1
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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2
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Gwak WS, Roy A. Genetic Diversity and Population Structure of Brown Croaker ( Miichthys miiuy) in Korea and China Inferred from mtDNA Control Region. Genes (Basel) 2023; 14:1692. [PMID: 37761832 PMCID: PMC10530706 DOI: 10.3390/genes14091692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Brown croaker (Miichthys miiuy), a species of fish with significant commercial value, is found in the coastal seas of Korea, China, and Japan. The genetic diversity and population structure of a representative sample of brown croaker specimens were assessed based on the control region of their mitochondrial DNA (mtDNA). Samples from a total of 115 individuals were collected from three separate locations, one in China (Lianyungang) and two in Korea (Mokpo and Gyeongnyeolbiyeoldo Island). Analysis of the 436-base-pair mtDNA control region revealed that the haplotype diversity ranged from 0.973 ± 0.025 to 0.988 ± 0.008, while the nucleotide diversity ranged from 0.012 ± 0.006 to 0.017 ± 0.009. The level of genetic diversity, star-shaped haplotype network, significant Fu's Fs test, and analysis of the mismatch distribution all suggested that this species has experienced population expansion. Fixation index analysis indicated that the population collected at the site in China differed significantly from the two populations obtained in Korea. The findings of this study extend the general understanding of the population structure of M. miiuy and can be used to develop strategies for effective resource management.
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Affiliation(s)
- Woo-Seok Gwak
- Department of Marine Biology and Aquaculture, The Institute of Marine Industry, Gyeongsang National University, Tongyeong 650-160, Republic of Korea;
| | - Animesh Roy
- Department of Marine Biology and Aquaculture, The Institute of Marine Industry, Gyeongsang National University, Tongyeong 650-160, Republic of Korea;
- Department of Fisheries Biology and Aquatic Environment, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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3
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Huang Q, Xu L, Xie L, Liu P, Rizo EZC, Han BP. Spatial and temporal variation of genetic diversity and genetic differentiation in Daphnia galeata populations in four large reservoirs in southern China. Front Microbiol 2022; 13:1041011. [PMID: 36439856 PMCID: PMC9691881 DOI: 10.3389/fmicb.2022.1041011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/24/2022] [Indexed: 03/21/2024] Open
Abstract
Daphnia galeata is a common and dominant species in warmer waters, and has a strong top-down effect on both phytoplankton and bacteria. The knowledge of its temporal and spatial patterns of genetic diversity is fundamental in understanding its population dynamics and potential ecological function in ecosystems. Its population genetics have been investigated at regional scales but few within regions or at smaller spatial scales. Here, we examined the fine-scale spatial genetic variation of D. galeata within four large, deep reservoirs in wet and dry seasons and the six-year variation of genetic diversity in one of the reservoirs by using cytochrome c oxidase subunit I and microsatellites (simple sequence repeat). Our study shows that fine-scale spatial genetic variation commonly occurred within the reservoirs, indicating strong environmental selection at least in the two of reservoirs with strong longitudinal gradients. Since the environmental gradients established in the dry season was largely reduced in the wet season, the fine-scale spatial genetic variation was much higher in the dry season. The dynamics of local genetic diversity did not follow the theoretical pattern of rapid erosion but peaked in mid or mid-late growth season. The local genetic diversity of D. galeata appears to be shaped and maintained not only by recruitment from resting egg banks but also by gene flow within reservoirs. The temporal and fine-scale genetic variation within a water body suggests that it is necessary to pay attention to sampling periods and locations of a given water body in regional studies.
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Affiliation(s)
- Qi Huang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
| | - Lei Xu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Lili Xie
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
| | - Ping Liu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Eric Zeus C. Rizo
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines-Visayas, Miagao, Iloilo, Philippines
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, Guangdong, China
- Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou, China
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4
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Singh P, Irisarri I, Torres-Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
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Affiliation(s)
- Pooja Singh
- Institute of Biology University of Graz Graz Austria.,Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg Hamburg Germany
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics Graz University of Technology Graz Austria.,OMICS Center Graz, BioTechMed Graz Graz Austria
| | - Hannes Svardal
- Department of Biology University of Antwerp Antwerp Belgium.,Naturalis Biodiversity Center Leiden The Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | - Alan R Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
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5
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Weber AAT, Rajkov J, Smailus K, Egger B, Salzburger W. Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes. SCIENCE ADVANCES 2021; 7:eabg5391. [PMID: 34731007 PMCID: PMC8565912 DOI: 10.1126/sciadv.abg5391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.
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6
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Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
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Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
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7
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Santos-Santos JH, Audenaert L, Verheyen E, Adriaens D. Ontogenetic divergence generates novel phenotypes in hybrid cichlids. J Anat 2021; 238:1116-1127. [PMID: 33417249 PMCID: PMC8053579 DOI: 10.1111/joa.13375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Hybridization is suggested to contribute to ecomorphological and taxonomic diversity in lacustrine East African cichlids. This is supported by studies demonstrating that genetic diversity within lake radiations has been influenced by hybridization events, leading to extensive phenotypic differentiation of genetically closely related species. Hybrid persistence and speciation in sympatry with gene flow can be explained by pleiotropy in traits involved in reproductive isolation; however, little attention has been given to how trait differentiation is established during hybrid ontogeny, and how this may relate to trophic and locomotor specialization. This study compares body shape changes in a Lake Victoria cichlid hybrid throughout its post-hatch ontogeny to those of its parental species. Across the considered age/size categories, hybrids occupy a distinct and intermediate morphological space, yet where several transgressive traits emerge. A between-group principal component analysis on body shapes across size categories reveals axes of shape variation exclusive to the hybrids in the youngest/smallest size categories. Shape differences in the hybrids involved morphological traits known to be implicated in trophic and locomotor specializations in the parental species. Combined, our findings suggest that phenotypic divergence in the hybrid can lead to functional differences that may potentially release them to some degree from competition with the parental species. These findings agree with recent literature that addresses the potential importance of hybridization for the unusually recent origin of the Lake Victoria cichlid super-species flock.
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Affiliation(s)
- Javier H Santos-Santos
- Evolutionary Morphology of Vertebrates, Ghent University, Gent, Belgium.,Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (MNCN-CSIC), Madrid, Spain
| | - Leen Audenaert
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Erik Verheyen
- OD Taxonomy and Phylogeny, Vertebrates, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerp, Belgium
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8
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Ronco F, Büscher HH, Indermaur A, Salzburger W. The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa. JOURNAL OF GREAT LAKES RESEARCH 2020; 46:1067-1078. [PMID: 33100489 PMCID: PMC7574848 DOI: 10.1016/j.jglr.2019.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ancient Lake Tanganyika in East Africa houses the world's ecologically and morphologically most diverse assemblage of cichlid fishes, and the third most species-rich after lakes Malawi and Victoria. Despite long-lasting scientific interest in the cichlid species flocks of the East African Great Lakes, for example in the context of adaptive radiation and explosive diversification, their taxonomy and systematics are only partially explored; and many cichlid species still await their formal description. Here, we provide a current inventory of the cichlid fish fauna of Lake Tanganyika, providing a complete list of all valid 208 Tanganyikan cichlid species, and discuss the taxonomic status of more than 50 undescribed taxa on the basis of the available literature as well as our own observations and collections around the lake. This leads us to conclude that there are at least 241 cichlid species present in Lake Tanganyika, all but two are endemic to the basin. We finally summarize some of the major taxonomic challenges regarding Lake Tanganyika's cichlid fauna. The taxonomic inventory of the cichlid fauna of Lake Tanganyika presented here will facilitate future research on the taxonomy and systematics and the ecology and evolution of the species flock, as well as its conservation.
