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  • 1. Alström, Per
    et al.
    Cibois, Alice
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Zuccon, Dario
    Gelang, Magnus
    Fjeldså, Jon
    Andersen, Michael J.
    Moyle, Robert G.
    Pasquet, Eric
    Olsson, Urban
    Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 127, p. 367-375Article in journal (Refereed)
    Abstract [en]

    The widespread Old World avian family Locustellidae (‘grassbirds and allies’) comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

  • 2. Alström, Per
    et al.
    Jønsson, Knud A.
    Fjeldså, Jon
    Ödeen, Anders
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dramatic niche shifts and morphological change in two insular bird species2015In: Royal Society Open Science, ISSN 2054-5703, Vol. 2, article id 140364Article in journal (Refereed)
    Abstract [en]

    Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.

  • 3. Batalha-Filho, Henrique
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Silveira, Luis F
    Miyaki, Cristina Y
    Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest.2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, no 1, p. 86-94Article in journal (Refereed)
    Abstract [en]

    The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, S. whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep divergence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75-0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period.

  • 4. Batalha-Filho, Henrique
    et al.
    Pessoa, Rodrigo O
    Fabre, Pierre-Henri
    Fjeldså, Jon
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Silveira, Luís F
    Miyaki, Cristina Y
    Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 79, p. 422-432Article in journal (Refereed)
    Abstract [en]

    We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae suggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatio-temporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

  • 5.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lagerholm, Vendela K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
  • 6.
    Dussex, Nicolas
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Taylor, Helen
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Robertson, Bruce
    When genetic and phenotypic data do not agree: the conservation implications of ignoring inconvenient taxonomic evidence2018In: New Zealand Journal of Ecology, ISSN 11777788, Vol. 42, no 2, p. 1-7Article in journal (Refereed)
  • 7.
    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.

  • 8.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Norman, Janette A
    Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds.2002In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 25, no 1, p. 53-62Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 bp obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu, are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Ericson et al., 2002; Irestedt et al., 2001).

  • 9.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Envall, Ida
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Norman, Janette A
    Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data.2003In: BMC evolutionary biology, ISSN 1471-2148, Vol. 3, p. 16-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria.

    RESULTS: Several novel phylogenetic relationships were recovered and strongly supported by the data, regardless of which method of analysis was employed. These include placing the gulls and allied groups as a sistergroup to the sandpiper-like birds, and not to the plover-like birds. The auks clearly belong to the clade with the gulls and allies, and are not basal to most other charadriiform birds as suggested in analyses of morphological data. Pluvialis, which has been supposed to belong to the plover family (Charadriidae), represents a basal branch that constitutes the sister taxon to a clade with plovers, oystercatchers and avocets. The thick-knees and sheathbills unexpectedly cluster together.

    CONCLUSION: The DNA sequence data contains a strong phylogenetic signal that results in a well-resolved phylogenetic tree with many strongly supported internodes. Taxonomically it is the most inclusive study of shorebird families that relies on nucleotide sequences. The presented phylogenetic hypothesis provides a solid framework for analyses of macroevolution of ecological, morphological and behavioural adaptations observed within the order Charadriiformes.

  • 10.
    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.

  • 11.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Klopfstein, Seraina
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nguyen, Jacqueline MT
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dating the diversification of the major lineages of Passeriformes (Aves)2014In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, no 8, p. 1-15Article in journal (Refereed)
    Abstract [en]

    Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.

  • 12.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Olson, Storrs L.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Alvarenga, Herculano
    Fjeldsa, Jon
    Circumscription of a monophyletic family for the tapaculos (Aves: Rhinocryptidae)2010In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 151, no 2, p. 337-345Article in journal (Refereed)
  • 13.
    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.

