1
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Suchocki CR, Ka'apu-Lyons C, Copus JM, Walsh CAJ, Lee AM, Carter JM, Johnson EA, Etter PD, Forsman ZH, Bowen BW, Toonen RJ. Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae). Sci Rep 2023; 13:15810. [PMID: 37737242 PMCID: PMC10517014 DOI: 10.1038/s41598-023-41719-9] [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: 02/28/2023] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
The Gila robusta species complex in the lower reaches of the Colorado River includes three nominal and contested species (G. robusta, G. intermedia, and G. nigra) originally defined by morphological and meristic characters. In subsequent investigations, none of these characters proved diagnostic, and species assignments were based on capture location. Two recent studies applied conservation genomics to assess species boundaries and reached contrasting conclusions: an ezRAD phylogenetic study resolved 5 lineages with poor alignment to species categories and proposed a single species with multiple population partitions. In contrast, a dd-RAD coalescent study concluded that the three nominal species are well-supported evolutionarily lineages. Here we developed a draft genome (~ 1.229 Gbp) to apply genome-wide coverage (10,246 SNPs) with nearly range-wide sampling of specimens (G. robusta N = 266, G. intermedia N = 241, and G. nigra N = 117) to resolve this debate. All three nominal species were polyphyletic, whereas 5 of 8 watersheds were monophyletic. AMOVA partitioned 23.1% of genetic variance among nominal species, 30.9% among watersheds, and the Little Colorado River was highly distinct (FST ranged from 0.79 to 0.88 across analyses). Likewise, DAPC identified watersheds as more distinct than species, with the Little Colorado River having 297 fixed nucleotide differences compared to zero fixed differences among the three nominal species. In every analysis, geography explains more of the observed variance than putative taxonomy, and there are no diagnostic molecular or morphological characters to justify species designation. Our analysis reconciles previous work by showing that species identities based on type location are supported by significant divergence, but natural geographic partitions show consistently greater divergence. Thus, our data confirm Gila robusta as a single polytypic species with roughly a dozen highly isolated geographic populations, providing a strong scientific basis for watershed-based future conservation.
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Affiliation(s)
- Christopher R Suchocki
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cassie Ka'apu-Lyons
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Cameron A J Walsh
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Anne M Lee
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Julie Meka Carter
- Arizona Game and Fish Department, 5000 W. Carefree Highway, Phoenix, AZ, 85086, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Paul D Etter
- Institute of Molecular Biology, University of Oregon, 1585 E 13th Ave., Eugene, OR, 97403, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
- Reefscape Restoration Initiative, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, 46-007 Lilipuna Road, Kāne'ohe, HI, 96744, USA.
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2
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Dean LL, Magalhaes IS, D’Agostino D, Hohenlohe P, MacColl ADC. On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback. Mol Biol Evol 2023; 40:msad191. [PMID: 37652053 PMCID: PMC10490448 DOI: 10.1093/molbev/msad191] [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: 03/02/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel Santos Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Department of Life Sciences, School of Health and Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Daniele D’Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Water Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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3
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Samad‐zada F, Kelemen EP, Rehan SM. The impact of geography and climate on the population structure and local adaptation in a wild bee. Evol Appl 2023; 16:1154-1168. [PMID: 37360027 PMCID: PMC10286232 DOI: 10.1111/eva.13558] [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: 11/09/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 06/28/2023] Open
Abstract
Deciphering processes that contribute to genetic differentiation and divergent selection of natural populations is useful for evaluating the adaptive potential and resilience of organisms faced with various anthropogenic stressors. Insect pollinator species, including wild bees, provide critical ecosystem services but are highly susceptible to biodiversity declines. Here, we use population genomics to infer the genetic structure and test for evidence of local adaptation in an economically important native pollinator, the small carpenter bee (Ceratina calcarata). Using genome-wide SNP data (n = 8302), collected from specimens across the species' entire distribution, we evaluated population differentiation and genetic diversity and identified putative signatures of selection in the context of geographic and environmental variation. Results of the analyses of principal component and Bayesian clustering were concordant with the presence of two to three genetic clusters, associated with landscape features and inferred phylogeography of the species. All populations examined in our study demonstrated a heterozygote deficit, along with significant levels of inbreeding. We identified 250 robust outlier SNPs, corresponding to 85 annotated genes with known functional relevance to thermoregulation, photoperiod, and responses to various abiotic and biotic stressors. Taken together, these data provide evidence for local adaptation in a wild bee and highlight genetic responses of native pollinators to landscape and climate features.
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4
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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5
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Piñeros VJ, Del R Pedraza-Marrón C, Betancourt-Resendes I, Calderón-Cortés N, Betancur-R R, Domínguez-Domínguez O. Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting. BMC Ecol Evol 2022; 22:108. [PMID: 36104671 PMCID: PMC9472351 DOI: 10.1186/s12862-022-02063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau. RESULTS Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system. CONCLUSIONS Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.
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Affiliation(s)
- Victor Julio Piñeros
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico
| | | | - Isaí Betancourt-Resendes
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de Las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, Mexico
| | - Nancy Calderón-Cortés
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico.
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
- Laboratorio Nacional de Análisis y Síntesis Ecológica Para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Apartado Postal 27-3 (Xangari), 58089, Michoacán, Morelia, Mexico.
