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Huang G, Zhang Y, Zhang W, Wei F. Genetic mechanisms of animal camouflage: an interdisciplinary perspective. Trends Genet 2024; 40:613-620. [PMID: 38644132 DOI: 10.1016/j.tig.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Abstract
Camouflage is a classic example of a trait wherein animals respond to natural selection to avoid predation or attract prey. This unique phenomenon has attracted significant recent attention and the rapid development of integrative research methods is facilitating advances in our understanding of the in-depth genetic mechanisms of camouflage. In this review article, we revisit camouflage definitions and strategies and then we examine the underlying mechanisms of the two most common forms of camouflage, crypsis and masquerade, that have recently been elucidated using multiple approaches. We also discuss unresolved questions related to camouflage. Ultimately, we highlight the implications of camouflage for informing various key issues in ecology and evolution.
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Affiliation(s)
- Guangping Huang
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fuwen Wei
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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2
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Judson JM, Hoekstra LA, Janzen FJ. Demographic history and genomic signatures of selection in a widespread vertebrate ectotherm. Mol Ecol 2024; 33:e17269. [PMID: 38234254 PMCID: PMC10922411 DOI: 10.1111/mec.17269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Environmental conditions vary greatly across large geographic ranges, and yet certain species inhabit entire continents. In such species, genomic sequencing can inform our understanding of colonization history and the impact of selection on the genome as populations experience diverse local environments. As ectothermic vertebrates are among the most vulnerable to environmental change, it is critical to understand the contributions of local adaptation to population survival. Widespread ectotherms offer an opportunity to explore how species can successfully inhabit such differing environments and how future climatic shifts will impact species' survival. In this study, we investigated the widespread painted turtle (Chrysemys picta) to assess population genomic structure, demographic history, and genomic signatures of selection in the western extent of the range. We found support for a substantial role of serial founder effects in shaping population genomic structure: demographic analysis and runs of homozygosity were consistent with bottlenecks of increasing severity from eastern to western populations during and following the Last Glacial Maximum, and edge populations were more strongly diverged and had less genetic diversity than those from the centre of the range. We also detected outlier loci, but allelic patterns in many loci could be explained by either genetic surfing or selection. While range expansion complicates the identification of loci under selection, we provide candidates for future study of local adaptation in a long-lived, widespread ectotherm that faces an uncertain future as the global climate continues to rapidly change.
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Affiliation(s)
- Jessica M. Judson
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Luke A. Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fredric J. Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
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3
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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4
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Parvizi E, Vaughan AL, Dhami MK, McGaughran A. Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni). Heredity (Edinb) 2024; 132:18-29. [PMID: 37903919 PMCID: PMC10798995 DOI: 10.1038/s41437-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/21/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.
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Affiliation(s)
- Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Amy L Vaughan
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Manpreet K Dhami
- Biocontrol and Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand.
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5
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Carbeck K, Arcese P, Lovette I, Pruett C, Winker K, Walsh J. Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule. Nat Commun 2023; 14:6974. [PMID: 37935683 PMCID: PMC10630373 DOI: 10.1038/s41467-023-42786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species' capacity to adapt to change. To identify genes underlying Bergmann's Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 - 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann's Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada.
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada
| | - Irby Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Christin Pruett
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR, 71998, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
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6
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de Jong M, van Rensburg AJ, Whiteford S, Yung CJ, Beaumont M, Jiggins C, Bridle J. Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range. Mol Ecol 2023; 32:5742-5756. [PMID: 37800849 DOI: 10.1111/mec.17138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023]
Abstract
Understanding the rate and extent to which populations can adapt to novel environments at their ecological margins is fundamental to predicting the persistence of biological communities during ongoing and rapid global change. Recent range expansion in response to climate change in the UK butterfly Aricia agestis is associated with the evolution of novel interactions with a larval food plant, and the loss of its ability to use an ancestral host species. Using ddRAD analysis of 61,210 variable SNPs from 261 females from throughout the UK range of this species, we identify genomic regions at multiple chromosomes that are associated with evolutionary responses, and their association with demographic history and ecological variation. Gene flow appears widespread throughout the range, despite the apparently fragmented nature of the habitats used by this species. Patterns of haplotype variation between selected and neutral genomic regions suggest that evolution associated with climate adaptation is polygenic, resulting from the independent spread of alleles throughout the established range of this species, rather than the colonization of pre-adapted genotypes from coastal populations. These data suggest that rapid responses to climate change do not depend on the availability of pre-adapted genotypes. Instead, the evolution of novel forms of biotic interaction in A. agestis has occurred during range expansion, through the assembly of novel genotypes from alleles from multiple localities.
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Affiliation(s)
- Maaike de Jong
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alexandra Jansen van Rensburg
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Samuel Whiteford
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Carl J Yung
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Chris Jiggins
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jon Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
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7
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Rosing-Asvid A, Löytynoja A, Momigliano P, Hansen RG, Scharff-Olsen CH, Valtonen M, Kammonen J, Dietz R, Rigét FF, Ferguson SH, Lydersen C, Kovacs KM, Holland DM, Jernvall J, Auvinen P, Tange Olsen M. An evolutionarily distinct ringed seal in the Ilulissat Icefjord. Mol Ecol 2023; 32:5932-5943. [PMID: 37855154 DOI: 10.1111/mec.17163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The Earth's polar regions are low rates of inter- and intraspecific diversification. An extreme mammalian example is the Arctic ringed seal (Pusa hispida hispida), which is assumed to be panmictic across its circumpolar Arctic range. Yet, local Inuit communities in Greenland and Canada recognize several regional variants; a finding supported by scientific studies of body size variation. It is however unclear whether this phenotypic variation reflects plasticity, morphs or distinct ecotypes. Here, we combine genomic, biologging and survey data, to document the existence of a unique ringed seal ecotype in the Ilulissat Icefjord (locally 'Kangia'), Greenland; a UNESCO World Heritage site, which is home to the most productive marine-terminating glacier in the Arctic. Genomic analyses reveal a divergence of Kangia ringed seals from other Arctic ringed seals about 240 kya, followed by secondary contact since the Last Glacial Maximum. Despite ongoing gene flow, multiple genomic regions appear under strong selection in Kangia ringed seals, including candidate genes associated with pelage coloration, growth and osmoregulation, potentially explaining the Kangia seal's phenotypic and behavioural uniqueness. The description of 'hidden' diversity and adaptations in yet another Arctic species merits a reassessment of the evolutionary processes that have shaped Arctic diversity and the traditional view of this region as an evolutionary freezer. Our study highlights the value of indigenous knowledge in guiding science and calls for efforts to identify distinct populations or ecotypes to understand how these might respond differently to environmental change.
