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The Peopling of the Americas: A Genetic Perspective
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The Peopling of the Americas: A Genetic Perspective

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 55359

Special Issue Editors

Prof. Dr. Ornella Semino

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, I-27100 Pavia, Italy
Interests: Y chromosome and mtDNA phylogeography; human genomic diversity; population genetics; human evolution; modern DNA variation and archeogenomics
Prof. Dr. Alessandro Achilli

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, I-27100 Pavia, Italy
Interests: Y-chromosome and mtDNA phylogeography; human genomic diversity; population genetics; human evolution; modern DNA variation and archeogenomics

Special Issue Information

Dear Colleagues,

The American double continent, the last to be colonized by modern humans, is characterized by an extraordinary cultural and linguistic diversity that, in the last decades, have fostered genetic analyses. However, its genetic history and demographic dynamics are far from being fully defined. Founder events, genetic drift, and admixture, as well as selection in native populations, together with the post-contact newcomers’ genetic contributions have made their reconstruction really challenging. Nowadays, with the advent of advanced sequencing technologies and bioinformatic tools able to acquire and analyze large amounts of modern and ancient genomic data, the knowledge of the Native American gene pool is enormously increasing with the possibility of integrating (modern and ancient) autosomal information with that derived from the mitochondrial DNA and the male-specific region of the Y chromosome.

This Special Issue will collect reviews and original research findings concerning the founding migrations from Beringia/Siberia (origins of Native Americans), the subsequent internal movements (pre-contact genetic history), and the genetic admixture during and after colonial times (post-contact genetic history), as well as historical events and socio-cultural habits that might have influenced the current genomic structure (an interdisciplinary perspective). In our view, an enriched genetic picture can be depicted not only through the analysis of the bi-parental and uni-parental genetic variation in modern and ancient individuals or groups, but also by intercepting indigenous-specific markers that survived in current general populations.

Sincerely

Prof. Ornella Semino
Prof. Alessandro Achilli
Guest Editors

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Keywords

  • Peopling of the Americas
  • Native American ancestries
  • Native American genetic history
  • Native American founding lineages
  • Admixture in the American double continent
  • Ancient and modern DNAs
  • MtDNA, Y chromosome, and autosomal markers

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Published Papers (8 papers)

