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  • 101. Müller, Johannes
    et al.
    Scheyer, Torsten M
    Head, Jason J
    Barrett, Paul M
    Werneburg, Ingmar
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pol, Diego
    Sánchez-Villagra, Marcelo R
    Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes.2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 5, p. 2118-23Article in journal (Refereed)
    Abstract [en]

    The development of distinct regions in the amniote vertebral column results from somite formation and Hox gene expression, with the adult morphology displaying remarkable variation among lineages. Mammalian regionalization is reportedly very conservative or even constrained, but there has been no study investigating vertebral count variation across Amniota as a whole, undermining attempts to understand the phylogenetic, ecological, and developmental factors affecting vertebral column variation. Here, we show that the mammalian (synapsid) and reptilian lineages show early in their evolutionary histories clear divergences in axial developmental plasticity, in terms of both regionalization and meristic change, with basal synapsids sharing the conserved axial configuration of crown mammals, and basal reptiles demonstrating the plasticity of extant taxa. We conducted a comprehensive survey of presacral vertebral counts across 436 recent and extinct amniote taxa. Vertebral counts were mapped onto a generalized amniote phylogeny as well as individual ingroup trees, and ancestral states were reconstructed by using squared-change parsimony. We also calculated the relationship between presacral and cervical numbers to infer the relative influence of homeotic effects and meristic changes and found no correlation between somitogenesis and Hox-mediated regionalization. Although conservatism in presacral numbers characterized early synapsid lineages, in some cases reptiles and synapsids exhibit the same developmental innovations in response to similar selective pressures. Conversely, increases in body mass are not coupled with meristic or homeotic changes, but mostly occur in concert with postembryonic somatic growth. Our study highlights the importance of fossils in large-scale investigations of evolutionary developmental processes.

  • 102. Norman, Janette A
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Jønsson, Knud A
    Fjeldså, Jon
    Christidis, Les
    A multi-gene phylogeny reveals novel relationships for aberrant genera of Australo-Papuan core Corvoidea and polyphyly of the Pachycephalidae and Psophodidae (Aves: Passeriformes).2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 52, no 2, p. 488-97Article in journal (Refereed)
    Abstract [en]

    The core Corvoidea is the largest and most diverse oscine assemblage within the Australo-Papuan region. Although central to an understanding of the evolutionary history and biogeography of the group the composition and intergeneric relationships of the Australo-Papuan radiation remain poorly understood. Here we analysed DNA sequence data from two nuclear gene regions and the mitochondrial cytochrome b gene, for 40 species of core Corvoidea to test the systematic affinities of key Australo-Papuan lineages. The families Pachycephalidae (whistlers, shrike-thrushes and allies) and Psophodidae (whipbirds, quail-thrush and allies) were both recovered as polyphyletic assemblages. The core pachycephaline assemblage comprised Pachycephala, Colluricincla, parts of Pitohui, and Falcunculus with the remaining genera resolving as four divergent lineages with no clearly defined affinities. Ptilorrhoa and Cinclosoma (Cinclosomatidae) formed a clade separate from Psophodes (Psophodidae) but neither clade showed clear affinities to any other taxa. Novel relationships were also identified for three aberrant New Guinean genera; ditypic Machaerirhynchus and monotypic Rhagologus were both nested within an assemblage that included the Artamidae and African malaconotoids (bush-shrikes and allies) while the enigmatic Ifrita was found to be part of an assemblage that included the Monarchidae and Paradisaeidae.

