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Joakim RL, Irham M, Haryoko T, Rowe KMC, Dalimunthe Y, Anita S, Achmadi AS, McGuire JA, Perkins S, Bowie RCK. Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia. Anim Microbiome 2023; 5:4. [PMID: 36647179 PMCID: PMC9841722 DOI: 10.1186/s42523-022-00219-3] [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: 02/04/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition. RESULTS The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae. CONCLUSIONS While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.
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Affiliation(s)
- Rachael L. Joakim
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA ,grid.241963.b0000 0001 2152 1081Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA ,grid.241963.b0000 0001 2152 1081The Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 USA
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Karen M. C. Rowe
- grid.436717.00000 0004 0500 6540Sciences Department, Museums Victoria, Carlton, VIC Australia ,grid.1008.90000 0001 2179 088XBioSciences Department, University of Melbourne, Parkville, VIC Australia
| | - Yohanna Dalimunthe
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Jimmy A. McGuire
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
| | - Susan Perkins
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA
| | - Rauri C. K. Bowie
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
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Mondal T, Dey P, Kumari D, Ray SD, Quadros G, Sastry Kochiganti VH, Singh RP. Genome survey sequencing and mining of genome-wide microsatellite markers in yellow-billed babbler ( Turdoides affinis). Heliyon 2023; 9:e12735. [PMID: 36647364 PMCID: PMC9840121 DOI: 10.1016/j.heliyon.2022.e12735] [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] [Received: 03/26/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 01/05/2023] Open
Abstract
Turdoides affinis is a species of group dwelling old world passerine of family Leiothrichidae. Unavailability of genome-wide sequence and species-specific molecular markers have hindered comprehensive understanding of cooperative breeding behaviour in T. affinis. Therefore, we generated genome-wide microsatellite markers through whole genome short read sequencing of T. affinis. A total of 68.8 gigabytes of paired-end raw data were sequenced containing 195,067,054 reads. Total sequenced reads spanned a coverage of 17X with genome size of 1.18 Gb. A large number of microsatellite markers (265,297) were mined in the T. affinis genome using Krait, and 50 most informative markers were identified and validated further. In-silico PCR results validated 47 markers. Of these 47 markers, five were randomly selected and validated in-vitro in twelve individuals of T. affinis. Genotyping data on these five loci estimated observed heterozygosity (H0) and expected heterozygosity (He) ratios between 0.333 - 0.833 and 0.851-0.906, respectively. Effective allele size ranged from 6.698 to 10.667, inbreeding coefficient of the population ranged from 0.080 to 0.631 and null allele frequency was calculated at 0.055 to 0.303. Polymorphic information content of all the five loci varied between 0.850 and 0.906. Probabilities of exclusion and identity across 5 loci was estimated to be 0.95 and 0.0036, respectively. All the loci showed significant adherence to Hardy-Weinberg equilibrium. The microsatellite markers reported in this study will facilitate future population genetics studies on T. affinis and other congeneric species.
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Affiliation(s)
- Trisha Mondal
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
| | - Prateek Dey
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India,Corresponding author.
| | - Divya Kumari
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
| | - Swapna Devi Ray
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India
| | - Goldin Quadros
- Wetland Ecology Division, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, 641108, Tamil Nadu, India
| | | | - Ram Pratap Singh
- Department of Life Science, Central University of South Bihar, Gaya, 824236, India,Corresponding author.