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6
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de Brito V, Betancur-R R, Burns MD, Buser TJ, Conway KW, Fontenelle JP, Kolmann MA, McCraney WT, Thacker CE, Bloom DD. Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes. Integr Comp Biol 2022; 62:406-423. [PMID: 35675320 DOI: 10.1093/icb/icac085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.
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Affiliation(s)
- Victor de Brito
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Room 314, Norman, OK 73019, USA
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell Museum of Vertebrates, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850-1923, USA
| | - Thaddaeus J Buser
- Department of BioSciences, Rice University, W100 George R. Brown Hall, 6100 Main Street, Houston, TX 77005, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX 77843, USA
| | - João Pedro Fontenelle
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks St., Toronto, ON M5S 3E8, Canada
| | - Matthew A Kolmann
- Museum of Paleontology, Biological Sciences Building, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109-1085, USA
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive South, Los Angeles, CA 90095-7246, USA
| | - Christine E Thacker
- Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007, USA.,Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Devin D Bloom
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA.,Institute of the Environment and Sustainability, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5419, USA
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7
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution 2022; 76:1301-1319. [PMID: 35398888 PMCID: PMC9320971 DOI: 10.1111/evo.14490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 01/21/2023]
Abstract
In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.
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Affiliation(s)
- David A. Marques
- Department of BiologyUniversity of VictoriaVictoriaBCV8W 3N5Canada
- Aquatic Ecology and Evolution, Institute of Ecology and EvolutionUniversity of BernBernCH‐3012Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (EAWAG), Eawag ‐ Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumCH‐6047Switzerland
- Natural History Museum BaselBaselCH‐4051Switzerland
| | - Felicity C. Jones
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA
- Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingen72076Germany
| | - Federica Di Palma
- Earlham InstituteNorwichNR4 7UZUnited Kingdom
- Department of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - David M. Kingsley
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA
- Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA
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8
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Wertman DL, Reimchen TE. Adaptive divergence of lateral plate ultrastructure in threespine stickleback. CAN J ZOOL 2022. [DOI: 10.1139/cjz-2021-0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lateral plates of threespine stickleback, Gasterosteus aculeatus Linnaeus, 1758, are well-studied for their adaptive morphological responses to predators, yet it is unknown whether habitat influences plate ultrastructure. We investigate using scanning electron microscopy the lateral plate ultrastructure (tubercles and ridges) of stickleback (<i>N</i> = 61 adult fish) from nine Haida Gwaii (coastal British Columbia) wild-type populations, two experimental transplants, and two lab-reared cohorts reared from source populations. Tubercle density, but not ridge density, differed significantly across habitat types and populations. Among wild-type fish, tubercle densities were greatest in dystrophic habitats containing predatory fish, and lowest in weakly dystrophic systems featuring bird–invertebrate predation and marine populations with diverse predatory fish. No differences in tubercle density were detected between source and transplant populations, despite major habitat shifts. Lab-reared fish exhibited significantly lower tubercle densities than their source populations (< one generation). Tubercle density differences across habitat types may reflect adaptation to divergent predation regimes, with tooth-bearing predators selecting for denser tubercles that disperse point forces. Conservation of ridge density across populations suggests an essential function in dispersing forces applied to dorsal spines during predator manipulation. Lateral plate ultrastructure in threespine stickleback thus results from both heritable effects and developmental plasticity.
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Affiliation(s)
- Debra L. Wertman
- University of Victoria, 8205, Department of Biology, Victoria, British Columbia, Canada
| | - Thomas E Reimchen
- University of Victoria, 8205, Department of Biology, Victoria, British Columbia, Canada,
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9
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James ME, O'Brien NLV, Bukkuri A. Digest: Stable phenotypes, fluid genotypes: how stochasticity impacts network evolution and speciation. Evolution 2022; 76:821-823. [PMID: 35149989 PMCID: PMC9303642 DOI: 10.1111/evo.14452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/04/2022] [Indexed: 01/21/2023]
Abstract
A longstanding goal of evolutionary biology is to understand the relationship between genotype and phenotype. Schiffman and Ralph use mathematical modeling to theoretically examine how the genetic network underlying a conserved phenotype can change over time. They found that when phenotypically identical populations with different gene network configurations interbreed, hybrid incompatibilities can arise. These results suggest that neutral processes could play a major role in driving speciation.
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Affiliation(s)
- Maddie E. James
- Australian Research Council Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQLD4072Australia,School of Biological SciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Nicholas L. V. O'Brien
- Australian Research Council Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQLD4072Australia,School of Biological SciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Anuraag Bukkuri
- Cancer Biology and Evolution Program and Department of Integrated Mathematical OncologyMoffitt Cancer CenterTampaFlorida33612
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10
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James ME, Wilkinson MJ, Bernal DM, Liu H, North HL, Engelstädter J, Ortiz-Barrientos D. Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio. Evolution 2021; 75:3115-3131. [PMID: 34687472 PMCID: PMC9299460 DOI: 10.1111/evo.14387] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022]
Abstract
The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune‐Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait‐environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Melanie J Wilkinson
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Diana M Bernal
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Biousos Neotropicales S.A.S, Bogotá, Colombia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Henry L North
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Current Address: Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, QLD, 4072, Australia
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11
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Samad‐zada F, van Poorten BT, Harris S, Godbout L, Russello MA. Genome-wide analysis reveals demographic and life-history patterns associated with habitat modification in landlocked, deep-spawning sockeye salmon ( Oncorhynchus nerka). Ecol Evol 2021; 11:13186-13205. [PMID: 34646462 PMCID: PMC8495803 DOI: 10.1002/ece3.8040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/11/2022] Open
Abstract
Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography, and life history of native biota, while disrupting the behavior of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last records of migrants occurring in the 1930s. Since that time, O. nerka persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life-history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir O. nerka using genome-wide SNP data (n = 7,709 loci) collected for resident and migrant individuals, as well as for neighboring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n = 312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other O. nerka populations in the Fraser River drainage. At a finer level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir O. nerka represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behavior associated with this life-history form. This finding punctuates the need for reassessment of conservation status and supports ongoing fisheries management activities in Alouette Reservoir.