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Affiliation(s)
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Paolo Momigliano
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, Spain
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | | | - Mia Valtonen
- Wildlife Ecology Group, Natural Resources Institute Finland, Helsinki, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | | | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, Tromsø, Norway
| | - David M Holland
- Mathematics and Atmosphere/Ocean Science, Courant Institute of Mathematical Sciences, New York University, New York City, New York, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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8
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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9
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de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC. Genomic architecture of migration timing in a long-distance migratory songbird. Sci Rep 2023; 13:2437. [PMID: 36765096 PMCID: PMC9918537 DOI: 10.1038/s41598-023-29470-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing.
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Affiliation(s)
- Evelien de Greef
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada.
| | - Alexander Suh
- Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TU, UK
| | - Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Kira E Delmore
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Kevin C Fraser
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada
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10
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Life on a beach leads to phenotypic divergence despite gene flow for an island lizard. Commun Biol 2023; 6:141. [PMID: 36732444 PMCID: PMC9895042 DOI: 10.1038/s42003-023-04494-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Limited spatial separation within small islands suggests that observed population divergence may occur due to habitat differences without interruption to gene flow but strong evidence of this is scarce. The wall lizard Teira dugesii lives in starkly contrasting shingle beach and inland habitats on the island of Madeira. We used a matched pairs sampling design to examine morphological and genomic divergence between four beach and adjacent (<1 km) inland areas. Beach populations are significantly darker than corresponding inland populations. Geometric morphometric analyses reveal divergence in head morphology: beach lizards have generally wider snouts. Genotyping-by-sequencing allows the rejection of the hypothesis that beach populations form a distinct lineage. Bayesian analyses provide strong support for models that incorporate gene flow, relative to those that do not, replicated at all pairs of matched sites. Madeiran lizards show morphological divergence between habitats in the face of gene flow, revealing how divergence may originate within small islands.
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11
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Nouhaud P, Martin SH, Portinha B, Sousa VC, Kulmuni J. Rapid and predictable genome evolution across three hybrid ant populations. PLoS Biol 2022; 20:e3001914. [PMID: 36538502 PMCID: PMC9767332 DOI: 10.1371/journal.pbio.3001914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Hybridization is frequent in the wild but it is unclear when admixture events lead to predictable outcomes and if so, at what timescale. We show that selection led to correlated sorting of genetic variation rapidly after admixture in 3 hybrid Formica aquilonia × F. polyctena ant populations. Removal of ancestry from the species with the lowest effective population size happened in all populations, consistent with purging of deleterious load. This process was modulated by recombination rate variation and the density of functional sites. Moreover, haplotypes with signatures of positive selection in either species were more likely to fix in hybrids. These mechanisms led to mosaic genomes with comparable ancestry proportions. Our work demonstrates predictable evolution over short timescales after admixture in nature.
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Affiliation(s)
- Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Beatriz Portinha
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- cE3c, Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Vitor C. Sousa
- cE3c, Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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12
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Wadgymar SM, DeMarche ML, Josephs EB, Sheth SN, Anderson JT. Local adaptation: Causal agents of selection and adaptive trait divergence. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022; 53:87-111. [PMID: 37790997 PMCID: PMC10544833 DOI: 10.1146/annurev-ecolsys-012722-035231] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation.
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Affiliation(s)
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Seema N Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602
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13
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Zacharias M, Pampuch T, Dauphin B, Opgenoorth L, Roland C, Schnittler M, Wilmking M, Bog M, Heer K. Genetic basis of growth reaction to drought stress differs in contrasting high-latitude treeline ecotones of a widespread conifer. Mol Ecol 2022; 31:5165-5181. [PMID: 35951000 DOI: 10.1111/mec.16648] [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: 03/01/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 12/15/2022]
Abstract
Climate change is increasing the frequency and intensity of drought events in many boreal forests. Trees are sessile organisms with a long generation time, which makes them vulnerable to fast climate change and hinders fast adaptations. Therefore, it is important to know how forests cope with drought stress and to explore the genetic basis of these reactions. We investigated three natural populations of white spruce (Picea glauca) in Alaska, located at one drought-limited and two cold-limited treelines with a paired plot design of one forest and one treeline plot. We obtained individual increment cores from 458 trees and climate data to assess dendrophenotypes, in particular the growth reaction to drought stress. To explore the genetic basis of these dendrophenotypes, we genotyped the individual trees at 3000 single nucleotide polymorphisms in candidate genes and performed genotype-phenotype association analysis using linear mixed models and Bayesian sparse linear mixed models. Growth reaction to drought stress differed in contrasting treeline populations. Therefore, the populations are likely to be unevenly affected by climate change. We identified 40 genes associated with dendrophenotypic traits that differed among the treeline populations. Most genes were identified in the drought-limited site, indicating comparatively strong selection pressure of drought-tolerant phenotypes. Contrasting patterns of drought-associated genes among sampled sites and in comparison to Canadian populations in a previous study suggest that drought adaptation acts on a local scale. Our results highlight genes that are associated with wood traits which in turn are critical for the establishment and persistence of future forests under climate change.
