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Gyllenhaal EF, Brady SS, DeCicco LH, Naikatini A, Hime PM, Manthey JD, Kelly J, Moyle RG, Andersen MJ. Waves of Colonization and Gene Flow in a Great Speciator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.603796. [PMID: 39091784 PMCID: PMC11291091 DOI: 10.1101/2024.07.18.603796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.
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Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Serina S. Brady
- Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA
| | - Lucas H. DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | | | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Present Address: McDonnell Genome Institute and Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph D. Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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DeCicco LH, DeRaad DA, Ostrow EN, Moyle RG. A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae). Mol Phylogenet Evol 2023; 187:107883. [PMID: 37481145 DOI: 10.1016/j.ympev.2023.107883] [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: 03/06/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.
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Affiliation(s)
- Lucas H DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA.
| | - Devon A DeRaad
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Emily N Ostrow
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
| | - Robert G Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, KS, USA
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DeRaad DA, Manthey JD, Ostrow EN, DeCicco LH, Andersen MJ, Hosner PA, Shult HT, Joseph L, Dumbacher JP, Moyle RG. Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves. Mol Phylogenet Evol 2021; 166:107333. [PMID: 34688879 DOI: 10.1016/j.ympev.2021.107333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022]
Abstract
Chalcophaps is a morphologically conserved genus of ground-walking doves distributed from India to mainland China, south to Australia, and across the western Pacific to Vanuatu. Here, we reconstruct the evolutionary history of this genus using DNA sequence data from two nuclear genes and one mitochondrial gene, sampled from throughout the geographic range of Chalcophaps. We find support for three major evolutionary lineages in our phylogenetic reconstruction, each corresponding to the three currently recognized Chalcophaps species. Despite this general concordance, we identify discordant mitochondrial and nuclear ancestries in the subspecies C. longirostris timorensis, raising further questions about the evolutionary history of this Timor endemic population. Within each of the three species, we find evidence for isolation by distance or hierarchical population structure, indicating an important role for geography in the diversification of this genus. Despite being distributed broadly across a highly fragmented geographic region known as a hotspot for avian diversification, the Chalcophaps doves show modest levels of phenotypic and genetic diversity, a pattern potentially explained by strong population connectivity owing to high overwater dispersal capability.
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Affiliation(s)
- Devon A DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
| | - Joseph D Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Emily N Ostrow
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87106, USA
| | - Peter A Hosner
- Natural History Museum of Denmark and Center for Global Mountain Biodiversity, University of Copenhagen, Copenhagen, Denmark
| | - Hannah T Shult
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT 2601, Australia
| | - John P Dumbacher
- California Academy of Sciences, Golden Gate Park, San Francisco, CA 94118, USA
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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Gyllenhaal EF, Mapel XM, Naikatini A, Moyle RG, Andersen MJ. A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations. Mol Ecol 2020; 29:4059-4073. [DOI: 10.1111/mec.15625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
| | - Xena M. Mapel
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
| | - Alivereti Naikatini
- South Pacific Regional Herbarium Institute of Applied Sciences University of the South Pacific Suva Fiji Islands
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology University of Kansas Lawrence KS USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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Hosner PA, Campillo LC, Andersen MJ, Sánchez-González LA, Oliveros CH, Urriza RC, Moyle RG. An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1085-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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