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  • 1. Black, Andrew B.
    et al.
    Jansen, Justin J.F.
    Frahnert, Sylke
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Provisional identification of historical grasswren(Amytornis: Maluridae) specimens in European collectionsdraws attention to the incomplete phylogeny of the group2019In: Bulletin of the British Ornithologists' Club, ISSN 0007-1595, Vol. 139, no 3, p. 228-237Article in journal (Refereed)
    Abstract [en]

    The phylogeny and systematics of grasswrens Amytornis species areincompletely resolved, in particular for three widely distributed members ofthe genus. In part this is a consequence of the dispersal to European and NorthAmerican collections of early specimens of now extinct populations. We describethree historical grasswren specimens from museums in Berlin and Stockholm, all ofwhich represent taxa for which phylogenetic and / or other data are incomplete. Wefurther identify other specimens that might contribute towards greater resolutionof grasswren phylogeny.

  • 2. Cappellini, Enrico
    et al.
    Gentry, Anthea
    Palkopoulou, Eleftheria
    Ishida, Yasuko
    Cram, David
    Roos, Anna-Marie
    Watson, Mick
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Fernholm, Bo
    Swedish Museum of Natural History, Department of Zoology.
    Agnelli, Paolo
    Barbagli, Fausto
    Littlewood, D. Tim. J.
    Kelstrup, Christian D.
    Olsen, Jesper V.
    Lister, Adrian M.
    Roca, Alfred L.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)2014In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 170, p. 222-232Article in journal (Refereed)
  • 3.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Anderson, Cajsa L
    Britton, Tom
    Elzanowski, Andrzej
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Källersjö, Mari
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Parsons, Thomas J
    Zuccon, Dario
    Mayr, Gerald
    Diversification of Neoaves: integration of molecular sequence data and fossils.2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 543-7Article in journal (Refereed)
    Abstract [en]

    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.

  • 4.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Cooper, Alan
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jackson, Jennifer
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Norman, Janette A
    A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens.2002In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 269, no 1488, p. 235-41Article in journal (Refereed)
    Abstract [en]

    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.

  • 5.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Evolution, biogeography, and patterns of diversification in passerine birds2003In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 34, no 1, p. 3-15Article in journal (Refereed)
    Abstract [en]

    This paper summarizes and discusses the many new insights into passerine evolution gained from an increased general interest in avian evolution among biologists, and particularly from the extensive use of DNA sequence data in phylogenetic reconstruction. The sister group relationship between the New Zealand rifleman and all other passerines, indicates the importance of the former southern supercontinent Gondwana in the earliest evolution of this group. Following the break-up of Gondwana, the ancestors of other major passerine groups became isolated in Australia (oscines), South America (New World suboscines), and possibly, the then connected Kerguelen Plateau/India/Madagascar tectonic plates (Old World suboscines). The oscines underwent a significant radiation in the Australo-Papuan region and only a few oscine lineages have spread further than to the nearby Southeast Asia. A remarkable exception is the ancestor to the vast Passerida radiation, which now comprises 35% of all bird species. This group obviously benefitted greatly from the increased diversity in plant seed size and morphology during the Tertiary. The lyrebirds (and possibly scrub-birds) constitute the sister group to all other oscines, which renders “Corvida” (sensu Sibley and Ahlquist 1990) paraphyletic. Sequence data suggests that Passerida, the other clade of oscines postulated based on the results of DNA–DNA hybridizations, is monophyletic, and that the rockfowl and rock-jumpers are the most basal members of this clade. The suboscines in the Old World (Eurylamides) and the New World (Tyrannides), respectively, are sister groups. A provisional, working classification of the passerines is presented based on the increased understanding of the major patterns of passerine evolution.

  • 6.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Jansén, Anna-Lee
    Stockholms universitet.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Ekman, Jan
    Uppsala universitet.
    Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data2005In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 36, no 3, p. 222-234Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto. The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.

  • 7.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data.2003In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 29, no 1, p. 126-38Article in journal (Refereed)
    Abstract [en]

    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.

