1
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Nakamura H, Aibara M, Nikaido M. Ancient standing genetic variation facilitated the adaptive radiation of Lake Victoria cichlids. Genes Genet Syst 2023; 98:93-99. [PMID: 37495512 DOI: 10.1266/ggs.23-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Cichlid fishes are textbook examples of explosive speciation and adaptive radiation, providing a great opportunity to understand how the genomic substrate yields extraordinary species diversity. Recently, we performed comparative genomic analyses of three Lake Victoria cichlids to reveal the genomic substrates underlying their rapid speciation and adaptation. We found that long divergent haplotypes derived from large-scale standing genetic variation, which originated before the adaptive radiation of Lake Victoria cichlids, may have contributed to their rapid diversification. In addition, the present study on genomic data from other East African cichlids suggested the reuse of alleles that may have originated in the ancestral lineages of Lake Tanganyika cichlids during cichlid evolution. Therefore, our results highlight that the primary factor that could drive repeated adaptive radiation across East African cichlids was allelic reuse from standing genetic variation to adapt to their own specific environment. In this report, we summarize the main results and discuss the evolutionary mechanisms of cichlids, based on our latest findings.
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Affiliation(s)
- Haruna Nakamura
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology
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2
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Pauers MJ, Hoffmann J, Ackley LJB. Differences among reciprocal hybrids of Labeotropheus. HYDROBIOLOGIA 2022; 850:2149-2164. [PMID: 36466299 PMCID: PMC9684848 DOI: 10.1007/s10750-022-05092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 11/04/2022] [Accepted: 11/12/2022] [Indexed: 06/14/2023]
Abstract
Current evidence suggests that hybridization played a crucial role in the early evolution and diversification of the species flocks of cichlid fishes in the African Great Lakes. Nonetheless, evidence for hybridization in the extant cichlid fauna is scant, suggesting that hybridization is rare in the modern era, perhaps enforced by natural or sexual selection acting against F1 hybrids. Additionally, most experimental studies of hybridization perform a hybrid cross in one direction, ignoring the reciprocal hybrid. In this study, we perform reciprocal crosses between sympatric congeners from Lake Malaŵi, Labeotropheus fuelleborni and L. trewavasae, in order to compare the body shape and coloration of males of both of these hybrids, as well as to examine how these hybrids fare during both inter- and intrasexual interactions. We found that L. trewavasae-sired hybrid males are intermediate to the parental species both morphologically and chromatically, while the reciprocal L. fuelleborni-sired hybrids are likely transgressive hybrids. Males of these transgressive hybrids also fare poorly during our mate choice experiments. While female L. trewavasae reject them as possible mates, male L. trewavasae do not make a distinction between them and conspecific males. Selection against transgressive F1 hybrids as observed in our crossing experiments may help explain why contemporary hybridization in Lake Malaŵi cichlids appears to be rare. Supplementary Information The online version contains supplementary material available at 10.1007/s10750-022-05092-4.
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Affiliation(s)
- Michael J. Pauers
- Section of Vertebrate Zoology, Milwaukee Public Museum, 800 W. Wells Street, Milwaukee, WI USA
- Department of Mathematics and Natural Science, University of Wisconsin-Milwaukee at Waukesha, 1500 N. University Drive, Waukesha, WI USA
- School of Freshwater Science, University of Wisconsin-Milwaukee, 600 E. Greenfield Avenue, Milwaukee, WI USA
| | - Jacob Hoffmann
- Department of Mathematics and Natural Science, University of Wisconsin-Milwaukee at Waukesha, 1500 N. University Drive, Waukesha, WI USA
| | - Leah Jiang-Bo Ackley
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 2900 N. Maryland Avenue, Milwaukee, WI USA
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3
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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4
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Gerwin J, Urban S, Meyer A, Kratochwil CF. Of bars and stripes: A Malawi cichlid hybrid cross provides insights into genetic modularity and evolution of modifier loci underlying colour pattern diversification. Mol Ecol 2021; 30:4789-4803. [PMID: 34322938 DOI: 10.1111/mec.16097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022]
Abstract
Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in colouration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common colour pattern in African cichlids, vertical bars, and potential interactions between the two colour patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both colour patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.
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Affiliation(s)
- Jan Gerwin
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sabine Urban
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Claudius F Kratochwil
- Department of Biology, University of Konstanz, Konstanz, Germany.,Institute of Biotechnology, HiLIFE, Helsinki, Finland
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5
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Patil C, Sylvester JB, Abdilleh K, Norsworthy MW, Pottin K, Malinsky M, Bloomquist RF, Johnson ZV, McGrath PT, Streelman JT. Genome-enabled discovery of evolutionary divergence in brains and behavior. Sci Rep 2021; 11:13016. [PMID: 34155279 PMCID: PMC8217251 DOI: 10.1038/s41598-021-92385-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Lake Malawi cichlid fishes exhibit extensive divergence in form and function built from a relatively small number of genetic changes. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants differed among the groups. We found that 96% of differentiated variants reside in non-coding sequence but these non-coding diverged variants are evolutionarily conserved. Genome regions near differentiated variants are enriched for craniofacial, neural and behavioral categories. Following leads from genome sequence, we used rock- vs. sand-species and their hybrids to (i) delineate the push-pull roles of BMP signaling and irx1b in the specification of forebrain territories during gastrulation and (ii) reveal striking context-dependent brain gene expression during adult social behavior. Our results demonstrate how divergent genome sequences can predict differences in key evolutionary traits. We highlight the promise of evolutionary reverse genetics-the inference of phenotypic divergence from unbiased genome sequencing and then empirical validation in natural populations.
