1
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Zhang C, Reid K, Sands AF, Fraimout A, Schierup MH, Merilä J. De Novo Mutation Rates in Sticklebacks. Mol Biol Evol 2023; 40:msad192. [PMID: 37648662 PMCID: PMC10503787 DOI: 10.1093/molbev/msad192] [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: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
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Affiliation(s)
- Chaowei Zhang
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Kerry Reid
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Arthur F Sands
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Antoine Fraimout
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Juha Merilä
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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2
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Wang Y, Wang Y, Cheng X, Ding Y, Wang C, Merilä J, Guo B. Prevalent Introgression Underlies Convergent Evolution in the Diversification of Pungitius Sticklebacks. Mol Biol Evol 2023; 40:7026025. [PMID: 36738166 PMCID: PMC9949714 DOI: 10.1093/molbev/msad026] [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: 08/26/2022] [Revised: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analyzed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures-important diagnostic traits in Pungitius systematics-and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the long-standing challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish.
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Affiliation(s)
- 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
| | - Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqi Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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3
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Feng X, Merilä J, Löytynoja A. Complex population history affects admixture analyses in nine-spined sticklebacks. Mol Ecol 2022; 31:5386-5401. [PMID: 35962788 PMCID: PMC9828525 DOI: 10.1111/mec.16651] [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: 01/25/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 01/12/2023]
Abstract
Introgressive hybridization is an important process in evolution but challenging to identify, undermining the efforts to understand its role and significance. On the contrary, many analytical methods assume direct descent from a single common ancestor, and admixture among populations can violate their assumptions and lead to seriously biased results. A detailed analysis of 888 whole-genome sequences of nine-spined sticklebacks (Pungitius pungitius) revealed a complex pattern of population ancestry involving multiple waves of gene flow and introgression across northern Europe. The two recognized lineages were found to have drastically different histories, and their secondary contact zone was wider than anticipated, displaying a smooth gradient of foreign ancestry with some curious deviations from the expected pattern. Interestingly, the freshwater isolates provided peeks into the past and helped to understand the intermediate states of evolutionary processes. Our analyses and findings paint a detailed picture of the complex colonization history of northern Europe and provide backdrop against which introgression and its role in evolution can be investigated. However, they also expose the challenges in analyses of admixed populations and demonstrate how hidden admixture and colonization history misleads the estimation of admixture proportions and population split times.
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Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Area of Ecology and Biodiversity, Kadoorie Science BuildingThe University of Hong KongHong Kong, SARChina
| | - Ari Löytynoja
- Institute of Biotechnology, University of HelsinkiHelsinkiFinland
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4
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Makaras T, Stankevičiūtė M. Swimming behaviour in two ecologically similar three-spined (Gasterosteus aculeatus L.) and nine-spined sticklebacks (Pungitius pungitius L.): a comparative approach for modelling the toxicity of metal mixtures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:14479-14496. [PMID: 34617211 DOI: 10.1007/s11356-021-16783-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Sticklebacks (Gasterosteiformes) are increasingly used in ecological and evolutionary research and have become well established as role model species for biologists. However, ecotoxicology studies concerning behavioural effects in sticklebacks regarding stress responses, mainly induced by chemical mixtures, have hardly been addressed. For this purpose, we investigated the swimming behaviour (including mortality rate based on 96-h LC50 values) of two ecologically similar three-spined (Gasterosteus aculeatus) and nine-spined sticklebacks (Pungitius pungitius) to short-term (up to 24 h) metal mixture (MIX) exposure. We evaluated the relevance and efficacy of behavioural responses of test species in the early toxicity assessment of chemical mixtures. Fish exposed to six (Zn, Pb, Cd, Cu, Ni, and Cr) metals in the mixture were either singled out by the Water Framework Directive as priority or as relevant substances in surface water, which was prepared according to the environmental quality standards (EQSs) of these metals set for inland waters in the European Union (EU) (Directive 2013/39/EU). The performed behavioural analysis showed the main effect on the interaction between time, species, and treatment variables. Although both species exposed to MIX revealed a decreasing tendency in swimming activity, these species' responsiveness to MIX was somewhat different. Substantial changes in the activity of G. aculeatus were established after a 3-h exposure to MIX solutions, which was 1.43-fold lower, while in the case of P. pungitius, 1.96-fold higher than established 96-h LC50 values for each species. This study demonstrated species-specific differences in response sensitivity to metal-based water pollution, indicating behavioural insensitivity of P. pungitius as model species for aquatic biomonitoring and environmental risk assessments.
