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Garg KM, Gwee CY, Chattopadhyay B, Ng NS, Prawiradilaga DM, David G, Fuchs J, Hung Le Manh, Martinez J, Olsson U, Vuong Tan Tu, Chhin S, Alström P, Lei F, Rheindt FE. When colors mislead: Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae). Mol Phylogenet Evol 2024; 193:107999. [PMID: 38160993 DOI: 10.1016/j.ympev.2023.107999] [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: 09/11/2023] [Revised: 11/10/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India; Department of Biology, Ashoka University, Sonipat, India
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munich, Germany
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biology, Ashoka University, Sonipat, India; Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Nathaniel S Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Dewi M Prawiradilaga
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor-Cibinong, West Java, Indonesia
| | - Gabriel David
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, 22 S U, EPHE, UA CP51, Paris, France
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Gothenburg Global Biodiversity Center, Göteborg, Sweden
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Sophea Chhin
- Department of Biodiversity, General Directorate of Policy and Strategy, Ministry of Environment, Phnom Penh, Cambodia
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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Hui TCY, Tang Q, Ng EYX, Chong JL, Slade EM, Rheindt FE. Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations. Animals (Basel) 2024; 14:426. [PMID: 38338069 PMCID: PMC10854910 DOI: 10.3390/ani14030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah's spiny rat Maxomys rajah, Whitehead's spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species.
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Affiliation(s)
- Tabitha C. Y. Hui
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Elize Y. X. Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, TAS 7005, Australia
| | - Ju Lian Chong
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia;
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
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A near-complete and time-calibrated phylogeny of the Old World flycatchers, robins and chats (Aves, Muscicapidae). Mol Phylogenet Evol 2023; 178:107646. [PMID: 36265831 DOI: 10.1016/j.ympev.2022.107646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recognized genera and ca. 92% of all the species, built using data from up to 15 mitochondrial and 13 nuclear loci. In addition to assembling nucleotide sequences available in public databases, we also extracted sequences from the genome assemblies and raw sequencing reads from GenBank and included a few unpublished sequences. Our analyses resolved the phylogenetic position for several previously unsampled taxa, for example, the Grand Comoro Flycatcher Humblotia flavirostris, the Collared Palm Thrush Cichladusa arquata, and the Taiwan Whistling-Thrush Myophonus insularis, etc. We also provide taxonomic recommendations for genera that exhibit paraphyly or polyphyly. Our results suggest that Muscicapidae diverged from Turdidae (thrushes and allies) in the early Miocene, and the most recent common ancestors for the four subfamilies (Muscicapinae, Niltavinae, Cossyphinae and Saxicolinae) all arose around the middle Miocene.
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