51
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Winkler DE, Chapin KJ, François O, Garmon JD, Gaut BS, Huxman TE. Multiple introductions and population structure during the rapid expansion of the invasive Sahara mustard ( Brassica tournefortii). Ecol Evol 2019; 9:7928-7941. [PMID: 31380061 PMCID: PMC6662425 DOI: 10.1002/ece3.5239] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 12/23/2022] Open
Abstract
The specific mechanisms that result in the success of any species invasion case are difficult to document. Reproductive strategies are often cited as a primary driver of invasive success, with human activities further facilitating invasions by, for example, acting as seed vectors for dispersal via road, train, air, and marine traffic, and by producing efficient corridors for movement including canals, drainages, and roadways. Sahara mustard (Brassica tournefortii) is a facultative autogamous annual native to Eurasia that has rapidly invaded the southwestern United States within the past century, displacing natives, and altering water-limited landscapes in the southwest. We used a genotyping-by-sequencing approach to study the population structure and spatial geography of Sahara mustard from 744 individuals from 52 sites across the range of the species' invasion. We also used herbaria records to model range expansion since its initial introduction in the 1920s. We found that Sahara mustard occurs as three populations in the United States unstructured by geography, identified three introduction sites, and combined herbaria records with genomic analyses to map the spread of the species. Low genetic diversity and linkage disequilibrium are consistent with self-fertilization, which likely promoted rapid invasive spread. Overall, we found that Sahara mustard experienced atypical expansion patterns, with a relatively constant rate of expansion and without the lag phase that is typical of many invasive species.
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Affiliation(s)
- Daniel E. Winkler
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
- U.S. Geological SurveySouthwest Biological Science CenterMoabUtah
| | - Kenneth J. Chapin
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCalifornia
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizona
| | | | | | - Brandon S. Gaut
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
| | - Travis E. Huxman
- Department of Ecology and Evolutionary BiologyUniversity of California, IrvineIrvineCalifornia
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52
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Willi Y. The relevance of mutation load for species range limits. AMERICAN JOURNAL OF BOTANY 2019; 106:757-759. [PMID: 31162640 DOI: 10.1002/ajb2.1296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
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53
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Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. SCIENCE ADVANCES 2019; 5:eaau0757. [PMID: 31149628 PMCID: PMC6541468 DOI: 10.1126/sciadv.aau0757] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 04/23/2019] [Indexed: 05/08/2023]
Abstract
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.
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Affiliation(s)
- Jacqueline A. Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Corresponding author.
| | - Jannikke Räikkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Leah M. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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54
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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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55
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Abstract
Factors that limit the geographic distribution of species are broadly important in ecology and evolutionary biology, and understanding distribution limits is imperative for predicting how species will respond to environmental change. Good data indicate that factors such as dispersal limitation, small effective population size, and isolation are sometimes important. But empirical research highlights no single factor that explains the ubiquity of distribution limits. In this article, we outline a guide to tackling distribution limits that integrates established causes, such as dispersal limitation and spatial environmental heterogeneity, with understudied causes, such as mutational load and genetic or developmental integration of traits limiting niche expansion. We highlight how modeling and quantitative genetic and genomic analyses can provide insight into sources of distribution limits. Our practical guide provides a framework for considering the many factors likely to determine species distributions and how the different approaches can be integrated to predict distribution limits using eco-evolutionary modeling. The framework should also help predict distribution limits of invasive species and of species under climate change.
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56
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Wan JSH, Rutherford S, Bonser SP. The invasion triangle in the range dynamics of invasive species following successful establishment. Evol Ecol 2019. [DOI: 10.1007/s10682-019-09986-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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57
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Javal M, Lombaert E, Tsykun T, Courtin C, Kerdelhué C, Prospero S, Roques A, Roux G. Deciphering the worldwide invasion of the Asian long‐horned beetle: A recurrent invasion process from the native area together with a bridgehead effect. Mol Ecol 2019; 28:951-967. [DOI: 10.1111/mec.15030] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Marion Javal
- INRA UR633 Zoologie Forestière Orléans Cedex 2 France
| | - Eric Lombaert
- INRA, Université Côte d'Azur, CNRS ISA Sophia Antipolis France
| | - Tetyana Tsykun
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | | | - Carole Kerdelhué
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro Université Montpellier Montpellier France
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | - Alain Roques
- INRA UR633 Zoologie Forestière Orléans Cedex 2 France
| | - Géraldine Roux
- INRA UR633 Zoologie Forestière Orléans Cedex 2 France
- COST Université d'Orléans Orléans France
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58
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van Boheemen LA, Atwater DZ, Hodgins KA. Rapid and repeated local adaptation to climate in an invasive plant. THE NEW PHYTOLOGIST 2019; 222:614-627. [PMID: 30367474 DOI: 10.1111/nph.15564] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
Biological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plant Ambrosia artemisiifolia. We explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for nonadaptive population differentiation using 11 598 single nucleotide polymorphisms. We revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines. Our data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.