  • 14. Ertz, Damien
    et al.
    Tehler, Anders
    Swedish Museum of Natural History, Department of Botany.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frisch, Andreas
    Thor, Göran
    Pieter, van den Boom
    A large-scale phylogenetic revision of Roccellaceae (Arthoniales) reveals eight new genera2015In: Fungal Diversity, Vol. 70, no 1, p. 31-53Article in journal (Refereed)
  • 15. Fjeldsa, Jon
    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.
    Zuccon, Dario
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    The Cinnamon Ibon Hypocryptadius cinnamomeus is a forest canopy sparrow2010In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 152, no 4, p. 747-760Article in journal (Refereed)
  • 16. Fjeldsa, Jon
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jonsson, Knud A.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogeny of the ovenbird genus Upucerthia: a case of independent adaptations for terrestrial life2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 2, p. 133-141Article in journal (Refereed)
  • 17. Fjeldså, Jon
    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.
    Molecular data reveal some major adaptational shifts in the early evolution of the most diverse avian family, the Furnariidae2005In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 146, no 1, p. 1-13Article in journal (Refereed)
    Abstract [en]

    A robust phylogeny estimate for the family Furnariidae (sensu lato) was obtained using sequences of two nuclear introns and one mitochondrial gene (cyt b). Contrary to the widely accepted sister-group relationship of ovenbirds (Furnariinae) and woodcreepers (Dendrocolaptinae), a basal clade is suggested for Sclerurus and Geositta, while Xenops, hitherto considered an aberrant ovenbird, was found to occupy a basal position on the woodcreeper lineage. The morphological variation is re-interpreted in view of this revised phylogenetic hypothesis. Presumably, the remarkable adaptive radiation in this family started as primitive, Sclerurus-likes forms, which used the tail as a prop during terrestrial feeding, lured up to seek food on tree-trunks. The two basal woodcreeper genera, Xenops and then Glyphorynchus, show strong cranial specializations for hammering in wood, thus presenting a remarkable parallelism with the family Picidae, Xenops resembling a piculet, Glyphorynchus, a diminutive woodpecker. However, this specialization was lost in other woodcreepers, which show a more normal passerine skull, adapted for probing and prying in tree-trunk crevices and sallying for escaping insects. The ovenbirds developed a more flexible (rhynchokinetic) bill, well suited for probing and retrieving hidden prey in dead-leaf clusters and debris suspended in the vegetation, and in epiphyte masses. Adaptations to live in open terrain are secondary.

  • 18. Fjeldså, Jon
    et al.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Batalha-Filho, Henrique
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Rapid expansion and diversification into new niche space by fluvicoline flycatchers2018In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 49, article id jav-01661Article in journal (Refereed)
  • 19. 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.

  • 20.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Batalha-Filho, Henrique
    Roselaar, Cees S.
    Christidis, Les
    Ericson, Per G. P.
    Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus): Phylogeography of Ailuroedus2016In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, ISSN - 1463-6409, Vol. - 45, no - 4, p. 365-379Article in journal (Refereed)
  • 21.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fabre, Pierre-Henri
    Batalha-Filho, Henrique
    Jønsson, Knud A
    Roselaar, Cees S
    Sangster, George
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The spatio-temporal colonization and diversification across the Indo-Pacific by a 'great speciator' (Aves, Erythropitta erythrogaster).2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1759, p. 20130309-Article in journal (Refereed)
    Abstract [en]

    The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea-level fluctuations during the Pleistocene may have promoted gene flow only locally. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a 'great speciator': it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.

  • 22.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae).2009In: BMC evolutionary biology, ISSN 1471-2148, Vol. 9, p. 268-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design, accompanied by expansions into new habitats, facilitates diversification. We present a multi-gene phylogeny and age estimates for the ovenbird-woodcreeper family and use these results to estimate the degree of convergent evolution in both phenotype and habitat utilisation. Furthermore, we discuss whether variation in species richness among ovenbird clades could be explained by differences in clade-specific diversification rates, and whether these rates differ among lineages with different nesting habits. In addition, the systematic positions of some enigmatic ovenbird taxa and the postulated monophyly of some species-rich genera are evaluated.

    RESULTS: The phylogenetic results reveal new examples of convergent evolution and show that ovenbirds have independently colonized open habitats at least six times. The calculated age estimates suggest that the ovenbird-woodcreeper family started to diverge at ca 33 Mya, and that the timing of habitat shifts into open environments may be correlated with the aridification of South America during the last 15 My. The results also show that observed large differences in species richness among clades can be explained by a substantial variation in net diversification rates. The synallaxines, which generally are adapted to dry habitats and build exposed vegetative nests, had the highest diversification rate of all major furnariid clades.

