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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Johansson US, Irestedt M, Ericson PGP. Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex. Mol Phylogenet Evol 2023; 189:107909. [PMID: 37611647 DOI: 10.1016/j.ympev.2023.107909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however. In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches. We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group. For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland. We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies. Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.
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Affiliation(s)
- Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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3
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Rancilhac L, Enbody ED, Harris R, Saitoh T, Irestedt M, Liu Y, Lei F, Andersson L, Alström P. Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation. Syst Biol 2023:syad062. [PMID: 37801684 DOI: 10.1093/sysbio/syad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 10/08/2023] Open
Abstract
Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a "complete evidence" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.
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Affiliation(s)
- Loïs Rancilhac
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Biomolecular Engineering, University of California, Santa Cruz, California, USA
| | | | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba 270-1145, Japan
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
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4
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Sangster G, Marki PZ, Gaudin J, Irestedt M, Jonsson KA. A new genus for Pycnopygius cinereus/P. ixoides (Aves: Meliphagidae). Zootaxa 2023; 5330:147-150. [PMID: 38220876 DOI: 10.11646/zootaxa.5330.1.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Indexed: 01/16/2024]
Affiliation(s)
- George Sangster
- Naturalis Biodiversity Center; Darwinweg 2; PO Box 9517; 2300 RA Leiden; the Netherlands.
| | - Petter Zahl Marki
- Division of Research and Innovation; University of Agder; Universitetsveien 25; 4630 Kristiansand; Norway.
| | - Jimmy Gaudin
- 34; avenue Antoine de Saint-Exupry; 17 000 La Rochelle; France.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; P.O. Box 50007; SE-10405; Stockholm; Sweden.
| | - Knud A Jonsson
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; P.O. Box 50007; SE-10405; Stockholm; Sweden.
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5
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Tan HZ, Jansen JJFJ, Allport GA, Garg KM, Chattopadhyay B, Irestedt M, Pang SEH, Chilton G, Gwee CY, Rheindt FE. Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds. eLife 2023; 12:e85422. [PMID: 37549057 PMCID: PMC10406428 DOI: 10.7554/elife.85422] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/27/2023] [Indexed: 08/09/2023] Open
Abstract
Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.
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Affiliation(s)
- Hui Zhen Tan
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | | | | | - Kritika M Garg
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Sean EH Pang
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Glen Chilton
- Department of Biology, St. Mary's UniversityCalgaryCanada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
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6
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Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A. Satellite DNA evolution in Corvoidea inferred from short and long reads. Mol Ecol 2023; 32:1288-1305. [PMID: 35488497 DOI: 10.1111/mec.16484] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
Satellite DNA (satDNA) is a fast-evolving portion of eukaryotic genomes. The homogeneous and repetitive nature of such satDNA causes problems during the assembly of genomes, and therefore it is still difficult to study it in detail in nonmodel organisms as well as across broad evolutionary timescales. Here, we combined the use of short- and long-read data to explore the diversity and evolution of satDNA between individuals of the same species and between genera of birds spanning ~40 millions of years of bird evolution using birds-of-paradise (Paradisaeidae) and crow (Corvus) species. These avian species highlighted the presence of a GC-rich Corvoidea satellitome composed of 61 satellite families and provided a set of candidate satDNA monomers for being centromeric on the basis of length, abundance, homogeneity and transcription. Surprisingly, we found that the satDNA of crow species rapidly diverged between closely related species while the satDNA appeared more similar between birds-of-paradise species belonging to different genera.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biological Sciences-Organisms and the Environment, University of East Anglia, Norwich, UK
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7
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Delling B, Thörn F, Norén M, Irestedt M. Museomics reveals the phylogenetic position of the extinct Moroccan trout Salmo pallaryi. J Fish Biol 2023; 102:619-627. [PMID: 36602189 DOI: 10.1111/jfb.15299] [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] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses, including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes, place S. pallaryi among other North African trouts. mtDNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure. They suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20th century.
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Affiliation(s)
- Bo Delling
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Filip Thörn
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Michael Norén
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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8
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Reeve AH, Gower G, Pujolar JM, Smith BT, Petersen B, Olsson U, Haryoko T, Koane B, Maiah G, Blom MPK, Ericson PGP, Irestedt M, Racimo F, Jønsson KA. Population genomics of the island thrush elucidates one of earth's great archipelagic radiations. Evol Lett 2023; 7:24-36. [PMID: 37065434 PMCID: PMC10091502 DOI: 10.1093/evlett/qrac006] [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] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 11/10/2022] [Accepted: 12/29/2022] [Indexed: 04/18/2023] Open
Abstract
Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.
