The Genomic Impact of Human Migrations

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 (15 September 2021) | Viewed by 33209

Special Issue Editors


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Guest Editor
Department of Mathematics and Computer Science, University of Ferrara, Ferrara, Italy
Interests: population genetics and genomics; molecular evolution; evolutionary genetics; molecular anthropology; demographic inference; demographic modeling

E-Mail Website
Guest Editor
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
Interests: molecular anthropology; human population prehistory; human migration; diffusion and contact; South American prehistory; congruence between gene and language transmission

Special Issue Information

Dear Colleagues,

Anatomically modern humans first appeared in the East African fossil record around 200,000 years ago, and colonized the rest of the world with an unprecedented fast pace, in less than 100,000 years.  Their journey was accompanied by various levels of interaction with different species and habitats: a substantial replacement of pre-existing archaic humans, a strong selection drive behind extensive domestication processes (of both animals and plants), a range of direct and indirect modifications to the landscape which created new niches for commensal and pathogenic species, and finally new challenges for the adaptation to different, and sometimes extreme, environments. After the main colonization dispersal, human genomic variation has been largely shaped by events of localized gene flow of different intensities. These movements have been favoured by geological changes, as the post-glacial migration from refugia, or by processes of cultural transition, as the spread of agriculture from the Levant and the Late Neolithic/Bronze Age migration from the Pontic-Caspian steppe.

This Special Issue will collect reviews and original contributions about migration dynamics and evolutionary trajectories of our species, and of the species that came into contact with us during our migration journey.  This includes studies of human-pathogens interaction and coevolution, human-driven selection, inference of past demographic dynamics and genomic adaptation to new environments. 

Prof. Silvia Ghirotto
Dr. Chiara Barbieri
Guest Editors

Manuscript Submission Information

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Keywords

  • Genomic variation
  • Human migration
  • Demographic inference
  • Genetic adaptation
  • Domestication
  • Pathogen evolution
  • Phylogeography

Published Papers (7 papers)

