201
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Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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202
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Rodriguez-Silva R, Weaver PF. A new livebearing fish of the genus Limia (Cyprinodontiformes: Poeciliidae) from Lake Miragoane, Haiti. JOURNAL OF FISH BIOLOGY 2020; 96:1360-1369. [PMID: 32112652 DOI: 10.1111/jfb.14301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Limia islai, a new species of livebearing fish, is described from Lake Miragoane in south-western Haiti on Hispaniola. The new species has a conspicuous barred pattern consisting of several (4-12) black bars along the body, ray 4p serrae of the gonopodium in males with 10 segments and origin of dorsal fin in females slightly behind the origin of the anal fin. Although the new species colour pattern is similar to that of the humpbacked limia Limia nigrofasciata Regan 1913, L. islai sp. nov. has exclusive morphological features, such as slender body, lack of hump anterior to dorsal fin in males and presence of specific features in the gonopodial suspensory, which allow an unambiguous diagnosis from L. nigrofasciata. L. islai further differs from L. nigrofasciata in reproductive behaviour since L. islai males rely on sneak copulations and gonopodial thrusting, whereas L. nigrofasciata display an elaborate courtship behaviour. The new species is also genetically distinct in both nuclear (Rh, Myh6) and mitochondrial (12S, ND2, D-loop, Cytb) genes from other species in the genus showing reciprocal monophyly. The description of this new Limia species from Lake Miragoane confirms this lake as an important centre of endemism for the genus, with a total of eight endemic species described so far.
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Affiliation(s)
| | - Pablo F Weaver
- Department of Biology, University of La Verne, La Verne, CA, USA
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203
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Carleton KL, Yourick MR. Axes of visual adaptation in the ecologically diverse family Cichlidae. Semin Cell Dev Biol 2020; 106:43-52. [PMID: 32439270 DOI: 10.1016/j.semcdb.2020.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
The family Cichlidae contains approximately 2000 species that live in diverse freshwater habitats including murky lakes, turbid rivers, and clear lakes from both the Old and New Worlds. Their visual systems are similarly diverse and have evolved specific sensitivities that differ along several axes of variation. Variation in cornea and lens transmission affect which wavelengths reach the retina. Variation in photoreceptor number and distribution affect brightness sensitivity, spectral sensitivity and resolution. Probably their most dynamic characteristic is the variation in visual pigment peak sensitivities. Visual pigments can be altered through changes in chromophore, opsin sequence and opsin expression. Opsin expression varies by altering which of the seven available cone opsins in their genomes are turned on. These opsins can even be coexpressed to produce seemingly infinitely tunable cone sensitivities. Both chromophore and opsin expression can vary on either rapid (hours or days), slower (seasonal or ontogenetic) or evolutionary timescales. Such visual system shifts have enabled cichlids to adapt to different habitats and foraging styles. Through both short term plasticity and longer evolutionary adaptations, cichlids have proven to be ecologically successful and an excellent model for studying organismal adaptation.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
| | - Miranda R Yourick
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
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204
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Davies KTJ, Yohe LR, Almonte J, Sánchez MKR, Rengifo EM, Dumont ER, Sears KE, Dávalos LM, Rossiter SJ. Foraging shifts and visual preadaptation in ecologically diverse bats. Mol Ecol 2020; 29:1839-1859. [PMID: 32293071 DOI: 10.1111/mec.15445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/28/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022]
Abstract
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye-expressed genes associated with shifts to new adaptive zones in ecologically diverse bats from the superfamily Noctilionoidea. Collectively, noctilionoids display remarkable ecological breadth, from highly divergent echolocation to flight strategies linked to specialized insectivory, the parallel evolution of diverse plant-based diets (e.g., nectar, pollen and fruit) from ancestral insectivory, and-unusually for echolocating bats-often have large, well-developed eyes. We report contrasting levels of positive selection in genes associated with the development, maintenance and scope of visual function, tracing back to the origins of noctilionoids and Phyllostomidae (the bat family with most dietary diversity), instead of during shifts to novel diets. Generalized plant visiting was not associated with exceptional molecular adaptation, and exploration of these novel niches took place in an ancestral phyllostomid genetic background. In contrast, evidence for positive selection in vision genes was found at subsequent shifts to either nectarivory or frugivory. Thus, neotropical noctilionoids that use visual cues for identifying food and roosts, as well as for orientation, were effectively preadapted, with subsequent molecular adaptations in nectar-feeding lineages and the subfamily Stenodermatinae of fig-eating bats fine-tuning pre-existing visual adaptations for specialized purposes.
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Affiliation(s)
- Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Department of Geology & Geophysics, Yale University, New Haven, CT, USA
| | - Jesus Almonte
- Independent Scientist, Santo Domingo, Dominican Republic
| | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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205
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Svardal H, Quah FX, Malinsky M, Ngatunga BP, Miska EA, Salzburger W, Genner MJ, Turner GF, Durbin R. Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation. Mol Biol Evol 2020; 37:1100-1113. [PMID: 31821500 PMCID: PMC7086168 DOI: 10.1093/molbev/msz294] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3-4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. "ruaha blue." The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.
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Affiliation(s)
- Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Milan Malinsky
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | - Eric A Miska
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - George F Turner
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
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206
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Faber-Hammond JJ, Bezault E, Lunt DH, Joyce DA, Renn SCP. The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biol Evol 2020; 11:2856-2874. [PMID: 31504491 DOI: 10.1093/gbe/evz185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50-100 CNVEs per individual. For those species represented by multiple samples, we identify 150-200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in "hotspots" and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.