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3
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Tian C, Yu X, Wang Z, Zou F, Gustafsson DR. PHYLOGENETIC RELATIONSHIPS OF GUIMARAESIELLA AND PRICEIELLA (PHTHIRAPTERA: ISCHNOCERA) FROM BABBLERS AND NON-BABBLERS (PASSERIFORMES). J Parasitol 2022; 108:107-121. [PMID: 35240688 DOI: 10.1645/21-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Babblers (Passeriformes: Leiothrichidae, Pellorneidae, Timaliidae) are parasitized by more genera of lice of the Brueelia complex than any other group of songbirds. However, the relationships of these louse groups are poorly known. We here try to resolve the relationships between Guimaraesiella (Guimaraesiella), Guimaraesiella (Cicchinella), and their putative sister group Priceiella by using mitochondrial cytochrome c subunit 1 (COI), 12S, and 16S sequences. Our data indicate that G. (Cicchinella) forms a monophyletic group of lice from babblers, but the relationship between G. (Guimaraesiella), G. (Cicchinella), and Priceiella could not be resolved. Moreover, the position of the third lineage of babbler-specific lice, containing only the aberrant species Guimaraesiella montisodalis, is unresolved. Morphologically, this species is different from all other Guimaraesiella in several characters and may represent a distinct lineage. We present some data indicating that (1) the Nanling Mountain range may be a biogeographical barrier to chewing lice and (2) host participation in mixed-species feeding flocks may influence host associations in Brueelia-complex chewing lice.
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Affiliation(s)
- Chunpo Tian
- College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Street, Chang'an District, Xi'an City, 710119, Shaanxi Province, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Street, Chang'an District, Xi'an City, 710119, Shaanxi Province, China
| | - Zhengzhen Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Fasheng Zou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
| | - Daniel R Gustafsson
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Library of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang West Road, Haizhu District, Guangzhou, 510260, Guangdong Province, China
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4
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Oliveros CH, Andersen MJ, Moyle RG. A phylogeny of white-eyes based on ultraconserved elements. Mol Phylogenet Evol 2021; 164:107273. [PMID: 34333115 DOI: 10.1016/j.ympev.2021.107273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. Zosterops white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian family Zosteropidae. We used concatenated maximum likelihood and species tree methods and found strong support for seven clades of white-eyes and three clades within the species-rich Zosterops radiation.
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Affiliation(s)
- Carl H Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA.
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5
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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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6
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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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7
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Li D, Shao S, Wang X, Wu X, Luo X. Complete mitochondrial genome of fire-tailed myzornis ( Myzornis pyrrhoura) and white-browed fulvetta ( Fulvetta vinipectus). Mitochondrial DNA B Resour 2020; 5:3307-3309. [PMID: 33458147 PMCID: PMC7782492 DOI: 10.1080/23802359.2020.1814884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In this study, the complete mitochondrial genomes of Myzornis pyrrhoura and Fulvetta vinipectus were sequenced and described for the first time. The whole mitochondrial genomes of M. pyrrhoura and F. vinipectus are 17,397 bp and 16,961 bp in length, with the G + C percentage 46.34% and 47.36%, respectively. Both genomes contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes, and 1 non-coding control region. The arrangement of genes is identical to mitochondrial genomes of Sylviidae species reported previously. A phylogenetic reconstruction supported that M. pyrrhoura and F. vinipectus are members of family Sylviidae. The mitochondrial genomes of these two species reported here would be helpful in better understanding the phylogeny and evolution of Sylviidae.
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Affiliation(s)
- Danjie Li
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan/Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Shimiao Shao
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan/Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Xiaoyi Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan/Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Xinran Wu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan/Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Xu Luo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan/Faculty of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
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8
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Gustafsson DR, Lei L, Luo K, Chu X, Zhao X, Zhang Q, Zou F. Chewing lice from high-altitude and migrating birds in Yunnan, China, with descriptions of two new species of Guimaraesiella. MEDICAL AND VETERINARY ENTOMOLOGY 2019; 33:407-419. [PMID: 31032960 DOI: 10.1111/mve.12378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/04/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
In total, 366 birds representing 55 species in 24 families and eight orders, were examined for chewing lice (Phthiraptera: Amblycera, Ischnocera) in two high-altitude localities in Yunnan Province, China. In Ailaoshan, almost all of the birds examined were resident passeriforms, of which 36% were parasitized by chewing lice. In Jinshanyakou, most birds were on migration, and included both passerine and non-passerine birds. Of the passerine birds caught in Jinshanyakou, only one bird (0.7%) was parasitized by chewing lice. The prevalence of Myrsidea and Brueelia-complex lice on birds caught in Ailaoshan was higher than in previous reports. Of the chewing lice identifiable to species level, three represent new records for China: Actornithophilus hoplopteri (Mjöberg, 1910), Maculinirmus ljosalfar Gustafsson & Bush, 2017 and Quadraceps sinensis Timmermann, 1954. In total, 17 new host records are included, of which we describe two as new species in the Brueelia-complex: Guimaraesiella (Cicchinella) ailaoshanensis sp. nov. ex Schoeniparus dubius dubius (Hume, 1874) and G. (C.) montisodalis sp. nov. ex Fulvetta manipurensis tonkinensis Delacour & Jabouille, 1930. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:9FC3D8EE-2CED-4DBE-A1DB-471B71260D27.
