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  • 1. Alerstam, Thomas
    et al.
    Rosén, Mikael
    Bäckman, Johan
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Hellgren, Olof
    Flight speeds among bird species: allometric and phylogenetic effects.2007In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 5, no 8, p. e197-Article in journal (Refereed)
    Abstract [en]

    Flight speed is expected to increase with mass and wing loading among flying animals and aircraft for fundamental aerodynamic reasons. Assuming geometrical and dynamical similarity, cruising flight speed is predicted to vary as (body mass)(1/6) and (wing loading)(1/2) among bird species. To test these scaling rules and the general importance of mass and wing loading for bird flight speeds, we used tracking radar to measure flapping flight speeds of individuals or flocks of migrating birds visually identified to species as well as their altitude and winds at the altitudes where the birds were flying. Equivalent airspeeds (airspeeds corrected to sea level air density, Ue) of 138 species, ranging 0.01-10 kg in mass, were analysed in relation to biometry and phylogeny. Scaling exponents in relation to mass and wing loading were significantly smaller than predicted (about 0.12 and 0.32, respectively, with similar results for analyses based on species and independent phylogenetic contrasts). These low scaling exponents may be the result of evolutionary restrictions on bird flight-speed range, counteracting too slow flight speeds among species with low wing loading and too fast speeds among species with high wing loading. This compression of speed range is partly attained through geometric differences, with aspect ratio showing a positive relationship with body mass and wing loading, but additional factors are required to fully explain the small scaling exponent of Ue in relation to wing loading. Furthermore, mass and wing loading accounted for only a limited proportion of the variation in Ue. Phylogeny was a powerful factor, in combination with wing loading, to account for the variation in Ue. These results demonstrate that functional flight adaptations and constraints associated with different evolutionary lineages have an important influence on cruising flapping flight speed that goes beyond the general aerodynamic scaling effects of mass and wing loading.

  • 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. Alstrom, Per
    et al.
    Olsson, Urban
    Rasmussen, Pamela C.
    Yao, Cheng-Te
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sundberg, Per
    Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)2007In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 149, no 3, p. 437-452Article in journal (Refereed)
  • 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.
    Höhna, Sebastian
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Olsson, Urban
    Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.2011In: BMC evolutionary biology, ISSN 1471-2148, Vol. 11, p. 352-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.

    RESULTS: There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).

    CONCLUSIONS: The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.

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

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

  • 9. 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.

  • 10. 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.

  • 11. Chiappe, Luis M
    et al.
    Lamb, James P
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    New enantiornithine bird from the marine Upper Cretaceous of Alabama2002In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 22, no 1, p. 170-174Article in journal (Refereed)
  • 12. Dalsätt, J
    et al.
    Zhou, Z
    Zhang, F
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Food remains in Confuciusornis sanctus suggest a fish diet.2006In: Die Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 93, no 9, p. 444-6Article in journal (Refereed)
    Abstract [en]

    Despite hundreds of excellent fossils of Confuciusornis, the most abundant group of birds in the Early Cretaceous, 'Jehol Biota' in China, there is yet no indication of the food choice of these birds. Here, we describe fish remains preserved in the alimentary system of a specimen of Confuciusornis sanctus from the Jiufotang Formation. This find is about five million years younger than all previously published confuciusornithid birds from the Yixian Formation. Although it is unknown how common fish was in the diet of Confuciusornis, the find does not support previous hypotheses that it fed on plants or grain.

  • 13.
    Dalsätt, Johan
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fossil birds from the Miocene and Pliocene of Hambach (NW Germany)2006In: Palaeontographica. Abteilung A, Palaozoologie, Stratigraphie, ISSN 0375-0442, Vol. 277, no 1-6, p. 113-+Article in journal (Refereed)
  • 14. Dickinson, Edward C
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Systematic notes on Asian birds 32: The type locality of Hirundo daurica Laxmann, 17692002In: Zoologische Verhandelingen Leiden, ISSN 0024-1652, Vol. 340, p. 205-206Article in journal (Refereed)
    Abstract [en]

    The restricted type locality suggested by Brooke (1974) for Hirundo daurica Laxmann, 1769 was apparently made without a translation of the original Swedish description. With this in hand we find it necessary to correct that restriction and move the type locality some 2500 km west.