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Affiliation(s)
- Andrew Hart Reeve
- Corresponding author: Universitetsparken 15, Office 345, Natural History Museum of Denmark, 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, National Institute of Aquatic Resources, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, United States
| | - Bent Petersen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, DK-1353 Copenhagen K, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Urban Olsson
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Bonny Koane
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
- Mauberema Ecotourism, Nature Conservation, Education, Research and Training Center, Simbu Province, Papua New Guinea
| | - Gibson Maiah
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | - Mozes P K Blom
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, DK-1350 Copenhagen K, Denmark
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
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9
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Ericson PGP, Irestedt M, Zuccon D, Larsson P, Tison JL, Emslie SD, Götherström A, Hume JP, Werdelin L, Qu Y. A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture. Commun Biol 2022; 5:857. [PMID: 35999361 PMCID: PMC9399080 DOI: 10.1038/s42003-022-03811-0] [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: 05/20/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution. 14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Dario Zuccon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR7205 CNRS MNHN UPMC EPHE Sorbonne Université, Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Petter Larsson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Jean-Luc Tison
- Department of Laboratory Medicine, Örebro University Hospital; Södra Grev Rosengatan, SE-70185, Örebro, Sweden
| | - Steven D Emslie
- Department of Biology and Marine Biology, University of North Carolina; Wilmington, 601S. College Road, Wilmington, NC, 28403, USA
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Archaeology and Classical Studies, Stockholm University, SE-10691, Stockholm, Sweden
| | - Julian P Hume
- Bird Group, Department of Life Sciences, Natural History Museum, Akeman St, Tring, Herts, UK
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-10405, Stockholm, Sweden. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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10
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Sangster G, Luksenburg JA, Päckert M, Roselaar CS, Irestedt M, Ericson PGP. Integrative taxonomy documents two additional cryptic
Erithacus
species on the Canary Islands (Aves). ZOOL SCR 2022. [DOI: 10.1111/zsc.12561] [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: 11/29/2022]
Affiliation(s)
- George Sangster
- Naturalis Biodiversity Center Leiden The Netherlands
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences Leiden University Leiden The Netherlands
- Department of Environmental Science and Policy George Mason University Fairfax Virginia USA
| | - Martin Päckert
- Senckenberg Natural History Collections Dresden Dresden Germany
| | | | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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11
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Ericson PGP, Irestedt M, Qu Y. Demographic history, local adaptation and vulnerability to climate change in a tropical mountain bird in New Guinea. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13614] [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: 11/28/2022] Open
Affiliation(s)
- Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences Beijing China
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12
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Irestedt M, Thörn F, Müller IA, Jønsson KA, Ericson PGP, Blom MPK. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins. Mol Ecol Resour 2022; 22:2672-2684. [PMID: 35661418 PMCID: PMC9542604 DOI: 10.1111/1755-0998.13660] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022]
Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
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Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Filip Thörn
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Ingo A Müller
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Mozes P K Blom
- Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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13
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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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14
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Reeve AH, Blom MPK, Zahl Marki P, Batista R, Olsson U, Edmark VN, Irestedt M, Jønsson KA. The Sulawesi Thrush (
Cataponera turdoides
; Aves: Passeriformes) belongs to the genus
Turdus. ZOOL SCR 2021. [DOI: 10.1111/zsc.12518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Andrew Hart Reeve
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Ø Denmark
| | - Mozes P. K. Blom
- Museum für Naturkunde BerlinInstitut für Evolutions‐ und Biodiversitätsforschung Germany
| | - Petter Zahl Marki
- Division of Research Management University of Agder Kristiansand Norway
| | - Romina Batista
- Instituto Nacional de Pesquisas da Amazônia Campus II Petrópolis CEP Brazil
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Urban Olsson
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
- Department of Biological and Environmental Sciences University of Göteborg Göteborg Sweden
| | - Veronica Nyström Edmark
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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15
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Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
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16
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Abstract
Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird (Amblyornis papuensis). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.