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Affiliation(s)
- Melanie Zacharias
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Timo Pampuch
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | | | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany
| | - Carl Roland
- Denali National Park and Preserve, Fairbanks, Alaska, USA
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Martin Wilmking
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Katrin Heer
- Forest Genetics, Faculty of Environment and Natural Resources, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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14
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Abstract
The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of 10 populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation-by-distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼650,000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.
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Affiliation(s)
- Takahiro Maruki
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Zhiqiang Ye
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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15
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An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proc Natl Acad Sci U S A 2022; 119:e2202862119. [PMID: 35776547 PMCID: PMC9271204 DOI: 10.1073/pnas.2202862119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Identifying the genetic basis of repeatedly evolved traits provides a way to reconstruct their evolutionary history and ultimately investigate the predictability of evolution. Here, we focus on the oldfield mouse (Peromyscus polionotus), which occurs in the southeastern United States, where it exhibits considerable color variation. Dorsal coats range from dark brown in mainland mice to near white in mice inhabiting sandy beaches; this light pelage has evolved independently on Florida's Gulf and Atlantic coasts as camouflage from predators. To facilitate genomic analyses, we first generated a chromosome-level genome assembly of Peromyscus polionotus subgriseus. Next, in a uniquely variable mainland population (Peromyscus polionotus albifrons), we scored 23 pigment traits and performed targeted resequencing in 168 mice. We find that pigment variation is strongly associated with an ∼2-kb region ∼5 kb upstream of the Agouti signaling protein coding region. Using a reporter-gene assay, we demonstrate that this regulatory region contains an enhancer that drives expression in the dermis of mouse embryos during the establishment of pigment prepatterns. Moreover, extended tracts of homozygosity in this Agouti region indicate that the light allele experienced recent and strong positive selection. Notably, this same light allele appears fixed in both Gulf and Atlantic coast beach mice, despite these populations being separated by >1,000 km. Together, our results suggest that this identified Agouti enhancer allele has been maintained in mainland populations as standing genetic variation and from there, has spread to and been selected in two independent beach mouse lineages, thereby facilitating their rapid and parallel evolution.
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16
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Portinha B, Avril A, Bernasconi C, Helanterä H, Monaghan J, Seifert B, Sousa VC, Kulmuni J, Nouhaud P. Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges. Mol Ecol 2022; 31:3416-3431. [PMID: 35460311 PMCID: PMC9320829 DOI: 10.1111/mec.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, for example, when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species Formica polyctena and F. aquilonia. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (c. 500 kya) and occurred with continuous asymmetrical gene flow from F. aquilonia to F. polyctena until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.
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Affiliation(s)
- Beatriz Portinha
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- cE3cCentre for Ecology, Evolution and Environmental changesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Amaury Avril
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | | | | | | | | | - Vitor C. Sousa
- cE3cCentre for Ecology, Evolution and Environmental changesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationUniversity of HelsinkiHankoFinland
| | - Pierre Nouhaud
- Organismal & Evolutionary Biology Research ProgrammeUniversity of HelsinkiHelsinkiFinland
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17
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Barton N, Olusanya O. The response of a metapopulation to a changing environment. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210009. [PMID: 35184588 PMCID: PMC8859523 DOI: 10.1098/rstb.2021.0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/15/2021] [Indexed: 01/10/2023] Open
Abstract
A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030-1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a 'fixed-state' approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m-1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Nick Barton
- Institute of Science and Technology Austria, Am Campus, 1, Klosterneuburg 3400, Austria
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18
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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19
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Liang S, Zhang X, Wei R. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Mol Ecol 2022; 31:2679-2697. [DOI: 10.1111/mec.16420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Si‐Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
- University of Chinese Academy of Sciences College of Life Sciences Beijing 100049 China
| | - Xian‐Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
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20
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Clark MI, Bradburd GS, Akopyan M, Vega A, Rosenblum EB, Robertson JM. Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas). Mol Ecol 2022; 31:1666-1681. [PMID: 35034406 PMCID: PMC8923152 DOI: 10.1111/mec.16350] [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: 05/22/2021] [Revised: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.
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Affiliation(s)
- Meaghan I. Clark
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Gideon S. Bradburd
- Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Maria Akopyan
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Jeanne M. Robertson
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
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21
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Local adaptation to climate anomalies relates to species phylogeny. Commun Biol 2022; 5:143. [PMID: 35177761 PMCID: PMC8854402 DOI: 10.1038/s42003-022-03088-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Climatic anomalies are increasing in intensity and frequency due to rapid rates of global change, leading to increased extinction risk for many species. The impacts of anomalies are likely to vary between species due to different degrees of sensitivity and extents of local adaptation. Here, we used long-term butterfly monitoring data of 143 species across six European bioclimatic regions to show how species’ population dynamics have responded to local or globally-calculated climatic anomalies, and how species attributes mediate these responses. Contrary to expectations, degree of apparent local adaptation, estimated from the relative population sensitivity to local versus global anomalies, showed no associations with species mobility or reproductive rate but did contain a strong phylogenetic signal. The existence of phylogenetically-patterned local adaptation to climate has important implications for forecasting species responses to current and future climatic conditions and for developing appropriate conservation practices. Melero et al. investigate butterfly responses to climatic anomalies from long-term monitoring observations in the field. They found the degree of adaptation to local fluctuations in climate had a strong phylogenetic signal but was not associated with mobility or reproductive rate of a species.