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Affiliation(s)
- Lotte A van Boheemen
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
| | - Daniel Z Atwater
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
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59
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Marin P, Genitoni J, Barloy D, Maury S, Gibert P, Ghalambor CK, Vieira C. Biological invasion: The influence of the hidden side of the (epi)genome. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13317] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pierre Marin
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Julien Genitoni
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Dominique Barloy
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRA Rennes France
| | - Stéphane Maury
- LBLGC EA 1207 INRA, Université d'Orléans, USC 1328 Orléans France
| | - Patricia Gibert
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
| | - Cameron K. Ghalambor
- Department of Biology and Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1 Université de Lyon Villeurbanne France
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60
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Willi Y, Fracassetti M, Zoller S, Van Buskirk J. Accumulation of Mutational Load at the Edges of a Species Range. Mol Biol Evol 2019; 35:781-791. [PMID: 29346601 DOI: 10.1093/molbev/msy003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Why species have geographically restricted distributions is an unresolved question in ecology and evolutionary biology. Here, we test a new explanation that mutation accumulation due to small population size or a history of range expansion can contribute to restricting distributions by reducing population growth rate at the edge. We examined genomic diversity and mutational load across the entire geographic range of the North American plant Arabidopsis lyrata, including old, isolated populations predominantly at the southern edge and regions of postglacial range expansion at the northern and southern edges. Genomic diversity in intergenic regions declined toward distribution edges and signatures of mutational load in exon regions increased. Genomic signatures of mutational load were highly linked to phenotypically expressed load, measured as reduced performance of individual plants and lower estimated rate of population growth. The geographic pattern of load and the connection between load and population growth demonstrate that mutation accumulation reduces fitness at the edge and helps restrict species' distributions.
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Affiliation(s)
- Yvonne Willi
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Marco Fracassetti
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.,Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre, ETH Zürich, Zürich, Switzerland
| | - Josh Van Buskirk
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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61
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Demastes JW, Hafner DJ, Hafner MS, Light JE, Spradling TA. Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei. Mol Ecol 2019; 28:703-720. [PMID: 30589151 DOI: 10.1111/mec.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post-bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225-generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid-based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.
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Affiliation(s)
- James W Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
| | - David J Hafner
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico
| | - Mark S Hafner
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas
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62
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Ferronato P, Woch AL, Soares PL, Bernardi D, Botton M, Andreazza F, Oliveira EE, Corrêa AS. A Phylogeographic Approach to the Drosophila suzukii (Diptera: Drosophilidae) Invasion in Brazil. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:425-433. [PMID: 30383249 DOI: 10.1093/jee/toy321] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 06/08/2023]
Abstract
Biological invasions have reached large parts of the globe, due to human actions across the planet. Drosophila suzukii (Matsumura, 1931) is a globally invasive species, always associated with enormous and costly damage to agricultural crops. Native to Southeast Asia, D. suzukii recently (i.e., 2013) invaded and is dispersing through South America. Here, we used a phylogeographic approach based on the cytochrome c oxidase subunit I gene fragment to explore the invasion dynamics of D. suzukii populations in Brazil. We identified five haplotypes and moderate genetic diversity in Brazilian populations, which are undergoing demographic and spatial expansion. The analyses of molecular variance indicated a high genetic structure among the populations, which is partially explained by their morphoclimatic origin and invasion history. Drosophila suzukii expanded from southern to southeastern Brazil, aided by human-mediated transport of fruits from region to region. The sharing of haplotypes among Brazilian and other invaded regions of the world suggests a single invasion event of D. suzukii in Brazil, originating from previously invaded areas (e.g., North America and Europe). The rapid geographic dispersal and wide variety of fruits attacked by of D. suzukii require immediate implementation of control strategies (legal and phytosanitary) to manage this pest in Brazil.
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Affiliation(s)
- Petra Ferronato
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, SP, Brazil
| | - Ana Luiza Woch
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, SP, Brazil
| | - Patricia Lima Soares
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, SP, Brazil
| | - Daniel Bernardi
- Department of Plant Health, Federal University of Pelotas, Capão do Leão, RS, Brazil
| | - Marcos Botton
- Embrapa Grape and Wine, Bento Gonçalves, Rio Grande do Sul, RS, Brazil
| | - Felipe Andreazza
- Department of Entomology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Eugênio E Oliveira
- Department of Entomology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Alberto Soares Corrêa
- Department of Entomology and Acarology, University of Sao Paulo, Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, SP, Brazil
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63
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Hu XS, Zhang XX, Zhou W, Hu Y, Wang X, Chen XY. Mating system shifts a species' range. Evolution 2018; 73:158-174. [PMID: 30592527 DOI: 10.1111/evo.13663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/05/2018] [Indexed: 01/20/2023]
Abstract
Understanding the ecological and evolutionary mechanisms that shape a species' range is an important goal in evolutionary biology. Evidence indicates that mating system is an effective predictor of the global range of native species or naturalized alien plants, but the mechanisms underlying this predictability are not elaborated. Here, we develop a theoretical model to account for the ranges of plants under different mating systems based on migration-selection processes (an idea proposed by Haldane). The model includes alternation of gametophyte and sporophyte generations in one life cycle and the dispersal of haploid pollen and diploid seeds as vectors for gene flow. We show that the interaction between selfing rates and gametophytic selection determines the role of mating system in shaping a species' range. Selfing restricts the species' range under gametophytic selection in nonrandom mating systems, but expands the species' range under the absence of gametophytic selection in any mating system. Gametophytic selection slightly restricts the species' range in random mating. Both logarithmic and logistic models of population demography yield similar conclusions in the case of fixed or evolving genetic variance. The theory also helps to explain a broader relationship between mating system and range size following biological invasion or plant naturalization.
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Affiliation(s)
- Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Xin-Xin Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Wei Zhou
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Ying Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Xi Wang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
| | - Xiao-Yang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong, 510642, China.,College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong, 510642, China
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64
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Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas. Curr Biol 2018; 29:165-170.e6. [PMID: 30595519 DOI: 10.1016/j.cub.2018.11.055] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022]
Abstract
Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.