  • 15. Drovetski, Sergei V.
    et al.
    Zink, Robert M.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fadeev, Igor V.
    A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats2010In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 37, no 4, p. 696-706Article in journal (Refereed)
  • 16. Ekman, Jan
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Out of Gondwanaland; the evolutionary history of cooperative breeding and social behaviour among crows, magpies, jays and allies.2006In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, no 1590, p. 1117-25Article in journal (Refereed)
    Abstract [en]

    Cooperative breeding is comparatively rare among birds in the mainly temperate and boreal Northern Hemisphere. Here we test if the distribution of breeding systems reflects a response to latitude by means of a phylogenetic analysis using correlates with geographical range among the corvids (crows, jays, magpies and allied groups). The corvids trace their ancestry to the predominantly cooperative 'Corvida' branch of oscine passerines from the Australo-Papuan region on the ancient Gondwanaland supercontinent, but we could not confirm the ancestral state of the breeding system within the family, while family cohesion may be ancestral. Initial diversification among pair-breeding taxa that are basal in the corvid phylogeny, represented by genera such as Pyrrhocorax and Dendrocitta, indicates that the corvid family in its current form could have evolved from pair-breeding ancestors only after they had escaped the Australo-Papuan shield. Within the family, cooperative breeding (alloparental care/family cohesion) is strongly correlated to latitude and its predominance in species maintaining a southerly distribution indicates a secondary evolution of cooperative breeding in the lineage leading away from the basal corvids. Multiple transitions show plasticity in the breeding system, indicating a response to latitude rather than evolutionary inertia. The evolutionary background to the loss of cooperative breeding among species with a northerly distribution is complex and differs between species, indicating a response to a variety of selection forces. Family cohesion where the offspring provide alloparental care is a main route to cooperatively breeding groups among corvids. Some corvid species lost only alloparental care, while maintaining coherent family groups. Other species lost family cohesion and, as a corollary, they also lost the behaviour where retained offspring provide alloparental care.

  • 17.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Aves: The living descendants of flying dinosaurs2014In: The tree of life: Evolution and classification of living organisms / [ed] Vargas, Pablo & Zardoya, Rafael, Sunderland, MA: Sinauer Associates, Inc. , 2014, p. 530-540Chapter in book (Refereed)
  • 18.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Current perspectives on the evolution of birds2008In: Contributions to zoology, ISSN 1383-4517, E-ISSN 1875-9866, Vol. 77, no 2, p. 109-116Article in journal (Refereed)
  • 19.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Evolution of terrestrial birds in three continents: biogeography and parallel radiations2012In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, no 5, p. 813-824Article in journal (Refereed)
  • 20.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Interpretations of Archaeological Bird Remains - a Taphonomic Approach1987In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 14, no 1, p. 65-75Article in journal (Refereed)
  • 21.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Systematic relationships of the palaeogene family Presbyornithidae (Aves: Anseriformes)1997In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 121, no 4, p. 429-483Article in journal (Refereed)
    Abstract [en]

    The early Tertiary (Paleocene and Eocene) family Presbyornithidae is one of the most completely known group of fossil birds. Essentially all parts of the skeleton are represented in the fossil record, allowing a thorough analysis of the phylogenetic position of the family. Forty-two families of nonpasserine birds representing the orders Ciconiiformes, Anseriformes, Galliformes, Gruiformes and Charadriiformes, were included in a cladistic analysis of 71 skeletal characters. The previously suggested anseriform affinity of the Presbyornithidae was confirmed. Furthermore, the family proved to be closer to the Anatidae than to the Anhimidae or Anseranatidae. The many postcranial similarities with certain charadriiform birds as the Burhinidae, obviously are plesiomorphies. By this observation, a better undestanding of character evolution in nonpasserine skeletal morphology is gained. The often suggested close relationship of anseriform and galliform birds is not confirmed by osteology. Instead, the Anseriformes and the Phoenicopteridae form a monophyletic clade that is the sister to the remaining ciconiiform birds. This result renders the Ciconiiformes sensu Wetmore (1960) polyphyletic. (C) 1997 The Linnean Society of London.