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Affiliation(s)
- Chinar Patil
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Jonathan B Sylvester
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Kawther Abdilleh
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael W Norsworthy
- Catalog Technologies Inc., Boston, MA, USA
- Freedom of Form Foundation, Inc., Cambridge, MA, USA
| | - Karen Pottin
- Laboratoire de Biologie du Dévelopement (IBPS-LBD, UMR7622), CNRS, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Milan Malinsky
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ryan F Bloomquist
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oral Biology and Diagnostic Sciences, Department of Restorative Sciences, Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - Zachary V Johnson
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick T McGrath
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey T Streelman
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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6
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. SCIENCE ADVANCES 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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7
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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8
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Inskeep KA, Doellman MM, Powell THQ, Berlocher SH, Seifert NR, Hood GR, Ragland GJ, Meyers PJ, Feder JL. Divergent diapause life history timing drives both allochronic speciation and reticulate hybridization in an adaptive radiation of Rhagoletis flies. Mol Ecol 2021; 31:4031-4049. [PMID: 33786930 DOI: 10.1111/mec.15908] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 12/18/2022]
Abstract
Divergent adaptation to new ecological opportunities can be an important factor initiating speciation. However, as niches are filled during adaptive radiations, trait divergence driving reproductive isolation between sister taxa may also result in trait convergence with more distantly related taxa, increasing the potential for reticulated gene flow across the radiation. Here, we demonstrate such a scenario in a recent adaptive radiation of Rhagoletis fruit flies, specialized on different host plants. Throughout this radiation, shifts to novel hosts are associated with changes in diapause life history timing, which act as "magic traits" generating allochronic reproductive isolation and facilitating speciation-with-gene-flow. Evidence from laboratory rearing experiments measuring adult emergence timing and genome-wide DNA-sequencing surveys supported allochronic speciation between summer-fruiting Vaccinium spp.-infesting Rhagoletis mendax and its hypothesized and undescribed sister taxon infesting autumn-fruiting sparkleberries. The sparkleberry fly and R. mendax were shown to be genetically discrete sister taxa, exhibiting no detectable gene flow and allochronically isolated by a 2-month average difference in emergence time corresponding to host availability. At sympatric sites across the southern USA, the later fruiting phenology of sparkleberries overlaps with that of flowering dogwood, the host of another more distantly related and undescribed Rhagoletis taxon. Laboratory emergence data confirmed broadly overlapping life history timing and genomic evidence supported on-going gene flow between sparkleberry and flowering dogwood flies. Thus, divergent phenological adaptation can drive the initiation of reproductive isolation, while also enhancing genetic exchange across broader adaptive radiations, potentially serving as a source of novel genotypic variation and accentuating further diversification.
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Affiliation(s)
- Katherine A Inskeep
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Meredith M Doellman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Thomas H Q Powell
- Department of Biological Sciences, Binghamton University (State University of New York), Binghamton, NY, USA
| | - Stewart H Berlocher
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas R Seifert
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Glen R Hood
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Peter J Meyers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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9
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Nakamura H, Aibara M, Kajitani R, Mrosso HDJ, Mzighani SI, Toyoda A, Itoh T, Okada N, Nikaido M. Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation. Mol Biol Evol 2021; 38:3111-3125. [PMID: 33744961 PMCID: PMC8321545 DOI: 10.1093/molbev/msab084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments-Haplochromis chilotes, H. sauvagei, and Lithochromis rufus-to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.
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Affiliation(s)
- Haruna Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hillary D J Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza Fisheries Research Center, Mwanza, Tanzania
| | - Semvua I Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), Headquarters, Dar es Salaam, Tanzania.,Fisheries Education and Training Agency, Dar es Salaam, Tanzania
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Norihiro Okada
- School of Pharmacy, Kitasato University, Kanagawa, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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10
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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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11
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Svardal H, Salzburger W, Malinsky M. Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes. Annu Rev Anim Biosci 2020; 9:55-79. [PMID: 33197206 DOI: 10.1146/annurev-animal-061220-023129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.
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Affiliation(s)
- Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium; .,Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
| | - Walter Salzburger
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
| | - Milan Malinsky
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
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12
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Baran NM, Streelman JT. Ecotype differences in aggression, neural activity and behaviorally relevant gene expression in cichlid fish. GENES BRAIN AND BEHAVIOR 2020; 19:e12657. [PMID: 32323443 DOI: 10.1111/gbb.12657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/17/2020] [Accepted: 04/18/2020] [Indexed: 12/18/2022]
Abstract
In Lake Malawi, two ecologically distinct lineages of cichlid fishes (rock- vs sand-dwelling ecotypes, each comprised of over 200 species) evolved within the last million years. The rock-dwelling species (Mbuna) are aggressively territorial year-round and males court and spawn with females over rocky substrate. In contrast, males of sand-dwelling species are not territorial and instead aggregate on seasonal breeding leks in which males construct courtship "bowers" in the sand. However, little is known about how phenotypic variation in aggression is produced by the genome. In this study, we first quantify and compare behavior in seven cichlid species, demonstrating substantial ecotype and species differences in unconditioned mirror-elicited aggression. Second, we compare neural activity in mirror-elicited aggression in two representative species, Mchenga conophoros (sand-dwelling) and Petrotilapia chitimba (rock-dwelling). Finally, we compare gene expression patterns between these two species, specifically within neurons activated during mirror aggression. We identified a large number of genes showing differential expression in mirror-elicited aggression, as well as many genes that differ between ecotypes. These genes, which may underly species differences in behavior, include several neuropeptides, genes involved in the synthesis of steroid hormones and neurotransmitter activity. This work lays the foundation for future experiments using this emerging genetic model system to investigate the genomic basis of evolved species differences in both brain and behavior.