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22
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Prado JR, Rubi TL, Baumgartner J, Hoffman SMG, Dantzer B, Lacey Knowles L. Postglacial colonization in the Great Lakes Region by the white-footed mouse (Peromyscus leucopus): conflicts between genomic and field data. J Mammal 2022. [DOI: 10.1093/jmammal/gyab158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
For regions that were covered by ice during the Pleistocene glaciations, species must have emigrated from unglaciated regions. However, it can be difficult to discern when and from what ancestral source populations such expansions took place, especially since warming climates introduce the possibility of very recent expansions. For example, in the Great Lakes region, pronounced climatic change includes past glaciations as well as recent, rapid warming. Here we evaluate different expansion hypotheses with a genomic study of the white-footed mouse (Peromyscus leucopus noveboracensis), which is one of the most common mammals throughout the Great Lakes region. Ecological surveys coupled with historical museum records suggest a recent range expansion of P. leucopus associated with the warming climate over the last decades. These detailed records have yet to be complemented by genomic data that provide the requisite resolution for detecting recent expansion, although some mitochondrial DNA (mtDNA) sequences have suggested possible hypotheses about the geography of expansion. With more than 7,000 loci generated using RADseq, we evaluate support for multiple hypotheses of a geographic expansion in the Upper Peninsula of Michigan (UP). Analysis of a single random single-nucleotide polymorphism per locus revealed a fine-scale population structure separating the Lower Peninsula (LP) population from all other populations in the UP. We also detected a genetic structure that reflects an evolutionary history of postglacial colonization from two different origins into the UP, one coming from the LP and one coming from the west. Instead of supporting a climate-driven range expansion, as suggested by field surveys, our results support more ancient postglacial colonization of the UP from two different ancestral sources. With these results, we offer new insights about P. leucopus geographic expansion history, as well as a more general phylogeographic framework for testing range shifts in the Great Lakes region.
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Affiliation(s)
- Joyce R Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Tricia L Rubi
- Department of Psychology, The University of Michigan, Ann Arbor, MI, USA
| | | | | | - Ben Dantzer
- Department of Psychology, The University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, MI, USA
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23
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Bertola LD, Miller SM, Williams VL, Naude VN, Coals P, Dures SG, Henschel P, Chege M, Sogbohossou EA, Ndiaye A, Kiki M, Gaylard A, Ikanda DK, Becker MS, Lindsey P. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion ( Panthera leo). Evol Appl 2022; 15:22-39. [PMID: 35126646 PMCID: PMC8792481 DOI: 10.1111/eva.13318] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.
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Affiliation(s)
- Laura D. Bertola
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- City College of New YorkNew YorkNew YorkUSA
| | - Susan M. Miller
- FitzPatrick Institute of African OrnithologyDSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Vivienne L. Williams
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Peter Coals
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Wildlife Conservation Research UnitUniversity of OxfordOxfordUK
| | | | | | - Monica Chege
- Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
- Kenya Wildlife ServiceNairobiKenya
| | | | | | - Martial Kiki
- Département de Génie de l’EnvironnementUniversité d’Abomey‐CalaviCotonouBenin
| | - Angela Gaylard
- Conservation Development & Assurance DepartmentAfrican Parks NetworkJohannesburgSouth Africa
| | | | | | - Peter Lindsey
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
- Wildlife Conservation NetworkSan FranciscoCaliforniaUSA
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24
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Orrock JL, Abueg L, Gammie S, Munshi‐South J. Exome sequencing of deer mice on two California Channel Islands identifies potential adaptation to strongly contrasting ecological conditions. Ecol Evol 2021; 11:17191-17201. [PMID: 34938502 PMCID: PMC8668806 DOI: 10.1002/ece3.8357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding the forces that drive genotypic and phenotypic change in wild populations is a central goal of evolutionary biology. We examined exome variation in populations of deer mice from two of the California Channel Islands: Peromyscus maniculatus elusus from Santa Barbara Island and P. m. santacruzae from Santa Cruz Island exhibit significant differences in olfactory predator recognition, activity timing, aggressive behavior, morphology, prevalence of Sin Nombre virus, and population densities. We characterized variation in protein-coding regions using exome capture and sequencing of 25 mice from Santa Barbara Island and 22 mice from Santa Cruz Island. We identified and examined 386,256 SNPs using three complementary methods (BayeScan, pcadapt, and LFMM). We found strong differences in molecular variation between the two populations and 710 outlier SNPs in protein-coding genes that were detected by all three methods. We identified 35 candidate genes from this outlier set that were related to differences in phenotypes between island populations. Enrichment analyses demonstrated that patterns of molecular variation were associated with biological processes related to response to chemical stimuli and regulation of immune processes. Candidate genes associated with olfaction (Gfy, Tlr2, Vmn13r2, numerous olfactory receptor genes), circadian activity (Cry1), anxiety (Brca1), immunity (Cd28, Eif2ak4, Il12a, Syne1), aggression (Cyp19a, Lama2), and body size (Bc16, Syne1) exhibited non-synonymous mutations predicted to have moderate to large effects. Variation in olfaction-related genes, including a stop codon in the Santa Barbara Island population, suggests loss of predator-recognition traits at the molecular level, consistent with a lack of behavioral aversion to fox feces. These findings also suggest that divergent pathogen prevalence and population density may have influenced adaptive immunity and behavioral phenotypes, such as reduced aggression. Overall, our study indicates that ecological differences between islands are associated with signatures of selection in protein-coding genes underlying phenotypes that promote success in those environments.
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Affiliation(s)
- John L. Orrock
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Linelle Abueg
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
| | - Stephen Gammie
- Department of Integrative BiologyUniversity of WisconsinMadisonWisconsinUSA
| | - Jason Munshi‐South
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNew YorkUSA
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25
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Prado JR, Percequillo AR, Pirani RM, Thomaz AT. Phenotypic and genomic differences between biomes of the South America marsh rat, Holochilus brasiliensis. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Abiotic factors can influence genetic and phenotypic divergence in several ways, and identifying the mechanisms responsible for generating this variation is challenging. However, when evaluated in combination, ecological characteristics and genetic and phenotypic information can help us to understand how habitat preferences can influence morphological and genetic patterns exhibited by taxa distributed between distinct biomes, such as the Atlantic Forest and Pampas biomes in South America. By combining distributional, environmental, phenotypic and genomic information from a habitat-specialist semi-aquatic rodent (Holochilus brasiliensis), we quantified the relationship between ecological niche differences and the phenotypic and genetic variation. The results demonstrate notable segregation among the ecological niches of H. brasiliensis within each biome, although we could not refute the hypothesis of niche similarity or equivalency. Such differences are consistent with a solid morphometric variation associated with the size of these rodents. However, the ecological and morphometric differentiation is not accompanied by the same pattern of genetic variation. Despite differences in the connectivity patterns in both biomes, the genetic differences corroborate a consistent level of migration history between biomes. Additionally, the association tests show that the environment explains a small and non- significant part of the genetic variation but a significant portion of the morphometric variation.