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Affiliation(s)
- D R Gustafsson
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - L Lei
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Changchun, China
| | - K Luo
- Ailaoshan Station for Subtropical Forest Ecosystem Studies, Chinese Academy of Sciences, Jingdong, China
| | - X Chu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - X Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Q Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - F Zou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
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9
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He W, Xu H, Li D, Xie M, Zhang M, Ni Q, Wu J, Wen A, Wang Q, Zhu G, Yao Y. Complete mitochondrial genome and phylogenetic analysis of Black-chinned Yuhina ( Yuhina nigrimenta). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1561226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Weiqiang He
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiayun Wu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Anxiang Wen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Guangxiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Yongfang Yao
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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10
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Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes). Mol Phylogenet Evol 2019; 130:346-356. [DOI: 10.1016/j.ympev.2018.10.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/04/2018] [Accepted: 10/09/2018] [Indexed: 11/21/2022]
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11
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Gustafsson DR, Chu X, Bush SE, Zou F. Seven new species of Resartor Gustafsson et Bush, 2017 (Phthiraptera: Ischnocera: Philopteridae) from Asian ʻbabblers' (Passeriformes: Leiothrichidae, Paradoxornithidae). Folia Parasitol (Praha) 2018; 65. [DOI: 10.14411/fp.2018.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/30/2018] [Indexed: 11/19/2022]
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12
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Tan DJX, Chattopadhyay B, Garg KM, Cros E, Ericson PGP, Irestedt M, Rheindt FE. Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis. Sci Rep 2018; 8:12804. [PMID: 30143731 PMCID: PMC6109123 DOI: 10.1038/s41598-018-31074-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 08/02/2018] [Indexed: 11/19/2022] Open
Abstract
Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.
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Affiliation(s)
- David J X Tan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Emilie Cros
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Per G P Ericson
- Department of Zoology, 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
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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13
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Cibois A, Gelang M, Alström P, Pasquet E, Fjeldså J, Ericson PGP, Olsson U. Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy. ZOOL SCR 2018. [DOI: 10.1111/zsc.12296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alice Cibois
- Natural History Museum of Geneva; Geneva Switzerland
| | | | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Swedish Species Information Centre; Swedish University of Agricultural Sciences; Uppsala Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology; Chinese Academy of Sciences; Beijing China
| | - Eric Pasquet
- UMS MNHN/CNRS 2700 Outils et Méthodes de la Systématique Intégrative (OMSI) and UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE; Sorbonne Universités, Muséum National d’Histoire Naturelle; Paris France
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate; Natural History Museum of Denmark, Zoological Museum; Copenhagen Denmark
| | - Per G. P. Ericson
- Department of Vertebrate Zoology; Molecular Systematics Laboratory; Swedish Museum of Natural History; Stockholm Sweden
| | - Urban Olsson
- Department of Zoology; University of Gothenburg; Göteborg Sweden
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14
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Alström P, Rheindt FE, Zhang R, Zhao M, Wang J, Zhu X, Gwee CY, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, Olsson U. Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation. Mol Phylogenet Evol 2018; 126:141-152. [PMID: 29631054 DOI: 10.1016/j.ympev.2018.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/24/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment,and we argue againstproliferation of taxonomic names,and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