  • 22.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    The skeletal evidence for a sister-group relationship of anseriform and galliform birds - A critical evaluation1996In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 27, no 3, p. 195-202Article in journal (Refereed)
    Abstract [en]

    The osteological basis for the proposed close phylogenetical relationship of anseriform and galliform birds is evaluated and found to be very weak. Out of eleven postulated synapomorphies in cranial morphology (Cracraft 1988), three must be excluded since they express variation that is already covered by any of the other eleven characters. Another six of the postulated synapomorhies either cannot be verified to occur in most anseriforms and galliforms, or have a wide distribution outside this group. A re-analysis of the combined morphological and biochemical data set of Cracraft and Mindell (1989) with the questionable osteological characters excluded, does not corroborate an anseriform-galliform sister-group relationship, but leaves the Neognathae unresolved.

  • 23.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Anderson, Caisa Lisa
    Mayr, Gerald
    Hangin' on to our rocks 'n clocks: a reply to Brown et al2007In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 3, no 3, p. 260-261Article in journal (Other academic)
  • 24.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Anderson, Cajsa L
    Britton, Tom
    Elzanowski, Andrzej
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Källersjö, Mari
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Parsons, Thomas J
    Zuccon, Dario
    Mayr, Gerald
    Diversification of Neoaves: integration of molecular sequence data and fossils.2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 543-7Article in journal (Refereed)
    Abstract [en]

    Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

  • 25.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Carrasquilla, F. H.
    Subspecific identity of prehistoric Baltic cormorants Phalacrocorax carbo1997In: Ardea, ISSN 0373-2266, E-ISSN 2213-1175, Vol. 85, no 1, p. 1-7Article in journal (Refereed)
    Abstract [en]

    Cormorants of the subspecies Phalacrocorax carbo sinensis breed in large numbers in the Baltic Sea. They migrate to the Mediterranean region to winter and are then replaced in the Baltic by wintering individuals of the Norwegian population of the nominate subspecies carbo. Cormorants bred in the Baltic during prehistoric times too, but as evident from a comparison of skeletal measurements in present-day and prehistoric Cormorants, these individuals belonged to the nominate subspecies carbo. The Swedish subfossil record of the Cormorants available for study, does not include any remains small enough to suggest the presence of sinensis. Precisely when the subspecies sinensis immigrated into the Baltic is unknown, but it must have occurred sometime between 1500 and 1800 AD.

  • 26.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Cooper, Alan
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jackson, Jennifer
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Norman, Janette A
    A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens.2002In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 269, no 1488, p. 235-41Article in journal (Refereed)
    Abstract [en]

    Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.

  • 27.
    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).

  • 28.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Envall, Ida
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Norman, Janette A
    Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data.2003In: BMC evolutionary biology, ISSN 1471-2148, Vol. 3, p. 16-Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 29.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Evolution, biogeography, and patterns of diversification in passerine birds2003In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 34, no 1, p. 3-15Article in journal (Refereed)
    Abstract [en]

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

  • 30.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Jansén, Anna-Lee
    Stockholms universitet.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Ekman, Jan
    Uppsala universitet.
    Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data2005In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 36, no 3, p. 222-234Article in journal (Refereed)
    Abstract [en]

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

  • 31.
    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.

  • 32.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Erratum: Major divisions of oscines revealed by insertions in the nuclear gene c-myc: A novel gene in avian phylogenetics (vol 117, pg 1077, 2000)2001In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 118, no 2, p. 563-563Article in journal (Other academic)
  • 33.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Parsons, Thomas J.
    Major divisions in oscines revealed by insertions in the nuclear gene c-myc: A novel gene in avian phylogenetics2000In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 117, no 4, p. 1069-1078Article in journal (Refereed)
  • 34.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Klopfstein, Seraina
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nguyen, Jacqueline MT
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dating the diversification of the major lineages of Passeriformes (Aves)2014In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, no 8, p. 1-15Article in journal (Refereed)
    Abstract [en]

