1
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Neto C, Hancock A. Genetic Architecture of Flowering Time Differs Between Populations With Contrasting Demographic and Selective Histories. Mol Biol Evol 2023; 40:msad185. [PMID: 37603463 PMCID: PMC10461413 DOI: 10.1093/molbev/msad185] [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: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Understanding the evolutionary factors that impact the genetic architecture of traits is a central goal of evolutionary genetics. Here, we investigate how quantitative trait variation accumulated over time in populations that colonized a novel environment. We compare the genetic architecture of flowering time in Arabidopsis populations from the drought-prone Cape Verde Islands and their closest outgroup population from North Africa. We find that trait polygenicity is severely reduced in the island populations compared to the continental North African population. Further, trait architectures and reconstructed allelic histories best fit a model of strong directional selection in the islands in accord with a Fisher-Orr adaptive walk. Consistent with this, we find that large-effect variants that disrupt major flowering time genes (FRI and FLC) arose first, followed by smaller effect variants, including ATX2 L125F, which is associated with a 4-day reduction in flowering time. The most recently arising flowering time-associated loci are not known to be directly involved in flowering time, consistent with an omnigenic signature developing as the population approaches its trait optimum. Surprisingly, we find no effect in the natural population of EDI-Cvi-0 (CRY2 V367M), an allele for which an effect was previously validated by introgression into a Eurasian line. Instead, our results suggest the previously observed effect of the EDI-Cvi-0 allele on flowering time likely depends on genetic background, due to an epistatic interaction. Altogether, our results provide an empirical example of the effects demographic history and selection has on trait architecture.
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Affiliation(s)
- Célia Neto
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela Hancock
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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2
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DeLorenzo L, Mathews D, Brandon AA, Joglekar M, Carmona Baez A, Moore EC, Ciccotto PJ, Roberts NB, Roberts RB, Powder KE. Genetic basis of ecologically relevant body shape variation among four genera of cichlid fishes. Mol Ecol 2023; 32:3975-3988. [PMID: 37161914 PMCID: PMC10502943 DOI: 10.1111/mec.16977] [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: 10/02/2021] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Divergence in body shape is one of the most widespread and repeated patterns of morphological variation in fishes and is associated with habitat specification and swimming mechanics. Such ecological diversification is the first stage of the explosive adaptive radiation of cichlid fishes in the East African Rift Lakes. We use two hybrid crosses of cichlids (Metriaclima sp. × Aulonocara sp. and Labidochromis sp. × Labeotropheus sp., >975 animals total) to determine the genetic basis of body shape diversification that is similar to benthic-pelagic divergence across fishes. Using a series of both linear and geometric shape measurements, we identified 34 quantitative trait loci (QTL) that underlie various aspects of body shape variation. These QTL are spread throughout the genome, each explaining 3.2-8.6% of phenotypic variation, and are largely modular. Further, QTL are distinct both between these two crosses of Lake Malawi cichlids and compared to previously identified QTL for body shape in fishes such as sticklebacks. We find that body shape is controlled by many genes of small effect. In all, we find that convergent body shape phenotypes commonly observed across fish clades are most likely due to distinct genetic and molecular mechanisms.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Destiny Mathews
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - A. Allyson Brandon
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Mansi Joglekar
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Aldo Carmona Baez
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Emily C. Moore
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Patrick J. Ciccotto
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biology, Warren Wilson College, Swannanoa, NC 28778, USA
| | - Natalie B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Reade B. Roberts
- Department of Biological Sciences, and Genetics and Genomics Academy, North Carolina State University, Raleigh, NC 27695, USA
| | - Kara E. Powder
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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3
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Roesti M, Groh JS, Blain SA, Huss M, Rassias P, Bolnick DI, Stuart YE, Peichel CL, Schluter D. Species divergence under competition and shared predation. Ecol Lett 2023; 26:111-123. [PMID: 36450600 DOI: 10.1111/ele.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Species competing for resources also commonly share predators. While competition often drives divergence between species, the effects of shared predation are less understood. Theoretically, competing prey species could either diverge or evolve in the same direction under shared predation depending on the strength and symmetry of their interactions. We took an empirical approach to this question, comparing antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that all live in the presence of a trout predator. We found divergence in antipredator traits between the species: in sympatry, antipredator adaptations were relatively increased in stickleback but decreased in sculpin. Shifts in feeding morphology, diet and habitat use were also divergent but driven primarily by stickleback evolution. Our results suggest that asymmetric ecological character displacement indirectly made stickleback more and sculpin less vulnerable to shared predation, driving divergence of antipredator traits between sympatric species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey S Groh
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, USA
| | - Stephanie A Blain
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Magnus Huss
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Aquatic Resources, Swedish University of Agricultural Sciences, Öregrund, Sweden
| | - Peter Rassias
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Yoel E Stuart
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dolph Schluter
- Zoology Department and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Characterizing phenotypic diversity in marine populations of the threespine stickleback. Sci Rep 2022; 12:17923. [PMID: 36289364 PMCID: PMC9606258 DOI: 10.1038/s41598-022-22872-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/20/2022] [Indexed: 01/20/2023] Open
Abstract
The threespine stickleback (Gasterosteus aculeatus) is an important model for studying the evolution of vertebrate morphology. Sticklebacks inhabit freshwater, brackish, and marine northern hemisphere waters. Anadromous and marine populations (hereafter marine) are assumed to have remained unchanged morphologically from ancestral marine sticklebacks, despite marine environments varying on regional and local scales. Recent studies suggest that genetic and phenotypic structure exists in marine populations, yet the scale of this variation, and its ecological causes remain unclear. Our goal was to assess morphological trait variation in marine stickleback populations around Southern British Columbia (BC) and determine if oceanographic and habitat characteristics were associated with this variation. Between May-July 2019, we sampled 534 sticklebacks from 15 sites around Vancouver Island, a region characterized by a large diversity of oceanographic and habitat features. We characterized trait variation using two-dimensional (2D) geometric morphometric analysis, comparing individuals between oceanographic regions and habitats. We focused on head and body shape. We found that marine sticklebacks varied morphologically among and between regions and habitats, but the variation did not appear to be related to environmental variation. Sexual dimorphism was the largest source of variation, but oceanographic and habitat variables influenced differences between sexes. We concluded that marine sticklebacks offer abundant opportunities for expanding our knowledge of drivers of morphology.