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65
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Chen Y, Shenkar N, Ni P, Lin Y, Li S, Zhan A. Rapid microevolution during recent range expansion to harsh environments. BMC Evol Biol 2018; 18:187. [PMID: 30526493 PMCID: PMC6286502 DOI: 10.1186/s12862-018-1311-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/27/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Adaptive evolution is one of the crucial mechanisms for organisms to survive and thrive in new environments. Recent studies suggest that adaptive evolution could rapidly occur in species to respond to novel environments or environmental challenges during range expansion. However, for environmental adaptation, many studies successfully detected phenotypic features associated with local environments, but did not provide ample genetic evidence on microevolutionary dynamics. It is therefore crucial to thoroughly investigate the genetic basis of rapid microevolution in response to environmental changes, in particular on what genes and associated variation are responsible for environmental challenges. Here, we genotyped genome-wide gene-associated microsatellites to detect genetic signatures of rapid microevolution of a marine tunicate invader, Ciona robusta, during recent range expansion to the harsh environment in the Red Sea. RESULTS The Red Sea population was significantly differentiated from the other global populations. The genome-wide scan, as well as multiple analytical methods, successfully identified a set of adaptive genes. Interestingly, the allele frequency largely varied at several adaptive loci in the Red Sea population, and we found significant correlations between allele frequency and local environmental factors at these adaptive loci. Furthermore, a set of genes were annotated to get involved in local temperature and salinity adaptation, and the identified adaptive genes may largely contribute to the invasion success to harsh environments. CONCLUSIONS All the evidence obtained in this study clearly showed that environment-driven selection had left detectable signatures in the genome of Ciona robusta within a few generations. Such a rapid microevolutionary process is largely responsible for the harsh environmental adaptation and therefore contributes to invasion success in different aquatic ecosystems with largely varied environmental factors.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China.
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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66
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Gidoin C, Peischl S. Range Expansion Theories Could Shed Light on the Spatial Structure of Intra-tumour Heterogeneity. Bull Math Biol 2018; 81:4761-4777. [DOI: 10.1007/s11538-018-00540-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/28/2018] [Indexed: 12/28/2022]
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67
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Ragsdale AP, Moreau C, Gravel S. Genomic inference using diffusion models and the allele frequency spectrum. Curr Opin Genet Dev 2018; 53:140-147. [PMID: 30366252 DOI: 10.1016/j.gde.2018.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/14/2018] [Accepted: 10/07/2018] [Indexed: 01/25/2023]
Abstract
Evolutionary, biological, and demographic processes together shape observed variation in populations. Understanding how these processes influence variation allows us to infer past demography and the nature of selection in populations. Forward in time models such as the diffusion approximation provide a powerful tool for performing inference based on the distribution of allele frequencies. Here, we discuss recent computational developments and their application to reconstructing human demographic history. Using whole-genome sequence data for 797 French Canadian individuals, we assess the neutrality of synonymous variants and show that selection can bias inferred demography, mutation rates, and distributions of fitness effects. We argue that the simple evolutionary models investigated by Kimura and Ohta still provide important insight into modern genetic research.
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Affiliation(s)
- Aaron P Ragsdale
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Claudia Moreau
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
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68
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Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet 2018; 14:e1007741. [PMID: 30346959 PMCID: PMC6233928 DOI: 10.1371/journal.pgen.1007741] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/13/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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Affiliation(s)
- Bernard Y. Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Christian D. Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- * E-mail:
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69
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Gilbert KJ, Peischl S, Excoffier L. Mutation load dynamics during environmentally-driven range shifts. PLoS Genet 2018; 14:e1007450. [PMID: 30265675 PMCID: PMC6179293 DOI: 10.1371/journal.pgen.1007450] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/10/2018] [Accepted: 08/29/2018] [Indexed: 11/29/2022] Open
Abstract
The fitness of spatially expanding species has been shown to decrease over time and space, but specialist species tracking their changing environment and shifting their range accordingly have been little studied. We use individual-based simulations and analytical modeling to compare the impact of range expansions and range shifts on genetic diversity and fitness loss, as well as the ability to recover fitness after either a shift or expansion. We find that the speed of a shift has a strong impact on fitness evolution. Fastest shifts show the strongest fitness loss per generation, but intermediate shift speeds lead to the strongest fitness loss per geographic distance. Range shifting species lose fitness more slowly through time than expanding species, however, their fitness measured at equal geographic distances from the source of expansion can be considerably lower. These counter-intuitive results arise from the combination of time over which selection acts and mutations enter the system. Range shifts also exhibit reduced fitness recovery after a geographic shift and may result in extinction, whereas range expansions can persist from the core of the species range. The complexity of range expansions and range shifts highlights the potential for severe consequences of environmental change on species survival.
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Affiliation(s)
- Kimberly J. Gilbert
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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70
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Wellband KW, Pettitt-Wade H, Fisk AT, Heath DD. Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species. Mol Ecol 2018; 27:1572-1585. [PMID: 29573310 DOI: 10.1111/mec.14557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 02/25/2018] [Accepted: 03/07/2018] [Indexed: 12/30/2022]
Abstract
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species, and thus, their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.