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Research

36 pages, 9881 KiB  
Article
Genomic Screening to Identify Food Trees Potentially Dispersed by Precolonial Indigenous Peoples
by Monica Fahey, Maurizio Rossetto, Emilie Ens and Andrew Ford
Genes 2022, 13(3), 476; https://doi.org/10.3390/genes13030476 - 8 Mar 2022
Cited by 7 | Viewed by 2542
Abstract
Over millennia, Indigenous peoples have dispersed the propagules of non-crop plants through trade, seasonal migration or attending ceremonies; and potentially increased the geographic range or abundance of many food species around the world. Genomic data can be used to reconstruct these histories. However, [...] Read more.
Over millennia, Indigenous peoples have dispersed the propagules of non-crop plants through trade, seasonal migration or attending ceremonies; and potentially increased the geographic range or abundance of many food species around the world. Genomic data can be used to reconstruct these histories. However, it can be difficult to disentangle anthropogenic from non-anthropogenic dispersal in long-lived non-crop species. We developed a genomic workflow that can be used to screen out species that show patterns consistent with faunal dispersal or long-term isolation, and identify species that carry dispersal signals of putative human influence. We used genotyping-by-sequencing (DArTseq) and whole-plastid sequencing (SKIMseq) to identify nuclear and chloroplast Single Nucleotide Polymorphisms in east Australian rainforest trees (4 families, 7 genera, 15 species) with large (>30 mm) or small (<30 mm) edible fruit, either with or without a known history of use by Indigenous peoples. We employed standard population genetic analyses to test for four signals of dispersal using a limited and opportunistically acquired sample scheme. We expected different patterns for species that fall into one of three broadly described dispersal histories: (1) ongoing faunal dispersal, (2) post-megafauna isolation and (3) post-megafauna isolation followed by dispersal of putative human influence. We identified five large-fruited species that displayed strong population structure combined with signals of dispersal. We propose coalescent methods to investigate whether these genomic signals can be attributed to post-megafauna isolation and dispersal by Indigenous peoples. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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18 pages, 1656 KiB  
Article
First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD)
by Flavio De Angelis, Marco Romboni, Virginia Veltre, Paola Catalano, Cristina Martínez-Labarga, Valentina Gazzaniga and Olga Rickards
Genes 2022, 13(1), 136; https://doi.org/10.3390/genes13010136 - 13 Jan 2022
Cited by 6 | Viewed by 3862
Abstract
This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the [...] Read more.
This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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17 pages, 2948 KiB  
Article
The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture
by Filipa Simão, Julyana Ribeiro, Carlos Vullo, Laura Catelli, Verónica Gomes, Catarina Xavier, Gabriela Huber, Martin Bodner, Alfredo Quiroz, Ana Paula Ferreira, Elizeu F. Carvalho, Walther Parson and Leonor Gusmão
Genes 2021, 12(11), 1788; https://doi.org/10.3390/genes12111788 - 12 Nov 2021
Cited by 10 | Viewed by 6769
Abstract
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of [...] Read more.
Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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21 pages, 4890 KiB  
Article
Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact
by Gludhug A. Purnomo, Kieren J. Mitchell, Sue O’Connor, Shimona Kealy, Leonard Taufik, Sophie Schiller, Adam Rohrlach, Alan Cooper, Bastien Llamas, Herawati Sudoyo, João C. Teixeira and Raymond Tobler
Genes 2021, 12(7), 965; https://doi.org/10.3390/genes12070965 - 24 Jun 2021
Cited by 15 | Viewed by 5755
Abstract
The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea [...] Read more.
The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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17 pages, 1325 KiB  
Article
The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea
by João Almeida, Anne-Maria Fehn, Margarida Ferreira, Teresa Machado, Tjerk Hagemeijer, Jorge Rocha and Magdalena Gayà-Vidal
Genes 2021, 12(6), 833; https://doi.org/10.3390/genes12060833 - 28 May 2021
Cited by 4 | Viewed by 3715
Abstract
The forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on [...] Read more.
The forced migration of millions of Africans during the Atlantic Slave Trade led to the emergence of new genetic and linguistic identities, thereby providing a unique opportunity to study the mechanisms giving rise to human biological and cultural variation. Here we focus on the archipelago of São Tomé and Príncipe in the Gulf of Guinea, which hosted one of the earliest plantation societies relying exclusively on slave labor. We analyze the genetic variation in 25 individuals from three communities who speak distinct creole languages (Forros, Principenses and Angolares), using genomic data from expanded exomes in combination with a contextual dataset from Europe and Africa, including newly generated data from 28 Bantu speakers from Angola. Our findings show that while all islanders display mixed contributions from the Gulf of Guinea and Angola, the Angolares are characterized by extreme genetic differentiation and inbreeding, consistent with an admixed maroon isolate. In line with a more prominent Bantu contribution to their creole language, we additionally found that a previously reported high-frequency Y-chromosome haplotype in the Angolares has a likely Angolan origin, suggesting that their genetic, linguistic and social characteristics were influenced by a small group of dominant men who achieved disproportionate reproductive success. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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18 pages, 4436 KiB  
Article
Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand
by Aornpriya Mawan, Nonglak Prakhun, Kanha Muisuk, Suparat Srithawong, Metawee Srikummool, Jatupol Kampuansai, Rasmi Shoocongdej, Angkhana Inta, Sukhum Ruangchai and Wibhu Kutanan
Genes 2021, 12(3), 383; https://doi.org/10.3390/genes12030383 - 8 Mar 2021
Cited by 2 | Viewed by 3360
Abstract
The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated [...] Read more.
The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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20 pages, 3260 KiB  
Article
More Rule than Exception: Parallel Evidence of Ancient Migrations in Grammars and Genomes of Finno-Ugric Speakers
by Patrícia Santos, Gloria Gonzàlez-Fortes, Emiliano Trucchi, Andrea Ceolin, Guido Cordoni, Cristina Guardiano, Giuseppe Longobardi and Guido Barbujani
Genes 2020, 11(12), 1491; https://doi.org/10.3390/genes11121491 - 11 Dec 2020
Cited by 3 | Viewed by 5376
Abstract
To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages [...] Read more.
To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Therefore, our analysis indicates that plausible cross-family linguistic interference effects were accompanied, and possibly caused, by recognizable demographic processes. In particular, based on the comparison of modern and ancient genomes, our study identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of FU languages into Europe. Full article
(This article belongs to the Special Issue The Genomic Impact of Human Migrations)
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