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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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2
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Kersten O, Star B, Krabberød AK, Atmore LM, Tørresen OK, Anker-Nilssen T, Descamps S, Strøm H, Johansson US, Sweet PR, Jakobsen KS, Boessenkool S. Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. Sci Adv 2023; 9:eadh1407. [PMID: 37801495 PMCID: PMC10558128 DOI: 10.1126/sciadv.adh1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
The Arctic is experiencing the fastest rates of global warming, leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidence of recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins (Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F. a. naumanni and the temperate, smaller-sized subspecies F. a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F. a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations. Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.
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Affiliation(s)
- Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Anders K. Krabberød
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - Hallvard Strøm
- Norwegian Polar Institute, Fram Centre, Langnes, Tromsø, Norway
| | | | - Paul R. Sweet
- American Museum of Natural History, New York, NY, USA
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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Cheng Y, Miller MJ, Zhang D, Xiong Y, Hao Y, Jia C, Cai T, Li SH, Johansson US, Liu Y, Chang Y, Song G, Qu Y, Lei F. Parallel genomic responses to historical climate change and high elevation in East Asian songbirds. Proc Natl Acad Sci U S A 2021; 118:e2023918118. [PMID: 34873033 PMCID: PMC8685689 DOI: 10.1073/pnas.2023918118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Accepted: 10/23/2021] [Indexed: 12/01/2022] Open
Abstract
Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Matthew J Miller
- Reneco International Wildlife Consultants, LLC, Abu Dhabi, UAE
- University of Alaska Museum, University of Alaska Fairbanks, AK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
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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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Cappellini E, Gentry A, Palkopoulou E, Ishida Y, Cram D, Roos AM, Watson M, Johansson US, Fernholm B, Agnelli P, Barbagli F, Littlewood DTJ, Kelstrup CD, Olsen JV, Lister AM, Roca AL, Dalén L, Gilbert MTP. Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae). Zool J Linn Soc 2014. [DOI: 10.1111/zoj12084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Anthea Gentry
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691, Stockholm, Sweden
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - David Cram
- Jesus College, Turl Street, Oxford, OX1 3DW, UK
| | - Anna-Marie Roos
- Lincoln School of Humanities, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Mick Watson
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Ulf S. Johansson
- Department of Zoology, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Bo Fernholm
- Department of Zoology, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Paolo Agnelli
- Natural History Museum of Florence, via Romana 17, 50125, Florence, Italy
| | - Fausto Barbagli
- Natural History Museum of Florence, via Romana 17, 50125, Florence, Italy
| | | | - Christian D. Kelstrup
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark
| | | | - Alfred L. Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
- Ancient DNA Laboratory, Murdoch University, South St, Perth, Western Australia, 6150, Australia
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Johansson US, Ekman J, Bowie RC, Halvarsson P, Ohlson JI, Price TD, Ericson PG. A complete multilocus species phylogeny of the tits and chickadees (Aves: Paridae). Mol Phylogenet Evol 2013; 69:852-60. [DOI: 10.1016/j.ympev.2013.06.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/19/2013] [Accepted: 06/25/2013] [Indexed: 11/28/2022]
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Cappellini E, Gentry A, Palkopoulou E, Ishida Y, Cram D, Roos AM, Watson M, Johansson US, Fernholm B, Agnelli P, Barbagli F, Littlewood DTJ, Kelstrup CD, Olsen JV, Lister AM, Roca AL, Dalén L, Gilbert MTP. Resolution of the type material of the Asian elephant,Elephas maximusLinnaeus, 1758 (Proboscidea, Elephantidae). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Anthea Gentry
- Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
- Department of Zoology; Stockholm University; SE-10691 Stockholm Sweden
| | - Yasuko Ishida
- Department of Animal Sciences; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - David Cram
