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van Rijssel JC, Moser FN, Mwaiko S, Seehausen O. Strong species structure but weak geographical structure in demersal Lake Victoria cichlids. Ecol Evol 2022; 12:e9669. [PMID: 36582774 PMCID: PMC9790821 DOI: 10.1002/ece3.9669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/27/2022] Open
Abstract
Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably <20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6-km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic, and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation by distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow.
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Affiliation(s)
- Jacco C. van Rijssel
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
- Wageningen Marine ResearchWageningen UniversityIJmuidenThe Netherlands
| | - Florian N. Moser
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Salome Mwaiko
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Ole Seehausen
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
- Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
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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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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: 20] [Impact Index Per Article: 2.9] [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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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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van Rijssel JC, Hoogwater ES, Kishe-Machumu MA, Reenen EV, Spits KV, van der Stelt RC, Wanink JH, Witte F. Fast adaptive responses in the oral jaw of Lake Victoria cichlids. Evolution 2014; 69:179-89. [DOI: 10.1111/evo.12561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/07/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Jacco C. van Rijssel
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
- Naturalis Biodiversity Center; P.O. Box 9517 2300 RA Leiden The Netherlands
- Current Address: Fish Ecology and Evolution, EAWAG Center of Ecology; Evolution and Biogeochemistry; 6047 Kastanienbaum Switzerland
- Current Address: Institute of Ecology and Evolution; University of Bern; CH-3012 Bern Switzerland
| | - Ellen S. Hoogwater
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
| | - Mary A. Kishe-Machumu
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
- Tanzania Fisheries Research Institute (TAFIRI); 9750 Dar Es Salaam Tanzania
| | - Elize van Reenen
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
| | - Kevin V. Spits
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
| | - Ronald C. van der Stelt
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
| | - Jan H. Wanink
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
- Koeman & Bijkerk B.V; Ecological Research and Consultancy; P.O. Box 111 9750 AC Haren The Netherlands
| | - Frans Witte
- Department of Integrative Zoology, Institute of Biology Leiden; Leiden University; P.O. Box 9505 2300 RA Leiden The Netherlands
- Naturalis Biodiversity Center; P.O. Box 9517 2300 RA Leiden The Netherlands
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Vitales D, García-Fernández A, Pellicer J, Vallès J, Santos-Guerra A, Cowan RS, Fay MF, Hidalgo O, Garnatje T. Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data. PLoS One 2014; 9:e113207. [PMID: 25412495 PMCID: PMC4239036 DOI: 10.1371/journal.pone.0113207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
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Affiliation(s)
- Daniel Vitales
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfredo García-Fernández
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | - Robyn S. Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
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Genetic structure of pelagic and littoral cichlid fishes from Lake Victoria. PLoS One 2013; 8:e74088. [PMID: 24040175 PMCID: PMC3765259 DOI: 10.1371/journal.pone.0074088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/25/2013] [Indexed: 11/20/2022] Open
Abstract
The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species and elucidate how this structure relates to the ecological conditions that caused their adaptation. We analyzed the genetic structure of two pelagic and seven littoral species sampled from the southeast area of Lake Victoria using sequences from the mtDNA control region and 12 microsatellite loci as markers. Using a Bayesian model-based clustering method to analyze the microsatellite data, we separated these nine species into four groups: one group composed of pelagic species and another three groups composed mainly of rocky-shore species. Furthermore, we found significant levels of genetic variation between species within each group at both marker loci using analysis of molecular variance (AMOVA), although the nine species often shared mtDNA haplotypes. We also found significant levels of genetic variation between populations within species. These results suggest that initial groupings, some of which appear to have been related to habitat differences, as well as divergence between species within groups took place among the cichlid species of Lake Victoria.
