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Peter BM. A geometric relationship of
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2
,
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3
and
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4
-statistics with principal component analysis. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200413. [PMID: 35430884 PMCID: PMC9014194 DOI: 10.1098/rstb.2020.0413] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Principal component analysis (PCA) and
F
-statistics
sensu
Patterson are two of the most widely used population genetic tools to study human genetic variation. Here, I derive explicit connections between the two approaches and show that these two methods are closely related.
F
-statistics have a simple geometrical interpretation in the context of PCA, and orthogonal projections are a key concept to establish this link. I show that for any pair of populations, any population that is admixed as determined by an
F
3
-statistic will lie inside a circle on a PCA plot. Furthermore, the
F
4
-statistic is closely related to an angle measurement, and will be zero if the differences between pairs of populations intersect at a right angle in PCA space. I illustrate my results on two examples, one of Western Eurasian, and one of global human diversity. In both examples, I find that the first few PCs are sufficient to approximate most
F
-statistics, and that PCA plots are effective at predicting
F
-statistics. Thus, while
F
-statistics are commonly understood in terms of discrete populations, the geometric perspective illustrates that they can be viewed in a framework of populations that vary in a more continuous manner.
This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Benjamin M. Peter
- Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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2
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Gnecchi-Ruscone GA, Szécsényi-Nagy A, Koncz I, Csiky G, Rácz Z, Rohrlach AB, Brandt G, Rohland N, Csáky V, Cheronet O, Szeifert B, Rácz TÁ, Benedek A, Bernert Z, Berta N, Czifra S, Dani J, Farkas Z, Hága T, Hajdu T, Jászberényi M, Kisjuhász V, Kolozsi B, Major P, Marcsik A, Kovacsóczy BN, Balogh C, Lezsák GM, Ódor JG, Szelekovszky M, Szeniczey T, Tárnoki J, Tóth Z, Tutkovics EK, Mende BG, Geary P, Pohl W, Vida T, Pinhasi R, Reich D, Hofmanová Z, Jeong C, Krause J. Ancient genomes reveal origin and rapid trans-Eurasian migration of 7 th century Avar elites. Cell 2022; 185:1402-1413.e21. [PMID: 35366416 PMCID: PMC9042794 DOI: 10.1016/j.cell.2022.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/28/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022]
Abstract
The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.
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Affiliation(s)
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - István Koncz
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - Gergely Csiky
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Zsófia Rácz
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - A B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Guido Brandt
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Veronika Csáky
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Bea Szeifert
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | | | | | | | | | | | | | | | | | - Tamás Hajdu
- Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary
| | | | | | | | | | - Antónia Marcsik
- Dept. of Biological Anthropology, Szeged University, 6701 Szeged, Hungary
| | | | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, 34720 Istanbul, Turkey
| | - Gabriella M Lezsák
- Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | | | | | - Tamás Szeniczey
- Dept. of Biological Anthropology, Eötvös Loránd University (ELTE), 1117 Budapest, Hungary
| | | | | | | | - Balázs G Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Patrick Geary
- Institute for Advanced Study, Princeton, NJ 08540, USA
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences, 1020 Vienna, Austria; Institute of Austrian Historical Research, University of Vienna, 1010 Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE Eötvös Loránd University, 1088 Budapest, Hungary
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Department of Archaeology and Museology, Faculty of Arts, Masaryk University, 60200 Brno, Czech Republic
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, 08826 Seoul, Republic of Korea.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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3
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Branco C, Kanellou M, González-Martín A, Arenas M. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes (Basel) 2022; 13:genes13020384. [PMID: 35205429 PMCID: PMC8871837 DOI: 10.3390/genes13020384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans.
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Affiliation(s)
- Catarina Branco
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Marina Kanellou
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonio González-Martín
- Department of Biodiversity, Ecology and Evolution, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Miguel Arenas
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Correspondence: ; Tel.: +34-986-130-047
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Rio J, Quilodrán CS, Currat M. Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations. Commun Biol 2021; 4:1163. [PMID: 34621003 PMCID: PMC8497574 DOI: 10.1038/s42003-021-02670-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023] Open
Abstract
The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.