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Affiliation(s)
- Kyle W Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Harri Pettitt-Wade
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Aaron T Fisk
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.,Department of Biological Sciences, University of Windsor, Windsor, ON, Canada
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71
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Shakeel M, Irfan M, Khan IA. Estimating the mutational load for cardiovascular diseases in Pakistani population. PLoS One 2018; 13:e0192446. [PMID: 29420653 PMCID: PMC5805289 DOI: 10.1371/journal.pone.0192446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/23/2018] [Indexed: 02/05/2023] Open
Abstract
The deleterious genetic variants contributing to certain diseases may differ in terms of number and allele frequency from population to population depending on their evolutionary background. Here, we prioritize the deleterious variants from Pakistani population in manually curated gene list already reported to be associated with common, Mendelian, and congenital cardiovascular diseases (CVDs) using the genome/exome sequencing data of Pakistani individuals publically available in 1000 Genomes Project (PJL), and Exome Aggregation Consortium (ExAC) South Asia. By applying a set of tools such as Combined Annotation Dependent Depletion (CADD), ANNOVAR, and Variant Effect Predictor (VEP), we highlighted 561 potentially detrimental variants from PJL data, and 7374 variants from ExAC South Asian data. Likewise, filtration from ClinVar for CVDs revealed 03 pathogenic and 02 likely pathogenic variants from PJL and 112 pathogenic and 42 likely pathogenic variants from ExAC South Asians. The comparison of derived allele frequencies (DAF) revealed many of these prioritized variants having two fold and higher DAF in Pakistani individuals than in other populations. The highest number of deleterious variants contributing to common CVDs in descending order includes hypertension, atherosclerosis, heart failure, aneurysm, and coronary heart disease, and for Mendelian and congenital CVDs cardiomyopathies, cardiac arrhythmias, and atrioventricular septal defects.
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Affiliation(s)
- Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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72
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73
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Sherpa S, Rioux D, Pougnet-Lagarde C, Després L. Genetic diversity and distribution differ between long-established and recently introduced populations in the invasive mosquito Aedes albopictus. INFECTION GENETICS AND EVOLUTION 2017; 58:145-156. [PMID: 29275191 DOI: 10.1016/j.meegid.2017.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/04/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022]
Abstract
The Asian tiger mosquito Aedes albopictus, native to South-eastern Asia, is currently the most invasive mosquito in the world. The spatio-temporal dynamics of its expansion through the genetic characterization of invasive populations has been challenged so far by the limited number of genetic markers variable enough to infer the genetic structure in recently invaded areas. Here we applied the double-digest Restriction-site Associated DNA sequencing method (ddRADseq) to mosquitoes collected in two invaded areas, Reunion Island (12 localities) and Europe (18 localities). Analyses of genetic diversity, Bayesian clustering, Maximum Likelihood inference and isolation-by-distance tests based on 1561 genome-wide distributed Single Nucleotide Polymorphisms (SNPs) revealed that Reunion Island and Europe form two distinct genetic clusters, supporting no contemporary gene flow and suggesting two different and independent invasion histories. Long-established populations (Reunion Island) were more genetically diverse than recently introduced European populations. The largest part of genetic variance was found at the intra-individual level (>85%) and most FIS values were positive, suggesting inbreeding at the local scale. The two invaded areas showed contrasting patterns of genetic structure. Significant isolation-by-distance was found among Reunion Island populations, suggesting that these populations are at the drift-migration equilibrium. In contrast, long-distance human-assisted transport is probably the main dispersal mechanism in Europe.
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Affiliation(s)
- Stéphanie Sherpa
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France
| | - Delphine Rioux
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France
| | | | - Laurence Després
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Grenoble Alpes, Grenoble, France.
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74
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Relaxed Selection During a Recent Human Expansion. Genetics 2017; 208:763-777. [PMID: 29187508 DOI: 10.1534/genetics.117.300551] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/22/2017] [Indexed: 01/15/2023] Open
Abstract
Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that: (i) both new and low-frequency variants are significantly more deleterious in front than in core individuals, (ii) equally deleterious mutations are at higher frequencies in front individuals, and (iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past six to nine generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection mainly due to higher rates of genetic drift on the wave front. Demographic inference and modeling of the evolution of rare variants suggest lower effective size on the front, and lead to an estimation of selection coefficients that increase with conservation scores. Even though range expansions have had a relatively limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions of Quebec.
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75
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Chapuis E, Lamy T, Pointier JP, Juillet N, Ségard A, Jarne P, David P. Bioinvasion Triggers Rapid Evolution of Life Histories in Freshwater Snails. Am Nat 2017; 190:694-706. [PMID: 29053358 DOI: 10.1086/693854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biological invasions offer interesting situations for observing how novel interactions between closely related, formerly allopatric species may trigger phenotypic evolution in situ. Assuming that successful invaders are usually filtered to be competitively dominant, invasive and native species may follow different trajectories. Natives may evolve traits that minimize the negative impact of competition, while trait shifts in invasives should mostly reflect expansion dynamics, through selection for colonization ability and transiently enhanced mutation load at the colonization front. These ideas were tested through a large-scale common-garden experiment measuring life-history traits in two closely related snail species, one invasive and one native, co-occurring in a network of freshwater ponds in Guadeloupe. We looked for evidence of recent evolution by comparing uninvaded or recently invaded sites with long-invaded ones. The native species adopted a life history favoring rapid population growth (i.e., increased fecundity, earlier reproduction, and increased juvenile survival) that may increase its prospects of coexistence with the more competitive invader. We discuss why these effects are more likely to result from genetic change than from maternal effects. The invader exhibited slightly decreased overall performances in recently colonized sites, consistent with a moderate expansion load resulting from local founder effects. Our study highlights a rare example of rapid life-history evolution following invasion.