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Affiliation(s)
- Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Box 7007, Uppsala SE-750 07, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jan Ohlson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
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15
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Opaev AS, Liu M, Kang Z. Behavioral Ecology of Elliot’s Laughingthrush (Trochalopteron (Garrulax) elliotii; Timaliidae): I. Breeding Biology and Social Behavior. BIOL BULL+ 2018. [DOI: 10.1134/s1062359017090072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Huang Z, Tu F, Tang S. Two new mitogenomes of Pellorneidae (Aves : Passeriformes) and a phylogeny of the superfamily Sylvioidea. AUST J ZOOL 2018. [DOI: 10.1071/zo18025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The superfamily Sylvioidea contains the most diversified species within the Passerida. The grey-cheeked fulvetta (Alcippe morrisonia) and the eyebrowed wren-babbler (Napothera epilepidota) are birds with a weak flight that live in lightly wooded or scrubland environments. In the present study, two new mitogenomes of A. morrisonia (KX376475) and N. epilepidota (KX831093) within the superfamily Sylvioidea were sequenced and their total lengths were 17788bp and 17913bp, respectively. Both mitogenomes comprised 13 protein-coding genes, 22 tRNAs, 2 rRNAs and two control regions (CR and CCR). Similar to most metazoans, both mitogenomes and their protein-coding genes encoded on the H-strand displayed typical positive AT skews and negative GC skews. Bayesian inference and maximum-likelihood phylogenetic analyses were conducted on the basis of partitioned data of mitogenomes and two identical topologies were observed. The family-level phylogenetic relationships ((((Pellorneidae, Leiothrichidae) Timaliidae) Zosteropidae) Sylviidae) among the superfamily Sylvioidea were strongly supported. Within the family Pellorneidae, A. morrisonia clustered with N. epilepidota. Within Leiothrichidae, we further demonstrated that Babax lanceolatus is sister to Garrulax perspicillatus, and Spizixos semitorques was nested within the genus Pycnonotus according to the mitogenomic data and we propose that the generic placement of Spizixos should be reconsidered.
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Ke DH, Deng YH, Guo WB, Huang ZH. A quadratic correlation between long-term mean group size and group density in a cooperatively breeding passerine. Ecol Evol 2017; 7:8719-8729. [PMID: 29152172 PMCID: PMC5677499 DOI: 10.1002/ece3.3405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/29/2017] [Accepted: 08/03/2017] [Indexed: 11/28/2022] Open
Abstract
Both mean group size (MGS) and mean group density (MGD) are critical indices to characterize a population of cooperatively breeding birds. When a population reaches its carrying capacity, both long‐term MGS and long‐term MGD will remain relatively stable. However, there has been little study of how these two variables relate. The Masked laughingthrush Garrulax perspicillatus is a cooperatively breeding bird living in fragmented habitats. During 2010 and 2012‐2016, we used song playback to observe and confirm the group sizes and territory ranges of the birds and the data of bird presence to determine habitat suitability. By grouping the nearest territories according to their geographical coordinates, we divided the whole study area into 12 subareas and the whole population into 12 subpopulations. Then, we calculated both MGS and MGD for different time durations for each subpopulation. Finally, using MGD as independent variable and MGS as the dependent variable, we explored the correlations between MGS and MGD by fitting quadratic functions and modeling quadratic regression. Both MGS and MGD were averaged for different time durations and were cross‐related. Our results show that the MGS for more than 2 years significantly correlated with MGD for more than 3 years in a reverse parabolic shape, differing from that of short‐term effects. Our findings suggest that long‐term MGD is a better predictor of long‐term habitat quality and that long‐term MGS is determined by long‐term habitat quality in Masked Laughingthrushes. Based on above findings, we can infer that: (1) Long‐term habitat quality determines the long‐term MGS, but it sets no prerequisite for the status and source of group members; (2) Long‐term MGS in certain populations is adapted to the corresponding level of long‐term habitat quality, it facilitates us to predict the helper effects on current or future survival or reproduction in different situations. These findings and inferences are both helpful for us to understand the evolution of cooperative breeding.