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Affiliation(s)
- Joyce R Prado
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Alexandre R Percequillo
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Renata M Pirani
- Biology Department, University of Nevada-Reno, Reno, NV, USA
| | - Andrea T Thomaz
- Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, DC, Colombia
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26
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Stephan W. Rapid Evolutionary Adaptation in Response to Selection on Quantitative Traits. Life (Basel) 2021; 11:life11080797. [PMID: 34440541 PMCID: PMC8398862 DOI: 10.3390/life11080797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 11/25/2022] Open
Abstract
Evolutionary adaptation after sudden environmental changes can occur very rapidly. The mechanisms facilitating rapid adaptation range from strong positive directional selection leading to large shifts in the allele frequencies at a few loci (selective sweeps) to polygenic selection causing small changes in allele frequencies at many loci. In addition, combinations of these two extreme mechanisms may also result in fast evolution. In recent years, following reports of new case studies of rapid adaptation, population genetic models have been proposed to explain these observations. In these models, the role of the major selective forces (positive directional and stabilizing selection) is highlighted as well as the genetic architecture of quantitative traits. Furthermore, the factors limiting the speed of adaptation are analyzed, in particular, the effects of random genetic drift and demography due to finite population size.
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Affiliation(s)
- Wolfgang Stephan
- Natural History Museum, 10115 Berlin, Germany;
- Faculty of Biology, Evolutionary Biology, Ludwig-Maximilian University of Munich, 82152 Planegg-Martinsried, Germany
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27
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Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Mol Ecol 2021; 30:3797-3814. [PMID: 33638231 DOI: 10.1111/mec.15861] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 12/28/2022]
Abstract
Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder-rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
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Affiliation(s)
- Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal
| | - Kerstin Johannesson
- Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger Butlin
- Animal & Plant Sciences, Western Bank, University of Sheffield, Sheffield, UK.,Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
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28
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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29
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Rautsaw RM, Schramer TD, Acuña R, Arick LN, DiMeo M, Mercier KP, Schrum M, Mason AJ, Margres MJ, Strickland JL, Parkinson CL. Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes. Mol Biol Evol 2021; 38:745-760. [PMID: 33035326 PMCID: PMC7947766 DOI: 10.1093/molbev/msaa266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.
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Affiliation(s)
- Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | | | - Rachel Acuña
- Department of Biology, University of Central Florida, Orlando, FL
| | - Lindsay N Arick
- Department of Biology, University of Central Florida, Orlando, FL
| | - Mark DiMeo
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Kathryn P Mercier
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, City College of New York, New York, NY.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, NY
| | - Michael Schrum
- Department of Biology, University of Central Florida, Orlando, FL
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Biology, University of South Alabama, Mobile, AL
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC.,Department of Biology, University of Central Florida, Orlando, FL.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC
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30
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Bal TMP, Llanos-Garrido A, Chaturvedi A, Verdonck I, Hellemans B, Raeymaekers JAM. Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species. Genes (Basel) 2021; 12:435. [PMID: 33803820 PMCID: PMC8003309 DOI: 10.3390/genes12030435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.
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Affiliation(s)
- Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway;
| | | | - Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland;
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
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31
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Depardieu C, Gérardi S, Nadeau S, Parent GJ, Mackay J, Lenz P, Lamothe M, Girardin MP, Bousquet J, Isabel N. Connecting tree-ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer. Mol Ecol 2021; 30:3898-3917. [PMID: 33586257 PMCID: PMC8451828 DOI: 10.1111/mec.15846] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/15/2021] [Accepted: 01/27/2021] [Indexed: 01/02/2023]
Abstract
As boreal forests face significant threats from climate change, understanding evolutionary trajectories of coniferous species has become fundamental to adapting management and conservation to a drying climate. We examined the genomic architecture underlying adaptive variation related to drought tolerance in 43 populations of a widespread boreal conifer, white spruce (Piceaglauca [Moench] Voss), by combining genotype–environment associations, genotype–phenotype associations, and transcriptomics. Adaptive genetic variation was identified by correlating allele frequencies for 6,153 single nucleotide polymorphisms from 2,606 candidate genes with temperature, precipitation and aridity gradients, and testing for significant associations between genotypes and 11 dendrometric and drought‐related traits (i.e., anatomical, growth response and climate‐sensitivity traits) using a polygenic model. We identified a set of 285 genes significantly associated with a climatic factor or a phenotypic trait, including 110 that were differentially expressed in response to drought under greenhouse‐controlled conditions. The interlinked phenotype–genotype–environment network revealed eight high‐confidence genes involved in white spruce adaptation to drought, of which four were drought‐responsive in the expression analysis. Our findings represent a significant step toward the characterization of the genomic basis of drought tolerance and adaptation to climate in conifers, which is essential to enable the establishment of resilient forests in view of new climate conditions. see also the Perspective by Lars Opgenoorth and Christian Rellstab
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Affiliation(s)
- Claire Depardieu
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Sébastien Gérardi
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Simon Nadeau
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Geneviève J. Parent
- Laboratory of GenomicsMaurice‐Lamontagne Institute, Fisheries and Oceans CanadaMont‐JoliQCCanada
| | - John Mackay
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Patrick Lenz
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceCanadian Wood Fibre CenterQuébecQCCanada
| | - Manuel Lamothe
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
| | - Martin P. Girardin
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
- Centre for Forest ResearchUniversité du Québec à MontréalMontréalQCCanada
| | - Jean Bousquet
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
| | - Nathalie Isabel
- Canada Research Chair in Forest GenomicsInstitute for Systems and Integrative BiologyUniversité LavalQuébecQCCanada
- Centre for Forest ResearchDépartement des sciences du bois et de la forêtUniversité LavalQuébecQCCanada
- Natural Resources CanadaCanadian Forest ServiceLaurentian Forestry CenterQuébecQCCanada
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32
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Hofmeister NR, Werner SJ, Lovette IJ. Environmental correlates of genetic variation in the invasive European starling in North America. Mol Ecol 2021; 30:1251-1263. [PMID: 33464634 DOI: 10.1111/mec.15806] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022]
Abstract
Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing of 17 winter-season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few FST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ~200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.