  • 103.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldsa, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A new genus for three species of tyrant flycatchers (Passeriformes: Tyrannidae), formerly placed in Myiophobus2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2290, p. 36-40Article in journal (Refereed)
  • 104.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular phylogeny of the manakins (Aves: Passeriformes2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, no 3, p. 796-804Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships within the manakin family (Pipridae) were investigated with sequence data from three nuclear introns and one mitochondrial protein-coding gene. This study confirms a sister group relationship between Neopelminae and Piprinae. We also find support for dividing the Piprinae into two principal clades: Ilicurini and Piprini. The genera Pipra and Chloropipo are found to be polyphyletic. Chloropipo species are placed in three different clades, including two species in an unresolved position alongside Ilicurini and Piprini. We propose a new classification of the family, where the most important modifications include recognizing the genus Ceratopipra for five species formerly placed in Pipra and the erection of a new genus for Chloropipo holochlora.

  • 105.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes)2008In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 3, p. 315-335Article in journal (Refereed)
    Abstract [en]

    Tyrant flycatchers constitute a substantial component of the land bird fauna in all South American habitats. Past interpretations of the morphological and ecological evolution in the group have been hampered by the lack of a well-resolved hypothesis of their phylogenetic interrelationships. Here, we present a well-resolved phylogeny based on DNA sequences from three nuclear introns for 128 taxa. Our results confirm much of the overall picture of Tyrannidae relationships, and also identify several novel relationships. The genera Onychorhynchus, Myiobius and Terenotriccus are placed outside Tyrannidae and may be more closely related to Tityridae. Tyrannidae consists of two main lineages. An expanded pipromorphine clade includes flatbills, tody-tyrants and antpipits, and also Phylloscartes and Pogonotriccus. The spadebills, Neopipo and Tachuris are their closest relatives. The remainder of the tyrant flycatchers forms a well-supported clade, subdivided in two large subclades, which differ consistently in foraging behaviour, the perch-gleaning elaeniines and the sallying myiarchines, tyrannines and fluvicolines. A third clade is formed by the genera Myiotriccus, Pyrrhomyias, Hirundinea and three species currently placed in Myiophobus. Ancestral habitat reconstruction and divergence date estimation suggest that early divergence events in Tyrannida took place in a humid forest environment during the Oligocene. Large-scale diversification in open habitats is confined to the clade consisting of the elaeniines, myiarchines, tyrannines and fluvicolines. This radiation correlates in time to the expansion of semi-open and open habitats from the mid-Miocene (c. 15 Mya) onwards. The pipromorphine, elaeniine and myiarchine–tyrannine–fluvicoline clades each employ distinct foraging strategies (upward striking, perch-gleaning and sallying, respectively), but the degree of diversity in morphology and microhabitat exploitation is markedly different between these clades. While the pipromorphines and elaeniines each are remarkably homogenous in morphology and exploit a restricted range of microhabitats, the myiarchine–tyrannine–fluvicoline clade is more diverse in these respects. This greater ecological diversity, especially as manifested in their success in colonizing a wider spectrum of open habitats, appears to be connected to a greater adaptive flexibility of the search-and-sally foraging behaviour.

  • 106.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fjeldså, Jon
    Phylogeny and classification of the New World suboscines (Aves, Passeriformes).2013In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 3613, p. 1-35Article in journal (Refereed)
    Abstract [en]

    Here we present a phylogenetic hypothesis for the New World suboscine radiation, based on a dataset comprising of 219 terminal taxa and five nuclear molecular markers (ca. 6300 bp). We also estimate ages of the main clades in this radiation. This study corroborates many of the recent insights into the phylogenetic relationships of New World suboscines. It further clarifies a number of cases for which previous studies have been inconclusive, such as the relationships of Conopophagidae, Melanopareiidae and Tityridae. We find a remarkable difference in age of the initial divergence events in Furnariida and Tyrannida. The deepest branches in Furnariida are of Eocene age, whereas the extant lineages of Tyrannida have their origin in the Oligocene. Approximately half of the New World suboscine species are harboured in 5 large clades that started to diversify around the Mid Miocene Climatic Optimum (16-12 Mya). Based on our phylogenetic results we propose a revised classification of the New World suboscines. We also erect new family or subfamily level taxa for four small and isolated clades: Berlepschiinae, Pipritidae, Tachurididae and Muscigrallinae.

