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  • 1.
    Abalde, Samuel
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Crocetta, Fabio
    Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Tenorio, Manuel J.
    Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
    D'Aniello, Salvatore
    Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Fassio, Giulia
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Rodríguez-Flores, Paula C.
    Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
    Uribe, Juan E.
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Afonso, Carlos M.L.
    Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal.
    Oliverio, Marco
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Zardoya, Rafael
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus2023In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 186, p. 107838-107838, article id 107838Article in journal (Refereed)
    Abstract [en]

    The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.

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  • 2. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Foerschler, Marc I.
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Erratum to: Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae) (vol 65, pg 35, 2012)2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 3, p. 1017-1019Article in journal (Refereed)
  • 3. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Förschler, Marc I
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 1, p. 35-45Article in journal (Refereed)
    Abstract [en]

    Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.

  • 4. 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.

  • 5. Alström, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Olsson, Urban
    Sundberg, Per
    Phylogeny and classification of the avian superfamily Sylvioidea.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 38, no 2, p. 381-97Article in journal (Refereed)
    Abstract [en]

    Sylvioidea is one of the three superfamilies recognized within the largest avian radiation, the parvorder Passerida. In the present study, which is the first taxon-dense analysis of the Sylvioidea based on sequence data (nuclear myoglobin intron II and mitochondrial cytochrome b gene), we investigate the interrelationships among the four "sylvioid" clades found by previous workers, as well as the relationships within the largest of these clades. The nuclear and mitochondrial loci estimate basically the same phylogeny, with minor differences in resolution. The trees based on myoglobin and the combined data identify a strongly supported clade that includes the taxa previously allocated to Sylvioidea, except for Sitta (nuthatches), Certhia (treecreepers), Parus (tits), Remiz (penduline tits), Troglodytes and Campylorhynchus (wrens), Polioptila (gnatcatchers), and Regulus (crests/kinglets); this clade also comprises larks, which have previously been placed in the superfamily Passeroidea. We refer to this clade as Sylvioidea. This clade is further divided into 10 main, well-supported clades, which we suggest form the basis for a revised classification.

  • 6. Alström, Per
    et al.
    Fregin, Silke
    Norman, Janette A
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Olsson, Urban
    Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 58, no 3, p. 513-26Article in journal (Refereed)
    Abstract [en]

    The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1×10(9) iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.

  • 7. Alström, Per
    et al.
    Zhang, R
    Zhao, M
    Wang, J
    Zhu, X
    Gwee, C.H.
    Hao, Y
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jia, C
    Prawiradilaga, D M
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lei, Fumin
    Olsson, Urban
    Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed)
  • 8. 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.

  • 9. 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.

  • 10.
    Beimforde, Christina
    et al.
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Feldberg, Kathrin
    Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Rikkinen, Jouko
    Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland.
    Tuovila, Hanna
    Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland.
    Dörfelt, Heinrich
    Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
    Gube, Matthias
    Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.
    Jackson, Daniel
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Reitner, Joachim
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Seyfullah, Leyla
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Schmidt, Alexander
    Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
    Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, no 78, p. 386-398Article in journal (Refereed)
    Abstract [en]

    The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualisticassociations such as mycorrhizae and lichens have evolved in this group, which are regarded as keyinnovations that supported the evolution of land plants. Only a few attempts have been made to date theorigin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack ofsatisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycetefossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils representfive major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes,and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 andRPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibrationpoints solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with aBayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician,followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuousdiversification was unaffected by mass extinctions. We suggest that the ecological diversity within eachlineage ensured that at least some taxa of each group were able to survive global crises and rapidlyrecovered.

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  • 11. Cai, T L
    et al.
    Cibois, Alice
    Alström, Per
    Moyle, R G
    Kennedy, J D
    Shao, S M
    Zhang, R Y
    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.
    Gelang, Magnus
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Lei, Fumin
    Fjeldså, Jon
    Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes)2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 346-356Article in journal (Refereed)
  • 12. Cole, Theresa
    et al.
    Rawlence, Nic
    Dussex, Nicolas
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elleberg, Ursulla
    Houston, Dave
    Mattern, Thomas
    Miskelly, Colin
    Morrisson, Kyle
    Scofield, Paul
    Tennyson, Alan
    Tompson, David
    Wood, Jamie
    Waters, Jonathan
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 131, p. 72-79Article in journal (Refereed)
    Abstract [en]

    Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as ‘Eudyptes spp.’, we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.

  • 13.
    Dussex, Nicolas
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’s most diverse penguin clade2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513Article in journal (Refereed)
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  • 14.
    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).

  • 15.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data.2003In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 29, no 1, p. 126-38Article in journal (Refereed)
    Abstract [en]

    Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.