- Jesus College; Turl Street Oxford OX1 3DW UK
| | - Anna-Marie Roos
- Lincoln School of Humanities; University of Lincoln; Brayford Pool Lincoln LN6 7TS UK
| | - Mick Watson
- The Roslin Institute; University of Edinburgh; Midlothian EH25 9RG UK
| | - Ulf S. Johansson
- Department of Zoology; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
| | - Bo Fernholm
- Department of Zoology; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
| | - Paolo Agnelli
- Natural History Museum of Florence; via Romana 17 50125 Florence Italy
| | - Fausto Barbagli
- Natural History Museum of Florence; via Romana 17 50125 Florence Italy
| | | | - Christian D. Kelstrup
- Novo Nordisk Foundation Center for Protein Research; Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research; Faculty of Health Sciences; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | | | - Alfred L. Roca
- Department of Animal Sciences; University of Illinois at Urbana-Champaign; Urbana Illinois 61801 USA
| | - Love Dalén
- Department of Bioinformatics and Genetics; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
- Ancient DNA Laboratory; Murdoch University; South St Perth Western Australia 6150 Australia
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Kuhn K, Schwenk K, Both C, Canal D, Johansson US, van der Mije S, Töpfer T, Päckert M. Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change. Ecol Evol 2013; 3:4799-814. [PMID: 24363905 PMCID: PMC3867912 DOI: 10.1002/ece3.855] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 11/11/2022] Open
Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
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Affiliation(s)
- Kerstin Kuhn
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Ecology and Evolution, Johann Wolfgang Goethe-UniversitätMax-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Institute of Environmental Sciences, University of Koblenz-LandauFortstraße 7, Landau in der Pfalz, 76829, Germany
| | - Christiaan Both
- Centre for Ecological and Evolutionary Studies (CEES), University of GroningenPO Box 11103, Groningen, 9700 CC, The Netherlands
| | - David Canal
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSICAv. Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural HistoryPO Box 50007, Stockholm, SE 10405, Sweden
| | | | - Till Töpfer
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| | - Martin Päckert
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
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Yamaguchi N, Driscoll CA, Werdelin L, Abramov AV, Csorba G, Cuisin J, Fernholm B, Hiermeier M, Hills D, Hunter L, Itakura H, Johansson US, Kascheev V, Krohmann K, Martin T, Nowak-Kemp M, Pavlinov IY, Renoud F, Tomsett L, Mije SVD, Zholnerovskaya E, Groves C, Kitchener AC, Nijman V, Macdonald DW. Locating Specimens of Extinct Tiger (Panthera tigris) Subspecies: Javan Tiger (P. T. sondaica), Balinese Tiger (P. T. balica), and Caspian Tiger (P. T. virgata), Including Previously Unpublished Specimens. Mammal Study 2013. [DOI: 10.3106/041.038.0307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
The New Zealand Thrush, or Piopio, is an extinct passerine that was endemic to New Zealand. It has often been placed in its own family (Turnagridae), unresolved relative to other passerines, but affinities with thrushes, Australaian magpies, manucodes, whistlers, birds-of-paradise and bowerbirds has been suggested based on morphological data. An affinity with the bowerbirds was also indicated in an early molecular study, but low statistical support make this association uncertain. In this study we use sequence data from three nuclear introns to examine the phylogenetic relationships of the piopios. All three genes independently indicate an oriole (Oriolidae) affinity of the piopios, and the monophyly of the typical orioles (Oriolus), figbirds (Sphecotheres), and the piopios is strongly supported in the Bayesian analysis of the concatenated data set (posterior probability = 1.0). The exact placement of the piopios within Oriolidae is, however, more uncertain but in the combined analysis and in two of the gene trees the piopios are placed basal to the typical orioles while the third gene suggest a sister relationship with the figbirds. This is the first time an oriole affinity has been proposed for the piopios. Divergence time estimates for the orioles suggest that the clade originated ca 20 million years ago, and based on these estimates it is evident that the piopios must have arrived on New Zealand by dispersal across the Tasman Sea and not as a result of vicariance when New Zealand separated from Gondwana in the late Cretaceous.
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Affiliation(s)
- Ulf S Johansson
- Department of Vertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden.