  • 107.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldsa, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Nuclear DNA from a 180-year-old study skin reveals the phylogenetic position of the Kinglet Calyptura Calyptura cristata (Passeriformes: Tyrannides)2012In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 154, no 3, p. 533-541Article in journal (Refereed)
  • 108.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Prum, Richard O
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A molecular phylogeny of the cotingas (Aves: Cotingidae).2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 42, no 1, p. 25-37Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. <http://www.museum.lsu.edu/~Remsen/SACCBaseline.html>]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.

  • 109. Olson, Storrs L
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fjeldså, Jon
    Independent evolution of two Darwinian marsh-dwelling ovenbirds (Furnariidae: Limnornis, Limnoctites)2005In: Ornitologia Neotropical, ISSN 1075-4377, Vol. 16, p. 347-359Article in journal (Refereed)
    Abstract [en]

    The Curve-billed Reedhaunter (Limnornis curvirostris) and the Straight-billed Reedhaunter (Limnoctitesrectirostris) are marsh-dwelling ovenbirds that were first collected by Charles Darwin in Uruguay.Each has a limited distribution in southernmost Brazil, Uruguay, and northern Argentina, within which thebirds occupy very distinct habitats. Originally described as congeners because of overall similarity of plumage,the two species have been treated as close relatives through most of their history despite obviousstructural differences. We analyzed DNA sequences from three different genes of these species, comparingthem with a wide variety of other species of Furnariidae and several outgroup taxa. Limnoctites rectirostrisbelongs among the species traditionally placed in Cranioleuca, being most closely related to the marshdwellingSulphur-throated Spinetail (C. sulphurifera) among the species we sampled. This is supported byvocalizations and nidification. Limnornis curvirostris forms a clade with the Wren-like Rushbird (Phleocryptesmelanops), with the Sharp-tailed Streamcreeper (Lochmias nematura) as a rather distant sister-taxon. A closerelationship between Limnornis and Phleocryptes is supported by the apparently unique nest architecture andblue-green egg color.

  • 110. Olsson, Urban
    et al.
    Alström, Per
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sundberg, Per
    Non-monophyletic taxa and cryptic species--evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves).2005In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 36, no 2, p. 261-76Article in journal (Refereed)
    Abstract [en]

    The avian taxa Cryptigata and Acanthopneuste have been treated either as subgenera within Phylloscopus (leaf-warblers), or as a distinct genus and an informal group, respectively. The circumscriptions of these taxa have varied between authors. We estimated the phylogeny, based on the mitochondrial cytochrome b and 12S genes and the nuclear myoglobin intron II, of all except two of the species placed in the Cryptigata and Acanthopneuste groups, as well as two recently described species and representatives of all subgenera and major clades in Phylloscopus and Seicercus recognized by previous studies. Neither Cryptigata nor Acanthopneuste is found to be monophyletic. The polytypic species P. reguloides and P. davisoni show deep divergences between some of their respective subspecies, and the latter species is non-monophyletic. We propose that the former be split into three species and the latter into two species. Seicercus xanthoschistos is nested in a clade that includes only Phylloscopus, and we recommend that it be placed in Phylloscopus. The rate of morphological divergence varies considerably among the taxa in this study. Our results emphasize the importance of dense taxon sampling in intrageneric phylogenetic studies.