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Affiliation(s)
- Per G. P. Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405, Stockholm, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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17
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Schodde R, Christidis L, Batalha-Filho H, Ericson PGP, Irestedt M. Why neotypification of emLophorina/em emsuperba/em (Pennant, 1781) (Aves: Paradisaeidae) is justified-and necessary. Zootaxa 2021; 4951:zootaxa.4951.2.5. [PMID: 33903404 DOI: 10.11646/zootaxa.4951.2.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/06/2021] [Indexed: 11/04/2022]
Abstract
We review Irestedt et al.'s (2017) neotypification of the senior species name superba Pennant, 1781 in the bird-of-paradise genus Lophorina in response to Elliott et al. (2020) who challenged the resultant shift in name from the small isolate in New Guinea's Vogelkop to the widespread species in the island's central cordillera. In nine male plumage traits which differentiate the two species, six of which had been identified as novel by Irestedt et al., we show that the only two figures of the perished male holotype of superba match the central cordillera species more closely than the Vogelkop. We find as well that not only was the trading of bird-of-paradise skins from the central cordillera to coastal ports in the Vogelkop feasible before European contact, but application of superba to the central cordillera species also promotes nomenclatural stability: the name has been used overwhelmingly at species rank for that widespread form throughout post-19th century media. Re-assessment of Irestedt et al.'s point-by-point justification of neotypification under Article 75.3 of the ICZN (1999) Code establishes, furthermore, that their case meets the requirements of every condition specified in the article; the neotypification is thus valid. Elliott et al.'s alternative to fix superba to the Vogelkop isolate by type locality restriction is not Code-compliant, nor is their evidence for interpreting J.R. Forster as the author of the name. In conclusion, we lay out the correct nomenclature for the taxa of Lophorina under the Code.
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Affiliation(s)
- R Schodde
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT 2601, Australia..
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18
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Ericson PGP, Irestedt M, Nylander JAA, Christidis L, Joseph L, Qu Y. Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics. Syst Biol 2021; 69:820-829. [PMID: 32415976 PMCID: PMC7440736 DOI: 10.1093/sysbio/syaa040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/07/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.]
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden
| | - Les Christidis
- School of Environment, Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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19
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Peona V, Blom MPK, Xu L, Burri R, Sullivan S, Bunikis I, Liachko I, Haryoko T, Jønsson KA, Zhou Q, Irestedt M, Suh A. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Mol Ecol Resour 2021; 21:263-286. [PMID: 32937018 PMCID: PMC7757076 DOI: 10.1111/1755-0998.13252] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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] [Received: 04/14/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/09/2023]
Abstract
Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic "dark matter") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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Affiliation(s)
- Valentina Peona
- Department of Ecology and Genetics—Evolutionary BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- Department of Organismal Biology—Systematic BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Museum für NaturkundeLeibniz Institut für Evolutions‐ und BiodiversitätsforschungBerlinGermany
| | - Luohao Xu
- Department of Neurosciences and Developmental BiologyUniversity of ViennaViennaAustria
| | - Reto Burri
- Department of Population EcologyInstitute of Ecology and EvolutionFriedrich‐Schiller‐University JenaJenaGermany
| | | | - Ignas Bunikis
- Department of Immunology, Genetics and PathologyScience for Life LaboratoryUppsala Genome CenterUppsala UniversityUppsalaSweden
| | | | - Tri Haryoko
- Research Centre for BiologyMuseum Zoologicum BogorienseIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Knud A. Jønsson
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Qi Zhou
- Department of Neurosciences and Developmental BiologyUniversity of ViennaViennaAustria
- MOE Laboratory of Biosystems Homeostasis & ProtectionLife Sciences InstituteZhejiang UniversityHangzhouChina
- Center for Reproductive MedicineThe 2nd Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Martin Irestedt
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Alexander Suh
- Department of Ecology and Genetics—Evolutionary BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- Department of Organismal Biology—Systematic BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- School of Biological Sciences—Organisms and the EnvironmentUniversity of East AngliaNorwichUK
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20
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Gwee CY, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Irestedt M, Lei F, Bloch LM, Lee JGH, Irham M, Haryoko T, Soh MCK, Peh KSH, Rowe KMC, Ferasyi TR, Wu S, Wogan GOU, Bowie RCK, Rheindt FE. Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity. eLife 2020; 9:e62765. [PMID: 33350381 PMCID: PMC7775107 DOI: 10.7554/elife.62765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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] [Received: 09/03/2020] [Accepted: 12/21/2020] [Indexed: 01/09/2023] Open
Abstract
Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.
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Affiliation(s)
- Chyi Yin Gwee
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Kritika M Garg
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Balaji Chattopadhyay
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
| | - Keren R Sadanandan
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholmSweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesKunmingChina
| | - Luke M Bloch
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Tri Haryoko
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science CenterCibinongIndonesia
| | - Malcolm CK Soh
- University of Western Australia, School of Biological SciencesPerthAustralia
| | - Kelvin S-H Peh
- University of Southampton, School of Biological Sciences, UniversitySouthamptonUnited Kingdom
| | - Karen MC Rowe
- Sciences Department, Museums VictoriaMelbourneAustralia
| | - Teuku Reza Ferasyi
- Faculty of Veterinary Medicine, Universitas Syiah KualaDarussalamIndonesia
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal UniversityXuzhouChina
| | - Shaoyuan Wu
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical UniversityTianjinChina
- Center for Tropical Veterinary Studies – One Health Collaboration Center, Universitas Syiah KualaDarussalamIndonesia
| | - Guinevere OU Wogan
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeleyUnited States
| | - Rauri CK Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Frank E Rheindt
- National University of Singapore, Department of Biological SciencesSingaporeSingapore
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21
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Xu L, Irestedt M, Zhou Q. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes (Basel) 2020; 11:E1267. [PMID: 33126459 PMCID: PMC7692361 DOI: 10.3390/genes11111267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 09/23/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin's finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.