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Affiliation(s)
- Nicole M Baran
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,Department of Psychology, Emory University, Atlanta, Georgia, USA
| | - J Todd Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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13
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Lindblad-Toh K. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 2020; 125:1-9. [PMID: 32054372 PMCID: PMC7054949 DOI: 10.1080/03009734.2020.1722298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
During the past 20 years, since I started as a postdoc, the world of genetics and genomics has changed dramatically. My main research goal throughout my career has been to understand human disease genetics, and I have developed comparative genomics and comparative genetics to generate resources and tools for understanding human disease. Through comparative genomics I have worked to sequence enough mammals to understand the functional potential of each base in the human genome as well as chosen vertebrates to study the evolutionary changes that have given many species their key traits. Through comparative genetics, I have developed the dog as a model for human disease, characterising the genome itself and determining a list of germ-line loci and somatic mutations causing complex diseases and cancer in the dog. Pulling all these findings and resources together opens new doors for understanding genome evolution, the genetics of complex traits and cancer in man and his best friend.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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14
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The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes. Genes (Basel) 2019; 10:genes10121027. [PMID: 31835491 PMCID: PMC6947334 DOI: 10.3390/genes10121027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022] Open
Abstract
Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development.
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15
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Pinho C, Cardoso V, Hey J. A population genetic assessment of taxonomic species: The case of Lake Malawi cichlid fishes. Mol Ecol Resour 2019; 19:1164-1180. [PMID: 31012255 PMCID: PMC6764894 DOI: 10.1111/1755-0998.13027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Accepted: 04/10/2019] [Indexed: 02/05/2023]
Abstract
Organisms sampled for population‐level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock‐dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified using adult male coloration patterns. Given high local endemism of male colour patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped and separately assigned: (a) to morphospecies using photographs; and (b) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (a) adult male‐limited sampling and (b) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well‐demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.
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Affiliation(s)
- Catarina Pinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Vera Cardoso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Jody Hey
- Rutgers, the State University of New Jersey, Piscataway, New Jersey.,CCGG, Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, Pennsylvania
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16
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Brock CD, Wagner CE. The smelly path to sympatric speciation? Mol Ecol 2019; 27:4153-4156. [PMID: 30375091 DOI: 10.1111/mec.14845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/28/2023]
Abstract
In this issue of Molecular Ecology, Poelstra et al. () use genomic data to show that cichlid species in the adaptive radiation in Lake Ejagham, Cameroon, experienced gene flow with a riverine relative, primarily prior to their diversification. Intriguingly, this introgression brought with it olfactory alleles that the authors suggest may play a sensory role in speciation. As a classic example of sympatric speciation due to the highly restricted geography of this small (0.49 km2 ) crater lake (Schliewen et al., ), this result sheds new light on the history of this fascinating radiation. As genomic data for cichlid radiations accumulate, finding evidence of introgression increasingly appears to be the rule rather than the exception (Kautt et al., ; Meier et al., , ). However, two points are pressing as evidence for introgression mounts: (a) It is crucial to understand the assumptions of analytical approaches used and (b) it is important to think clearly about the divergent contexts in which evidence for introgression has been invoked as an important feature of adaptive radiation.
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Affiliation(s)
- Chad D Brock
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
| | - Catherine E Wagner
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
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17
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Takuno S, Miyagi R, Onami JI, Takahashi-Kariyazono S, Sato A, Tichy H, Nikaido M, Aibara M, Mizoiri S, Mrosso HDJ, Mzighani SI, Okada N, Terai Y. Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'. BMC Evol Biol 2019; 19:68. [PMID: 30832572 PMCID: PMC6399900 DOI: 10.1186/s12862-019-1387-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/12/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species. RESULTS Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels. CONCLUSIONS These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.
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Affiliation(s)
- Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Biological sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 197-0397 Japan
| | - Jun-ichi Onami
- JST (Japan Science and Technology Agency), NBDC (National Bioscience Database Center), 5-3, Yonbancho, Chiyoda-ku, Tokyo, 102-0081 Japan
| | - Shiho Takahashi-Kariyazono
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
| | - Akie Sato
- Department of Anatomy and Cytohistology, School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Herbert Tichy
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Corrensstrasse 42, D-72076 Tübingen, Germany
| | - Masato Nikaido
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology (Tokyo Tech), 2-12-1, Ookayama, Meguro ward, Tokyo, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
| | | | - Semvua I. Mzighani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Tanzania Fisheries Research Institute (TAFIRI), Mwanza, Tanzania
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
- Department of Life Sciences, National Cheng Kung University, 701 Tainan, Taiwan
- Foundation for Advancement of International Science (FAIS), Tsukuba, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193 Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501 Japan
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18
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Abstract
The tremendous diversity of animal behaviors has inspired generations of scientists from an array of biological disciplines. To complement investigations of ecological and evolutionary factors contributing to behavioral evolution, modern sequencing, gene editing, computational and neuroscience tools now provide a means to discover the proximate mechanisms upon which natural selection acts to generate behavioral diversity. Social behaviors are motivated behaviors that can differ tremendously between closely related species, suggesting phylogenetic plasticity in their underlying biological mechanisms. In addition, convergent evolution has repeatedly given rise to similar forms of social behavior and mating systems in distantly related species. Social behavioral divergence and convergence provides an entry point for understanding the neurogenetic mechanisms contributing to behavioral diversity. We argue that the greatest strides in discovering mechanisms contributing to social behavioral diversity will be achieved through integration of interdisciplinary comparative approaches with modern tools in diverse species systems. We review recent advances and future potential for discovering mechanisms underlying social behavioral variation; highlighting patterns of social behavioral evolution, oxytocin and vasopressin neuropeptide systems, genetic/transcriptional "toolkits," modern experimental tools, and alternative species systems, with particular emphasis on Microtine rodents and Lake Malawi cichlid fishes.