  • 8.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Erratum: Major divisions of oscines revealed by insertions in the nuclear gene c-myc: A novel gene in avian phylogenetics (vol 117, pg 1077, 2000)2001In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 118, no 2, p. 563-563Article in journal (Other academic)
  • 9.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Major divisions in oscines revealed by insertions in the nuclear gene c-myc: A novel gene in avian phylogenetics2000In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 117, no 4, p. 1069-1078Article in journal (Refereed)
  • 10.
    Ericson, Per G. P.
    et al.
    Swedish Museum of Natural History, Research Division.
    Qu, Yanhua
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blom, Mozes P. K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    A genomic perspective of the pink-headed duck Rhodonessa caryophyllacea suggests a long history of low effective population size2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 16853Article in journal (Refereed)
    Abstract [en]

    The first molecular phylogenetic hypothesis for the possibly extinct pink-headed duck Rhodonessa caryophyllacea unambiguously shows that it belongs to the pochard radiation that also includes the genera Aythya and Netta. It is the sister to all modern-day pochards and belongs to a lineage that branched off from the others more than 2.8 million years ago. Rhodonessa caryophyllacea is believed to never have been common in modern time and we show this has probably been the situation for as long as 100,000 years. Our results suggest that their effective population size varied between 15,000 and 25,000 individuals during the last 150,000 years of the Pleistocene. The reasons behind this are largely unknown as very little is known about the life-history and biology of this species. Presumably it is due to factors related to feeding or to breeding, but we may never know this for sure.

  • 11.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Alvarenga, Herculano
    Prum, Richard O
    Higher-level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannida).2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, no 2, p. 471-83Article in journal (Refereed)
    Abstract [en]

    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.

  • 12. Farris, James S.
    et al.
    Källersjö, Mari
    Crowe, Timothy M.
    Lipscomb, Diana
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Frigatebirds, Tropicbirds and Ciconiida: Excesses of Confidence Probability1999In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 15, no 1, p. 1-7Article in journal (Refereed)
  • 13. Fjeldså, Jon
    et al.
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Lokugalappatti, L.G. Sampath
    Bowie, Rauri
    Diversification of African greenbuls in space and time: linking ecological and historical processes2007In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 148, no suppl. 2, p. 359-367Article in journal (Refereed)
  • 14. Fjeldså, Jon
    et al.
    Zuccon, Dario
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sapayoa aenigma: a New World representative of 'Old World suboscines'.2003In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 270 Suppl 2, p. S238-41Article in journal (Refereed)
    Abstract [en]

    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.

  • 15. Haase, Martin
    et al.
    Höljte, Henriette
    Blahy, Beate
    Bridge, Damon
    Henne, Eberhard
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Kaldma, Katrin
    Khudyakov, Ekaterina A
    King, Amy
    Leito, Aivar
    Mewes, Wolfgang
    Mudrik, Elena A.
    Ojaste, Ivar
    Politov, Dmitry V. 
    Popken, Ronald
    Rinne, Juhani
    Stanbury, Andrew
    Tofft, Jesper
    Väli, Ülo
    Schmitz Ornés, Angela
    Shallow genetic population structure in an expanding migratory bird with high breeding site fidelity, the Western Eurasian Crane Grus grus grus2019In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 160, p. 965-972Article in journal (Refereed)
    Abstract [en]