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Affiliation(s)
- Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden;
| | - Qi Zhou
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090 Vienna, Austria;
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310012, China
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310012, China
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22
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Ghorbani F, Aliabadian M, Zhang R, Irestedt M, Hao Y, Sundev G, Lei F, Ma M, Olsson U, Alström P. Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark (
Alaudala rufescens
) — Sand Lark (
A. raytal
) species complex (Aves, Passeriformes) reveal cryptic diversity. ZOOL SCR 2020. [DOI: 10.1111/zsc.12422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fatemeh Ghorbani
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
- Zoological Innovations Research Department Institute of Applied Zoology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Martin Irestedt
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Gombobaatar Sundev
- National University of Mongolia and Mongolian Ornithological Society Ulaanbaatar Mongolia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Ming Ma
- Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Xinjiang China
| | - Urban Olsson
- Systematics and Biodiversity Department of Biology and Environmental Sciences University of Gothenburg Göteborg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - 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 Uppsala Sweden
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23
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Cros E, Ng EYX, Oh RRY, Tang Q, Benedick S, Edwards DP, Tomassi S, Irestedt M, Ericson PGP, Rheindt FE. Fine-scale barriers to connectivity across a fragmented South-East Asian landscape in six songbird species. Evol Appl 2020; 13:1026-1036. [PMID: 32431750 PMCID: PMC7232758 DOI: 10.1111/eva.12918] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 12/08/2019] [Indexed: 12/28/2022] Open
Abstract
Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome-wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge-tolerant and forest-canopy species as compared to forest-dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.
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Affiliation(s)
- Emilie Cros
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Elize Y. X. Ng
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Rachel R. Y. Oh
- Centre for Urban Greenery and EcologyNational Parks BoardSingaporeSingapore
- School of Biological SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Qian Tang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Suzan Benedick
- Sustainable Agriculture SchoolUniversiti Malaysia SabahSabahMalaysia
| | - David P. Edwards
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Suzanne Tomassi
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Martin Irestedt
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Per G. P. Ericson
- Department of ZoologySwedish Museum of Natural HistoryStockholmSweden
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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24
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Martins FC, Cox SC, Irestedt M, Prŷs-Jones RP, Day JJ. A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history. Mol Phylogenet Evol 2020; 149:106843. [PMID: 32330543 DOI: 10.1016/j.ympev.2020.106843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 09/16/2019] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 10/24/2022]
Abstract
White-eyes (Zosterops) are a hyper-diverse genus of passerine birds that have rapidly radiated across the Afrotropics and Southeast Asia. Despite their broad range, a disproportionately large number of species are currently recognised from islands compared to the mainland. Described species-level diversity of this 'great speciator' from continental Africa-Arabia is strikingly low, despite the vast size and environmental complexity of this region. However, efforts to identify natural groups using traditional approaches have been hindered by the remarkably uniform morphology and plumage of these birds. Here, we investigated the phylogenetic relationships and systematics of Afrotropical Zosterops, including the Gulf of Guinea and western Indian Ocean islands. We included exceptional sampling (~160 individuals) from all except one subspecies of the 55 taxa (32 species, plus 23 additional named sub-species) currently recognized throughout the region, in addition to a subset of extra-Afrotropical taxa, by exploiting blood and archival samples. Employing a multi-locus phylogenetic approach and applying quantitative species delimitation we tested: (1) if there has been a single colonisation event of the Afrotropical realm; (2) if constituent mainland and island birds are monophyletic; and (3) if mainland diversity has been underestimated. Our comprehensive regional phylogeny revealed a single recent colonisation of the Afrotropical realm c.1.30 Ma from Asia, but a subsequent complex colonisation history between constituent island and mainland lineages during their radiation across this vast area. Our findings suggest a significant previous underestimation of continental species diversity and, based on this, we propose a revised taxonomy. Our study highlights the need to densely sample species diversity across ranges, providing key findings for future conservation assessments and establishing a robust framework for evolutionary studies.
