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  • 51. Fuchs, Jérôme
    et al.
    Pons, Jean-Marc
    Liu, Liang
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Couloux, Arnaud
    Pasquet, Eric
    A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae).2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, no 3, p. 578-88Article in journal (Refereed)
    Abstract [en]

    The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the 'wrong' phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that (1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and (2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome.

  • 52.
    Gelang, Magnus
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Cibois, Alice
    Pasquet, Eric
    Olsson, Urban
    Alstrom, Per
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification2009In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 3, p. 225-236Article in journal (Refereed)
  • 53. Gilbert, M Thomas P
    et al.
    Drautz, Daniela I
    Lesk, Arthur M
    Ho, Simon Y W
    Qi, Ji
    Ratan, Aakrosh
    Hsu, Chih-Hao
    Sher, Andrei
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Götherström, Anders
    Tomsho, Lynn P
    Rendulic, Snjezana
    Packard, Michael
    Campos, Paula F
    Kuznetsova, Tatyana V
    Shidlovskiy, Fyodor
    Tikhonov, Alexei
    Willerslev, Eske
    Iacumin, Paola
    Buigues, Bernard
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Germonpré, Mietje
    Kosintsev, Pavel
    Nikolaev, Vladimir
    Nowak-Kemp, Malgosia
    Knight, James R
    Irzyk, Gerard P
    Perbost, Clotilde S
    Fredrikson, Karin M
    Harkins, Timothy T
    Sheridan, Sharon
    Miller, Webb
    Schuster, Stephan C
    Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 24, p. 8327-32Article in journal (Refereed)
    Abstract [en]

    We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

  • 54. Gilbert, M Thomas P
    et al.
    Tomsho, Lynn P
    Rendulic, Snjezana
    Packard, Michael
    Drautz, Daniela I
    Sher, Andrei
    Tikhonov, Alexei
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Kuznetsova, Tatyana
    Kosintsev, Pavel
    Campos, Paula F
    Higham, Thomas
    Collins, Matthew J
    Wilson, Andrew S
    Shidlovskiy, Fyodor
    Buigues, Bernard
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Germonpré, Mietje
    Götherström, Anders
    Iacumin, Paola
    Nikolaev, Vladimir
    Nowak-Kemp, Malgosia
    Willerslev, Eske
    Knight, James R
    Irzyk, Gerard P
    Perbost, Clotilde S
    Fredrikson, Karin M
    Harkins, Timothy T
    Sheridan, Sharon
    Miller, Webb
    Schuster, Stephan C
    Whole-genome shotgun sequencing of mitochondria from ancient hair shafts.2007In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 317, no 5846, p. 1927-30Article in journal (Refereed)
    Abstract [en]

    Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

  • 55. Hou, Lianhai
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A middle Eocene shorebird from China2002In: The Condor, ISSN 0010-5422, E-ISSN 1938-5129, Vol. 104, p. 896-899Article in journal (Refereed)
    Abstract [en]

    We describe a new species of shorebird, tentatively referred to the family Charadriidae, from the Huadian Formation (Middle Eocene) in Jilin Province, China. In general morphology the specimen closely matches that of an extant charadriid, and correspondsin size to the Killdeer (Charadrius vociferus). If correctly identified this is the oldest record of the Charadriidae. The Middle Eocene paleoenvironment of the Huadian region is thought to have resembled a subtropical swamp.

  • 56.
    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.

  • 57.
    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.

  • 58.
    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.

  • 59.
    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.

  • 60.
    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.

  • 61.
    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.

  • 62.
    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)
  • 63.
    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)
  • 64.
    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.

  • 65.
    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.