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Affiliation(s)
- Jérémy Rio
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Claudio S Quilodrán
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
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5
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Deng J, Assandri G, Chauhan P, Futahashi R, Galimberti A, Hansson B, Lancaster LT, Takahashi Y, Svensson EI, Duplouy A. Wolbachia-driven selective sweep in a range expanding insect species. BMC Ecol Evol 2021; 21:181. [PMID: 34563127 PMCID: PMC8466699 DOI: 10.1186/s12862-021-01906-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022] Open
Abstract
Background Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. Method The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). Results Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000 years before present, which is consistent with the end of the last glacial period about 20,000 years. Conclusions Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.
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Affiliation(s)
- Junchen Deng
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden.,Institute of Environmental Sciences, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
| | - Giacomo Assandri
- Area per l'Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPA), Via Ca' Fornacetta 9, 40064, Ozzano Emilia, BO, Italy
| | - Pallavi Chauhan
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advance Industrial Science and Technology (AIST), Trukuba, Ibaraki, 305-8566, Japan
| | - Andrea Galimberti
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Bengt Hansson
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Lesley T Lancaster
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Yuma Takahashi
- Graduate School of Science, Chiba University, Chiba, Japan
| | - Erik I Svensson
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Anne Duplouy
- Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden. .,Insect Symbiosis Ecology and Evolution Lab, Organismal and Evolutionary Biology Research Program, The University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
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Ferreiro D, Núñez-Estévez B, Canedo M, Branco C, Arenas M. Evaluating Causes of Current Genetic Gradients of Modern Humans of the Iberian Peninsula. Genome Biol Evol 2021; 13:6219947. [PMID: 33837782 PMCID: PMC8086631 DOI: 10.1093/gbe/evab071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
The history of modern humans in the Iberian Peninsula includes a variety of population arrivals sometimes presenting admixture with resident populations. Genetic data from current Iberian populations revealed an overall east–west genetic gradient that some authors interpreted as a direct consequence of the Reconquista, where Catholic Kingdoms expanded their territories toward the south while displacing Muslims. However, this interpretation has not been formally evaluated. Here, we present a qualitative analysis of the causes of the current genetic gradient observed in the Iberian Peninsula using extensive spatially explicit computer simulations based on a variety of evolutionary scenarios. Our results indicate that the Neolithic range expansion clearly produces the orientation of the observed genetic gradient. Concerning the Reconquista (including political borders among Catholic Kingdoms and regions with different languages), if modeled upon a previous Neolithic expansion, it effectively favored the orientation of the observed genetic gradient and shows local isolation of certain regions (i.e., Basques and Galicia). Despite additional evolutionary scenarios could be evaluated to more accurately decipher the causes of the Iberian genetic gradient, here we show that this gradient has a more complex explanation than that previously hypothesized.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, Spain.,Universidade de Vigo, Departamento de Bioquímica, Xenética e Immunoloxía, Spain
| | - Bernabé Núñez-Estévez
- CINBIO, Universidade de Vigo, Spain.,Universidade de Vigo, Departamento de Bioquímica, Xenética e Immunoloxía, Spain
| | - Mateo Canedo
- CINBIO, Universidade de Vigo, Spain.,Universidade de Vigo, Departamento de Bioquímica, Xenética e Immunoloxía, Spain
| | - Catarina Branco
- CINBIO, Universidade de Vigo, Spain.,Universidade de Vigo, Departamento de Bioquímica, Xenética e Immunoloxía, Spain
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, Spain.,Universidade de Vigo, Departamento de Bioquímica, Xenética e Immunoloxía, Spain
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Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics 2020; 35:4480-4483. [PMID: 31077292 PMCID: PMC6821363 DOI: 10.1093/bioinformatics/btz311] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
SUMMARY SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework. The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a large variety of DNA mutation models. These implementations have been applied independently to various studies, but grouped together in the current version. AVAILABILITY AND IMPLEMENTATION SPLATCHE3 is written in C++ and is freely available for non-commercial use from the website http://www.splatche.com/splatche3. It includes console versions for Linux, MacOs and Windows and a user-friendly GUI for Windows, as well as detailed documentation and ready-to-use examples.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva 1211, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, Vigo 36310, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Claudio S Quilodràn
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva 1205, Switzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern 3012, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicolas Ray
- Institute of Global Health, GeoHealth Group, University of Geneva, Geneva 1205, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva 1205, Switzerland
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Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia. Mol Ecol 2020; 29:2150-2159. [PMID: 32436243 DOI: 10.1111/mec.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Nicolas Ray
- GeoHealth Group, Institute of Global Health, University of Geneva, Geneva, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
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Abstract
Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.
