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Coll-Costa C, Dahms C, Kemppainen P, Alexandre CM, Ribeiro F, Zanella D, Zanella L, Merilä J, Momigliano P. Parallel evolution despite low genetic diversity in three-spined sticklebacks. Proc Biol Sci 2024; 291:20232617. [PMID: 38593844 PMCID: PMC11003780 DOI: 10.1098/rspb.2023.2617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback (Gasterosteus aculeatus) repeatedly colonized and adapted to brackish and freshwater. Most parallel evolution studies in G. aculeatus were conducted at high latitudes, where freshwater populations maintain connectivity to the source marine populations. Here, we analysed southern and northern European marine and freshwater populations to test two hypotheses. First, that southern European freshwater populations (which currently lack connection to marine populations) lost genetic diversity due to bottlenecks and inbreeding compared to their northern counterparts. Second, that the degree of genetic parallelism is higher among northern than southern European freshwater populations, as the latter have been subjected to strong drift due to isolation. The results show that southern populations exhibit lower genetic diversity but a higher degree of genetic parallelism than northern populations. Hence, they confirm the hypothesis that southern populations have lost genetic diversity, but this loss probably happened after they had already adapted to freshwater conditions, explaining the high degree of genetic parallelism in the south.
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Affiliation(s)
- Carla Coll-Costa
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Carolin Dahms
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Petri Kemppainen
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Carlos M. Alexandre
- MARE—Marine and Environmental Sciences Centre, Universidade de Évora, Évora, 7004-516, Portugal
| | - Filipe Ribeiro
- MARE—Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Davor Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Linda Zanella
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb, 10000, Croatia
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, FI-00014, Finland
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Paolo Momigliano
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong SAR, People's Republic of China
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2
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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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3
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Hudson CM, Ladd SN, Leal MC, Schubert CJ, Seehausen O, Matthews B. Fit and fatty freshwater fish: contrasting polyunsaturated fatty acid phenotypes between hybridizing stickleback lineages. OIKOS 2021. [DOI: 10.1111/oik.08558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Cameron M. Hudson
- Dept of Fish Ecology and Evolution, Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry Kastanienbaum Switzerland
- Aquatic Ecology and Evolution, Inst. of Ecology and Evolution, Univ. of Bern Bern Switzerland
| | - S. Nemiah Ladd
- Dept of Surface Waters – Research and Management, Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry Kastanienbaum Switzerland
- Ecosystem Physiology, Univ. of Freiburg Freiburg Germany
| | - Miguel C. Leal
- ECOMARE, CESAM – Center for Environmental and Marine Studies, Dept of Biology, Univ. of Aveiro, Campus Universitário de Santiago Aveiro Portugal
| | - Carsten J. Schubert
- Dept of Surface Waters – Research and Management, Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry Kastanienbaum Switzerland
| | - Ole Seehausen
- Dept of Fish Ecology and Evolution, Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry Kastanienbaum Switzerland
- Aquatic Ecology and Evolution, Inst. of Ecology and Evolution, Univ. of Bern Bern Switzerland
| | - Blake Matthews
- Dept of Fish Ecology and Evolution, Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry Kastanienbaum Switzerland
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin". Nat Commun 2021; 12:2807. [PMID: 33990586 PMCID: PMC8121787 DOI: 10.1038/s41467-021-23096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
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5
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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6
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Kakioka R, Mori S, Kokita T, Hosoki TK, Nagano AJ, Ishikawa A, Kume M, Toyoda A, Kitano J. Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. BMC Evol Biol 2020; 20:143. [PMID: 33143638 PMCID: PMC7641863 DOI: 10.1186/s12862-020-01713-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/27/2020] [Indexed: 12/03/2022] Open
Abstract
Background The three-spined stickleback (Gasterosteus aculeatus) is a remarkable system to study the genetic mechanisms underlying parallel evolution during the transition from marine to freshwater habitats. Although the majority of previous studies on the parallel evolution of sticklebacks have mainly focused on postglacial freshwater populations in the Pacific Northwest of North America and northern Europe, we recently use Japanese stickleback populations for investigating shared and unique features of adaptation and speciation between geographically distant populations. However, we currently lack a comprehensive phylogeny of the Japanese three-spined sticklebacks, despite the fact that a good phylogeny is essential for any evolutionary and ecological studies. Here, we conducted a phylogenomic analysis of the three-spined stickleback in the Japanese Archipelago. Results We found that freshwater colonization occurred in multiple waves, each of which may reflect different interglacial isolations. Some of the oldest freshwater populations from the central regions of the mainland of Japan (hariyo populations) were estimated to colonize freshwater approximately 170,000 years ago. The next wave of colonization likely occurred approximately 100,000 years ago. The inferred origins of several human-introduced populations showed that introduction occurred mainly from nearby habitats. We also found a new habitat of the three-spined stickleback sympatric with the Japan Sea stickleback (Gasterosteus nipponicus). Conclusions These Japanese stickleback systems differ from those in the Pacific Northwest of North America and northern Europe in terms of divergence time and history. Stickleback populations in the Japanese Archipelago offer valuable opportunities to study diverse evolutionary processes in historical and contemporary timescales.