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11
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Johansson US, Bowie RCK, Hackett SJ, Schulenberg TS. The phylogenetic affinities of Crossley's babbler (Mystacornis crossleyi): adding a new niche to the vanga radiation of Madagascar. Biol Lett 2009; 4:677-80. [PMID: 18832056 DOI: 10.1098/rsbl.2008.0444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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
Crossley's babbler (Mystacornis crossleyi) is a passerine endemic to Madagascar. Traditionally, it has been classified as a babbler (Timaliidae), although affinities with warblers and vangas have been suggested. We investigated the phylogenetic affinities of Crossley's babbler using sequence data from two nuclear introns (myoglobin intron 2 and beta-fibrinogen intron 5) and one mitochondrial gene (ND2). We present for the first time (to our knowledge) a molecular phylogeny that confidently places this enigmatic species within the vangas (Vangidae). The inclusion of Crossley's babbler within the vangas adds another foraging niche--gleaning small invertebrates from the ground-to this already large adaptive radiation of songbirds.
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Affiliation(s)
- Ulf S Johansson
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute, University of Cape Town, Rondebosch 77014, Cape Town, South Africa.
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12
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Johansson US, Fjeldså J, Bowie RC. Phylogenetic relationships within Passerida (Aves: Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers. Mol Phylogenet Evol 2008; 48:858-76. [DOI: 10.1016/j.ympev.2008.05.029] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 05/05/2008] [Accepted: 05/22/2008] [Indexed: 10/22/2022]
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Johansson US, Fjeldså J, Lokugalappatti LGS, Bowie RCK. A nuclear DNA phylogeny and proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae). ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00290.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Johansson US, Alström P, Olsson U, Ericson PGP, Sundberg P, Price TD. Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers. Evolution 2007; 61:324-33. [PMID: 17348943 DOI: 10.1111/j.1558-5646.2007.00024.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Himalayan mountain range is one of the most species-rich areas in the world, harboring about 8% of the world's bird species. In this study, we compare the relative importance of immigration versus in situ speciation to the build-up of the Himalayan avifauna, by evaluating the biogeographic history of the Phylloscopus/Seicercus warblers, a speciose clade that is well represented in Himalayan forests. We use a comprehensive, multigene phylogeny in conjunction with dispersal-vicariance analysis to discern patterns of speciation and dispersal within this clade. The results indicate that virtually no speciation has occurred within the Himalayas. Instead, several speciation events are attributed to dispersal into the Himalayas followed by vicariance between the Himalayas and China/Southeast Asia. Most, perhaps all, of these events appear to be pre-Pleistocene. The apparent lack of speciation within the Himalayas stands in contrast to the mountain-driven Pleistocene speciation suggested for the Andes and the East African mountains.
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Affiliation(s)
- Ulf S Johansson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th St., Chicago, Illinois 60637, USA.
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Ericson PGP, Anderson CL, Britton T, Elzanowski A, Johansson US, Källersjö M, Ohlson JI, Parsons TJ, Zuccon D, Mayr G. Diversification of Neoaves: integration of molecular sequence data and fossils. Biol Lett 2006; 2:543-7. [PMID: 17148284 PMCID: PMC1834003 DOI: 10.1098/rsbl.2006.0523] [Citation(s) in RCA: 368] [Impact Index Per Article: 20.4] [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: 05/30/2006] [Accepted: 07/06/2006] [Indexed: 11/12/2022] Open
Abstract
Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.
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Affiliation(s)
- Per G P Ericson
- Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural History, PO Box 50007, 10405 Stockholm, Sweden.