  • 16.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Alvarenga, Herculano
    Prum, Richard O
    Higher-level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannida).2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, no 2, p. 471-83Article in journal (Refereed)
    Abstract [en]

    Despite increased understanding of higher-level relationships in passerine birds in the last 15 years, the taxonomic boundaries and phylogenetic interrelationships of the major groups of the Tyrannida (including the cotingas, manakins, tityrines, and tyrant flycatchers) remain unclear. Here, we present an analysis of DNA sequence data obtained from two nuclear exons, three introns, and one mitochondrial gene for 26 genera of Tyrannida and 6 tracheophone outgroups. The analysis resulted in well-supported hypotheses about the earliest evolution within Tyrannida. The Cotingidae, Pipridae, Tityrinae (sensu) [Prum, R.O., Rice, N.H., Mobley, J.A., Dimmick, W.W., 2000. A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 117, 236-241], Tyrannidae, and the tyrannid subfamiles Tyranninae and Pipromorphinae (sensu) [Sibley, C.G., Monroe, B. L. Jr., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT] were all found to be reciprocally monophyletic (given the present taxon sampling). The Cotingidae and Pipridae form a clade that is the sister group to a well-supported clade including Oxyruncus, the Tityrinae, Piprites, and the Tyrannidae. Oxyruncus is the sister group to the Tityrinae, and Piprites is placed as the sister group to the Tyrannidae. The tyrannid subfamilies Tyranninae and Pipromorphinae are monophyletic sister taxa, but the relationships of Platyrinchus mystaceus to these two clades remains ambiguous. The presence of medial (=internal) cartilages in the syrinx is a synapomorphy for the Oxyruncus-Tityrinae-Piprites-Tyrannidae clade. Although morphological synapomorphies currently support the monophyly of both the Pipridae and the Cotingidae, convergences and/or reversals in morphological character states are common in Tyrannida. The relationship between Oxyruncus and the Tityrinae is congruent with additional syringeal synapomorphies and allozyme distance data. Accordingly, we propose the recognition the family Tityridae within the Tyrannida to include the genera Schiffornis, Laniisoma, Laniocera, Iodopleura, Xenopsaris, Pachyramphus, Tityra, and Oxyruncus.

  • 17.
    Erséus, Christer
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Ida, Envall
    Pierre, De Wit
    Gustavsson, Lena
    Swedish Museum of Natural History, Department of Zoology.
    Molecular data reveal a tropical freshwater origin of Naidinae (Annelida, Clitellata, Naididae)2017In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, ISSN 1055-7903, Vol. 115, p. 115-127Article in journal (Refereed)
  • 18. Ewen, John G
    et al.
    Flux, Ian
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Systematic affinities of two enigmatic New Zealand passerines of high conservation priority, the hihi or stitchbird Notiomystis cincta and the kokako Callaeas cinerea.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, no 1, p. 281-4Article in journal (Refereed)
  • 19. Freire-Rallo, Sandra
    et al.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Diederich, Paul
    Millanes, Ana M.
    To explore strange new worlds – The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae2023In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 180, p. 107680-107680, article id 107680Article in journal (Refereed)
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  • 20. Fuchs, Jérôme
    et al.
    Pons, Jean-Marc
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bonillo, Céline
    Couloux, Arnaud
    Pasquet, Eric
    Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae).2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 34-46Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that the woodpecker genus Picus (Aves: Picidae) may not be monophyletic. In order to evaluate this hypothesis, we analyzed DNA sequences from all but two species of Picus, as well as from representatives of all genera in the tribe Malarpicini, within which Picus is nested. We sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics. The species currently placed in Picus fall into two subclades that may not form a monophyletic assemblage. Consequently, we propose to place miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 in the genus Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion-deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting.

  • 21. 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.

  • 22.
    Hansen, Karen
    et al.
    Swedish Museum of Natural History, Department of Botany. Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Perry, Brian A.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Dranginis, Andrew W.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Pfister, Donald H.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected lifehistory traits2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, p. 311-335Article in journal (Refereed)
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  • 23.
    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.