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

  • 35.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Olson, Storrs L.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Alvarenga, Herculano
    Fjeldsa, Jon
    Circumscription of a monophyletic family for the tapaculos (Aves: Rhinocryptidae)2010In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 151, no 2, p. 337-345Article in journal (Refereed)
  • 36.
    Ericson, Per G P
    et al.
    Swedish Museum of Natural History, Research Division.
    Tyrberg, T.
    Kjellberg, A. S.
    Jonsson, L.
    Ullen, I.
    The earliest record of house sparrows (Passer domesticus) in northern Europe1997In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 24, no 2, p. 183-190Article in journal (Refereed)
    Abstract [en]

    Remains of the house sparrow (Passer domesticus) recovered from a late Bronze Age (1200-800 sc) settlement in central Sweden are described. The house sparrow is conspicuously rare in prehistoric Europe, and this record constitutes the earliest from the northern part. The find predates the introduction of domestic fowl (Gallus gallus) to Sweden, a species with which the house sparrow has been assumed to be spread simultaneously. Instead, it is here suggested that house sparrows most likely spread over Europe along with the horse Equus caballus. (C) 1997 Academic Press Limited

  • 37.
    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.

  • 38. 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)
  • 39. Fjeldsa, Jon
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    The Cinnamon Ibon Hypocryptadius cinnamomeus is a forest canopy sparrow2010In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 152, no 4, p. 747-760Article in journal (Refereed)
  • 40. Fjeldsa, Jon
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jonsson, Knud A.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogeny of the ovenbird genus Upucerthia: a case of independent adaptations for terrestrial life2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 2, p. 133-141Article in journal (Refereed)
  • 41. Fjeldså, Jon
    et al.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Molecular data reveal some major adaptational shifts in the early evolution of the most diverse avian family, the Furnariidae2005In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 146, no 1, p. 1-13Article in journal (Refereed)
    Abstract [en]

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

  • 42. Fjeldså, Jon
    et al.
    Zuccon, Dario
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sapayoa aenigma: a New World representative of 'Old World suboscines'.2003In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 270 Suppl 2, p. S238-41Article in journal (Refereed)
    Abstract [en]

    Passerine birds are very plastic in their adaptations, which has made it difficult to define phylogenetic lineages and correctly allocate all species to these. Sapayoa aenigma, a member of the large group of New World flycatchers, has been difficult to place, and DNA-DNA hybridization experiments have indicated that it may have been misplaced. This is confirmed here, as base sequencing of two nuclear genes places it as a deep branch in the group of broadbills and pittas of the Old World tropics. The peculiar distribution of this lineage may be best explained in terms of a Gondwanic and Late Cretaceous origin of the passerine birds, as this particular lineage dispersed from the Antarctic landmass, reaching the Old World tropics via the drifting Indian plate, and South America via the West Antarctic Peninsula.

  • 43.
    Fuchs, Jerome
    et al.
    Departement Systematique et Evolution, UMR7205 Institut de Systematique, Evolution, Biodiversite CNRS MNHN UPMC EPHE, Sorbonne Universites, Museum National d’Histoire Naturelle, CP 51, 57 rue Cuvier, F-75231 Paris Cedex 05, France.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bonillo, Céline
    Couloux, Arnaud
    Pasquet, Eric
    The complex phylogeography of the Indo-Malayan Alophoixus bulbuls with the description of a putativenew ring species complex2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, p. 5460-5474Article in journal (Refereed)
    Abstract [en]

    The Indo-Malayan bioregion has provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such that their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from Sundaland with sequential divergence of taxa from southwest to northeast characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a ring species model driven by geographic isolation. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo-Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo-Malaya.

  • 44. Fuchs, Jerome
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Mitochondrial phylogeographic structure of the white-browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina2008In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 35, no 3, p. 565-575Article in journal (Refereed)
  • 45. Fuchs, Jerome
    et al.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)2006In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 37, no 5, p. 487-496Article in journal (Refereed)
  • 46. Fuchs, Jerome
    et al.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 1, p. 11-25Article in journal (Refereed)
  • 47. 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.

  • 48. 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.

  • 49.
    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)
  • 50. 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.

123 1 - 50 of 118
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