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5
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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6
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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] [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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7
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Sprengelmeyer QD, Lack JB, Braun DT, Monette MJ, Pool JE. The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture. G3 GENES|GENOMES|GENETICS 2022; 12:6493269. [PMID: 35100377 PMCID: PMC8895999 DOI: 10.1093/g3journal/jkab454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/21/2021] [Indexed: 11/12/2022]
Abstract
Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.
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Affiliation(s)
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dylan T Braun
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J Monette
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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8
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Chhina AK, Thompson KA, Schluter D. Adaptive divergence and the evolution of hybrid trait mismatch in threespine stickleback. Evol Lett 2022; 6:34-45. [PMID: 35127136 PMCID: PMC8802241 DOI: 10.1002/evl3.264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 10/31/2021] [Indexed: 12/31/2022] Open
Abstract
Selection against mismatched traits in hybrids is the phenotypic analogue of intrinsic hybrid incompatibilities. Mismatch occurs when hybrids resemble one parent population for some phenotypic traits and the other parent population for other traits, and is caused by dominance in opposing directions or from segregation of alleles in recombinant hybrids. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to test the theoretical prediction that trait mismatch in hybrids should increase with the magnitude of phenotypic divergence between parent populations. We measured morphological traits in parents and hybrids in crosses between a marine population representing the ancestral form and twelve freshwater populations that have diverged from this ancestral state to varying degrees according to their environments. We found that trait mismatch was greater in more divergent crosses for both F1 and F2 hybrids. In the F1, the divergence–mismatch relationship was caused by traits having dominance in different directions, whereas it was caused by increasing segregating phenotypic variation in the F2. Our results imply that extrinsic hybrid incompatibilities accumulate as phenotypic divergence proceeds.
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Affiliation(s)
- Avneet K. Chhina
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
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9
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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10
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Connallon T, Hodgins KA. Allen Orr and the genetics of adaptation. Evolution 2021; 75:2624-2640. [PMID: 34606622 DOI: 10.1111/evo.14372] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023]
Abstract
Over most of the 20th century, evolutionary biologists predominantly subscribed to a strong form of "micro-mutationism," in which adaptive phenotypic divergence arises from allele frequency changes at many loci, each with a small effect on the phenotype. To be sure, there were well-known examples of large-effect alleles contributing to adaptation, yet such cases were generally regarded as atypical and unrepresentative of evolutionary change in general. In 1998, Allen Orr published a landmark theoretical paper in Evolution, which showed that both small- and large-effect mutations are likely to contribute to "adaptive walks" of a population to an optimum. Coupled with a growing set of empirical examples of large-effect alleles contributing to divergence (e.g., from QTL studies), Orr's paper provided a mathematical formalism that converted many evolutionary biologists from micro-mutationism to a more pluralistic perspective on the genetic basis of evolutionary change. We revisit the theoretical insights emerging from Orr's paper within the historical context leading up to 1998, and track the influence of this paper on the field of evolutionary biology through an examination of its citations over the last two decades and an analysis of the extensive body of theoretical and empirical research that Orr's pioneering paper inspired.
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Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Australia
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11
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Wang Y, Wang Y, Zhao Y, Kravchenko AY, Merilä J, Guo B. Phylogenomics of Northeast Asian
Pungitius
sticklebacks. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yu Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Yahui Zhao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Alexandra Yu Kravchenko
- A. V. Zhirmunsky National Scientific Center of Marine Biology Far Eastern Branch Russian Academy of Sciences Vladivostok Russia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
- Research Division for Ecology and Biodiversity, School of Biological Sciences Faculty of Science The University of Hong Kong Hong Kong SAR China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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12
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Roberts Kingman GA, Lee D, Jones FC, Desmet D, Bell MA, Kingsley DM. Longer or shorter spines: Reciprocal trait evolution in stickleback via triallelic regulatory changes in Stanniocalcin2a. Proc Natl Acad Sci U S A 2021; 118:e2100694118. [PMID: 34321354 PMCID: PMC8346906 DOI: 10.1073/pnas.2100694118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different freshwater environments. Here we identify a regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (major spine enhancer). Maser maps in a closely linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. The distinct freshwater alleles either increase or decrease expression of the bone growth inhibitor gene Stanniocalcin2a in developing spines, providing a simple genetic mechanism for either increasing or decreasing spine lengths in natural populations. Genomic surveys suggest many recurrently differentiated loci in sticklebacks are similarly specialized into three or more distinct alleles, providing multiple ancient standing variants in particular genes that may contribute to a range of phenotypes in different environments.
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Affiliation(s)
| | - David Lee
- Stanford University School of Humanities and Sciences, Stanford University, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Danielle Desmet
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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13
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Schluter D, Marchinko KB, Arnegard ME, Zhang H, Brady SD, Jones FC, Bell MA, Kingsley DM. Fitness maps to a large-effect locus in introduced stickleback populations. Proc Natl Acad Sci U S A 2021; 118:e1914889118. [PMID: 33414274 PMCID: PMC7826376 DOI: 10.1073/pnas.1914889118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
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Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Kerry B Marchinko
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Matthew E Arnegard
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Haili Zhang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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14
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Kong S, Zhou Z, Zhou T, Zhao J, Chen L, Lin H, Pu F, Ke Q, Bai H, Xu P. Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:631-643. [PMID: 32666363 DOI: 10.1007/s10126-020-09983-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection.
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Affiliation(s)
- Shengnan Kong
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lin Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huanling Lin
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
| | - Qiaozhen Ke
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Huaqiang Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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15
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Stanford BC, Clake DJ, Morris MR, Rogers SM. The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. Evol Appl 2020; 13:1166-1182. [PMID: 32684953 PMCID: PMC7359838 DOI: 10.1111/eva.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid environmental changes impact the global distribution and abundance of species, highlighting the urgency to understand and predict how populations will respond. The analysis of differentially expressed genes has elucidated areas of the genome involved in adaptive divergence to past and present environmental change. Such studies however have been hampered by large numbers of differentially expressed genes and limited knowledge of how these genes work in conjunction with each other. Recent methods (broadly termed "pathway analyses") have emerged that aim to group genes that behave in a coordinated fashion to a factor of interest. These methods aid in functional annotation and uncovering biological pathways, thereby collapsing complex datasets into more manageable units, providing more nuanced understandings of both the organism-level effects of modified gene expression, and the targets of adaptive divergence. Here, we reanalyze a dataset that investigated temperature-induced changes in gene expression in marine-adapted and freshwater-adapted threespine stickleback (Gasterosteus aculeatus), using Weighted Gene Co-expression Network Analysis (WGCNA) with PANTHER Gene Ontology (GO)-Slim overrepresentation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Six modules exhibited a conserved response and six a divergent response between marine and freshwater stickleback when acclimated to 7°C or 22°C. One divergent module showed freshwater-specific response to temperature, and the remaining divergent modules showed differences in height of reaction norms. PPARAa, a transcription factor that regulates fatty acid metabolism and has been implicated in adaptive divergence, was located in a module that had higher expression at 7°C and in freshwater stickleback. This updated methodology revealed patterns that were not found in the original publication. Although such methods hold promise toward predicting population response to environmental stressors, many limitations remain, particularly with regard to module expression representation, database resources, and cross-database integration.
