1
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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2
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Yang C, Dong X, Wang Q, Hou X, Yuan H, Li X. Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication. PeerJ 2023; 11:e16233. [PMID: 37842035 PMCID: PMC10576491 DOI: 10.7717/peerj.16233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
The mitochondrial genomes of six Phylloscopus species-small insectivores belonging to the Phylloscopidae family-were obtained using the Illumina sequencing platform. The mitogenomes were closed circular molecules 16,922-17,007 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions (CR1 and remnant CR2). The gene orders were conserved in 35 sampled Phylloscopus mitogenomes in the GenBank database, with a gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. The average base compositions of the six Phylloscopus mitogenomes were 29.43% A, 32.75% C, 14.68% G, and 23.10% T, with the A+T content slightly higher than that of G+C. ATG and TAA were the most frequent initiating and terminating codons, respectively. Several conserved boxes were identified in CR1, including C-string in domain I; F, E, D, and C boxes, as well as bird similarity and B boxes, in domain II; and CSB1 in domain III. Tandem repeats were observed in remnant CR2 of the Phylloscopus fuscatus and Phylloscopus proregulus mitogenomes. A phylogenetic analysis with maximum likelihood (ML) and Bayesian inference (BI) methods, based on 13 protein-coding genes and two rRNA genes, indicated that the Phylloscopus species was divided into two larger clades, with a splitting time approximately 11.06 million years ago (mya). The taxa of Phylloscopus coronatus/Phylloscopus burkii and Phylloscopus inornatus/P. proregulus were located at the basal position of the different clades. The phylogenetic result of the cox1 gene showed that Seicercus was nested within Phylloscopus. The complete set of mitogenomes of the Phylloscopus species provides potentially useful resources for the further exploration of the taxonomic status and phylogenetic history of Phylloscopidae.
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Affiliation(s)
- Chao Yang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiaomei Dong
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qingxiong Wang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiang Hou
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Hao Yuan
- School of Basic Medical Sciences, Xi’an Medical University, Xi’an, China
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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3
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Lundberg M, Mackintosh A, Petri A, Bensch S. Inversions maintain differences between migratory phenotypes of a songbird. Nat Commun 2023; 14:452. [PMID: 36707538 PMCID: PMC9883250 DOI: 10.1038/s41467-023-36167-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.
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Affiliation(s)
- Max Lundberg
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Anna Petri
- Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
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4
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de Raad J, Päckert M, Irestedt M, Janke A, Kryukov AP, Martens J, Red'kin YA, Sun Y, Töpfer T, Schleuning M, Neuschulz EL, Nilsson MA. Speciation and population divergence in a mutualistic seed dispersing bird. Commun Biol 2022; 5:429. [PMID: 35534538 PMCID: PMC9085801 DOI: 10.1038/s42003-022-03364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/14/2022] [Indexed: 11/29/2022] Open
Abstract
Bird-mediated seed dispersal is crucial for the regeneration and viability of ecosystems, often resulting in complex mutualistic species networks. Yet, how this mutualism drives the evolution of seed dispersing birds is still poorly understood. In the present study we combine whole genome re-sequencing analyses and morphometric data to assess the evolutionary processes that shaped the diversification of the Eurasian nutcracker (Nucifraga), a seed disperser known for its mutualism with pines (Pinus). Our results show that the divergence and phylogeographic patterns of nutcrackers resemble those of other non-mutualistic passerine birds and suggest that their early diversification was shaped by similar biogeographic and climatic processes. The limited variation in foraging traits indicates that local adaptation to pines likely played a minor role. Our study shows that close mutualistic relationships between bird and plant species might not necessarily act as a primary driver of evolution and diversification in resource-specialized birds. Genomic and phylogeographic analyses indicate that resource-specialization did not play a major role in the diversification and speciation of seed dispersing nutcrackers
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Affiliation(s)
- Jordi de Raad
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Museum für Tierkunde, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Russian Academy of Sciences, Stoletiya Avenue 159, 690022, Vladivostok, Russia
| | - Jochen Martens
- Institut für Organismische und Molekulare Evolutionsbiologie (iomE), Johannes Gutenberg-Universität Mainz, 55099, Mainz, Germany
| | - Yaroslav A Red'kin
- Department of Ornithology, Zoological Museum of Moscow State University, Bol'shaya Nikitskaya Street 2, 125009, Moscow, Russia
| | - Yuehua Sun
- Institute of Zoology, Chinese Academy of Sciences, CN-100101, Beijing, PR China
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Adenauerallee 127, 53113, Bonn, Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F, Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.
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5
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Zhang D, Rheindt FE, She H, Cheng Y, Song G, Jia C, Qu Y, Alström P, Lei F. Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow. Syst Biol 2021; 70:961-975. [PMID: 33787929 PMCID: PMC8357342 DOI: 10.1093/sysbio/syab024] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leaf warblers) using one de novo genome assembly and 78 resequenced genomes. On the basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the "winner-takes-all democratic majority tree" is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.[Bifurcation; introgression; recombination; reticulation; Phylloscopus.].
