1
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Berman LM, Wu MY, Baveja P, Cros E, Sin YCK, Prawiradilaga DM, Rheindt FE. Population structure in Mixornis tit-babblers across Sunda Shelf matches interfluvia of paleo-rivers. Mol Phylogenet Evol 2024; 197:108105. [PMID: 38754709 DOI: 10.1016/j.ympev.2024.108105] [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: 11/05/2023] [Revised: 04/04/2024] [Accepted: 05/12/2024] [Indexed: 05/18/2024]
Abstract
Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent - Sundaland - during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis, respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today.
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Affiliation(s)
- Laura Marie Berman
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore.
| | - Meng Yue Wu
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore
| | - Pratibha Baveja
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore
| | - Emilie Cros
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore
| | - Yong Chee Keita Sin
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore.
| | - Dewi M Prawiradilaga
- Museum Zoologicum Bogoriense, Research Centre for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jalan Raya, Jakarta Bogor KM 46, Cibinong 16911, Indonesia.
| | - Frank E Rheindt
- National University of Singapore, Department of Biological Sciences, 16 Science Drive 4, 117558, Singapore.
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2
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Muenzel D, Bani A, De Brauwer M, Stewart E, Djakiman C, Halwi, Purnama R, Yusuf S, Santoso P, Hukom FD, Struebig M, Jompa J, Limmon G, Dumbrell A, Beger M. Combining environmental DNA and visual surveys can inform conservation planning for coral reefs. Proc Natl Acad Sci U S A 2024; 121:e2307214121. [PMID: 38621123 PMCID: PMC11047114 DOI: 10.1073/pnas.2307214121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/14/2023] [Indexed: 04/17/2024] Open
Abstract
Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia's hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning.
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Affiliation(s)
- Dominic Muenzel
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Alessia Bani
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- School of Life Sciences, University of Essex, ColchesterCO4 3SQ, United Kingdom
- College of Science and Engineering, School of Built and Natural Environment,University of Derby, DerbyDE22 1 GB, United Kingdom
| | - Maarten De Brauwer
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Commonwealth Scientific and Industrial Research Organisation Oceans & Atmosphere, Battery Point, Hobart, TAS7004, Australia
| | - Eleanor Stewart
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Cilun Djakiman
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
| | - Halwi
- Graduate School, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Ray Purnama
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
| | - Syafyuddin Yusuf
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Prakas Santoso
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor16680, Indonesia
| | - Frensly D. Hukom
- Research Centre for Oceanography, Badan Riset dan Inovasi Nasional, Jakarta14430, Indonesia
- The Center for Collaborative Research on Aquatic Ecosystem in Eastern Indonesia, Pattimura University, Ambon97234, Indonesia
| | - Matthew Struebig
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, CanterburyCT2 7NR, United Kingdom
| | - Jamaluddin Jompa
- Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar90245, Indonesia
| | - Gino Limmon
- Maritime and Marine Science Center of Excellence, Pattimura University, Ambon85XW+H66, Indonesia
- The Center for Collaborative Research on Aquatic Ecosystem in Eastern Indonesia, Pattimura University, Ambon97234, Indonesia
| | - Alex Dumbrell
- School of Life Sciences, University of Essex, ColchesterCO4 3SQ, United Kingdom
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, LeedsLS2 9JT, United Kingdom
- Centre for Biodiversity and Conservation Science, School of Biological Sciences, University of Queensland, Brisbane, QLD4072, Australia
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3
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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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4
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Reeve AH, Kennedy JD, Pujolar JM, Petersen B, Blom MPK, Alström P, Haryoko T, Ericson PGP, Irestedt M, Nylander JAA, Jønsson KA. The formation of the Indo-Pacific montane avifauna. Nat Commun 2023; 14:8215. [PMID: 38081809 PMCID: PMC10713610 DOI: 10.1038/s41467-023-43964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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Affiliation(s)
- Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark.