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Affiliation(s)
- Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa, 903-0213, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu Kyoritsu University, Ogaki, Gifu, 503-8550, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, 917-0003, Japan
| | - Takuya K Hosoki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan
| | - Manabu Kume
- Field Science Education and Research Center, Kyoto University, Kyoto, 606-8502, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, 411-8540, Japan.
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7
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nat Commun 2019; 10:4240. [PMID: 31534121 PMCID: PMC6751218 DOI: 10.1038/s41467-019-12182-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2019] [Indexed: 01/25/2023] Open
Abstract
Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation. Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.
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Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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8
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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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9
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Vila M, Hermida M, Fernández C, Perea S, Doadrio I, Amaro R, San Miguel E. Phylogeography and Conservation Genetics of the Ibero-Balearic Three-Spined Stickleback (Gasterosteus aculeatus). PLoS One 2017; 12:e0170685. [PMID: 28118391 PMCID: PMC5261773 DOI: 10.1371/journal.pone.0170685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/09/2017] [Indexed: 02/03/2023] Open
Abstract
Genetic isolation and drift may imperil peripheral populations of wide-ranging species more than central ones. Therefore, information about species genetic variability and population structure is invaluable for conservation managers. The Iberian populations of three-spined stickleback lie at the southwestern periphery of the European distribution of Gasterosteus aculeatus. This teleost is a protected species in Portugal and Spain and local extinctions have been reported in both countries during the last decades. Our objectives were (i) to determine whether the Iberian populations of G. aculeatus are unique or composed of any of the major evolutionary lineages previously identified and (ii) to assess the evolutionary potential of these peripheral populations. We genotyped 478 individuals from 17 sites at 10 polymorphic microsatellite loci to evaluate the genetic variability and differentiation of the Ibero-Balearic populations. We also sequenced 1,165 bp of the mitochondrial genome in 331 of those individuals in order to complement the estimates of genetic diversity in the Ibero-Balearic region. We predicted the evolutionary potential of the different sites analysed based on the contribution of each of them to total allelic/mitochondrial diversity. An intraspecific phylogeny at European level was reconstructed using our data from the mitochondrial cytochrome b gene (755 bp) and published sequences. The so-called Transatlantic, European and Mediterranean mitochondrial lineages were found to be present in the Ibero-Balearic region. Their phylogeography suggests a history of multiple colonisations. The nuclear results show, however, a strong correlation between population structure and drainage system. The following basins should be prioritised by conservation policies in order to preserve those populations with the highest evolutionary potential: the Portuguese Vouga and Tagus as well as the Spanish Majorca and Limia. Maintenance of their connectivity, control of exotic species and monitoring of habitat properties are strongly recommended in those areas. Genetic variation alone cannot, however, ensure the persistence of these peripheral southern populations of G. aculeatus. On the one hand, the analysis of a historical sample from Eastern Spain (Penyscola) revealed no genetic erosion, which suggests a fairly sudden extinction of that population. On the other hand, the reintroduction program implemented in the Valencian Community has mostly failed despite our finding of similar level of genetic diversity between the wild source and the captive-bred released individuals.