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Affiliation(s)
| | - Danielle J. Clake
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
| | | | - Sean M. Rogers
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
- Bamfield Marine Sciences CentreBamfieldBCCanada
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16
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Miller SE, Roesti M, Schluter D. A Single Interacting Species Leads to Widespread Parallel Evolution of the Stickleback Genome. Curr Biol 2019; 29:530-537.e6. [PMID: 30686736 DOI: 10.1016/j.cub.2018.12.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 11/07/2018] [Accepted: 12/24/2018] [Indexed: 11/26/2022]
Abstract
Biotic interactions are potent, widespread causes of natural selection and divergent phenotypic evolution and can lead to genetic differentiation with gene flow among wild populations ("isolation by ecology") [1-4]. Biotic selection has been predicted to act on more genes than abiotic selection thereby driving greater adaptation [5]. However, difficulties in isolating the genome-wide effect of single biotic agents of selection have limited our ability to identify and quantify the number and type of genetic regions responding to biotic selection [6-9]. We identified geographically interspersed lakes in which threespine stickleback fish (Gasterosteus aculeatus) have repeatedly adapted to the presence or absence of a single member of the ecological community, prickly sculpin (Cottus asper), a fish that is both a competitor and a predator of the stickleback [10]. Whole-genome sequencing revealed that sculpin presence or absence accounted for the majority of genetic divergence among stickleback populations, more so than geography. The major axis of genomic variation within and between the two lake types was correlated with multiple traits, indicating parallel natural selection across a gradient of biotic environments. A large proportion of the genome-about 1.8%, encompassing more than 600 genes-differentiated stickleback from the two biotic environments. Divergence occurred in 141 discrete genomic clumps located mainly in regions of low recombination, suggesting that genes brought to lakes by the colonizing ancestral population often evolved together in linked blocks. Strong selection and a wealth of standing genetic variation explain how a single member of the biotic community can have such a rapid and profound evolutionary impact.
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Affiliation(s)
- Sara E Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA; Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Marius Roesti
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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17
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Complexity Theory: An Overview with Potential Applications for the Social Sciences. SYSTEMS 2019. [DOI: 10.3390/systems7010004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Systems theory has been challenged in the recent literature due to its perceived disconnection from today’s research and practice demands. Moving away from the reductionist frameworks and the complicated domain predominated by known unknowns and order, a call is being made to the social sciences to begin adopting complexity theory and newer connectionist methods that better address complexity and open social systems. Scholars and scholar-practitioners will continue to find the need to apply complexity theory as wicked problems become more prevalent in the social sciences. This paper differentiates between general systems theory (GST) and complexity theory, as well as identifies advantages for the social sciences in incorporating complexity theory as a formal theory. Complexity theory is expanded upon and identified as providing a new perspective and a new method of theorizing that can be practiced by disciplines within the social sciences. These additions could better position the social sciences to address the complexity associated with advancing technology, globalization, intricate markets, cultural change, and the myriad of challenges and opportunities to come.
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18
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Wucherpfennig JI, Miller CT, Kingsley DM. Efficient CRISPR-Cas9 editing of major evolutionary loci in sticklebacks. EVOLUTIONARY ECOLOGY RESEARCH 2019; 20:107-132. [PMID: 34899072 PMCID: PMC8664273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Stickleback fish are widely used to study the genetic and ecological basis of phenotypic evolution. Although several major loci have now been identified that contribute to evolutionary differences between wild populations, further study of the phenotypes associated with particular genes and mutations has been limited by the difficulty of generating targeted mutations at precise locations in the stickleback genome. APPROACH AND AIMS We compared different methods of expressing single-guide RNAs (sgRNAs) and Cas9 activity in fertilized stickleback eggs. We used an easily scored pigmentation gene (SLC24A5) to screen for molecular lesions, phenotypic effects, and possible germline transmission of newly induced alleles. We then used the optimized CRISPR methods to target two major evolutionary loci in sticklebacks, KITLG and EDA. We hypothesized that coding region mutations in the KITLG gene would alter body pigmentation and possibly sex determination, and that mutations in the EDA gene would disrupt the formation of most armor plates, fin rays, spines, teeth, and gill rakers. RESULTS Targeted deletions were successfully induced at each target locus by co-injecting one-cell stage stickleback embryos with either Cas9 mRNA or Cas9 protein, together with sgRNAs designed to protein-coding exons. Founder animals were typically mosaic for multiple mutations, which they transmitted through the germline at overall rates of 21 to 100%. We found that the copy of KITLG on the X chromosome (KITLGX) has diverged from the KITLG on the Y chromosome (KITLGY). Predicted loss-of-function mutations in the KITLGX gene dramatically altered pigmentation in both external skin and internal organ, but the same was not true for KITLGY mutations. Predicted loss-of-function mutations in either the KITLGX or KITLGY genes did not lead to sex reversal or prevent fertility. Homozygous loss-of-function mutations in the EDA gene led to complete loss of armor plates, severe reduction or loss of most soft rays in the dorsal, anal, and caudal fins, and severe reductions in tooth and gill raker number. In contrast, long dorsal and pelvic spines remained intact in EDA mutant animals, suggesting that common co-segregation of plate loss and spine reduction in wild populations is unlikely to be due to pleiotropic effects of EDA mutations. CONCLUSION CRISPR-Cas9 approaches can be used to induce germline mutations in key evolutionary loci in sticklebacks. Targeted coding region mutations confirm an important role for KITLG and EDA in skin pigmentation and armor plate reduction, respectively. They also provide new information about the functions of these genes in other body structures.