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Affiliation(s)
- Dian-Hua Ke
- School of Life Sciences Jinggangshan University Ji'An China
| | - Yan-Hui Deng
- Library of Jinggangshan University Jinggangshan University Ji'An China
| | - Wei-Bin Guo
- School of Life Sciences Jinggangshan University Ji'An China
| | - Zu-Hao Huang
- School of Life Sciences Jinggangshan University Ji'An China
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18
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Robin VV, Vishnudas CK, Gupta P, Rheindt FE, Hooper DM, Ramakrishnan U, Reddy S. Two new genera of songbirds represent endemic radiations from the Shola Sky Islands of the Western Ghats, India. BMC Evol Biol 2017; 17:31. [PMID: 28114902 PMCID: PMC5259981 DOI: 10.1186/s12862-017-0882-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/11/2017] [Indexed: 12/03/2022] Open
Abstract
Background A long-standing view of Indian biodiversity is that while rich in species, there are few endemics or in-situ radiations within the subcontinent. One exception is the Western Ghats biodiversity hotspot, an isolated mountain range with many endemic species. Understanding the origins of the montane-restricted species is crucial to illuminate both taxonomic and environmental history. Results With evidence from genetic, morphometric, song, and plumage data, we show that two songbird lineages endemic to the Western Ghats montane forest each have diversified into multiple distinct species. Historically labeled as single species of widespread Asian genera, these two lineages are highly divergent and do not group with the taxa in which they were previously classified but rather are distinct early divergences in larger Asian clades of flycatchers and babblers. Here we designated two new genera, the Western Ghats shortwings as Sholicola and the laughingthrushes as Montecincla, and evaluated species-limits to reflect distinct units by revising six previously named taxa and describing one novel species. Divergence dating showed that both these montane groups split from their Himalayan relatives during the Miocene, which is coincident with a shift towards arid conditions that fragmented the previously contiguous humid forest across peninsular India and isolated these lineages in the Western Ghats. Furthermore, these two genera showed congruent patterns of diversification across the Western Ghats Sky Islands, coincident with other climatic changes. Conclusion Our study reveals the existence of two independent endemic radiations in the high montane Western Ghats or Shola Sky Islands with coincident divergence times, highlighting the role of climate in the diversification of these ancient lineages. The endemic and highly divergent nature of these previously unrecognized species underscores the dearth of knowledge about the biogeography of the Asian tropics, even for comparatively well-known groups such as birds. The substantial increase in the diversity of this region underscores the need for more rigorous systematic analysis to inform biodiversity studies and conservation efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0882-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V V Robin
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India. .,Present address - Indian Institute of Science Education and Research Tirupati, Mangalam, Tirupati, 517507, India.
| | - C K Vishnudas
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India
| | - Pooja Gupta
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India
| | - Frank E Rheindt
- Avian Evolution Lab, Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Daniel M Hooper
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India
| | - Sushma Reddy
- National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore, 560065, India. .,Biology Department, Loyola University Chicago, Chicago, IL, 60660, USA.
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19
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Li B, Yao Y, Li D, Ni Q, Zhang M, Xie M, Xu H. Complete mitochondrial genome of Minla ignotincta (Passeriformes: Timaliidae). Mitochondrial DNA B Resour 2016; 1:140-141. [PMID: 33473437 PMCID: PMC7799491 DOI: 10.1080/23802359.2016.1144099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
We sequenced the complete mitochondrial genome from Minla ignotincta. The genome sequence was 17 868 bp in length, and the gene arrangement and contents were identical to those of previously reported Timaliidae mitochondrial genomes. The overall base composition of the mitogenome is biased toward A + T content at 54.04%. All protein-coding genes (PCGs) began with ATG. Nine of the 13 PCGs used complete (TAA) or incomplete (TA or T) stop codon, while ND1 and ND5 ended with AGA, COI ended with AGG and ND6 with TAG. All the genes in M. ignotincta were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.