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Research

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22 pages, 4799 KiB  
Article
Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent
by Giulia Colombo, Luca Traverso, Lucia Mazzocchi, Viola Grugni, Nicola Rambaldi Migliore, Marco Rosario Capodiferro, Gianluca Lombardo, Rodrigo Flores, Monika Karmin, Siiri Rootsi, Luca Ferretti, Anna Olivieri, Antonio Torroni, Rui Martiniano, Alessandro Achilli, Alessandro Raveane and Ornella Semino
Genes 2022, 13(2), 220; https://doi.org/10.3390/genes13020220 - 25 Jan 2022
Cited by 4 | Viewed by 7544
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native [...] Read more.
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813). Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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17 pages, 3745 KiB  
Article
Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas
by Nicola Rambaldi Migliore, Giulia Colombo, Marco Rosario Capodiferro, Lucia Mazzocchi, Ana Maria Chero Osorio, Alessandro Raveane, Maribel Tribaldos, Ugo Alessandro Perego, Tomás Mendizábal, Alejandro García Montón, Gianluca Lombardo, Viola Grugni, Maria Garofalo, Luca Ferretti, Cristina Cereda, Stella Gagliardi, Richard Cooke, Nicole Smith-Guzmán, Anna Olivieri, Bethany Aram, Antonio Torroni, Jorge Motta, Ornella Semino and Alessandro Achilliadd Show full author list remove Hide full author list
Genes 2021, 12(12), 1921; https://doi.org/10.3390/genes12121921 - 29 Nov 2021
Cited by 3 | Viewed by 7662
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in [...] Read more.
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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12 pages, 1215 KiB  
Article
Evaluating the Impact of Sex-Biased Genetic Admixture in the Americas through the Analysis of Haplotype Data
by Linda Ongaro, Ludovica Molinaro, Rodrigo Flores, Davide Marnetto, Marco R. Capodiferro, Marta E. Alarcón-Riquelme, Andrés Moreno-Estrada, Nedio Mabunda, Mario Ventura, Kristiina Tambets, Alessandro Achilli, Cristian Capelli, Mait Metspalu, Luca Pagani and Francesco Montinaro
Genes 2021, 12(10), 1580; https://doi.org/10.3390/genes12101580 - 7 Oct 2021
Cited by 9 | Viewed by 2996
Abstract
A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of [...] Read more.
A general imbalance in the proportion of disembarked males and females in the Americas has been documented during the Trans-Atlantic Slave Trade and the Colonial Era and, although less prominent, more recently. This imbalance may have left a signature on the genomes of modern-day populations characterised by high levels of admixture. The analysis of the uniparental systems and the evaluation of continental proportion ratio of autosomal and X chromosomes revealed a general sex imbalance towards males for European and females for African and Indigenous American ancestries. However, the consistency and degree of this imbalance are variable, suggesting that other factors, such as cultural and social practices, may have played a role in shaping it. Moreover, very few investigations have evaluated the sex imbalance using haplotype data, containing more critical information than genotypes. Here, we analysed genome-wide data for more than 5000 admixed American individuals to assess the presence, direction and magnitude of sex-biased admixture in the Americas. For this purpose, we applied two haplotype-based approaches, ELAI and NNLS, and we compared them with a genotype-based method, ADMIXTURE. In doing so, besides a general agreement between methods, we unravelled that the post-colonial admixture dynamics show higher complexity than previously described. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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14 pages, 1424 KiB  
Article
The Mitochondrial DNA Landscape of Modern Mexico
by Martin Bodner, Ugo A. Perego, J. Edgar Gomez, Ricardo M. Cerda-Flores, Nicola Rambaldi Migliore, Scott R. Woodward, Walther Parson and Alessandro Achilli
Genes 2021, 12(9), 1453; https://doi.org/10.3390/genes12091453 - 21 Sep 2021
Cited by 12 | Viewed by 11839
Abstract
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has [...] Read more.
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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15 pages, 2401 KiB  
Article
Uniparental Lineages from the Oldest Indigenous Population of Ecuador: The Tsachilas
by Tullia Di Corcia, Giuseppina Scano, Cristina Martínez-Labarga, Stefania Sarno, Sara De Fanti, Donata Luiselli and Olga Rickards
Genes 2021, 12(8), 1273; https://doi.org/10.3390/genes12081273 - 20 Aug 2021
Cited by 2 | Viewed by 3250
Abstract
Together with Cayapas, the Tsachilas constitute the oldest population in the country of Ecuador and, according to some historians, they are the last descendants of the ancient Yumbos. Several anthropological issues underlie the interest towards this peculiar population: the uncertainty of their origin, [...] Read more.
Together with Cayapas, the Tsachilas constitute the oldest population in the country of Ecuador and, according to some historians, they are the last descendants of the ancient Yumbos. Several anthropological issues underlie the interest towards this peculiar population: the uncertainty of their origin, their belonging to the Barbacoan linguistic family, which is still at the center of an intense linguistic debate, and the relations of their Yumbo ancestors with the Inca invaders who occupied their ancient territory. Our contribution to the knowledge of their complex past was the reconstruction of their genetic maternal and paternal inheritance through the sequencing of 70 entire mitochondrial genomes and the characterization of the non-recombinant region of the Y chromosome in 26 males. For both markers, we built comprehensive datasets of various populations from the surrounding geographical area, northwestern South America, NW, with a known linguistic affiliation, and we could then compare our sample against the overall variability to infer relationships with other Barbacoan people and with other NW natives. We found contrasting patterns of genetic diversity for the two markers, but generally, our results indicated a possible common origin between the Tsachilas, the Chachi, and other Ecuadorian and Colombian Barbacoans and are suggestive of an interesting ancient linkage to the Inca invaders in Yumbo country. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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Review

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12 pages, 2390 KiB  
Review
Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics
by John Lindo and Michael DeGiorgio
Genes 2021, 12(3), 360; https://doi.org/10.3390/genes12030360 - 2 Mar 2021
Cited by 3 | Viewed by 3731
Abstract
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. [...] Read more.
The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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16 pages, 2189 KiB  
Review
A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations
by Roberta Davidson, Lars Fehren-Schmitz and Bastien Llamas
Genes 2021, 12(2), 215; https://doi.org/10.3390/genes12020215 - 2 Feb 2021
Cited by 5 | Viewed by 5671
Abstract
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438–1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that [...] Read more.
The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438–1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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19 pages, 3883 KiB  
Review
Ancient DNA Studies in Pre-Columbian Mesoamerica
by Xavier Roca-Rada, Yassine Souilmi, João C. Teixeira and Bastien Llamas
Genes 2020, 11(11), 1346; https://doi.org/10.3390/genes11111346 - 13 Nov 2020
Cited by 6 | Viewed by 10705
Abstract
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and [...] Read more.
Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE–150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900–1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses. Full article
(This article belongs to the Special Issue The Peopling of the Americas: A Genetic Perspective)
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