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Affiliation(s)
- Tomas Makaras
- Nature Research Centre, Akademijos Str. 2, 08412, Vilnius, Lithuania.
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5
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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6
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Dahms C, Kemppainen P, Zanella LN, Zanella D, Carosi A, Merilä J, Momigliano P. Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks. Mol Ecol 2021; 31:1234-1253. [PMID: 34843145 DOI: 10.1111/mec.16295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely. This is expected to limit parallel evolution, that is the extent to which phylogenetically related alleles can be shared among independently colonized freshwater populations. Using whole genome and 2b-RAD sequencing data, we compared levels of genetic differentiation and genetic parallelism of 15 Adriatic stickleback populations to 19 Pacific, Atlantic and Caspian populations, where gene flow between freshwater populations across extant marine populations is still possible. Our findings support previous studies suggesting that Adriatic populations are highly differentiated (average FST ≈ 0.45), of low genetic diversity and connectivity, and likely to stem from multiple independent colonizations during the Pleistocene. Linkage disequilibrium network analyses in combination with linear mixed models nevertheless revealed several parallel marine-freshwater differentiated genomic regions, although still not to the extent observed elsewhere in the world. We hypothesize that current levels of genetic parallelism in the Adriatic lineages are a relic of freshwater adaptation from SGV prior to the extinction of marine sticklebacks in the Mediterranean that has persisted despite substantial genetic drift experienced by the Adriatic stickleback isolates.
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Affiliation(s)
- Carolin Dahms
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Linda N Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division for Ecology and Biodiversity, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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7
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. SCIENCE ADVANCES 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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8
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Kivikoski M, Rastas P, Löytynoja A, Merilä J. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Mol Ecol Resour 2021; 21:2166-2176. [PMID: 33955177 DOI: 10.1111/1755-0998.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/06/2023]
Abstract
We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
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Affiliation(s)
- Mikko Kivikoski
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong, SAR
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9
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Bal TMP, Llanos-Garrido A, Chaturvedi A, Verdonck I, Hellemans B, Raeymaekers JAM. Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species. Genes (Basel) 2021; 12:435. [PMID: 33803820 PMCID: PMC8003309 DOI: 10.3390/genes12030435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.
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Affiliation(s)
- Thijs M. P. Bal
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway;
| | | | - Anurag Chaturvedi
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland;
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000 Leuven, Belgium; (I.V.); (B.H.)
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10
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Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA. Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution. Genome Biol 2020; 21:177. [PMID: 32684159 PMCID: PMC7368989 DOI: 10.1186/s13059-020-02097-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/08/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. RESULTS We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we find no evidence for large amplicons identified in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). CONCLUSIONS Together, our work shows that the evolutionary forces shaping sex chromosomes can cause relatively rapid changes in the overall genetic architecture of Y chromosomes.