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9
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Carleton KL, Yourick MR. Axes of visual adaptation in the ecologically diverse family Cichlidae. Semin Cell Dev Biol 2020; 106:43-52. [PMID: 32439270 DOI: 10.1016/j.semcdb.2020.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
The family Cichlidae contains approximately 2000 species that live in diverse freshwater habitats including murky lakes, turbid rivers, and clear lakes from both the Old and New Worlds. Their visual systems are similarly diverse and have evolved specific sensitivities that differ along several axes of variation. Variation in cornea and lens transmission affect which wavelengths reach the retina. Variation in photoreceptor number and distribution affect brightness sensitivity, spectral sensitivity and resolution. Probably their most dynamic characteristic is the variation in visual pigment peak sensitivities. Visual pigments can be altered through changes in chromophore, opsin sequence and opsin expression. Opsin expression varies by altering which of the seven available cone opsins in their genomes are turned on. These opsins can even be coexpressed to produce seemingly infinitely tunable cone sensitivities. Both chromophore and opsin expression can vary on either rapid (hours or days), slower (seasonal or ontogenetic) or evolutionary timescales. Such visual system shifts have enabled cichlids to adapt to different habitats and foraging styles. Through both short term plasticity and longer evolutionary adaptations, cichlids have proven to be ecologically successful and an excellent model for studying organismal adaptation.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Miranda R Yourick
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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10
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Weak population structure and recent demographic expansion of the monogenean parasite Kapentagyrus spp. infecting clupeid fishes of Lake Tanganyika, East Africa. Int J Parasitol 2020; 50:471-486. [PMID: 32277985 DOI: 10.1016/j.ijpara.2020.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 11/22/2022]
Abstract
Lake Tanganyika, East Africa, is the oldest and deepest African Great Lake and harbours one of the most diverse fish assemblages on earth. Two clupeid fishes, Limnothrissa miodon and Stolothrissa tanganicae, constitute a major part of the total fish catch, making them indispensable for local food security. Parasites have been proposed as indicators of stock structure in highly mobile pelagic hosts. We examined the monogeneans Kapentagyrus limnotrissae and Kapentagyrus tanganicanus (Dactylogyridae) infecting these clupeids to explore the parasites' lake-wide population structure and patterns of demographic history. Samples were collected at seven sites distributed across three sub-basins of the lake. Intraspecific morphological variation of the monogeneans (n = 380) was analysed using morphometrics and geomorphometrics of sclerotised structures. Genetic population structure of both parasite species (n = 246) was assessed based on a 415 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Overall, we observed a lack of clear geographical morphological differentiation in both parasites along a north-south axis. This lack of geographical population structure was also reflected by a large proportion of shared haplotypes, and a pattern of seemingly unrestricted gene flow between populations. Significant morphological and genetic differentiation between some populations might reflect temporal differentiation rather than geographical isolation. Overall, the shallow population structure of both species of Kapentagyrus reflects the near-panmictic population structure of both host species as previously reported. Morphological differences related to host species identity of K. tanganicanus were consistent with incipient speciation at the genetic level. Both parasite species experienced a recent demographic expansion, which might be linked to paleohydrological events. Finally, interspecific hybridisation was found in Kapentagyrus, representing the first case in dactylogyrid monogeneans.
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11
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Jones BP, Norman BF, Borrett HE, Attwood SW, Mondal MMH, Walker AJ, Webster JP, Rajapakse RPVJ, Lawton SP. Divergence across mitochondrial genomes of sympatric members of the Schistosoma indicum group and clues into the evolution of Schistosoma spindale. Sci Rep 2020; 10:2480. [PMID: 32051431 PMCID: PMC7015907 DOI: 10.1038/s41598-020-57736-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 01/07/2020] [Indexed: 11/21/2022] Open
Abstract
Schistosoma spindale and Schistosoma indicum are ruminant-infecting trematodes of the Schistosoma indicum group that are widespread across Southeast Asia. Though neglected, these parasites can cause major pathology and mortality to livestock leading to significant welfare and socio-economic issues, predominantly amongst poor subsistence farmers and their families. Here we used mitogenomic analysis to determine the relationships between these two sympatric species of schistosome and to characterise S. spindale diversity in order to identify possible cryptic speciation. The mitochondrial genomes of S. spindale and S. indicum were assembled and genetic analyses revealed high levels of diversity within the S. indicum group. Evidence of functional changes in mitochondrial genes indicated adaptation to environmental change associated with speciation events in S. spindale around 2.5 million years ago. We discuss our results in terms of their theoretical and applied implications.
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Affiliation(s)
- Ben P Jones
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Billie F Norman
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Hannah E Borrett
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Stephen W Attwood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Mohammed M H Mondal
- Department of Parasitology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Anthony J Walker
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK
| | - Joanne P Webster
- Centre for Emerging, Endemic and Exotic Diseases, Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, Hertfordshire, AL9 7TA, United Kingdom
| | - R P V Jayanthe Rajapakse
- Faculty of Veterinary Medicine and Animal Science, Department of Veterinary Pathobiology, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Scott P Lawton
- Molecular Parasitology Laboratory, School of Life Sciences, Pharmacy & Chemistry, Kingston University London, Kingston Upon Thames, Surrey, KT1 2EE, UK.
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12
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Clark FE, Kocher TD. Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish. Sci Rep 2019; 9:20213. [PMID: 31882583 PMCID: PMC6934658 DOI: 10.1038/s41598-019-55774-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/02/2019] [Indexed: 01/16/2023] Open
Abstract
B chromosomes are extra, non-essential chromosomes present in addition to the normal complement of A chromosomes. Many species of cichlid fish in Lake Malawi carry a haploid, female-restricted B chromosome. Here we show that this B chromosome exhibits drive, with an average transmission rate of 70%. The offspring of B-transmitting females exhibit a strongly female-biased sex ratio. Genotyping of these offspring reveals the B chromosome carries a female sex determiner that is epistatically dominant to an XY system on linkage group 7. We suggest that this sex determiner evolved to enhance the meiotic drive of the B chromosome. This is some of the first evidence that female meiotic drive can lead to the invasion of new sex chromosomes solely to benefit the driver, and not to compensate for skewed sex ratios.
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Affiliation(s)
- Frances E Clark
- Department of Biology, University of Maryland College Park, College Park, MD, 20742, USA.
| | - Thomas D Kocher
- Department of Biology, University of Maryland College Park, College Park, MD, 20742, USA
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13
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Niu SF, Wu RX, Zhai Y, Zhang HR, Li ZL, Liang ZB, Chen YH. Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence. PeerJ 2019; 7:e7953. [PMID: 31681517 PMCID: PMC6822595 DOI: 10.7717/peerj.7953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/26/2019] [Indexed: 11/24/2022] Open
Abstract
Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.
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Affiliation(s)
- Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yun Zhai
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Hao-Ran Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhong-Lu Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yu-Hang Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong, China
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14
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Zhang X, Zhang X, Song N, Gao T, Zhao L. Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:825-834. [PMID: 31571512 DOI: 10.1080/24701394.2019.1670820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.