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Affiliation(s)
- Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Larry J Young
- Center for Translational Social Neuroscience, Silvio O. Conte Center for Oxytocin and Social Cognition, Department of Psychiatry and Behavioral Sciences, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
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19
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Doellman MM, Egan SP, Ragland GJ, Meyers PJ, Hood GR, Powell THQ, Lazorchak P, Hahn DA, Berlocher SH, Nosil P, Feder JL. Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies. Ecol Evol 2019; 9:393-409. [PMID: 30680122 PMCID: PMC6342182 DOI: 10.1002/ece3.4758] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer whether standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early vs. late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430-km transect, where the host races co-occur in sympatry in the Midwest United States. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion-associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.
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Affiliation(s)
| | - Scott P. Egan
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Advanced Diagnostics and Therapeutics InitiativeUniversity of Notre DameNotre DameIndiana
- Department of BiosciencesRice UniversityHoustonTexas
| | - Gregory J. Ragland
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana
- Department of Integrative BiologyUniversity of Colorado–DenverDenverColorado
| | - Peter J. Meyers
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
| | - Glen R. Hood
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Biological SciencesWayne State UniversityDetroitMichigan
| | - Thomas H. Q. Powell
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Biological SciencesState University of New York–BinghamtonBinghamtonNew York
| | - Peter Lazorchak
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMaryland
| | - Daniel A. Hahn
- Department of Entomology and NematologyUniversity of FloridaGainesvilleFlorida
| | - Stewart H. Berlocher
- Department of EntomologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Patrik Nosil
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Jeffrey L. Feder
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Advanced Diagnostics and Therapeutics InitiativeUniversity of Notre DameNotre DameIndiana
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana
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20
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Nandamuri SP, Conte MA, Carleton KL. Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids. BMC Genomics 2018; 19:945. [PMID: 30563463 PMCID: PMC6299527 DOI: 10.1186/s12864-018-5328-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/28/2018] [Indexed: 01/22/2023] Open
Abstract
Background Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of complex traits, knowledge about the proximate genetic causes underlying these traits is still limited. African cichlids have diverse visual systems, with different species expressing different combinations of seven cone opsin genes. Using opsin expression variation in African cichlids as a model for gene expression evolution, this study aims to investigate the genetic architecture of opsin expression divergence in this group. Results Results from a genome-wide linkage mapping on the F2 progeny of an intergeneric cross, between two species with differential opsin expression show that opsins in Lake Malawi cichlids are controlled by multiple quantitative trait loci (QTLs). Most of these QTLs are located in trans to the opsins except for one cis-QTL for SWS1 on LG17. A closer look at this major QTL revealed the presence of a 691 bp deletion in the promoter of the SWS1 opsin (located 751 bp upstream of the start site) that is associated with a decrease in its expression. Phylogenetic footprinting indicates that the region spanning the deletion harbors a microRNA miR-729 and a conserved non-coding element (CNE) that also occurs in zebrafish and other teleosts. This suggests that the deletion might contain ancestrally preserved regulators that have been tuned for SWS1 gene expression in Lake Malawi. While this deletion is not common, it does occur in several other species within the lake. Conclusions Differential expression of cichlid opsins is associated with multiple overlapping QTL, with all but one in trans to the opsins they regulate. The one cis-acting factor is a deletion in the promoter of the SWS1 opsin, suggesting that ancestral polymorphic deletions may contribute to cichlid’s visual diversity. In addition to expanding our understanding of the molecular landscape of opsin expression in African cichlids, this study sheds light on the molecular mechanisms underlying phenotypic variation in natural populations. Electronic supplementary material The online version of this article (10.1186/s12864-018-5328-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sri Pratima Nandamuri
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, 1210 Biology / Psychology Bldg #144, College Park, MD, 20742, USA.
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21
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Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes. Proc Natl Acad Sci U S A 2018; 115:E11081-E11090. [PMID: 30397142 PMCID: PMC6255178 DOI: 10.1073/pnas.1810140115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683-1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809-820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.
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22
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Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ, Schmutz J, Jenkins J, Grimwood J, Shu S, Hayes RD, Hellsten U, Barry K, Yan J, Mihaltcheva S, Karafiátová M, Nizhynska V, Kramer EM, Lysak MA, Hodges SA, Nordborg M. The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. eLife 2018; 7:e36426. [PMID: 30325307 PMCID: PMC6255393 DOI: 10.7554/elife.36426] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.