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Affiliation(s)
- Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, California 94720, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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19
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Hume JB, Recknagel H, Bean CW, Adams CE, Mable BK. RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry. Mol Ecol 2018; 27:4572-4590. [PMID: 30252984 DOI: 10.1111/mec.14881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023]
Abstract
Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater-resident nonparasitic lampreys from anadromous-parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction-associated DNA sequencing), we found that a freshwater-parasitic ecotype was highly distinct from an anadromous-parasitic form (Qlake-P = 96.8%, Fst = 0.154), but that a freshwater-nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous-parasitic ecotype (Qanad-P = 37.7%), there is no evidence of introgression into the freshwater-parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater-parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post-glacial regions, followed by periods of extensive gene flow among such diverging populations.
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Affiliation(s)
- John B Hume
- Department of Fisheries and Wildlife, College of Agriculture & Natural Resources, Michigan State University, East Lansing, Michigan.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Hans Recknagel
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Natural Heritage, Clydebank, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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20
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Abstract
The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.
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21
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Morris MRJ, Bowles E, Allen BE, Jamniczky HA, Rogers SM. Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback. BMC Evol Biol 2018; 18:113. [PMID: 30021523 PMCID: PMC6052716 DOI: 10.1186/s12862-018-1228-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/03/2018] [Indexed: 11/25/2022] Open
Abstract
Background Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence – particularly if some individuals persist in the ancestral habitat. Such “contemporary ancestors” can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these “contemporary ancestors” can complicate inferences about the source (standing genetic variation, de novo mutation) and pace of adaptive divergence. Marine threespine stickleback (Gasterosteus aculeatus) have colonized freshwater environments along the Pacific coast of North America, but have also persisted in the marine environment. To what extent are marine stickleback good proxies of the ancestral condition? Results We sequenced > 5800 variant loci in over 250 marine stickleback from eight locations extending from Alaska to California, and phenotyped them for platedness and body shape. Pairwise FST varied from 0.02 to 0.18. Stickleback were divided into five genetic clusters, with a single cluster comprising stickleback from Washington to Alaska. Plate number, Eda, body shape, and candidate loci showed evidence of being under selection in the marine environment. Comparisons to a freshwater population demonstrated that candidate loci for freshwater adaptation varied depending on the choice of marine populations. Conclusions Marine stickleback are structured into phenotypically and genetically distinct populations that have been evolving as freshwater stickleback evolved. This variation complicates their usefulness as proxies of the ancestors of freshwater populations. Lessons from stickleback may be applied to other “contemporary ancestor”-derived population studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1228-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew R J Morris
- Department of Biology, Ambrose University, 150 Ambrose Circle SW, Calgary, AB, T3H 0L5, Canada.
| | - Ella Bowles
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Brandon E Allen
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Heather A Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4Z6, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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22
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Nosil P, Villoutreix R, de Carvalho CF, Farkas TE, Soria-Carrasco V, Feder JL, Crespi BJ, Gompert Z. Natural selection and the predictability of evolution in Timema stick insects. Science 2018; 359:765-770. [PMID: 29449486 DOI: 10.1126/science.aap9125] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 12/21/2017] [Indexed: 01/03/2023]
Abstract
Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time (r2 = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection (r2 = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process.
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Affiliation(s)
- Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Romain Villoutreix
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | | | - Timothy E Farkas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06369, USA
| | - Víctor Soria-Carrasco
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Bernard J Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA.
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23
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Higham TE, Rogers SM, Langerhans RB, Jamniczky HA, Lauder GV, Stewart WJ, Martin CH, Reznick DN. Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation. Proc Biol Sci 2017; 283:rspb.2016.1294. [PMID: 27629033 DOI: 10.1098/rspb.2016.1294] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/24/2016] [Indexed: 11/12/2022] Open
Abstract
Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator-prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.
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Affiliation(s)
- Timothy E Higham
- Department of Biology, University of California, Riverside, CA, USA
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - R Brian Langerhans
- Department of Biological Sciences and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | | | - David N Reznick
- Department of Biology, University of California, Riverside, CA, USA
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24
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Peichel CL, Marques DA. The genetic and molecular architecture of phenotypic diversity in sticklebacks. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0486. [PMID: 27994127 DOI: 10.1098/rstb.2015.0486] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 11/12/2022] Open
Abstract
A major goal of evolutionary biology is to identify the genotypes and phenotypes that underlie adaptation to divergent environments. Stickleback fish, including the threespine stickleback (Gasterosteus aculeatus) and the ninespine stickleback (Pungitius pungitius), have been at the forefront of research to uncover the genetic and molecular architecture that underlies phenotypic diversity and adaptation. A wealth of quantitative trait locus (QTL) mapping studies in sticklebacks have provided insight into long-standing questions about the distribution of effect sizes during adaptation as well as the role of genetic linkage in facilitating adaptation. These QTL mapping studies have also provided a basis for the identification of the genes that underlie phenotypic diversity. These data have revealed that mutations in regulatory elements play an important role in the evolution of phenotypic diversity in sticklebacks. Genetic and molecular studies in sticklebacks have also led to new insights on the genetic basis of repeated evolution and suggest that the same loci are involved about half of the time when the same phenotypes evolve independently. When the same locus is involved, selection on standing variation and repeated mutation of the same genes have both contributed to the evolution of similar phenotypes in independent populations.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Catherine L Peichel
- Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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25
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Higham TE, Jamniczky HA, Jagnandan K, Smith SJ, Barry TN, Rogers SM. Comparative dynamics of suction feeding in marine and freshwater three-spined stickleback, Gasterosteus aculeatus: kinematics and geometric morphometrics. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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26
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Miller SE, Barrueto M, Schluter D. A comparative analysis of experimental selection on the stickleback pelvis. J Evol Biol 2017; 30:1165-1176. [DOI: 10.1111/jeb.13085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/27/2017] [Accepted: 03/30/2017] [Indexed: 11/28/2022]
Affiliation(s)
- S. E. Miller
- Department of Zoology; University of British Columbia; Vancouver BC Canada
- Department of Neurobiology and Behavior; Cornell University; Ithaca NY USA
| | - M. Barrueto
- Department of Zoology; University of British Columbia; Vancouver BC Canada
| | - D. Schluter
- Department of Zoology; University of British Columbia; Vancouver BC Canada
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27
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McGirr JA, Martin CH. Novel Candidate Genes Underlying Extreme Trophic Specialization in Caribbean Pupfishes. Mol Biol Evol 2017; 34:873-888. [PMID: 28028132 PMCID: PMC5850223 DOI: 10.1093/molbev/msw286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic changes responsible for evolutionary transitions from generalist to specialist phenotypes are poorly understood. Here we examine the genetic basis of craniofacial traits enabling novel trophic specialization in a sympatric radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist species and two novel specialists: a small-jawed "snail-eater" and a large-jawed "scale-eater." We genotyped 12 million single nucleotide polymorphisms (SNPs) by whole-genome resequencing of 37 individuals of all three species from nine populations and integrated genome-wide divergence scans with association mapping to identify divergent regions containing putatively causal SNPs affecting jaw size-the most rapidly diversifying trait in this radiation. A mere 22 fixed variants accompanied extreme ecological divergence between generalist and scale-eater species. We identified 31 regions (20 kb) containing variants fixed between specialists that were significantly associated with variation in jaw size which contained 11 genes annotated for skeletal system effects and 18 novel candidate genes never previously associated with craniofacial phenotypes. Six of these 31 regions showed robust signs of hard selective sweeps after accounting for demographic history. Our data are consistent with predictions based on quantitative genetic models of adaptation, suggesting that the effect sizes of regions influencing jaw phenotypes are positively correlated with distance between fitness peaks on a complex adaptive landscape.