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Affiliation(s)
- Dezhi Zhang
- 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, Singapore 117543, Republic of Singapore
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
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6
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Forcina G, Boesman P, Jowers MJ. Cryptic diversity in a neotropical avian species complex untangled by neglected genetic evidence. Studies on Neotropical Fauna and Environment 2021. [DOI: 10.1080/01650521.2021.1915674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Giovanni Forcina
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | | | - Michael J. Jowers
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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7
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Opaev AS, Shishkina EM. Song amplitude and population density in two sympatric warblers, Phylloscopus schwarzi and P. fuscatus. BIOACOUSTICS 2021. [DOI: 10.1080/09524622.2020.1720816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- A. S. Opaev
- Laboratory of Comparative Ethology and Biocommunication, Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russian Federation
| | - E. M. Shishkina
- Laboratory of Comparative Ethology and Biocommunication, Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Moscow, Russian Federation
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8
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Recuerda M, Vizueta J, Cuevas-Caballé C, Blanco G, Rozas J, Milá B. Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology. Genome Biol Evol 2021; 13:evab034. [PMID: 33616654 PMCID: PMC8046334 DOI: 10.1093/gbe/evab034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe and parts of Asia, North Africa, and the Macaronesian archipelagos. We present a high-quality genome assembly of the common chaffinch generated using Illumina shotgun sequencing in combination with Chicago and Hi-C libraries. The final genome is a 994.87-Mb chromosome-level assembly, with 98% of the sequence data located in chromosome scaffolds and a N50 statistic of 69.73 Mb. Our genome assembly shows high completeness, with a complete BUSCO score of 93.9% using the avian data set. Around 7.8% of the genome contains interspersed repetitive elements. The structural annotation yielded 17,703 genes, 86.5% of which have a functional annotation, including 7,827 complete universal single-copy orthologs out of 8,338 genes represented in the BUSCO avian data set. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Joel Vizueta
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristian Cuevas-Caballé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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9
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Rheindt FE, Prawiradilaga DM, Ashari H, Suparno, Gwee CY, Lee GWX, Wu MY, Ng NSR. A lost world in Wallacea: Description of a montane archipelagic
avifauna. Science 2020; 367:167-170. [DOI: 10.1126/science.aax2146] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
Birds are the best-known animal class, with only about five or six new
species descriptions per year since 1999. Integrating genomic and phenotypic
research with arduous fieldwork in remote regions, we describe five new songbird
species and five new subspecies from a small area near Sulawesi, Indonesia, all
collected in a single 6-week expedition. Two factors contributed to the
description of this large number of species from such a small geographic area: (i)
Knowledge of Quaternary Period land connections helped pinpoint isolated islands
likely to harbor substantial endemism and (ii) studying accounts of historic
collectors such as Alfred Wallace facilitated the identification of undercollected
islands. Our findings suggest that humans’ understanding of biogeographically
complex regions such as Wallacea remains incomplete.
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Affiliation(s)
- Frank E. Rheindt
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Dewi M. Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong 16911, Indonesia
| | - Chyi Yin Gwee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Geraldine W. X. Lee
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Meng Yue Wu
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
| | - Nathaniel S. R. Ng
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543
- Department of Conservation and Research, Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore 729826
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10
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Forcina G, Guerrini M, Panayides P, Hadjigerou P, Khan AA, Barbanera F. Molecular taxonomy and intra-Palaearctic boundary: new insights from the biogeography of the black francolin (Francolinus francolinus) by means of microsatellite DNA. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1691673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Giovanni Forcina
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal
- Department of Biology, University of Pisa, Via A. Volta 4, Pisa, I-56126, Italy
| | - Monica Guerrini
- Department of Biology, University of Pisa, Via A. Volta 4, Pisa, I-56126, Italy
| | - Panicos Panayides
- Game & Fauna Service, Ministry of Interior, Nicosia, CY-1453, Cyprus
| | | | - Aleem Ahmed Khan
- Institute of Pure & Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, Pisa, I-56126, Italy
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11
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Fuchs J, Alström P, Yosef R, Olsson U. Miocene diversification of an open‐habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jérôme Fuchs
- UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle Sorbonne Université Paris France
| | - 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
| | | | - Urban Olsson
- Department of Biology and Environmental Science University of Gothenburg Gothenburg Sweden
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12
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Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, Lei F. 'Ghost introgression' as a cause of deep mitochondrial divergence in a bird species complex. Mol Biol Evol 2019; 36:2375-2386. [PMID: 31364717 DOI: 10.1093/molbev/msz170] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022] Open
Abstract
In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genetic introgression. Here we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of 'ghost introgression' as the cause of DMD, and we suggest that 'ghost introgression' may be a widely overlooked phenomenon in nature.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, Sweden.,Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, Uppsala, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Ng NSR, Prawiradilaga DM, Ng EYX, Suparno, Ashari H, Trainor C, Verbelen P, Rheindt FE. A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics. Sci Rep 2018; 8:15646. [PMID: 30353148 PMCID: PMC6199301 DOI: 10.1038/s41598-018-34101-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/27/2018] [Indexed: 11/09/2022] Open
Abstract
Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.
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Affiliation(s)
- Nathaniel S R Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Colin Trainor
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, 0909, Australia
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 129801, Singapore.
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