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Affiliation(s)
- Danièle L Filiault
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Evangeline S Ballerini
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Terezie Mandáková
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Gökçe Aköz
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
| | - Nathan J Derieg
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Jeremy Schmutz
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jerry Jenkins
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Jane Grimwood
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
- HudsonAlpha Institute of BiotechnologyAlabamaUnited States
| | - Shengqiang Shu
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Richard D Hayes
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Uffe Hellsten
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Kerrie Barry
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | - Juying Yan
- Department of EnergyJoint Genome InstituteWalnut CreekUnited States
| | | | - Miroslava Karafiátová
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
| | - Elena M Kramer
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
| | - Martin A Lysak
- Central-European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraUnited States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of SciencesVienna BioCenterViennaAustria
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23
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Salzburger W. Understanding explosive diversification through cichlid fish genomics. Nat Rev Genet 2018; 19:705-717. [DOI: 10.1038/s41576-018-0043-9] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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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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25
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Meyer BS, Matschiner M, Salzburger W. Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes. Syst Biol 2018; 66:531-550. [PMID: 27539485 DOI: 10.1093/sysbio/syw069] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Basel, Switzerland.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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26
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Ramakrishnan Varadarajan A, Mopuri R, Streelman JT, McGrath PT. Genome-wide protein phylogenies for four African cichlid species. BMC Evol Biol 2018; 18:1. [PMID: 29368592 PMCID: PMC5784529 DOI: 10.1186/s12862-017-1072-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background The thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species. Results We used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented. Conclusion These phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species. Electronic supplementary material The online version of this article (10.1186/s12862-017-1072-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rohini Mopuri
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - J Todd Streelman
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA
| | - Patrick T McGrath
- Department of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr., Atlanta, GA, 30332, USA.
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27
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Trucchi E, Frajman B, Haverkamp THA, Schönswetter P, Paun O. Genomic analyses suggest parallel ecological divergence in Heliosperma pusillum (Caryophyllaceae). THE NEW PHYTOLOGIST 2017; 216:267-278. [PMID: 28782803 PMCID: PMC5601199 DOI: 10.1111/nph.14722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/20/2017] [Indexed: 05/24/2023]
Abstract
The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south-eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high-coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes. The data are consistent with repeated ecological divergence in H. pusillum, uncovering up to five polytopic origins of one ecotype from the other. A complex evolutionary history is evidenced, with local isolation-with-migration in two population pairs and intra-ecotype migration in two others. In all cases, the time of divergence or secondary contact was inferred as postglacial. A metagenomic analysis on exogenous contaminant RAD sequences suggests divergent microbial communities between the ecotypes. The lack of shared genomic regions of high divergence across population pairs illustrates the action of drift and/or local selection in shaping genetic divergence across repeated cases of ecological divergence.
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Affiliation(s)
- Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
- Department of Life Sciences and BiotechnologyUniversity of FerraraVia L. Borsari 46Ferrara44121Italy
| | - Božo Frajman
- Institute of BotanyUniversity of InnsbruckSternwartestraße 15Innsbruck6020Austria
| | - Thomas H. A. Haverkamp
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloPO Box, 1066 BlindernOslo0316Norway
| | - Peter Schönswetter
- Institute of BotanyUniversity of InnsbruckSternwartestraße 15Innsbruck6020Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14Vienna1030Austria
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28
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Alter SE, Munshi-South J, Stiassny MLJ. Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River. Mol Ecol 2017; 26:1401-1419. [PMID: 28028845 DOI: 10.1111/mec.13973] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/13/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.
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Affiliation(s)
- S Elizabeth Alter
- Department of Biology, York College/The City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, NY, 11451, USA.,The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Jason Munshi-South
- Louis Calder Center-Biological Field Station, Fordham University, Armonk, NY, 10504, USA
| | - Melanie L J Stiassny
- The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
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29
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Bloomquist RF, Fowler TE, Sylvester JB, Miro RJ, Streelman JT. A compendium of developmental gene expression in Lake Malawi cichlid fishes. BMC DEVELOPMENTAL BIOLOGY 2017; 17:3. [PMID: 28158974 PMCID: PMC5291978 DOI: 10.1186/s12861-017-0146-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/26/2017] [Indexed: 12/24/2022]
Abstract
BACKGROUND Lake Malawi cichlids represent one of a growing number of vertebrate models used to uncover the genetic and developmental basis of trait diversity. Rapid evolutionary radiation has resulted in species that share similar genomes but differ markedly in phenotypes including brains and behavior, nuptial coloration and the craniofacial skeleton. Research has begun to identify the genes, as well as the molecular and developmental pathways that underlie trait divergence. RESULTS We assemble a compendium of gene expression for Lake Malawi cichlids, across pharyngula (the phylotypic stage) and larval stages of development, encompassing hundreds of gene transcripts. We chart patterns of expression in Bone morphogenetic protein (BMP), Fibroblast growth factor (FGF), Hedgehog (Hh), Notch and Wingless (Wnt) signaling pathways, as well as genes involved in neurogenesis, calcium and endocrine signaling, stem cell biology, and numerous homeobox (Hox) factors-in three planes using whole-mount in situ hybridization. Because of low sequence divergence across the Malawi cichlid assemblage, the probes we employ are broadly applicable in hundreds of species. We tabulate gene expression across general tissue domains, and highlight examples of unexpected expression patterns. CONCLUSIONS On the heels of recently published genomes, this compendium of developmental gene expression in Lake Malawi cichlids provides a valuable resource for those interested in the relationship between evolution and development.
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Affiliation(s)
- R F Bloomquist
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA.,Medical College of Georgia, School of Dentistry, Augusta, GA, USA
| | - T E Fowler
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - J B Sylvester
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - R J Miro
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA
| | - J T Streelman
- Georgia Institute of Technology, School of Biological Sciences and Institute for Bioengineering and Bioscience, Atlanta, GA, USA.