    CONCLUSION: Several key features may have played an important role for the radiation and evolution of convergent phenotypes in the ovenbird-woodcreeper family. Our results suggest that changes in nest building strategy and adaptation to novel habitats may have played an important role in a diversification that included multiple radiations into more open and bushy environments. The synallaxines were found to have had a particularly high diversification rate, which may be explained by their ability to build exposed vegetative nests and thus to expand into a variety of novel habitats that emerged during a period of cooling and aridification in South America.

  • 23.
    Irestedt, Martin
    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.
    Evolution of the ovenbird-woodcreeper assemblage(Aves: Furnariidae) - major shifts in nest architecture and adaptive radiation2006In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 37, no 3, p. 260-272Article in journal (Refereed)
    Abstract [en]

    The Neotropical ovenbirds (Furnariidae) form an extraordinary morphologically and ecologically diverse passerine radiation, which includes many examples of species that are superficially similar to other passerine birds as a resulting from their adaptations to similar lifestyles. The ovenbirds further exhibits a truly remarkable variation in nest types, arguably approaching that found in the entire passerine clade. Herein we present a genus-level phylogeny of ovenbirds based on both mitochondrial and nuclear DNA including a more complete taxon sampling than in previous molecular studies of the group. The phylogenetic results are in good agreement with earlier molecular studies of ovenbirds, and supports the suggestion that Geositta and Sclerurus form the sister clade to both core-ovenbirds and woodcreepers. Within the core-ovenbirds several relationships that are incongruent with traditional classifications are suggested. Among other things, the philydorine ovenbirds are found to be non-monophyletic. The mapping of principal nesting strategies onto the molecular phylogeny suggests cavity nesting to be plesiomorphic within the ovenbird–woodcreeper radiation. It is also suggested that the shift from cavity nesting to building vegetative nests is likely to have happened at least three times during the evolution of the group. We suggest that the shifts in nest architecture within the furnariine and synallaxine ovenbirds have served as an ecological release that has facilitated diversification into new habitats and new morphological specializations.

  • 24.
    Irestedt, Martin
    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.
    Phylogenetic relationships of woodcreepers (Aves: Dendrocolaptinae) – incongruence between molecular and morphological data2004In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 35, no 3, p. 280-288-Article in journal (Refereed)
    Abstract [en]

    The woodcreepers is a highly specialized lineage within the New World suboscine radiation. Most systematic studies of higher level relationships of this group rely on morphological characters, and few studies utilizing molecular data exist. In this paper, we present a molecular phylogeny of the major lineages of woodcreepers (Aves: Dendrocolaptinae), based on nucleotide sequence data from a nuclear non-coding gene region (myoglobin intron II) and a protein-coding mitochondrial gene (cytochrome b). A good topological agreement between the individual gene trees suggests that the resulting phylogeny reflects the true evolutionary history of woodcreepers well. However, the DNA-based phylogeny conflicts with the results of a parsimony analysis of morphological characters. The topological differences mainly concern the basal branches of the trees. The morphological data places the genus Drymornis in a basal position (mainly supported by characters in the hindlimb), while our data suggests it to be derived among woodcreepers. Unlike most other woodcreepers, Drymornis is ground-adapted, as are the ovenbirds. The observed morphological similarities between Drymornis and the ovenbird outgroup may thus be explained with convergence or with reversal to an ancestral state. This observation raises the question of the use of characters associated with locomotion and feeding in phylogenetic reconstruction based on parsimony.

  • 25.
    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.

  • 26.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors.2004In: BMC evolutionary biology, ISSN 1471-2148, Vol. 4, p. 23-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.

    RESULTS: The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata), the spot-winged antshrike (Pygiptila stellaris) and the russet antshrike (Thamnistes anabatinus) are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood.

    CONCLUSIONS: The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and morphological adaptations to new habitats or food sources, and genera like Myrmeciza antbirds and the Myrmotherula antwrens obviously need taxonomic revisions. Although, Bayes factors seem promising for evaluating the relative contribution of components to an evolutionary model, the results suggests that even if strong evidence for a model allowing separate topology parameters is found, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing.

  • 27.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fuchs, Jérôme
    Jønsson, Knud A
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The systematic affinity of the enigmatic Lamprolia victoriae (Aves: Passeriformes) - an example of avian dispersal between New Guinea and Fiji over Miocene intermittent land bridges?2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 3, p. 1218-22Article in journal (Refereed)
  • 28.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Sangster, George
    Swedish Museum of Natural History, Department of Zoology.
    Olsson, Urban
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Alstrom, Per
    Neumann's Warbler Hemitesia neumanni (Sylvioidea): the sole African member of a Palaeotropic Miocene avifauna2011In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 153, no 1, p. 78-86Article in journal (Refereed)
  • 29.
    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.