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Affiliation(s)
- Catherine L. Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Shaugnessy R. McCann
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
| | - Joseph A. Ross
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | | | - James R. Urton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jennifer N. Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195 USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - David M. Kingsley
- Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael A. White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
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11
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Yamasaki YY, Kakioka R, Takahashi H, Toyoda A, Nagano AJ, Machida Y, Møller PR, Kitano J. Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190548. [PMID: 32654635 DOI: 10.1098/rstb.2019.0548] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Yoshiyasu Machida
- Bihoro Museum, Midori 253-4, Bihoro, Abashiri, Hokkaido 092-0002, Japan
| | - Peter R Møller
- Natural History Museum of Denmark, University of Copenhagen, Universitatetsparken 15, Copenhagen 2100, Denmark
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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12
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Evolution of novel genes in three-spined stickleback populations. Heredity (Edinb) 2020; 125:50-59. [PMID: 32499660 PMCID: PMC7413265 DOI: 10.1038/s41437-020-0319-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes frequently acquire new protein-coding genes which may significantly impact an organism’s fitness. Novel genes can be created, for example, by duplication of large genomic regions or de novo, from previously non-coding DNA. Either way, creation of a novel transcript is an essential early step during novel gene emergence. Most studies on the gain-and-loss dynamics of novel genes so far have compared genomes between species, constraining analyses to genes that have remained fixed over long time scales. However, the importance of novel genes for rapid adaptation among populations has recently been shown. Therefore, since little is known about the evolutionary dynamics of transcripts across natural populations, we here study transcriptomes from several tissues and nine geographically distinct populations of an ecological model species, the three-spined stickleback. Our findings suggest that novel genes typically start out as transcripts with low expression and high tissue specificity. Early expression regulation appears to be mediated by gene-body methylation. Although most new and narrowly expressed genes are rapidly lost, those that survive and subsequently spread through populations tend to gain broader and higher expression levels. The properties of the encoded proteins, such as disorder and aggregation propensity, hardly change. Correspondingly, young novel genes are not preferentially under positive selection but older novel genes more often overlap with FST outlier regions. Taken together, expression of the surviving novel genes is rapidly regulated, probably via epigenetic mechanisms, while structural properties of encoded proteins are non-debilitating and might only change much later.
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13
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Wang Y, Zhao Y, Wang Y, Li Z, Guo B, Merilä J. Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine‐spined sticklebacks. Mol Ecol 2020; 29:1642-1656. [DOI: 10.1111/mec.15435] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022]
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
| | - Yongxin Zhao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology 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
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - 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
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
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14
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Yoshida K, Ravinet M, Makino T, Toyoda A, Kokita T, Mori S, Kitano J. Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations. Genome Biol Evol 2020; 12:479-492. [PMID: 32232440 PMCID: PMC7197494 DOI: 10.1093/gbe/evaa065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 02/06/2023] Open
Abstract
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Mark Ravinet
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway.,School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Seiichi Mori
- Biological Laboratories, Gifu-kyoritsu University, Ogaki, Gifu, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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15
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Ishikawa A, Kabeya N, Ikeya K, Kakioka R, Cech JN, Osada N, Leal MC, Inoue J, Kume M, Toyoda A, Tezuka A, Nagano AJ, Yamasaki YY, Suzuki Y, Kokita T, Takahashi H, Lucek K, Marques D, Takehana Y, Naruse K, Mori S, Monroig O, Ladd N, Schubert CJ, Matthews B, Peichel CL, Seehausen O, Yoshizaki G, Kitano J. A key metabolic gene for recurrent freshwater colonization and radiation in fishes. Science 2019; 364:886-889. [PMID: 31147520 DOI: 10.1126/science.aau5656] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
Abstract
Colonization of new ecological niches has triggered large adaptive radiations. Although some lineages have made use of such opportunities, not all do so. The factors causing this variation among lineages are largely unknown. Here, we show that deficiency in docosahexaenoic acid (DHA), an essential ω-3 fatty acid, can constrain freshwater colonization by marine fishes. Our genomic analyses revealed multiple independent duplications of the fatty acid desaturase gene Fads2 in stickleback lineages that subsequently colonized and radiated in freshwater habitats, but not in close relatives that failed to colonize. Transgenic manipulation of Fads2 in marine stickleback increased their ability to synthesize DHA and survive on DHA-deficient diets. Multiple freshwater ray-finned fishes also show a convergent increase in Fads2 copies, indicating its key role in freshwater colonization.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan.,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Koki Ikeya