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76
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Accumulation of Deleterious Mutations During Bacterial Range Expansions. Genetics 2017; 207:669-684. [PMID: 28821588 PMCID: PMC5629331 DOI: 10.1534/genetics.117.300144] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/28/2017] [Indexed: 12/15/2022] Open
Abstract
Recent theory predicts that the fitness of pioneer populations can decline when species expand their range, due to high rates of genetic drift on wave fronts making selection less efficient at purging deleterious variants. To test these predictions, we studied the fate of mutator bacteria expanding their range for 1650 generations on agar plates. In agreement with theory, we find that growth abilities of strains with a high mutation rate (HMR lines) decreased significantly over time, unlike strains with a lower mutation rate (LMR lines) that present three to four times fewer mutations. Estimation of the distribution of fitness effect under a spatially explicit model reveals a mean negative effect for new mutations (-0.38%), but it suggests that both advantageous and deleterious mutations have accumulated during the experiment. Furthermore, the fitness of HMR lines measured in different environments has decreased relative to the ancestor strain, whereas that of LMR lines remained unchanged. Contrastingly, strains with a HMR evolving in a well-mixed environment accumulated less mutations than agar-evolved strains and showed an increased fitness relative to the ancestor. Our results suggest that spatially expanding species are affected by deleterious mutations, leading to a drastic impairment of their evolutionary potential.
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77
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Range Expansion Compromises Adaptive Evolution in an Outcrossing Plant. Curr Biol 2017; 27:2544-2551.e4. [DOI: 10.1016/j.cub.2017.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/22/2017] [Accepted: 07/04/2017] [Indexed: 01/04/2023]
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78
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Fraimout A, Debat V, Fellous S, Hufbauer RA, Foucaud J, Pudlo P, Marin JM, Price DK, Cattel J, Chen X, Deprá M, François Duyck P, Guedot C, Kenis M, Kimura MT, Loeb G, Loiseau A, Martinez-Sañudo I, Pascual M, Polihronakis Richmond M, Shearer P, Singh N, Tamura K, Xuéreb A, Zhang J, Estoup A. Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest. Mol Biol Evol 2017; 34:980-996. [PMID: 28122970 PMCID: PMC5400373 DOI: 10.1093/molbev/msx050] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios.
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Affiliation(s)
- Antoine Fraimout
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - Vincent Debat
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - Simon Fellous
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France
| | - Ruth A Hufbauer
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France.,Colorado State University, Fort Collins, CO
| | - Julien Foucaud
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France
| | - Pierre Pudlo
- Centre de Mathématiques et Informatique, Aix-Marseille Université, Marseille, France
| | - Jean-Michel Marin
- Institut Montpelliérain Alexander Grothendieck, Université de Montpellier, Montpellier, France
| | - Donald K Price
- Tropical Conservation Biology & Environmental Science, University of Hawaii at Hilo, HI
| | - Julien Cattel
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Xiao Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, People's Republic of China
| | - Marindia Deprá
- Programa de Pós Graduação em Genética e Biologia Molecular, Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | | | - Masahito T Kimura
- Graduate School of Environmental Earth Science, Hokkaido Daigaku University, Sapporo, Hokkaido Prefecture, Japan
| | - Gregory Loeb
- Department of Entomology, Cornell University, Ithaca, NY
| | - Anne Loiseau
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France
| | - Isabel Martinez-Sañudo
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Universita degli Studi di Padova, Padova, Italy
| | - Marta Pascual
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
| | | | - Peter Shearer
- Mid-Columbia Agricultural Research and Extension Center, Oregon State University, Hood River, OR
| | - Nadia Singh
- Department of Genetics, North Carolina State University, Raleigh, NC
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Anne Xuéreb
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France
| | - Jinping Zhang
- MoA-CABI Joint Laboratory for Bio-safety, Chinese Academy of Agricultural Sciences, BeiXiaGuan, Haidian Qu, China
| | - Arnaud Estoup
- INRA, Centre de Biologie et de Gestion des Populations (UMR INRA IRD Cirad Montpellier SupAgro), Montferrier-Sur-Lez, France
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79
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Goubert C, Henri H, Minard G, Valiente Moro C, Mavingui P, Vieira C, Boulesteix M. High-throughput sequencing of transposable element insertions suggests adaptive evolution of the invasive Asian tiger mosquito towards temperate environments. Mol Ecol 2017; 26:3968-3981. [DOI: 10.1111/mec.14184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Clement Goubert
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
- Department of Human Genetics; University of Utah; Salt Lake City UT USA
| | - Helene Henri
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
| | - Guillaume Minard
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
- Department of Biosciences; Metapopulation Research Center; University of Helsinki; Helsinki Finland
| | - Claire Valiente Moro
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
| | - Patrick Mavingui
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Ecologie Microbienne; UMR CNRS 5557; UMR INRA 1418; Villeurbanne France
- UMR PIMIT; INSERM 1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI; Universite de La Reunion; Sainte-Clotilde Reunion
| | - Cristina Vieira
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
| | - Matthieu Boulesteix
- Université de Lyon; Lyon France
- Université Lyon 1; Villeurbanne France
- Laboratoire de Biometrie et Biologie Evolutive; UMR CNRS 5558; Villeurbanne France
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80
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Vandepitte K, Helsen K, Van Acker K, Mergeay J, Honnay O. Retention of gene diversity during the spread of a non-native plant species. Mol Ecol 2017; 26:3141-3150. [PMID: 28345193 DOI: 10.1111/mec.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/23/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022]
Abstract
Spatial expansion, which is a crucial stage in the process to successful biological invasion, is anticipated to profoundly affect the magnitude and spatial distribution of genetic diversity in novel colonized areas. Here, we show that, contrasting common expectations, Pyrenean rocket (Sisymbrium austriacum), retained SNP diversity as this introduced plant species descended in the Meuse River Basin. Allele frequencies did not mirror between-population distances along the predominant expansion axis. Reconstruction of invasion history based on the genotypes of historical herbarium specimens indicated no influence of additional introductions or multiple points of entry on this nongradual pattern. Assignment analysis suggested the admixture of distant upstream sources in recently founded downstream populations. River dynamics seem to have facilitated occasional long-distance dispersal which brought diversity to the expansion front and so maintained evolutionary potential. Our findings highlight the merit of a historical framework in interpreting extant patterns of genetic diversity in introduced species and underscore the need to integrate long-distance dispersal events in theoretical work on the genetic consequences of range expansion.
