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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 161-176Article in journal (Refereed)
  • 2. Alström, Per
    et al.
    Jønsson, Knud A.
    Fjeldså, Jon
    Ödeen, Anders
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dramatic niche shifts and morphological change in two insular bird species2015In: Royal Society Open Science, ISSN 2054-5703, Vol. 2, article id 140364Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

  • 5.
    Bengtson, Annika
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Pruski, John F.
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    Phylogeny of the Athroismeae (Asteraceae), with a new circumscription of the tribe2017In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 66, no 2, p. 408-420Article in journal (Refereed)
    Abstract [en]

    Athroismeae is a small tribe of the Asteraceae-Asteroideae, the members of which show considerable variation in morphology. A molecular phylogenetic study of the tribe is presented for the first time, based on plastid (ndhF, trnH-psbA, trnL-trnF) and nuclear data (ETS, ITS). The phylogenetic relationships between the different genera within Athroismeae are discussed, and in addition, three unispecific genera: Anisochaeta, Artemisiopsis and Symphyllocarpus as well as Duhaldea (Inula) stuhlmannii, all earlier placed in other tribes, are here shown to belong within Athroismeae. Symphyllocarpus is sister to Centipeda and the earlier Symphyllocarpinae includes Centipedinae in synonymy. Furthermore, Cardosoa and Philyrophyllum are found to be integrated within Anisopappus and their generic status cannot be maintained. An outline of an amended circumscription of the Athroismeae is presented, with three new combinations and a description of the new subtribe Lowryanthinae.

  • 6. Brace, Selina
    et al.
    Thomas, Jessica A.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Burger, Joachim
    MacPhee, Ross D. E.
    Barnes, Ian
    Turvey, Samuel T.
    Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 12, p. 3095-3103Article in journal (Refereed)
    Abstract [en]

    The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a similar to 750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.

  • 7. Cahill, James A
    et al.
    Stirling, Ian
    Kistler, Logan
    Salamzade, Rauf
    Ersmark, Erik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Stockholms Universitet.
    Fulton, Tara L
    Stiller, Mathias
    Green, Richard E
    Shapiro, Beth
    Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed a remarkable episode of polar bear gene flow into the population of brown bears that colonized the Admiralty, Baranof, and Chichagof Islands (ABC Islands) of Alaska. Here, we present an analysis of data from a large panel of polar bear and brown bear genomes that includes brown bears from the ABC Islands, the Alaskan mainland and Europe. Our results provide clear evidence that gene flow between the two species had a geographically wide impact, with polar bear DNA found within the genomes of brown bears living both on the ABC Islands and in the Alaskan mainland. Intriguingly, while brown bear genomes contain up to 8.8% polar bear ancestry, polar bear genomes appear to be devoid of brown bear ancestry, suggesting the presence of a barrier to gene flow in that direction. This article is protected by copyright. All rights reserved.

  • 8.
    Cannon, Johanna
    et al.
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Vellutini, Bruno
    Sars International Centre for Marine Molecular Biology.
    Smith, Julian
    Winthrop University.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jondelius, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Hejnol, Andreas
    Sars International Centre for Marine Molecular Biology.
    Xenacoelomorpha is the sister group to Nephrozoa2016In: Nature, ISSN ISSN: 0028-0836, Vol. 530, p. 89-93Article in journal (Refereed)
    Abstract [en]

    The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships1. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (= Nephrozoa, namely protostomes and deuterostomes)2,3 or is a clade inside Deuterostomia4. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long- branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa. 

