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  • 1.
    Abalde, Samuel
    Naturhistoriska riksmuseet, Enheten för zoologi.
    MATEdb: a new phylogenomic-driven database for Metazoa2022Övrigt (Övrig (populärvetenskap, debatt, mm))
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  • 2.
    Abalde, Samuel
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Crocetta, Fabio
    Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Tenorio, Manuel J.
    Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
    D'Aniello, Salvatore
    Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Fassio, Giulia
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Rodríguez-Flores, Paula C.
    Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
    Uribe, Juan E.
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Afonso, Carlos M.L.
    Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal.
    Oliverio, Marco
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Zardoya, Rafael
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus2023Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 186, s. 107838-107838, artikel-id 107838Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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  • 3.
    Abalde, Samuel
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Dutertre, Sébastien
    IBMM, Université de Montpellier CNRS.
    Zardoya, Rafael
    Museo Nacional de Ciencias Naturales.
    A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae)2021Ingår i: Toxins, ISSN 2072-6651, E-ISSN 2072-6651, Vol. 13, nr 9, s. 642-642Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Venoms are complex mixtures of proteins that have evolved repeatedly in the animal kingdom. Cone snail venoms represent one of the best studied venom systems. In nature, this venom can be dynamically adjusted depending on its final purpose, whether to deter predators or hunt prey. Here, the transcriptome of the venom gland and the proteomes of the predation-evoked and defensive venoms of the molluscivorous cone snail Cylinder ammiralis were catalogued. A total of 242 venom-related transcripts were annotated. The conotoxin superfamilies presenting more different peptides were O1, O2, T, and M, which also showed high expression levels (except T). The three precursors of the J superfamily were also highly expressed. The predation-evoked and defensive venoms showed a markedly distinct profile. A total of 217 different peptides were identified, with half of them being unique to one venom. A total of 59 peptides ascribed to 23 different protein families were found to be exclusive to the predatory venom, including the cono-insulin, which was, for the first time, identified in an injected venom. A total of 43 peptides from 20 protein families were exclusive to the defensive venom. Finally, comparisons of the relative abundance (in terms of number of peptides) of the different conotoxin precursor superfamilies showed that most of them present similar abundance regardless of the diet.

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  • 4.
    Abalde, Samuel
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Tellgren-Roth, Christian
    Heintz, Julia
    Vinnere Pettersson, Olga
    Jondelius, Ulf
    Naturhistoriska riksmuseet, Enheten för zoologi.
    The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes2023Ingår i: Frontiers in Genetics, E-ISSN 1664-8021, Vol. 14, artikel-id 1244493Artikel i tidskrift (Refereegranskat)
  • 5.
    Adroit, Benjamin
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Grímsson, Friðgeir
    University of Vienna, Department of Botany and Biodiversity Research, 1030 Vienna, Austria.
    Suc, Jean-Pierre
    Sorbonne Université, CNRS-INSU, Institut des Sciences de la Terre Paris, ISTeP UMR7193, 75005 Paris, France.
    Escarguel, Gilles
    Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés UMR CNRS 5023 LEHNA, Université Claude Bernard Lyon 1, France.
    Zetter, Reinhard
    University of Vienna, Department of Palaeontology, 1090 Vienna, Austria.
    Bouchal, Johannes M.
    University of Vienna, Department of Botany and Biodiversity Research, 1030 Vienna, Austria.
    Fauquette, Séverine
    ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
    Zhuang, Xin
    Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, Finland.
    Djamali, Morteza
    Institut Méditerranéen de Biodiversité et d'Ecologie–IMBE (Aix Marseille Univ, Avignon Université, CNRS, IRD), Europôle de l'Arbois, Aix-en-Provence, France.
    Are morphological characteristics of Parrotia (Hamamelidaceae) pollen species diagnostic?2022Ingår i: Review of Palaeobotany and Palynology, ISSN 0034-6667, E-ISSN 1879-0615, Vol. 307, s. 104776-104776, artikel-id 104776Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Parrotia persica is one of the most notable endemic relict tree species growing in the Hyrcanian forest at the southern Caspian Sea. The recent discovery of sibling species Parrotia subaequalis, occurring in the temperate forests of south-eastern China, offers the opportunity to compare their morphology and ecological preferences and to dig deeper into the paleophytogeographic history of the genus from a perspective. Since pollen morphology of these species would be essential to unravel the origin and evolution of these Arcto-Tertiary species, the present study aimed to investigate whether it is possible to segregate pollen from these two species. Therefore, a detailed combined light- and scanning electron microscopy-based pollen-analysis of each taxon was conducted, the pollen was described, measured, and compared using statistical approaches and principal component analyses to establish unbiased results. The correlation-based principal component analysis achieved for each species shows an overall good superposition of pollen grains measured in equatorial and polar views in the first principal plane, revealing that the P. persica pollen is morphometrically as homogeneous as that of P. subaequalis. Then, the significant difference, mainly driven by lumen density, has been highlighted between the two species. Ultimately, the cross-validation of the resulting two-species linear discriminants classifier shows that based upon this reference dataset, (sub)fossil pollen grain can now be confidently assigned to either of the two species with an 85.8% correct-assignment rate. This opens new doors in the affiliation of fossil Parrotia pollen and suggests that previous pollen records need to be revised.