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Affiliation(s)
| | - Etienne Bezault
- BOREA Research Unit, MNHN, CNRS 7208, Sorbonne Université, IRD 207, UCN, UA, Paris, France
| | - David H Lunt
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Domino A Joyce
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Suzy C P Renn
- Department of Biology, Reed College, Portland OR 97202
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207
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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208
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Barth JMI, Gubili C, Matschiner M, Tørresen OK, Watanabe S, Egger B, Han YS, Feunteun E, Sommaruga R, Jehle R, Schabetsberger R. Stable species boundaries despite ten million years of hybridization in tropical eels. Nat Commun 2020; 11:1433. [PMID: 32188850 PMCID: PMC7080837 DOI: 10.1038/s41467-020-15099-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 02/07/2020] [Indexed: 02/01/2023] Open
Abstract
Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla) and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past introgression across a time-calibrated phylogeny. We show that the seven species have remained distinct for up to 10 million years and find that the current frequencies of hybridization across species pairs contrast with genomic signatures of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we suggest cytonuclear incompatibilities, hybrid breakdown, and purifying selection as mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of clades.
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Affiliation(s)
- Julia M I Barth
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Chrysoula Gubili
- Fisheries Research Institute, Hellenic Agricultural Organisation-DEMETER, Nea Peramos, 64 007, Kavala, Greece
| | - Michael Matschiner
- Department of Palaeontology and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006, Zurich, Switzerland.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway.
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316, Oslo, Norway
| | - Shun Watanabe
- Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Eric Feunteun
- Laboratoire Biologie des Organismes et Écosystèmes Aquatiques (BOREA), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, Université de Caen Normandie, Université des Antilles, IRD, 61 Rue Buffon, CP 53, 75231, Paris Cedex 05, France
- MNHN-Station Marine de Dinard, Centre de Recherche et d'Enseignement Sur les Systèmes Côtiers (CRESCO), 38 Rue du Port Blanc, 35800, Dinard, France
| | - Ruben Sommaruga
- Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford Crescent, Salford, M5 4WT, UK.
| | - Robert Schabetsberger
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
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209
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Korshunova T, Malmberg K, Prkić J, Petani A, Fletcher K, Lundin K, Martynov A. Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity. Zookeys 2020; 917:15-50. [PMID: 32206016 PMCID: PMC7076062 DOI: 10.3897/zookeys.917.47444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 11/12/2022] Open
Abstract
Using the nudibranch genus Amphorina as a model, ongoing speciation is demonstrated, as well as how periodic-like patterns in colouration can be included in an integrated method of fine-scale species delimitation. By combining several methods, including BPP analysis and the study of molecular, morphological, and ecological data from a large number of specimens within a broad geographic range from northern Europe to the Mediterranean, five species are recognised within the genus Amphorina, reviewed here for the first time. Two new species from the southwestern coast of Sweden are described, A. viriola sp. nov. and A. andra sp. nov. Evidence is provided of a recent speciation process between the two closely related, yet separate, species which inhabit the same geographic localities but demonstrate strict water depth differentiation, with one species inhabiting the shallow brackish top layer above the halocline and the other species inhabiting the underlying saltier water. The results presented here are of relevance for currently debated issues such as conservation in relation to speciation, fine species delimitation, and integration of molecular, morphological and ecological information in biodiversity studies. The periodic approach to biological taxonomy has considerable practical potential for various organismal groups.
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Affiliation(s)
- Tatiana Korshunova
- Koltzov Institute of Developmental Biology RAS, 26 Vavilova Str., 119334 Moscow, Russia Koltzov Institute of Developmental Biology RAS Moscow Russia.,Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia Moscow State University Moscow Russia
| | - Klas Malmberg
- Aquatilis, Nostravägen 11, S-41743, Gothenburg, Sweden Aquatilis Gothenburgh Sweden
| | - Jakov Prkić
- Getaldiceva 11, C 21000 Split, Croatia Unaffiliated Split Croatia
| | - Alen Petani
- Put Kotlara 6, C 23000 Zadar, Croatia Unaffiliated Zadar Croatia
| | - Karin Fletcher
- Port Orchard, Washington, 98366, USA Unaffiliated Port Orchard United States of America
| | - Kennet Lundin
- Gothenburg Natural History Museum, Box 7283, SE-40235, Gothenburg, Sweden Gothenburg Natural History Museum Gothenburg Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-40530, Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Alexander Martynov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 125009 Moscow, Russia Moscow State University Moscow Russia
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210
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Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes. COPEIA 2020. [DOI: 10.1643/cg-18-139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403;
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael D. Burns
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503;
| | - Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Fábio F. Roxo
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil;
| | - Prosanta Chakrabarty
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Brian L. Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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211
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Olave M, Meyer A. Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish. Syst Biol 2020; 69:848-862. [DOI: 10.1093/sysbio/syaa005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/09/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022] Open
Abstract
AbstractThe Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]
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Affiliation(s)
- Melisa Olave
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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212
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Exploratory behaviour is associated with microhabitat and evolutionary radiation in Lake Malawi cichlids. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2019.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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213
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Eldridge MDB, Pearson DJ, Potter S. Identification of a novel hybrid zone within the black-footed rock-wallaby (Petrogale lateralis) in Western Australia. AUST J ZOOL 2020. [DOI: 10.1071/zo20052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.
