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Imamoto M, Nakamura H, Aibara M, Hatashima R, Kimirei IA, Kashindye BB, Itoh T, Nikaido M. Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria. Mol Biol Evol 2024; 41:msae093. [PMID: 38782570 PMCID: PMC11166178 DOI: 10.1093/molbev/msae093] [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: 08/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.
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Affiliation(s)
- Minami Imamoto
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Haruna Nakamura
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Kanagawa, Japan
| | - Mitsuto Aibara
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ryo Hatashima
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ismael A Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | | | - Takehiko Itoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masato Nikaido
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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Nakamura H, Aibara M, Kajitani R, Mrosso HDJ, Mzighani SI, Toyoda A, Itoh T, Okada N, Nikaido M. Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation. Mol Biol Evol 2021; 38:3111-3125. [PMID: 33744961 PMCID: PMC8321545 DOI: 10.1093/molbev/msab084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments-Haplochromis chilotes, H. sauvagei, and Lithochromis rufus-to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.
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Affiliation(s)
- Haruna Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hillary D J Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza Fisheries Research Center, Mwanza, Tanzania
| | - Semvua I Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), Headquarters, Dar es Salaam, Tanzania.,Fisheries Education and Training Agency, Dar es Salaam, Tanzania
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Norihiro Okada
- School of Pharmacy, Kitasato University, Kanagawa, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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Takuno S, Miyagi R, Onami JI, Takahashi-Kariyazono S, Sato A, Tichy H, Nikaido M, Aibara M, Mizoiri S, Mrosso HDJ, Mzighani SI, Okada N, Terai Y. Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'. BMC Evol Biol 2019; 19:68. [PMID: 30832572 PMCID: PMC6399900 DOI: 10.1186/s12862-019-1387-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/12/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. RESULTS Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. CONCLUSIONS These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.
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Affiliation(s)
- Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Biological sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 197-0397 Japan
| | - Jun-ichi Onami
- JST (Japan Science and Technology Agency), NBDC (National Bioscience Database Center), 5-3, Yonbancho, Chiyoda-ku, Tokyo, 102-0081 Japan
| | - Shiho Takahashi-Kariyazono
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Akie Sato
- Department of Anatomy and Cytohistology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Herbert Tichy
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Corrensstrasse 42, D-72076 Tübingen, Germany
| | - Masato Nikaido
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology (Tokyo Tech), 2-12-1, Ookayama, Meguro ward, Tokyo, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | | | - Semvua I. Mzighani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza, Tanzania
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Life Sciences, National Cheng Kung University, 701 Tainan, Taiwan
- Foundation for Advancement of International Science (FAIS), Tsukuba, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
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Kordbacheh A, Wallace RL, Walsh EJ. Evidence supporting cryptic species within two sessile microinvertebrates, Limnias melicerta and L. ceratophylli (Rotifera, Gnesiotrocha). PLoS One 2018; 13:e0205203. [PMID: 30379825 PMCID: PMC6209156 DOI: 10.1371/journal.pone.0205203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/20/2018] [Indexed: 11/25/2022] Open
Abstract
Microorganisms, including rotifers, are thought to be capable of long distance dispersal. Therefore, they should show little population genetic structure due to high gene flow. Nevertheless, substantial genetic structure has been reported among populations of many taxa. In rotifers, genetic studies have focused on planktonic taxa leaving sessile groups largely unexplored. Here, we used COI gene and ITS region sequences to study genetic structure and delimit cryptic species in two sessile species (Limnias melicerta [32 populations]; L. ceratophylli [21 populations]). Among populations, ITS region sequences were less variable as compared to those of the COI gene (ITS; L. melicerta: 0-3.1% and L. ceratophylli: 0-4.4%; COI; L. melicerta: 0-22.7% and L. ceratophylli: 0-21.7%). Moreover, L. melicerta and L. ceratophylli were not resolved in phylogenetic analyses based on ITS sequences. Thus, we used COI sequences for species delimitation. Bayesian Species Delimitation detected nine putative cryptic species within L. melicerta and four putative cryptic species for L. ceratophylli. The genetic distance in the COI gene was 0-15.4% within cryptic species of L. melicerta and 0.5-0.6% within cryptic species of L. ceratophylli. Among cryptic species, COI genetic distance ranged 8.1-21.9% for L. melicerta and 15.1-21.2% for L. ceratophylli. The correlation between geographic and genetic distance was weak or lacking; thus geographic isolation cannot be considered a strong driver of genetic variation. In addition, geometric morphometric analyses of trophi did not show significant variation among cryptic species. In this study we used a conservative approach for species delimitation, yet we were able to show that species diversity in these sessile rotifers is underestimated.