| | - Jonathan David Kennedy
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - José Martín Pujolar
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Centre for Gelatinous Plankton Ecology and Evolution, DTU Aqua, Kemitorvet, Building 202, DK-2800, Kongens Lyngby, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Mozes P K Blom
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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5
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Sadanandan KR, Tan HZ, Lim HY, Tan YG, Lee G, Chan L, Pei Y, Rheindt FE, Baldwin MW. Spatial and temporal resource partitioning in a mixed-species colony of avian echolocators. Ecol Evol 2023; 13:e9805. [PMID: 36818536 PMCID: PMC9936513 DOI: 10.1002/ece3.9805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/18/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Resource partitioning may facilitate the coexistence of sympatric species with similar ecological requirements. Here, we study a colony of unusual echolocating birds called swiftlets, which nest underground on an island off the coast of Singapore. The colony comprises two congeneric swiftlet species, black-nest swiftlets (Aerodramus maximus) and edible-nest swiftlets (A. fuciphagus), nesting at high densities and in close proximity. Bioacoustic recordings and monitoring of nesting biology at the site across multiple seasons revealed significant differences in echolocation calls as well as survival rates between the species, with the larger black-nest swiftlet nesting at locations with the highest fledging rates. We also observe an additional off-season breeding peak by the smaller species, the edible-nest swiftlet. Unexpectedly, off-season egg-hatching rates were significantly higher compared with the rates during the shared breeding season (mean difference = 14%). Our study on the breeding biology of these echolocating cave-dwelling birds provides an example of spatial and temporal strategies that animals employ to partition resources within a confined habitat.
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Affiliation(s)
- Keren R. Sadanandan
- Evolution of Sensory Systems Research GroupMax Planck Institute for Biological IntelligenceSeewiesenGermany
| | - Hui Zhen Tan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Hong Yao Lim
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Yi Gain Tan
- Sentosa Development CorporationSingaporeSingapore
| | - Grace Lee
- Sentosa Development CorporationSingaporeSingapore
| | - Lena Chan
- International Biodiversity Conservation DivisionNational Parks Board of SingaporeSingaporeSingapore
| | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for Biological IntelligenceSeewiesenGermany
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Maude W. Baldwin
- Evolution of Sensory Systems Research GroupMax Planck Institute for Biological IntelligenceSeewiesenGermany
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6
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Hay EM, McGee MD, Chown SL. Geographic range size and speciation in honeyeaters. BMC Ecol Evol 2022; 22:86. [PMID: 35768772 PMCID: PMC9245323 DOI: 10.1186/s12862-022-02041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Darwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin’s proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae).
Results
We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation.
Conclusions
Honeyeater speciation rate differs considerably between islands and the continental setting across the clade’s distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin’s original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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7
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Melo M, Freitas B, Verbelen P, da Costa SR, Pereira H, Fuchs J, Sangster G, Correia MN, de Lima RF, Crottini A. A new species of scops-owl (Aves, Strigiformes, Strigidae, Otus) from Príncipe Island (Gulf of Guinea, Africa) and novel insights into the systematic affinities within Otus. Zookeys 2022; 1126:1-54. [PMID: 36763062 PMCID: PMC9836643 DOI: 10.3897/zookeys.1126.87635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/08/2022] [Indexed: 12/25/2022] Open
Abstract
A new species of scops-owl (Aves, Strigiformes, Strigidae, Otus) is described from Príncipe Island, São Tomé and Príncipe (Gulf of Guinea, Africa). This species was discovered for science in 2016, although suspicions of its occurrence gained traction from 1998, and testimonies from local people suggesting its existence could be traced back to 1928. Morphometrics, plumage colour and pattern, vocalisations, and molecular evidence all support the species status of the scops-owl from Príncipe, which is described here as Otusbikegila sp. nov. Phylogenetic analyses suggest that this species descended from the first colonisation of the Gulf of Guinea islands, being sister to the clade including the mainland African Scops-Owl O.senegalensis, and the island endemics Sao Tome Scops-Owl O.hartlaubi and Pemba Scops-Owl O.pembaensis. The most diagnostic trait in the field is its unique call which, curiously, is most similar to a distantly related Otus species, the Sokoke Scops-Owl O.ireneae. The new species occurs at low elevations of the old-growth native forest of Príncipe, currently restricted to the south of the island but fully included within Príncipe Obô Natural Park. Otusbikegila sp. nov. takes the number of single-island endemic bird species of Príncipe to eight, further highlighting the unusually high level of bird endemism for an island of only 139 km2.