- Gifu World Freshwater Aquarium, Gifu, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Jennifer N Cech
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naoki Osada
- Graduate School of Bioengineering and Bioinformatics, Hokkaido University, Sapporo, Japan
| | - Miguel C Leal
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Manabu Kume
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | | | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Yuto Suzuki
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi, Japan
| | - Kay Lucek
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Yusuke Takehana
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, Japan
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Ribera de Cabanes, Castellón, Spain
| | - Nemiah Ladd
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Earth Sciences, ETH-Zurich, Zurich Switzerland
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Department of Aquatic Ecology, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag Swiss Federal Institute of Aquatic Science and Technology, Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan. .,Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
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16
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Brock CD, Wagner CE. The smelly path to sympatric speciation? Mol Ecol 2019; 27:4153-4156. [PMID: 30375091 DOI: 10.1111/mec.14845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/28/2023]
Abstract
In this issue of Molecular Ecology, Poelstra et al. () use genomic data to show that cichlid species in the adaptive radiation in Lake Ejagham, Cameroon, experienced gene flow with a riverine relative, primarily prior to their diversification. Intriguingly, this introgression brought with it olfactory alleles that the authors suggest may play a sensory role in speciation. As a classic example of sympatric speciation due to the highly restricted geography of this small (0.49 km2 ) crater lake (Schliewen et al., ), this result sheds new light on the history of this fascinating radiation. As genomic data for cichlid radiations accumulate, finding evidence of introgression increasingly appears to be the rule rather than the exception (Kautt et al., ; Meier et al., , ). However, two points are pressing as evidence for introgression mounts: (a) It is crucial to understand the assumptions of analytical approaches used and (b) it is important to think clearly about the divergent contexts in which evidence for introgression has been invoked as an important feature of adaptive radiation.
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Affiliation(s)
- Chad D Brock
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
| | - Catherine E Wagner
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
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17
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Worldwide phylogeny of three-spined sticklebacks. Mol Phylogenet Evol 2018; 127:613-625. [DOI: 10.1016/j.ympev.2018.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/16/2018] [Accepted: 06/04/2018] [Indexed: 11/23/2022]
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18
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Poelstra JW, Richards EJ, Martin CH. Speciation in sympatry with ongoing secondary gene flow and a potential olfactory trigger in a radiation of Cameroon cichlids. Mol Ecol 2018; 27:4270-4288. [DOI: 10.1111/mec.14784] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/30/2018] [Accepted: 05/14/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Jelmer W. Poelstra
- Department of Biology; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
- Department of Biology; Duke University; Durham North Carolina
| | - Emilie J. Richards
- Department of Biology; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
| | - Christopher H. Martin
- Department of Biology; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
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19
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Liu S, Ferchaud AL, Grønkjaer P, Nygaard R, Hansen MM. Genomic parallelism and lack thereof in contrasting systems of three-spined sticklebacks. Mol Ecol 2018; 27:4725-4743. [DOI: 10.1111/mec.14782] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Shenglin Liu
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - Anne-Laure Ferchaud
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Peter Grønkjaer
- Department of Bioscience; Aarhus University; Aarhus C Denmark
| | - Rasmus Nygaard
- Greenland Institute of Natural Resources; Nuuk Greenland
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20
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Abstract
Recombination often differs markedly between males and females. Here we present the first analysis of sex-specific recombination in Gasterosteus sticklebacks. Using whole-genome sequencing of 15 crosses between G. aculeatus and G. nipponicus, we localized 698 crossovers with a median resolution of 2.3 kb. We also used a bioinformatic approach to infer historical sex-averaged recombination patterns for both species. Recombination is greater in females than males on all chromosomes, and overall map length is 1.64 times longer in females. The locations of crossovers differ strikingly between sexes. Crossovers cluster toward chromosome ends in males, but are distributed more evenly across chromosomes in females. Suppression of recombination near the centromeres in males causes crossovers to cluster at the ends of long arms in acrocentric chromosomes, and greatly reduces crossing over on short arms. The effect of centromeres on recombination is much weaker in females. Genomic differentiation between G. aculeatus and G. nipponicus is strongly correlated with recombination rate, and patterns of differentiation along chromosomes are strongly influenced by male-specific telomere and centromere effects. We found no evidence for fine-scale correlations between recombination and local gene content in either sex. We discuss hypotheses for the origin of sexual dimorphism in recombination and its consequences for sexually antagonistic selection and sex chromosome evolution.