  • 24.
    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)
  • 25.
    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)
  • 26.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Fjeldså, Jon
    Bowie, Rauri C.K.
    Phylogenetic relationships witihn Passerida (Aves: Passeriformes): A review and a new molecular phylogeny based on three nuclear intron markers.2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 3, p. 858-876Article in journal (Refereed)
  • 27.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Irestedt, Martin
    Ericson, Per G.P.
    Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex2023In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 189, article id 107909Article in journal (Refereed)
  • 28.
    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)
  • 29. Jonsson, Knud Andreas
    et al.
    Blom, Mozes P. K.
    Marki, Petter Zahl
    Joseph, Leo
    Sangster, George
    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.
    Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 137, p. 200-209Article in journal (Refereed)
    Abstract [en]

    Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on (i) 21 nuclear genes, (ii) whole mito-genomes, and (iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or groups of subspecies may warrant species rank and we find a continental example of two morphologically distinct species (O. mellianus/O. traillii) being genetically (mtDNA) very similar. Biogeographically, we confirm previous findings that members of the Oriolidae originated in Australo-Papua. Dispersal out of this area took place around 15 Mya to southeast Asia and Africa, and from Africa to the Palearctic followed by recolonization of the Indonesian and Philippine island region during the Plio-Pleistocene. Recolonisation of the Indonesian and Philippine islands coincided with an increase in body size, which may have facilitated the ability to co-exist with other congenerics.

  • 30. 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)
  • 31. 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.

  • 32. 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.

  • 33.
    Marki, Petter Z.
    et al.
    Univ Copenhagen, Nat Hist Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark.;Univ Oslo, Nat Hist Museum, POB 1172, N-0318 Oslo, Norway..
    Jønsson, Knud A.
    Univ Copenhagen, Nat Hist Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark..
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Paleobiology.
    Nguyen, Jacqueline M. T.
    Australian Museum, Australian Museum Res Inst, 1 William St, Sydney, NSW 2010, Australia..
    Rahbek, Carsten
    Univ Copenhagen, Nat Hist Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark.;Imperial Coll London, Dept Life Sci, Silwood Pk Campus, Ascot SL5 7PY, Berks, England..
    Fjeldsa, Jon
    Univ Copenhagen, Nat Hist Museum, Ctr Macroecol Evolut & Climate, Univ Pk 15, DK-2100 Copenhagen, Denmark..
    Supermatrix phylogeny and biogeography of the Australasian Meliphagides radiation (Aves: Passeriformes)2017In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 107, p. 516-529Article in journal (Refereed)
    Abstract [en]

    With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3 Mya, 95% HPD 25.2-38.2 Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change. (C) 2016 Elsevier Inc. All rights reserved.

  • 34. Martins, Frederico C.
    et al.
    Cox, Siobhan C.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Prys-Jones, Robert P.
    Day, Julia J.
    A comprehensive molecular phylogeny of Afrotropical white-eyes (Aves: Zosteropidae) highlights prior underestimation of mainland diversity and complex colonisation history2020In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, ISSN - 1055-7903, Vol. 149, article id 108843Article in journal (Refereed)
    Abstract [en]

    White-eyes (Zosterops) are a hyper-diverse genus of passerine birds that have rapidly radiated across the Afrotropics and Southeast Asia. Despite their broad range, a disproportionately large number of species are currently recognised from islands compared to the mainland. Described species-level diversity of this ´great speciator´ from continental Africa-Arabia is strikingly low, despite the vast size and environmental complexity of this region. However, efforts to identify natural groups using traditional approaches have been hindered by the remarkably uniform morphology and plumage of these birds. Here, we investigated the phylogenetic relationships and systematics of Afrotropical Zosterops, including the Gulf of Guinea and western Indian Ocean islands. We included exceptional sampling (~160 individuals) from all except one subspecies of the 55 taxa (32 species, plus 23 additional named sub-species) currently recognized throughout the region, in addition to a subset of extra-Afrotropical taxa, by exploiting blood and archival samples. Employing a multi-locus phylogenetic approach and applying quantitative species delimitation we tested: (1) if there has been a single colonisation event of the Afrotropical realm; (2) if constituent mainland and island birds are monophyletic; and (3) if mainland diversity has been underestimated. Our comprehensive regional phylogeny revealed a single recent colonisation of the Afrotropical realm c.1.30 Ma from Asia, but a subsequent complex colonisation history between constituent island and mainland lineages during their radiation across this vast area. Our findings suggest a significant previous underestimation of continental species diversity and, based on this, we propose a revised taxonomy. Our study highlights the need to densely sample species diversity across ranges, providing key findings for future conservation assessments and establishing a robust framework for evolutionary studies.

  • 35. 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.

  • 36. Norhazrina, Nik
    et al.
    Vanderpoorten, Alain
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Patiño, Jairo
    What are the evolutionary mechanisms explaining the similar species richness patterns in tropical mosses? Insights from the phylogeny of the pantropical genus Pelekium2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 105, p. 139-145Article in journal (Refereed)
  • 37. 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.