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Affiliation(s)
- Katrien Vandepitte
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Heverlee, Belgium
| | - Kenny Helsen
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Heverlee, Belgium.,Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kasper Van Acker
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Heverlee, Belgium
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Heverlee, Belgium
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81
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Gilbert KJ, Sharp NP, Angert AL, Conte GL, Draghi JA, Guillaume F, Hargreaves AL, Matthey-Doret R, Whitlock MC. Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load. Am Nat 2017; 189:368-380. [PMID: 28350500 DOI: 10.1086/690673] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The biotic and abiotic factors that facilitate or hinder species range expansions are many and complex. We examine the impact of two genetic processes and their interaction on fitness at expanding range edges: local maladaptation resulting from the presence of an environmental gradient and expansion load resulting from increased genetic drift at the range edge. Results from spatially explicit simulations indicate that the presence of an environmental gradient during range expansion reduces expansion load; conversely, increasing expansion load allows only locally adapted populations to persist at the range edge. Increased maladaptation reduces the speed of range expansion, resulting in less genetic drift at the expanding front and more immigration from the range center, therefore reducing expansion load at the range edge. These results may have ramifications for species being forced to shift their ranges because of climate change or other anthropogenic changes. If rapidly changing climate leads to faster expansion as populations track their shifting climatic optima, populations may suffer increased expansion load beyond previous expectations.
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82
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Fijarczyk A, Dudek K, Babik W. Selective Landscapes in newt Immune Genes Inferred from Patterns of Nucleotide Variation. Genome Biol Evol 2016; 8:3417-3432. [PMID: 27702815 PMCID: PMC5203778 DOI: 10.1093/gbe/evw236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Host–pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases. Here, we present an analysis of polymorphism and divergence of 634 immune genes in two lineages of Lissotriton newts: L. montandoni and L. vulgaris graecus. Variation in newt immune genes has been shaped predominantly by widespread purifying selection and strong evolutionary constraint, implying long-term importance of these genes for functioning of the immune system. The two evolutionary lineages differ in the overall strength of purifying selection which can partially be explained by demographic history but may also signal differences in long-term pathogen pressure. The prevalent constraint notwithstanding, 23 putative targets of positive selection and 11 putative targets of balancing selection were identified. The latter were detected by composite tests involving the demographic model and further validated in independent population samples. Putative targets of balancing selection encode proteins which may interact closely with pathogens but include also regulators of immune response. The identified candidates will be useful for testing whether genes affected by balancing selection are more prone to interspecific introgression than other genes in the genome.
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Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Wieslaw Babik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
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83
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Haenel GJ. Introgression of mtDNA inUrosauruslizards: historical and ecological processes. Mol Ecol 2016; 26:606-623. [DOI: 10.1111/mec.13930] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023]
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84
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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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85
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Viard F, David P, Darling JA. Marine invasions enter the genomic era: three lessons from the past, and the way forward. Curr Zool 2016; 62:629-642. [PMID: 29491950 PMCID: PMC5804250 DOI: 10.1093/cz/zow053] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/15/2016] [Indexed: 01/22/2023] Open
Abstract
The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.
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Affiliation(s)
- Frédérique Viard
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Lab. Adaptation Et Diversité En Milieu Marin, Team Div&Co, Station Biologique De Roscoff, Roscoff 29682, France
| | - Patrice David
- CEFE UMR 5175, CNRS-Université De Montpellier-UM III-EPHE, 1919 Route De Mende, Montpellier Cedex 34293, France
| | - John A. Darling
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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86
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Estoup A, Ravigné V, Hufbauer R, Vitalis R, Gautier M, Facon B. Is There a Genetic Paradox of Biological Invasion? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032116] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arnaud Estoup
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Virginie Ravigné
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
| | - Ruth Hufbauer
- Department of Bioagricultural Science and Pest Management, Colorado State University, Fort Collins, Colorado 80523
| | - Renaud Vitalis
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Mathieu Gautier
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
| | - Benoit Facon
- Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, 34988 Montferrier sur Lez, France;
- Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, 97410 Saint-Pierre, La Réunion, France
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87
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Le Gros A, Clergeau P, Zuccon D, Cornette R, Mathys B, Samadi S. Invasion history and demographic processes associated with rapid morphological changes in the Red-whiskered bulbul established on tropical islands. Mol Ecol 2016; 25:5359-5376. [DOI: 10.1111/mec.13853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 07/22/2016] [Accepted: 09/04/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Ariane Le Gros
- Sorbonne Paris Cité; Université Paris Diderot; 5 Rue Thomas Mann 75013 Paris France
- MNHN; CNRS; UPMC; CP51; Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204); Sorbonne Universités; 55 rue Buffon 75005 Paris France
- MNHN; CNRS; UPMC; CP26; Institut de Systématique; Evolution; Biodiversité (ISYEB UMR 7205); Sorbonne Universités; 57 rue Cuvier 75005 Paris France
| | - Philippe Clergeau
- MNHN; CNRS; UPMC; CP51; Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204); Sorbonne Universités; 55 rue Buffon 75005 Paris France
| | - Dario Zuccon
- MNHN; CNRS; UPMC; CP26; Institut de Systématique; Evolution; Biodiversité (ISYEB UMR 7205); Sorbonne Universités; 57 rue Cuvier 75005 Paris France
| | - Raphaël Cornette
- MNHN; CNRS; UPMC; CP26; Institut de Systématique; Evolution; Biodiversité (ISYEB UMR 7205); Sorbonne Universités; 57 rue Cuvier 75005 Paris France
| | - Blake Mathys
- Division of Mathematics; Computer and Natural Sciences; Ohio Dominican University; Columbus OH 43219 USA
| | - Sarah Samadi
- MNHN; CNRS; UPMC; CP26; Institut de Systématique; Evolution; Biodiversité (ISYEB UMR 7205); Sorbonne Universités; 57 rue Cuvier 75005 Paris France
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88
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Gralka M, Stiewe F, Farrell F, Möbius W, Waclaw B, Hallatschek O. Allele surfing promotes microbial adaptation from standing variation. Ecol Lett 2016; 19:889-98. [PMID: 27307400 DOI: 10.1111/ele.12625] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/08/2016] [Accepted: 04/18/2016] [Indexed: 01/19/2023]
Abstract
The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges.