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21
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Ravinet M, Yoshida K, Shigenobu S, Toyoda A, Fujiyama A, Kitano J. The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression. PLoS Genet 2018; 14:e1007358. [PMID: 29791436 PMCID: PMC5988309 DOI: 10.1371/journal.pgen.1007358] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 06/05/2018] [Accepted: 04/11/2018] [Indexed: 12/17/2022] Open
Abstract
Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.
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Affiliation(s)
- Mark Ravinet
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Kohta Yoshida
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Jun Kitano
- Division of Ecological Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
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22
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Abstract
Recent years have seen an increase in studies that associate genomic loci with behavioral variation both within and across animal species. Ryan York compiles and analyzes over 1,000 of these loci, finding that the genetic... Although most animal behaviors are associated with some form of heritable genetic variation, we do not yet understand how genes sculpt behavior across evolution, either directly or indirectly. To address this, I here compile a data set comprised of over 1000 genomic loci representing a spectrum of behavioral variation across animal taxa. Comparative analyses reveal that courtship and feeding behaviors are associated with genomic regions of significantly greater effect than other traits, on average threefold greater than other behaviors. Investigations of whole-genome sequencing and phenotypic data for 87 behavioral traits from the Drosophila Genetics Reference Panel indicate that courtship and feeding behaviors have significantly greater genetic contributions and that, in general, behavioral traits overlap little in individual base pairs but increasingly interact at the levels of genes and traits. These results provide evidence that different types of behavior are associated with variable genetic bases and suggest that, across animal evolution, the genetic landscape of behavior is more rugged, yet predictable, than previously thought.
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23
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Raeymaekers JAM, Chaturvedi A, Hablützel PI, Verdonck I, Hellemans B, Maes GE, De Meester L, Volckaert FAM. Adaptive and non-adaptive divergence in a common landscape. Nat Commun 2017; 8:267. [PMID: 28814718 PMCID: PMC5559485 DOI: 10.1038/s41467-017-00256-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes. The three-spined stickleback is a model species for the study of adaptive divergence. Here, Raeymaekers et al. compare how the three-spined stickleback and its relative the nine-spined stickleback vary at the phenotypic and genomic levels in response to the same spatial and environmental drivers.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium. .,Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway. .,Faculty of Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway.
| | - Anurag Chaturvedi
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Pascal I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Flanders Marine Institute, B-8400, Oostende, Belgium
| | - Io Verdonck
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
| | - Gregory E Maes
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium.,Genomics Core, Center for Human Genetics, UZ Leuven, B-3000, Leuven, Belgium.,Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, B-3000, Leuven, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, B-3000, Leuven, Belgium
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24
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Yang L, Zhang Z, He S. Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes. Genome Biol Evol 2016; 8:3433-3445. [PMID: 27742722 PMCID: PMC5203780 DOI: 10.1093/gbe/evw239] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
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Liu S, Hansen MM, Jacobsen MW. Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences. Mol Ecol 2016; 25:5187-5202. [PMID: 27569902 DOI: 10.1111/mec.13827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 02/04/2023]
Abstract
We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations.