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Affiliation(s)
- Martim Melo
- MHNC-UP, Museu de História Natural e da Ciência da Universidade do Porto, Praça Gomes Teixeira, 4050-368 Porto, PortugalGulf of Guinea Biodiversity CentreSão ToméSão Tomé and Príncipe,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal,FitzPatrick Institute of African Ornithology, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South AfricaUniversidade do PortoVairaoPortugal,Gulf of Guinea Biodiversity Centre, São Tomé, São Tomé and PríncipeBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIOVairãoPortugal,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, PortugalUniversity of Cape TownCape TownSouth Africa
| | - Bárbara Freitas
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, PortugalUniversity of Cape TownCape TownSouth Africa,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, PortugalUniversidade do PortoPortoPortugal,MNCN-CSIC, National Museum of Natural Sciences, Spanish National Research Council, Calle José Gutiérrez Abascal 2, Madrid 28006, SpainNational Museum of Natural SciencesMadridSpain,EDB, Laboratory of Evolution and Biologic Diversity, UMR 5174 CNRS-IRD, University of Toulouse III Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, FranceUniversity of Toulouse III Paul SabatierToulouseFrance
| | | | - Sátiro R. da Costa
- Praia Lapa, Príncipe, São Tomé and Príncipe, São Tomé and PríncipeUnaffiliatedPríncipeSão Tomé and Príncipe
| | - Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, GermanyUniversidade do PortoVairãoPortugal,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA CP51, 57 rue Cuvier, 75005 Paris, FranceBielefeld UniversityBielefeldGermany
| | - Jérôme Fuchs
- Naturalis Biodiversity Center, Darwinweg 2, PO Box 9517, 2300, RA, Leiden, NetherlandsMuséum national d’Histoire naturelleParisFrance
| | - George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, SwedenNaturalis Biodiversity CenterLeidenNetherlands,LIDA, School of Arts and Design, Polytechnic of Leiria, Rua Isidoro Inácio Alves de Carvalho, 2500-321 Caldas da Rainha, Leiria, PortugalSwedish Museum of Natural HistoryStockholmSweden
| | - Marco N. Correia
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalSchool of Arts and DesignLeiriaPortugal
| | - Ricardo F. de Lima
- Gulf of Guinea Biodiversity Centre, São Tomé, São Tomé and PríncipeBIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIOVairãoPortugal,Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalUniversidade de LisboaLisboaPortugal
| | - Angelica Crottini
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, PortugalUniversity of Cape TownCape TownSouth Africa,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, PortugalUniversidade do PortoPortoPortugal,Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, GermanyUniversidade do PortoVairãoPortugal
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8
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Martin TE, Bennett GC, Fairbairn A, Mooers AO. ‘Lost’ taxa and their conservation implications. Anim Conserv 2022. [DOI: 10.1111/acv.12788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- T. E. Martin
- Operation Wallacea Ltd Spilsby UK
- Biodiversity Inventory for Conservation NPO (BINCO) Glabbeek Belgium
- Wild Planet Trust, Paignton Zoo Paignton UK
| | - G. C. Bennett
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
| | - A. Fairbairn
- Terrestrial Ecology Research Group, Department for Life Science Systems, School of Life Science Technical University of Munich Freising Germany
| | - A. O. Mooers
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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9
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Lum D, Rheindt FE, Chisholm RA. Tracking scientific discovery of avian phylogenetic diversity over 250 years. Proc Biol Sci 2022; 289:20220088. [PMID: 35440208 PMCID: PMC9019523 DOI: 10.1098/rspb.2022.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Estimating the total number of species on Earth has been a longstanding pursuit. Models project anywhere between 2 and 10 million species, and discovery of new species continues to the present day. Despite this, we hypothesized that our current knowledge of phylogenetic diversity (PD) may be almost complete because new discoveries may be less phylogenetically distinct than past discoveries. Focusing on birds, which are well studied, we generated a robust phylogenetic tree for most extant species by combining existing published trees and calculated each discovery's marginal contribution to known PD since the first formal species descriptions in 1758. We found that PD contributions began to plateau in the early 1900s, about half a century earlier than species richness. Relative contributions of each phylogenetic order to known PD shifted over the first 150 years, with a growing contribution of the hyper-diverse perching birds (Passeriformes) in particular, but after the early 1900s this has remained relatively stable. Altogether, this suggests that our knowledge of the evolutionary history of extant birds is mostly complete, with few discoveries of high evolutionary novelty left to be made, and that conclusions of studies using avian phylogenies are likely to be robust to future species discoveries.