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Affiliation(s)
- Bo Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongfang Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meng Xie
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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20
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Li B, Yao Y, Li D, Ni Q, Zhang M, Xie M, Xu H. The complete mitochondrial genome sequence of White-collared Yuhina (Yuhina diademata). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:21-22. [PMID: 26641536 DOI: 10.3109/19401736.2015.1106524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced the complete mitochondrial DNA genome of Yuhina diademata by means of polymerase chain reaction. The circle genome (17 834 bp in length) contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions (Dloop1 and Dloop2), which was similar to the other published mitogenome of Timaliidae species. Most PCGs began with ATG, while COI and ND2 genes started with GTG. Nine of the PCGs used complete (TAA) or incomplete (TA- or T--) stop codon, while ND1 and ND6 genes ended with AGA, COI gene ended with AGG, and ND6 gene with TAG. Overall base composition of the complete mtDNA was 30.30% A, 23.81% T, 31.72% C, and 14.17% G. All the PCGs in Y. diademata were distributed on the H-strand, except for the ND6 gene and eight tRNA genes which were encoded on the L-strand.
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Affiliation(s)
- Bo Li
- a College of Life Science, Sichuan Agricultural University , Ya'an , China , and.,b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Yongfang Yao
- b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Diyan Li
- b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Qingyong Ni
- b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Mingwang Zhang
- b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Meng Xie
- a College of Life Science, Sichuan Agricultural University , Ya'an , China , and
| | - Huailiang Xu
- a College of Life Science, Sichuan Agricultural University , Ya'an , China , and
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21
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Reddy S, Sharief S, Yohe LR, Witkowski J, Hosner PA, Nyári ÁS, Moyle RG. Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia. Mol Phylogenet Evol 2014; 82 Pt A:183-92. [PMID: 25450499 DOI: 10.1016/j.ympev.2014.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/07/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022]
Abstract
Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Sarah Sharief
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Laurel R Yohe
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Julie Witkowski
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Peter A Hosner
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
| | - Árpád S Nyári
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA.
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
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22
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Ericson PGP, Klopfstein S, Irestedt M, Nguyen JMT, Nylander JAA. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol Biol 2014; 14:8. [PMID: 24422673 PMCID: PMC3917694 DOI: 10.1186/1471-2148-14-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% of all living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the late Cretaceous. However, previous molecular dating studies have relied heavily on the geological split between New Zealand and Antarctica, assumed to have occurred 85-82 Mya, for calibrating the molecular clock and might thus be circular in their argument. RESULTS This study provides a time-scale for the evolution of the major clades of passerines using seven nuclear markers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealand split from Antarctica 85-52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretations of the New Zealand-Antarctica vicariance event influence our age estimates. Our results suggest that the diversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration for the New Zealand-Antarctica vicariance event (85-52 Mya) dramatically increases the 95% credibility intervals and leads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genes analyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines, which can be used as secondary calibration points in future molecular studies. CONCLUSIONS Our analysis takes recent paleontological and geological findings into account and provides the best estimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporal framework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, and adds to the growing support for a Cretaceous origin of Passeriformes.