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Affiliation(s)
- Shenglin Liu
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark.
| | - Magnus W Jacobsen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
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26
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Kautt AF, Machado-Schiaffino G, Torres-Dowdall J, Meyer A. Incipient sympatric speciation in Midas cichlid fish from the youngest and one of the smallest crater lakes in Nicaragua due to differential use of the benthic and limnetic habitats? Ecol Evol 2016; 6:5342-57. [PMID: 27551387 PMCID: PMC4984508 DOI: 10.1002/ece3.2287] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Understanding how speciation can occur without geographic isolation remains a central objective in evolutionary biology. Generally, some form of disruptive selection and assortative mating are necessary for sympatric speciation to occur. Disruptive selection can arise from intraspecific competition for resources. If this competition leads to the differential use of habitats and variation in relevant traits is genetically determined, then assortative mating can be an automatic consequence (i.e., habitat isolation). In this study, we caught Midas cichlid fish from the limnetic (middle of the lake) and benthic (shore) habitats of Crater Lake Asososca Managua to test whether some of the necessary conditions for sympatric speciation due to intraspecific competition and habitat isolation are given. Lake As. Managua is very small (<900 m in diameter), extremely young (maximally 1245 years of age), and completely isolated. It is inhabited by, probably, only a single endemic species of Midas cichlids, Amphilophus tolteca. We found that fish from the limnetic habitat were more elongated than fish collected from the benthic habitat, as would be predicted from ecomorphological considerations. Stable isotope analyses confirmed that the former also exhibit a more limnetic lifestyle than the latter. Furthermore, split‐brood design experiments in the laboratory suggest that phenotypic plasticity is unlikely to explain much of the observed differences in body elongation that we observed in the field. Yet, neutral markers (microsatellites) did not reveal any genetic clustering in the population. Interestingly, demographic inferences based on RAD‐seq data suggest that the apparent lack of genetic differentiation at neutral markers could simply be due to a lack of time, as intraspecific competition may only have begun a few hundred generations ago.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | | | - Julian Torres-Dowdall
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
| | - Axel Meyer
- Department of Biology University of Konstanz Universitätsstrasse 10 78457 Konstanz Germany
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Kautt AF, Machado-Schiaffino G, Meyer A. Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids. PLoS Genet 2016; 12:e1006157. [PMID: 27362536 PMCID: PMC4928843 DOI: 10.1371/journal.pgen.1006157] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
The formation of species in the absence of geographic barriers (i.e. sympatric speciation) remains one of the most controversial topics in evolutionary biology. While theoretical models have shown that this most extreme case of primary divergence-with-gene-flow is possible, only a handful of accepted empirical examples exist. And even for the most convincing examples uncertainties remain; complex histories of isolation and secondary contact can make species falsely appear to have originated by sympatric speciation. This alternative scenario is notoriously difficult to rule out. Midas cichlids inhabiting small and remote crater lakes in Nicaragua are traditionally considered to be one of the best examples of sympatric speciation and lend themselves to test the different evolutionary scenarios that could lead to apparent sympatric speciation since the system is relatively small and the source populations known. Here we reconstruct the evolutionary history of two small-scale radiations of Midas cichlids inhabiting crater lakes Apoyo and Xiloá through a comprehensive genomic data set. We find no signs of differential admixture of any of the sympatric species in the respective radiations. Together with coalescent simulations of different demographic models our results support a scenario of speciation that was initiated in sympatry and does not result from secondary contact of already partly diverged populations. Furthermore, several species seem to have diverged simultaneously, making Midas cichlids an empirical example of multispecies outcomes of sympatric speciation. Importantly, however, the demographic models strongly support an admixture event from the source population into both crater lakes shortly before the onset of the radiations within the lakes. This opens the possibility that the formation of reproductive barriers involved in sympatric speciation was facilitated by genetic variants that evolved in a period of isolation between the initial founding population and the secondary migrants that came from the same source population. Thus, the exact mechanisms by which these species arose might be different from what had been thought before.