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Affiliation(s)
| | - Brett T. van Poorten
- Applied Freshwater Ecology Research UnitBritish Columbia Ministry of Environment and Climate Change StrategyVancouverBCCanada
- School of Resource and Environmental ManagementSimon Fraser UniversityBurnabyBCCanada
| | - Shannon Harris
- Applied Freshwater Ecology Research UnitBritish Columbia Ministry of Environment and Climate Change StrategyVancouverBCCanada
| | - Lyse Godbout
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimoBCCanada
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12
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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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13
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Haenel Q, Oke KB, Laurentino TG, Hendry AP, Berner D. Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish. Nat Commun 2021; 12:4850. [PMID: 34381033 PMCID: PMC8358029 DOI: 10.1038/s41467-021-25039-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.
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Affiliation(s)
- Quiterie Haenel
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
| | - Krista B Oke
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, AK, USA
- Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada
| | - Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.
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14
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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15
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Ecological predictors of lateral line asymmetry in stickleback (Gasterosteus aculeatus). Evol Ecol 2021. [DOI: 10.1007/s10682-021-10117-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Flanagan SP, Rose E, Jones AG. The population genomics of repeated freshwater colonizations by Gulf pipefish. Mol Ecol 2021; 30:1672-1687. [PMID: 33580570 DOI: 10.1111/mec.15841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/30/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022]
Abstract
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome-level changes underlying local adaptation. Here, we present a genomic analysis of colonization of freshwater habitats by a primarily marine fish, the Gulf pipefish (Syngnathus scovelli). We sample pipefish from four geographically distinct freshwater locations and use double-digest restriction site associated DNA sequencing to compare them to 12 previously studied saltwater populations. The two most geographically distant and isolated freshwater populations are the most genetically distinct, although demographic analysis suggests that these populations are experiencing ongoing migration with their saltwater neighbours. Additionally, outlier regions were found genome-wide, showing parallelism across ecotype pairs. We conclude that these multiple freshwater colonizations involve similar genomic regions, despite the large geographical distances and different underlying mechanisms. These similar patterns are probably facilitated by the interacting effects of intrinsic barriers, gene flow among populations and ecological selection in the Gulf pipefish.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily Rose
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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17
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Kemppainen P, Li Z, Rastas P, Löytynoja A, Fang B, Yang J, Guo B, Shikano T, Merilä J. Genetic population structure constrains local adaptation in sticklebacks. Mol Ecol 2021; 30:1946-1961. [PMID: 33464655 DOI: 10.1111/mec.15808] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/19/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022]
Abstract
Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to 10 novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large-effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterized on empirical data, we hypothesize that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2× stronger population structuring among freshwater populations and >10× stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.
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Affiliation(s)
- Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Pasi Rastas
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jing Yang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Chinese Sturgeon Research Institute, Three Gorges Corporation, Yichang, China
| | - Baocheng Guo
- The Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takahito Shikano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, The University of Hong Kong, Pokfulam, Hong Kong, SAR
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18
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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19
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McCulloch GA, Foster BJ, Dutoit L, Harrop TWR, Guhlin J, Dearden PK, Waters JM. Genomics Reveals Widespread Ecological Speciation in Flightless Insects. Syst Biol 2020; 70:863-876. [DOI: 10.1093/sysbio/syaa094] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/04/2023] Open
Abstract
Abstract
Recent genomic analyses have highlighted parallel divergence in response to ecological gradients, but the extent to which altitude can underpin such repeated speciation remains unclear. Wing reduction and flight loss have apparently evolved repeatedly in montane insect assemblages and have been suggested as important drivers of hexapod diversification. We test this hypothesis using genomic analyses of a widespread wing-polymorphic stonefly species complex in New Zealand. We identified over 50,000 polymorphic genetic markers generated across almost 200 Zelandoperla fenestrata stonefly specimens using a newly generated plecopteran reference genome, to reveal widespread parallel speciation between sympatric full-winged and wing-reduced ecotypes. Rather than the existence of a single, widespread, flightless taxon (Zelandoperla pennulata), evolutionary genomic data reveal that wing-reduced upland lineages have speciated repeatedly and independently from full-winged Z. fenestrata. This repeated evolution of reproductive isolation between local ecotype pairs that lack mitochondrial DNA differentiation suggests that ecological speciation has evolved recently. A cluster of outlier single-nucleotide polymorphisms detected in independently wing-reduced lineages, tightly linked in an approximately 85 kb genomic region that includes the developmental “supergene” doublesex, suggests that this “island of divergence” may play a key role in rapid ecological speciation. [Ecological speciation; genome assembly; genomic island of differentiation; genotyping-by-sequencing; incipient species; plecoptera; wing reduction.]