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Affiliation(s)
- Azar Kordbacheh
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Robert L. Wallace
- Department of Biology, Ripon College, Ripon, Wisconsin, United States of America
| | - Elizabeth J. Walsh
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
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Lehtonen TK, Elmer KR, Lappalainen M, Meyer A. Genetic evidence for panmixia in a colony-breeding crater lake cichlid fish. Sci Rep 2018; 8:1166. [PMID: 29348515 PMCID: PMC5773479 DOI: 10.1038/s41598-018-19266-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/22/2017] [Indexed: 11/21/2022] Open
Abstract
Fine-scaled genetic structuring, as seen for example in many lacustrine fish, typically relates to the patterns of migration, habitat use, mating system or other ecological factors. Because the same processes can also affect the propensity of population differentiation and divergence, assessments of species from rapidly speciating clades, or with particularly interesting ecological traits, can be especially insightful. For this study, we assessed the spatial genetic relationships, including the genetic evidence for sex-biased dispersal, in a colony-breeding cichlid fish, Amphilophus astorquii, endemic to Crater Lake Apoyo in Nicaragua, using 11 polymorphic microsatellite loci (n = 123 individuals from three colonies). We found no population structure in A. astorquii either within colonies (no spatial genetic autocorrelation, r ~0), or at the lake-wide level (pairwise population differentiation FST = 0-0.013 and no clustering), and there was no sex-bias (male and female AIc values bounded 0) to this lack of genetic structure. These patterns may be driven by the colony-breeding reproductive behaviour of A. astorquii. The results suggest that strong philopatry or spatial assortative mating are unlikely to explain the rapid speciation processes associated with the history of this species in Lake Apoyo.
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Affiliation(s)
- T K Lehtonen
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- School of Biological Sciences, Monash University, Victoria, 3800, Australia
| | - K R Elmer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - M Lappalainen
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - A Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
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6
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Terai Y, Miyagi R, Aibara M, Mizoiri S, Imai H, Okitsu T, Wada A, Takahashi-Kariyazono S, Sato A, Tichy H, Mrosso HDJ, Mzighani SI, Okada N. Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms. BMC Evol Biol 2017; 17:200. [PMID: 28830359 PMCID: PMC5568302 DOI: 10.1186/s12862-017-1040-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Background For Lake Victoria cichlid species inhabiting rocky substrates with differing light regimes, it has been proposed that adaptation of the long-wavelength-sensitive (LWS) opsin gene triggered speciation by sensory drive through color signal divergence. The extensive and continuous sand/mud substrates are also species-rich, and a correlation between male nuptial coloration and the absorption of LWS pigments has been reported. However, the factors driving genetic and functional diversity of LWS pigments in sand/mud habitats are still unresolved. Results To address this issue, nucleotide sequences of eight opsin genes were compared in ten Lake Victoria cichlid species collected from sand/mud bottoms. Among eight opsins, the LWS and rod-opsin (RH1) alleles were diversified and one particular allele was dominant or fixed in each species. Natural selection has acted on and fixed LWS alleles in each species. The functions of LWS and RH1 alleles were measured by absorption of reconstituted A1- and A2-derived visual pigments. The absorption of pigments from RH1 alleles most common in deep water were largely shifted toward red, whereas those of LWS alleles were largely shifted toward blue in both A1 and A2 pigments. In both RH1 and LWS pigments, A2-derived pigments were closer to the dominant light in deep water, suggesting the possibility of the adaptation of A2-derived pigments to depth-dependent light regimes. Conclusions The RH1 and LWS sequences may be diversified for adaptation of A2-derived pigments to different light environments in sand/mud substrates. Diversification of the LWS alleles may have originally taken place in riverine environments, with a new mutation occurring subsequently in Lake Victoria. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1040-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan. .,Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
| | - Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Kyoto, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Shiho Takahashi-Kariyazono
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Akie Sato
- Department of Anatomy and Cytohistology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama, 230-8501, Japan
| | - Herbert Tichy
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Corrensstrasse 42, 72076, Tübingen, Germany
| | | | - Semvua I Mzighani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.,Tanzania Fisheries Research Institute (TAFIRI), Mwanza, Tanzania
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan. .,Present address: Department of Life Sciences, National Cheng Kung University, 701, Tainan, Taiwan. .,Present address: Foundation for Advancement of International Science (FAIS), Tsukuba, Japan.