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Affiliation(s)
- Xiaomeng Zhang
- Fisheries College, Ocean University of China, Qingdao, China
| | - Xiumei Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.,Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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15
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Ekimova I, Valdés Á, Chichvarkhin A, Antokhina T, Lindsay T, Schepetov D. Diet-driven ecological radiation and allopatric speciation result in high species diversity in a temperate-cold water marine genus Dendronotus (Gastropoda: Nudibranchia). Mol Phylogenet Evol 2019; 141:106609. [PMID: 31494182 DOI: 10.1016/j.ympev.2019.106609] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 07/11/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
While the majority nudibranch clades are more species rich in the tropics, the genus Dendronotus is mainly represented in Arctic and boreal regions. This distribution pattern remains poorly understood. An integrative approach and novel data provided valuable insights into processes driving Dendronotus radiation and speciation. We propose an evolutionary scenario based on molecular phylogenetics and morphological, ecological, ontogenetic data, combined with data on complex geology and paleoclimatology of this region. Estimated phylogenetic relationships based on four molecular markers (COI, 16S, H3 and 28S) shows strong correlation with radular morphology, diet and biogeographical pattern. Ancestral area reconstruction (AAR) provides evidence for a tropical Pacific origin of the genus. Based on AAR and divergence time estimates we conclude that the evolution of Dendronotus has been shaped by different processes: initial migration out of the tropics, diet-driven adaptive radiation in the North Pacific influenced by Miocene climate change, and subsequent allopatric speciation resulting from successive closings of the Bering strait and cooling of the Arctic Ocean during the Pliocene-Pleistocene. At the same time, contemporary amphiboreal species appear to have dispersed into the Atlantic fairly recently.
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Affiliation(s)
- Irina Ekimova
- Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; Far Eastern Federal University, Sukhanova str., 8, 690950 Vladivostok, Russia.
| | - Ángel Valdés
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Anton Chichvarkhin
- Far Eastern Federal University, Sukhanova str., 8, 690950 Vladivostok, Russia; A.V. Zhirmunsky Institute of Marine Biology, Russian Academy of Sciences, Palchevskogo 17, 690041 Vladivostok, Russia
| | - Tatiana Antokhina
- A.N. Severstov Institute of Ecology and Evolution, Leninskiy prosp. 33, 119071 Moscow, Russia
| | - Tabitha Lindsay
- Department of Biology, South Seattle Community College, 6000 16th Ave SW, Seattle, WA 98106, USA
| | - Dimitry Schepetov
- Lomonosov Moscow State University, Leninskie Gory 1-12, 119234 Moscow, Russia; N.K. Koltzov Institute of Developmental Biology RAS, Vavilov Str. 26, 119334 Moscow, Russia; National Research University Higher School of Economics, Myasnitskaya Str. 20, 101000 Moscow, Russia
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16
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Schedel FDB, Musilova Z, Schliewen UK. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol Biol 2019; 19:94. [PMID: 31023223 PMCID: PMC6482553 DOI: 10.1186/s12862-019-1417-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates. RESULTS Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43-33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89-20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88-25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23-18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40-26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93-5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: 'Orthochromis' indermauri and 'Haplochormis' vanheusdeni. CONCLUSIONS Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated "Melting-Pot Tanganyika" hypothesis. The radiation of the 'Lower Congo Lamprologus clade' might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi.
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Affiliation(s)
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44 Prague, Czech Republic
| | - Ulrich Kurt Schliewen
- Department of Ichthyology, SNSB - Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
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17
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De Keyzer ELR, De Corte Z, Van Steenberge M, Raeymaekers JAM, Calboli FCF, Kmentová N, N’Sibula Mulimbwa T, Virgilio M, Vangestel C, Mulungula PM, Volckaert FAM, Vanhove MPM. First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species. BMC Evol Biol 2019; 19:6. [PMID: 30621593 PMCID: PMC6323704 DOI: 10.1186/s12862-018-1325-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population. RESULTS We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a north-south axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046-0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data. CONCLUSION Our results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management.
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Affiliation(s)
- Els L. R. De Keyzer
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
- Capacities for Biodiversity and Sustainable Development (CEBioS), Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
| | - Zoë De Corte
- Joint Experimental Molecular Unit & Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
- Joint Experimental Molecular Unit & Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Maarten Van Steenberge
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
- Joint Experimental Molecular Unit & Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
- Joint Experimental Molecular Unit & Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Joost A. M. Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
- Faculty of Bioscience and Aquaculture, Nord University, Universitetsalléen 11, N-8026 Bodø, Norway
| | - Federico C. F. Calboli
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
| | | | - Massimiliano Virgilio
- Joint Experimental Molecular Unit & Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Carl Vangestel
- Joint Experimental Molecular Unit & Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Pascal Masilya Mulungula
- Département de Biologie, Centre de Recherche en Hydrobiologie, B.P. 73, Uvira, Democratic Republic of Congo
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Maarten P. M. Vanhove
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
- Capacities for Biodiversity and Sustainable Development (CEBioS), Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O.Box 17, FI-00014 Helsinki, Finland
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
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18
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Miura O, Urabe M, Nishimura T, Nakai K, Chiba S. Recent lake expansion triggered the adaptive radiation of freshwater snails in the ancient Lake Biwa. Evol Lett 2018; 3:43-54. [PMID: 30788141 PMCID: PMC6369999 DOI: 10.1002/evl3.92] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/09/2018] [Indexed: 01/08/2023] Open
Abstract
Lake expansion that leads to the formation of new habitats has potential to drive intralacustrine diversification. The ancient Lake Biwa in central Japan has historically experienced substantial changes in the lake size, and it provides a useful system for evaluating the role of lake-size fluctuations in the diversification of endemic fauna. Here, we used genome-wide DNA analyses and reconstructed the diversification history of the endemic freshwater snails belonging to the subgenus Biwamelania with respect to the geological history of Lake Biwa. We found that two genetically distinct snail lineages independently colonized Lake Biwa and they concurrently and rapidly radiated into 15 extant Biwamelania species. A combination of paleontological evidence and molecular dating technique demonstrated that the radiation of Biwamelania was tightly linked to the latest enlargement of the lake about 0.4 million years ago and suggested that increased ecological opportunity associated with the lake expansion drove the rapid adaptive radiation. We propose that the Biwamelania snails in Lake Biwa offer a promising new system for understanding the association between the geological history of the lake and rapid intralacustrine diversification.
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Affiliation(s)
- Osamu Miura
- Faculty of Agriculture and Marine Science Kochi University 200 Monobe Nankoku Kochi 783-8502 Japan
| | - Misako Urabe
- Department of Ecosystem Studies, School of Environmental Science The University of Shiga Prefecture 2500 Hassaka-cho Hikone, Shiga 522-8533 Japan
| | - Tomohiro Nishimura
- Faculty of Agriculture and Marine Science Kochi University 200 Monobe Nankoku Kochi 783-8502 Japan.,Current address: Cawthron Institute 98 Halifax Street East Nelson 7010 New Zealand
| | - Katsuki Nakai
- Lake Biwa Museum 1091 Oroshimo Kusatsu Shiga 525-0001 Japan
| | - Satoshi Chiba
- Department of Environmental Life Sciences, Graduate School of Life Sciences Tohoku University Kawauchi 41 Aoba-ku Sendai 980-0862 Japan
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19
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Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
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Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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20
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Koblmüller S, Zangl L, Börger C, Daill D, Vanhove MPM, Sturmbauer C, Sefc KM. Only true pelagics mix: comparative phylogeography of deepwater bathybatine cichlids from Lake Tanganyika. HYDROBIOLOGIA 2018; 832:93-103. [PMID: 30880831 PMCID: PMC6394743 DOI: 10.1007/s10750-018-3752-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/28/2018] [Accepted: 08/29/2018] [Indexed: 05/15/2023]
Abstract
In the absence of dispersal barriers, species with great dispersal ability are expected to show little, if at all, phylogeographic structure. The East African Great Lakes and their diverse fish faunas provide opportunities to test this hypothesis in pelagic fishes, which are presumed to be highly mobile and unrestricted in their movement by physical barriers. Here, we address the link between panmixis and pelagic habitat use by comparing the phylogeographic structure among four deepwater cichlid species of the tribe Bathybatini from Lake Tanganyika. We show that the mitochondrial genealogies (based on the most variable part or the control region) of the four species are very shallow (0.8-4% intraspecific divergence across entire distribution ranges) and that all species experienced recent population growth. A lack of phylogeographic structure in the two eupelagic species, Bathybates fasciatus and B. leo, was consistent with expectations and with findings in other pelagic cichlid species. Contrary to expectations, a clear phylogeographic structure was detected in the two benthopelagic species, B. graueri and Hemibates stenosoma. Differences in genetic diversity between eupelagic and benthopelagic species may be due to differences in their dispersal propensity, mediated by their respective predatory niches, rather than precipitated by external barriers to dispersal.
