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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ostrow EN, DeCicco LH, Moyle RG. Range-wide phylogenomics of the Great Horned Owl ( Bubo virginianus) reveals deep north-south divergence in northern Peru. PeerJ 2023; 11:e15787. [PMID: 37576505 PMCID: PMC10422955 DOI: 10.7717/peerj.15787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023] Open
Abstract
The Great Horned Owl (Bubo virginianus) inhabits myriad habitats throughout the Americas and shows complex patterns of individual and geographic morphological variation. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger's rule. Although untested at the species level, these ecogeographic rules may affect B. virginianus plumage coloration and body size. Previous studies have indicated that, despite this species' morphological variability, little genetic differentiation exists across parts of their range. This study uses reduced representation genome-wide nuclear and complete mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) of the central and southern Andes. We found shallow phylogenetic relationships generally structured latitudinally to the north of the central Andes, and a deep divergence between a southern and northern clade close to the Marañón Valley in the central Andes, a common biogeographic barrier. We identify evidence of gene flow between B. v. magellanicus and other subspecies based on mitonuclear discordance and F-branch statistics. Overall differences in morphology, plumage coloration, voice, and genomic divergence support species status for B. v. magellanicus.
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Affiliation(s)
- Emily N. Ostrow
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
| | - Lucas H. DeCicco
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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