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Abstract
Despite the efforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the first humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions.
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Illera JC, Arenas M, López-Sánchez CA, Obeso JR, Laiolo P. Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper. Genes (Basel) 2019; 10:E590. [PMID: 31387238 PMCID: PMC6724060 DOI: 10.3390/genes10080590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
The location of the high mountains of southern Europe has been crucial in the phylogeography of most European species, but how extrinsic (topography of sky islands) and intrinsic features (dispersal dynamics) have interacted to shape the genetic structure in alpine restricted species is still poorly known. Here we investigated the mechanisms explaining the colonisation of Cantabrian sky islands in an endemic flightless grasshopper. We scrutinised the maternal genetic variability and haplotype structure, and we evaluated the fitting of two migration models to understand the extant genetic structure in these populations: Long-distance dispersal (LDD) and gradual distance dispersal (GDD). We found that GDD fits the real data better than the LDD model, with an onset of the expansion matching postglacial expansions after the retreat of the ice sheets. Our findings suggest a scenario with small carrying capacity, migration rates, and population growth rates, being compatible with a slow dispersal process. The gradual expansion process along the Cantabrian sky islands found here seems to be conditioned by the suitability of habitats and the presence of alpine corridors. Our findings shed light on our understanding about how organisms which have adapted to live in alpine habitats with limited dispersal abilities have faced new and suitable environmental conditions.
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Affiliation(s)
- Juan Carlos Illera
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
| | - Carlos A López-Sánchez
- Department of Biology, Organisms and Systems, GIS-Forest Group, Oviedo University, 33600 Mieres, Spain
| | - José Ramón Obeso
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain
| | - Paola Laiolo
- Research Unit of Biodiversity (UMIB, UO-CSIC-PA), Oviedo University, 33600 Mieres, Spain
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Braga RT, Rodrigues JFM, Diniz-Filho JAF, Rangel TF. Genetic Population Structure and Allele Surfing During Range Expansion in Dynamic Habitats. AN ACAD BRAS CIENC 2019; 91:e20180179. [PMID: 31038531 DOI: 10.1590/0001-3765201920180179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 09/10/2018] [Indexed: 12/24/2022] Open
Abstract
Expanding populations may loss genetic diversity because sequential founder events throughout a wave of demographic expansion may cause "allele surfing", as the alleles of founder individuals may propagate rapidly through space. The spatial components of allele surfing have been studied by geneticists, but have never been investigate on dynamic and shifting habitats. Here we used an individual-based-model (IBM) to study how interactions between different habitat restoration scenarios and biological characteristics (dispersal capacity) affect the spatial patterns of the genetic structure of a population during demographic expansion. We found that both habitat dynamics and dispersal capacity, as well as their interaction, were the drivers of emergent pattern of genetic diversity and allele surfing. Specifically, allele surfing is more common when a species with low dispersal capacity colonizes a large geographic area with slow restoration (low carrying capacity). Despite this, we showed that allele surfing can be reduced, or even avoided, by dispersal management through suitable habitat restoration. Thus, investigating how colonization generates a spatial variation in genetic diversity, and which parameters control the emergent genetic pattern, are essential steps to planning assisted gene flow, which is fundamental for an effective planning of habitat restoration.
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Affiliation(s)
- Rosana T Braga
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - João F M Rodrigues
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - José A F Diniz-Filho
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
| | - Thiago F Rangel
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Avenida Esperança, s/n, 74001-970 Goiânia, GO, Brazil
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13
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Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes (Basel) 2018; 9:genes9100506. [PMID: 30340387 PMCID: PMC6210830 DOI: 10.3390/genes9100506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022] Open
Abstract
Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species.