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Affiliation(s)
- Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Května 8, 603 65 Brno, Czech Republic
| | - Lukas Zangl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Christine Börger
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Daniel Daill
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
- Consultants in Aquatic Ecology and Engineering – blattfisch e.U., Gabelsbergerstraße 7, 4600 Wels, Austria
| | - Maarten P. M. Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 34 Brno, Czech Republic
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014 Helsinki, Finland
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, 3000 Louvain, Belgium
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M. Sefc
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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21
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Basiita RK, Zenger KR, Mwanja MT, Jerry DR. Gene flow and genetic structure in Nile perch, Lates niloticus, from African freshwater rivers and lakes. PLoS One 2018; 13:e0200001. [PMID: 29995906 PMCID: PMC6040733 DOI: 10.1371/journal.pone.0200001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Geological evolution of the African continent has been subject to complex processes including uplift, volcanism, desert formation and tectonic rifting. This complex geology has created substantial biogeographical barriers, and coupled with anthropogenic introductions of freshwater fishes, has influenced the genetic diversity, connectivity and sub-structuring of the teleost fauna. Nile perch, Lates niloticus, is an iconic fish in Africa and is of high commercial importance, both in the species' native range and where it has been translocated. However, the species is in decline and there is a need to understand its population genetic structure to facilitate sustainable management of the fishery and aquaculture development. METHODOLOGY Nile perch tissue samples were acquired from two West and four East (Lakes; Albert, Kyoga, Victoria and Turkana) African locations. Nineteen polymorphic microsatellite loci were used to study the genetic variation among populations across regions (West and East Africa), as well as between native and introduced environments within East Africa. PRINCIPAL FINDINGS AND THEIR SIGNIFICANCE Results revealed strong and significant genetic structuring among populations across the sampled distribution (divergence across regions, FCT = 0.26, P = 0.000). STRUCTURE analysis at a broad scale revealed K = 2 clusters, the West African individuals were assigned to one cluster, while all individuals from the East African region, regardless of whether native or introduced, were assigned to another cluster. The distinct genetic clusters identified in the current study between the West and East African Nile perch, appear to have been maintained by presence of biogeographic barriers and restricted gene flow between the two regions. Therefore, any translocations of Nile perch should be carefully considered across the regions of West and East Africa. Further analysis at a regional scale revealed further structuring of up to K = 3 genetic clusters in East African Nile perch. Significantly (P < 0.05) lower genetic diversity based on analysis of allelic richness (AR) was obtained for the two translocated populations of Lake Kyoga (AR = 3.61) and Lake Victoria (AR = 3.52), compared to Nile perch populations from their putative origins of Lakes Albert (AR = 4.12) and Turkana (AR = 4.43). The lower genetic diversity in the translocated populations may be an indication of previous bottlenecks and may also indicate a difficulty for these populations to persist and adapt to climatic changes and anthropogenic pressures that are currently present in the East African region.
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Affiliation(s)
- Rose K. Basiita
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- National Agricultural Research Organization, National Fisheries Resources Research Institute, Aquaculture Research and Development Center Kajjansi, Kampala, Uganda
- WorldFish Zambia Office, Ridgeway Lusaka, Zambia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Matthew T Mwanja
- National Agricultural Research Organization, National Fisheries Resources Research Institute, Aquaculture Research and Development Center Kajjansi, Kampala, Uganda
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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22
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Gao TX, Yang TY, Yanagimoto T, Xiao YS. Levels and patterns of genetic variation in Japanese whiting (Sillago japonica) based on mitochondrial DNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:172-183. [DOI: 10.1080/24701394.2018.1467411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tian-Xiang Gao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhejiang, China
| | - Tian-Yan Yang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhejiang, China
| | - Takashi Yanagimoto
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Japan
| | - Yong-Shuang Xiao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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23
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Pauquet G, Salzburger W, Egger B. The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni. Ecol Evol 2018; 8:5637-5648. [PMID: 29938080 PMCID: PMC6010872 DOI: 10.1002/ece3.4092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Astatotilapia burtoni is a member of the "modern haplochromines," the most species-rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d-loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction-associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP-based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake-level fluctuations leading to past contact zones between otherwise isolated populations and large-scale migration events.
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Affiliation(s)
| | | | - Bernd Egger
- Zoological InstituteUniversity of BaselBaselSwitzerland
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24
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Rahmouni C, Vanhove MPM, Šimková A. Underexplored diversity of gill monogeneans in cichlids from Lake Tanganyika: eight new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) from the northern basin of the lake, with remarks on the vagina and the heel of the male copulatory organ. Parasit Vectors 2017; 10:591. [PMID: 29197419 PMCID: PMC5712084 DOI: 10.1186/s13071-017-2460-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 10/09/2017] [Indexed: 11/17/2022] Open
Abstract
Background Lake Tanganyika harbours the most diverse cichlid assemblage of the Great African Lakes. Considering its cichlid flocks consist of approximately 250 endemic species, we can hypothesize a high species-richness in their often quite host-specific monogenean ectoparasites belonging to Cichlidogyrus Paperna, 1960. Yet, only 24 species were described from Tanganyikan hosts and some host tribes have never been investigated for monogeneans. This study presents the first parasitological examination of species of the tribes Cyprichromini (Cyprichromis microlepidotus (Poll, 1956)), Eretmodini (Eretmodus marksmithi Burgess, 2012 and Tanganicodus irsacae Poll, 1950) and Ectodini (Aulonocranus dewindti (Boulenger, 1899)). Specimens of the ectodine Ophthalmotilapia nasuta (Poll & Matthes, 1962) from which four Cichlidogyrus spp. have been previously described from more southern localities were also studied. Further, we discuss the haptor configuration in Tanganyikan Cichlidogyrus spp. and highlight the morphological diversity of the vagina, and that of the heel, a sclerotized part of the male copulatory organ, absent in some species of Cichlidogyrus. Methods Cichlidogyrus spp. were isolated from gills and fixed using GAP. Haptoral and genital hard parts were measured and drawn by means of a phase contrast microscopic examination. Results We describe eight new species: Cichlidogyrus milangelnari n. sp. on C. microlepidotus; C. jeanloujustinei n. sp. on E. marksmithi; C. evikae n. sp. on T. irsacae; C. aspiralis n. sp., C. glacicremoratus n. sp. and C. rectangulus n. sp. on O. nasuta; and C. pseudoaspiralis n. sp. and C. discophonum n. sp. on A. dewindti. Three haptoral morphotypes were recognized among the new species. Species of Cichlidogyrus from closely related hosts exhibited the same morphotypes. Geographical variation in Cichlidogyrus spp. fauna as observed in O. nasuta and three morphotypes were distinguished. Finally, we listed 111 Cichlidogyrus species, of which 27 and three Tanganyikan species lack sclerotized vagina and heel, respectively, just like 19 and seven species outside of the lake. Conclusions Haptoral and genital features in the Tanganyikan Cichlidogyrus fauna reflect the phylogenetic relationships of their cichlid hosts. It seems that several lineages of Cichlidogyrus spp. exist in Lake Tanganyika but further studies are necessary to confirm this hypothesis and answer questions related to Lake Tanganyika and its cichlids. Electronic supplementary material The online version of this article (10.1186/s13071-017-2460-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chahrazed Rahmouni
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic.