  • 111. Olsson, Urban
    et al.
    Alström, Per
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sundberg, Per
    Phylogeography of Indonesian and Sino-Himalayan region bush warblers (Cettia, Aves).2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 41, no 3, p. 556-65Article in journal (Refereed)
    Abstract [en]

    We present a hypothesis for the phylogeny and phylogeography of a group of bush warblers in the genus Cettia, based on parts of the mitochondrial Cytochrome b gene and the nuclear myoglobin intron II (in all approximately 1.7 kb). Ancestral areas were reconstructed by dispersal-vicariance analysis and constrained Bayesian inference. The results suggest that the insular taxa in the Cettia vulcania group are most closely related to Cettia flavolivacea, and originated from a dispersal by an ancestral population in the Himalayas towards the south, to the Sunda region. From this population, a second dispersal along a different route colonized China and northern Vietnam. Hence, the Chinese taxon intricata and Vietnamese oblita, currently allocated to C. flavolivacea, are more closely related to the vulcania group than to the other taxa in the flavolivacea group, and we propose that they be treated as conspecific with C. vulcania, restricting C. flavolivacea to Myanmar and the Himalayas.

  • 112. Olsson, Urban
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sangster, George
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Alström, Per
    Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera.2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 66, no 3, p. 790-9Article in journal (Refereed)
    Abstract [en]

    The avian taxon Cisticolidae includes c. 110 species which are distributed throughout the tropical and subtropical parts of the Old World. We estimated the phylogeny of 47 species representing all genera assumed to be part of Cisticolidae based on sequence data from two mitochondrial and two nuclear markers, in total 3495bp. Bayesian inference and maximum likelihood analyses resulted in a generally well-supported phylogeny which clarified the position of several previously poorly known taxa. The placement of Drymocichla, Malcorus, Micromacronus, Oreophilais, Phragmacia, Phyllolais, Poliolais and Urorhipis in Cisticolidae is corroborated, whereas Rhopophilus and Scotocerca are removed from Cisticolidae. Urorhipis and Heliolais are placed in the genus Prinia whereas Prinia burnesii is shown to be part of Timaliidae, and is placed in the genus Laticilla. Although not recovered by all single loci independently, four major clades were identified within Cisticolidae, and one of these is here described as a new taxon (Neomixinae).

  • 113. Olsson, Urban
    et al.
    Sundberg, Per
    Alström, Per
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    What is proper vouchering in phylogenetic studies of birds?--a reply to Peterson et al. (2007).2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 383-5Article in journal (Refereed)
  • 114. Paśko, Łukasz
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Elzanowski, Andrzej
    Phylogenetic utility and evolution of indels: a study in neognathous birds.2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 61, no 3, p. 760-71Article in journal (Refereed)
    Abstract [en]

    Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.

  • 115.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lei, Fu Min
    Li, Shou Hsien
    Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis.2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 6, p. 1767-81Article in journal (Refereed)
    Abstract [en]

    Most phylogeographical studies of postglacial colonization focus on high latitude locations in the Northern Hemisphere. Here, we studied the phylogeographical structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analysed 879 base pairs (bp) of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h = 0.94); nucleotide diversity was low (eth = 0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07-0.19 million years ago (Ma). Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5-0.175 Ma), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the post-glacial phylogeographical structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semicontinuous and thus promoting population mixing.

  • 116.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lei, Fumin
    Gebauer, Axel
    Kaiser, Martin
    Helbig, Andreas J
    Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, no 1, p. 218-26Article in journal (Refereed)
    Abstract [en]

    The snow finch complex (Montifringilla, Pyrgilauda, and Onychostruthus) has its center of distribution on the Tibetan plateau, with six out of seven species in the genera occurring there. Phylogenetic relationships among these six species of three genera have been studied based on DNA sequence data obtained from the mitochondrial cytochrome b gene and the nuclear myoglobin gene. The results support monophyly of the snow finch complex group and three major evolutionary lineages are recognized. The first clade consists of ruficollis, blanfordi, and davidiana. These three taxa are sometimes placed in their own genus, Pyrgilauda, and the DNA data supports this. The three taxa nivalis, henrici, and adamsi have traditionally been placed in the genus Montifringilla, and they group together strongly in the present analysis. The results further suggest that nivalis and adamsi are more closely related to each other than are nivalis and henrici, despite that the latter two are often regarded as conspecific. The third distinct lineage within the snow finch complex consists of taczanowskii, which has been placed its own genus, Onychostruthus. This taxon has a basal position in the phylogenetic tree and is sister to all other snow finches. We estimated that taczanowskii split from the other taxa between 2 and 2.5 mya, i.e., about the time for the most recent uplift of the Tibetan plateau, "the Tibet movement", 3.6-1.7 mya. Cladogenesis within the Montifringilla and Pyrgilauda clades seems to be contemporary with the second phase of "Tibet movement" at 2.5 mya and the third phase at 1.7 mya and "Kunhuang movement" in 1.5-0.6 mya. The dramatic climatic and ecological changes following from the uplift of the Tibetan plateau, together with the cyclic contraction and expansion of suitable habitats during the Pleistocene, are probably the most important factors for the cladogenesis in snow finch complex.