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Affiliation(s)
- Matti Gralka
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Fabian Stiewe
- Biophysics and Evolutionary Dynamics Group, Max Planck Institute for Dynamics and Self-Organization, 37077, Göttingen, Germany
| | - Fred Farrell
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, UK
| | - Wolfram Möbius
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Bartlomiej Waclaw
- SUPA, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ, UK.,Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh, UK
| | - Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA, 94720, USA
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89
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Robinson JA, Ortega-Del Vecchyo D, Fan Z, Kim BY, vonHoldt BM, Marsden CD, Lohmueller KE, Wayne RK. Genomic Flatlining in the Endangered Island Fox. Curr Biol 2016; 26:1183-9. [PMID: 27112291 DOI: 10.1016/j.cub.2016.02.062] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/11/2022]
Abstract
Genetic studies of rare and endangered species often focus on defining and preserving genetically distinct populations, especially those having unique adaptations [1, 2]. Much less attention is directed at understanding the landscape of deleterious variation, an insidious consequence of geographic isolation and the inefficiency of natural selection to eliminate harmful variants in small populations [3-5]. With population sizes of many vertebrates decreasing and isolation increasing through habitat fragmentation and loss, understanding the extent and nature of deleterious variation in small populations is essential for predicting and enhancing population persistence. The Channel Island fox (Urocyon littoralis) is a dwarfed species that inhabits six of California's Channel Islands and is derived from the mainland gray fox (U. cinereoargenteus). These isolated island populations have persisted for thousands of years at extremely small population sizes [6, 7] and, consequently, are a model for testing ideas about the accumulation of deleterious variation in small populations under natural conditions. Analysis of complete genome sequence data from island foxes shows a dramatic decrease in genome-wide variation and a sharp increase in the homozygosity of deleterious variants. The San Nicolas Island population has a near absence of variation, demonstrating a unique genetic flatlining that is punctuated by heterozygosity hotspots, enriched for olfactory receptor genes and other genes with high levels of ancestral variation. These findings question the generality of the small-population paradigm that maintains substantial genetic variation is necessary for short- and long-term persistence.
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Affiliation(s)
- Jacqueline A Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diego Ortega-Del Vecchyo
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Bernard Y Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Clare D Marsden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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90
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Adrian-Kalchhauser I, Hirsch PE, Behrmann-Godel J, N'Guyen A, Watzlawczyk S, Gertzen S, Borcherding J, Burkhardt-Holm P. The invasive bighead goby Ponticola kessleri displays large-scale genetic similarities and small-scale genetic differentiation in relation to shipping patterns. Mol Ecol 2016; 25:1925-43. [PMID: 26928748 DOI: 10.1111/mec.13595] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
Abstract
Colonization events, range expansions and species invasions leave genetic signatures in the genomes of invasive organisms and produce intricate special patterns. Predictions have been made as to how those patterns arise, but only very rarely, genetic processes can be monitored in real time during range expansions. In an attempt to change that, we track a very recently established invasive population of a fish species, the bighead goby Ponticola kessleri, with high temporal and spatial resolution through 2 years to identify patterns over time. We then compare Swiss and German samples of bighead goby along the river Rhine using microsatellites, mitochondrial D-loop sequences and geometric morphometrics to investigate geographic patterns. We detect weak temporal and strong geographic patterns in the data, which are inconsistent with isolation by distance and indicate long range transport. In search of an explanation for our observations, we analyse the vector properties and travel patterns of commercial vessels on the river Rhine. We present evidence that freshwater cargo ships and tankers are plausible vectors for larvae of invasive goby species. We also present indications that cargo ships and tankers act as differential vectors for this species. In summary, we present genetic data at unique temporal resolution from a vertebrate invasion front and substantiate the paramount role of commercial shipping in freshwater fish translocations.
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Affiliation(s)
- I Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - P E Hirsch
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.,Research Centre for Sustainable Energy and Water Supply, University of Basel, Peter Merian Weg 6, CH-4002, Basel, Switzerland
| | - J Behrmann-Godel
- Limnological Institute, University of Konstanz, Mainaustrasse 252, D-78457, Konstanz, Germany
| | - A N'Guyen
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - S Watzlawczyk
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - S Gertzen
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - J Borcherding
- Zoological Institute of the University of Cologne, Department of General Ecology & Limnology, Ecological Field Station Grietherbusch, D-50923, Cologne, Germany
| | - P Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, Canada
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91
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Brandvain Y, Wright SI. The Limits of Natural Selection in a Nonequilibrium World. Trends Genet 2016; 32:201-210. [PMID: 26874998 DOI: 10.1016/j.tig.2016.01.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022]
Abstract
Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance.