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Affiliation(s)
- Marta Vila
- Universidade da Coruña, Evolutionary Biology Group (GIBE), Facultade de Ciencias, Campus da Zapateira, A Coruña, Spain
- * E-mail:
| | - Miguel Hermida
- Universidade de Santiago de Compostela, Departamento de Xenética, Facultade de Veterinaria, Avenida Carballo Calero s/n, Lugo, Spain
| | - Carlos Fernández
- Universidade de Santiago de Compostela, Departamento de Xenética, Facultade de Veterinaria, Avenida Carballo Calero s/n, Lugo, Spain
| | - Silvia Perea
- Museo Nacional de Ciencias Naturales, Departamento de Biodiversidad y Biología Evolutiva, CSIC, José Gutiérrez Abascal 2, Madrid, Spain
| | - Ignacio Doadrio
- Museo Nacional de Ciencias Naturales, Departamento de Biodiversidad y Biología Evolutiva, CSIC, José Gutiérrez Abascal 2, Madrid, Spain
| | - Rafaela Amaro
- Universidade de Santiago de Compostela, Departamento de Xenética, Facultade de Veterinaria, Avenida Carballo Calero s/n, Lugo, Spain
| | - Eduardo San Miguel
- Universidade de Santiago de Compostela, Departamento de Xenética, Facultade de Veterinaria, Avenida Carballo Calero s/n, Lugo, Spain
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Lumme J, Mäkinen H, Ermolenko AV, Gregg JL, Ziętara MS. Displaced phylogeographic signals from Gyrodactylus arcuatus, a parasite of the three-spined stickleback Gasterosteus aculeatus, suggest freshwater glacial refugia in Europe. Int J Parasitol 2016; 46:545-54. [PMID: 27155331 DOI: 10.1016/j.ijpara.2016.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/25/2016] [Accepted: 03/06/2016] [Indexed: 11/17/2022]
Abstract
We examined the global mitochondrial phylogeography of Gyrodactylus arcuatus, a flatworm ectoparasite of three-spined stickleback Gasterosteus aculeatus. In accordance with the suggested high divergence rate of 13%/million years, the genetic variation of the parasite was high: haplotype diversity h=0.985 and nucleotide diversity π=0.0161. The differentiation among the parasite populations was substantial (Φst=0.759), with two main allopatric clades (here termed Euro and North) accounting for 54% of the total genetic variation. The diversity center of the Euro clade was in the Baltic Sea, while the North clade was spread across the Barents and White Seas. A single haplotype within the North clade was found in the western and eastern Pacific Ocean. Divergence of main clades was estimated to be circa 200 thousand years ago. Each main clade was further divided into six distinct subclades, estimated to have diverged in isolation since 135 thousand years ago. This second division corresponds approximately to the Eemian interglacial predating the last glacial maximum. A demographic expansion of the subclades is associated with colonisation of northern Europe since the last glacial maximum, circa 15-40 thousand years ago. The parasite phylogeny is most likely explained by sequential isolated bottlenecks and expansions in numerous allopatric refugia. The postglacial intermingling and high variation in the marine parasite populations, separately in the Baltic and Barents Seas, suggest low competition of divergent parasite matrilines, coupled with a large population size and high rate of dispersal of hosts. The genetic contribution of the assumed refugial fish populations maintaining the parasite during the last glacial maximum was not detected among the marine sticklebacks, which perhaps were infected after range expansion.