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de Zeeuw MP, Westbroek I, van Oijen MJ, Witte F. Two new species of zooplanktivorous haplochromine cichlids from Lake Victoria, Tanzania. Zookeys 2013; 256:1-34. [PMID: 23717179 PMCID: PMC3650828 DOI: 10.3897/zookeys.256.3871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 12/05/2012] [Indexed: 11/12/2022] Open
Abstract
Two new species of zooplanktivorous haplochromine cichlids from Lake Victoria, Tanzania, are described and illustrated. These species closely resemble each other. Their affinities to other zooplanktivorous haplochromines from Lake Victoria are discussed. Haplochromis argens sp. n., which featured under nicknames (mainly Haplochromis "argens") in more than 50 papers, was caught both in the Mwanza Gulf and the Emin Pasha Gulf, whereas Haplochromis goldschmidti sp. n. was only found in the Emin Pasha Gulf. Of the latter species only males are available, but it seems unlikely that it represents a case of male colour polymorphism as several presumably unrelated characters differ in sympatry between the two species, suggesting that there is no gene flow. Statistical analysis revealed that the overall difference between the two species is greater than that between the populations from the two locations. Body depth of the two species in sympatry in the Emin Pasha Gulf was more similar than that of Haplochromis goldschmidti sp. n. and the allopatric population of Haplochromis argens sp. n. from the Mwanza Gulf,which mayindicate an overall environmental effect. However, several measurements related to the width of snout and mouth differed more between the populations of the two species in sympatry than between the allopatric populations. In contrast to a group of zooplanktivorous species that recovered successfully after environmental changes in the lake, Haplochromis argens sp. n. is among a group that became extremely rare and probably is in danger of extinction; the conservation status of Haplochromis goldschmidti sp. n. is currently unknown.
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Affiliation(s)
| | - Irene Westbroek
- Institute of Biology Leiden, Leiden University, The Netherlands
| | | | - Frans Witte
- Naturalis Biodiversity Center, The Netherlands
- Institute of Biology Leiden, Leiden University, The Netherlands
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Wagner CE, Keller I, Wittwer S, Selz OM, Mwaiko S, Greuter L, Sivasundar A, Seehausen O. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Mol Ecol 2012; 22:787-98. [PMID: 23057853 DOI: 10.1111/mec.12023] [Citation(s) in RCA: 310] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/26/2012] [Accepted: 07/04/2012] [Indexed: 01/08/2023]
Abstract
Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction-site-associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence-based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher-level relationships. These patterns have generally been attributed to the very recent origin (<15,000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post-speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.
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Affiliation(s)
- Catherine E Wagner
- Department of Fish Ecology & Evolution, EAWAG Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
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10
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Miyagi R, Terai Y, Aibara M, Sugawara T, Imai H, Tachida H, Mzighani SI, Okitsu T, Wada A, Okada N. Correlation between nuptial colors and visual sensitivities tuned by opsins leads to species richness in sympatric Lake Victoria cichlid fishes. Mol Biol Evol 2012; 29:3281-96. [PMID: 22617953 DOI: 10.1093/molbev/mss139] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reproductive isolation that prevents interspecific hybridization between closely related coexisting species maintains sympatric species diversity. One of the reproductive isolations is mate choice based on color signals (breeding color perceived by color vision). This is well known in several animal taxa, yet little is known about its genetic and molecular mechanism. Lake Victoria cichlid fishes are thought to be an example of sympatric species diversity. In the species inhabiting different light environments in rocky shore, speciation by sensory drive through color signals has been proposed by analyses of the long wavelength-sensitive (LWS) opsin gene and the male nuptial coloration. However, the genetic and molecular mechanism of how diversity of sympatric species occurring in the same habitat is maintained remains unknown. To address this issue, we determined nucleotide sequences of eight opsins of six sympatric species collected from a sandy-muddy shore--an ideal model system for studying sympatric species. Among eight opsins, the LWS and RH1 alleles were diversified and one particular allele is dominant or fixed in each species, and we propose that this is due to natural selection. The functions of their LWS alleles were also diversified as shown by absorption measurements of reconstituted visual pigments. To analyze the relationship between nuptial coloration and the absorption of LWS pigments, we systematically evaluated and defined nuptial coloration. We showed that the coloration was species specific with respect to hue and significantly differentiated by the index values of hue (dominant wavelength: λ(d)). The λ(d) value of the male nuptial coloration correlated with the absorption of LWS pigments from all the species, suggesting that reproductive isolation through mate choice using color signals may prevent sympatric interspecific hybridization, thereby maintaining the species diversity in sympatric species in Lake Victoria.