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Affiliation(s)
- Frederico C Martins
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Siobhan C Cox
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK; Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Herts HP23 6AP, UK
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Robert P Prŷs-Jones
- Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Herts HP23 6AP, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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25
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Ohlson JI, Irestedt M, Filho HB, Ericson PGP, Fjeldså J. A revised classification of the fluvicoline tyrant flycatchers (Passeriformes, Tyrannidae, Fluvicolinae). Zootaxa 2020; 4747:zootaxa.4747.1.7. [PMID: 32230123 DOI: 10.11646/zootaxa.4747.1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/02/2020] [Indexed: 11/04/2022]
Abstract
A new classification is proposed for the subfamily Fluvicolinae in the New World Flycatchers (Tyrannidae), based on the results of a previously published phylogeny including more than 90% of the species. In this classification we propose one new family level name (Ochthoecini) and one new generic name (Scotomyias). We also resurrect three genera (Heteroxolmis, Pyrope and Nengetus) and subsume five (Tumbezia, Lathrotriccus, Polioxolmis, Neoxolmis and Myiotheretes) into other genera to align the classification with the current understanding of phylogenetic relationships in Fluvicolinae.
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Affiliation(s)
- Jan I Ohlson
- Dept of Bioinformatics and Genetics, Swedish Museum of Natural History, Sweden..
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26
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Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, Irestedt M, Lundin K, Larsson E, Matos-Maraví P, Müller J, von Proschwitz T, Roderick GK, Schliep A, Wahlberg N, Wiedenhoeft J, Källersjö M. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 2020; 8:e8225. [PMID: 32025365 PMCID: PMC6993751 DOI: 10.7717/peerj.8225] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
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Affiliation(s)
- Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Nuno Ferrand
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Magnus Gelang
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Rosemary G Gillespie
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Kennet Lundin
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Johannes Müller
- Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Ted von Proschwitz
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - George K Roderick
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander Schliep
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | | | - John Wiedenhoeft
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | - Mari Källersjö
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Botanical Garden, Göteborg, Sweden
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27
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Jønsson KA, Blom MP, Marki PZ, Joseph L, Sangster G, Ericson PG, Irestedt M. Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return. Mol Phylogenet Evol 2019; 137:200-209. [DOI: 10.1016/j.ympev.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/05/2019] [Accepted: 03/22/2019] [Indexed: 12/01/2022]
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28
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Ericson PGP, Qu Y, Rasmussen PC, Blom MPK, Rheindt FE, Irestedt M. Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. BMC Evol Biol 2019; 19:151. [PMID: 31340765 PMCID: PMC6657069 DOI: 10.1186/s12862-019-1481-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
Background Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. Results We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. Conclusions We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, “stepping-stone” dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea. Electronic supplementary material The online version of this article (10.1186/s12862-019-1481-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pamela C Rasmussen
- Department of Integrative Biology and MSU Museum, Michigan State University, East Lansing, 48824, MI, USA.,Bird Group, The Natural History Museum, Akeman Street, Tring, HP23 6AP, UK
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 119077, Singapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
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29
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Prost S, Armstrong EE, Nylander J, Thomas GWC, Suh A, Petersen B, Dalen L, Benz BW, Blom MPK, Palkopoulou E, Ericson PGP, Irestedt M. Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. Gigascience 2019; 8:giz003. [PMID: 30689847 PMCID: PMC6497032 DOI: 10.1093/gigascience/giz003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/30/2018] [Accepted: 01/10/2019] [Indexed: 12/14/2022] Open
Abstract
The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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Affiliation(s)
- Stefan Prost
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
- Department of Integrative Biology, University of California, 3040 Valley Life Science Building, Berkeley, CA 94720-3140, USA
| | - Ellie E Armstrong
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305–5020, USA
| | - Johan Nylander
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Gregg W C Thomas
- Department of Biology and School of Informatics, Computing, and Engineering, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Norbyvaegen 14-18, 75236 Uppsala, Sweden
| | - Bent Petersen
- Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology,Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia
| | - Love Dalen
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Brett W Benz
- Department of Ornithology, American Museum of Natural History, Central Park West, New York, NY 10024, USA
| | - Mozes P K Blom
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Eleftheria Palkopoulou
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Per G P Ericson
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
| | - Martin Irestedt
- Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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Johansson US, Irestedt M, Qu Y, Ericson PGP. Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes. Mol Phylogenet Evol 2018; 126:17-22. [PMID: 29631051 DOI: 10.1016/j.ympev.2018.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/06/2017] [Revised: 03/08/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The rollers (Coraciidae) constitute a relative small avian family with ca. 12 species distributed in Africa, western and southern Eurasia, and eastern Australia. In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgun sequencing on degraded DNA from museum study skins we have been able to recover complete mitochondrial genomes as well as 15 nuclear genes for in total 16 taxa. The gene sequences were analyzed both concatenated in a maximum likelihood framework as well in a species tree approach using MP-EST. The different analytical approaches yield similar, highly supported trees and support the current division of the rollers into two genera, Coracias and Eurystomus. The only conflict relates to the placement of the Blue-bellied Roller (C. cyanogaster), where the mitochondrial, and the concatenated nuclear and mitochondrial data set, place this taxon as sister to the other Coracias species, whereas nuclear data and the species tree analysis place it as the sister taxon of C. naevia and C. spatulatus. All analyses place the Eurasian roller (C. garrulus) with the two African species, Abyssinian Roller (C. abyssinica) and Liliac-breasted Roller (C. caudatus), and place this clade as the sister group to the Asian Coracias rollers. In addition, our results support a sister group relationship between the morphologically rather dissimilar Purple Roller (C. naevia) and Racquet-tailed Roller (C. spatulatus) and also support the division of Eurystomus in an African and an Asian clade. However, within the Asian clade the Azure Roller (E. azureus) from Halmahera appears to be nested within the Dollarbird (E. orientalis), indicating that that this taxon is a morphological divergent, but a rather recent offshoot, of the widespread Dollarbird. Similarly, the Purple-winged Roller (C. temminickii) from Sulawesi group together with C. benghalensis affinis from Southeast Asia and these two in turn comprises the sister group to C. benghalensis benghalensis from India and western Asia.