    For more than half a century, the Western Eurasian Crane (Grus grus grus) has been expanding its range toward western Europe, recolonizing areas where it had been previously driven to extinction, including the UK, the Netherlands and Denmark. The Western Eurasian Crane is, on the one hand, a very mobile, migratory species, but on the other, is territorial and shows high breeding site fidelity. Hence, its genetic population structure is subject to antagonizing forces, which have different consequences. Based on the genotyping of six highly variable microsatellite loci, we inferred the population structure of the Western Eurasian Crane from samples from eight regions. We integrated classic F-statistics including analyses of molecular variance with a priori designation of structure and divisive clustering approaches, i.e. a Bayesian procedure (STRU CTU RE) and discriminant analysis of principal components, which infer structure a posteriori. According to the F-statistics, populations were only weakly differentiated, and the majority of the genetic variance (> 90%) was attributed to individuals. At first glance, the divisive approaches appeared to agree in finding four clusters. Yet, there was no correspondence regarding the composition of the clusters and none of the results were biologically meaningful. However, STRU CTU RE delivered an alternative interpretation, designating the highest likelihood to a scenario without subdivision, in clear agreement with the findings based on the F-statistics. In conclusion, the Western Eurasian Crane is genetically largely homogeneous, probably as a consequence of the rapid growth and range expansion of its population.

  • 16.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G. P.
    Johansson, Ulf S.
    Oliver, Paul
    Joseph, Leo
    Blom, Mozes P. K.
    No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)2019In: DIVERSITY-BASEL, Vol. 11, no 4Article in journal (Refereed)
    Abstract [en]

    The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.

  • 17.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes).2002In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 23, no 3, p. 499-512Article in journal (Refereed)
    Abstract [en]

    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.

  • 18.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data2001In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 32, no 1, p. 15-25Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c-myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade. The New World suboscines clustered into two clades. The first contained Conopophaga (Conopophagidae), Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridisation data. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridisation. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma. Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines. The presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridisation data. The precise age of the divergences studied herein are unknown but based on interpretations of the fossil record of passerine birds many of them might date back to the early Tertiary. The agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergences in birds.

  • 19.
    Johansson, Ulf S
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Alström, Per
    Olsson, Urban
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sundberg, Per
    Price, Trevor D
    Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers.2007In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 61, no 2, p. 324-33Article in journal (Refereed)
    Abstract [en]

    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.

  • 20.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Bowie, Rauri C.K.
    Hackett, Shannon J.
    Schulenberg, Thomas S.
    The Phylogenetic affinities of Crossley's Babbler (Mystacornis crossleyi): adding a new niche to the vanga radiation of Madagascar.2008In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 4, no 6, p. 677-680Article in journal (Refereed)
  • 21.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ekman, Jan
    Bowie, Rauri C.K.
    Halvarsson, Peter
    Ohlson, Jan I.
    Price, Trevor D.
    Ericson, Per G.P.
    Swedish Museum of Natural History, Research Division.
    A complete multilocus species phylogeny of the tits and chickadees (Aves: Paridae)2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, p. 852-860Article in journal (Refereed)
  • 22.
    Johansson, Ulf S
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A re-evaluation of basal phylogenetic relationships within trogons (Aves: Trogonidae) based on nuclear DNA sequences2005In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 43, no 2, p. 166-173Article in journal (Refereed)
    Abstract [en]

    The avian clade Trogonidae (trogons) consists of approximately 40 species distributed pantropically in the Neotropical, Afrotropical and Indomalayan zoogeographical regions. In this study, we evaluate the basal phylogenetic relationships within the trogons based on DNA sequences from three nuclear introns [myoglobin intron 2, β-fibrinogen intron 7 and glyceraldehydes-3-phosphodehydrogenase (G3PDH) intron 11]. In addition, previously published cytochrome b and 12S sequences were re-analysed and combined with the nuclear data set. The analysis of the three nuclear genes combined suggests a sister group relationship between the Afrotropical (Apaloderma) and Indomalayan (Harpactes) clades, whereas the Neotropical taxa (Trogon, Pharomachrus, and Priotelus) form an unresolved polytomy basal to these two groups. In addition, two of the three individual gene trees also support a sister group relationship between the Afrotropical and Indomalayan trogons. This is at odds with previously published studies based on mitochondrial sequence data and DNA–DNA hybridization. The third nuclear intron (G3PDH), however, suggests that the Afrotropical trogons are basal relative the other trogons. This was also suggested by the mitochondrial data set, as well as the analysis of the combined nuclear and mitochondrial data. Both of these conflicting hypotheses are supported by high posterior probabilities. An insertion in β-fibrinogen further supports a basal position of the Afrotropical clade. Analyses of the myoglobin intron with additional outgroups place the root differently and strongly support monophyly of each of the zoogeographical regions (including the Neotropics), and these three clades form a basal trichotomy. This suggests that that rooting is a serious problem in resolving basal phylogenetic relationships among the trogons.