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic.,Capacities for Biodiversity and Sustainable Development (CEBioS), Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Charles Deberiotstraat 32, B-3000, Leuven, Belgium.,Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, B-3590, Diepenbeek, Belgium
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37, Brno, Czech Republic
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25
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Egger B, Roesti M, Böhne A, Roth O, Salzburger W. Demography and genome divergence of lake and stream populations of an East African cichlid fish. Mol Ecol 2017; 26:5016-5030. [DOI: 10.1111/mec.14248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Bernd Egger
- Zoological Institute; University of Basel; Basel Switzerland
| | - Marius Roesti
- Zoological Institute; University of Basel; Basel Switzerland
- Department of Zoology; Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada
| | - Astrid Böhne
- Zoological Institute; University of Basel; Basel Switzerland
| | - Olivia Roth
- Evolutionary Ecology of Marine Fishes; Helmholtz Zentrum für Ozeanforschung Kiel (GEOMAR); Kiel Germany
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26
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Basiita RK, Zenger KR, Jerry DR. Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish, Bagrus docmak, in East Africa. Ecol Evol 2017; 7:6172-6187. [PMID: 28861223 PMCID: PMC5574809 DOI: 10.1002/ece3.3153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 11/18/2022] Open
Abstract
The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (-3.769 and -5.049; p < .05). Heterozygosity deficiencies and restricted effective population size (NeLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (ɸST = 0.62 for mtDNA; p < .001) and contemporary (microsatellite FST = 0.460; p < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro- and micro-evolutionary forces in the formation of the East African teleost fauna.
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Affiliation(s)
- Rose Komugisha Basiita
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
- National Agricultural Research OrganizationNational Fisheries Resources Research InstituteAquaculture Research and Development Center KajjansiKampalaUganda
| | - Kyall Richard Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
| | - Dean Robert Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Marine and Environmental SciencesJames Cook UniversityTownsvilleQldAustralia
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27
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Hata H, Ochi H. Depth and substratum differentiations among coexisting herbivorous cichlids in Lake Tanganyika. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160229. [PMID: 28018609 PMCID: PMC5180107 DOI: 10.1098/rsos.160229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
Cichlid fish in Lake Tanganyika represent a system of adaptive radiation in which eight ancestral lineages have diversified into hundreds of species through adaptation to various niches. However, Tanganyikan cichlids have been thought to be oversaturated, that is, the species number exceeds the number of niches and ecologically equivalent and competitively even species coexist. However, recent studies have shed light on niche segregation on a finer scale among apparently equivalent species. We observed depth and substratum preferences of 15 herbivorous cichlids from four ecomorphs (i.e. grazer, browser, scraper and scooper) on a rocky littoral slope for 14 years. Depth differentiation was detected among grazers that defended feeding territories and among browsers with feeding territories. Cichlid species having no feeding territory also showed specificity on depth and substratum, resulting in habitat segregation among species that belong to the same ecomorph. Phylogenetically close species did not occupy adjacent depths, nor the opposite depth zones. Our findings suggest that apparently equivalent species of the same ecomorph coexist parapatrically along depth on a few-metre scale, or coexist with different substratum preferences on the rocky shore, and this niche segregation may have been acquired by competition between encountering equivalent species through repetitive lake-level fluctuations.
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Affiliation(s)
- Hiroki Hata
- Graduate School of Science and Engineering, Ehime University, 2–5 Bunkyo, Matsuyama, Ehime, Japan
| | - Haruki Ochi
- 4-4-7 Higashimon-cho, Imabari 794-0033, Japan
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28
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Hablützel PI, Grégoir AF, Vanhove MPM, Volckaert FAM, Raeymaekers JAM. Weak link between dispersal and parasite community differentiation or immunogenetic divergence in two sympatric cichlid fishes. Mol Ecol 2016; 25:5451-5466. [PMID: 27596520 DOI: 10.1111/mec.13833] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 02/03/2023]
Abstract
Geographical isolation, habitat variation and trophic specialization have contributed to a large extent to the astonishing diversity of cichlid fishes in the Great East African lakes. Because parasite communities often vary across space and environments, parasites can accompany and potentially enhance cichlid species diversification. However, host dispersal may reduce opportunities for parasite-driven evolution by homogenizing parasite communities and allele frequencies of immunity genes. To test for the relationships between parasite community variation, host dispersal and parasite-induced host evolution, we studied two sympatric cichlid species with contrasting dispersal capacities along the shores of southern Lake Tanganyika. Whereas the philopatric Tropheus moorii evolved into several genetically differentiated colour morphs, Simochromis diagramma is phenotypically rather uniform across its distribution range and shows only weak population structure. Populations of both species were infected with divergent parasite communities and harbour differentiated variant pools of an important set of immune genes, the major histocompatibility complex (MHC). The overall extent of geographical variation of parasites and MHC genes was similar between host species. This indicates that immunogenetic divergence among populations of Lake Tanganyika cichlids can occur even in species that are strongly dispersing. However, because this also includes species that are phenotypically uniform, parasite-induced evolution may not represent a key factor underlying species diversification in this system.
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Affiliation(s)
- P I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium.
| | - A F Grégoir
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium
| | - M P M Vanhove
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - F A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium
| | - J A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. de Bériotstraat 32, B-3000, Leuven, Belgium.,Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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29
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Clark FE, Conte MA, Ferreira-Bravo IA, Poletto AB, Martins C, Kocher TD. Dynamic Sequence Evolution of a Sex-Associated B Chromosome in Lake Malawi Cichlid Fish. J Hered 2016; 108:53-62. [PMID: 27630131 DOI: 10.1093/jhered/esw059] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
B chromosomes are extra chromosomes found in many species of plants, animals, and fungi. B chromosomes often manipulate common cellular processes to increase their frequency, sometimes to the detriment of organismal fitness. Here, we characterize B chromosomes in several species of Lake Malawi cichlid fish. Whole genome sequencing of Metriaclima zebra "Boadzulu" individuals revealed blocks of sequence with unusually high sequence coverage, indicative of increased copy number of those sequences. These regions of high sequence coverage were found only in females. SNPs unique to the high copy number sequences permitted the design of specific amplification primers. These primers amplified fragments only in Metriaclima lombardoi individuals that carried a cytologically identified B chromosome (B-carriers), indicating these extra copies are located on the B chromosome. These same primers were used to identify B-carrying individuals in additional species from Lake Malawi. Across 7 species, a total of 43 B-carriers were identified among 323 females. B-carriers were exclusively female; no B chromosomes were observed in the 317 males surveyed from these species. Quantitative analysis of the copy number variation of B-specific sequence blocks suggests that B-carriers possess a single B chromosome, consistent with previous karyotyping of M. lombardoi A single B chromosome in B-carriers is consistent with 2 potential drive mechanisms: one involving nondisjunction and preferential segregation in a mitotic division prior to the germ-line, and the other involving preferential segregation during meiosis I.
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Affiliation(s)
- Frances E Clark
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Matthew A Conte
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Irani A Ferreira-Bravo
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Andreia B Poletto
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Cesar Martins
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Thomas D Kocher
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins).