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Affiliation(s)
- Deon Lum
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117558, Singapore
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10
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Liu J, Slik F, Zheng S, Lindenmayer DB. Undescribed species have higher extinction risk than known species. Conserv Lett 2022. [DOI: 10.1111/conl.12876] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Jiajia Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai China
| | - Ferry Slik
- Environmental and Life Sciences Department Faculty of Science Universiti Brunei Darussalam Bandar Seri Begawan Brunei Darussalam
| | - Shilu Zheng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences Fudan University Shanghai China
| | - David B. Lindenmayer
- Fenner School of Environment and Society The Australian National University Canberra Australia
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11
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The formation of avian montane diversity across barriers and along elevational gradients. Nat Commun 2022; 13:268. [PMID: 35022441 PMCID: PMC8755808 DOI: 10.1038/s41467-021-27858-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.
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12
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Garg KM, Chattopadhyay B, Cros E, Tomassi S, Benedick S, Edwards DP, Rheindt FE. Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland. Mol Biol Evol 2022; 39:msab340. [PMID: 34893875 PMCID: PMC8789277 DOI: 10.1093/molbev/msab340] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
- Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India
- Department of Biology, Ashoka University, Sonipat, India
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Emilie Cros
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Suzanne Tomassi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Suzan Benedick
- Faculty of Sustainable Agriculture, University of Malaysia, Sabah, Malaysia
| | - David P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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13
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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14
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Ó Marcaigh F, Kelly DJ, O'Connell DP, Dunleavy D, Clark A, Lawless N, Karya A, Analuddin K, Marples NM. Evolution in the understorey: The Sulawesi babbler Pellorneum celebense (Passeriformes: Pellorneidae) has diverged rapidly on land-bridge islands in the Wallacean biodiversity hotspot. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Buainain N, Maximiano MFA, Ferreira M, Aleixo A, Faircloth BC, Brumfield RT, Cracraft J, Ribas CC. Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860) (Aves: Vireonidae). Mol Phylogenet Evol 2021; 162:107206. [PMID: 34015447 DOI: 10.1016/j.ympev.2021.107206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 11/20/2022]
Abstract
Several bird taxa have been recently described or elevated to full species and almost twice as many bird species than are currently recognized may exist. Defining species is one of the most basic and important issues in biological science because unknown or poorly defined species hamper subsequent studies. Here, we evaluate the species limits and evolutionary history of Tunchiornis ochraceiceps-a widespread forest songbird that occurs in the lowlands of Central America, Chocó and Amazonia-using an integrative approach that includes plumage coloration, morphometrics, vocalization and genomic data. The species has a relatively old crown age (~9 Ma) and comprises several lineages with little, if any, evidence of gene flow among them. We propose a taxonomic arrangement composed of four species, three with a plumage coloration diagnosis and one deeply divergent cryptic species. Most of the remaining lineages have variable but unfixed phenotypic characters despite their relatively old origin. This decoupling of genomic and phenotypic differentiation reveals a remarkable case of phenotypic conservatism, possibly due to strict habitat association. Lineages are geographically delimited by the main Amazonian rivers and the Andes, a pattern observed in studies of other understory upland forest Neotropical birds, although phylogenetic relationships and divergence times among populations are idiosyncratic.