  • 66.
    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)
  • 67. James, Helen F
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Slikas, Beth
    Lei, Fumin
    Gill, Frank B
    Olson, Storrs L
    Pseudopodoces humilis, a misclassified terrestrial tit (Paridae) of the Tibetan Plateau: evolutionary consequences of shifting adaptive zones2003In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 145, no 2, p. 185-202Article in journal (Refereed)
    Abstract [en]

    Pseudopodoces humilis (Hume's Ground-Jay) is a small passerine bird that inhabits the high rocky steppes of the Tibetan (Qinghai–Xizang) Plateau. Although it was long classified as a small species of ground jay (Podoces), two previous anatomical studies cast doubt on its assignment to the Corvidae (crows and jays). We studied the evolutionary relationships of Pseudopodoces using three independent datasets drawn from comparative osteology, the nuclear c-myc gene, and the mitochondrial cytochrome b gene. All three datasets agree on the placement of Pseudopodoces in the family Paridae (tits and chickadees). The cytochrome b data further suggest that Pseudopodoces may be closest to the Great Tit Parus major species group. Pseudopodoces is the only species of parid whose distribution is limited to treeless terrain. Its evolutionary relationships were long obscured by adaptations to open habitat, including pale, cryptic plumage; a long, decurved bill for probing in crevices among rocks or in the ground; and long legs for terrestrial locomotion. Despite these accommodations to a novel adaptive zone, its evolutionary affinity with the Paridae is clearly expressed in comparative osteology and genetics, and is supported by its habit of nesting in cavities.

  • 68.
    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.

  • 69.
    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)
  • 70.
    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.

  • 71.
    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.

  • 72.
    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.

  • 73.
    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)
  • 74.
    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.

  • 75. Johnsen, Arild
    et al.
    Rindal, Eirik
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Kerr, Kevin C. R.
    Stoeckle, Mark Y.
    Lifjeld, Jan T.
    DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species2010In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 151, no 3, p. 565-578Article in journal (Refereed)
  • 76. 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)
  • 77. 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.

  • 78. 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.

  • 79. 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.

  • 80. 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)
  • 81. 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.

  • 82. Mayr, Gerald
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Evidence for a sister group relationship between the Madagascan mesites (Mesitornithidae) and cuckoos (Cuculidae)2004In: Senckenbergiana Biologica, ISSN 0037-2102, Vol. 84, no 1/2, p. 119-135Article in journal (Refereed)
  • 83. Miller, Webb
    et al.
    Drautz, Daniela I
    Janecka, Jan E
    Lesk, Arthur M
    Ratan, Aakrosh
    Tomsho, Lynn P
    Packard, Mike
    Zhang, Yeting
    McClellan, Lindsay R
    Qi, Ji
    Zhao, Fangqing
    Gilbert, M Thomas P
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Arsuaga, Juan Luis
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Huson, Daniel H
    Helgen, Kristofer M
    Murphy, William J
    Götherström, Anders
    Schuster, Stephan C
    The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).2009In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 19, no 2, p. 213-20Article in journal (Refereed)
    Abstract [en]

    We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

  • 84. 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.

  • 85.
    Murphy, Melissa
    et al.
    University of Oxford.
    Porcelli, Don
    University of Oxford.
    Pogge von Strandmann, Philip
    University College London.
    Hirst, Catherine
    Swedish Museum of Natural History, Department of Geology.
    Kutscher, Liselott
    Swedish Museum of Natural History, Department of Geology.
    Katchinoff, Joachim
    Yale University.
    Mörth, Carl-Magnus
    Stockholm University.
    Maximov, Trofim
    Institute for Biological Problems in the Cryolitic Zone, Yakutsk.
    Andersson, Per
    Swedish Museum of Natural History, Research Division.
    Tracingsilicate weathering processes in the permafrost-dominated Lena River watershedusing lithium isotopes2019In: Geochimica et Cosmochimica Acta, ISSN 0016-7037, E-ISSN 1872-9533, Vol. 245, p. 154-171Article in journal (Refereed)
    Abstract [en]

    Increasing global temperatures are causing widespread changes in the Arctic, including permafrost thawing and altered freshwater inputs and trace metal and carbon fluxes into the ocean and atmosphere. Changes in the permafrost active layer thickness can affect subsurface water flow paths and water-rock interaction times, and hence weathering processes. Riverine lithium isotope ratios (reported as δ7Li) are tracers of silicate weathering that are unaffected by biological uptake, redox, carbonate weathering and primary lithology. Here we use Li isotopes to examine silicate weathering processes in one of the largest Russian Arctic rivers: the Lena River in eastern Siberia. The Lena River watershed is a large multi-lithological catchment, underlain by continuous permafrost. An extensive dataset of dissolved Li isotopic compositions of waters from the Lena River main channel, two main tributaries (the Aldan and Viliui Rivers) and a range of smaller sub tributaries are presented from the post-spring flood/early-summer period at the onset of active layer development and enhanced water-rock interactions. The Lena River main channel (average δ7Lidiss ~19‰) has a slightly lower isotopic composition than the mean global average of 23‰ (Huh