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Affiliation(s)
- Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE 104 05 Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm 10405, Sweden
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Marki PZ, Fjeldså J, Irestedt M, Jønsson KA. Molecular phylogenetics and species limits in a cryptically coloured radiation of Australo-Papuan passerine birds (Pachycephalidae: Colluricincla). Mol Phylogenet Evol 2018. [PMID: 29526804 DOI: 10.1016/j.ympev.2018.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds. In line with previous studies, we find that one species, the little shrikethrush (C. megarhyncha) is characterized by deep divergences among populations. Delimitation results suggest that these clades represent distinct species and we consequently propose a new classification. Furthermore, our findings suggest that C. megarhyncha melanorhyncha of Biak Island does not belong in this genus, but is nested within the whistlers (Pachycephala) as sister to P. phaionota. This study represents a useful example of species delimitation when phenotypic variation is limited or poorly defined.
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Affiliation(s)
- Petter Z Marki
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark; Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318 Oslo, Norway.
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Knud A Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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Dussex N, Taylor H, Irestedt M, Robertson B. When genetic and phenotypic data do not agree: the conservation implications of ignoring inconvenient taxonomic evidence. NEW ZEAL J ECOL 2018. [DOI: 10.20417/nzjecol.42.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Low GW, Chattopadhyay B, Garg KM, Irestedt M, Ericson P, Yap G, Tang Q, Wu S, Rheindt FE. Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive. Heredity (Edinb) 2018; 120:138-153. [PMID: 29225353 PMCID: PMC5837122 DOI: 10.1038/s41437-017-0026-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/13/2017] [Accepted: 10/19/2017] [Indexed: 11/09/2022] Open
Abstract
Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore. We inferred limited population subdivision at a micro-geographic level, a genetic patch size (~13-14 km) indicative of a pronounced dispersal ability, and barely an increase in effective population size since introduction despite an increase of four to five orders of magnitude in actual population size, suggesting that low population-genetic diversity following a bottleneck has not impeded establishment success. Landscape genomic analyses identified urban features, such as low-rise neighborhoods, that constitute pronounced barriers to gene flow. Based on our data, we consider an approach targeting the complete eradication of Javan Mynas across Singapore to be unfeasible. Instead, a mixed approach of localized mitigation measures taking into account urban geographic features and planning policy may be the most promising avenue to reducing the adverse impacts of this urban pest. Our study demonstrates how genomic methods can directly inform the management and control of invasive species, even in geographically limited datasets with high gene flow rates.