  • 23.
    Johansson, Ulf S
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960)2003In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 34, no 2, p. 185-197Article in journal (Refereed)
    Abstract [en]

    Woodpeckers, honeyguides, barbets, and toucans form a well-supported clade with approximately 355 species. This clade, commonly referred to as Pici, share with the South American clade Galbulae (puffbirds and jacamars) a zygodactyls foot with a unique arrangement of the deep flexor tendons (Gadow's Type VI). Based on these characters, Pici and Galbulae are often considered sister taxa, and have in traditional classification been placed in the order Piciformes. There are, however, a wealth of other morphological characters that contradicts this association, and indicates that Pici is closer related to the Passeriformes (passerines) than to Galbulae. Galbulae, in turn, is considered more closely related to the rollers and ground-rollers (Coracii). In this study, we evaluate these two hypotheses by using DNA sequence data from exons of the nuclear RAG-1 and c-myc genes, and an intron of the nuclear myoglobin gene, totally including 3400 basepairs of aligned sequences. The results indicate a sister group relationship between Pici and Galbulae, i.e. monophyly of the Piciformes, and this association has high statistical support in terms of bootstrap values and posterior probabilities. This study also supports several associations within the traditional order Coraciiformes, including a sister group relationship between the kingfishers (Alcedinidae) and a clade with todies (Todidae) and motmots (Momotidae), and with the bee-eaters (Meropidae) placed basal relative to these three groups.

  • 24.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G.P.
    Blom, Mozes
    Irestedt, Martin
    The phylogenetic position of the extinct Cuban Macaw Ara tricolor based on complete mitochondrial genome sequences2018In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 160, p. 666-672Article in journal (Refereed)
  • 25.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G.P.
    Fjeldså, Jon
    Irestedt, Martin
    The phylogenetic position of the world´s smallest passerine, the Pygmy Bushtit Psaltria exilis2016In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 158, p. 519-529Article in journal (Refereed)
  • 26.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Fjeldså, Jon
    Bowie, Rauri C.K.
    Phylogenetic relationships witihn Passerida (Aves: Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers.2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 3, p. 858-876Article in journal (Refereed)
  • 27.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Fjeldså, Jon
    Lokugalappatti, L.G. Sampath
    Bowie, Rauri C.K.
    A nuclear DNA phylogeny and a proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae)2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 5, p. 417-427Article in journal (Refereed)
  • 28.
    Johansson, Ulf S
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Parsons, Thomas J.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Basal phylogeny of the Tyrannoidea based on comparisons of cytochrome b and exons of nuclear c-myc and RAG-1 genes2002In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 119, no 4, p. 984-995Article in journal (Refereed)
    Abstract [en]

    The outlines of the phylogenetic relationships within the New World suboscine clade Tyrannoidea were investigated on the basis of nucleotide sequence data from two nuclear genes (c-myc and RAG-1) and one mitochondrial gene (cytochrome b), totaling over 2,400 bp. Representatives of the major tyrannoid lineages were sequenced, including Pachyramphus, Schiffornis, Tityra, and Oxyruncus. The data set with the three genes combined was analyzed under both the parsimony and maximum-likelihood criteria and under different character weighting schemes. The analyses resulted in similar topologies that differed only in poorly supported nodes. The three manakins (Pipra, Manacus, and Chiroxiphia) included in this study were found to be monophyletic, whereas Schiffornis—sometimes also considered to be a manakin—did not group with the manakins, but occurred with Pachyramphus and Tityra in the clade Tityrinae. The two clades Pipromorphinae and Tyranninae are also strongly supported in this analysis and appear as sister groups, thus supporting the monophyly of the tyrant flycatcher assemblage. Phytotoma was placed with the only cotingid species included in this analysis, whereas the position of Oxyruncus was unresolved.