  • 117.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Quan, Qing
    Song, Gang
    Zhang, Ruiying
    Gao, Bin
    Lei, Fumin
    Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya.2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 3, p. 705-20Article in journal (Refereed)
    Abstract [en]

    China's Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3-0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.

  • 118.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Song, Gang
    Gao, Bin
    Quan, Qing
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lei, Fumin
    The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 1, p. 179-192Article in journal (Refereed)
    Abstract [en]

    Aim: East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps).

    Location: East Asia.

    Methods: We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits.

    Results: The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages.

    Main conclusions: Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations,allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China, thus obscuring the genetic endemism of the Taiwanese populations.

  • 119.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Tian, Shilin
    Han, Nanjian
    Zhao, Hongwei
    Gao, Bin
    Fu, Jun
    Cheng, Yalin
    Song, Gang
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zhang, Yong E.
    Wang, Dawei
    Quan, Qing
    Jiang, Zhi
    Li, Ruiquang
    Lei, Fumin
    Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas2015In: Scientific Reports, E-ISSN 2045-2322, Vol. 5, article id 14256Article in journal (Refereed)
    Abstract [en]

    Species that undertake altitudinal migrations are exposed to a considerable seasonal variationin oxygen levels and temperature. How they cope with this was studied in a population of greattit (Parus major) that breeds at high elevations and winters at lower elevations in the easternHimalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (aminosugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR andMAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategiesobserved in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectionin lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparativepopulation genomics also revealed selection for larger body size in high altitudinal great tits.

  • 120.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Zhao, Hongwei
    Han, Naijian
    Zhou, Guangyu
    Song, Gang
    Gao, Bin
    Tian, Shilin
    Zhang, Jinbo
    Zhang, Ruiying
    Meng, Xuehong
    Zhang, Yuan
    Zhang, Yong
    Zhu, Xiaojia
    Wang, Wenjuan
    Lambert, David
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Subramanian, Sankar
    Yeung, Carol
    Zhu, Hongmei
    Jiang, Zhi
    Li, Ruiqiang
    Lei, Fumin
    Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.2013In: Nature communications, ISSN 2041-1723, Vol. 4, p. 2071-Article in journal (Refereed)
    Abstract [en]

    The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.

  • 121.
    Razafimandimbison, Sylvain
    et al.
    Swedish Museum of Natural History, Department of Botany. Swedish Museum of Natural History, Research Division.
    Kainulainen, Kent
    De Block, Petra
    Rubiaceae of Madagascar: progress since 20032022In: The new Natural History of Madagascar / [ed] S. Goodman, USA: Princeton University Press, 2022, p. 744-752Chapter in book (Other academic)
  • 122.
    Razafimandimbison, Sylvain
    et al.
    Swedish Museum of Natural History, Department of Botany. Swedish Museum of Natural History, Research Division.
    Wikström, Niklas
    Khodabandeh, Anbar
    Rydin, Catarina
    Phylogeny of the Madagascar-centred tribe Danaideae (Rubiaceae) as a precursor of taxonomic revision: insights into its generic and species limits, affinities and distribution2022In: Annals of Botany, Vol. 130, p. 849-867Article in journal (Refereed)
    Abstract [en]