  • 9. Cappellini, Enrico
    et al.
    Gentry, Anthea
    Palkopoulou, Eleftheria
    Ishida, Yasuko
    Cram, David
    Roos, Anna-Marie
    Watson, Mick
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Fernholm, Bo
    Swedish Museum of Natural History, Department of Zoology.
    Agnelli, Paolo
    Barbagli, Fausto
    Littlewood, D. Tim. J.
    Kelstrup, Christian D.
    Olsen, Jesper V.
    Lister, Adrian M.
    Roca, Alfred L.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Resolution of the type material of the Asian elephant, Elephas maximus Linnaeus, 1758 (Proboscidea, Elephantidae)2014In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 170, p. 222-232Article in journal (Refereed)
  • 10. Chang, Dan
    et al.
    Knapp, Michael
    Enk, Jacob
    Lippold, Sebastian
    Kircher, Martin
    Lister, Adrian
    MacPhee, Ross D. E.
    Widga, Christopher
    Czechowski, Paul
    Sommer, Robert
    Hodges, Emily
    Stuempel, Nikolaus
    Barnes, Ian
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Derevianko, Anatoly
    Germonpre, Mietje
    Hillebrand-Voiculescu, Alexandra
    Constantin, Silviu
    Kuznetsova, Tatyana
    Mol, Dick
    Rathgeber, Thomas
    Rosendahl, Wilfried
    Tikhonov, Alexey N.
    Willerslev, Eske
    Hannon, Greg
    Lalueza-Fox, Carles
    Joger, Ulrich
    Poinar, Hendrik
    Hofreiter, Michael
    Shapiro, Beth
    The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44585Article in journal (Refereed)
  • 11. Collinson, J M
    et al.
    McGowan, R Y
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    First British records of ‘Eastern’ and ‘Western’ Subalpine Warblers2014In: British birds, Vol. 107, p. 282-285Article, book review (Other (popular science, discussion, etc.))
  • 12.
    Dalen, Love
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lagerholm, Vendela K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barton, Nick
    Bochenski, Zbigniew M.
    Tomek, Teresa
    Rudling, David
    Ericson, Per G. P.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Stewart, John R.
    Identifying Bird Remains Using Ancient DNA Barcoding2017In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 8, no 6, article id 169Article in journal (Refereed)
  • 13. Dalerum, Fredrik
    et al.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frojd, Christina
    Lecomte, Nicolas
    Lindgren, Asa
    Meijer, Tomas
    Pecnerova, Patricia
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Angerbjorn, Anders
    Spatial variation in Arctic hare (Lepus arcticus) populations around the Hall Basin2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 10, p. 2113-2118Article in journal (Refereed)
  • 14.
    Daume, Stefan
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University of Göttingen; Stockholm Resilience Centre.
    Mining Twitter to monitor Invasive Alien Species – An analytical framework and sample information topologies2016In: Ecological Informatics, ISSN 1574-9541, E-ISSN 1878-0512, Vol. 31, p. 70-82Article in journal (Refereed)
    Abstract [en]

    Social online media increasingly emerge as important informal information sources that can contribute to the detection of trends and early warnings in critical fields such as public health monitoring or emergency management. In the face of global environmental challenges the utilization of this information in ecological monitoring contexts has been called for, but examples remain sparse. This can be attributed to the significant technical challenges in processing this data and concerns about the quality, reliability and applicability of information mined from social media to the ecological domain. Here the strength and weaknesses of social media mining for ecological monitoring are assessed using the micro-blogging service Twitter and invasive alien species (IAS) monitoring as an example. The assessment is based on a manual analysis of 2842 Tweets sampled from Twitter data with potential direct or descriptive references to IAS impacting forest ecosystems, which was collected over a period of nearly three years. The results are presented as information topologies for Twitter messages of observational and non-observational character for three IAS with distinctive characteristics (Oak Processionary Moth, Emerald Ash Borer, Eastern Grey Squirrel). The results show that the social media channel Twitter is a rich source of primary and secondary observational biodiversity information. It also provides useful insights in the topical landscape of public communications on IAS as well as the public perception of IAS and IAS management. The analysis suggests broad application opportunities in IAS monitoring and management, and points at applications for related environmental questions. The results highlight that social media mining for ecological monitoring needs to be approached with the same best practices as ecological monitoring in general, requiring a good understanding of the monitored subjects and specific monitoring questions. The challenges in utilizing this information for operational systems are of technical rather than conceptual nature and include extending the degree of automation, especially with regard to image recognition and the automatic provisioning of location information.

  • 15.
    Daume, Stefan
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University Göttingen, Germany.
    Albert, Matthias
    Northwest German Forest Research Institute.
    Gadow, von, Klaus
    University Göttingen, Germany.
    Assessing citizen science opportunities in forest monitoring using probabilistic topic modelling2014In: Forest Ecosystems, ISSN 2197-5620, Vol. 1, no 11, p. 1-12Article in journal (Refereed)
    Abstract [en]

    Background

    With mounting global environmental, social and economic pressures the resilience and stability of forests and thus the provisioning of vital ecosystem services is increasingly threatened. Intensified monitoring can help to detect ecological threats and changes earlier, but monitoring resources are limited. Participatory forest monitoring with the help of “citizen scientists” can provide additional resources for forest monitoring and at the same time help to communicate with stakeholders and the general public. Examples for citizen science projects in the forestry domain can be found but a solid, applicable larger framework to utilise public participation in the area of forest monitoring seems to be lacking. We propose that a better understanding of shared and related topics in citizen science and forest monitoring might be a first step towards such a framework.