    et al., 1998a). The greatest range of [Li] and δ7Lidiss are observed in catchments draining the south facing slopes of the Verkhoyansk Mountain Range. South-facing slopes in high-latitude, permafrost dominated regions are typically characterised by increased summer insolation and higher daytime temperatures relative to other slope aspects. The increased solar radiation on south-facing catchments promotes repeated freeze-thaw cycles, and contributes to more rapid melting of snow cover, warmer soils, and increased active layer thaw depths. The greater variability in δ7Li and [Li] in the south-facing rivers likely reflect the greater infiltration of melt water and enhanced water rock interactions within the active layer. A similar magnitude of isotopic fractionation is observed between the low-lying regions of the Central Siberian Plateau (and catchments draining into the Viliui River), and catchments draining the Verkhoyansk Mountain Range into the Aldan River. This is in contrast to global rivers in non permafrost terrains that drain high elevations or areas of rapid uplift, where high degrees of physical erosion promote dissolution of freshly exposed primary rock typically yielding low δ7Lidiss, and low lying regions exhibit high riverine δ7Li values resulting from greater water-rock interaction and formation of secondary mineral that fractionates Li isotopes. Overall, the range of Li concentrations and δ7Lidiss observed within the Lena River catchment are comparable to global rivers located in temperate and tropical regions. This suggests that cryogenic weathering features specific to permafrost regions (such as the continual exposure of fresh primary minerals due to seasonal freeze-thaw cycles, frost shattering and salt weathering), and climate (temperature and runoff), are not a dominant control on δ7Li variations. Despite vastly different climatic and weathering regimes, the same range of riverine δ7Li values globally suggests that the same processes govern Li geochemistry – that is, the balance between primary silicate mineral dissolution and the formation (or exchange with) secondary minerals. This has implications for the use of δ7Li as a palaeo weathering tracer for interpreting changes in past weathering regimes.

  • 86. Möllerstrom, A. E.
    et al.
    Soder, P. O.
    Frithiof, L.
    Wouters, F.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Marginal Bone Loss in a Medieval Population in Stockholm1987In: Swedish Dental Journal, ISSN 0347-9994, Vol. 11, no 6, p. 287-287Article in journal (Refereed)
  • 87. Möllerstrom, A. E.
    et al.
    Soder, P. O.
    Frithiof, L.
    Wouters, F. R.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Marginal Bone Loss in a Medieval Population in Stockholm1989In: Journal of Dental Research, ISSN 0022-0345, E-ISSN 1544-0591, Vol. 68, no 4, p. 703-703Article in journal (Other academic)
  • 88. Müller, Johannes
    et al.
    Scheyer, Torsten M
    Head, Jason J
    Barrett, Paul M
    Werneburg, Ingmar
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pol, Diego
    Sánchez-Villagra, Marcelo R
    Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes.2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 5, p. 2118-23Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 90.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldsa, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A new genus for three species of tyrant flycatchers (Passeriformes: Tyrannidae), formerly placed in Myiophobus2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2290, p. 36-40Article in journal (Refereed)
  • 91.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular phylogeny of the manakins (Aves: Passeriformes2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 69, no 3, p. 796-804Article in journal (Refereed)
    Abstract [en]

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

  • 92.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Fjeldså, Jon
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes)2008In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 3, p. 315-335Article in journal (Refereed)
    Abstract [en]

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

  • 93.
    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.

  • 94.
    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)
  • 95.
    Ohlson, Jan I
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Prum, Richard O
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    A molecular phylogeny of the cotingas (Aves: Cotingidae).2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 42, no 1, p. 25-37Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

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

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

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

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

  • 100. Olsson, Urban
    et al.
    Sundberg, Per
    Alström, Per
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    What is proper vouchering in phylogenetic studies of birds?--a reply to Peterson et al. (2007).2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 383-5Article in journal (Refereed)
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