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Affiliation(s)
- Nelson Buainain
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil.
| | - Marina F A Maximiano
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de Pós-Graduação em Ecologia, Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, Roraima, RR 69304-000, Brazil
| | - Alexandre Aleixo
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Brant C Faircloth
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Louisiana State University, Department of Biological Sciences, Baton Rouge, LA 70803, USA; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Joel Cracraft
- American Museum of Natural History, Department of Ornithology, New York, NY, USA
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo, 2936, Manaus, AM 69067-375, Brazil
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16
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Garg KM, Chattopadhyay B. Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change. J Indian Inst Sci 2021; 101:165-176. [PMID: 34155425 PMCID: PMC8207815 DOI: 10.1007/s41745-021-00239-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023]
Abstract
Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.
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Affiliation(s)
- Kritika M. Garg
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka India ,grid.449178.70000 0004 5894 7096Department of Biology, Ashoka University, Sonipat, Haryana India
| | - Balaji Chattopadhyay
- grid.449178.70000 0004 5894 7096Trivedi School of Biosciences, Ashoka University, Sonipat, Haryana India
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17
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Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KSH, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity. eLife 2020; 9:e62765. [PMID: 33350381 PMCID: PMC7775107 DOI: 10.7554/elife.62765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
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Affiliation(s)
- Chyi Yin Gwee
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Kritika M Garg
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Balaji Chattopadhyay
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Keren R Sadanandan
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Tri Haryoko
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Malcolm CK Soh
- University of Western Australia, School of Biological SciencesPerthAustralia
| | - Kelvin S-H Peh
- University of Southampton, School of Biological Sciences, UniversitySouthamptonUnited Kingdom
| | - Karen MC Rowe
- Sciences Department, Museums VictoriaMelbourneAustralia
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah KualaDarussalamIndonesia
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal UniversityXuzhouChina
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
- Center for Tropical Veterinary Studies – One Health Collaboration Center, Universitas Syiah KualaDarussalamIndonesia
| | - Guinevere OU Wogan
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeleyUnited States
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Frank E Rheindt
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
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18
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Gwee CY, Lee QL, Mahood SP, Hung Le Manh, Tizard R, Eiamampai K, Round PD, Rheindt FE. The interplay of colour and bioacoustic traits in the differentiation of a Southeast Asian songbird complex. Mol Ecol 2020; 30:297-309. [PMID: 33135269 DOI: 10.1111/mec.15718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/26/2022]
Abstract
Morphological traits have served generations of biologists as a taxonomic indicator, and have been the main basis for defining and classifying species diversity for centuries. A quantitative integration of behavioural characters, such as vocalizations, in studies on biotic differentiation has arisen more recently, and the relative importance of these different traits in the diversification process remains poorly understood. To provide a framework within which to interpret the evolutionary interplay between morphological and behavioural traits, we generated a draft genome of a cryptic Southeast Asian songbird, the limestone wren-babbler Napothera crispifrons. We resequenced whole genomes of multiple individuals of all three traditional subspecies and of a distinct leucistic population. We demonstrate strong genomic and mitochondrial divergence among all three taxa, pointing to the existence of three species-level lineages. Despite its great phenotypic distinctness, the leucistic population was characterized by shallow genomic differentiation from its neighbour, with only a few localized regions emerging as highly diverged. Quantitative bioacoustic analysis across multiple traits revealed deep differences especially between the two taxa characterized by limited plumage differentiation. Our study demonstrates that differentiation in these furtive songbirds has resulted in a complex mosaic of colour-based and bioacoustic differences among populations. Extreme colour differences can be anchored in few genomic loci and may therefore arise and subside rapidly.