    Methods

    We conduct a systematic meta-analysis of 1015 publication abstracts addressing “forest monitoring” and “citizen science” in order to explore the combined topical landscape of these subjects. We employ ‘topic modelling’, an unsupervised probabilistic machine learning method, to identify latent shared topics in the analysed publications.

    Results

    We find that large shared topics exist, but that these are primarily topics that would be expected in scientific publications in general. Common domain-specific topics are under-represented and indicate a topical separation of the two document sets on “forest monitoring” and “citizen science” and thus the represented domains. While topic modelling as a method proves to be a scalable and useful analytical tool, we propose that our approach could deliver even more useful data if a larger document set and full-text publications would be available for analysis.

    Conclusions

    We propose that these results, together with the observation of non-shared but related topics, point at under-utilised opportunities for public participation in forest monitoring. Citizen science could be applied as a versatile tool in forest ecosystems monitoring, complementing traditional forest monitoring programmes, assisting early threat recognition and helping to connect forest management with the general public. We conclude that our presented approach should be pursued further as it may aid the understanding and setup of citizen science efforts in the forest monitoring domain.

  • 16.
    Daume, Stefan
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University of Göttingen; Stockholm Resilience Centre.
    Galaz, Victor
    Stockholm Resilience Centre, Stockholm University.
    “Anyone Know What Species This Is?” – Twitter Conversations as Embryonic Citizen Science Communities2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3Article in journal (Refereed)
    Abstract [en]

    Social media like blogs, micro-blogs or social networks are increasingly being investigated and employed to detect and predict trends for not only social and physical phenomena, but also to capture environmental information. Here we argue that opportunistic biodiversity observations published through Twitter represent one promising and until now unexplored example of such data mining. As we elaborate, it can contribute to real-time information to traditional ecological monitoring programmes including those sourced via citizen science activities. Using Twitter data collected for a generic assessment of social media data in ecological monitoring we investigated a sample of what we denote biodiversity observations with species determination requests (N = 191). These entail images posted as messages on the micro-blog service Twitter. As we show, these frequently trigger conversations leading to taxonomic determinations of those observations. All analysed Tweets were posted with species determination requests, which generated replies for 64% of Tweets, 86% of those contained at least one suggested determination, of which 76% were assessed as correct. All posted observations included or linked to images with the overall image quality categorised as satisfactory or better for 81% of the sample and leading to taxonomic determinations at the species level in 71% of provided determinations. We claim that the original message authors and conversation participants can be viewed as implicit or embryonic citizen science communities which have to offer valuable contributions both as an opportunistic data source in ecological monitoring as well as potential active contributors to citizen science programmes.