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14
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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15
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Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. Consequences of diverse evolutionary processes on american genetic gradients of modern humans. Heredity (Edinb) 2018; 121:548-556. [PMID: 30022169 DOI: 10.1038/s41437-018-0122-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
European genetic gradients of modern humans were initially interpreted as a consequence of the demic diffusion of expanding Neolithic farmers. However, recent studies showed that these gradients may also be influenced by other evolutionary processes such as population admixture or range contractions. Genetic gradients were observed in the Americas, although their specific evolutionary causes were not investigated. Here we extended the approach used to study genetic gradients in Europe to analyze the influence of diverse evolutionary scenarios on American genetic gradients. Using extensive computer simulations, we evaluated the impact of (i) admixture between expansion waves of modern humans, (ii) the presence of ice-sheets during the last glacial maximum (LGM) and (iii) long-distance dispersal (LDD) events, on the genetic gradients (detected by principal component analysis) of the entire continent, North America and South America. The specific simulation of North and South America showed that genetic gradients are usually orthogonal to the direction of range expansions-either expansions from Bering or posterior re-expansions to recolonize northern regions after ice sheets melting-and we suggest that they result from allele surfing processes. Conversely, our results on the entire continent show a northwest-southeast gradient obtained with any scenario, which we interpreted as a consequence of isolation by distance along the long length of the continent. These findings suggest that distinct genetic gradients can be detected at different regions of the Americas and that subcontinent regions present gradients more sensible to evolutionary and environmental factors (such as LDD and the LGM) than the whole continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Miguel Velasco
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Macarena Benguigui
- Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mathias Currat
- Anthropology, Genetics and Peopling History Lab, Department of Genetics & Evolution -Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Nicolas Ray
- EnviroSPACE Lab, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland.,Institute of Global Health, University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal. .,Centre for Molecular Biology "Severo Ochoa", Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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16
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Thouzeau V, Mennecier P, Verdu P, Austerlitz F. Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. Proc Biol Sci 2018; 284:rspb.2017.0706. [PMID: 28835553 DOI: 10.1098/rspb.2017.0706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/17/2017] [Indexed: 11/12/2022] Open
Abstract
Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.
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Affiliation(s)
- Valentin Thouzeau
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Philippe Mennecier
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Paul Verdu
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Frédéric Austerlitz
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
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17
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Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Mol Biol Evol 2017; 34:3232-3242. [DOI: 10.1093/molbev/msx256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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18
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Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep 2017; 7:46044. [PMID: 28387361 PMCID: PMC5384202 DOI: 10.1038/srep46044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 01/17/2023] Open
Abstract
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.
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Amorim CEG, Hofer T, Ray N, Foll M, Ruiz-Linares A, Excoffier L. Long-distance dispersal suppresses introgression of local alleles during range expansions. Heredity (Edinb) 2017; 118:135-142. [PMID: 27577693 PMCID: PMC5234476 DOI: 10.1038/hdy.2016.68] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 07/15/2016] [Accepted: 07/18/2016] [Indexed: 12/24/2022] Open
Abstract
During range expansions, even low levels of interbreeding can lead to massive introgression of local alleles into an invader's genome. Nonetheless, this pattern is not always observed in human populations. For instance, European Americans in North America are barely introgressed by Amerindian genes in spite of known contact and admixture. With coalescent spatially explicit simulations, we examined the impact of long-distance dispersal (LDD) events on introgression of local alleles into the invading population using a set of different demographic scenarios applicable to a diverse range of natural populations and species. More specifically, we consider two distinct LDD models: one where LDD events originate in the range core and targets only the expansion front and a second one where LDD events can occur from any area to any other. We find that LDD generally prevents introgression, but that LDD events specifically targeting the expansion front are most efficient in suppressing introgression. This is likely due to the fact that LDD allows for the presence of a larger number of invader alleles at the wave front, where effective population size is thus increased and local introgressed alleles are rapidly outnumbered. We postulate that the documented settlement of pioneers directly on the wave front in North America has contributed to low levels of Amerindian admixture observed in European Americans and that this phenomenon may well explain the lack of introgression after a range expansion in natural populations without the need to evoke other mechanisms such as natural selection.