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Affiliation(s)
- Joseph A. McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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28
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Henning F, Machado-Schiaffino G, Baumgarten L, Meyer A. Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes. Evolution 2017; 71:1297-1312. [PMID: 28211577 DOI: 10.1111/evo.13206] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/04/2017] [Indexed: 12/14/2022]
Abstract
Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and Pundamilia nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive-effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick-lipped ecomorph is the result of selection on numerous loci distributed throughout the genome.
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Affiliation(s)
- Frederico Henning
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.,Department of Genetics, CCS, Federal University of Rio de Janeiro, Ilha do Fundão, 21941-599, Rio de Janeiro, Brazil
| | | | - Lukas Baumgarten
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
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29
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Rogers SM, Xu S, Schlüter PM. Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation. Mol Ecol 2017; 26:1-6. [DOI: 10.1111/mec.13947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/30/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Sean M. Rogers
- Department of Biological Sciences; University of Calgary; Calgary Alberta Canada T3L 2R9
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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30
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Regulatory Architecture of Gene Expression Variation in the Threespine Stickleback Gasterosteus aculeatus. G3-GENES GENOMES GENETICS 2017; 7:165-178. [PMID: 27836907 PMCID: PMC5217106 DOI: 10.1534/g3.116.033241] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Much adaptive evolutionary change is underlain by mutational variation in regions of the genome that regulate gene expression rather than in the coding regions of the genes themselves. An understanding of the role of gene expression variation in facilitating local adaptation will be aided by an understanding of underlying regulatory networks. Here, we characterize the genetic architecture of gene expression variation in the threespine stickleback (Gasterosteus aculeatus), an important model in the study of adaptive evolution. We collected transcriptomic and genomic data from 60 half-sib families using an expression microarray and genotyping-by-sequencing, and located expression quantitative trait loci (eQTL) underlying the variation in gene expression in liver tissue using an interval mapping approach. We identified eQTL for several thousand expression traits. Expression was influenced by polymorphism in both cis- and trans-regulatory regions. Trans-eQTL clustered into hotspots. We did not identify master transcriptional regulators in hotspot locations: rather, the presence of hotspots may be driven by complex interactions between multiple transcription factors. One observed hotspot colocated with a QTL recently found to underlie salinity tolerance in the threespine stickleback. However, most other observed hotspots did not colocate with regions of the genome known to be involved in adaptive divergence between marine and freshwater habitats.
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31
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Martin CH, Erickson PA, Miller CT. The genetic architecture of novel trophic specialists: larger effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation. Mol Ecol 2016; 26:624-638. [PMID: 27873369 DOI: 10.1111/mec.13935] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 12/14/2022]
Abstract
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here, we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas, containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion. These specialized niches and trophic traits are unique among over 2000 related species. Measurements of the fitness landscape on San Salvador demonstrate multiple fitness peaks and a larger fitness valley isolating the scale-eater from the putative ancestral intermediate phenotype of the generalist, suggesting that more large-effect QTL should contribute to its unique phenotype. We evaluated this prediction using an F2 intercross between these specialists. We present the first linkage map for pupfishes and detect significant QTL for sex and eight skeletal traits. Large-effect QTL contributed more to enlarged scale-eater jaws than the molluscivore nasal protrusion, consistent with predictions from the adaptive landscape. The microevolutionary genetic architecture of large-effect QTL for oral jaws parallels the exceptional diversification rates of oral jaws within the San Salvador radiation observed over macroevolutionary timescales and may have facilitated exceptional trophic novelty in this system.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, Campus Box 3280, 120 South Rd, Chapel Hill, NC 27599-3280, USA
| | - Priscilla A Erickson
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA.,Department of Biology, University of Virginia, 229 Gilmer Hall, 485 McCormick Road, P.O. Box 400328, Charlottesville, VA 22904, USA
| | - Craig T Miller
- Molecular and Cell Biology Department, University of California, Berkeley, CA 94720, USA
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32
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Marques DA, Lucek K, Haesler MP, Feller AF, Meier JI, Wagner CE, Excoffier L, Seehausen O. Genomic landscape of early ecological speciation initiated by selection on nuptial colour. Mol Ecol 2016; 26:7-24. [DOI: 10.1111/mec.13774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/30/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Affiliation(s)
- David Alexander Marques
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Kay Lucek
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
- University of Sheffield; Sheffield UK
| | - Marcel Philipp Haesler
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Anna Fiona Feller
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Joana Isabel Meier
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
| | - Catherine E. Wagner
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
- Department of Botany, Biodiversity Institute; University of Wyoming; Laramie WY USA
| | - Laurent Excoffier
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Swiss Institute of Bioinformatics; Lausanne Switzerland
| | - Ole Seehausen
- Institute of Ecology & Evolution; University of Bern; Bern Switzerland
- Eawag: Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum Switzerland
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33
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Pistore A, Barry T, Bowles E, Sharma R, Vanderzwan S, Rogers S, Jamniczky H. Characterizing phenotypic divergence using three-dimensional geometric morphometrics in four populations of threespine stickleback (Gasterosteus aculeatus; Pisces: Gasterosteidae) in Katmai National Park and Preserve, Alaska. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The threespine stickleback (Gasterosteus aculeatus L., 1758) is a vertebrate model for the study of the relationship between phenotype and environment in facilitating rapid evolutionary change. Using four populations from a system of lakes in Katmai National Park and Preserve, Alaska, and microcomputed tomography and three-dimensional geometric morphometrics, we test the hypothesis that stickleback populations inhabiting freshwater environments display cranial phenotypes that are intermediate between the putative ancestral form and the low-plated freshwater populations that demonstrate substantial divergence toward new phenotypic optima. We further test the hypothesis that phenotypic covariance structure is disrupted in the context of such putatively recent adaptive events. We report significant phenotypic differences among all four populations that includes a component of sexual dimorphism. Furthermore, we show evidence of disrupted phenotypic covariance structure among these populations. Taken together, these findings indicate the importance of phenotypic quantification as a key step in elucidating both the ecological processes responsible for rapid adaptive radiations and the role of developmental mechanisms in biasing evolutionary change.