  • 17.
    de Jong, Yde
    et al.
    University of Amsterdam.
    Kouwenberg, Juiana
    Boumans, Louis
    Hussey, Charles
    Hyam, Roger
    Nicolson, Nicola
    Kirk, Paul
    Paton, Alan
    Michel, Ellinor
    Guiry, Michael D,
    Boegh, Phillip S.
    Aerenlund Pedersen, Henrik
    Enghoff, Henrik
    von Raab-Straube, Eckhard
    Güntsch, Anton
    Geoffroy, Marc
    Müller, Andreas
    Kohlbecker, Andreas
    Berendsohn, Walter
    Appeltans, Ward
    Arvantidis, Christos
    Vanhoorne, Bart
    Declerck, Joram
    Vandepitte, Leen
    Hernandez, Francisco
    Nash, Róisín
    Costello, Mark John
    Ouvrard, David
    Bezard-Falgas, Pascale
    Bourgoin, Thierry
    Wetzel, Florian Tobias
    Glöckler, Falko
    Korb, Günther
    Ring, Caroline
    Hagedorn, Gregor
    Häuser, Christoph
    Aktaç, Nihat
    Asan, Ahmet
    Ardelean, Adorian
    Vieira Borges, Paulo Alexandre
    Dhora, Dhimiter
    Khachatryan, Hasmik
    Malicky, Michael
    Ibrahimov, Shaig
    Tuzikov, Alexander
    De Wever, Aike
    Moncheva, Snejana
    Spassov, Nikolai
    Chobot, Karel
    Popov, Alexei
    Borsíc, Igor
    Sfenthourakis, Spyros
    Köljalg, Urmas
    Uotila, Pertti
    Olivier, Gargominy
    Dauvin, Jean-Claude
    Tarkhnishvili, David
    Chaladze, Giorgi
    Tuerkay, Michael
    Legakis, Anastasios
    Peregovits, LáslZó
    Gudmundsson, Gudmundur
    Ólafsson, Erling
    Lysaght, Liam
    Galil, Bella Sarah
    Raimondo, Francesco M.
    Domina, Gianniantonio
    Stoch, Fabio
    Minelli, Alessandro
    Spungis, Voldemars
    Budrys, Eduardas
    Olenin, Sergei
    Turpel, Armand
    Walisch, Tania
    Krpach, Vladimir
    Gambin, Marie Therese
    Ungureano, Laurentia
    Karaman, Gordan
    Kleukers, Roy M. J. C.
    Stur, Elisabeth
    Aagaard, Kaare
    Valland, Nils
    Loennechen Moen, Tori
    Bogdanowicz, Wieslaw
    Tykarski, Piotr
    Wieslawski, Jan Marcin
    Kedra, Monika
    de frias Martins, ntonio M.
    Domingos Abreu, António
    Silva, Ricardo
    Medvedev, Sergei
    Ryss, Alexander
    Simic, Smilijka
    Marhold, Karel
    Stloukal, Eduard
    Tome, Davorin
    Ramos, Marian A.
    Valdés, Benito
    Pina, Francisco
    Kullander, Sven
    Swedish Museum of Natural History, Department of Zoology.
    Anders, Telenius
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gonseth, Yves
    Tschudin, Pascal
    Sergeyeva, Oleksandra
    Vladymyrov, Volodymyr
    Bogdanovych Rizun, Volodymyr
    Raper, Chris
    Lear, Dan
    Stoev, Pavel
    Penev, Lyubomir
    Casino Rubio, Ana
    Backeljau, Thierry
    Saarenmaa, Hannu
    Ullenberg, Sandrine
    PESI - a taxonomic backbone for Europe2015In: Biodiversity Data Journal, ISSN 1314-2836, E-ISSN 1314-2828, Vol. 3, p. 1-51, article id e5848Article in journal (Refereed)
    Abstract [en]

    Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.

    The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

    This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

  • 18. Divakar, Pradeep K.
    et al.
    Crespo, Ana
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi2015In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, p. 1217-1226Article in journal (Refereed)
  • 19. Dupont, Chris L
    et al.
    Larsson, John
    Yooseph, Shibu
    Ininbergs, Karolina
    Goll, Johannes
    Asplund-Samuelsson, Johannes
    McCrow, John P
    Celepli, Narin
    Allen, Lisa Zeigler
    Ekman, Martin
    Lucas, Andrew J
    Hagström, Åke
    Thiagarajan, Mathangi
    Brindefalk, Björn
    Richter, Alexander R
    Andersson, Anders F
    Tenney, Aaron
    Lundin, Daniel
    Tovchigrechko, Andrey
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Brami, Daniel
    Badger, Jonathan H
    Allen, Andrew E
    Rusch, Douglas B
    Hoffman, Jeff
    Norrby, Erling
    Friedman, Robert
    Pinhassi, Jarone
    Venter, J Craig
    Bergman, Birgitta
    Functional tradeoffs underpin salinity-driven divergence in microbial community composition.2014In: PloS one, ISSN 1932-6203, Vol. 9, no 2, p. e89549-Article in journal (Refereed)
    Abstract [en]

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  • 20. Díez, Beatriz
    et al.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Ininbergs, Karolina
    Dupont, Christopher L
    Allen, Andrew E
    Yooseph, Shibu
    Rusch, Douglas B
    Bergman, Birgitta
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5Article in journal (Refereed)
    Abstract [en]