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30
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Bupp G, Ricono A, Peterson CL, Pruett CL. Conservation implications of small population size and habitat fragmentation in an endangered lupine. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0883-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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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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Franchini P, Xiong P, Fruciano C, Meyer A. The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua. Genome Biol Evol 2016; 8:1543-55. [PMID: 27189980 PMCID: PMC4898811 DOI: 10.1093/gbe/evw097] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cichlid fishes are an ideal model system for studying biological diversification because they provide textbook examples of rapid speciation. To date, there has been little focus on the role of gene regulation during cichlid speciation. However, in recent years, gene regulation has been recognized as a powerful force linking diversification in gene function to speciation. Here, we investigated the potential role of miRNA regulation in the diversification of six cichlid species of the Midas cichlid lineage (Amphilophus spp.) inhabiting the Nicaraguan crater lakes. Using several genomic resources, we inferred 236 Midas miRNA genes that were used to predict the miRNA target sites on 8,232 Midas 3′-UTRs. Using population genomic calculations of SNP diversity, we found the miRNA genes to be more conserved than protein coding genes. In contrast to what has been observed in other cichlid fish, but similar to what has been typically found in other groups, we observed genomic signatures of purifying selection on the miRNA targets by comparing these sites with the less conserved nontarget portion of the 3′-UTRs. However, in one species pair that has putatively speciated sympatrically in crater Lake Apoyo, we recovered a different pattern of relaxed purifying selection and high genetic divergence at miRNA targets. Our results suggest that sequence evolution at miRNA binding sites could be a critical genomic mechanism contributing to the rapid phenotypic evolution of Midas cichlids.
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Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Carmelo Fruciano
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany School of Earth Environmental & Biological Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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33
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Rocha S, Perera A, Silva A, Posada D, Harris DJ. Evolutionary history ofTrachylepisskinks in the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Rocha
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Bioquímica; Genética e Inmunología; Facultad de Biología; Universidad de Vigo; Vigo 36310 Spain
| | - Anna Perera
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
| | - Andreia Silva
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Rua do Campo Alegre FC4; 4169-007 Porto Portugal
| | - David Posada
- Departamento de Bioquímica; Genética e Inmunología; Facultad de Biología; Universidad de Vigo; Vigo 36310 Spain
| | - D. James Harris
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Rua do Campo Alegre FC4; 4169-007 Porto Portugal
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34
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Breman FC, Loix S, Jordaens K, Snoeks J, Van Steenberge M. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika. Mol Ecol Resour 2016; 16:1455-1464. [DOI: 10.1111/1755-0998.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Floris C. Breman
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Sara Loix
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Kurt Jordaens
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Jos Snoeks
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Maarten Van Steenberge
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
- Operational Directorate Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
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35
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Tabata R, Kakioka R, Tominaga K, Komiya T, Watanabe K. Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecol Evol 2016; 6:2601-23. [PMID: 27066244 PMCID: PMC4798153 DOI: 10.1002/ece3.2070] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 01/21/2023] Open
Abstract
To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3–13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.
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Affiliation(s)
- Ryoichi Tabata
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Ryo Kakioka
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan; Research Institute for Humanity and Nature 457-4 Kamigamo-Motoyama Kita-ku Kyoto 603-8047 Japan
| | - Koji Tominaga
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto606-8502 Japan; Kwansei Gakuin Senior High School 1-155 Uegahara-ichibancho Nishinomiya Hyogo 662-8501 Japan
| | - Takefumi Komiya
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
| | - Katsutoshi Watanabe
- Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho Sakyo Kyoto 606-8502 Japan
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36
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Genner MJ, Ngatunga BP, Mzighani S, Smith A, Turner GF. Geographical ancestry of Lake Malawi's cichlid fish diversity. Biol Lett 2016; 11:20150232. [PMID: 26063752 DOI: 10.1098/rsbl.2015.0232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Lake Malawi haplochromine cichlid flock is one of the largest vertebrate adaptive radiations. The geographical source of the radiation has been assumed to be rivers to the south and east of Lake Malawi, where extant representatives of the flock are now present. Here, we provide mitochondrial DNA evidence suggesting the sister taxon to the Lake Malawi radiation is within the Great Ruaha river in Tanzania, north of Lake Malawi. Estimates of the time of divergence between the Lake Malawi flock and this riverine sister taxon range from 2.13 to 6.76 Ma, prior to origins of the current radiation 1.20-4.06 Ma. These results are congruent with evaluations of 2-3.75 Ma fossil material that suggest past faunal connections between Lake Malawi and the Ruaha. We propose that ancestors of the Malawi radiation became isolated within the catchment during Pliocene rifting that formed both Lake Malawi and the Kipengere/Livingstone mountain range, before colonizing rivers to the south and east of the lake region and radiating within the lake basin. Identification of this sister taxon allows tests of whether standing genetic diversity has predisposed Lake Malawi cichlids to rapid speciation and adaptive radiation.
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Affiliation(s)
- Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS81TQ, UK
| | - Benjamin P Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), PO Box 9750, Dar-es-Salaam, Tanzania
| | - Semvua Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), PO Box 9750, Dar-es-Salaam, Tanzania
| | - Alan Smith
- School of Biological, Biomedical and Environmental Science, University of Hull, Hull HU67RX, UK
| | - George F Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL572UW, UK
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Continuous 1.3-million-year record of East African hydroclimate, and implications for patterns of evolution and biodiversity. Proc Natl Acad Sci U S A 2015; 112:15568-73. [PMID: 26644580 DOI: 10.1073/pnas.1512864112] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9-15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world's largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including 15 lowstands when water levels were more than 400 m lower than modern. A dramatic shift is observed at the Mid-Pleistocene Transition (MPT), consistent with far-field climate forcing, which separates vastly different hydroclimate regimes before and after ∼800,000 years ago. Before 800 ka, lake levels were lower, indicating a climate drier than today, and water levels changed frequently. Following the MPT high-amplitude lake level variations dominate the record. From 800 to 100 ka, a deep, often overfilled lake occupied the basin, indicating a wetter climate, but these highstands were interrupted by prolonged intervals of extreme drought. Periods of high lake level are observed during times of high eccentricity. The extreme hydroclimate variability exerted a profound influence on the Lake Malawi endemic cichlid fish species flock; the geographically extensive habitat reconfiguration provided novel ecological opportunities, enabling new populations to differentiate rapidly to distinct species.