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Affiliation(s)
- Graham A McCulloch
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Brodie J Foster
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Thomas W R Harrop
- Genomics Aotearoa and Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Joseph Guhlin
- Genomics Aotearoa and Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Jonathan M Waters
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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20
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Haines GE, Stuart YE, Hanson D, Tasneem T, Bolnick DI, Larsson HCE, Hendry AP. Adding the third dimension to studies of parallel evolution of morphology and function: An exploration based on parapatric lake-stream stickleback. Ecol Evol 2020; 10:13297-13311. [PMID: 33304538 PMCID: PMC7713967 DOI: 10.1002/ece3.6929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/04/2022] Open
Abstract
Recent methodological advances have led to a rapid expansion of evolutionary studies employing three-dimensional landmark-based geometric morphometrics (GM). GM methods generally enable researchers to capture and compare complex shape phenotypes, and to quantify their relationship to environmental gradients. However, some recent studies have shown that the common, inexpensive, and relatively rapid two-dimensional GM methods can distort important information and produce misleading results because they cannot capture variation in the depth (Z) dimension. We use micro-CT scanned threespine stickleback (Gasterosteus aculeatus Linnaeus, 1758) from six parapatric lake-stream populations on Vancouver Island, British Columbia, to test whether the loss of the depth dimension in 2D GM studies results in misleading interpretations of parallel evolution. Using joint locations described with 2D or 3D landmarks, we compare results from separate 2D and 3D shape spaces, from a combined 2D-3D shape space, and from estimates of biomechanical function. We show that, although shape is distorted enough in 2D projections to strongly influence the interpretation of morphological parallelism, estimates of biomechanical function are relatively robust to the loss of the Z dimension.
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Affiliation(s)
- Grant E. Haines
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | | | - Dieta Hanson
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | - Tania Tasneem
- Kealing Middle SchoolAustin Independent School DistrictAustinTXUSA
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
| | - Hans C. E. Larsson
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
| | - Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill UniversityMontréalQCCanada
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21
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Salisbury SJ, McCracken GR, Perry R, Keefe D, Layton KK, Kess T, Nugent CM, Leong JS, Bradbury IR, Koop BF, Ferguson MM, Ruzzante DE. Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (
Salvelinus alpinus
). Mol Ecol 2020; 29:4280-4294. [DOI: 10.1111/mec.15634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Robert Perry
- Department of Environment Fish and Wildlife Division Government of Yukon Whitehorse YT Canada
| | - Donald Keefe
- Department of Environment and Conservation Wildlife Division Government of Newfoundland and Labrador Corner Brook NL Canada
| | - Kara K.S. Layton
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Tony Kess
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
| | - Cameron M. Nugent
- Department of Integrative Biology University of Guelph Guelph ON Canada
| | - Jong S. Leong
- Department of Biology University of Victoria Victoria BC Canada
| | - Ian R. Bradbury
- Department of Biology Dalhousie University Halifax NS Canada
- Department of Fisheries and Oceans Northwest Atlantic Fisheries Centre St. John's NL Canada
- Department of Ocean Sciences Memorial University of Newfoundland St. John's NL Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria BC Canada
- Centre for Biomedical Research University of Victoria Victoria BC Canada
| | - Moira M. Ferguson
- Department of Integrative Biology University of Guelph Guelph ON Canada
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22
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Esin EV, Bocharova ES, Borisova EA, Markevich GN. Interaction among morphological, trophic and genetic groups in the rapidly radiating Salvelinus fishes from Lake Kronotskoe. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10048-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Laurentino TG, Moser D, Roesti M, Ammann M, Frey A, Ronco F, Kueng B, Berner D. Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish. Nat Commun 2020; 11:1928. [PMID: 32317640 PMCID: PMC7174299 DOI: 10.1038/s41467-020-15657-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/19/2020] [Indexed: 11/29/2022] Open
Abstract
How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dario Moser
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Matthias Ammann
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Anja Frey
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Benjamin Kueng
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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24
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Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes. Genome Biol Evol 2020; 11:2344-2359. [PMID: 31298693 PMCID: PMC6735750 DOI: 10.1093/gbe/evz148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Münster, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, USA
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25
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Ríos N, Casanova A, Hermida M, Pardo BG, Martínez P, Bouza C, García G. Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region. Genes (Basel) 2020; 11:genes11010109. [PMID: 31963477 PMCID: PMC7017130 DOI: 10.3390/genes11010109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/16/2022] Open
Abstract
Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.