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30
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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31
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Powder KE, Albertson RC. Cichlid fishes as a model to understand normal and clinical craniofacial variation. Dev Biol 2016; 415:338-346. [PMID: 26719128 PMCID: PMC4914429 DOI: 10.1016/j.ydbio.2015.12.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/14/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023]
Abstract
We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.
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Affiliation(s)
- Kara E Powder
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
| | - R Craig Albertson
- Department of Biology, University of Massachusetts Amherst, 221 Morrill Science Center South, 611 North Pleasant Street, Amherst, MA 01003, USA.
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32
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Takahashi T, Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 2016; 100:234-242. [PMID: 27068840 DOI: 10.1016/j.ympev.2016.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/16/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.
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Affiliation(s)
- Tetsumi Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; National Institute of Genetics, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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33
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Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection. Sci Rep 2016; 6:20954. [PMID: 26879532 PMCID: PMC4754680 DOI: 10.1038/srep20954] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/13/2016] [Indexed: 12/30/2022] Open
Abstract
Schistosoma mansoni is a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics to S. mansoni based on high-coverage resequencing data from 10 global isolates and an isolate of the closely-related Schistosoma rodhaini, which infects rodents. Using population genetic tests, we document genes under directional and balancing selection in S. mansoni that may facilitate adaptation to the human host. Coalescence modeling reveals the speciation of S. mansoni and S. rodhaini as 107.5-147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate that S. mansoni originated in East Africa and experienced a decline in effective population size 20-90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence that S. mansoni migrated to the New World with the 16-19th Century Atlantic Slave Trade.
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34
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Developmental basis of phenotypic integration in two Lake Malawi cichlids. EvoDevo 2016; 7:3. [PMID: 26798449 PMCID: PMC4721197 DOI: 10.1186/s13227-016-0040-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Background Cichlid fishes from the Rift Lakes of East Africa have undergone the most spectacular adaptive radiations in vertebrate history. Eco-morphological adaptations in lakes Victoria, Malawi and Tanganyika have resulted in a vast array of skull shapes and sizes, yet primary axes of morphological variation are conserved in all three radiations, prominently including the size of the preorbital region of the skull. This conserved pattern suggests that development may constrain the trajectories of cichlid head morphological evolution. Results Here, we (1) present a comparative analysis of adult head morphology in two sand-dweller cichlids from Lake Malawi with preorbital size differences representative of the main axis of variation among the three lakes and (2) analyze the ontogeny of shape and size differences by focusing on known developmental modules throughout the head. We find that (1) developmental differences between the two species correlate with known developmental modules; (2) differences in embryonic cartilage development result in phenotypically integrated changes among all bones derived from a single cartilage, while differences in dermal bone development tend to influence isolated regions within a bone; and lastly (3) species-specific morphologies appear in the embryo as subtle differences, which become progressively amplified throughout ontogeny. We propose that this amplification takes place at skeletal growth zones, the locations and shapes of which are patterned during embryogenesis. Conclusions This study is the most anatomically comprehensive analysis of the developmental differences underlying cichlid skull evolution in the Rift Lakes of East Africa. The scale of our analysis reveals previously unnoticed correlations between developmental modules and patterns of phenotypic integration. We propose that the primary axes of morphological variation among East African cichlid adaptive radiations are constrained by the hierarchical modularity of the teleost head skeleton.
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35
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Elderkin CL, Clewing C, Wembo Ndeo O, Albrecht C. Molecular phylogeny and DNA barcoding confirm cryptic species in the African freshwater oysterEtheria ellipticaLamarck, 1807 (Bivalvia: Etheriidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12734] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Curt L. Elderkin
- Department of Biology; The College of New Jersey; Ewing NJ 08638 USA
| | - Catharina Clewing
- Department of Animal Ecology and Systematics; Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 IFZ; 35392 Giessen Germany
| | - Oscar Wembo Ndeo
- Hydrobiological Department; Faculty of Sciences; University of Kisangani; Kisangani Oriental Province DR Congo
| | - Christian Albrecht
- Department of Animal Ecology and Systematics; Justus Liebig University Giessen; Heinrich-Buff-Ring 26-32 IFZ; 35392 Giessen Germany
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Cruz-Jofré F, Morales P, Vila I, Esquer-Garrigos Y, Hugueny B, Gaubert P, Poulin E, Méndez MA. Geographical isolation and genetic differentiation: the case ofOrestias ascotanensis(Teleostei: Cyprinodontidae), an Andean killifish inhabiting a highland salt pan. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Franco Cruz-Jofré
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Escuela de Medicina Veterinaria; Facultad de Medicina Veterinaria y Recursos Naturales; Universidad Santo Tomás; Avenida Limonares 190 Viña del Mar Chile
| | - Pamela Morales
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
| | - Irma Vila
- Laboratorio de Limnología; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Yareli Esquer-Garrigos
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Bernard Hugueny
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
| | - Philippe Gaubert
- UMR BOREA; Département Milieux et Peuplements Aquatiques; MNHN-CNRS 7208-IRD 207-UPMC; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris France
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UM2/CNRS/IRD; Université de Montpellier; Place Eugène Bataillon, CC 64 34095 Montpellier, Cedex 05 France
| | - Elie Poulin
- Laboratorio de Ecología Molecular; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
| | - Marco A. Méndez
- Laboratorio de Genética y Evolución; Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Casilla 653 Ñuñoa Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB), Departamento de Ciencias Ecológicas; Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425, Casilla 653 Ñuñoa Santiago Chile
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37
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Morris J, Ford AGP, Ali JR, Peart CR, Bills R, Day JJ. High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jake Morris
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Antonia G. P. Ford
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Jarome R. Ali
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Claire R. Peart
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Roger Bills
- South African Institute for Aquatic Biodiversity; Private Bag 1015 Grahamstown 6140 South Africa
| | - Julia J. Day
- Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
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38
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Kavembe GD, Franchini P, Irisarri I, Machado-Schiaffino G, Meyer A. Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa. J Mol Evol 2015; 81:90-109. [DOI: 10.1007/s00239-015-9696-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/29/2015] [Indexed: 11/29/2022]
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39
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Vanhove MPM, Pariselle A, Van Steenberge M, Raeymaekers JAM, Hablützel PI, Gillardin C, Hellemans B, Breman FC, Koblmüller S, Sturmbauer C, Snoeks J, Volckaert FAM, Huyse T. Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites. Sci Rep 2015; 5:13669. [PMID: 26335652 PMCID: PMC4558575 DOI: 10.1038/srep13669] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 07/23/2015] [Indexed: 11/09/2022] Open
Abstract
The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebrate radiation, we study monogenean parasites infecting tropheine cichlids from Lake Tanganyika. Monogeneans are flatworms usually infecting the body surface and gills of fishes. In contrast to many other parasites, they depend only on a single host species to complete their lifecycle. Our spatially comprehensive combined nuclear-mitochondrial DNA dataset of the parasites covering almost all tropheine host species (N = 18), reveals species-rich parasite assemblages and shows consistent host-specificity. Statistical comparisons of host and parasite phylogenies based on distance and topology-based tests demonstrate significant congruence and suggest that host-switching is rare. Molecular rate evaluation indicates that species of Cichlidogyrus probably diverged synchronically with the initial radiation of the tropheines. They further diversified through within-host speciation into an overlooked species radiation. The unique life history and specialisation of certain parasite groups has profound evolutionary consequences. Hence, evolutionary parasitology adds a new dimension to the study of biodiversity hotspots like Lake Tanganyika.