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Affiliation(s)
- Natalie R Hofmeister
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
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33
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Yamamoto N, Sota T. Evolutionary fine-tuning of background-matching camouflage among geographical populations in the sandy beach tiger beetle. Proc Biol Sci 2020; 287:20202315. [PMID: 33323087 PMCID: PMC7779511 DOI: 10.1098/rspb.2020.2315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/20/2020] [Indexed: 11/12/2022] Open
Abstract
Background-matching camouflage is a widespread adaptation in animals; however, few studies have thoroughly examined its evolutionary process and consequences. The tiger beetle Chaetodera laetescripta exhibits pronounced variation in elytral colour pattern among sandy habitats of different colour in the Japanese Archipelago. In this study, we performed digital image analysis with avian vision modelling to demonstrate that elytral luminance, which is attributed to proportions of elytral colour components, is fine-tuned to match local backgrounds. Field predation experiments with model beetles showed that better luminance matching resulted in a lower attack rate and corresponding lower mortality. Using restriction site-associated DNA (RAD) sequence data, we analysed the dispersal and evolution of colour pattern across geographical locations. We found that sand colour matching occurred irrespective of genetic and geographical distances between populations, suggesting that locally adapted colour patterns evolved after the colonization of these habitats. Given that beetle elytral colour patterns presumably have a quantitative genetic basis, our findings demonstrate that fine-tuning of background-matching camouflage to local habitat conditions can be attained through selection by visual predators, as predicted by the earliest proponent of natural selection.
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Affiliation(s)
- Nayuta Yamamoto
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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34
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Jones MR, Mills LS, Jensen JD, Good JM. The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares. Am Nat 2020; 196:316-332. [DOI: 10.1086/710022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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35
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Stephan W, John S. Polygenic Adaptation in a Population of Finite Size. ENTROPY 2020; 22:e22080907. [PMID: 33286676 PMCID: PMC7517530 DOI: 10.3390/e22080907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/31/2020] [Accepted: 08/15/2020] [Indexed: 12/15/2022]
Abstract
Polygenic adaptation in response to selection on quantitative traits has become an important topic in evolutionary biology. Here we review the recent literature on models of polygenic adaptation. In particular, we focus on a model that includes mutation and both directional and stabilizing selection on a highly polygenic trait in a population of finite size (thus experiencing random genetic drift). Assuming that a sudden environmental shift of the fitness optimum occurs while the population is in a stochastic equilibrium, we analyze the adaptation of the trait to the new optimum. When the shift is not too large relative to the equilibrium genetic variance and this variance is determined by loci with mostly small effects, the approach of the mean phenotype to the optimum can be approximated by a rapid exponential process (whose rate is proportional to the genetic variance). During this rapid phase the underlying changes to allele frequencies, however, may depend strongly on genetic drift. While trait-increasing alleles with intermediate equilibrium frequencies are dominated by selection and contribute positively to changes of the trait mean (i.e., are aligned with the direction of the optimum shift), alleles with low or high equilibrium frequencies show more of a random dynamics, which is expected when drift is dominating. A strong effect of drift is also predicted for population size bottlenecks. Our simulations show that the presence of a bottleneck results in a larger deviation of the population mean of the trait from the fitness optimum, which suggests that more loci experience the influence of drift.
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Affiliation(s)
- Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Natural History Museum, 10115 Berlin, Germany;
| | - Sona John
- Department of Life Science Systems, Technical University of Munich, 85354 Freising, Germany
- Correspondence:
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36
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Li LF, Cushman SA, He YX, Li Y. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. HORTICULTURE RESEARCH 2020; 7:130. [PMID: 32821413 PMCID: PMC7395120 DOI: 10.1038/s41438-020-00352-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 05/06/2023]
Abstract
Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.
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Affiliation(s)
- Lin-Feng Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, Arizona USA
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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37
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Sun SJ, Catherall AM, Pascoal S, Jarrett BJM, Miller SE, Sheehan MJ, Kilner RM. Rapid local adaptation linked with phenotypic plasticity. Evol Lett 2020; 4:345-359. [PMID: 32774883 PMCID: PMC7403679 DOI: 10.1002/evl3.176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 11/05/2022] Open
Abstract
Models of "plasticity-first" evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can facilitate rapid microevolutionary change between diverging populations. Here, we show how plasticity may have generated adaptive differences in fecundity between neighboring wild populations of burying beetles Nicrophorus vespilloides. These populations occupy distinct Cambridgeshire woodlands that are just 2.5 km apart and that probably originated from a common ancestral population about 1000-4000 years ago. We find that populations are divergently adapted to breed on differently sized carrion. Adaptive differences in clutch size and egg size are associated with divergence at loci connected with oogenesis. The populations differ specifically in the elevation of the reaction norm linking clutch size to carrion size (i.e., genetic accommodation), and in the likelihood that surplus offspring will be lost after hatching. We suggest that these two processes may have facilitated rapid local adaptation on a fine-grained spatial scale.