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214
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Diversification and Evolutionary Histories of Patagonian Steppe Lizards. NATURAL AND SOCIAL SCIENCES OF PATAGONIA 2020. [DOI: 10.1007/978-3-030-42752-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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215
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Lecaudey LA, Sturmbauer C, Singh P, Ahi EP. Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii. Sci Rep 2019; 9:20296. [PMID: 31889116 PMCID: PMC6937230 DOI: 10.1038/s41598-019-56771-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
East African cichlid fishes represent a model to tackle adaptive changes and their connection to rapid speciation and ecological distinction. In comparison to bony craniofacial tissues, adaptive morphogenesis of soft tissues has been rarely addressed, particularly at the molecular level. The nuchal hump in cichlids fishes is one such soft-tissue and exaggerated trait that is hypothesized to play an innovative role in the adaptive radiation of cichlids fishes. It has also evolved in parallel across lakes in East Africa and Central America. Using gene expression profiling, we identified and validated a set of genes involved in nuchal hump formation in the Lake Malawi dolphin cichlid, Cyrtocara moorii. In particular, we found genes differentially expressed in the nuchal hump, which are involved in controlling cell proliferation (btg3, fosl1a and pdgfrb), cell growth (dlk1), craniofacial morphogenesis (dlx5a, mycn and tcf12), as well as regulators of growth-related signals (dpt, pappa and socs2). This is the first study to identify the set of genes associated with nuchal hump formation in cichlids. Given that the hump is a trait that evolved repeatedly in several African and American cichlid lineages, it would be interesting to see if the molecular pathways and genes triggering hump formation follow a common genetic track or if the trait evolved in parallel, with distinct mechanisms, in other cichlid adaptive radiations and even in other teleost fishes.
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Affiliation(s)
- Laurène Alicia Lecaudey
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
| | - Pooja Singh
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria
- Institute of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Ehsan Pashay Ahi
- Institute of Biology, University of Graz, Universitätsplatz 2, A-8010, Graz, Austria.
- Department of Comparative Physiology, Uppsala University, Norbyvägen 18A, SE-75 236, Uppsala, Sweden.
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216
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York RA, Byrne A, Abdilleh K, Patil C, Streelman T, Finger TE, Fernald RD. Behavioral evolution contributes to hindbrain diversification among Lake Malawi cichlid fish. Sci Rep 2019; 9:19994. [PMID: 31882605 PMCID: PMC6934501 DOI: 10.1038/s41598-019-55894-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/20/2019] [Indexed: 12/30/2022] Open
Abstract
The evolutionary diversification of animal behavior is often associated with changes in the structure and function of nervous systems. Such evolutionary changes arise either through alterations of individual neural components (“mosaically”) or through scaling of the whole brain (“concertedly”). Here we show that the evolution of a courtship behavior in Malawi cichlid fish is associated with rapid, extensive, and specific diversification of orosensory, gustatory centers in the hindbrain. We find that hindbrain volume varies significantly between species that build pit (depression) compared to castle (mound) type bowers and that this trait is evolving rapidly among castle-building species. Molecular analyses of neural activity via immediate early gene expression indicate a functional role for hindbrain structures during bower building. Finally, comparisons of bower building species in neighboring Lake Tanganyika suggest parallel patterns of neural diversification to those in Lake Malawi. Our results suggest that mosaic brain evolution via alterations to individual brain structures is more extensive and predictable than previously appreciated.
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Affiliation(s)
- Ryan A York
- Department of Biology, Stanford University, Stanford, California, 94305, USA. .,Department of Neurobiology, Stanford University, Stanford, California, 94305, USA.
| | - Allie Byrne
- Department of Biology, Stanford University, Stanford, California, 94305, USA
| | - Kawther Abdilleh
- School of Biological Sciences and Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Chinar Patil
- School of Biological Sciences and Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Todd Streelman
- School of Biological Sciences and Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Thomas E Finger
- Department of Cell and Developmental Biology, University of Colorado Denver, Aurora, CO, 80045, USA.,Rocky Mountain Taste and Smell Center, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Russell D Fernald
- Department of Biology, Stanford University, Stanford, California, 94305, USA.,Neuroscience Institute, Stanford University, Stanford, California, 94305, USA
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217
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Meier JI, Stelkens RB, Joyce DA, Mwaiko S, Phiri N, Schliewen UK, Selz OM, Wagner CE, Katongo C, Seehausen O. The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes. Nat Commun 2019; 10:5391. [PMID: 31796733 PMCID: PMC6890737 DOI: 10.1038/s41467-019-13278-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Great Lakes to test these hypotheses. Greater biotic isolation (fewer lineages) predicts fewer constraints by competition and hence more ecological opportunity in Lake Bangweulu, whereas opportunity for hybridization predicts increased genetic potential in Lake Mweru. In Lake Bangweulu, we find no evidence for hybridization but also no adaptive radiation. We show that the Bangweulu lineages also colonized Lake Mweru, where they hybridized with Congolese lineages and then underwent multiple adaptive radiations that are strikingly complementary in ecology and morphology. Our data suggest that the presence of several related lineages does not necessarily prevent adaptive radiation, although it constrains the trajectories of morphological diversification. It might instead facilitate adaptive radiation when hybridization generates genetic variation, without which radiation may start much later, progress more slowly or never occur.
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Affiliation(s)
- Joana I Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK
| | - Rike B Stelkens
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Division of Population Genetics, Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, 106 91, Stockholm, Sweden
| | - Domino A Joyce
- Evolutionary and Ecological Genomics Group, Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Salome Mwaiko
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Numel Phiri
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ulrich K Schliewen
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany
| | - Oliver M Selz
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Biodiversity Institute and Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland.