    Background and aims The tribe Danaideae (Rubiaceae) is almost

    exclusively endemic to the Western Indian Ocean Region (WIOR), encompassing the

    genera Danais, Payera and Schismatoclada that occur in humid and sub-humid

    climates. Much of the species diversity is endemic to restricted, remote and/or

    mountainous areas of the WIOR, and recent field work on Madagascar indicates

    substantial unknown diversity of the Danaideae. Further, the monophyly of the

    Malagasy genera Payera and Schismatoclada has been questioned in previous work,

    species delimitations and phylogenetic relationships within the genera are poorly

    understood, and distribution and evolution of gross morphological features have not

    been assessed.

    Methods We conducted morphological investigations, and produced robust

    phylogenies of Danaideae based on nuclear and plastid sequence data from 193

    terminals. Ample plant material has been newly collected in the WIOR for the

    purpose of the present study, including potentially new species unknown to science.

    We performed Bayesian non-clock and relaxed-clock analyses employing three

    alternative clock models of a dataset with a dense sample of taxa from the entire

    geographic ranges of Danaideae. Based on the results, we discuss species diversity

    and distribution, relationships, and morphology in Danaideae.

    Key results Our results demonstrate the monophyly of Danaideae, its three

    genera, and 43 species. Nine species are resolved as non-monophyletic. Many

    geographically distinct but morphologically heterogeneous lineages were identified,

    and morphological features traditionally considered diagnostic of subgroups of the

    genera, used e.g. in species identification keys, are not clade-specific.

    Conclusions Our results demonstrate that Madagascar contains ample hereto

    undocumented morphological and species diversity of Danaideae. Our novel approach

    to perform molecular phylogenetic analyses as a precursor to taxonomic revisions

    provides numerous benefits for the latter. There are tentative indications of parallel

    northward diversification in Payera and Schismatoclada on Madagascar, and of

    geographic phylogenetic clustering despite the anemochorous condition of Danaideae

  • 123.
    Sangster, George
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Roselaar, Cees S.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G. P.
    Swedish Museum of Natural History, Research Division.
    Sillem’s Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Carpodacus, Fringillidae)2016In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 158, no 1, p. 184-189Article in journal (Refereed)
  • 124. Sodhi, Navjot S.
    et al.
    Astuti, Dwi
    Diesmos, Arvin C.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fernandopulle, Neil
    Kotagama, Sarath
    Kudavidanege, Enoka
    Lim, Haw Chuan
    Lee, Benjamin
    Lim, Susan L. H.
    Lin, Yangchen
    Lohman, David J.
    Meckvichai, Wina
    Miranda, Hector
    Moyle, Robert G.
    Ong, Perry
    Pan, Khang Aun
    Prawiradilaga, Dewi
    Rahman, Mustafa Abdul
    Rahmani, Asad
    Sheldon, Frederick H.
    Stoeckle, Mark Y.
    Sulandari, Sri
    Wang, Luan Keng
    Winker, Kevin
    Barcoding Indo-Malayan birds2007In: The Raffles bulletin of zoology, ISSN 0217-2445, Vol. 55, no 2, p. 397-398Article in journal (Other academic)
  • 125. Song, Gang
    et al.
    Zhang, Ruiying
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Wang, Zhiheng
    Kristin, Anton
    Alström, Per
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lambert, David M
    Fjeldså, Jon
    Lei, Fumin
    A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China2016In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 43, p. 2099-2112Article in journal (Refereed)
    Abstract [en]

    Aim.The location of zoogeographical boundaries in eastern China has longbeen the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China.Location. Eastern China.Methods.Two mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny,tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods.Results. A congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c.40°N in easternChina. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene.Main conclusions. Our results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.