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Affiliation(s)
- Syuan-Jyun Sun
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Andrew M Catherall
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Benjamin J M Jarrett
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom.,Department of Entomology Michigan State University East Lansing Michigan 48824
| | - Sara E Miller
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Michael J Sheehan
- Department of Neurobiology and Behavior Cornell University Ithaca New York 14853
| | - Rebecca M Kilner
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
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38
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Jones MR, Mills LS, Jensen JD, Good JM. Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range*. Evolution 2020; 74:2033-2045. [DOI: 10.1111/evo.13976] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew R. Jones
- Division of Biological Sciences University of Montana Missoula Montana 59812
| | - L. Scott Mills
- Wildlife Biology Program University of Montana Missoula Montana 59812
- Office of Research and Creative Scholarship University of Montana Missoula Montana 59812
| | - Jeffrey D. Jensen
- School of Life Sciences Arizona State University Tempe Arizona 85281
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula Montana 59812
- Wildlife Biology Program University of Montana Missoula Montana 59812
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39
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Apata M, Pfeifer SP. Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity (Edinb) 2020; 124:253-262. [PMID: 31776483 PMCID: PMC6972707 DOI: 10.1038/s41437-019-0285-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in genomics have enabled researchers to shed light on the evolutionary processes driving human adaptation, by revealing the genetic architectures underlying traits ranging from lactase persistence, to skin pigmentation, to hypoxic response, to arsenic tolerance. Complicating the identification of targets of positive selection in modern human populations is their complex demographic history, characterized by population bottlenecks and expansions, population structure, migration, and admixture. In particular, founder effects and recent strong population size reductions, such as those experienced by the indigenous peoples of the Americas, have severe impacts on genetic variation that can lead to the accumulation of large allele frequency differences between populations due to genetic drift rather than natural selection. While distinguishing the effects of demographic history from selection remains challenging, neglecting neutral processes can lead to the incorrect identification of candidate loci. We here review the recent population genomic insights into the genetic basis of arsenic tolerance in Andean populations, and utilize this example to highlight both the difficulties pertaining to the identification of local adaptations in strongly bottlenecked populations, as well as the importance of controlling for demographic history in selection scans.
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Affiliation(s)
- Mario Apata
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA
| | - Susanne P Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA.
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40
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Moest M, Van Belleghem SM, James JE, Salazar C, Martin SH, Barker SL, Moreira GRP, Mérot C, Joron M, Nadeau NJ, Steiner FM, Jiggins CD. Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation. PLoS Biol 2020; 18:e3000597. [PMID: 32027643 PMCID: PMC7029882 DOI: 10.1371/journal.pbio.3000597] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/19/2020] [Accepted: 01/15/2020] [Indexed: 11/21/2022] Open
Abstract
Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation.
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Affiliation(s)
- Markus Moest
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Steven M. Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Jennifer E. James
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota D.C., Colombia
| | - Simon H. Martin
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L. Barker
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Gilson R. P. Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Claire Mérot
- IBIS, Department of Biology, Université Laval, Québec, Canada
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS—Université de Montpellier—Université Paul Valéry Montpellier—EPHE, Montpellier, France
| | - Nicola J. Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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41
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Slatyer RA, Schoville SD, Nufio CR, Buckley LB. Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community? Ecol Evol 2020; 10:980-997. [PMID: 32015859 PMCID: PMC6988534 DOI: 10.1002/ece3.5961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023] Open
Abstract
Species responses to environmental change are likely to depend on existing genetic and phenotypic variation, as well as evolutionary potential. A key challenge is to determine whether gene flow might facilitate or impede genomic divergence among populations responding to environmental change, and if emergent phenotypic variation is dependent on gene flow rates. A general expectation is that patterns of genetic differentiation in a set of codistributed species reflect differences in dispersal ability. In less dispersive species, we predict greater genetic divergence and reduced gene flow. This could lead to covariation in life-history traits due to local adaptation, although plasticity or drift could mirror these patterns. We compare genome-wide patterns of genetic structure in four phenotypically variable grasshopper species along a steep elevation gradient near Boulder, Colorado, and test the hypothesis that genomic differentiation is greater in short-winged grasshopper species, and statistically associated with variation in growth, reproductive, and physiological traits along this gradient. In addition, we estimate rates of gene flow under competing demographic models, as well as potential gene flow through surveys of phenological overlap among populations within a species. All species exhibit genetic structure along the elevation gradient and limited gene flow. The most pronounced genetic divergence appears in short-winged (less dispersive) species, which also exhibit less phenological overlap among populations. A high-elevation population of the most widespread species, Melanoplus sanguinipes, appears to be a sink population derived from low elevation populations. While dispersal ability has a clear connection to the genetic structure in different species, genetic distance does not predict growth, reproductive, or physiological trait variation in any species, requiring further investigation to clearly link phenotypic divergence to local adaptation.
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Affiliation(s)
| | | | - César R. Nufio
- University of Colorado Natural History MuseumUniversity of ColoradoBoulderCOUSA
- National Science FoundationAlexandriaVAUSA
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42
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Benham PM, Cheviron ZA. Population history and the selective landscape shape patterns of osmoregulatory trait divergence in tidal marsh Savannah sparrows (Passerculus sandwichensis). Evolution 2019; 74:57-72. [DOI: 10.1111/evo.13886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/12/2019] [Accepted: 11/02/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Phred M. Benham
- Division of Biological SciencesUniversity of Montana Missoula Montana 59812
- Current Address: Museum of Vertebrate ZoologyUniversity of California Berkeley 3101 Valley Life Sciences Building Berkeley CA 94720‐3160
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43
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Cabalzar AP, Fields PD, Kato Y, Watanabe H, Ebert D. Parasite-mediated selection in a natural metapopulation of Daphnia magna. Mol Ecol 2019; 28:4770-4785. [PMID: 31591747 DOI: 10.1111/mec.15260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/03/2023]
Abstract
Parasite-mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease-related traits. However, nonadaptive processes like migration and extinction-(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life-history and disease-related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite-mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life-history and disease traits in common garden experiments. Combining phenotypic and genotypic data a QST -FST -like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction-(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.