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Affiliation(s)
- Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qiao Le Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon P Mahood
- Wildlife Conservation Society Cambodia Program, Sangkat Tonle Bassac, Phnom Penh, Cambodia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduated University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Caugiay, Hanoi, Vietnam
| | - Robert Tizard
- Global Conservation Program, Wildlife Conservation Society, Bronx, NY, USA
| | - Krairat Eiamampai
- Wildlife Research Division, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, Thailand
| | - Philip D Round
- Department of Biology, Faculty of Science, Mahidol University, Rachadhavi, Bangkok, Thailand
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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19
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Ó Marcaigh F, Kelly DJ, Analuddin K, Karya A, Lawless N, Marples NM. Cryptic sexual dimorphism reveals differing selection pressures on continental islands. Biotropica 2020. [DOI: 10.1111/btp.12852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Fionn Ó Marcaigh
- Department of Zoology School of Natural Sciences Trinity College Dublin Dublin Ireland
| | - David J. Kelly
- Department of Zoology School of Natural Sciences Trinity College Dublin Dublin Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology Universitas Halu Oleo Kendari Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology Universitas Halu Oleo Kendari Indonesia
| | - Naomi Lawless
- Department of Zoology School of Natural Sciences Trinity College Dublin Dublin Ireland
| | - Nicola M. Marples
- Department of Zoology School of Natural Sciences Trinity College Dublin Dublin Ireland
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20
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O'Connell DP, Kelly DJ, Analuddin K, Karya A, Marples NM, Martin TE. Adapt taxonomy to conservation goals. Science 2020; 369:1172. [PMID: 32883855 DOI: 10.1126/science.abd7717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Darren P O'Connell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK. darren.o'.,Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo, Southeast Sulawesi, Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo, Southeast Sulawesi, Indonesia
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - Thomas E Martin
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, Spilsby, Lincolnshire, PE23 4EX, UK
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21
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Chen D, Liu Y, Davison G, Yong DL, Gao S, Hu J, Li SH, Zhang Z. Disentangling the evolutionary history and biogeography of hill partridges (Phasianidae, Arborophila) from low coverage shotgun sequences. Mol Phylogenet Evol 2020; 151:106895. [PMID: 32562823 DOI: 10.1016/j.ympev.2020.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/06/2020] [Accepted: 06/12/2020] [Indexed: 11/18/2022]
Abstract
The advent of the phylogenomic era has significantly improved our understanding of the evolutionary history and biogeography of Southeast Asia's diverse avian fauna. However, the taxonomy and phylogenetic relationships of many Southeast Asian birds remain poorly resolved, especially for those with large geographic ranges, which might have experienced both ancient and recent geological and environmental changes. In this study, we examined the evolutionary history and biogeography of the hill partridges (Galliformes: Phasianidae: Arborophila spp.), currently the second most speciose galliform genus, and thought to have colonized Southeast Asia from Africa. We present a well-resolved phylogeny of 14 Arborophila species inferred from ultra-conserved elements, exons, and mitochondrial genomes from both fresh and museum samples, which representing almost complete coverage of the genus. Our fossil-calibrated divergence time estimates and biogeographic modeling showed the ancestor of Arborophila arrived in Indochina during the early Miocene, but the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification within Arborophila were driven by several tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling and extensive dispersal and speciation of Sundaic Arborophila during the Pleistocene sea-level fluctuations. Taken together, these results suggest that the evolutionary history and biogeography of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia.
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Affiliation(s)
- De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Geoffrey Davison
- National Biodiversity Centre, National Parks Board, 1 Cluny Road, 259569, Singapore
| | - Ding Li Yong
- BirdLife International (Asia), 354 Tanglin Road, #01-16/17, Tanglin International Centre, Singapore 247672, Singapore; Fenner School of Environment and Society, The Australian National University, Linnaeus Way, Canberra, ACT 2601, Australia
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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22
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Affiliation(s)
- Jonathan D Kennedy
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.,Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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