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Affiliation(s)
- Per GP Ericson
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Seraina Klopfstein
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Martin Irestedt
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
| | - Jacqueline MT Nguyen
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Johan AA Nylander
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Box 50007, SE–10405 Stockholm, Sweden
- BILS – Bioinformatics Infrastructure for Life Sciences, University of Linköping, SE–58183 Linköping, Sweden
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23
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Johansson US, Ekman J, Bowie RC, Halvarsson P, Ohlson JI, Price TD, Ericson PG. A complete multilocus species phylogeny of the tits and chickadees (Aves: Paridae). Mol Phylogenet Evol 2013; 69:852-60. [DOI: 10.1016/j.ympev.2013.06.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/19/2013] [Accepted: 06/25/2013] [Indexed: 11/28/2022]
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24
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Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus). PLoS One 2013; 8:e55629. [PMID: 23405183 PMCID: PMC3566057 DOI: 10.1371/journal.pone.0055629] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/02/2013] [Indexed: 12/01/2022] Open
Abstract
We present the first extensive and integrative analysis of niche evolution based on climatic variables and a dated molecular phylogeny of a heterogeneous avian group of Southeast Asian scimitar babblers of the genus Pomatorhinus. The four main clades of scimitar babblers have species that co-occur in similar areas across southern Asia but some have diverged at different timeframes, with the most recently evolved clade harboring the highest number of species. Ecological niche models and analysis of contributing variables within a phylogenetic framework indicate instances of convergent evolution of members of different clades onto similar ecological parameter space, as well as divergent evolution of members from within clades. Pomatorhinus species from different clades occupying Himalayan foothills show convergence towards similar climatic tolerances, whereas within a clade, allopatric sister-species occurring in the Himalayas have diverged to occupy different climatic parameter spaces. Comparisons of climatic tolerances of Himalayan foothills taxa with species distributed further south in Assam/Burma and Burma/Thailand indicate convergence towards similar parameter spaces in several climatic variables. Niche overlap was observed to be lower among species of the youngest clade (ruficollis) and higher among species of older clades (ferruginosus). Analysis of accumulation of ecological disparity through time indicates rapid divergence within recent time frames. As a result, Himalayan taxa originating at different temporal scales within the four main scimitar babbler clades have differentiated ecologically only in recently diverged taxa. Our study suggests that the repeated orogenic and climatic fluctuations of the Pliocene and Pleistocene within mainland Southeast Asia served as an important ecological speciation driver within scimitar babblers, by providing opportunities for rapid geographic expansion and filling of novel environmental niches.
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25
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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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26
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Matysioková B, Remeš V. Faithful females receive more help: the extent of male parental care during incubation in relation to extra-pair paternity in songbirds. J Evol Biol 2012. [PMID: 23176707 DOI: 10.1111/jeb.12039] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Parental care provided by males occurs in a diverse array of animals and there are large differences among species in its extent compared with female care. However, social and ecological factors responsible for interspecific differences in male's share of parental duties remain unclear. Genetic fidelity of females has been long considered important. Theory predicts that females should receive more help from their mates in raising the offspring in species with high genetic fidelity. Using avian incubation behaviour as a model system, we confirmed this prediction. The extent of male's help during incubation increased with decreasing rate of extra-pair paternity across species (22 species of socially monogamous songbirds from 13 families; male's share of incubation ranged from 6% to 58%), even after accounting for covariates, biases in species selection and intraspecific variability. Moreover, this result was not sensitive to two different phylogenies and branch length estimates. We suggest that our findings support the notion, backed by theory, that genetic fidelity is an important factor in the evolution of male parental care. We offer several behavioural scenarios for the coevolution between male's share of parental duties and the genetic mating system.
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Affiliation(s)
- B Matysioková
- Laboratory of Ornithology, Department of Zoology, Palacký University, Olomouc, Czech Republic.
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27
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Fregin S, Haase M, Olsson U, Alström P. New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers. BMC Evol Biol 2012; 12:157. [PMID: 22920688 PMCID: PMC3462691 DOI: 10.1186/1471-2148-12-157] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 08/17/2012] [Indexed: 11/20/2022] Open
Abstract
Background The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade.
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Affiliation(s)
- Silke Fregin
- Vogelwarte Hiddensee, Zoological Institute and Museum, Ernst Moritz Arndt University of Greifswald, Greifswald, 17489, Germany.