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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218
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Kratochwil CF, Liang Y, Urban S, Torres-Dowdall J, Meyer A. Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes. Genome Biol Evol 2019; 11:3452-3465. [PMID: 31821504 PMCID: PMC6916709 DOI: 10.1093/gbe/evz261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8-12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
| | - Sabine Urban
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
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219
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Piñeiro Fernández L, Byers KJR.P, Cai J, Sedeek KEM, Kellenberger RT, Russo A, Qi W, Aquino Fournier C, Schlüter PM. A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia. FRONTIERS IN PLANT SCIENCE 2019; 10:1553. [PMID: 31850034 PMCID: PMC6895147 DOI: 10.3389/fpls.2019.01553] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/07/2019] [Indexed: 05/30/2023]
Abstract
The orchids (Orchidaceae) constitute one of the largest and most diverse families of flowering plants. They have evolved a great variety of adaptations to achieve pollination by a diverse group of pollinators. Many orchids reward their pollinators, typically with nectar, but the family is also well-known for employing deceptive pollination strategies in which there is no reward for the pollinator, in the most extreme case by mimicking sexual signals of pollinators. In the European flora, two examples of these different pollination strategies are the sexually deceptive genus Ophrys and the rewarding genus Gymnadenia, which differ in their level of pollinator specialization; Ophrys is typically pollinated by pseudo-copulation of males of a single insect species, whilst Gymnadenia attracts a broad range of floral visitors. Here, we present and describe the annotated floral transcriptome of Ophrys iricolor, an Andrena-pollinated representative of the genus Ophrys that is widespread throughout the Aegean. Furthermore, we present additional floral transcriptomes of both sexually deceptive and rewarding orchids, specifically the deceptive Ophrys insectifera, Ophrys aymoninii, and an updated floral transcriptome of Ophrys sphegodes, as well as the floral transcriptomes of the rewarding orchids Gymnadenia conopsea, Gymnadenia densiflora, Gymnadenia odoratissima, and Gymnadenia rhellicani (syn. Nigritella rhellicani). Comparisons of these novel floral transcriptomes reveal few annotation differences between deceptive and rewarding orchids. Since together, these transcriptomes provide a representative sample of the genus-wide taxonomic diversity within Ophrys and Gymnadenia (Orchidoideae: Orchidinae), we employ a phylogenomic approach to address open questions of phylogenetic relationships within the genera. Specifically, this includes the controversial placement of O. insectifera within the Ophrys phylogeny and the placement of "Nigritella"-type morphologies within the phylogeny of Gymnadenia. Whereas in Gymnadenia, several conflicting topologies are supported by a similar number of gene trees, a majority of Ophrys gene topologies clearly supports a placement of O. insectifera as sister to a clade containing O. sphegodes.
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Affiliation(s)
- Laura Piñeiro Fernández
- Institute of Botany, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Kelsey J. R .P. Byers
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Jing Cai
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Khalid E. M. Sedeek
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Centre, Giza, Egypt
| | - Roman T. Kellenberger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alessia Russo
- Institute of Botany, University of Hohenheim, Stuttgart, Germany
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Centre Zurich, Zurich, Switzerland
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220
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Hybridization increases population variation during adaptive radiation. Proc Natl Acad Sci U S A 2019; 116:23216-23224. [PMID: 31659024 DOI: 10.1073/pnas.1913534116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
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221
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Selz OM, Seehausen O. Interspecific hybridization can generate functional novelty in cichlid fish. Proc Biol Sci 2019; 286:20191621. [PMID: 31640510 DOI: 10.1098/rspb.2019.1621] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has been suggested to facilitate the evolution of ecological novelty, and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether ecological opportunities, beyond those of the parental species, do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental species when feeding on food either parent is adapted to, and if the same hybrids perform better than their parents when feeding on food none of the species are adapted to. We generated two first-generation hybrid crosses between species of African cichlids. In feeding efficiency experiments we measured the performance of hybrids and parental species on food types representing both parental species niches and additional 'novel' niches, not used by either of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the 'novel' food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.
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Affiliation(s)
- O M Selz
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - O Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
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222
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Musilova Z, Indermaur A, Bitja‐Nyom AR, Omelchenko D, Kłodawska M, Albergati L, Remišová K, Salzburger W. Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon. Mol Ecol 2019; 28:5010-5031. [DOI: 10.1111/mec.15217] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Zuzana Musilova
- Department of Zoology Charles University in Prague Prague Czech Republic
- Zoological Institute University of Basel Basel Switzerland
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological Sciences University of Ngaoundéré Ngaoundéré Cameroon
- Department of Management of Fisheries and Aquatic Ecosystems University of Douala Douala Cameroon
| | - Dmytro Omelchenko
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Monika Kłodawska
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Lia Albergati
- Zoological Institute University of Basel Basel Switzerland
| | - Kateřina Remišová
- Department of Physiology Charles University in Prague Prague Czech Republic
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223
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Yuan H, Atta C, Tornabene L, Li C. Assexon: Assembling Exon Using Gene Capture Data. Evol Bioinform Online 2019; 15:1176934319874792. [PMID: 31523128 PMCID: PMC6732846 DOI: 10.1177/1176934319874792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Exon capture across species has been one of the most broadly applied approaches
to acquire multi-locus data in phylogenomic studies of non-model organisms.
Methods for assembling loci from short-read sequences (eg, Illumina platforms)
that rely on mapping reads to a reference genome may not be suitable for studies
comprising species across a wide phylogenetic spectrum; thus, de novo assembling
methods are more generally applied. Current approaches for assembling targeted
exons from short reads are not particularly optimized as they cannot (1)
assemble loci with low read depth, (2) handle large files efficiently, and (3)
reliably address issues with paralogs. Thus, we present Assexon: a streamlined
pipeline that de novo assembles targeted exons and their flanking sequences from
raw reads. We tested our method using reads from Lepisosteus
osseus (4.37 Gb) and Boleophthalmus pectinirostris
(2.43 Gb), which are captured using baits that were designed based on genome
sequence of Lepisosteus oculatus and Oreochromis
niloticus, respectively. We compared performance of Assexon to
PHYLUCE and HybPiper, which are commonly used pipelines to assemble
ultra-conserved element (UCE) and Hyb-seq data. A custom exon capture analysis
pipeline (CP) developed by Yuan et al was compared as well. Assexon accurately
assembled more than 3400 to 3800 (20%-28%) loci than PHYLUCE and more than 1900
to 2300 (8%-14%) loci than HybPiper across different levels of phylogenetic
divergence. Assexon ran at least twice as fast as PHYLUCE and HybPiper. Number
of loci assembled using CP was comparable with Assexon in both tests, while
Assexon ran at least 7 times faster than CP. In addition, some steps of CP
require the user’s interaction and are not fully automated, and this user time
was not counted in our calculation. Both Assexon and CP retrieved no paralogs in
the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is a tool
for accurate and efficient assembling of large read sets from exon capture
experiments. Furthermore, Assexon includes scripts to filter poorly aligned
coding regions and flanking regions, calculate summary statistics of loci, and
select loci with reliable phylogenetic signal. Assexon is available at https://github.com/yhadevol/Assexon.
