 101:307-323; Malhi et al. [2001] Hum. Biol. 73:17-55), those from the Southeast instead exhibit haplogroup frequency distributions that differ significantly from one another. Such divergent haplogroup frequency distributions are unexpected for the Muskogean-speaking southeastern populations, which share many sociocultural traits, speak closely related languages, and have experienced extensive admixture both with each other and with other eastern North American populations. Independent origins, genetic isolation from other Native American populations due to matrilocality, differential admixture, or a genetic bottleneck could be responsible for this heterogeneous distribution of haplogroup frequencies. Within a given haplogroup, however, the HVS I sequences from the four Muskogean-speaking populations appear relatively similar to one another, providing evidence for close relationships among them and for reduced diversity within haplogroups in the Southeast. Given additional archaeological, linguistic, and ethnographic evidence, these results suggest that a genetic bottleneck associated with the historical population decline is the most plausible explanation for such patterns of mtDNA variation.     

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.     

mtDNA variability in two Bantu‐speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub‐Saharan Africa

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu‐speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu‐speaking populations. Moreover, by comparing our data with those from other Niger‐Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub‐Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu‐speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu‐speaking populations, but also between Bantu and non‐Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu‐speakers, with strong interactions between the different lines of Bantu‐speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Languages, geography and HLA haplotypes in native American and Asian populations

A number of studies based on linguistic, dental and genetic data have proposed that the colonization of the New World took place in three separate waves of migration from North-East Asia. Recently, other studies have suggested that only one major migration occurred. It is the aim of this study to assess these opposing migration hypotheses using molecular-typed HLA class II alleles to compare the relationships between linguistic and genetic data in contemporary Native American populations. Our results suggest that gene flow and genetic drift have been important factors in shaping the genetic landscape of Native American populations. We report significant correlations between genetic and geographical distances in Native American and East Asian populations. In contrast, a less clear-cut relationship seems to exist between genetic distances and linguistic affiliation. In particular, the close genetic relationship of the neighbouring Na-Dene Athabaskans and Amerindian Salishans suggests that geography is the more important factor. Overall, our results are most congruent with the single migration model.     

Affinities among Melanesians,Micronesians, and Polynesians: a neutral biparental genetic perspective

The human colonization of Remote Oceania, the vast Pacific region including Micronesia, Polynesia, and Melanesia beyond the northern Solomon Islands, ranks as one of the greatest achievements of prehistory. Many aspects of human diversity have been examined in an effort to reconstruct this late Holocene expansion. Archaeolinguistic analyses describe a rapid expansion of Austronesian-speaking "Lapita people" from Taiwan out into the Pacific. Analyses of biological markers, however, indicate genetic contributions from Pleistocene-settled Near Oceania into Micronesia and Polynesia, and genetic continuity across Melanesia. Thus, conflicts between archaeolinguistic and biological patterns suggest either linguistic diffusion or gene flow across linguistic barriers throughout Melanesia. To evaluate these hypotheses and the general utility of linguistic patterns for conceptualizing Pacific prehistory, we analyzed 14 neutral, biparental genetic (short tandem repeat) loci from 965 individuals representing 27 island Southeast Asian, Melanesian, Micronesian, and Polynesian populations. Population bottlenecks during the colonization of Remote Oceania are indicated by a statistically significant regression of loss of heterozygosity on migration distance from island Southeast Asia (r = 0.78, p < 0.001). Genetic and geographic distances were consistently correlated (r > 0.35, p < 0.006), indicating extensive gene flow primarily focused among neighboring populations. Significant correlations between linguistic and geographic patterns and between genetic and linguistic patterns depended upon the inclusion of Papuan speakers in the analyses. These results are consistent with an expansion of Austronesian-speaking populations out of island Southeast Asia and into Remote Oceania, followed by substantial gene flow from Near Oceanic populations. Although linguistic and genetic distinctions correspond at times, particularly between Western and Central-Eastern Micronesia, gene flow has reduced the utility of linguistic data within Melanesia. Overall, geographic proximity is a better predictor of biparental genetic relationships than linguistic affinities.     

Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

The Uto‐Aztecan premolar among North and South Amerindians: Geographic variation and genetics

The Uto‐Aztecan premolar (UAP) is a dental polymorphism characterized by an exaggerated distobuccal rotation of the paracone in combination with the presence of a fossa at the intersection of the distal occlusal ridge and distal marginal ridge of upper first premolars. This trait is important because, unlike other dental variants, it has been found exclusively in Native American populations. However, the trait's temporal and geographic variation has never been fully documented. The discovery of a Uto‐Aztecan premolar in a prehistoric skeletal series from northern South America calls into question the presumed linguistic and geographic limits of this trait. We examined published and unpublished data for this rare but highly distinctive trait in samples representing over 5,000 Native Americans from North and South America. Our findings in living Southwest Amerindian populations corroborate the notion that the variable goes beyond the bounds of the Uto‐Aztecan language family. It is found in prehistoric Native Americans from South America, eastern North America, Northern and Central Mexico, and in living and prehistoric populations in the American Southwest that are not members of the Uto‐Aztecan language stock. The chronology of samples, its geographic distribution, and trait frequencies suggests a North American origin (Southwest) for UAP perhaps between 15,000 BP and 4,000 BP and a rapid and widespread dispersal into South America during the late Holocene. Family data indicate that it may represent an autosomal recessive mutation that occurred after the peopling of the Americas as its geographic range appears to be limited to North and South Amerindian populations. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

mtDNA variation in East Africa unravels the history of afro‐asiatic groups

East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long‐term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro‐Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno‐linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations—explored using spatial Principal Component Analysis and Model‐based clustering—turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA‐speaking populations, and shows shared ancestry with Semitic‐speaking groups from Yemen and Egypt and AA‐Chadic‐speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene‐flow (Bantu, Nilo‐Saharan pastoralists), one of them is associated with a more ancient AA‐Cushitic stratum. Most North‐African and Levantine populations (AA‐Berber, AA‐Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Population Histories and Genomic Diversity of South American Natives

South America is home to one of the most culturally diverse present-day native populations. However, the dispersion pattern, genetic substructure, and demographic complexity within South America are still poorly understood. Based on genome-wide data of 58 native populations, we provide a comprehensive scenario of South American indigenous groups considering the genomic, environmental, and linguistic data. Clear patterns of genetic structure were inferred among the South American natives, presenting at least four primary genetic clusters in the Amazonian and savanna regions and three clusters in the Andes and Pacific coast. We detected a cline of genetic variation along a west-east axis, contradicting a hard Andes-Amazon divide. This longitudinal genetic variation seemed to have been shaped by both serial population bottlenecks and isolation by distance. Results indicated that present-day South American substructures recapitulate ancient macroregional ancestries and western Amazonia groups show genetic evidence of cultural exchanges that led to language replacement in precontact times. Finally, demographic inferences pointed to a higher resilience of the western South American groups regarding population collapses caused by the European invasion and indicated precontact population reductions and demic expansions in South America.     

A formal test of linguistic and genetic coevolution in native Central and South America

This paper investigates a mechanism of linguistic and genetic coevolution in Native Central and South America. This mechanism proposes that a process of population fissions, expansions into new territories, and isolation of ancestral and descendant groups will produce congruent language and gene trees. To evaluate this population fissions mechanism, we collected published mtDNA sequences for 1,381 individuals from 17 Native Central and South American populations. We then tested the hypothesis that three well-known language classifications also represented the genetic structure of these populations. We rejected the hypothesis for each language classification. Our tests revealed linguistic and genetic correspondence in several shallow branches common to each classification, but no linguistic and genetic correspondence in the deeper branches contained in two of the language classifications. We discuss the possible causes for the lack of congruence between linguistic and genetic structure in the region, and describe alternative mechanisms of linguistic and genetic correspondence and their predictions.     