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Affiliation(s)
- Andreas F. Kautt
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
| | | | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, Germany
- * E-mail:
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28
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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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Guo B, Li Z, Merilä J. Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Mol Ecol 2016; 25:2833-52. [DOI: 10.1111/mec.13657] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 03/31/2016] [Accepted: 04/14/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Zitong Li
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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30
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Meguro YI, Takahashi H, Machida Y, Shirakawa H, Gaither M, Goto A. Assortative mating and divergent male courtship behaviours between two cryptic species of nine-spined sticklebacks (genus Pungitius). BEHAVIOUR 2016. [DOI: 10.1163/1568539x-00003396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Assortative mating based on ecologically divergent traits is a major driver of speciation among three-spined sticklebacks, however, little is known about reproductive isolation and variations in courtship behaviour among nine-spined sticklebacks. Here we demonstrate assortative mating and divergent courtship behaviours between two cryptic species of nine-spined sticklebacks using no-choice mate trials and kinematic analyses. Strong assortative mating was demonstrated in our tank experiments, highlighting the importance of prezygotic reproductive isolation in these species. Kinematic analyses showed that the freshwater type exhibited aggressive courtship behaviour with frequent ‘Attacking’ and spent more time exhibiting displacement activities. In contrast, the brackish-water type demonstrated a higher frequency of the ‘Zigzag-dance’ and ‘Nest-showing’. Our study highlights the value of nine-spined sticklebacks as a comparative system for the study of speciation and paves the way for future studies on the role of courtship behaviours and assortative mating in the evolution of sticklebacks.
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Affiliation(s)
- Yu-ichiro Meguro
- Division of Marine Biosciences, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
| | - Hiroshi Takahashi
- Department of Applied Aquabiology, National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki 759-6595, Japan
| | | | - Hokuto Shirakawa
- Field Science Center for Northern Biosphere, Hokkaido University, 20-5 Benten-cho, Hakodate, 040-005, Japan
- JST CREST, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan
| | - Michelle R. Gaither
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Honolulu, HI 96744, USA
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Akira Goto
- Division of Marine Biosciences, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan
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31
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Rastas P, Calboli FCF, Guo B, Shikano T, Merilä J. Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example. Genome Biol Evol 2015; 8:78-93. [PMID: 26668116 PMCID: PMC4758246 DOI: 10.1093/gbe/evv250] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5–2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates.
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Affiliation(s)
- Pasi Rastas
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Baocheng Guo
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes. G3-GENES GENOMES GENETICS 2015; 6:141-8. [PMID: 26564948 PMCID: PMC4704712 DOI: 10.1534/g3.115.024448] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Glyptosternoid fishes (Siluriformes), one of the three broad fish lineages (the two other are schizothoracines and Triplophysa), have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes.
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33
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Yang L, Wang Y, Zhang Z, He S. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. Genome Biol Evol 2014; 7:251-61. [PMID: 25543049 PMCID: PMC4316632 DOI: 10.1093/gbe/evu279] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.
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Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ying Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Ontario, Canada Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
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Extensive copy-number variation of young genes across stickleback populations. PLoS Genet 2014; 10:e1004830. [PMID: 25474574 PMCID: PMC4256280 DOI: 10.1371/journal.pgen.1004830] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation. After a locus is duplicated in a genome, individuals from a population instantaneously differ in the number of copies of this locus producing a copy-number variation (CNV). Over time, the joint effects of selection and other evolutionary forces will act to either eliminate the extra genetic copy or retain it. Depending on this evolutionary interplay, young duplications, including newly duplicated genes, can persist for millions of years as CNVs. CNVs may especially be prevalent between populations that have colonized and adapted to disparate environments in which selective pressures differ. Using whole genome sequences from several populations of three-spined sticklebacks that inhabit different environments, we find that a third of young duplicated genes are CNVs. These young CNV genes are enriched with environmental response functions and evolving rapidly at the molecular level, making them promising candidates for a role in the rapid ecological adaptation to novel environments.
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