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Affiliation(s)
- Hao Yuan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean Universitiy), Ministry of Education, Shanghai, China
| | - Calder Atta
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean Universitiy), Ministry of Education, Shanghai, China
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224
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Conith MR, Conith AJ, Albertson RC. Evolution of a soft-tissue foraging adaptation in African cichlids: Roles for novelty, convergence, and constraint. Evolution 2019; 73:2072-2084. [PMID: 31418824 DOI: 10.1111/evo.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Abstract
Understanding the origins of biodiversity demands consideration of both extrinsic (e.g., ecological opportunity) and intrinsic (e.g., developmental constraint) factors. Here, we use a combination of phylogenetic and genetic tools to address the origin of novelty in African cichlids. In particular, we focus on an extreme hypertrophied snout that is structurally integrated with the upper jaw. We show that this bizarre trait has evolved independently in at least two distinct and ecologically successful cichlid clades. We find that snout dimensions are decoupled both phenotypically and genetically, which has enabled it to evolve independently in multiple directions. Further, patterns of variation among species and within a genetic mapping pedigree suggest that relative to snout length, depth is under greater genetic and/or developmental constraint. Models of evolution suggest that snout shape is under selection for feeding behavior, with snout depth being important for algae scraping and snout length for sand sifting. Indeed, the deep snout of some algivores is achieved via an expansion of the intermaxillary ligament, which is important for jaw stability and may increase feeding performance. Overall, our data imply that the evolution of exaggerated snout depth required overcoming a genetic/developmental constraint, which led to expanded ecological opportunity via foraging adaptation.
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Affiliation(s)
- Moira R Conith
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Andrew J Conith
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - R Craig Albertson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003.,Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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225
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Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K. Evidence for sympatric speciation in a Wallacean ancient lake. Evolution 2019; 73:1898-1915. [DOI: 10.1111/evo.13821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Nobu Sutra
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Junko Kusumi
- Faculty of Social and Cultural StudiesKyushu University Fukuoka 819‐0395 Japan
| | - Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Shingo Fujimoto
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | | | | | - Atsushi Toyoda
- Comparative Genomics LaboratoryNational Institute of Genetics Mishima 411‐8540 Japan
| | | | - Ryosuke Kimura
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
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226
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Franchini P, Xiong P, Fruciano C, Schneider RF, Woltering JM, Hulsey CD, Meyer A. MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Mol Biol Evol 2019; 36:2498-2511. [PMID: 31397871 DOI: 10.1093/molbev/msz168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
AbstractCichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.
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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
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France
| | - Ralf F Schneider
- Marine Ecology, Helmholtz-Zentrum für Ozeanforschung Kiel (GEOMAR), Düsternbrooker Weg 20, Kiel, Germany
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Joost M Woltering
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christopher Darrin Hulsey
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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227
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Ben Jemaa S, Kdidi S, Gdura AM, Dayhum AS, Eldaghayes IM, Boussaha M, Rebours E, Yahyaoui MH. Inferring the population structure of the Maghreb sheep breeds using a medium-density SNP chip. Anim Genet 2019; 50:526-533. [PMID: 31385357 DOI: 10.1111/age.12831] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2019] [Indexed: 01/26/2023]
Abstract
North Africa has a great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics and to certain historical events that took place in the region. To date, few genome-wide studies have been conducted to investigate the population structure of North African indigenous sheep. The objective of the present study was to provide a detailed assessment of the genetic structure and admixture patterns of six Maghreb sheep populations using the Illumina 50K Ovine BeadChip and comparisons with 22 global populations of sheep and mouflon. Regardless of the method of analysis used, patterns of multiple hybridization events were observed within all North African populations, leading to a heterogeneous genetic architecture that varies according to the breed. The Barbarine population showed the lowest genetic heterogeneity and major southwest Asian ancestry, providing additional support to the Asian origin of the North African fat-tailed sheep. All other breeds presented substantial Merino introgression ranging from 15% for D'man to 31% for Black Thibar. We highlighted several signals of ancestral introgression between North African and southern European sheep. In addition, we identified two opposite gradients of ancestry, southwest Asian and central European, occurring between North Africa and central Europe. Our results provide further evidence of the weak global population structure of sheep resulting from high levels of gene flow among breeds occurring worldwide. At the regional level, signs of recent admixture among North African populations, resulting in a change of the original genomic architecture of minority breeds, were also detected.