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Affiliation(s)
- A.E. Pistore
- McCaig Institute for Bone and Joint Health, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive Northwest, Calgary, AB T2N 4Z6, Canada
| | - T.N. Barry
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - E. Bowles
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - R. Sharma
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - S.L. Vanderzwan
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - S.M. Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Drive Northwest, Calgary, AB T2N 1N4, Canada
| | - H.A. Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive Northwest, Calgary, AB T2N 4Z6, Canada
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34
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Di Poi C, Bélanger D, Amyot M, Rogers S, Aubin-Horth N. Receptors rather than signals change in expression in four physiological regulatory networks during evolutionary divergence in threespine stickleback. Mol Ecol 2016; 25:3416-27. [DOI: 10.1111/mec.13690] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/13/2016] [Accepted: 05/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Carole Di Poi
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Quebec Canada, G1V 0A6
| | - Dominic Bélanger
- Département de Sciences Biologiques; Université de Montréal; Montréal Quebec Canada H3C 3J7
| | - Marc Amyot
- Département de Sciences Biologiques; Université de Montréal; Montréal Quebec Canada H3C 3J7
| | - Sean Rogers
- Department of Biological Sciences; University of Calgary; Calgary Alberta Canada T2N 1N4
| | - Nadia Aubin-Horth
- Département de Biologie & Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec Quebec Canada, G1V 0A6
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35
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Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
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36
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Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW. Factors influencing the effect size distribution of adaptive substitutions. Proc Biol Sci 2016; 283:20153065. [PMID: 27053750 PMCID: PMC4843649 DOI: 10.1098/rspb.2015.3065] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/15/2016] [Indexed: 12/17/2022] Open
Abstract
The distribution of effect sizes of adaptive substitutions has been central to evolutionary biology since the modern synthesis. Early theory proposed that because large-effect mutations have negative pleiotropic consequences, only small-effect mutations contribute to adaptation. More recent theory suggested instead that large-effect mutations could be favoured when populations are far from their adaptive peak. Here we suggest that the distributions of effect sizes are expected to differ among study systems, reflecting the wide variation in evolutionary forces and ecological conditions experienced in nature. These include selection, mutation, genetic drift, gene flow, and other factors such as the degree of pleiotropy, the distance to the phenotypic optimum, whether the optimum is stable or moving, and whether new mutation or standing genetic variation provides the source of adaptive alleles. Our goal is to review how these factors might affect the distribution of effect sizes and to identify new research directions. Until more theory and empirical work is available, we feel that it is premature to make broad generalizations about the effect size distribution of adaptive substitutions important in nature.
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Affiliation(s)
- Emily L Dittmar
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Christopher G Oakley
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey K Conner
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Douglas W Schemske
- Department of Plant Biology and W. K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
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37
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Marques DA, Lucek K, Meier JI, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback. PLoS Genet 2016; 12:e1005887. [PMID: 26925837 PMCID: PMC4771382 DOI: 10.1371/journal.pgen.1005887] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/29/2016] [Indexed: 01/18/2023] Open
Abstract
Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes have focused on advanced stages of the speciation process after thousands of generations of divergence. As a consequence, we still do not know what genomic signatures of the early onset of ecological speciation look like. Here, we examined genomic differentiation among migratory lake and resident stream ecotypes of threespine stickleback reproducing in sympatry in one stream, and in parapatry in another stream. Importantly, these ecotypes started diverging less than 150 years ago. We obtained 34,756 SNPs with restriction-site associated DNA sequencing and identified genomic islands of differentiation using a Hidden Markov Model approach. Consistent with incipient ecological speciation, we found significant genomic differentiation between ecotypes both in sympatry and parapatry. Of 19 islands of differentiation resisting gene flow in sympatry, all were also differentiated in parapatry and were thus likely driven by divergent selection among habitats. These islands clustered in quantitative trait loci controlling divergent traits among the ecotypes, many of them concentrated in one region with low to intermediate recombination. Our findings suggest that adaptive genomic differentiation at many genetic loci can arise and persist in sympatry at the very early stage of ecotype divergence, and that the genomic architecture of adaptation may facilitate this.
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Affiliation(s)
- David A. Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- * E-mail:
| | - Kay Lucek
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Animal and Plant Science, University of Sheffield, Sheffield, United Kingdom
| | - Joana I. Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Biodiversity Institute, University of Wyoming, Wyoming, United States of America
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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38
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Miller SE, Metcalf D, Schluter D. Intraguild predation leads to genetically based character shifts in the threespine stickleback. Evolution 2015; 69:3194-203. [PMID: 26527484 DOI: 10.1111/evo.12811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/22/2015] [Accepted: 10/24/2015] [Indexed: 11/30/2022]
Abstract
Intraguild predation is a common ecological interaction that occurs when a species preys upon another species with which it competes. The interaction is potentially a mechanism of divergence between intraguild prey (IG-prey) populations, but it is unknown if cases of character shifts in IG-prey are an environmental or evolutionary response. We investigated the genetic basis and inducibility of character shifts in threespine stickleback from lakes with and without prickly sculpin, a benthic intraguild predator (IG-predator). Wild populations of stickleback sympatric with sculpin repeatedly show greater defensive armor and water column height preference. We laboratory-raised stickleback from lakes with and without sculpin, as well as marine stickleback, and found that differences between populations in armor, body shape, and behavior persisted in a common garden. Within the common garden, we raised stickleback half-families from multiple populations in the presence and absence of sculpin. Although the presence of sculpin induced trait changes in the marine stickleback, we did not observe an induced response in the freshwater stickleback. Behavioral and morphological trait differences between freshwater populations thus have a genetic basis and suggest an evolutionary response to intraguild predation.