  • 126. Sundberg, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bachmann, Lutz
    Zoologica Scripta in the dynamic field of systematics2013In: Zoologica Scripta, Vol. 42, no 6, p. 551-552Article in journal (Other academic)
  • 127. Sundberg, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bachmann, Lutz
    Slagsvold, Tore
    Jacobson, Carl-Olof
    Untitled2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 3, p. 229-230Article in journal (Other academic)
  • 128. Taylor, Charlotte
    et al.
    Razafimandimbison, Sylvain
    Swedish Museum of Natural History, Department of Botany. Swedish Museum of Natural History, Research Division.
    Psychotrieae alliance and some related groups (subfamily Rubioideae)2022In: The new Natural History of Madagascar / [ed] S. Goodman, USA: Princeton University Press, 2022, p. 765-769Chapter in book (Other academic)
  • 129. Thureborn, Olle
    et al.
    Razafimandimbison, Sylvain
    Swedish Museum of Natural History, Department of Botany. Swedish Museum of Natural History, Research Division.
    Rydin, Catarina
    Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)2022In: Frontiers in Plant ScienceArticle in journal (Refereed)
    Abstract [en]

    Subfamily Rubioideae is the largest of the main lineages in the coffee family

    (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships

    among tribes and other major clades within this group of plants are still

    only partly resolved despite considerable efforts. While previous studies have

    mainly utilized data from the organellar genomes and nuclear ribosomal DNA,

    we here use a large number of low-copy nuclear genes obtained via a target

    capture approach to infer phylogenetic relationships within Rubioideae. We

    included 101 Rubioideae species representing all but two (the monogeneric

    tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes,

    and all but one non-monogeneric tribe were represented by more than

    one genus. Using data from the 353 genes targeted with the universal

    Angiosperms353 probe set we investigated the impact of data type, analytical

    approach, and potential paralogs on phylogenetic reconstruction. We inferred

    a robust phylogenetic hypothesis of Rubioideae with the vast majority (or

    all) nodes being highly supported across all analyses and datasets and few

    incongruences between the inferred topologies. The results were similar to

    those of previous studies but novel relationships were also identified. We

    found that supercontigs [coding sequence (CDS) C non-coding sequence]

    clearly outperformed CDS data in levels of support and gene tree congruence.

    The full datasets (353 genes) outperformed the datasets with potentially

    paralogous genes removed (186 genes) in levels of support but increased

    gene tree incongruence slightly. The pattern of gene tree conflict at short

    internal branches were often consistent with high levels of incomplete lineage

    sorting (ILS) due to rapid speciation in the group. While concatenationand

    coalescence-based trees mainly agreed, the observed phylogenetic

    discordance between the two approaches may be best explained by

    their differences in accounting for ILS. The use of target capture data 

    greatly improved our confidence and understanding of the Rubioideae

    phylogeny, highlighted by the increased support for previously uncertain

    relationships and the increased possibility to explore sources of underlying

    phylogenetic discordance.

    Download (pdf)
    Rubioideae
  • 130. Zhang, Fucheng
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zhou, Zhonghe
    Description of a new enantiornithine bird from the Early Cretaceous of Hebei, northern China2004In: Canadian journal of earth sciences (Print), ISSN 0008-4077, E-ISSN 1480-3313, Vol. 41, no 9, p. 1097-1107Article in journal (Refereed)
    Abstract [en]

    This paper describes a new enantiornithine fossil bird, Vescornis hebeiensis, nov. sp. from the Early Cretaceous of China. We refer Vescornis to the crown clade Euenantiornithes based on several characteristics observed in the thoracic girdle and wing. Vescornis also exhibits characteristics that separate it from other enantiornithine birds, such as the short alular phalanx, the vestigial manual claws, and the well-developed and long foot claws. These features suggest an adaptation towards an improved flight capability, while the ability of Vescornis to climb is reduced compared with many other enantiornithine birds.