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Gillespie RG. Island time and the interplay between ecology and evolution in species diversification. Evol Appl 2015; 9:53-73. [PMID: 27087839 PMCID: PMC4780372 DOI: 10.1111/eva.12302] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/30/2015] [Indexed: 01/12/2023] Open
Abstract
Research on the dynamics of biodiversity has progressed tremendously over recent years, although in two separate directions – ecological, to determine change over space at a given time, and evolutionary, to understand change over time. Integration of these approaches has remained elusive. Archipelagoes with a known geological chronology provide an opportunity to study ecological interactions over evolutionary time. Here, I focus on the Hawaiian archipelago and summarize the development of ecological and evolutionary research; I emphasize spiders because they have attributes allowing analysis of ecological affinities in concert with diversification. Within this framework, I highlight recent insights from the island chronosequence, in particular the importance of (i) selection and genetic drift in generating diversity; (ii) fusion and fission in fostering diversification; and (iii) variability upon which selection can act. Insights into biodiversity dynamics at the nexus of ecology and evolution are now achievable by integrating new tools, in particular (i) ecological metrics (interaction networks, maximum entropy inference) across the chronosequence to uncover community dynamics and (ii) genomic tools to understand contemporaneous microevolutionary change. The work can inform applications of invasion and restoration ecology by elucidating the importance of changes in abundances, interaction strengths, and rates of evolutionary response in shaping biodiversity.
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Affiliation(s)
- Rosemary G Gillespie
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
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39
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Berner D, Salzburger W. The genomics of organismal diversification illuminated by adaptive radiations. Trends Genet 2015; 31:491-9. [DOI: 10.1016/j.tig.2015.07.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
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40
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Concannon MR, Albertson RC. The genetic and developmental basis of an exaggerated craniofacial trait in East African cichlids. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:662-70. [DOI: 10.1002/jez.b.22641] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/01/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Moira R. Concannon
- Graduate Program in Organismic and Evolutionary Biology; University of Massachusetts Amherst; Morrill Science Center South; Amherst Massachusetts
| | - R. Craig Albertson
- Department of Biology; University of Massachusetts Amherst; Morrill Science Center; Amherst Massachusetts
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41
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Kakioka R, Kokita T, Kumada H, Watanabe K, Okuda N. Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes. Mol Ecol 2015; 24:4159-74. [PMID: 26179373 DOI: 10.1111/mec.13309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 01/19/2023]
Abstract
Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat-related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat-related divergence in the body shape of Gnathopogon fishes, a novel example of lake-stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream-dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2 interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction-site associated DNA sequencing-derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape-related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape-related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.
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Affiliation(s)
- Ryo Kakioka
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Hiroki Kumada
- Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, Obama, 917-0003, Japan
| | - Katsutoshi Watanabe
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, 509-3 Hirano 2-chome, Otsu, 520-2113, Japan
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42
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Nichols P, Genner MJ, van Oosterhout C, Smith A, Parsons P, Sungani H, Swanstrom J, Joyce DA. Secondary contact seeds phenotypic novelty in cichlid fishes. Proc Biol Sci 2015; 282:20142272. [PMID: 25392475 PMCID: PMC4262179 DOI: 10.1098/rspb.2014.2272] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species to overcome environmental challenges and adapt to novel environments, including during adaptive radiation. To date, this has largely been considered from the perspective of interspecific hybridization at contact zones. However, it is also possible that this process occurs more commonly between natural populations of a single species, and thus its importance in adaptive evolution may have been underestimated. In this study, we tested the consequences of genomic introgression during apparent secondary contact between phenotypically similar lineages of the riverine cichlid fish Astatotilapia calliptera. We provide population genetic evidence of a secondary contact zone in the wild, and then demonstrate using mate-choice experiments that both lineages can reproduce together successfully in laboratory conditions. Finally, we show that genomically admixed individuals display extreme phenotypes not observed in the parental lineages. Collectively, the evidence shows that secondary contact can drive the evolution of phenotypic novelty, suggesting that pulses of secondary contact may repeatedly seed genetic novelty, which when coupled with ecological opportunity could promote rapid adaptive evolution in natural circumstances.