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Affiliation(s)
- S Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - S Kdidi
- Livestock and Wildlife Laboratory, Arid Lands Institute, Route Djorf Km 22, 4119, Medenine, Tunisia
| | - A M Gdura
- Animal Improvement Project, Ministry of Agriculture, Tripoli, Libya
| | - A S Dayhum
- Faculty of Veterinary Medicine, University of Tripoli, 13662, Tripoli, Libya
| | - I M Eldaghayes
- Faculty of Veterinary Medicine, University of Tripoli, 13662, Tripoli, Libya
| | - M Boussaha
- GABI, INRA, AgroParisTech, Paris Saclay University, 78350, Jouy-en-Josas, France
| | - E Rebours
- GABI, INRA, AgroParisTech, Paris Saclay University, 78350, Jouy-en-Josas, France
| | - M H Yahyaoui
- Livestock and Wildlife Laboratory, Arid Lands Institute, Route Djorf Km 22, 4119, Medenine, Tunisia
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228
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Cui R, Medeiros T, Willemsen D, Iasi LN, Collier GE, Graef M, Reichard M, Valenzano DR. Relaxed Selection Limits Lifespan by Increasing Mutation Load. Cell 2019; 178:385-399.e20. [DOI: 10.1016/j.cell.2019.06.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/18/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
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229
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Marques DA, Meier JI, Seehausen O. A Combinatorial View on Speciation and Adaptive Radiation. Trends Ecol Evol 2019; 34:531-544. [DOI: 10.1016/j.tree.2019.02.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 01/28/2023]
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230
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Foote AD, Martin MD, Louis M, Pacheco G, Robertson KM, Sinding MHS, Amaral AR, Baird RW, Baker CS, Ballance L, Barlow J, Brownlow A, Collins T, Constantine R, Dabin W, Dalla Rosa L, Davison NJ, Durban JW, Esteban R, Ferguson SH, Gerrodette T, Guinet C, Hanson MB, Hoggard W, Matthews CJD, Samarra FIP, de Stephanis R, Tavares SB, Tixier P, Totterdell JA, Wade P, Excoffier L, Gilbert MTP, Wolf JBW, Morin PA. Killer whale genomes reveal a complex history of recurrent admixture and vicariance. Mol Ecol 2019; 28:3427-3444. [PMID: 31131963 DOI: 10.1111/mec.15099] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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Affiliation(s)
- Andrew D Foote
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Marie Louis
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - George Pacheco
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Kelly M Robertson
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Mikkel-Holger S Sinding
- Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Ana R Amaral
- American Museum of Natural History, New York City, New York.,Faculdade de Ciências Universidade de Lisboa, Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | | | - Charles Scott Baker
- Department of Fisheries and Wildlife, Marine Mammal Institute, Oregon State University, Newport, Oregon.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Lisa Ballance
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Jay Barlow
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, New York City, New York
| | | | - Willy Dabin
- Observatoire Pelagis, Université de La Rochelle-CNRS, La Rochelle, France
| | - Luciano Dalla Rosa
- Laboratório de Ecologia e Conservação da Megafauna Marinha, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Nicholas J Davison
- Scottish Marine Animal Stranding Scheme, SRUC Veterinary Services Drummondhill, Inverness, UK
| | - John W Durban
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Ruth Esteban
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | | | - Tim Gerrodette
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France
| | - M Bradley Hanson
- National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Northwest Fisheries Science Center, Seattle, Washington
| | - Wayne Hoggard
- National Marine Fisheries Service, NOAA, Southeast Fisheries Science Center, Pascagoula, Mississippi
| | | | | | - Renaud de Stephanis
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras, Spain
| | - Sara B Tavares
- Scottish Oceans Institute, East Sands, University of St. Andrews, St. Andrews, UK
| | - Paul Tixier
- Centre d'Etudes Biologiques de Chizé (CEBC), CNRS-ULR, UMR, Chizé, France.,School of Life and Environmental Sciences (Burwood Campus), Deakin University, Geelong, Victoria, Australia
| | - John A Totterdell
- Marine Information and Research Group-Australia (MIRG), Quinns Rocks, Western Australia, Australia
| | - Paul Wade
- National Marine Mammal Laboratory, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Alaska Fisheries Science Center, Seattle, Washington
| | - Laurent Excoffier
- CMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - M Thomas P Gilbert
- NTNU University Museum, Trondheim, Norway.,Department of Biology, Section for Evolutionary Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany.,Department of Evolutionary Biology, Science of Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Phillip A Morin
- Marine Mammal and Turtle Division, National Marine Fisheries Service, National Oceanographic and Atmospheric Administration, Southwest Fisheries Science Center, La Jolla, California
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231
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Edgley DE, Genner MJ. Adaptive Diversification of the Lateral Line System during Cichlid Fish Radiation. iScience 2019; 16:1-11. [PMID: 31146127 PMCID: PMC6542376 DOI: 10.1016/j.isci.2019.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/06/2019] [Accepted: 05/10/2019] [Indexed: 01/19/2023] Open
Abstract
The mechanosensory lateral line system is used by fishes to sense hydrodynamic stimuli in their environment. It provides information about flow regimes, proximity to substrate, and the presence and identity of prey and predators and represents a means of receiving communication signals from other fish. Thus we may expect lateral line system structures to be under strong divergent selection during adaptive radiation. Here, we used X-ray micro-computed tomography scans to quantify variation in cranial lateral line canal morphology within the adaptive radiation of Lake Malawi cichlids. We report that cranial lateral line canal morphology is strongly correlated with diet and other aspects of craniofacial morphology, including the shape of oral jaws. These results indicate an adaptive role for the lateral line system in prey detection and suggest that diversification of this system has taken an important role in the spectacular evolution of Lake Malawi's cichlid fish diversity.
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Affiliation(s)
- Duncan E Edgley
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK.