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Affiliation(s)
- G W Low
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| | - B Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - K M Garg
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - M Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 54, Plan 3, Stockholm, 114018, Sweden
| | - Pgp Ericson
- Department of Zoology, Swedish Museum of Natural History, Frescativägen 54, Plan 3, Stockholm, 114018, Sweden
| | - G Yap
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way, Singapore, 138667, Singapore
| | - Q Tang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - S Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, 101 Shanghai Road, Xuzhou, Jiangsu, 221116, China
| | - F E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
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Jønsson KA, Delhey K, Sangster G, Ericson PGP, Irestedt M. The evolution of mimicry of friarbirds by orioles (Aves: Passeriformes) in Australo-Pacific archipelagos. Proc Biol Sci 2017; 283:rspb.2016.0409. [PMID: 27335418 DOI: 10.1098/rspb.2016.0409] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/25/2016] [Indexed: 11/12/2022] Open
Abstract
Observations by Alfred Wallace and Jared Diamond of plumage similarities between co-occurring orioles (Oriolus) and friarbirds (Philemon) in the Malay archipelago led them to conclude that the former represent visual mimics of the latter. Here, we use molecular phylogenies and plumage reflectance measurements to test several key predictions of the mimicry hypothesis. We show that friarbirds originated before brown orioles, that the two groups did not co-speciate, although there is one plausible instance of co-speciation among species on the neighbouring Moluccan islands of Buru and Seram. Furthermore, we show that greater size disparity between model and mimic and a longer history of co-occurrence have resulted in a stronger plumage similarity (mimicry). This suggests that resemblance between orioles and friarbirds represents mimicry and that colonization of islands by brown orioles has been facilitated by their ability to mimic the aggressive friarbirds.
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Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen Ø, Denmark Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Kaspar Delhey
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, 3800 Victoria, Australia Max Planck Institute for Ornithology, Radolfzell 78315, Germany
| | - George Sangster
- Department of Zoology, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Per G P Ericson
- Department of Zoology, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
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Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M. Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji. Mol Phylogenet Evol 2017; 120:28-32. [PMID: 29199105 DOI: 10.1016/j.ympev.2017.11.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/22/2017] [Accepted: 11/29/2017] [Indexed: 11/30/2022]
Abstract
Molecular studies have revealed a number of cases in which traditional assessments of evolutionary relationships have been incorrect. This has implications not only for systematics and taxonomy but also for our understanding of how diversity patterns on Earth have been formed. Here, we use high-throughput sequencing technology to obtain molecular data from the holotype specimen of the elusive Eutrichomyias rowleyi, which is endemic to the Indonesian island of Sangihe. We show that E. rowleyi unexpectedly is a member of the family Lamproliidae, which dates back some 20 Million years and only include two other species, Lamprolia victoriae from Fiji and Chaetorhynchus papuensis from New Guinea. Tectonic reconstructions suggest that the Melanesian island arc, which included land masses on the northern edge of the Australian plate (present day New Guinea) stretched as a string of islands from the Philippines (including proto-Sangihe) to Fiji from 25 to 20 My. Consequently, our results are indicative of an ancient distribution along the Melanesian island arc followed by relictualization, which led to members of the Lamproliidae to be distributed on widely separated islands across the Indo-Pacific.
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Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark.
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Martin Päckert
- Senckenberg Natural History Collections, Museum of Zoology, Königsbrücker Landstraße 159, D-01109 Dresden, Germany
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
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Irestedt M, Batalha-Filho H, Ericson PGP, Christidis L, Schodde R. Phylogeny, biogeography and taxonomic consequences in a bird-of-paradise species complex, Lophorina–Ptiloris (Aves: Paradisaeidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Marki PZ, Jønsson KA, Irestedt M, Nguyen JM, Rahbek C, Fjeldså J. Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes). Mol Phylogenet Evol 2017; 107:516-529. [DOI: 10.1016/j.ympev.2016.12.021] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 11/15/2022]
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Jønsson KA, Delhey K, Sangster G, Ericson PGP, Irestedt M. Correction to 'The evolution of mimicry of friarbirds by orioles (Aves: Passeriformes) in Australo-Pacific archipelagos'. Proc Biol Sci 2016; 283:rspb.2016.1497. [PMID: 27581886 DOI: 10.1098/rspb.2016.1497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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40
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Irestedt M, Batalha-Filho H, Roselaar CS, Christidis L, Ericson PGP. Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus). ZOOL SCR 2015. [DOI: 10.1111/zsc.12163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Irestedt
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
| | | | - Cees S. Roselaar
- Naturalis Biodiversity Center; Darwinweg 2 PO Box 9517 RA Leiden 2300 The Netherlands
| | - Les Christidis
- National Marine Science Centre; Southern Cross University; Coffs Harbour NSW 2450 Australia
| | - Per G. P. Ericson
- Department of Zoology; Swedish Museum of Natural History; PO Box 50007 Stockholm 10405 Sweden
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41
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Alström P, Jønsson KA, Fjeldså J, Ödeen A, Ericson PGP, Irestedt M. Dramatic niche shifts and morphological change in two insular bird species. R Soc Open Sci 2015; 2:140364. [PMID: 26064613 PMCID: PMC4448822 DOI: 10.1098/rsos.140364] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.