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Affiliation(s)
- C E G Amorim
- Department of Biological Sciences,
Columbia University, New York, NY,
USA
- CAPES Foundation, Ministry of
Education of Brazil, Brasília, Distrito
Federal, Brazil
| | - T Hofer
- Computational and Molecular
Population Genetics Lab, Institute of Ecology and Evolution, University of
Bern, Bern, Switzerland
- Swiss Institute of
Bioinformatics, Lausanne, Switzerland
| | - N Ray
- EnviroSPACE Laboratory, Institute for
Environmental Sciences, University of Geneva, Geneva,
Switzerland
| | - M Foll
- Genetic Cancer Susceptibility Group,
International Agency for Research on Cancer, Lyon,
France
| | - A Ruiz-Linares
- Department of Genetics, Evolution and
Environment, University College London, London,
UK
| | - L Excoffier
- Computational and Molecular
Population Genetics Lab, Institute of Ecology and Evolution, University of
Bern, Bern, Switzerland
- Swiss Institute of
Bioinformatics, Lausanne, Switzerland
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20
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Genetic surfing in human populations: from genes to genomes. Curr Opin Genet Dev 2016; 41:53-61. [DOI: 10.1016/j.gde.2016.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 12/20/2022]
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21
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Hunley K, Gwin K, Liberman B. A Reassessment of the Impact of European Contact on the Structure of Native American Genetic Diversity. PLoS One 2016; 11:e0161018. [PMID: 27579784 PMCID: PMC5007009 DOI: 10.1371/journal.pone.0161018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
Our current understanding of pre-Columbian history in the Americas rests in part on several trends identified in recent genetic studies. The goal of this study is to reexamine these trends in light of the impact of post-Columbian admixture and the methods used to study admixture. The previously-published data consist of 645 autosomal microsatellite genotypes from 1046 individuals in 63 populations. We used STRUCTURE to estimate ancestry proportions and tested the sensitivity of these estimates to the choice of the number of clusters, K. We used partial correlation analyses to examine the relationship between gene diversity and geographic distance from Beringia, controlling for non-Native American ancestry (from Africa, Europe and East Asia), and taking into account alternative paths of migration. Principal component analysis and multidimensional scaling were used to investigate the relationships between Andean and non-Andean populations and to explore gene-language correspondence. We found that 1) European and East Asian ancestry estimates decline as K increases, especially in Native Canadian populations, 2) a north-south decline in gene diversity is driven by low diversity in Amazonian and Paraguayan populations, not serial founder effects from Beringia, 3) controlling for non-Native American ancestry, populations in the Andes and Mesoamerica have higher gene diversity than populations in other regions, and 4) patterns of genetic and linguistic diversity are poorly correlated. We conclude that patterns of diversity previously attributed to pre-Columbian processes may in part reflect post-Columbian admixture and the choice of K in STRUCTURE analyses. Accounting for admixture, the pattern of diversity is inconsistent with a north-south founder effect process, though the genetic similarities between Mesoamerican and Andean populations are consistent with rapid dispersal along the western coast of the Americas. Further, even setting aside the disruptive effects of European contact, gene-language congruence is unlikely to have ever existed at the geographic scale analyzed here.
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Affiliation(s)
- Keith Hunley
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
- * E-mail:
| | - Kiela Gwin
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Brendan Liberman
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, United States of America
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Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity (Edinb) 2016; 117:316-325. [PMID: 27485668 DOI: 10.1038/hdy.2016.54] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from >1000 nuclear single-nucleotide polymorphisms (SNPs) and find evidence of incomplete lineage sorting so that the genealogies of SNPs do not all conform to a single topology. To disentangle whether uncertainty in the phylogenetic inference of the relationships among ecotypes could also result from ancestral admixture events we reconstructed the relationship among the ecotypes as an admixture graph and estimated f4-statistics using TreeMix. The results were consistent with episodes of admixture between two of the North Pacific ecotypes and the two outgroups (populations from the Southern Ocean and the North Atlantic). Gene flow may have occurred via unsampled 'ghost' populations rather than directly between the populations sampled here. Our results indicate that because of ancestral admixture events and incomplete lineage sorting, a single bifurcating tree does not fully describe the relationship among these populations. The data are therefore most consistent with the genomic variation among North Pacific killer whale ecotypes resulting from multiple colonisation events, and secondary contact may have facilitated evolutionary divergence. Thus, the present-day populations of North Pacific killer whale ecotypes have a complex ancestry, confounding the tree-based inference of ancestral geography.
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