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232
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Lavretsky P, DaCosta JM, Sorenson MD, McCracken KG, Peters JL. ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America. Mol Ecol 2019; 28:2594-2609. [DOI: 10.1111/mec.15091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 03/05/2019] [Accepted: 03/29/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Philip Lavretsky
- Department of Biological Sciences University of Texas at El Paso El Paso Texas
- Department of Biological Sciences Wright State University Dayton Ohio
- Department of Biology University of Miami Miami Florida
| | - Jeffrey M. DaCosta
- Biology Department Boston College Chestnut Hill Massachusetts
- Biology Department Boston College Boston Massachusetts
| | | | - Kevin G. McCracken
- Department of Biology University of Miami Miami Florida
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences University of Miami Miami Florida
- Human Genetics and Genomics Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami Florida
- Institute of Arctic Biology and University of Alaska Museum University of Alaska Fairbanks Fairbanks Alaska
| | - Jeffrey L. Peters
- Department of Biological Sciences Wright State University Dayton Ohio
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233
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Oziolor EM, Reid NM, Yair S, Lee KM, Guberman VerPloeg S, Bruns PC, Shaw JR, Whitehead A, Matson CW. Adaptive introgression enables evolutionary rescue from extreme environmental pollution. Science 2019; 364:455-457. [DOI: 10.1126/science.aav4155] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/25/2019] [Indexed: 12/19/2022]
Abstract
Radical environmental change that provokes population decline can impose constraints on the sources of genetic variation that may enable evolutionary rescue. Adaptive toxicant resistance has rapidly evolved in Gulf killifish (Fundulus grandis) that occupy polluted habitats. We show that resistance scales with pollution level and negatively correlates with inducibility of aryl hydrocarbon receptor (AHR) signaling. Loci with the strongest signatures of recent selection harbor genes regulating AHR signaling. Two of these loci introgressed recently (18 to 34 generations ago) from Atlantic killifish (F. heteroclitus). One introgressed locus contains a deletion in AHR that confers a large adaptive advantage [selection coefficient (s) = 0.8]. Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change.
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234
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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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235
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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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236
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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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237
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Böhne A, Weber AAT, Rajkov J, Rechsteiner M, Riss A, Egger B, Salzburger W. Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine Cichlid Pseudocrenilabrus philander. Genome Biol Evol 2019; 11:439-458. [PMID: 30649313 PMCID: PMC6375353 DOI: 10.1093/gbe/evz003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/15/2022] Open
Abstract
Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX-XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX-XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.
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Affiliation(s)
- Astrid Böhne
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Alexandra Anh-Thu Weber
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Museums Victoria, Melbourne, Victoria, Australia
| | - Jelena Rajkov
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Michael Rechsteiner
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Andrin Riss
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Program Man Society Environment, University of Basel, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
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238
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Conith AJ, Lam DT, Albertson RC. Muscle-induced loading as an important source of variation in craniofacial skeletal shape. Genesis 2018; 57:e23263. [PMID: 30418689 DOI: 10.1002/dvg.23263] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 10/27/2018] [Indexed: 01/01/2023]
Abstract
The shape of the craniofacial skeleton is constantly changing through ontogeny and reflects a balance between developmental patterning and mechanical-load-induced remodeling. Muscles are a major contributor to producing the mechanical environment that is crucial for "normal" skull development. Here, we use an F5 hybrid population of Lake Malawi cichlids to characterize the strength and types of associations between craniofacial bones and muscles. We focus on four bones/bone complexes, with different developmental origins, alongside four muscles with distinct functions. We used micro-computed tomography to extract 3D information on bones and muscles. 3D geometric morphometrics and volumetric measurements were used to characterize bone and muscle shape, respectively. Linear regressions were performed to test for associations between bone shape and muscle volume. We identified three types of associations between muscles and bones: weak, strong direct (i.e., muscles insert directly onto bone), and strong indirect (i.e., bone is influenced by muscles without a direct connection). In addition, we show that although the shape of some bones is relatively robust to muscle-induced mechanical stimulus, others appear to be highly sensitive to muscular input. Our results imply that the roles for muscular input on skeletal shape extend beyond specific points of origin or insertion and hold significant potential to influence broader patterns of craniofacial geometry. Thus, changes in the loading environment, either as a normal course of ontogeny or if an organism is exposed to a novel environment, may have pronounced effects on skeletal shape via near and far-ranging effects of muscular loading.
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Affiliation(s)
- Andrew J Conith
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Daniel T Lam
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
| | - R Craig Albertson
- Biology Department, University of Massachusetts Amherst, Amherst, Massachusetts
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239
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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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240
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Darrin Hulsey C, Zheng J, Holzman R, Alfaro ME, Olave M, Meyer A. Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes? BMC Evol Biol 2018; 18:179. [PMID: 30486792 PMCID: PMC6263179 DOI: 10.1186/s12862-018-1296-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 11/16/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibiting greatly hypertrophied lips. RESULTS The hypertrophied lip cichlids Cheilochromis euchilus, Eclectochromis ornatus, Placidochromis "Mbenji fatlip", and Placidochromis milomo are all nested within the non-mbuna clade of Malawi cichlids based on both concatenated sequence and single nucleotide polymorphism (SNP) inferred phylogenies. Lichnochromis acuticeps that exhibits slightly hypertrophied lips also appears to have evolutionary affinities to this group. However, Chilotilapia rhoadesii that lacks hypertrophied lips was recovered as nested within the species Cheilochromis euchilus. Species tree reconstructions and analyses of introgression provided largely ambiguous patterns of Malawi cichlid evolution. CONCLUSIONS Contrary to mitochondrial DNA phylogenies, bifurcating trees based on our 1024 UCE loci supported close affinities of Lake Malawi lineages with hypertrophied lips. However, incomplete lineage sorting in Malawi tends to render these inferences more tenuous. Phylogenomic analyses will continue to provide powerful inferences about whether phenotypic novelties arose once or multiple times during adaptive radiation.
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Affiliation(s)
- C. Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jimmy Zheng
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Roi Holzman
- Department of Zoology, Tel Aviv University and the Inter-University Institute for Marine Sciences in Eilat, 88103 Eilat, Israel
| | - Michael E. Alfaro
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA USA
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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241
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Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol 2018; 27:4397-4416. [PMID: 30252986 PMCID: PMC6261294 DOI: 10.1111/mec.14877] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022]
Abstract
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our data set. The two lineages likely diverged much more recently than previous mitochondrial estimates of 5-7 mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161 and 191 k generations ago. The favoured demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified gene flow among all lineages sampled. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite gene flow with surface populations. The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift. Finally, we show that a key trogolomorphic phenotype QTL is enriched for genomic regions with low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. Our study shows that gene flow must be considered in studies of independent, repeated trait evolution.