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Affiliation(s)
- Paul Nichols
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Martin J Genner
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Cock van Oosterhout
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, UK School of Environmental Science, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Alan Smith
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Paul Parsons
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harold Sungani
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jennifer Swanstrom
- School of Biological Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Domino A Joyce
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull HU6 7RX, UK
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Nested Levels of Adaptive Divergence: The Genetic Basis of Craniofacial Divergence and Ecological Sexual Dimorphism. G3-GENES GENOMES GENETICS 2015; 5:1613-24. [PMID: 26038365 PMCID: PMC4528318 DOI: 10.1534/g3.115.018226] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exemplary systems for adaptive divergence are often characterized by their large degrees of phenotypic variation. This variation represents the outcome of generations of diversifying selection. However, adaptive radiations can also contain a hierarchy of differentiation nested within them where species display only subtle phenotypic differences that still have substantial effects on ecology, function, and ultimately fitness. Sexual dimorphisms are also common in species displaying adaptive divergence and can be the result of differential selection between sexes that produce ecological differences between sexes. Understanding the genetic basis of subtle variation (between certain species or sexes) is therefore important for understanding the process of adaptive divergence. Using cichlids from the dramatic adaptive radiation of Lake Malawi, we focus on understanding the genetic basis of two aspects of relatively subtle phenotypic variation. This included a morphometric comparison of the patterns of craniofacial divergence between two ecologically similar species in relation to the larger adaptive radiation of Malawi, and male-female morphological divergence between their F2 hybrids. We then genetically map craniofacial traits within the context of sex and locate several regions of the genome that contribute to variation in craniofacial shape that is relevant to sexual dimorphism within species and subtle divergence between closely related species, and possibly to craniofacial divergence in the Malawi radiation as a whole. To enhance our search for candidate genes we take advantage of population genomic data and a genetic map that is anchored to the cichlid genome to determine which genes within our QTL regions are associated with SNPs that are alternatively fixed between species. This study provides a holistic understanding of the genetic underpinnings of adaptive divergence in craniofacial shape.
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44
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Weiss JD, Cotterill FPD, Schliewen UK. Lake Tanganyika--a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae)? PLoS One 2015; 10:e0125043. [PMID: 25928886 PMCID: PMC4415804 DOI: 10.1371/journal.pone.0125043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/08/2015] [Indexed: 11/19/2022] Open
Abstract
A long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika (“ancient mouthbrooders”) was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor lineages which diversified in ancient rivers and precursor lakes and then amalgamated in the extant L. Tanganyika basin is put forward as an alternative: the 'melting pot Tanganyika' hypothesis.
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Affiliation(s)
- Juliane D. Weiss
- Department of Ichthyology, Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
| | - Fenton P. D. Cotterill
- Geoecodynamics Research Hub, c/o Department of Botany and Zoology, University of Stellenbosch, Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Ulrich K. Schliewen
- Department of Ichthyology, Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
- * E-mail:
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45
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Meyer BS, Indermaur A, Ehrensperger X, Egger B, Banyankimbona G, Snoeks J, Salzburger W. Back to Tanganyika: a case of recent trans-species-flock dispersal in East African haplochromine cichlid fishes. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140498. [PMID: 26064619 PMCID: PMC4448823 DOI: 10.1098/rsos.140498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/09/2015] [Indexed: 05/15/2023]
Abstract
The species flocks of cichlid fishes in the East African Great Lakes are the largest vertebrate adaptive radiations in the world and illustrious textbook examples of convergent evolution between independent species assemblages. Although recent studies suggest some degrees of genetic exchange between riverine taxa and the lake faunas, not a single cichlid species is known from Lakes Tanganyika, Malawi and Victoria that is derived from the radiation associated with another of these lakes. Here, we report the discovery of a haplochromine cichlid species in Lake Tanganyika, which belongs genetically to the species flock of haplochromines of the Lake Victoria region. The new species colonized Lake Tanganyika only recently, suggesting that faunal exchange across watersheds and, hence, between isolated ichthyofaunas, is more common than previously thought.
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Affiliation(s)
- Britta S. Meyer
- Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Adrian Indermaur
- Zoological Institute, University of Basel, Basel 4051, Switzerland
| | | | - Bernd Egger
- Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Gaspard Banyankimbona
- Department of Biology, University of Burundi, Bujumbura, Burundi
- Royal Museum for Central Africa, Tervuren 3080, Belgium
| | - Jos Snoeks
- Royal Museum for Central Africa, Tervuren 3080, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Leuven 3000, Belgium
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel 4051, Switzerland
- Author for correspondence: Walter Salzburger e-mail:
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46
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York RA, Patil C, Hulsey CD, Streelman JT, Fernald RD. Evolution of bower building in Lake Malawi cichlid fish: phylogeny, morphology, and behavior. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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47
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A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids. Gene 2015; 560:156-64. [PMID: 25639358 DOI: 10.1016/j.gene.2015.01.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/06/2023]
Abstract
Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.
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48
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Brewer MS, Carter RA, Croucher PJP, Gillespie RG. Shifting habitats, morphology, and selective pressures: Developmental polyphenism in an adaptive radiation of Hawaiian spiders. Evolution 2014; 69:162-78. [DOI: 10.1111/evo.12563] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 10/14/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Michael S. Brewer
- Department of Environmental Science; Policy, and Management; University of California; Berkeley California 94720
- Department of Biology; East Carolina University; Greenville North Carolina 27858
| | - Rebecca A. Carter
- Department of Environmental Science; Policy, and Management; University of California; Berkeley California 94720
| | - Peter J. P. Croucher
- Department of Environmental Science; Policy, and Management; University of California; Berkeley California 94720
| | - Rosemary G. Gillespie
- Department of Environmental Science; Policy, and Management; University of California; Berkeley California 94720
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49
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Abstract
The extraordinary species richness of freshwater fishes has attracted much research on mechanisms and modes of speciation. We here review research on speciation in freshwater fishes in light of speciation theory, and place this in a context of broad-scale diversity patterns in freshwater fishes. We discuss several major repeated themes in freshwater fish speciation and the speciation mechanisms they are frequently associated with. These include transitions between marine and freshwater habitats, transitions between discrete freshwater habitats, and ecological transitions within habitats, as well as speciation without distinct niche shifts. Major research directions in the years to come include understanding the transition from extrinsic environment-dependent to intrinsic reproductive isolation and its influences on species persistence and understanding the extrinsic and intrinsic constraints to speciation and how these relate to broad-scale diversification patterns through time.
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Affiliation(s)
- Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Catherine E. Wagner
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
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50
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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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