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Affiliation(s)
- Maarten P M Vanhove
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic.,Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research, 46.7 km Athens-Sounio Avenue, PO Box 712, Anavyssos GR-190 13, Greece
| | - Antoine Pariselle
- Institut des Sciences de l'Évolution, IRD-CNRS-Université Montpellier 2, CC 063, Place Eugène Bataillon, F-34095 Montpellier cedex 05, France
| | - Maarten Van Steenberge
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium.,Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Pascal I Hablützel
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Céline Gillardin
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Floris C Breman
- Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Christian Sturmbauer
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
| | - Jos Snoeks
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Tine Huyse
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium.,Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
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40
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Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis GM, Ferguson SH, Ford JK, Ford MJ, Garilao C, Gilbert MTP, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SYW, Foote AD. Geographic and temporal dynamics of a global radiation and diversification in the killer whale. Mol Ecol 2015; 24:3964-79. [PMID: 26087773 DOI: 10.1111/mec.13284] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 02/05/2023]
Abstract
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Kim M Parsons
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Lance G Barrett-Lennard
- Vancouver Aquarium Marine Science Centre, 845 Avison Way, Vancouver, British Columbia, V6G 3E2, Canada
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Av. Itália km. 8 s/n, Campus Carreiros, Rio Grande, RS, 96201-900, Brazil
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - John W Durban
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA.,Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Graeme M Ellis
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Steven H Ferguson
- Fisheries & Oceans Canada, 501 University Crescent, Winnipeg, Manitoba, R3T 2N6, Canada
| | - John K Ford
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, British Columbia, Canada
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA 2725 Montlake Blvd E, Seattle, WA, USA
| | - Cristina Garilao
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 2, 24105, Kiel, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Trace and Environmental DNA laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6845, Australia
| | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, Albert-Ludwigs-University of Freiburg, Tennenbacher Strasse 4, 79106, Freiburg, Germany
| | - Craig O Matkin
- North Gulf Oceanic Society, 3430 Main St. Ste. B1, Homer, AK, 99603, USA
| | - Stephen D Petersen
- Assiniboine Park Zoo, 2595 Roblin Blvd, Winnipeg, Manitoba, R3P 2N7, Canada
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Ingrid N Visser
- Orca Research Trust, P.O. Box 402043, Tutukaka, Northland, 0153, New Zealand
| | - Paul R Wade
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew D Foote
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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41
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Seehausen O. Process and pattern in cichlid radiations - inferences for understanding unusually high rates of evolutionary diversification. THE NEW PHYTOLOGIST 2015; 207:304-312. [PMID: 25983053 DOI: 10.1111/nph.13450] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/26/2015] [Indexed: 05/15/2023]
Abstract
The cichlid fish radiations in the African Great Lakes differ from all other known cases of rapid speciation in vertebrates by their spectacular trophic diversity and richness of sympatric species, comparable to the most rapid angiosperm radiations. I review factors that may have facilitated these radiations and compare these with insights from recent work on plant radiations. Work to date suggests that it was a coincidence of ecological opportunity, intrinsic ecological versatility and genomic flexibility, rapidly evolving behavioral mate choice and large amounts of standing genetic variation that permitted these spectacular fish radiations. I propose that spatially orthogonal gradients in the fit of phenotypes to the environment facilitate speciation because they allow colonization of alternative fitness peaks during clinal speciation despite local disruptive selection. Such gradients are manifold in lakes because of the interaction of water depth as an omnipresent third spatial dimension with other fitness-relevant variables. I introduce a conceptual model of adaptive radiation that integrates these elements and discuss its applicability to, and predictions for, plant radiations.
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Affiliation(s)
- Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- EAWAG Centre for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
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42
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Givnish TJ. Adaptive radiation versus 'radiation' and 'explosive diversification': why conceptual distinctions are fundamental to understanding evolution. THE NEW PHYTOLOGIST 2015; 207:297-303. [PMID: 26032979 DOI: 10.1111/nph.13482] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 05/01/2015] [Indexed: 05/23/2023]
Abstract
Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within a lineage. Recently, some researchers have begun to use 'adaptive radiation' or 'radiation' as synonymous with 'explosive species diversification'. This essay aims to clarify distinctions between these concepts, and the related ideas of geographic speciation, sexual selection, key innovations, key landscapes and ecological keys. Several examples are given to demonstrate that adaptive radiation and explosive diversification are not the same phenomenon, and that focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some 'radiations' involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of 'adaptive radiation' appear to involve effects driven partly by geographic speciation, species' dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity.
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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43
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Stelkens RB, Schmid C, Seehausen O. Hybrid breakdown in cichlid fish. PLoS One 2015; 10:e0127207. [PMID: 25996870 PMCID: PMC4440740 DOI: 10.1371/journal.pone.0127207] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/13/2015] [Indexed: 12/22/2022] Open
Abstract
Studies from a wide diversity of taxa have shown a negative relationship between genetic compatibility and the divergence time of hybridizing genomes. Theory predicts the main breakdown of fitness to happen after the F1 hybrid generation, when heterosis subsides and recessive allelic (Dobzhansky-Muller) incompatibilities are increasingly unmasked. We measured the fitness of F2 hybrids of African haplochromine cichlid fish bred from species pairs spanning several thousand to several million years divergence time. F2 hybrids consistently showed the lowest viability compared to F1 hybrids and non-hybrid crosses (crosses within the grandparental species), in agreement with hybrid breakdown. Especially the short- and long-term survival (2 weeks to 6 months) of F2 hybrids was significantly reduced. Overall, F2 hybrids showed a fitness reduction of 21% compared to F1 hybrids, and a reduction of 43% compared to the grandparental, non-hybrid crosses. We further observed a decrease of F2 hybrid viability with the genetic distance between grandparental lineages, suggesting an important role for negative epistatic interactions in cichlid fish postzygotic isolation. The estimated time window for successful production of F2 hybrids resulting from our data is consistent with the estimated divergence time between the multiple ancestral lineages that presumably hybridized in three major adaptive radiations of African cichlids.
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Affiliation(s)
| | - Corinne Schmid
- Department of Aquatic Ecology and Macroevolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Ole Seehausen
- Department of Aquatic Ecology and Macroevolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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44
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Husemann M, Nguyen R, Ding B, Danley PD. A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling. Mol Ecol 2015; 24:2686-701. [DOI: 10.1111/mec.13205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Martin Husemann
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
- Department of General Zoology; Institute of Biology; Martin-Luther University Halle-Wittenberg; Hoher Weg 8 Halle (Saale) D-06120 Germany
| | - Rachel Nguyen
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
| | - Baoqing Ding
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
| | - Patrick D. Danley
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
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45
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Hata H, Shibata J, Omori K, Kohda M, Hori M. Depth segregation and diet disparity revealed by stable isotope analyses in sympatric herbivorous cichlids in Lake Tanganyika. ZOOLOGICAL LETTERS 2015; 1:15. [PMID: 26605060 PMCID: PMC4657292 DOI: 10.1186/s40851-015-0016-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/15/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Lake Tanganyika in the African Great Rift Valley is known as a site of adaptive radiation in cichlid fishes. Diverse herbivorous fishes coexist on a rocky littoral of the lake. Herbivorous cichlids have acquired multiple feeding ecomorphs, including grazer, browser, scraper, and scooper, and are segregated by dietary niche. Within each ecomorph, however, multiple species apparently coexist sympatrically on a rocky slope. Previous observations of their behavior show that these cichlid species inhabit discrete depths separated by only a few meters. In this paper, using carbon (C) and nitrogen (N) stable isotope ratios as markers, we followed the nutritional uptake of cichlid fishes from periphyton in their feeding territories at various depths. RESULTS δ(15)N of fish muscles varied among cichlid ecomorphs; this was significantly lower in grazers than in browsers and scoopers, although δ(15)N levels in periphyton within territories did not differ among territorial species. This suggests that grazers depend more directly on primary production of periphyton, while others ingest animal matter from higher trophic levels. With respect to δ(13)C, only plankton eaters exhibited lower values, suggesting that these fishes depend on production of phytoplankton, while the others depend on production of periphyton. Irrespective of cichlid ecomorph, δ(13)C of periphyton correlated significantly with habitat depth, and decreased as habitat depth became deeper. δ(13)C in territorial fish muscles was significantly related to that of periphyton within their territories, regardless of cichlid ecomorph, which suggests that these herbivorous cichlids depend on primary production of periphyton within their territories. CONCLUSIONS Carbon and nitrogen stable isotope ratios varied among ecomorphs and among cichlid species in the same ecomorphs sympatrically inhabiting a littoral area of Lake Tanganyika, suggesting that these cichlids are segregated by nutrient source due to varying dependency on periphyton in different ecomorphs (especially between grazers and browsers), and due to segregation of species of the same ecomorph by feeding depth, grazers and browsers in particular.