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

  • 21. Elmhagen, Bodil
    et al.
    Destouni, Georgia
    Angerbjorn, Anders
    Borgstrom, Sara
    Boyd, Emily
    Cousins, Sara A. O.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ehrlen, Johan
    Ermold, Matti
    Hamback, Peter A.
    Hedlund, Johanna
    Hylander, Kristoffer
    Jaramillo, Fernando
    Lagerholm, Vendela K.
    Lyon, Steve W.
    Moor, Helen
    Nykvist, Bjorn
    Pasanen-Mortensen, Marianne
    Plue, Jan
    Prieto, Carmen
    van der Velde, Ype
    Lindborg, Regina
    Interacting effects of change in climate, human population, land use, and water use on biodiversity and ecosystem services2015In: Ecology & society, ISSN 1708-3087, E-ISSN 1708-3087, Vol. 20, no 1, article id UNSP 23Article in journal (Refereed)
  • 22.
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Konsten att göra en höna av en fjäder: DNA-streckkoder i praktiken2014In: Bi-lagan, ISSN 2000-8139, Vol. 1, p. 17-18Article in journal (Other (popular science, discussion, etc.))
    Abstract [sv]

    Med hjälp av korta artspecifika delar av DNA:t, så kallade DNA-streckkoder, är det möjligt att artbestämma till exempel en fågel utifrån bara en fjäder. I och med att tekniken blivit både enklare och billigare har tiden nu blivit mogen för att introducera DNA-streckkoder i skolundervisningen.

  • 23.
    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.

  • 24.
    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.

  • 25.
    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).

  • 26.
    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.

  • 27.
    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.

  • 28.
    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.

  • 29.
    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)
  • 30.
    Ericson, Per G. P.
    et al.
    Swedish Museum of Natural History, Research Division.
    Qu, Yanhua
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blom, Mozes P. K.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Johansson, Ulf S.
    Swedish Museum of Natural History, Department of Zoology.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    A genomic perspective of the pink-headed duck Rhodonessa caryophyllacea suggests a long history of low effective population size2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 16853Article in journal (Refereed)
    Abstract [en]

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

  • 31.
    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.

  • 32.
    Ersmark, Erik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Orlando, Ludovic
    Sandoval-Castellanos, Edson
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Barnes, Ian
    Barnett, Ross
    Stuart, Anthony
    Lister, Adrian
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Population Demography and Genetic Diversity in the Pleistocene Cave Lion2015In: Open Quaternary, Vol. 1, no 4, p. 1-14Article in journal (Refereed)
  • 33. Ertz, Damien
    et al.
    Tehler, Anders
    Swedish Museum of Natural History, Department of Botany.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frisch, Andreas
    Thor, Göran
    Pieter, van den Boom
    A large-scale phylogenetic revision of Roccellaceae (Arthoniales) reveals eight new genera2015In: Fungal Diversity, Vol. 70, no 1, p. 31-53Article in journal (Refereed)
  • 34. Fabre, Pierre-Henri
    et al.
    Moltensen, Maria
    Fjeldsa, Jon
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lessard, Jean-Philippe
    Jonsson, Knud A.
    Multiple waves of colonization by monarch flycatchers (Myiagra, Monarchidae) across the Indo-Pacific and their implications for coexistence and speciation2014In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 41, no 2, p. 274-286Article in journal (Refereed)
    Abstract [en]

    Aim Islands and archipelagos have played an important role in the development of ecological and evolutionary theories. Using a newly compiled molecular phylogeny we infer the biogeographical history of a monarch flycatcher genus, Myiagra, which is distributed across the Indo-Pacific. We subsequently integrate biogeographical and ecomorphological data to examine the role of dispersal and trait evolution in the build-up of avian assemblages. Location Australia, the Moluccas, New Guinea and Pacific islands. Methods We generated a taxonomically densely sampled mitochondrial DNA dataset that included almost all species and subspecies of the reciprocally monophyletic genera Myiagra and Arses. We then used maximum likelihoood and Bayesian inference to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the tree topology and then used Lagrange to infer ancestral geographical areas. Finally, we combined ancestral area reconstructions with information on ecomorphological traits to infer mechanisms underlying community assembly. Results We provide the first comprehensive molecular phylogenetic reconstruction for Myiagra and Arses monarch flycatchers. Our phylogenetic reconstruction reveals a relatively recent diversification from the Miocene associated with several major dispersal events. Ancestral area reconstruction reveals several independent colonizations of the Moluccas, Melanesia, Fiji and the Micronesian islands. Ancestral state reconstruction of ecological traits suggests that the diversity of traits in co-occurring species of monarch flycatchers results from independent colonization events and ecological niche conservatism rather than in situ diversification. Main conclusions Three waves of colonization, non-overlapping in time, led to independent speciation events in the Bismarcks, Fiji and the Moluccas, in addition to in situ speciation events on remote islands of Micronesia, the Solomons, Vanuatu and Samoa. Few of these colonizations have led to the co-occurrence of congenerics or species with similar ecomorphological profiles on the same island. Thus, we suggest that priority effects might prevent new colonizers from establishing themselves if they share high levels of ecological similarity with resident species. We conclude that historical dispersal to and colonization of new islands, combined with ecologically deterministic priority effects, drove the assembly of insular monarch flycatcher communities across the Indo-Pacific.