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Santos‐Santos JH, Audenaert L, Verheyen E, Adriaens D. Divergent ontogenies of trophic morphology in two closely related haplochromine cichlids. J Morphol 2015; 276:860-71. [DOI: 10.1002/jmor.20385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 02/15/2015] [Accepted: 02/17/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Javier H. Santos‐Santos
- Evolutionary Morphology of Vertebrates, Department of BiologyGhent UniversityK.L. Ledeganckstraat 35B‐9000Gent Belgium
- Integrative Biogeography and Global Change DepartmentMuseo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (MNCN‐CSIC)28006Madrid Spain
| | - Leen Audenaert
- Operational Direction, Taxonomy, and Phylogeny VertebratesRoyal Belgian Institute of Natural SciencesVautierstraat 29B‐1000Brussels Belgium
| | - Erik Verheyen
- Operational Direction, Taxonomy, and Phylogeny VertebratesRoyal Belgian Institute of Natural SciencesVautierstraat 29B‐1000Brussels Belgium
- Evolutionary Ecology Group, Biology DepartmentUniversity of Antwerp Belgium
| | - Dominique Adriaens
- Evolutionary Morphology of Vertebrates, Department of BiologyGhent UniversityK.L. Ledeganckstraat 35B‐9000Gent Belgium
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A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids. Gene 2015; 560:156-64. [PMID: 25639358 DOI: 10.1016/j.gene.2015.01.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/06/2023]
Abstract
Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.
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Shirai K, Inomata N, Mizoiri S, Aibara M, Terai Y, Okada N, Tachida H. High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria. Gene 2014; 552:239-45. [PMID: 25241383 DOI: 10.1016/j.gene.2014.09.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 08/28/2014] [Accepted: 09/17/2014] [Indexed: 10/24/2022]
Abstract
When a population size is reduced, genetic drift may fix slightly deleterious mutations, and an increase in nonsynonymous substitution is expected. It has been suggested that past aridity has seriously affected and decreased the populations of cichlid fishes in Lake Victoria, while geographical studies have shown that the water levels in Lake Tanganyika and Lake Malawi have remained fairly constant. The comparably stable environments in the latter two lakes might have kept the populations of cichlid fishes large enough to remove slightly deleterious mutations. The difference in the stability of cichlid fish population sizes between Lake Victoria and the Lakes Tanganyika and Malawi is expected to have caused differences in the nonsynonymous/synonymous ratio, ω (=dN/dS), of the evolutionary rate. Here, we estimated ω and compared it between the cichlids of the three lakes for 13 mitochondrial protein-coding genes using maximum likelihood methods. We found that the lineages of the cichlids in Lake Victoria had a significantly higher ω for several mitochondrial loci. Moreover, positive selection was indicated for several codons in the mtDNA of the Lake Victoria cichlid lineage. Our results indicate that both adaptive and slightly deleterious molecular evolution has taken place in the Lake Victoria cichlids' mtDNA genes, whose nonsynonymous sites are generally conserved.
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Affiliation(s)
- Kazumasa Shirai
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuyuki Inomata
- International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Japan
| | | | - Mitsuto Aibara
- Foundation for Advancement of International Science, Tsukuba, Japan
| | - Yohey Terai
- The Graduate University for Advanced Studies, Kanagawa, Japan
| | - Norihiro Okada
- Foundation for Advancement of International Science, Tsukuba, Japan; Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hidenori Tachida
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.
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