  • 29.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Martin, Irestedt
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Qu, Yanhua
    Ericson, Per G.P.
    Swedish Museum of Natural History, Research Division.
    Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomesand fifteen nuclear genes2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 17-22Article in journal (Refereed)
  • 30.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Nylinder, Stephan
    Ohlson, Jan I.
    Tietze, Dieter Thomas
    Reconstruction of the Late Miocene Biogeographic History of Tits and Chickadees (Aves: Passeriformes: Paridae) – a Comparison between Discrete Area Analyses and ProbabilisticDiffusion Approach2018In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 45, p. 14-25Article in journal (Refereed)
  • 31.
    Johansson, Ulf S
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Clades within the 'higher land birds', evaluated bg nuclear DNA sequences2001In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 39, no 1-2, p. 37-51Article in journal (Refereed)
    Abstract [en]

    In this study we investigated the phylogenetic relationships within the 'higher land birds' by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c-myc and RAG-I. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c-myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbers more closely related to the Ramphastidae than to the Old World barbers. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively.

  • 32.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Pasquet, Eric
    Irestedt, Martin
    The New Zealand: Thrush: An extinct Oriole2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, article id e24317Article in journal (Refereed)
  • 33. Kuhn, Kerstin
    et al.
    Schwenk, Klaus
    Both, Christiaan
    Canal, David
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    van der Mije, Steven
    Töpfer, Till
    Päckert, Martin
    Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track globalclimate change2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 14, p. 4799-4799Article in journal (Refereed)
  • 34. Mayr, Gerald
    et al.
    Manegold, Albrecht
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Monophyletic groups within "higher land birds" - comparison of morphological and molecular data.2003In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 41, no 4, p. 233-248Article in journal (Refereed)
  • 35. Movalli, Paola
    et al.
    Duke, Guy
    Ramello, Gloria
    Dekker, René
    Vrezec, Al
    Shore, Richard F.
    García-Fernández, Antonio
    Wernham, Chris
    Krone, Oliver
    Alygizakis, Nikiforos
    Badry, Alexander
    Barbagli, Fausto
    Biesmeijer, Koos
    Boano, Giovanni
    Bond, Alexander L.
    Choresh, Yael
    Christensen, Jan Bolding
    Cincinelli, Alessandra
    Danielsson, Sara
    Dias, Andreia
    Dietz, Rune
    Eens, Marcel
    Espín, Silvia
    Eulaers, Igor
    Frahnert, Sylke
    Fuiz, Tibor I.
    Gkotsis, Georgios
    Glowacka, Natalia
    Gómez-Ramírez, Pilar
    Grotti, Marco
    Guiraud, Michel
    Hosner, Peter
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Jaspers, Veerle L.B.
    Kamminga, Pepijn
    Koschorreck, Jan
    Knopf, Burkhard
    Kubin, Eero
    LoBrutto, Sabrina
    Lourenco, Rui
    Martellini, Tania
    Martínez-López, Emma
    Mateo, Rafael
    Nika, Maria-Christina
    Nikolopoulou, Varvara
    Osborn, Dan
    Pauwels, Olivier
    Pavia, Marco
    Pereira, M. Glória
    Rüdel, Heinz
    Sanchez-Virosta, Pablo
    Slobodnik, Jaroslav
    Sonne, Christian
    Thomaidis, Nikolaos
    Töpfer, Till
    Treu, Gabriele
    Väinölä, Risto
    Valkama, Jari
    van der Mije, Steven
    Vangeluwe, Didier
    Warren, Ben H.
    Woog, Friederike
    Progress on bringing together raptor collections in Europe for contaminant research and monitoring in relation to chemicals regulation2019In: Environmental science and pollution research international, ISSN 0944-1344, E-ISSN 1614-7499, Vol. 26, p. 20132-20136Article in journal (Other academic)
  • 36. Price, Trevor D.
    et al.
    Hooper, Daniel M.
    Buchanan, Caitlyn D.
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Tietze, D. Thomas
    Alström, Per
    Olsson, Urban
    Ghosh-Harihar, Mousumi
    Ishtiaq, Farah
    Gupta, Sandeep K.
    Martens, Jochen
    Harr, Bettina
    Singh, Pratap
    Mohan, Dhananjai
    Niche filling slows the diversification of Himalayan songbirds2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 509, p. 222-225Article in journal (Refereed)
  • 37.
    Werdelin, Lars
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Yamaguchi, Nobuyuki
    Driscoll, C. A.
    Abramov, A.
    Csorba, G.
    Cuisin, J.
    Fernholm, Bo
    Swedish Museum of Natural History, Department of Zoology.
    Hiermeier, M.
    Hills, D.
    Hunter, L.
    Itakura, H.
    Johansson, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Kascheev, V.
    Krohmann, K.
    Martin, T.
    Nowak-Kemp, M.
    Pavlinov, I.
    Renoud, F.
    Tomsett, L.
    van der Mije, S.
    Zholnerovskaya, E.
    Groves, Colin
    Kitchener, Andrew C.
    Nijman, V.
    Macdonald, David W.
    Locating specimens of extinct tiger (Panthera tigris) subspecies: Caspian tiger (P. t. virgata), Javan tiger (P. t. sondaica), and Balinese tiger (P. t. balica) – including previously unpublished specimens2013In: Mammal Study, ISSN 1343-4152, E-ISSN 1348-6160, Vol. 38, p. 187-198Article in journal (Refereed)
    Abstract [en]