Contrasting maternal and paternal histories in the linguistic context of Burkina Faso

Burkina Faso is located in the heart of West Africa and is a representative of the local structured patterns of human variability. Here, different cultures and languages are found in a geographic contiguity, as a result of several waves of migration and the succession of long- and short-term empires. However, historical documentation for this area is only partial, focusing predominantly on the recent empires, and linguistic surveys lack the power to fully elucidate the social context of the contact-induced changes. In this paper, we report Y-chromosomal data and complete mtDNA genome sequences for ten populations from Burkina Faso whose languages belong to two very distantly related branches of the Niger-Congo phylum, the Gur and Mande language families. In addition, two further populations, the Mande-speaking Mandenka from Senegal and the Yoruba from Nigeria, were included for regional comparison. We focus on the different historical trajectories undergone by the maternal and paternal lineages. Our results reveal a striking structure in the paternal line, which matches the linguistic affiliation of the ethnolinguistic groups, in contrast to the near-complete homogeneity of the populations in the maternal line. However, while the ancient structure along the linguistic lines is apparent in the Y-chromosomal haplogroup affiliation, this has clearly been overlain by more recent migrations, as shown by significant correlations between the genetic distances based on Y chromosome short tandem repeats and geographic distances between the populations, as well as by the patterns of shared haplotypes. Using the complete mtDNA sequences, we are able to reconstruct population size variation in the past, showing a strong sign of expansion in the concomitance with the Holocene Climate Optimum approximately 12,000-10,000 years ago, which has been suggested as the cause of the spread of the Niger-Congo phylum in the area. However, subsequent climatic fluctuations do not appear to have had an impact on the demography of the inhabitants of West Africa, probably reflecting the adaptive advantages of cultural innovations, such as pastoralism and agriculture.     

Patterns of genetic variation in Native America.

Allele frequencies from seven polymorphic red cell antigen loci (ABO, Rh, MN, S, P, Duffy, and Diego) were examined in 144 Native American populations. Mean genetic distances (Nei's D) and the fixation index FST are approximately equal for the North and South American samples but are reduced in the Central American geographic area. The relationship between genetic distance and geographic distance differs markedly across geographic areas. The correlation between geographic distance and genetic distance for the North and Central American data is twice as large as that observed for the South American samples. This geographic difference is confirmed in spatial autocorrelation analyses; no geographic structure is apparent in the South American data but geographic structure is prominent in North and Central American samples. These results confirm earlier observations regarding differences between North and South American gene frequency patterns.     

Unraveling the complex maternal history of Southern African Khoisan populations

The Khoisan populations of southern Africa are known to harbor some of the deepest‐rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre‐Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari. Am J Phys Anthropol 153:435–448, 2014. © 2013 Wiley Periodicals, Inc.     

Demographic History of Indigenous Populations in Mesoamerica Based on mtDNA Sequence Data

The genetic characterization of Native American groups provides insights into their history and demographic events. We sequenced the mitochondrial D-loop region (control region) of 520 samples from eight Mexican indigenous groups. In addition to an analysis of the genetic diversity, structure and genetic relationship between 28 Native American populations, we applied Bayesian skyline methodology for a deeper insight into the history of Mesoamerica. AMOVA tests applying cultural, linguistic and geographic criteria were performed. MDS plots showed a central cluster of Oaxaca and Maya populations, whereas those from the North and West were located on the periphery. Demographic reconstruction indicates higher values of the effective number of breeding females (Nef) in Central Mesoamerica during the Preclassic period, whereas this pattern moves toward the Classic period for groups in the North and West. Conversely, Nef minimum values are distributed either in the Lithic period (i.e. founder effects) or in recent periods (i.e. population declines). The Mesomerican regions showed differences in population fluctuation as indicated by the maximum Inter-Generational Rate (IGRmax): i) Center-South from the lithic period until the Preclassic; ii) West from the beginning of the Preclassic period until early Classic; iii) North characterized by a wide range of temporal variation from the Lithic to the Preclassic. Our findings are consistent with the genetic variations observed between central, South and Southeast Mesoamerica and the North-West region that are related to differences in genetic drift, structure, and temporal survival strategies (agriculture versus hunter-gathering, respectively). Interestingly, although the European contact had a major negative demographic impact, we detect a previous decline in Mesoamerica that had begun a few hundred years before.