  • 30.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jønsson, Knud A
    Fjeldså, Jon
    Christidis, Les
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    An unexpectedly long history of sexual selection in birds-of-paradise.2009In: BMC evolutionary biology, ISSN 1471-2148, Vol. 9, p. 235-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The birds-of-paradise (Paradisaeidae) form one of the most prominent avian examples of sexual selection and show a complex biogeographical distribution. The family has accordingly been used as a case-study in several significant evolutionary and biogeographical syntheses. As a robust phylogeny of the birds-of-paradise has been lacking, these hypotheses have been tentative and difficult to assess. Here we present a well supported species phylogeny with divergence time estimates of the birds-of-paradise. We use this to assess if the rates of the evolution of sexually selected traits and speciation have been excessively high within the birds-of-paradise, as well as to re-interpret biogeographical patterns in the group.

    RESULTS: The phylogenetic results confirm some traditionally recognized relationships but also suggest novel ones. Furthermore, we find that species pairs are geographically more closely linked than previously assumed. The divergence time estimates suggest that speciation within the birds-of-paradise mainly took place during the Miocene and the Pliocene, and that several polygynous and morphologically homogeneous genera are several million years old. Diversification rates further suggest that the speciation rate within birds-of-paradise is comparable to that of the enitre core Corvoidea.

    CONCLUSION: The estimated ages of morphologically homogeneous and polygynous genera within the birds-of-paradise suggest that there is no need to postulate a particularly rapid evolution of sexually selected morphological traits. The calculated divergence rates further suggest that the speciation rate in birds-of-paradise has not been excessively high. Thus the idea that sexual selection could generate high speciation rates and rapid changes in sexual ornamentations is not supported by our birds-of-paradise data. Potentially, hybridization and long generation times in polygynous male birds-of-paradise have constrained morphological diversification and speciation, but external ecological factors on New Guinea may also have allowed the birds-of-paradise to develop and maintain magnificent male plumages. We further propose that the restricted but geographically complex distributions of birds-of-paradise species may be a consequence of the promiscuous breeding system.

  • 31.
    Irestedt, Martin
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Zuccon, Dario
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Kallersjo, Mari
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes)2006In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 35, no 6, p. 567-580Article in journal (Refereed)
  • 32.
    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)
  • 33.
    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)
  • 34.
    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.

  • 35.
    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)
  • 36.
    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.

  • 37.
    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)
  • 38. Jonsson, Knud A.
    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.
    Fjeldsa, Jon
    A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus): implications for biogeography and convergent plumage evolution2010In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 39, no 1, p. 1-8Article in journal (Refereed)
  • 39. Jönsson, Knud A.
    et al.
    Blom, Mozes P.K.
    Päckert, Martin
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 120, p. 28-32Article in journal (Refereed)
  • 40. Jønsson, Knud A
    et al.
    Fabre, Pierre-Henri
    Fritz, Susanne A
    Etienne, Rampal S
    Ricklefs, Robert E
    Jørgensen, Tobias B
    Fjeldså, Jon
    Rahbek, Carsten
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Woog, Friederike
    Pasquet, Eric
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas.2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 17, p. 6620-5Article in journal (Refereed)
    Abstract [en]

    Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)--or even larger (size variation)--as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.

  • 41. Jønsson, Knud A
    et al.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Systematic placement of an enigmatic Southeast Asian taxon Eupetes macrocerus and implications for the biogeography of a main songbird radiation, the Passerida.2007In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, no 3, p. 323-6Article in journal (Refereed)
    Abstract [en]

    Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocerus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea on the other side of Wallace's Line, but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops, and their sister taxon in turn being Picathartes, with a divergence in the Eocene. Thus, this clade is distributed in remote corners of Africa and Asia, which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.

  • 42. Jønsson, Knud A
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fuchs, Jérôme
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Bowie, Rauri C K
    Norman, Janette A
    Pasquet, Eric
    Fjeldså, Jon
    Explosive avian radiations and multi-directional dispersal across Wallacea: evidence from the Campephagidae and other Crown Corvida (Aves).2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 47, no 1, p. 221-36Article in journal (Refereed)
    Abstract [en]

    The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35 Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace's line have revealed a particularly complex movement of terranes over the last 20-30 Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace's line are complex and began at least 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 Myr, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographic pattern in the region.