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Affiliation(s)
- Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
- Correspondence: ; Tel.: +598-25258618 (ext. 140)
| | - Adrián Casanova
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Belén G. Pardo
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
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26
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Planidin N, Reimchen T. Spatial, sexual, and rapid temporal differentiation in neuromast expression on lateral plates of Haida Gwaii threespine stickleback (Gasterosteus aculeatus). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2019-0005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lateral lines, a major sensory modality in fishes, are diverse among taxa, but their intraspecific variation has received limited attention. We examined numbers of superficial neuromasts on the buttressing lateral plates (LP) of 1910 threespine stickleback (Gasterosteus aculeatus Linnaeus, 1758) from 26 ecologically and morphologically diverse populations on the Haida Gwaii archipelago, western Canada. Extending from previous studies, we predicted that (i) highly stained dystrophic localities would have threespine stickleback with elevated numbers of neuromasts per plate due to a greater reliance on non-visual sensory modalities and (ii) that LP count and neuromast numbers per plate would functionally covary with predatory assemblage. We found that there were no differences in neuromast count across major habitats (marine, lake, stream), but clear-water populations and those with predatory fish had significantly more neuromasts per plate than most populations in highly stained dystrophic lakes, the effects being accentuated on the first buttressing plate (LP4). We also report the first evidence that neuromast counts per plate are sexually dimorphic, with males having a greater density of neuromasts in most populations. Two transplant experiments between ecologically opposite habitats indicate that within 12 generations, neuromast counts per plate can rapidly shift in response to a change in habitat.
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Affiliation(s)
- N.P. Planidin
- Department of Biology, University of Victoria, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
- Department of Biology, University of Victoria, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
| | - T.E. Reimchen
- Department of Biology, University of Victoria, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
- Department of Biology, University of Victoria, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
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27
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Dermond P, Sperlich N, Brodersen J. Heritable morphological differentiation in salmonids from two distinct stream types. JOURNAL OF FISH BIOLOGY 2019; 95:1215-1222. [PMID: 31418819 DOI: 10.1111/jfb.14121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
We tested for phenotype-to-habitat associations in brown trout Salmo trutta populations from two ecologically different habitat types; i.e., groundwater and surface-water-fed streams. Additionally, we raised captive offspring from two such populations under standardised conditions to test whether potential phenotypic differentiation would be passed on to offspring. We found analogous differentiation by habitat in multiple wild populations. Some of these morphological differences were at least partially inherited by offspring. We suggest that this could have implications for both scientists and fisheries authorities studying or managing trout populations.
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Affiliation(s)
- Philip Dermond
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Nicola Sperlich
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jakob Brodersen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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28
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Blankers T, Oh KP, Shaw KL. Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets. Proc Biol Sci 2019; 286:20191479. [PMID: 31594503 PMCID: PMC6790767 DOI: 10.1098/rspb.2019.1479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and whether the likelihood of QTL sharing is related to QTL effect size. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more frequently than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
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29
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Currey MC, Bassham SL, Cresko WA. Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats. Biol J Linn Soc Lond 2019; 128:415-434. [PMID: 36846094 PMCID: PMC9957565 DOI: 10.1093/biolinnean/blz106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Species such as threespine stickleback (Gasterosteus aculeatus) that inhabit divergent selective environments and that have diversified on different time scales can be of value for understanding evolutionary processes. Here we synthesize high-resolution genotypic and phenotypic data to explore a largely unstudied distribution of threespine stickleback populations living in oceanic and freshwater habitats along coastal and inland regions of Oregon. Many inland aquatic habitats of Oregon remained unglaciated during the last ice age, meaning that some extant Oregon lake and river stickleback may have descended from freshwater populations established long before more well-studied, post-glacial freshwater populations. To address the degree of congruence between genetic and phenotypic divergence, we directly compared Oregon stickleback to much younger (post-glacial) Alaskan populations. We found phenotypic variation in Oregon stickleback to be primarily partitioned between oceanic and freshwater habitats, as has been documented in other stickleback systems. However, the main axis of genetic divergence was between coastal and inland regions regardless of habitat type. Furthermore, when comparing patterns between Oregon and Alaska we found similar levels of phenotypic divergence, but much greater genetic divergence among Oregon's populations. The Oregon stickleback system therefore appears well suited for future studies linking genotypic and phenotypic change, further extending the utility of this small fish to provide general insights into evolutionary processes.
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Affiliation(s)
- Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-1254, USA
| | - Susan L Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-1254, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-1254, USA
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30
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Rougeux C, Gagnaire P, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol 2019; 28:4388-4403. [DOI: 10.1111/mec.15226] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Clément Rougeux
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
| | | | - Kim Praebel
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland
| | - Louis Bernatchez
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
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31
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Nelson TC, Crandall JG, Ituarte CM, Catchen JM, Cresko WA. Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes. Genetics 2019; 212:1367-1382. [PMID: 31213503 PMCID: PMC6707445 DOI: 10.1534/genetics.119.302261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/11/2019] [Indexed: 11/18/2022] Open
Abstract
The outcome of selection on genetic variation depends on the geographic organization of individuals and populations as well as the organization of loci within the genome. Spatially variable selection between marine and freshwater habitats has had a significant and heterogeneous impact on patterns of genetic variation across the genome of threespine stickleback fish. When marine stickleback invade freshwater habitats, more than a quarter of the genome can respond to divergent selection, even in as little as 50 years. This process largely uses standing genetic variation that can be found ubiquitously at low frequency in marine populations, can be millions of years old, and is likely maintained by significant bidirectional gene flow. Here, we combine population genomic data of marine and freshwater stickleback from Cook Inlet, Alaska, with genetic maps of stickleback fish derived from those same populations to examine how linkage to loci under selection affects genetic variation across the stickleback genome. Divergent selection has had opposing effects on linked genetic variation on chromosomes from marine and freshwater stickleback populations: near loci under selection, marine chromosomes are depauperate of variation, while these same regions among freshwater genomes are the most genetically diverse. Forward genetic simulations recapitulate this pattern when different selective environments also differ in population structure. Lastly, dense genetic maps demonstrate that the interaction between selection and population structure may impact large stretches of the stickleback genome. These findings advance our understanding of how the structuring of populations across geography influences the outcomes of selection, and how the recombination landscape broadens the genomic reach of selection.
