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Kemppainen P, Schembri R, Momigliano P. Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data. Mol Biol Evol 2024; 41:msae091. [PMID: 38743590 PMCID: PMC11135943 DOI: 10.1093/molbev/msae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.
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Affiliation(s)
- Petri Kemppainen
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Rhiannon Schembri
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Paolo Momigliano
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
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Freund F, Kerdoncuff E, Matuszewski S, Lapierre M, Hildebrandt M, Jensen JD, Ferretti L, Lambert A, Sackton TB, Achaz G. Interpreting the pervasive observation of U-shaped Site Frequency Spectra. PLoS Genet 2023; 19:e1010677. [PMID: 36952570 PMCID: PMC10072462 DOI: 10.1371/journal.pgen.1010677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 04/04/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.
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Affiliation(s)
- Fabian Freund
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Elise Kerdoncuff
- Department of Genetics, University of California, Berkeley, California, United States of America
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Marguerite Lapierre
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Jeffrey D Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Amaury Lambert
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, Paris, France
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy B Sackton
- Éco-anthropologie, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Guillaume Achaz
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
- SMILE group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Paris, France
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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Mas-Sandoval A, Pope NS, Nielsen KN, Altinkaya I, Fumagalli M, Korneliussen TS. Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data. Gigascience 2022; 11:giac032. [PMID: 35579549 PMCID: PMC9112775 DOI: 10.1093/gigascience/giac032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The site frequency spectrum summarizes the distribution of allele frequencies throughout the genome, and it is widely used as a summary statistic to infer demographic parameters and to detect signals of natural selection. The use of high-throughput low-coverage DNA sequencing data can lead to biased estimates of the site frequency spectrum due to high levels of uncertainty in genotyping. RESULTS Here we design and implement a method to efficiently and accurately estimate the multidimensional joint site frequency spectrum for large numbers of haploid or diploid individuals across an arbitrary number of populations, using low-coverage sequencing data. The method maximizes a likelihood function that represents the probability of the sequencing data observed given a multidimensional site frequency spectrum using genotype likelihoods. Notably, it uses an advanced binning heuristic paired with an accelerated expectation-maximization algorithm for a fast and memory-efficient computation, and can generate both unfolded and folded spectra and bootstrapped replicates for haploid and diploid genomes. On the basis of extensive simulations, we show that the new method requires remarkably less storage and is faster than previous implementations whilst retaining the same accuracy. When applied to low-coverage sequencing data from the fungal pathogen Neonectria neomacrospora, results recapitulate the patterns of population differentiation generated using the original high-coverage data. CONCLUSION The new implementation allows for accurate estimation of population genetic parameters from arbitrarily large, low-coverage datasets, thus facilitating cost-effective sequencing experiments in model and non-model organisms.
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Affiliation(s)
- Alex Mas-Sandoval
- Department of Life Sciences, Silwood Park campus, Imperial College London, SL5 7PY, Ascot, UK
| | - Nathaniel S Pope
- Department of Entomology, The Pennsylvania State University, 201 Old Main, University Park, PA 16802, USA
| | - Knud Nor Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Isin Altinkaya
- GLOBE, Section for Geogenetics, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Matteo Fumagalli
- Department of Life Sciences, Silwood Park campus, Imperial College London, SL5 7PY, Ascot, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez AS, Ballinger MA, Agwamba K, Nachman MW. The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics 2022; 220:iyab226. [PMID: 34897431 PMCID: PMC9097263 DOI: 10.1093/genetics/iyab226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/04/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the genetic basis of environmental adaptation in natural populations is a central goal in evolutionary biology. The conditions at high elevation, particularly the low oxygen available in the ambient air, impose a significant and chronic environmental challenge to metabolically active animals with lowland ancestry. To understand the process of adaptation to these novel conditions and to assess the repeatability of evolution over short timescales, we examined the signature of selection from complete exome sequences of house mice (Mus musculus domesticus) sampled across two elevational transects in the Andes of South America. Using phylogenetic analysis, we show that house mice colonized high elevations independently in Ecuador and Bolivia. Overall, we found distinct responses to selection in each transect and largely nonoverlapping sets of candidate genes, consistent with the complex nature of traits that underlie adaptation to low oxygen availability (hypoxia) in other species. Nonetheless, we also identified a small subset of the genome that appears to be under parallel selection at the gene and SNP levels. In particular, three genes (Col22a1, Fgf14, and srGAP1) bore strong signatures of selection in both transects. Finally, we observed several patterns that were common to both transects, including an excess of derived alleles at high elevation, and a number of hypoxia-associated genes exhibiting a threshold effect, with a large allele frequency change only at the highest elevations. This threshold effect suggests that selection pressures may increase disproportionately at high elevations in mammals, consistent with observations of some high-elevation diseases in humans.
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Affiliation(s)
- Elizabeth J Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felipe Martins
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Taichi A Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Evolution, Ecology, and Organismal Biology and the Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Mallory A Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kennedy Agwamba
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021; 111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
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Affiliation(s)
- Alex Mercier
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
- Université Paris-Saclay, Orsay, France
| | - Adeline Simon
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Marc Bardin
- UR0407 Pathologie Végétale, INRAE, 84143 Montfavet, France
| | - Anne-Sophie Walker
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Adaptive Evolution in Cities: Progress and Misconceptions. Trends Ecol Evol 2020; 36:239-257. [PMID: 33342595 DOI: 10.1016/j.tree.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022]
Abstract
Current narratives suggest that urban adaptation - the adaptive evolution of organisms to cities - is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.
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