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Affiliation(s)
- Andrea P Cabalzar
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Tvärminne Zoological Station, Tvärminne, Finland
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44
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The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity (Edinb) 2019; 124:1-14. [PMID: 31399719 PMCID: PMC6906368 DOI: 10.1038/s41437-019-0257-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/16/2019] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on background matching, a particular facet of crypsis that involves the ability of an organism to conceal itself through matching its color to the surrounding environment. While interesting in and of itself, the study of this phenotype has also provided fruitful population genetic insights into the interplay of strong positive selection with other evolutionary processes. Specifically, and predicated upon the findings of previous candidate gene association studies, a primary focus of this recent literature involves the realization that the inference of selection from DNA sequence data first requires a robust model of population demography in order to identify genomic regions which do not conform to neutral expectations. Moreover, these demographic estimates provide crucial information about the origin and timing of the onset of selective pressures associated with, for example, the colonization of a novel environment. Furthermore, such inference has revealed crypsis to be a particularly useful phenotype for investigating the interplay of migration and selection—with examples of gene flow constraining rates of adaptation, or alternatively providing the genetic variants that may ultimately sweep through the population. Here, we evaluate the underlying evidence, review the strengths and weaknesses of the many population genetic methodologies used in these studies, and discuss how these insights have aided our general understanding of the evolutionary process.
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45
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Hämälä T, Savolainen O. Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata. Mol Biol Evol 2019; 36:2557-2571. [PMID: 31236594 DOI: 10.1093/molbev/msz149] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/02/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
AbstractShort-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged <2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
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46
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Margres MJ, Patton A, Wray KP, Hassinger ATB, Ward MJ, Lemmon EM, Lemmon AR, Rokyta DR. Tipping the Scales: The Migration-Selection Balance Leans toward Selection in Snake Venoms. Mol Biol Evol 2019; 36:271-282. [PMID: 30395254 DOI: 10.1093/molbev/msy207] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The migration-selection interaction is the strongest determinant of whether a beneficial allele increases in frequency within a population. Results of empirical studies examining the role of gene flow in an adaptive context, however, have largely been equivocal, with examples of opposing outcomes being repeatedly documented (e.g., local adaptation with high levels of gene flow vs. gene swamping). We compared neutral genomic and venom expression divergence for three sympatric pit vipers with differing ecologies to determine if and how migration-selection disequilibria result in local adaptation. We specifically tested whether neutral differentiation predicted phenotypic differentiation within an isolation-by-distance framework. The decoupling of neutral and phenotypic differentiation would indicate selection led to adaptive divergence irrespective of migration, whereas a significant relationship between neutral and venom expression differentiation would provide evidence in favor of the constraining force of gene flow. Neutral differentiation and geographic distance predicted phenotypic differentiation only in the generalist species, indicating that selection was the predominant mechanism in the migration-selection balance underlying adaptive venom evolution in both specialists. Dispersal is thought to be a stronger influence on genetic differentiation than specialization, but our results suggest the opposite. Greater specialization may lead to greater diversification rates, and extreme spatial and temporal variation in selective pressures can favor generalist phenotypes evolving under strong stabilizing selection. Our results are consistent with these expectations, suggesting that the equivocal findings of studies examining the role of gene flow in an adaptive context may be explained by ecological specialization theory.
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Affiliation(s)
- Mark J Margres
- Department of Biological Science, Florida State University, Tallahassee, FL.,School of Biological Sciences, Washington State University, Pullman, WA.,Department of Biological Sciences, Clemson University, Clemson, SC
| | - Austin Patton
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Kenneth P Wray
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Alyssa T B Hassinger
- Department of Biological Science, Florida State University, Tallahassee, FL.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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47
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Miller AD, Hoffmann AA, Tan MH, Young M, Ahrens C, Cocomazzo M, Rattray A, Ierodiaconou DA, Treml E, Sherman CDH. Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (
Haliotis rubra
) from southeastern Australia. Mol Ecol 2019; 28:3053-3072. [DOI: 10.1111/mec.15128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/17/2019] [Accepted: 05/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Adam D. Miller
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Ary A. Hoffmann
- School of BioSciences Bio21 Institute, The University of Melbourne Parkville Victoria Australia
| | - Mun Hua Tan
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
| | - Mary Young
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Collin Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University Penrith New South Wales Australia
| | - Michael Cocomazzo
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Alex Rattray
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Daniel A. Ierodiaconou
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Eric Treml
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
| | - Craig D. H. Sherman
- School of Life and Environmental Sciences Centre for Integrative Ecology, Deakin University Geelong Victoria Australia
- Deakin Genomics Centre Deakin University Geelong Victoria Australia
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48
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Amish SJ, Ali O, Peacock M, Miller M, Robinson M, Smith S, Luikart G, Neville H. Assessing thermal adaptation using family‐based association and
F
ST
outlier tests in a threatened trout species. Mol Ecol 2019; 28:2573-2593. [DOI: 10.1111/mec.15100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Stephen J. Amish
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | - Omar Ali
- Department of Animal Science University of California Davis California
| | - Mary Peacock
- Department of Biology University of Nevada Reno Nevada
| | - Michael Miller
- Department of Animal Science University of California Davis California
| | | | - Seth Smith
- Flathead Biological Station University of Montana Polson Montana
| | - Gordon Luikart
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
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49
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O'Connell KA, Mulder KP, Maldonado J, Currie KL, Ferraro DM. Sampling related individuals within ponds biases estimates of population structure in a pond-breeding amphibian. Ecol Evol 2019; 9:3620-3636. [PMID: 30962914 PMCID: PMC6434569 DOI: 10.1002/ece3.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Effective conservation and management of pond-breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding-site connectivity. Population-level studies of pond-breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within-pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome-wide SNPs generated using a double-digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within-pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.
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Affiliation(s)
- Kyle A O'Connell
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington District of Columbia
- Global Genome Initiative National Museum of Natural History, Smithsonian Institution Washington District of Columbia
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Kevin P Mulder
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington District of Columbia
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Porto Portugal
| | - Jose Maldonado
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Kathleen L Currie
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Dennis M Ferraro
- School of Natural Resources University of Nebraska Lincoln Lincoln Nebraska
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50
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