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Affiliation(s)
- Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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92
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Patterns of deleterious variation between human populations reveal an unbalanced load. Proc Natl Acad Sci U S A 2016; 113:809-11. [PMID: 26787891 DOI: 10.1073/pnas.1524016113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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93
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Li SL, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. ANNALS OF BOTANY 2016; 117:187-194. [PMID: 26420202 PMCID: PMC4701146 DOI: 10.1093/aob/mcv145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. METHODS Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. KEY RESULTS It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. CONCLUSIONS The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity.
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Affiliation(s)
- Shou-Li Li
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA,
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia and
| | - Satu Ramula
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Aronia Coastal Zone Research Team, Åbo Akademi University and Novia University of Applied Sciences, Raseborgsvägen 9, 10600 Ekenäs, Finland
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94
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Rieseberg L, Geraldes A. Editorial 2016. Mol Ecol 2016; 25:433-49. [DOI: 10.1111/mec.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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95
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Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A 2015; 113:E440-9. [PMID: 26712023 DOI: 10.1073/pnas.1510805112] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Out-of-Africa (OOA) dispersal ∼ 50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.
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96
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Balick DJ, Do R, Cassa CA, Reich D, Sunyaev SR. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck. PLoS Genet 2015; 11:e1005436. [PMID: 26317225 PMCID: PMC4552954 DOI: 10.1371/journal.pgen.1005436] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/09/2015] [Indexed: 11/30/2022] Open
Abstract
Population bottlenecks followed by re-expansions have been common throughout history of many populations. The response of alleles under selection to such demographic perturbations has been a subject of great interest in population genetics. On the basis of theoretical analysis and computer simulations, we suggest that this response qualitatively depends on dominance. The number of dominant or additive deleterious alleles per haploid genome is expected to be slightly increased following the bottleneck and re-expansion. In contrast, the number of completely or partially recessive alleles should be sharply reduced. Changes of population size expose differences between recessive and additive selection, potentially providing insight into the prevalence of dominance in natural populations. Specifically, we use a simple statistic, BR≡∑xipop1/∑xjpop2, where xi represents the derived allele frequency, to compare the number of mutations in different populations, and detail its functional dependence on the strength of selection and the intensity of the population bottleneck. We also provide empirical evidence showing that gene sets associated with autosomal recessive disease in humans may have a BR indicative of recessive selection. Together, these theoretical predictions and empirical observations show that complex demographic history may facilitate rather than impede inference of parameters of natural selection. Dominance has played a central role in classical genetics since its inception. However, the effect of dominance introduces substantial technical complications into theoretical models describing dynamics of alleles in populations. As a result, dominance is often ignored in population genetic models. Statistical tests for selection built on these models do not discriminate between recessive and additive alleles. We show that historical changes in population size can provide a way to differentiate between recessive and additive selection. Our analysis compares two sub-populations with different demographic histories. History of our own species provides plenty of examples of sub-populations that went through population bottlenecks followed by re-expansions. We show that demographic differences, which generally complicate the analysis, can instead aid in the inference of features of natural selection.
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Affiliation(s)
- Daniel J. Balick
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Ron Do
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher A. Cassa
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - David Reich
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail:
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97
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Dlugosch KM, Anderson SR, Braasch J, Cang FA, Gillette HD. The devil is in the details: genetic variation in introduced populations and its contributions to invasion. Mol Ecol 2015; 24:2095-111. [PMID: 25846825 DOI: 10.1111/mec.13183] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/14/2022]
Abstract
The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself.
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Affiliation(s)
- Katrina M Dlugosch
- Department of Ecology & Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
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98
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Colautti RI, Lau JA. Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation. Mol Ecol 2015; 24:1999-2017. [PMID: 25891044 DOI: 10.1111/mec.13162] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 01/15/2023]
Abstract
Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change.
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Affiliation(s)
- Robert I Colautti
- Plant Evolutionary Ecology Group, Department for Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, D-72076, Tübingen, Germany
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99
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Bock DG, Caseys C, Cousens RD, Hahn MA, Heredia SM, Hübner S, Turner KG, Whitney KD, Rieseberg LH. What we still don't know about invasion genetics. Mol Ecol 2015; 24:2277-97. [PMID: 25474505 DOI: 10.1111/mec.13032] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/12/2022]
Abstract
Publication of The Genetics of Colonizing Species in 1965 launched the field of invasion genetics and highlighted the value of biological invasions as natural ecological and evolutionary experiments. Here, we review the past 50 years of invasion genetics to assess what we have learned and what we still don't know, focusing on the genetic changes associated with invasive lineages and the evolutionary processes driving these changes. We also suggest potential studies to address still-unanswered questions. We now know, for example, that rapid adaptation of invaders is common and generally not limited by genetic variation. On the other hand, and contrary to prevailing opinion 50 years ago, the balance of evidence indicates that population bottlenecks and genetic drift typically have negative effects on invasion success, despite their potential to increase additive genetic variation and the frequency of peak shifts. Numerous unknowns remain, such as the sources of genetic variation, the role of so-called expansion load and the relative importance of propagule pressure vs. genetic diversity for successful establishment. While many such unknowns can be resolved by genomic studies, other questions may require manipulative experiments in model organisms. Such studies complement classical reciprocal transplant and field-based selection experiments, which are needed to link trait variation with components of fitness and population growth rates. We conclude by discussing the potential for studies of invasion genetics to reveal the limits to evolution and to stimulate the development of practical strategies to either minimize or maximize evolutionary responses to environmental change.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Room 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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