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Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers. Mol Phylogenet Evol 2012; 63:606-16. [DOI: 10.1016/j.ympev.2012.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 01/31/2012] [Accepted: 02/01/2012] [Indexed: 11/23/2022]
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Lovette IJ, Arbogast BS, Curry RL, Zink RM, Botero CA, Sullivan JP, Talaba AL, Harris RB, Rubenstein DR, Ricklefs RE, Bermingham E. Phylogenetic relationships of the mockingbirds and thrashers (Aves: Mimidae). Mol Phylogenet Evol 2012; 63:219-29. [DOI: 10.1016/j.ympev.2011.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Revised: 06/03/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
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Moyle RG, Andersen MJ, Oliveros CH, Steinheimer FD, Reddy S. Phylogeny and Biogeography of the Core Babblers (Aves: Timaliidae). Syst Biol 2012; 61:631-51. [DOI: 10.1093/sysbio/sys027] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Michael J. Andersen
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Carl H. Oliveros
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Frank D. Steinheimer
- Natural History Collections, Martin-Luther-University Halle-Wittenberg, Domplatz 4, D-06108 Halle (Saale), Germany; and
| | - Sushma Reddy
- Department of Biology, Loyola University, Chicago, IL 60660, USA
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Voelker G, Light JE. Palaeoclimatic events, dispersal and migratory losses along the Afro-European axis as drivers of biogeographic distribution in Sylvia warblers. BMC Evol Biol 2011; 11:163. [PMID: 21672229 PMCID: PMC3123607 DOI: 10.1186/1471-2148-11-163] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Old World warbler genus Sylvia has been used extensively as a model system in a variety of ecological, genetic, and morphological studies. The genus is comprised of about 25 species, and 70% of these species have distributions at or near the Mediterranean Sea. This distribution pattern suggests a possible role for the Messinian Salinity Crisis (from 5.96-5.33 Ma) as a driving force in lineage diversification. Other species distributions suggest that Late Miocene to Pliocene Afro-tropical forest dynamics have also been important in the evolution of Sylvia lineages. Using a molecular phylogenetic hypothesis and other methods, we seek to develop a biogeographic hypothesis for Sylvia and to explicitly assess the roles of these climate-driven events. RESULTS We present the first strongly supported molecular phylogeny for Sylvia. With one exception, species fall into one of three strongly supported clades: one small clade of species distributed mainly in Africa and Europe, one large clade of species distributed mainly in Africa and Asia, and another large clade with primarily a circum-Mediterranean distribution. Asia is reconstructed as the ancestral area for Sylvia. Long-distance migration is reconstructed as the ancestral character state for the genus, and sedentary behavior subsequently evolved seven times. CONCLUSION Molecular clock calibration suggests that Sylvia arose in the early Miocene and diverged into three main clades by 12.6 Ma. Divergence estimates indicate that the Messinian Salinity Crisis had a minor impact on Sylvia. Instead, over-water dispersals, repeated loss of long-distance migration, and palaeo-climatic events in Africa played primary roles in Sylvia divergence and distribution.
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Affiliation(s)
- Gary Voelker
- Department of Wildlife and Fisheries Sciences and Texas Cooperative Wildlife Collections, Texas A&M University, College Station, TX 77843, USA
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences and Texas Cooperative Wildlife Collections, Texas A&M University, College Station, TX 77843, USA
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Alström P, Fregin S, Norman JA, Ericson PG, Christidis L, Olsson U. Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae. Mol Phylogenet Evol 2011; 58:513-26. [DOI: 10.1016/j.ympev.2010.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 11/29/2022]
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Martens J, Tietze DT, Päckert M. Phylogeny, Biodiversity, and Species Limits of Passerine Birds in the Sino-Himalayan Region—A Critical Review. ACTA ACUST UNITED AC 2011. [DOI: 10.1525/om.2011.70.1.64] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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REDDY SUSHMA, MOYLE ROBERTG. Systematics of the scimitar babblers (Pomatorhinus: Timaliidae): phylogeny, biogeography, and species-limits of four species complexes. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2010.01611.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dong F, Li SH, Yang XJ. Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences. Mol Phylogenet Evol 2010; 57:1268-75. [DOI: 10.1016/j.ympev.2010.09.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 09/27/2010] [Accepted: 09/28/2010] [Indexed: 11/28/2022]
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