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Ericson PGP, Zuccon D, Ohlson JI, Johansson US, Alvarenga H, Prum RO. Higher-level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannida). Mol Phylogenet Evol 2006; 40:471-83. [PMID: 16678446 DOI: 10.1016/j.ympev.2006.03.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [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: 11/16/2005] [Revised: 03/08/2006] [Accepted: 03/29/2006] [Indexed: 10/24/2022]
Abstract
Despite increased understanding of higher-level relationships in passerine birds in the last 15 years, the taxonomic boundaries and phylogenetic interrelationships of the major groups of the Tyrannida (including the cotingas, manakins, tityrines, and tyrant flycatchers) remain unclear. Here, we present an analysis of DNA sequence data obtained from two nuclear exons, three introns, and one mitochondrial gene for 26 genera of Tyrannida and 6 tracheophone outgroups. The analysis resulted in well-supported hypotheses about the earliest evolution within Tyrannida. The Cotingidae, Pipridae, Tityrinae (sensu) [Prum, R.O., Rice, N.H., Mobley, J.A., Dimmick, W.W., 2000. A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 117, 236-241], Tyrannidae, and the tyrannid subfamiles Tyranninae and Pipromorphinae (sensu) [Sibley, C.G., Monroe, B. L. Jr., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT] were all found to be reciprocally monophyletic (given the present taxon sampling). The Cotingidae and Pipridae form a clade that is the sister group to a well-supported clade including Oxyruncus, the Tityrinae, Piprites, and the Tyrannidae. Oxyruncus is the sister group to the Tityrinae, and Piprites is placed as the sister group to the Tyrannidae. The tyrannid subfamilies Tyranninae and Pipromorphinae are monophyletic sister taxa, but the relationships of Platyrinchus mystaceus to these two clades remains ambiguous. The presence of medial (=internal) cartilages in the syrinx is a synapomorphy for the Oxyruncus-Tityrinae-Piprites-Tyrannidae clade. Although morphological synapomorphies currently support the monophyly of both the Pipridae and the Cotingidae, convergences and/or reversals in morphological character states are common in Tyrannida. The relationship between Oxyruncus and the Tityrinae is congruent with additional syringeal synapomorphies and allozyme distance data. Accordingly, we propose the recognition the family Tityridae within the Tyrannida to include the genera Schiffornis, Laniisoma, Laniocera, Iodopleura, Xenopsaris, Pachyramphus, Tityra, and Oxyruncus.
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Affiliation(s)
- Per G P Ericson
- Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
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17
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Abstract
Passerine birds are very plastic in their adaptations, which has made it difficult to define phylogenetic lineages and correctly allocate all species to these. Sapayoa aenigma, a member of the large group of New World flycatchers, has been difficult to place, and DNA-DNA hybridization experiments have indicated that it may have been misplaced. This is confirmed here, as base sequencing of two nuclear genes places it as a deep branch in the group of broadbills and pittas of the Old World tropics. The peculiar distribution of this lineage may be best explained in terms of a Gondwanic and Late Cretaceous origin of the passerine birds, as this particular lineage dispersed from the Antarctic landmass, reaching the Old World tropics via the drifting Indian plate, and South America via the West Antarctic Peninsula.
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Affiliation(s)
- Jon Fjeldså
- Zoological Museum, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Abstract
Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.
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Affiliation(s)
- Per G P Ericson
- Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural History, Frescativagen 44, P.O. Box 50007, SE-10405 Stockholm, Sweden.
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Abstract
Based on their highly specialized "tracheophone" syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos), and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1, and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. The results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, but several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic and that Sclerurus is the sister taxon to an ovenbird-woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent.
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Affiliation(s)
- Martin Irestedt
- Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden.
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Ericson PGP, Christidis L, Cooper A, Irestedt M, Jackson J, Johansson US, Norman JA. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc Biol Sci 2002; 269:235-41. [PMID: 11839192 PMCID: PMC1690883 DOI: 10.1098/rspb.2001.1877] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.
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Affiliation(s)
- Per G P Ericson
- Department of Vertebrate Zoology and Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden.
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Ericson PGP, Johansson US, Parsons TJ. Major Divisions in Oscines Revealed by Insertions in the Nuclear Gene c-myc: A Novel Gene in Avian Phylogenetics. ACTA ACUST UNITED AC 2000. [DOI: 10.1093/auk/117.4.1069] [Citation(s) in RCA: 6] [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: 11/14/2022]
Affiliation(s)
- Per G. P. Ericson
- Department of Vertebrate Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Ulf S. Johansson
- Department of Vertebrate Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Department of Zoology, University of Stockholm, SE-106 91 Stockholm, Sweden
| | - Thomas J. Parsons
- U.S. Armed Forces DNA Identification Laboratory, Armed Forces Institute for Pathology, 1413 Research Boulevard, Rockville, Maryland 20850, USA
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