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Cerca J, Cotoras DD, Santander CG, Bieker VC, Hutchins L, Morin-Lagos J, Prada CF, Kennedy S, Krehenwinkel H, Rominger AJ, Meier J, Dimitrov D, Struck TH, Gillespie RG. Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i). Mol Ecol 2023; 32:4971-4985. [PMID: 37515430 DOI: 10.1111/mec.17082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny-leg Tetragnatha adaptive radiation, which includes four microhabitat-specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low-coverage, whole-genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re-evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny-leg Tetragnatha is influenced by multiple evolutionary processes.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Department of Entomology, California Academy of Sciences, San Francisco, California, USA
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Leke Hutchins
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
| | - Jaime Morin-Lagos
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Sanger Institute, Hinxton, UK
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Torsten H Struck
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
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4
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Cerca J, Cotoras DD, Bieker VC, De-Kayne R, Vargas P, Fernández-Mazuecos M, López-Delgado J, White O, Stervander M, Geneva AJ, Guevara Andino JE, Meier JI, Roeble L, Brée B, Patiño J, Guayasamin JM, Torres MDL, Valdebenito H, Castañeda MDR, Chaves JA, Díaz PJ, Valente L, Knope ML, Price JP, Rieseberg LH, Baldwin BG, Emerson BC, Rivas-Torres G, Gillespie R, Martin MD. Evolutionary genomics of oceanic island radiations. Trends Ecol Evol 2023:S0169-5347(23)00032-0. [PMID: 36870806 DOI: 10.1016/j.tree.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico, 28014 Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Calle Darwin 2, 28049 Madrid, Spain
| | - Julia López-Delgado
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Oliver White
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Anthony J Geneva
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Joana Isabel Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Baptiste Brée
- Université de Pau et des Pays de l'Adour (UPPA), Energy Environment Solutions (E2S), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), 64000 Pau, France
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Calle Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - Hugo Valdebenito
- Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador; Herbarium of Economic Botany of Ecuador (Herabario QUSF), Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador
| | | | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA; Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Department of Botany and Plant Physiology, University of Málaga, Málaga, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Jonathan P Price
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building 2465, University of California, Berkeley, CA 94720-2465, USA
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Spain
| | - Gonzalo Rivas-Torres
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Rosemary Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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5
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Piñeros VJ, Del R Pedraza-Marrón C, Betancourt-Resendes I, Calderón-Cortés N, Betancur-R R, Domínguez-Domínguez O. Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting. BMC Ecol Evol 2022; 22:108. [PMID: 36104671 PMCID: PMC9472351 DOI: 10.1186/s12862-022-02063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau. RESULTS Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system. CONCLUSIONS Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.
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Affiliation(s)
- Victor Julio Piñeros
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico
| | | | - Isaí Betancourt-Resendes
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de Las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, Mexico
| | - Nancy Calderón-Cortés
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico.
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
- Laboratorio Nacional de Análisis y Síntesis Ecológica Para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Apartado Postal 27-3 (Xangari), 58089, Michoacán, Morelia, Mexico.
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6
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Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
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Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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