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Affiliation(s)
- Adam Herman
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Yaniv Brandvain
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - James Weagley
- Ecology, Evolution, and Behavior, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Helena Bilandžija
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
- Department of Biology, University of Maryland, College Park, Maryland
| | | | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, New York
| | - Kelly O'Quin
- Department of Biology, Centre College, Danville, Kentucky
| | - Claudia P Ornelas-García
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | - Brian Carlson
- Department of Biology, College of Wooster, Wooster, Ohio
| | - Ernesto Maldonado
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St Louis, Missouri
| | - Suzanne E McGaugh
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
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242
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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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243
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Ahi EP, Sefc KM. Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation. PeerJ 2017; 5:e4080. [PMID: 29158996 PMCID: PMC5695249 DOI: 10.7717/peerj.4080] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/01/2017] [Indexed: 01/04/2023] Open
Abstract
Morphological differentiation among closely related species provides opportunities to study mechanisms shaping natural phenotypic variation. Here, we address variation in the orientation of melanin-colored body stripes in three cichlid species of the tribe Haplochromini. Melanochromis auratus displays a common pattern of dark, straight horizontal body stripes, whereas in Aristochromis christyi and Buccochromis rhoadesii, oblique stripes extend from the anterior dorsal to the posterior mid-lateral trunk. We first validated a stably reference gene, and then, investigated the chromatophore distribution in the skin by assessing the expression levels of the iridophore and melanophore marker genes, ltk and slc24a5, respectively, as well as pmel, a melanophore pigmentation marker gene. We found anterior-posterior differences in the expression levels of the three genes in the oblique-striped species. The higher anterior expression of ltk, indicates increased iridophore density in the anterior region, i.e., uneven horizontal distribution of iridophores, which coincides with the anterior dorsalization of melanophore stripe in these species. The obliqueness of the horizontal body stripes might be a result of distinct migratory or patterning abilities of melanophores in anterior and posterior stripe regions which could be reflected by variation in the expression of genes involved in melanophore patterning. To address this, we investigated anterior-posterior expression levels of a primary set of candidate target genes with known functions in melanophore migration and stripe patterning in the adult zebrafish, and their related gene regulatory network. Among these genes, those with differences in anterior-posterior expression showed only species-specific differential expression, e.g., sdf1a, col14a1a, ifitm5, and agpat3, with the exception of fbxw4/hagoromo (differentially expressed in an oblique-and the straight-striped species). In summary, distinct anterior-posterior gradients in iridophore density found to be more similar characteristic between the two oblique-striped species. Furthermore, the species-specific differential expression of genes involved in stripe patterning might also implicate distinct molecular processes underlying the obliqueness of body stripe in two closely related cichlid species.
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Affiliation(s)
- Ehsan Pashay Ahi
- Institute of Zoology, Universitätsplatz 2, Universität Graz, Graz, Austria
| | - Kristina M Sefc
- Institute of Zoology, Universitätsplatz 2, Universität Graz, Graz, Austria
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244
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Parsons PJ, Bridle JR, Rüber L, Genner MJ. Evolutionary divergence in life history traits among populations of the Lake Malawi cichlid fish Astatotilapia calliptera. Ecol Evol 2017; 7:8488-8506. [PMID: 29075465 PMCID: PMC5648681 DOI: 10.1002/ece3.3311] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/26/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
Abstract
During the early stages of adaptive radiation, populations diverge in life history traits such as egg size and growth rates, in addition to eco‐morphological and behavioral characteristics. However, there are few studies of life history divergence within ongoing adaptive radiations. Here, we studied Astatotilapia calliptera, a maternal mouthbrooding cichlid fish within the Lake Malawi haplochromine radiation. This species occupies a rich diversity of habitats, including the main body of Lake Malawi, as well as peripheral rivers and shallow lakes. We used common garden experiments to test for life history divergence among populations, focussing on clutch size, duration of incubation, egg mass, offspring size, and growth rates. In a first experiment, we found significant differences among populations in average clutch size and egg mass, and larger clutches were associated with smaller eggs. In a second experiment, we found significant differences among populations in brood size, duration of incubation, juvenile length when released, and growth rates. Larger broods were associated with smaller juveniles when released and shorter incubation times. Although juvenile growth rates differed between populations, these were not strongly related to initial size on release. Overall, differences in life history characters among populations were not predicted by major habitat classifications (Lake Malawi or peripheral habitats) or population genetic divergence (microsatellite‐based FST). We suggest that the observed patterns are consistent with local selective forces driving the observed patterns of trait divergence. The results provide strong evidence of evolutionary divergence and covariance of life history traits among populations within a radiating cichlid species, highlighting opportunities for further work to identify the processes driving the observed divergence.
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Affiliation(s)
- Paul J Parsons
- School of Biological Sciences University of Bristol Bristol UK.,University of Exeter Penryn UK
| | - Jon R Bridle
- School of Biological Sciences University of Bristol Bristol UK
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland.,Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Martin J Genner
- School of Biological Sciences University of Bristol Bristol UK
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245
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Feng C, Pettersson M, Lamichhaney S, Rubin CJ, Rafati N, Casini M, Folkvord A, Andersson L. Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate. eLife 2017; 6:e23907. [PMID: 28665273 PMCID: PMC5524536 DOI: 10.7554/elife.23907] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 × 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.
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Affiliation(s)
- Chungang Feng
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sangeet Lamichhaney
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nima Rafati
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden
| | - Arild Folkvord
- Department of Biology, University of Bergen and the Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway
- Institute of Marine Research, Bergen, Norway
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, United States
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