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Affiliation(s)
- Sara E Miller
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Daniel Metcalf
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dolph Schluter
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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39
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Abstract
The fundamental features of growth may be universal, because growth trajectories of most animals are very similar, but a unified mechanistic theory of growth remains elusive. Still needed is a synthetic explanation for how and why growth rates vary as body size changes, both within individuals over their ontogeny and between populations and species over their evolution. Here, we use Bertalanffy growth equations to characterize growth of ray-finned fishes in terms of two parameters, the growth rate coefficient, K, and final body mass, m∞. We derive two alternative empirically testable hypotheses and test them by analyzing data from FishBase. Across 576 species, which vary in size at maturity by almost nine orders of magnitude, K scaled as [Formula: see text]. This supports our first hypothesis that growth rate scales as [Formula: see text] as predicted by metabolic scaling theory; it implies that species that grow to larger mature sizes grow faster as juveniles. Within fish species, however, K scaled as [Formula: see text]. This supports our second hypothesis, which predicts that growth rate scales as [Formula: see text] when all juveniles grow at the same rate. The unexpected disparity between across- and within-species scaling challenges existing theoretical interpretations. We suggest that the similar ontogenetic programs of closely related populations constrain growth to [Formula: see text] scaling, but as species diverge over evolutionary time they evolve the near-optimal [Formula: see text] scaling predicted by metabolic scaling theory. Our findings have important practical implications because fish supply essential protein in human diets, and sustainable yields from wild harvests and aquaculture depend on growth rates.
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40
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Oke KB, Bukhari M, Kaeuffer R, Rolshausen G, Räsänen K, Bolnick DI, Peichel CL, Hendry AP. Does plasticity enhance or dampen phenotypic parallelism? A test with three lake–stream stickleback pairs. J Evol Biol 2015; 29:126-43. [DOI: 10.1111/jeb.12767] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 12/19/2022]
Affiliation(s)
- K. B. Oke
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - M. Bukhari
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - R. Kaeuffer
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - G. Rolshausen
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
| | - K. Räsänen
- Department of Aquatic Ecology Eawag and Institute of Integrative Biology ETH‐Zurich Duebendorf Switzerland
| | - D. I. Bolnick
- Department of Integrative Biology University of Texas at Austin Austin TX USA
| | - C. L. Peichel
- Divisions of Basic Sciences and Human Biology Fred Hutchinson Cancer Research Center Seattle WA USA
| | - A. P. Hendry
- Redpath Museum and Department of Biology McGill University Montreal QC Canada
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41
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Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes. Mol Ecol 2015; 24:4159-74. [PMID: 26179373 DOI: 10.1111/mec.13309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 01/19/2023]
Abstract
Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat-related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat-related divergence in the body shape of Gnathopogon fishes, a novel example of lake-stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream-dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2 interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction-site associated DNA sequencing-derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape-related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape-related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.
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Affiliation(s)
- Ryo Kakioka
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Hiroki Kumada
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Katsutoshi Watanabe
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, 509-3 Hirano 2-chome, Otsu, 520-2113, Japan
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Alexandre H, Vrignaud J, Mangin B, Joly S. Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae). PeerJ 2015; 3:e1028. [PMID: 26157613 PMCID: PMC4476130 DOI: 10.7717/peerj.1028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/26/2015] [Indexed: 12/16/2022] Open
Abstract
Adaptation to pollinators is a key factor of diversification in angiosperms. The Caribbean sister genera Rhytidophyllum and Gesneria present an important diversification of floral characters. Most of their species can be divided in two major pollination syndromes. Large-open flowers with pale colours and great amount of nectar represent the generalist syndrome, while the hummingbird-specialist syndrome corresponds to red tubular flowers with a less important nectar volume. Repeated convergent evolution toward the generalist syndrome in this group suggests that such transitions rely on few genes of moderate to large effect. To test this hypothesis, we built a linkage map and performed a QTL detection for divergent pollination syndrome traits by crossing one specimen of the generalist species Rhytidophyllum auriculatum with one specimen of the hummingbird pollinated R. rupincola. Using geometric morphometrics and univariate traits measurements, we found that floral shape among the second-generation hybrids is correlated with morphological variation observed between generalist and hummingbird-specialist species at the genus level. The QTL analysis showed that colour and nectar volume variation between syndromes involve each one major QTL while floral shape has a more complex genetic basis and rely on few genes of moderate effect. Finally, we did not detect any genetic linkage between the QTLs underlying those traits. This genetic independence of traits could have facilitated evolution toward optimal syndromes.
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Affiliation(s)
- Hermine Alexandre
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada
| | - Justine Vrignaud
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada
| | - Brigitte Mangin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM) UMR , Castanet-Tolosan , France ; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM) UMR , Castanet-Tolosan , France
| | - Simon Joly
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada ; Montreal Botanical Garden , Montreal, QC , Canada
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RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish (Coregonus clupeaformis) Species Pairs. G3-GENES GENOMES GENETICS 2015; 5:1481-91. [PMID: 26002924 PMCID: PMC4502382 DOI: 10.1534/g3.115.019067] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site−associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.