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Affiliation(s)
- Thomas C Nelson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | | | - Catherine M Ituarte
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Julian M Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Department of Animal Biology, University of Illinois at Urbana-Champaign, Illinois 61801
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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32
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Phair NL, Toonen RJ, Knapp I, von der Heyden S. Shared genomic outliers across two divergent population clusters of a highly threatened seagrass. PeerJ 2019; 7:e6806. [PMID: 31106053 PMCID: PMC6497040 DOI: 10.7717/peerj.6806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.
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Affiliation(s)
- Nikki Leanne Phair
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert John Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Ingrid Knapp
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Sophie von der Heyden
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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33
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Hohenlohe PA, Magalhaes IS. The Population Genomics of Parallel Adaptation: Lessons from Threespine Stickleback. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2019_67] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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34
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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35
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Liu S, Ferchaud AL, Grønkjaer P, Nygaard R, Hansen MM. Genomic parallelism and lack thereof in contrasting systems of three-spined sticklebacks. Mol Ecol 2018; 27:4725-4743. [DOI: 10.1111/mec.14782] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Shenglin Liu
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - Anne-Laure Ferchaud
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Peter Grønkjaer
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - Rasmus Nygaard
- Greenland Institute of Natural Resources; Nuuk Greenland
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36
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nat Ecol Evol 2018; 2:1128-1138. [PMID: 29942074 PMCID: PMC6519129 DOI: 10.1038/s41559-018-0581-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages adapted to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-years selection experiment, we let giant stickleback from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the adaptive genomic change between 12,000 years old ecotypes. Adaptive genomic change was as fast as phenotypic change in defence and trophic morphology and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived adaptive radiation members, allowing adaptive radiations to unfold very rapidly.
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Affiliation(s)
- David A Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada. .,Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Felicity C Jones
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK.,Department of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David M Kingsley
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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37
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Nelson TC, Cresko WA. Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations. Evol Lett 2018; 2:9-21. [PMID: 30283661 PMCID: PMC6121857 DOI: 10.1002/evl3.37] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/16/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We extend restriction site-associated DNA sequencing (RAD-seq) to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by dXY , reaches tenfold higher than background levels and genomic variation is structured into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback (Pungitius pungitius), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local adaptation in stickleback has therefore been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on ecological timescales is a result of genome evolution over geological timescales, and vice versa.
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Affiliation(s)
- Thomas C Nelson
- Institute of Ecology and Evolution University of Oregon Eugene, Oregon 97403.,Current Address: Division of Biological Sciences University of Montana Missoula, Montana 59812
| | - William A Cresko
- Institute of Ecology and Evolution University of Oregon Eugene, Oregon 97403
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38
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Andersen JC, Mills NJ. Comparative genetics of invasive populations of walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, in California. Ecol Evol 2018; 8:801-811. [PMID: 29321915 PMCID: PMC5756880 DOI: 10.1002/ece3.3667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 01/08/2023] Open
Abstract
Coevolution may be an important component of the sustainability of importation biological control, but how frequently introduced natural enemies coevolve with their target pests is unclear. Here we explore whether comparative population genetics of the invasive walnut aphid, Chromaphis juglandicola, and its introduced parasitoid, Trioxys pallidus, provide insights into the localized breakdown of biological control services in walnut orchards in California. We found that sampled populations of C. juglandicola exhibited higher estimates of genetic differentiation (FST) than co-occurring populations of T. pallidus. In contrast, estimates of both the inbreeding coefficient (GIS) and contemporary gene flow were higher for T. pallidus than for C. juglandicola. We also found evidence of reciprocal outlier loci in some locations, but none showed significant signatures of selection. Synthesis and applications. Understanding the importance of coevolutionary interactions for the sustainability of biological control remains an important and understudied component of biological control research. Given the observed differences in gene flow and genetic differentiation among populations of T. pallidus and C. juglandicola, we suspect that temporary local disruption of biological control services may occur more frequently than expected while remaining stable at broader regional scales. Further research that combines genomewide single nucleotide polymorphism genotyping with measurements of phenotypic traits is needed to provide more conclusive evidence of whether the occurrence of outlier loci that display significant signatures of selection can be interpreted as evidence of the presence of a geographic mosaic of coevolution in this system.