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Affiliation(s)
- Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences, PO Box 7007, Uppsala 75007, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, People's Republic of China
| | - Knud A. Jønsson
- Center for Macroecology, Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders Ödeen
- Department of Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Per G. P. Ericson
- Department of Zoology, and, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
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42
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Batalha-Filho H, Pessoa RO, Fabre PH, Fjeldså J, Irestedt M, Ericson PG, Silveira LF, Miyaki CY. Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests. Mol Phylogenet Evol 2014; 79:422-32. [DOI: 10.1016/j.ympev.2014.06.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 05/31/2014] [Accepted: 06/13/2014] [Indexed: 12/01/2022]
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43
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Ertz D, Tehler A, Irestedt M, Frisch A, Thor G, van den Boom P. A large-scale phylogenetic revision of Roccellaceae (Arthoniales) reveals eight new genera. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0286-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jønsson KA, Irestedt M, Christidis L, Clegg SM, Holt BG, Fjeldså J. Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala). Proc Biol Sci 2014; 281:20131727. [PMID: 24403319 DOI: 10.1098/rspb.2013.1727] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).
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Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, , Copenhagen, Denmark, Department of Life Sciences, Imperial College London, , Silwood Park Campus, Ascot SL5 7PY, UK, Department of Life Sciences, Natural History Museum, , Cromwell Road, London SW7 5BD, UK, Department of Biodiversity Informatics and Genetics, Swedish Museum of Natural History, , PO Box 50007, Stockholm 104 05, Sweden, National Marine Science Centre, Southern Cross University, , Coffs Harbour, New South Wales 2450, Australia, Environmental Futures Centre and Griffith School of Environment, Griffith University, , Gold Coast Campus, Queensland 4222, Australia
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Bristol RM, Fabre PH, Irestedt M, Jønsson KA, Shah NJ, Tatayah V, Warren BH, Groombridge JJ. Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: Undetected evolutionary diversity revealed amongst island populations. Mol Phylogenet Evol 2013; 67:336-47. [DOI: 10.1016/j.ympev.2013.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 01/23/2013] [Accepted: 01/30/2013] [Indexed: 11/25/2022]
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47
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Irestedt M, Fabre PH, Batalha-Filho H, Jønsson KA, Roselaar CS, Sangster G, Ericson PGP. The spatio-temporal colonization and diversification across the Indo-Pacific by a 'great speciator' (Aves, Erythropitta erythrogaster). Proc Biol Sci 2013; 280:20130309. [PMID: 23554394 DOI: 10.1098/rspb.2013.0309] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea-level fluctuations during the Pleistocene may have promoted gene flow only locally. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a 'great speciator': it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.
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Affiliation(s)
- Martin Irestedt
- Department of Biodiversity Informatics and Genetics, Swedish Museum of Natural History, PO Box 50007, 10405 Stockholm, Sweden.
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48
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Olsson U, Irestedt M, Sangster G, Ericson PG, Alström P. Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera. Mol Phylogenet Evol 2013; 66:790-9. [DOI: 10.1016/j.ympev.2012.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/28/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
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Moltesen M, Irestedt M, Fjeldså J, Ericson PGP, Jønsson KA. Molecular phylogeny of Chloropseidae and Irenidae - cryptic species and biogeography. Mol Phylogenet Evol 2012; 65:903-14. [PMID: 22960142 DOI: 10.1016/j.ympev.2012.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 08/03/2012] [Accepted: 08/16/2012] [Indexed: 11/16/2022]
Abstract
Chloropseidae (Leafbirds) and Irenidae (Fairy-bluebirds) are colourful Oriental birds, which have been placed as a deep (old) branch in the radiation of passeroid songbirds. We present a densely sampled molecular phylogeny of the two families based on two nuclear introns (GAPDH and ODC) and two mitochondrial genes (ND3 and cyt-b) largely stemming from old museum specimens. Our results show that several subspecies within both Chloropseidae and Irenidae are genetically distinct and separated in the Miocene some 10-11Million years ago (Mya), indicating a substantial underestimation of species numbers within the two families. Based on our molecular findings, plumage distinctiveness and contemporary distributions we propose that several subspecies be recognised at the species level. Furthermore, we use the molecular data to examine biogeographical patterns of the two families in the light of historical geological re-arrangements in the region. The results indicate that the Philippines were colonised in the Pliocene and that colonisation probably progressed via the Sulu islands from Borneo and not via Palawan, which was first colonised in the Pleistocene.
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Affiliation(s)
- Maria Moltesen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100 Copenhagen Ø, Denmark
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Abstract
BACKGROUND Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos. RESULTS This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows. CONCLUSIONS Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.
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Affiliation(s)
- Knud A Jønsson
- Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100, Copenhagen Ø, Denmark
| | - Pierre-Henri Fabre
- Center for Macroecology Evolution and Climate at the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken, 15, DK-2100, Copenhagen Ø, Denmark
| | - Martin Irestedt
- Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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