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Affiliation(s)
- Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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VAN DER MEER HENNYJ, VAN RIJSSEL JACCOC, WAGENAAR LEONC, WITTE FRANS. Photopic adaptations to a changing environment in two Lake Victoria cichlids. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01859.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Odhiambo EA, Mautner SI, Bock O, Sturmbauer C. Genetic distinction of four haplochromine cichlid fish species in a satellite lake of Lake Victoria, East Africa. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2011.00641.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Konijnendijk N, Joyce DA, Mrosso HDJ, Egas M, Seehausen O. Community Genetics Reveal Elevated Levels of Sympatric Gene Flow among Morphologically Similar but Not among Morphologically Dissimilar Species of Lake Victoria Cichlid Fish. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:616320. [PMID: 22164342 PMCID: PMC3227470 DOI: 10.4061/2011/616320] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 05/18/2011] [Accepted: 07/11/2011] [Indexed: 11/20/2022]
Abstract
We examined genetic structure among five species of Lake Victoria haplochromine cichlids in four island communities, using a full factorial sampling design that compared genetic differentiation between pairs of species and populations of varying morphological similarity and geographical proximity. We found that allopatric conspecific populations were on average significantly more strongly differentiated than sympatric heterospecific populations of morphologically similar species. Allopatric heterospecific populations of morphologically dissimilar species were most differentiated. Our work demonstrates that phenotypic divergence can be maintained and perhaps even evolve in sympatry despite considerable gene flow between species. Conversely, phenotypic resemblance among conspecific populations can be maintained despite geographical isolation. Additionally we show that anthropogenically increased hybridization does not affect all sympatric species evenly but predominantly affects morphologically similar and closely related species. This has important implications for the evolution of reproductive isolation between species These findings are also consistent with the hypothesis of speciation reversal due to weakening of divergent selection and reproductive isolation as a consequence of habitat homogenization and offers an evolutionary mechanistic explanation for the observation that species poor assemblages in turbid areas of the lake are characterized by just one or two species in each of a few morphologically distinct genera.
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Affiliation(s)
- N Konijnendijk
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
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Hermann CM, Sefc KM, Koblmüller S. Ancient origin and recent divergence of a haplochromine cichlid lineage from isolated water bodies in the East African Rift system. JOURNAL OF FISH BIOLOGY 2011; 79:1356-1369. [PMID: 22026612 DOI: 10.1111/j.1095-8649.2011.03101.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phylogenetic analysis identified haplochromine cichlids from isolated water bodies in the eastern branch of the East African Rift system as an ancient lineage separated from their western sister group in the course of the South Kenyan-North Tanzanian rift system formation. Within this lineage, the close phylogenetic relatedness among taxa indicates a recent common ancestry and historical connections between now separated water bodies. In connection with a total lack of local genetic diversity attributable to population bottlenecks, the data suggest cycles of extinction and colonization in the unstable habitat provided by the small lakes and rivers in this geologically highly active area.
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Affiliation(s)
- C M Hermann
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, A-8010 Graz, Austria
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Bezault E, Mwaiko S, Seehausen O. POPULATION GENOMIC TESTS OF MODELS OF ADAPTIVE RADIATION IN LAKE VICTORIA REGION CICHLID FISH. Evolution 2011; 65:3381-97. [DOI: 10.1111/j.1558-5646.2011.01417.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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