  • 38. O'Hara, Timothy D
    et al.
    Hugall, Andrew F
    Thuy, Ben
    Stöhr, Sabine
    Swedish Museum of Natural History, Department of Zoology.
    Martynov, Alexander
    Restructuring Higher Taxonomy using Broad-scale Phylogenomics: the Living Ophiuroidea2017In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 107, p. 415-430Article in journal (Refereed)
    Abstract [en]

    The power and throughput of next-generation sequencing is instigating a major transformation in our understanding of evolution and classification of life on our planet. The new trees of life are robust and comprehensive. Here we provide a landmark phylogeny of the living ophiuroids and use it as the basis for a major revision of the higher classification of this class of marine invertebrates. We used an exon-capture system to generate a 1484 exon (273kbp) data-matrix from DNA extracted from ethanol-preserved museum samples. We successfully obtained an average of 92% of our target sequence from 576 species spread across the known taxonomic diversity. The topology of the major lineages was robust to taxon sampling, exon-sampling, models and methods. However, estimates of node age were much less precise, varying by about a quarter of mean age. We used a combination of phylogenetic distinctiveness and temporal-banding to guide our revision of the family-level classification. Empirically, we determined that limiting family crown age to 110 ± 10 Ma (mid Cretaceous) selected phylogenetically distinct nodes while minimising disruption to the existing taxonomy. The resulting scheme of 32 families and six orders considerably expands the number of higher taxa. The families are generally longitudinally widespread across the world's oceans, although 17 are largely confined to temperate and equatorial latitudes and six to relatively shallow water (less than 1000 m depth).

  • 39.
    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.

  • 40.
    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.

  • 41. 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.

  • 42. 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.

  • 43. 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).

  • 44. 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)
  • 45. Otálora, Monica A.G.
    et al.
    Aragón, Gregorio
    Martínez, Isabel
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Cardinal characters on a slippery slope - A re-evaluation of phylogeny, character evolution, and evolutionary rates in the jelly lichens (Collemataceae s. str.)2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 68, p. 185-198Article in journal (Refereed)
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  • 46. Paśko, Łukasz
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Elzanowski, Andrzej
    Phylogenetic utility and evolution of indels: a study in neognathous birds.2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 61, no 3, p. 760-71Article in journal (Refereed)
    Abstract [en]

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

  • 47.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Lei, Fumin
    Gebauer, Axel
    Kaiser, Martin
    Helbig, Andreas J
    Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, no 1, p. 218-26Article in journal (Refereed)
    Abstract [en]

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

  • 48.
    Razafimandimbison, Sylvain
    Swedish Museum of Natural History, Department of Botany.
    Evolution of sexual systems and growth habit in Mussaenda (Rubiaceae): Insights into the evolutionary pathways of dioecy2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 123, p. 113-122Article in journal (Refereed)
  • 49. Terra-Araujo, Mario
    et al.
    de Faria, Aparecida
    Vicentini, Alberto
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Swenson, Ulf
    Swedish Museum of Natural History, Department of Botany.
    Species tree phylogeny and biogeography of the Neotropical genus Pradosia (Sapotaceae, Chrysophylloideae).2015In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 87, p. 1-13Article in journal (Refereed)
    Abstract [en]

    Recent phylogenetic studies in Sapotaceae have demonstrated that many genera need to be redefined to better correspond to natural groups. The Neotropical genus Pradosia is believed to be monophyletic and includes 26 recognized species. Here we reconstruct the generic phylogeny by a species-tree approach using ∗BEAST, 21 recognized species (36 accessions), sequence data from three nuclear markers (ITS, ETS, and RPB2), a relaxed lognormal clock model, and a fossil calibration. We explore the evolution of five selected morphological characters, reconstruct the evolution of habitat (white-sand vs. clayish soils) preference, as well as space and time by using a recently developed continuous diffusion model in biogeography. We find Pradosia to be monophyletic in its current circumscription and to have originated in the Amazon basin at ∼ 47.5 Ma. Selected morphological characters are useful to readily distinguish three clades. Preferences to white-sand and/or clay are somewhat important for the majority of species, but speciation has not been powered by habitat shifts. Pradosia brevipes is a relative young species (∼ 1.3 Ma) that has evolved a unique geoxylic life strategy within Pradosia and is restricted to savannahs. Molecular dating and phylogenetic pattern indicate that Pradosia reached the Brazilian Atlantic coast at least three times: at 34.4 Ma (P. longipedicellata), at 11.7 Ma (P. kuhlmannii), and at 3.9 Ma (weakly supported node within the red-flowered clade).

  • 50.
    Wahlberg, Emma
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Johanson, Kjell Arne
    Swedish Museum of Natural History, Department of Zoology.
    The age, ancestral distribution and radiation of Chimarra (Trichoptera: Philopotamidae) using molecular methods2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 79, p. 433-442Article in journal (Refereed)
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