  • 43. Jønsson, Knud Andreas
    et al.
    Delhey, Kaspar
    Sangster, George
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Correction to 'The evolution of mimicry of friarbirds by orioles (Aves: Passeriformes) in Australo-Pacific archipelagos'.2016In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, no 1837, article id 20161497Article in journal (Refereed)
  • 44. Jønsson, Knud Andreas
    et al.
    Delhey, Kaspar
    Sangster, George
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    The evolution of mimicry of friarbirds by orioles (Aves: Passeriformes) in Australo-Pacific archipelagos.2016In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, no 1833, article id 20160409Article in journal (Refereed)
    Abstract [en]

    Observations by Alfred Wallace and Jared Diamond of plumage similarities between co-occurring orioles (Oriolus) and friarbirds (Philemon) in the Malay archipelago led them to conclude that the former represent visual mimics of the latter. Here, we use molecular phylogenies and plumage reflectance measurements to test several key predictions of the mimicry hypothesis. We show that friarbirds originated before brown orioles, that the two groups did not co-speciate, although there is one plausible instance of co-speciation among species on the neighbouring Moluccan islands of Buru and Seram. Furthermore, we show that greater size disparity between model and mimic and a longer history of co-occurrence have resulted in a stronger plumage similarity (mimicry). This suggests that resemblance between orioles and friarbirds represents mimicry and that colonization of islands by brown orioles has been facilitated by their ability to mimic the aggressive friarbirds.

  • 45. Jønsson, Knud Andreas
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Christidis, Les
    Clegg, Sonya M
    Holt, Ben G
    Fjeldså, Jon
    Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala).2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1777, p. 20131727-Article in journal (Refereed)
    Abstract [en]

    Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles).

  • 46. Low, Gabriel
    et al.
    Chattopadhyay, Balaji
    Garg, Kritika
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Yap, G
    Tang, Q
    Wu, S
    Rheindt, Frank E.
    Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive2018In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 120, p. 138-153Article in journal (Refereed)
  • 47. Marki, Petter Z.
    et al.
    Fjeldså, Jon
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jønsson, Knud A.
    Molecular phylogenetics and species limits in a cryptically coloured radiation of Australo-Papuan passerine birds (Pachycephalidae: Colluricincla)2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 124, p. 100-105Article in journal (Refereed)
    Abstract [en]

    Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds. In line with previous studies, we find that one species, the little shrikethrush (C. megarhyncha) is characterized by deep divergences among populations. Delimitation results suggest that these clades represent distinct species and we consequently propose a new classification. Furthermore, our findings suggest that C. megarhyncha melanorhyncha of Biak Island does not belong in this genus, but is nested within the whistlers (Pachycephala) as sister to P. phaionota. This study represents a useful example of species delimitation when phenotypic variation is limited or poorly defined.

  • 48. Moltesen, Maria
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Jønsson, Knud A
    Molecular phylogeny of Chloropseidae and Irenidae - cryptic species and biogeography.2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 3, p. 903-14Article in journal (Refereed)
    Abstract [en]

    Chloropseidae (Leafbirds) and Irenidae (Fairy-bluebirds) are colourful Oriental birds, which have been placed as a deep (old) branch in the radiation of passeroid songbirds. We present a densely sampled molecular phylogeny of the two families based on two nuclear introns (GAPDH and ODC) and two mitochondrial genes (ND3 and cyt-b) largely stemming from old museum specimens. Our results show that several subspecies within both Chloropseidae and Irenidae are genetically distinct and separated in the Miocene some 10-11Million years ago (Mya), indicating a substantial underestimation of species numbers within the two families. Based on our molecular findings, plumage distinctiveness and contemporary distributions we propose that several subspecies be recognised at the species level. Furthermore, we use the molecular data to examine biogeographical patterns of the two families in the light of historical geological re-arrangements in the region. The results indicate that the Philippines were colonised in the Pliocene and that colonisation probably progressed via the Sulu islands from Borneo and not via Palawan, which was first colonised in the Pleistocene.

  • 49.
    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.

  • 50.
    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)
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