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Affiliation(s)
| | | | - Alexey V Ermolenko
- Institute of Biology and Soil Science, Russian Academy of Sciences, Vladivostok, Russia
| | - Jacob L Gregg
- U.S. Geological Survey, Marrowstone Marine Field Station, Nordland, WA, USA
| | - Marek S Ziętara
- University of Oulu, Oulu, Finland; Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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Palandačić A, Bravničar J, Zupančič P, Šanda R, Snoj A. Molecular data suggest a multispecies complex of Phoxinus (Cyprinidae) in the Western Balkan Peninsula. Mol Phylogenet Evol 2015; 92:118-23. [DOI: 10.1016/j.ympev.2015.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/28/2015] [Indexed: 11/26/2022]
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12
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Distinctive insular forms of threespine stickleback (Gasterosteus aculeatus) from western Mediterranean islands. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0742-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Zanella LN, DeFaveri J, Zanella D, Merilä J, Šanda R, Mrakovčić M. Does predation drive morphological differentiation among Adriatic populations of the three-spined stickleback? Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda N. Zanella
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| | - Jacquelin DeFaveri
- Ecological Genetic Research Unit; Department of Biological Sciences; University of Helsinki; PO Box 65 FI-00014 Helsinki Finland
| | - Davor Zanella
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
| | - Juha Merilä
- Ecological Genetic Research Unit; Department of Biological Sciences; University of Helsinki; PO Box 65 FI-00014 Helsinki Finland
| | - Radek Šanda
- Department of Zoology; National Museum; Václavské nám. 68 11579 Praha 1 Czech Republic
| | - Milorad Mrakovčić
- Department of Zoology; Faculty of Science; University of Zagreb; Rooseveltov trg 6 10000 Zagreb Croatia
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14
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Ravinet M, Takeuchi N, Kume M, Mori S, Kitano J. Comparative analysis of Japanese three-spined stickleback clades reveals the Pacific Ocean lineage has adapted to freshwater environments while the Japan Sea has not. PLoS One 2014; 9:e112404. [PMID: 25460163 PMCID: PMC4251985 DOI: 10.1371/journal.pone.0112404] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/06/2014] [Indexed: 12/02/2022] Open
Abstract
Divergent selection and adaptive divergence can increase phenotypic diversification amongst populations and lineages. Yet adaptive divergence between different environments, habitats or niches does not occur in all lineages. For example, the colonization of freshwater environments by ancestral marine species has triggered adaptive radiation and phenotypic diversification in some taxa but not in others. Studying closely related lineages differing in their ability to diversify is an excellent means of understanding the factors promoting and constraining adaptive evolution. A well-known example of the evolution of increased phenotypic diversification following freshwater colonization is the three-spined stickleback. Two closely related stickleback lineages, the Pacific Ocean and the Japan Sea occur in Japan. However, Japanese freshwater stickleback populations are derived from the Pacific Ocean lineage only, suggesting the Japan Sea lineage is unable to colonize freshwater. Using stable isotope data and trophic morphology, we first show higher rates of phenotypic and ecological diversification between marine and freshwater populations within the Pacific Ocean lineage, confirming adaptive divergence has occurred between the two lineages and within the Pacific Ocean lineage but not in the Japan Sea lineage. We further identified consistent divergence in diet and foraging behaviour between marine forms from each lineage, confirming Pacific Ocean marine sticklebacks, from which all Japanese freshwater populations are derived, are better adapted to freshwater environments than Japan Sea sticklebacks. We suggest adaptive divergence between ancestral marine populations may have played a role in constraining phenotypic diversification and adaptive evolution in Japanese sticklebacks.
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Affiliation(s)
- Mark Ravinet
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Naoko Takeuchi
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Manabu Kume
- Biological Laboratory, Gifu-keizai University, Ogaki, Japan
| | - Seiichi Mori
- Biological Laboratory, Gifu-keizai University, Ogaki, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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15
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Ravinet M, Harrod C, Eizaguirre C, Prodöhl PA. Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization? Ecol Evol 2014; 4:2488-504. [PMID: 25360281 PMCID: PMC4203293 DOI: 10.1002/ece3.853] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 11/24/2022] Open
Abstract
Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.
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Affiliation(s)
- Mark Ravinet
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Lovén Centre-Tjärnö, Department of Biology and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Chris Harrod
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta Chile
| | - Christophe Eizaguirre
- GEOMAR
- Helmholtz Centre for Ocean Research Duesternbrooker weg 20, 24105, Kiel, Germany ; Max Planck Institute for Evolutionary Biology August Thienemannstr. 2, 24306, Ploen, Germany
| | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K
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16
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Previšić A, Schnitzler J, Kučinić M, Graf W, Ibrahimi H, Kerovec M, Pauls SU. Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification. FRESHWATER SCIENCE (PRINT) 2014; 33:250-262. [PMID: 27042385 PMCID: PMC4813752 DOI: 10.1086/674430] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor. Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.
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Affiliation(s)
- Ana Previšić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Jan Schnitzler
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Mladen Kučinić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecology Management, University of Natural Resources and Applied Life Sciences, Max-Emanuel-Straße 17, 1180 Vienna, Austria
| | - Halil Ibrahimi
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Prishtina, Mother Theresa p.n., 10000 Prishtina, Kosovo
| | - Mladen Kerovec
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Steffen U Pauls
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt/Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
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