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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [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: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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2
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Friis G, Vizueta J, Ketterson ED, Milá B. A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird. G3 (BETHESDA, MD.) 2022; 12:jkac083. [PMID: 35404451 PMCID: PMC9157146 DOI: 10.1093/g3journal/jkac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022]
Abstract
The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.
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Affiliation(s)
- Guillermo Friis
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid 28006, Spain
| | - Joel Vizueta
- Centre for Social Evolution, University of Copenhaguen, Copenhaguen 1165, Denmark
| | - Ellen D Ketterson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Borja Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid 28006, Spain
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5
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Jaynes KE, Myers EA, Gvoždík V, Blackburn DC, Portik DM, Greenbaum E, Jongsma GFM, Rödel MO, Badjedjea G, Bamba-Kaya A, Baptista NL, Akuboy JB, Ernst R, Kouete MT, Kusamba C, Masudi FM, McLaughlin PJ, Nneji LM, Onadeko AB, Penner J, Vaz Pinto P, Stuart BL, Tobi E, Zassi-Boulou AG, Leaché AD, Fujita MK, Bell RC. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits. Mol Ecol 2021; 31:3979-3998. [PMID: 34516675 DOI: 10.1111/mec.16169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/18/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
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Affiliation(s)
- Kyle E Jaynes
- Department of Biology, Adrian College, Michigan, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Integrative Biology, W.K. Kellogg Biological Station, Michigan State University, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, Michigan, USA
| | - Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Daniel M Portik
- Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Gregory F M Jongsma
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,Department of Biology, University of Florida, Florida, USA
| | - Mark-Oliver Rödel
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des Ressources Aquatiques, Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, République Démocratique du Congo
| | | | - Ninda L Baptista
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Faculdade de Ciências da, Universidade do Porto, Porto, Portugal.,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, Angola
| | - Jeannot B Akuboy
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Marcel T Kouete
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,School of Natural Resources and Environment, University of Florida, Florida, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, République Démocratique du Congo, Lwiro
| | - Franck M Masudi
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Patrick J McLaughlin
- Bioko Biodiversity Protection Project, Drexel University, Philadelphia, Pennsylvania, USA.,Institute of Conservation Science and Learning, Bristol Zoological Society, Bristol, UK
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
| | - Abiodun B Onadeko
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Johannes Penner
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.,Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Pedro Vaz Pinto
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Fundação Kissama, Luanda, Angola
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, North Carolina, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | | | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
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6
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Recuerda M, Carlos Illera J, Blanco G, Zardoya R, Milá B. Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs). Mol Phylogenet Evol 2021; 164:107291. [PMID: 34384903 DOI: 10.1016/j.ympev.2021.107291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/28/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022]
Abstract
Oceanic archipelagos are excellent systems for studying speciation, yet inference of evolutionary process requires that the colonization history of island organisms be known with accuracy. Here, we used phylogenomics and patterns of genetic diversity to infer the sequence and timing of colonization of Macaronesia by mainland common chaffinches (Fringilla coelebs), and assessed whether colonization of the different archipelagos has resulted in a species-level radiation. To reconstruct the evolutionary history of the complex we generated a molecular phylogeny based on genome-wide SNP loci obtained from genotyping-by-sequencing, we ran ancestral range biogeographic analyses, and assessed fine-scale genetic structure between and within archipelagos using admixture analysis. To test for a species-level radiation, we applied a probabilistic tree-based species delimitation method (mPTP) and an integrative taxonomy approach including phenotypic differences. Results revealed a circuitous colonization pathway in Macaronesia, from the mainland to the Azores, followed by Madeira, and finally the Canary Islands. The Azores showed surprisingly high genetic diversity, similar to that found on the mainland, and the other archipelagos showed the expected sequential loss of genetic diversity. Species delimitation methods supported the existence of several species within the complex. We conclude that the common chaffinch underwent a rapid radiation across Macaronesia that was driven by the sequential colonization of the different archipelagos, resulting in phenotypically and genetically distinct, independent evolutionary lineages. We recommend a taxonomic revision of the complex that takes into account its genetic and phenotypic diversity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain.
| | - Juan Carlos Illera
- Biodiversity Research Unit (UO-CSIC-PA), Oviedo University, 33600 Mieres, Asturias, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
| | - Rafael Zardoya
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC),Madrid 28006, Spain
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