  • 35. 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)
  • 36. 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)
  • 37. 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.

  • 38. 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.

  • 39. 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)
  • 40. 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)
  • 41. 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.

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

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

  • 43.
    Gopalakrishnan, Shyam
    et al.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Samaniego Castruita, Jose A.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Sinding, Mikkel-Holger S.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Kuderna, Lukas F. K.
    Institute of Evolutionary Biology (UPF-CSIC), PRBB Dr. CNAG-CRG, Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) .
    Räikkönen, Jannikke
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Petersen, Bent
    Department of Bio and Health Informatics Technical University of Denmark .
    Sicheritz-Ponten, Thomas
    Department of Bio and Health Informatics Technical University of Denmark .
    Larson, Greger
    Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art University of Oxford .
    Orlando, Ludovic
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Marques-Bonet, Tomas
    Institute of Evolutionary Biology (UPF-CSIC), PRBB Dr. CNAG-CRG, Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology (BIST) Catalan Institution of Research and Advanced Studies (ICREA).
    Hansen, Anders J.
    Centre for GeoGenetics, Natural History Museum of Denmark University of Copenhagen.
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gilbert, M. Thomas P.
    Centre for GeoGenetics, Natural History Museum of Denmark University of CopenhagenTrace and Environmental DNA Laboratory, Department of Environment and Agriculture Curtin University, NTNU University Museum, Norwegian University of Science and Technology.
    The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics2017In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, no 495, p. 1-11Article in journal (Refereed)
  • 44. Haddad, Nizar Jamal
    et al.
    Al-Nakeeb, Kosai
    Petersen, Bent
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Blom, Nikolaj
    Sicheritz-Ponten, Thomas
    Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)2017In: MITOCHONDRIAL DNA PART B-RESOURCES, ISSN 2380-2359, Vol. 2, p. 139-140Article in journal (Refereed)
  • 45. Hambäck, Peter A.
    et al.
    Weingartner, Elisabeth
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Wirta, Helena
    Roslin, Tomas
    Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes2016In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 23, p. 8431-8439Article in journal (Refereed)
  • 46.
    Hovmöller, Rasmus
    et al.
    Swedish Museum of Natural History, Department of Zoology. Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Forshage, Mattias
    Swedish Museum of Natural History, Department of Zoology. Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Streckkodning av den svenska floran och faunan – förutsättningar och utmaningar.2017Report (Other academic)
  • 47.
    Hsiang, Allison
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elder, Leanne (Contributor)
    Yale University.
    Sibert, Elizabeth (Contributor)
    Harvard University.
    Kahanamoku, Sara (Contributor)
    University of California, Berkeley.
    Burke, Janet (Contributor)
    Yale University.
    Kelly, Abigail (Contributor)
    Smithsonian Tropical Research Institute.
    Liu, Yusu (Contributor)
    Massachusetts Institute of Technology.
    Hull, Pincelli (Contributor)
    Yale University.
    AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction2017In: Methods in Ecology and Evolution, ISSN 2041-210X, EISSN 2041-210XArticle in journal (Refereed)
    Abstract [en]
    1. Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.

    2. Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage- scale morphological data.

    3. We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.

    4. AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms. 

  • 48.
    Häggqvist, Sibylle
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ulefors, Sven Olof
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    A new species group in Megaselia, the lucifrons group, with description of a new species (Diptera, Phoridae)2015In: ZooKeys, ISSN 1313-2989, E-ISSN 1313-2970, Vol. 512, p. 89-108Article in journal (Refereed)
  • 49.
    Höhna, Sebastian
    et al.
    Stockholms universitet.
    Heath, Tracy A.
    Boussau, Bastien
    Landis, Michael J.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Huelsenbeck, John P.
    Probabilistic graphical model representation in phylogenetics2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 753-771Article in journal (Refereed)
    Abstract [en]

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution.

  • 50. Höhna, Sebastian
    et al.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 726-736Article in journal (Refereed)
123 1 - 50 of 131
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