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Affiliation(s)
- Jeremy C. Andersen
- Department of Environmental Science Policy and ManagementUniversity of California BerkeleyBerkeleyCAUSA
| | - Nicholas J. Mills
- Department of Environmental Science Policy and ManagementUniversity of California BerkeleyBerkeleyCAUSA
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39
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Berner D, Roesti M. Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate. Mol Ecol 2017; 26:6351-6369. [PMID: 28994152 DOI: 10.1111/mec.14373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Genetic differentiation between divergent populations is often greater in chromosome centres than peripheries. Commonly overlooked, this broadscale differentiation pattern is sometimes ascribed to heterogeneity in crossover rate and hence linked selection within chromosomes, but the underlying mechanisms remain incompletely understood. A literature survey across 46 organisms reveals that most eukaryotes indeed exhibit a reduced crossover rate in chromosome centres relative to the peripheries. Using simulations of populations diverging into ecologically different habitats through sorting of standing genetic variation, we demonstrate that such chromosome-scale heterogeneity in crossover rate, combined with polygenic divergent selection, causes stronger hitchhiking and especially barriers to gene flow across chromosome centres. Without requiring selection on new mutations, this rapidly leads to elevated population differentiation in the low-crossover centres relative to the high-crossover peripheries of chromosomes ("Chromosome Centre-Biased Differentiation", CCBD). Using simulated and empirical data, we then show that strong CCBD between populations can provide evidence of polygenic adaptive divergence with a phase of gene flow. We further demonstrate that chromosome-scale heterogeneity in crossover rate impacts analyses beyond that of population differentiation, including the inference of phylogenies and parallel adaptive evolution among populations, the detection of genetic loci under selection, and the interpretation of the strength of selection on genomic regions. Overall, our results call for a greater appreciation of chromosome-scale heterogeneity in crossover rate in evolutionary genomics.
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Affiliation(s)
- Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Marius Roesti
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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40
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Divergence of insulin superfamily ligands, receptors and Igf binding proteins in marine versus freshwater stickleback: Evidence of selection in known and novel genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 25:53-61. [PMID: 29149730 DOI: 10.1016/j.cbd.2017.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/04/2017] [Accepted: 10/23/2017] [Indexed: 11/20/2022]
Abstract
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations. Next, we analysed genome-wide transcriptome data from eight tissues to assess differential gene expression. Two Igfbp's (Igfbp2a and Igfbp5a) show evidence of divergent adaptation between life-history types, and a cluster of nonsynonymous mutations in Igfbp5a exhibit high Fst in exons apparently alternatively spliced in gill. We find evidence of selection on the relaxin family ligand-receptor gene pair, Insl3-Rxfp2, known to be involved in male spermatogenesis and bone metabolism, and in the 5' regulatory region of Igf2. We also confirmed the gene and coding sequence of two unannotated relaxin family ligands. These analyses underscore the utility of candidate gene studies and indicate directions for further exploration of the function of insulin superfamily genes in FW adaptation.
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41
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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42
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Hanson D, Hu J, Hendry AP, Barrett RDH. Heritable gene expression differences between lake and stream stickleback include both parallel and antiparallel components. Heredity (Edinb) 2017; 119:339-348. [PMID: 28832577 PMCID: PMC5637370 DOI: 10.1038/hdy.2017.50] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
The repeated phenotypic patterns that characterize populations undergoing parallel evolution provide support for a deterministic role of adaptation by natural selection. Determining the level of parallelism also at the genetic level is thus central to our understanding of how natural selection works. Many studies have looked for repeated genomic patterns in natural populations, but work on gene expression is less common. The studies that have examined gene expression have found some support for parallelism, but those studies almost always used samples collected from the wild that potentially confounds the effects of plasticity with heritable differences. Here we use two independent pairs of lake and stream threespine stickleback (Gasterosteus aculeatus) raised in common garden conditions to assess both parallel and antiparallel (that is, similar versus different directions of lake–stream expression divergence in the two watersheds) heritable gene expression differences as measured by total RNA sequencing. We find that more genes than expected by chance show either parallel (22 genes, 0.18% of expressed genes) or antiparallel (24 genes, 0.20% of expressed genes) lake–stream expression differences. These results correspond well with previous genomic studies in stickleback ecotype pairs that found similar levels of parallelism. We suggest that parallelism might be similarly constrained at the genomic and transcriptomic levels.
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Affiliation(s)
- D Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - A P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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43
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Raeymaekers JAM, Chaturvedi A, Hablützel PI, Verdonck I, Hellemans B, Maes GE, De Meester L, Volckaert FAM. Adaptive and non-adaptive divergence in a common landscape. Nat Commun 2017; 8:267. [PMID: 28814718 PMCID: PMC5559485 DOI: 10.1038/s41467-017-00256-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes. The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium. .,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway. .,Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway.