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  • 6. Alerstam, Thomas
    et al.
    Rosén, Mikael
    Bäckman, Johan
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Hellgren, Olof
    Flight speeds among bird species: allometric and phylogenetic effects.2007Ingår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 5, nr 8, s. e197-Artikel i tidskrift (Refereegranskat)
    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.

  • 7. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Foerschler, Marc I.
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    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)2012Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, nr 3, s. 1017-1019Artikel i tidskrift (Refereegranskat)
  • 8. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Förschler, Marc I
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Zuccon, Dario
    Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).2012Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, nr 1, s. 35-45Artikel i tidskrift (Refereegranskat)
    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.

  • 9. Alstrom, Per
    et al.
    Olsson, Urban
    Rasmussen, Pamela C.
    Yao, Cheng-Te
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Sundberg, Per
    Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)2007Ingår i: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 149, nr 3, s. 437-452Artikel i tidskrift (Refereegranskat)
  • 10. Alström, Per
    et al.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Olsson, Urban
    Sundberg, Per
    Phylogeny and classification of the avian superfamily Sylvioidea.2006Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 38, nr 2, s. 381-97Artikel i tidskrift (Refereegranskat)
    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.

  • 11. Alström, Per
    et al.
    Fregin, Silke
    Norman, Janette A
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Christidis, Les
    Olsson, Urban
    Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.2011Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 58, nr 3, s. 513-26Artikel i tidskrift (Refereegranskat)
    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.

  • 12. Alström, Per
    et al.
    Höhna, Sebastian
    Gelang, Magnus
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Olsson, Urban
    Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.2011Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 11, s. 352-Artikel i tidskrift (Refereegranskat)
    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.

  • 13.
    Bachmann, Lutz
    et al.
    University of Oslo Natural History Museum P.O. Box 1172 Blindern NO 0318 Oslo Norway.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Sundberg, Per
    University of Gothenburg Department of Marine Sciences P.O. Box 463 SE 40530 Gothenburg Sweden.
    Systematics and biodiversity research in the era of genomics2016Ingår i: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 45, nr S1, s. 3-4Artikel i tidskrift (Övrigt vetenskapligt)
  • 14.
    Barani-Beiranvand, Hossein
    et al.
    Dept of Biology, Faculty of Science, Ferdowsi Univ. of Mashhad, Iran Mashhad, Khorasan-e Razavi; Mashhad Iran.
    Aliabadian, Mansour
    Dept of Biology, Faculty of Science, Ferdowsi Univ. of Mashhad, Iran Mashhad, Khorasan-e Razavi; Mashhad Iran;Research Dept of Zoological Innovation (RDZI), Inst. of Applied Zoology, Ferdowsi Univ. of Mashhad; Mashhad Iran.
    Irestedt, Martin
    Dept of Bioinformatics and Genetics, Swedish Museum of Natural History; Stockholm Sweden.
    Qu, Yanhua
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Darvish, Jamshid
    Research Dept of Rodentology, Inst. of Applied Zoology, Ferdowsi Univ. of Mashhad; Mashhad Iran.
    Székely, Tamás
    Dept of Biology and Biochemistry, Univ. of Bath; Bath UK.
    Van Dijk, René E.
    Dept of Animal and Plant Sciences, Univ. of Sheffield; Sheffield UK.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Phylogeny of penduline tits inferred from mitochondrial and microsatellite genotyping2017Ingår i: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 48, nr 7, s. 932-940Artikel i tidskrift (Refereegranskat)
  • 15. Barlow, A
    et al.
    Paijmans, J L A
    Alberti, F
    Gasparyan, B
    Bar-Oz, G
    Pinhasi, R
    Foronova, I
    Puzachenko, A Y
    Pacher, M
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Baryshnikov, G
    Hofreiter, M
    Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears2021Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 31, nr 8, s. 1771-+Artikel i tidskrift (Refereegranskat)
  • 16. Barnett, Ross
    et al.
    Westbury, Michael V.
    Sandoval-Velasco, Marcela
    Vieira, Filipe Garrett
    Jeon, Sungwon
    Zazula, Grant
    Martin, Michael D.
    Ho, Simon Y.W.
    Mather, Niklas
    Gopalakrishnan, Shyam
    Ramos-Madrigal, Jazmín
    de Manuel, Marc
    Zepeda-Mendoza, M. Lisandra
    Antunes, Agostinho
    Baez, Aldo Carmona
    De Cahsan, Binia
    Larson, Greger
    O’Brien, Stephen J.
    Eizirik, Eduardo
    Johnson, Warren E.
    Koepfli, Klaus-Peter
    Wilting, Andreas
    Fickel, Jörns
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lorenzen, Eline D.
    Marques-Bonet, Tomas
    Hansen, Anders J.
    Zhang, Guojie
    Bhak, Jong
    Yamaguchi, Nobuyuki
    Gilbert, M. Thomas P.
    Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens2020Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Summary Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6, 7, 8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11, 12, 13, 14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.