  • 131. Zhang, Ruiying
    et al.
    Song, Gang
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Alström, Per
    Ramos, Raül
    Xing, Xiaoying
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fjeldså, Jon
    Wang, Haitao
    Yang, Xiaojun
    Kristin, Anton
    Shestopalov, Alexander M
    Choe, Jae Chun
    Lei, Fumin
    Comparative phylogeography of two widespread magpies: importance of habitat preference and breeding behavior on genetic structure in China.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 2, p. 562-72Article in journal (Refereed)
    Abstract [en]

    Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and perhaps also breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.

  • 132. Zuccon, Dario
    et al.
    Cibois, Alice
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 41, no 2, p. 333-44Article in journal (Refereed)
    Abstract [en]

    We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group.

  • 133.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A multi-gene phylogeny disentangles the chat-flycatcher complex (Aves: Muscicapidae)2010In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 39, no 3, p. 213-224Article in journal (Refereed)
  • 134. Zuccon, Dario
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular and morphological evidences place the extinct New Zealand endemic Turnagra capensis in the Oriolidae.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 62, no 1, p. 414-26Article in journal (Refereed)
    Abstract [en]

    The affinities of Piopio Turnagra capensis, an extinct New Zealand passerine, remain poorly known. It has been included into or associated with several bird families (Calleatidae, Cracticidae, Pachycephalidae, Ptilonorhynchidae, Turdidae), often on tenuous grounds. We reassessed Turnagra phylogenetic relationships using nuclear and mitochondrial sequences and a set of morphological and behavioural traits. Molecular and phenotypic characters strongly suggest a novel hypothesis, congruently placing Turnagra in Oriolidae, a highly dispersive corvoid family distributed from the Austro-Papuan landmass to Eurasia and Africa, but missing from the Pacific islands. We show also that the published molecular support to link Turnagra with Ptilonorhynchidae was biased by the use of incorrect genetic data and weak analyses.

  • 135. Zuccon, Dario
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The Monticola rock-thrushes: phylogeny and biogeography revisited.2010In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 3, p. 901-10Article in journal (Refereed)
    Abstract [en]

    We investigated the phylogenetic relationships within the Monticola rock-thrushes, an open-habitat genus inhabiting a large part of the Old World. Our results support one Oriental clade and one clade including African, Malagasy and Eurasian taxa. The biogeographic reconstruction obtained with the dispersal-vicariance analysis suggested Southern Africa plus Palearctic as the Monticola ancestral area. Our phylogenetic hypothesis suggests also some taxonomic changes. The polytypic Monticola solitarius includes two reciprocally monophyletic clades that should be recognized as full species, M. solitarius s.s. and M. philippensis. With the exclusion of the south-western population, M. imerinus, all other Malagasy rock-thrush populations should be merged in the monotypic, albeit polymorphic, M. sharpei. The genus Thamnolaea is shown to be non-monophyletic, with T. semirufa being part of the Monticola radiation, while T. cinnamomeiventris is related to other chat species inhabiting open-habitats. We demonstrate that a previous phylogenetic hypothesis for the rock-thrushes was flawed by the inclusion of contaminated sequences obtained from study-skins and we suggest some working guidelines to improve the reliability of the sequences obtained from old or degraded DNA.

  • 136.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The phylogenetic position of the Black-collared Bulbul Neolestes torquatus2010In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 152, no 2, p. 386-392Article in journal (Refereed)
  • 137.
    Zuccon, Dario
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogenetic relationships among Palearctic-Oriental starlings and mynas (genera Sturnus and Acridotheres: Sturnidae)2008In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 5, p. 469-481Article in journal (Refereed)
  • 138. Zuccon, Dario
    et al.
    Prŷs-Jones, Robert
    Rasmussen, Pamela C
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The phylogenetic relationships and generic limits of finches (Fringillidae).2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 62, no 2, p. 581-96Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.

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