    Recent advances in multivariate statistics, and in ancient DNA techniques, have greatly increased understanding of tiger phylogeography. However, regardless of advances in analytical methodology, researchers will continue to need access to specimens for morphological measurements and sampling for genetic analysis. The tiger has become increasingly endangered, and out of the nine putative tiger subspecies, three (Javan, Balinese, and Caspian) have become extinct in the last 100 years, leaving the specimens kept in natural history collections as the only materials available for research. Frustratingly little information is widely available concerning the specimens of these extinct tiger subspecies. We conducted an extensive search for specimens of extinct tiger subspecies, and also developed a simple on-site method to assign unprovenanced and probable Indonesian specimens to either Javan/Balinese or Sumatran subspecies. We located a total of 88 Javan, 11 Balinese, and 46 Caspian tigers, including seven new Javan tigers, and three Balinese tigers that were not widely known previously. These specimens are critical for research in order to understand the intraspecific phylogeny and evolutionary history of the tiger.

  • 38. Yamaguchi, Nobuyuki
    et al.
    Driscoll, Carlos A.
    Werdelin, Lars
    Swedish Museum of Natural History, Department of Paleobiology.
    Abramov, Alexei V.
    Csorba, Gabor
    Cuisin, Jacques
    Fernholm, Bo
    Swedish Museum of Natural History, Department of Zoology.
    Hiermeier, Michael
    Hills, Daphne
    Hunter, Luke
    Itakura, Hiroyuki
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Kascheev, Vitaliy
    Krohmann, Katrin
    Martin, Thomas
    Nowak-Kemp, Malgosia
    Pavlinov, Igor Ya.
    Renoud, Francis
    Tomsett, Louise
    van der Mije, Steven
    Zholnerovskaya, Elena
    Groves, Colin
    Kitchener, Andrew C.
    Nijman, Vincent
    Macdonald, David W.
    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 specimens2013In: Mammal Study, ISSN 1343-4152, E-ISSN 1348-6160, Vol. 38, p. 187-198Article in journal (Refereed)
  • 39.
    Åhlander, Erik
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Johansson, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Vem var egentligen först med azurmesen2014In: Roadrunner, ISSN 1402-2451, no 2, p. 45-Article in journal (Other (popular science, discussion, etc.))
1 - 39 of 39
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