| | - Anurag Chaturvedi
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Pascal I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Flanders Marine Institute, B-8400, Oostende, Belgium
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Gregory E Maes
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Genomics Core, Center for Human Genetics, UZ Leuven, B-3000, Leuven, Belgium.,Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
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44
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Oke KB, Rolshausen G, LeBlond C, Hendry AP. How Parallel Is Parallel Evolution? A Comparative Analysis in Fishes. Am Nat 2017; 190:1-16. [DOI: 10.1086/691989] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Stuart YE, Veen T, Weber JN, Hanson D, Ravinet M, Lohman BK, Thompson CJ, Tasneem T, Doggett A, Izen R, Ahmed N, Barrett RDH, Hendry AP, Peichel CL, Bolnick DI. Contrasting effects of environment and genetics generate a continuum of parallel evolution. Nat Ecol Evol 2017; 1:158. [DOI: 10.1038/s41559-017-0158] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/07/2017] [Indexed: 12/25/2022]
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46
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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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47
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Steane DA, Potts BM, McLean EH, Collins L, Holland BR, Prober SM, Stock WD, Vaillancourt RE, Byrne M. Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon. Genome Biol Evol 2017; 9:253-265. [PMID: 28391293 PMCID: PMC5381606 DOI: 10.1093/gbe/evw290] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2016] [Indexed: 01/01/2023] Open
Abstract
Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
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Affiliation(s)
- Dorothy A. Steane
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
- CSIRO Land and Water, Wembley, Western Australia, Australia
| | - Brad M. Potts
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Elizabeth H. McLean
- CSIRO Land and Water, Wembley, Western Australia, Australia
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
| | - Lesley Collins
- Faculty of Health Science, Universal College of Learning, Palmerston North, New Zealand
| | - Barbara R. Holland
- School of Physical Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | | | - William D. Stock
- Centre for Ecosystem Management, School of Natural Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - René E. Vaillancourt
- School of Biological Sciences and ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Bentley Delivery Centre, Western Australia, Australia
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48
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Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines. Genetics 2016; 205:871-890. [PMID: 28007884 DOI: 10.1534/genetics.116.187104] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022] Open
Abstract
Adaptation to environmental stress is critical for long-term species persistence. With climate change and other anthropogenic stressors compounding natural selective pressures, understanding the nature of adaptation is as important as ever in evolutionary biology. In particular, the number of alternative molecular trajectories available for an organism to reach the same adaptive phenotype remains poorly understood. Here, we investigate this issue in a set of replicated Drosophila melanogaster lines selected for increased desiccation resistance-a classical physiological trait that has been closely linked to Drosophila species distributions. We used pooled whole-genome sequencing (Pool-Seq) to compare the genetic basis of their selection responses, using a matching set of replicated control lines for characterizing laboratory (lab-)adaptation, as well as the original base population. The ratio of effective population size to census size was high over the 21 generations of the experiment at 0.52-0.88 for all selected and control lines. While selected SNPs in replicates of the same treatment (desiccation-selection or lab-adaptation) tended to change frequency in the same direction, suggesting some commonality in the selection response, candidate SNP and gene lists often differed among replicates. Three of the five desiccation-selection replicates showed significant overlap at the gene and network level. All five replicates showed enrichment for ovary-expressed genes, suggesting maternal effects on the selected trait. Divergence between pairs of replicate lines for desiccation-candidate SNPs was greater than between pairs of control lines. This difference also far exceeded the divergence between pairs of replicate lines for neutral SNPs. Overall, while there was overlap in the direction of allele frequency changes and the network and functional categories affected by desiccation selection, replicates showed unique responses at all levels, likely reflecting hitchhiking effects, and highlighting the challenges in identifying candidate genes from these types of experiments when traits are likely to be polygenic.
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49
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Berner D, Ammann M, Spencer E, Rüegg A, Lüscher D, Moser D. Sexual isolation promotes divergence between parapatric lake and stream stickleback. J Evol Biol 2016; 30:401-411. [PMID: 27862535 DOI: 10.1111/jeb.13016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 12/26/2022]
Abstract
Speciation can be initiated by adaptive divergence between populations in ecologically different habitats, but how sexually based reproductive barriers contribute to this process is less well understood. We here test for sexual isolation between ecotypes of threespine stickleback fish residing in adjacent lake and stream habitats in the Lake Constance basin, Central Europe. Mating trials exposing females to pairings of territorial lake and stream males in outdoor mesocosms allowing for natural reproductive behaviour reveal that mating occurs preferentially between partners of the same ecotype. Compared to random mating, this sexual barrier reduces gene flow between the ecotypes by some 36%. This relatively modest strength of sexual isolation is surprising because comparing the males between the two ecotypes shows striking differentiation in traits generally considered relevant to reproductive behaviour (body size, breeding coloration, nest size). Analysing size differences among the individuals in the mating trials further indicates that assortative mating is not related to ecotype differences in body size. Overall, we demonstrate that sexually based reproductive isolation promotes divergence in lake-stream stickleback along with other known reproductive barriers, but we also caution against inferring strong sexual isolation from the observation of strong population divergence in sexually relevant traits.
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Affiliation(s)
- D Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - M Ammann
- Zoological Institute, University of Basel, Basel, Switzerland
| | - E Spencer
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
| | - A Rüegg
- Zoological Institute, University of Basel, Basel, Switzerland
| | - D Lüscher
- Zoological Institute, University of Basel, Basel, Switzerland
| | - D Moser
- Zoological Institute, University of Basel, Basel, Switzerland
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50
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Weber JN, Bradburd GS, Stuart YE, Stutz WE, Bolnick DI. Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback. Evolution 2016; 71:342-356. [DOI: 10.1111/evo.13110] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/15/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Jesse N. Weber
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
- Division of Biological Sciences University of Montana Missoula Montana 59801
| | - Gideon S. Bradburd
- Department of Integrative Biology Michigan State University East Lansing Michigan 48824
| | - Yoel E. Stuart
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
| | - William E. Stutz
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder Boulder Colorado 80309
| | - Daniel I. Bolnick
- Department of Integrative Biology University of Texas at Austin Austin Texas 78712
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