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Affiliation(s)
- Hiroki Hata
- />Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo, Matsuyama, Ehime Japan
| | - Jyunya Shibata
- />Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo, Matsuyama, Ehime Japan
- />Environmental Research and Management Center, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima Japan
| | - Koji Omori
- />Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo, Matsuyama, Ehime Japan
| | - Masanori Kohda
- />Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka Japan
| | - Michio Hori
- />Kyoto University, Yoshida-Honmachi, Sakyo, Kyoto Japan
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46
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Koblmüller S, Odhiambo EA, Sinyinza D, Sturmbauer C, Sefc KM. Big fish, little divergence: phylogeography of Lake Tanganyika's giant cichlid, Boulengerochromis microlepis. HYDROBIOLOGIA 2015; 748:29-38. [PMID: 25983338 PMCID: PMC4430823 DOI: 10.1007/s10750-014-1863-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The largely endemic cichlid species flocks of the East African Great Lakes are among the prime examples for explosive speciation and adaptive radiation. Speciation rates differ among cichlid lineages, and the propensity to radiate has been linked to intrinsic and extrinsic factors such as sexual selection and ecological opportunity. Remarkably, only one cichlid tribe-the Boulengerochromini-comprises just a single species, Boulengerochromis microlepis, a predominantly piscivorous endemic of Lake Tanganyika and the world's largest cichlid. While the lineage diverged from its closest relatives at the onset of the Lake Tanganyika radiation >8 MYA, mitochondrial control region sequences collected in this study dated the most recent common ancestor of B. microlepis to ~60-110 KYA. There was no evidence of phylogeographic structure in the lake-wide sample. Patterns of genetic diversity and demographic analyses were consistent with slow and steady population growth throughout the reconstructed timescale. Additionally, the shallow divergence within the species may be related to a possibly large variance in reproductive success in this highly fecund species. Trophic niche space restriction by sympatric piscivores, lack of geographic structure, low potential for sexual selection arising from the monogamous mating system and extinction may have contributed to keeping the lineage monotypic.
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Affiliation(s)
- Stephan Koblmüller
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | - Elizabeth A Odhiambo
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria; Ichthyology Section, National Museums of Kenya, Nairobi, Kenya
| | - Danny Sinyinza
- Department of Fisheries, Ministry of Agriculture and Lifestock, Mpulungu, Zambia
| | - Christian Sturmbauer
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M Sefc
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria
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Daniels SR, Phiri EE, Klaus S, Albrecht C, Cumberlidge N. Multilocus Phylogeny of the Afrotropical Freshwater Crab Fauna Reveals Historical Drainage Connectivity and Transoceanic Dispersal Since the Eocene. Syst Biol 2015; 64:549-67. [PMID: 25649930 DOI: 10.1093/sysbio/syv011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/28/2015] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensive taxonomic sampling of any freshwater crab family globally, and explores the impact of paleodrainage interconnectivity on cladogenesis among freshwater crabs. Phylogenetic analyses of the total evidence data using maximum-likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) produced a robust statistically well-supported tree topology that reaffirmed the monophyly of the Afrotropical freshwater crab fauna. The estimated divergence times suggest that the Afrotropical Potamonautidae diverged during the Eocene. Cladogenesis within and among several genera occurred predominantly during the Miocene, which was associated with major tectonic and climatic ameliorations throughout the region. Paleodrainage connectivity was observed with specimens from the Nilo-Sudan and East African coast proving to be sister to specimens from the Upper Guinea Forests in West Africa. In addition, we observed strong sister taxon affinity between specimens from East Africa and the Congo basin, including specimens from Lake Tanganyika, while the southern African fauna was retrieved as sister to the Angolan taxa. Within the East African clade we observed two independent transoceanic dispersal events, one to the Seychelles Archipelago and a second to Madagascar, while we observe a single transoceanic dispersal event from West Africa to São Tomé. The ancestral area estimation suggested a West African/East African ancestral range for the family with multiple dispersal events between southern Africa and East Africa, and between East Africa and Central Africa The taxonomic implications of our results are discussed in light of the widespread paraphyly evident among a number of genera.
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Affiliation(s)
- Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA
| | - Ethel E Phiri
- Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA
| | - Sebastian Klaus
- Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA
| | - Christian Albrecht
- Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA
| | - Neil Cumberlidge
- Department of Botany and Zoology, Private Bag X1, University of Stellenbosch, Matieland 7602, South Africa; Department of Ecology and Evolution, J. W. Goethe-University, Biologicum, Frankfurt am Main 60438, Germany; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Peoples Republic of China; Department of Animal Ecology and Systematics, Justus Liebig University, Giessen 35392, Germany; and Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USA
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Xiao Y, Li J, Ren G, Ma D, Wang Y, Xiao Z, Xu S. Pronounced population genetic differentiation in the rock bream Oplegnathus fasciatus inferred from mitochondrial DNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2045-52. [PMID: 25427804 DOI: 10.3109/19401736.2014.982553] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034, hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005, лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007, лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity of O. fasciatus in south China was significantly higher than those of north China. Three genealogical clades were checked in the O. fasciatus populations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on the Fst (0.331, p = 0.000) and exact p (0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations of O. fasciatus was shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169-175 kya before present.
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Affiliation(s)
- Yongshuang Xiao
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Jun Li
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Guijing Ren
- b East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences , Shanghai , China
| | - Daoyuan Ma
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Yanfeng Wang
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - ZhiZhong Xiao
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
| | - Shihong Xu
- a Institute of Oceanology, Chinese Academy of Sciences , Qingdao , China and
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Salzburger W, Van Bocxlaer B, Cohen AS. Ecology and Evolution of the African Great Lakes and Their Faunas. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091804] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Bert Van Bocxlaer
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013;
- Department of Geology and Soil Science, Ghent University, 9000 Ghent, Belgium
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Andrew S. Cohen
- Department of Geosciences, University of Arizona, Tucson, Arizona 85721;
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Theis A, Ronco F, Indermaur A, Salzburger W, Egger B. Adaptive divergence between lake and stream populations of an East African cichlid fish. Mol Ecol 2014; 23:5304-22. [DOI: 10.1111/mec.12939] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Anya Theis
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Fabrizia Ronco
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Adrian Indermaur
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Walter Salzburger
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Bernd Egger
- Zoological Institute; University of Basel; Vesalgasse 1 4051 Basel Switzerland
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