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Jamniczky HA, Barry TN, Rogers SM. Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus). Integr Comp Biol 2015; 55:166-78. [DOI: 10.1093/icb/icv018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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Three-Dimensional Morphometrics for Quantitative Trait Locus Analysis: Tackling Complex Questions with Complex Phenotypes. Evol Biol 2015. [DOI: 10.1007/s11692-015-9318-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0706-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Ravinet M, Takeuchi N, Kume M, Mori S, Kitano J. Comparative analysis of Japanese three-spined stickleback clades reveals the Pacific Ocean lineage has adapted to freshwater environments while the Japan Sea has not. PLoS One 2014; 9:e112404. [PMID: 25460163 PMCID: PMC4251985 DOI: 10.1371/journal.pone.0112404] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/06/2014] [Indexed: 12/02/2022] Open
Abstract
Divergent selection and adaptive divergence can increase phenotypic diversification amongst populations and lineages. Yet adaptive divergence between different environments, habitats or niches does not occur in all lineages. For example, the colonization of freshwater environments by ancestral marine species has triggered adaptive radiation and phenotypic diversification in some taxa but not in others. Studying closely related lineages differing in their ability to diversify is an excellent means of understanding the factors promoting and constraining adaptive evolution. A well-known example of the evolution of increased phenotypic diversification following freshwater colonization is the three-spined stickleback. Two closely related stickleback lineages, the Pacific Ocean and the Japan Sea occur in Japan. However, Japanese freshwater stickleback populations are derived from the Pacific Ocean lineage only, suggesting the Japan Sea lineage is unable to colonize freshwater. Using stable isotope data and trophic morphology, we first show higher rates of phenotypic and ecological diversification between marine and freshwater populations within the Pacific Ocean lineage, confirming adaptive divergence has occurred between the two lineages and within the Pacific Ocean lineage but not in the Japan Sea lineage. We further identified consistent divergence in diet and foraging behaviour between marine forms from each lineage, confirming Pacific Ocean marine sticklebacks, from which all Japanese freshwater populations are derived, are better adapted to freshwater environments than Japan Sea sticklebacks. We suggest adaptive divergence between ancestral marine populations may have played a role in constraining phenotypic diversification and adaptive evolution in Japanese sticklebacks.
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Affiliation(s)
- Mark Ravinet
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Naoko Takeuchi
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Manabu Kume
- Biological Laboratory, Gifu-keizai University, Ogaki, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu-keizai University, Ogaki, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6. Proc Natl Acad Sci U S A 2014; 111:13912-7. [PMID: 25205810 DOI: 10.1073/pnas.1407567111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Developmental genetic studies of evolved differences in morphology have led to the hypothesis that cis-regulatory changes often underlie morphological evolution. However, because most of these studies focus on evolved loss of traits, the genetic architecture and possible association with cis-regulatory changes of gain traits are less understood. Here we show that a derived benthic freshwater stickleback population has evolved an approximate twofold gain in ventral pharyngeal tooth number compared with their ancestral marine counterparts. Comparing laboratory-reared developmental time courses of a low-toothed marine population and this high-toothed benthic population reveals that increases in tooth number and tooth plate area and decreases in tooth spacing arise at late juvenile stages. Genome-wide linkage mapping identifies largely separate sets of quantitative trait loci affecting different aspects of dental patterning. One large-effect quantitative trait locus controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, and no coding changes are found between the high- and low-toothed populations. However, quantitative allele-specific expression assays of Bmp6 in developing teeth in F1 hybrids show that cis-regulatory changes have elevated the relative expression level of the freshwater benthic Bmp6 allele at late, but not early, stages of stickleback development. Collectively, our data support a model where a late-acting cis-regulatory up-regulation of Bmp6 expression underlies a significant increase in tooth number in derived benthic sticklebacks.
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Matuszewski S, Hermisson J, Kopp M. Fisher's geometric model with a moving optimum. Evolution 2014; 68:2571-88. [PMID: 24898080 PMCID: PMC4285815 DOI: 10.1111/evo.12465] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 05/15/2014] [Indexed: 12/29/2022]
Abstract
Fisher's geometric model has been widely used to study the effects of pleiotropy and organismic complexity on phenotypic adaptation. Here, we study a version of Fisher's model in which a population adapts to a gradually moving optimum. Key parameters are the rate of environmental change, the dimensionality of phenotype space, and the patterns of mutational and selectional correlations. We focus on the distribution of adaptive substitutions, that is, the multivariate distribution of the phenotypic effects of fixed beneficial mutations. Our main results are based on an “adaptive-walk approximation,” which is checked against individual-based simulations. We find that (1) the distribution of adaptive substitutions is strongly affected by the ecological dynamics and largely depends on a single composite parameter γ, which scales the rate of environmental change by the “adaptive potential” of the population; (2) the distribution of adaptive substitution reflects the shape of the fitness landscape if the environment changes slowly, whereas it mirrors the distribution of new mutations if the environment changes fast; (3) in contrast to classical models of adaptation assuming a constant optimum, with a moving optimum, more complex organisms evolve via larger adaptive steps.
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Affiliation(s)
- Sebastian Matuszewski
- Mathematics and BioSciences Group, Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, A-1090, Vienna, Austria.
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Rogers SM, Jamniczky HA. The shape of things to come in the study of the origin of species? Mol Ecol 2014; 23:1650-2. [PMID: 24667008 DOI: 10.1111/mec.12695] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/10/2014] [Accepted: 02/14/2014] [Indexed: 12/13/2022]
Abstract
Perhaps Darwin would agree that speciation is no longer the mystery of mysteries that it used to be. It is now generally accepted that evolution by natural selection can contribute to ecological adaptation, resulting in the evolution of reproductive barriers and, hence, to the evolution of new species (Schluter & Conte 2009; Meyer 2011; Nosil 2012). From genes that encode silencing proteins that cause infertility in hybrid mice (Mihola et al. 2009), to segregation distorters linked to speciation in fruit flies (Phadnis & Orr 2009), or pollinator-mediated selection on flower colour alleles driving reinforcement in Texan wildflowers (Hopkins & Rausher 2012), characterization of the genes that drive speciation is providing clues to the origin of species (Nosil & Schluter 2011). It is becoming apparent that, while recent work continues to overturn historical ideas about sympatric speciation (e.g. Barluenga et al. 2006), ecological circumstances strongly influence patterns of genomic divergence, and ultimately the establishment of reproductive isolation when gene flow is present (Elmer & Meyer 2011). Less clear, however, are the genetic mechanisms that cause speciation, particularly when ongoing gene flow is occurring. Now, in this issue, Franchini et al. (2014) employ a classic genetic mapping approach augmented with new genomic tools to elucidate the genomic architecture of ecologically divergent body shapes in a pair of sympatric crater lake cichlid fishes. From over 450 segregating SNPs in an F2 cross, 72 SNPs were linked to 11 QTL associated with external morphology measured by means of traditional and geometric morphometrics. Annotation of two highly supported QTL further pointed to genes that might contribute to ecological divergence in body shape in Midas cichlids, overall supporting the hypothesis that genomic regions of large phenotypic effect may be contributing to early-stage divergence in Midas cichlids.
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Affiliation(s)
- Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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