  • 17. Batalha-Filho, Henrique
    et al.
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Fjeldså, Jon
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Silveira, Luis F
    Miyaki, Cristina Y
    Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest.2013Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, nr 1, s. 86-94Artikel i tidskrift (Refereegranskat)
    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.

  • 18. Batalha-Filho, Henrique
    et al.
    Pessoa, Rodrigo O
    Fabre, Pierre-Henri
    Fjeldså, Jon
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Silveira, Luís F
    Miyaki, Cristina Y
    Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests.2014Ingår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 79, s. 422-432Artikel i tidskrift (Refereegranskat)
    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.

  • 19.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Presentation of the 2010 Charles Schuchert Award of the Paleontological Society to Philip C. J. Donoghue.2011Ingår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Journal of Paleontology, Vol. 85, nr 5, s. 1015-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    LADIES AND gentlemen, friends and colleagues, the winner of the 2010 Charles Schuchert Award is Professor Philip Donoghue of the University of Bristol. In the natural progression of our personal lives, the transition from young snot to old fart is so gradual that one tends not to recognize it, least of all in oneself. Most of us— those further along in their careers— have passed through the stage of young, promising paleontologist to become middleaged promising paleontologists. Not so Phil Donoghue. I first met him when he was a graduate student at the University of Leicester. We got into a discussion about the nature of conodonts and certain pet ideas of mine that I had published. Phil did not agree with me so he went down in my book as a young snot. Soon thereafter, he published a ground-breaking, paradigm-changing paper, together with Peter Forey and Dick Aldridge, on the phylogenetic position of conodonts. Now, I realized that it was I who was the old fart. Phil had demonstrated that he had skipped the young-and-promising stage. He was, and is, young and delivering. Most people who start working on conodonts tend to remain with them. There is something about that mouth apparatus and the way in which it grabs hold of you. But Phil quickly tore himself loose from its grip. He quickly demonstrated an unquenchable zeal in attacking central issues in evolutionary paleontology, such as the origin of microstructures in teeth, the origin of teeth in jaws, the origin of jaws in vertebrates, the origin of vertebrates among animals, the origin of animals in the biosphere, and so on. I fear he will not stop until he has solved the question of the origin of life, the universe, and everything else. The breadth of questions he has already addressed is one aspect of Phil’s work. The diversity of tools he brings to bear on them is another. There is a lot of grinding powder under his fingernails, and lots of devo in his evo. After a sabbatical at the University of Bath, where he seems to have broken every rule of the Sabbath, he came out as a full-fledged molecular biologist, with RNA libraries at his fingertips. He is at the forefront in marrying data from living organisms with that from fossil taxa in phylogenetic analyses. Recently, he came out in defense of the paraphyletic stem group with arguments such that I have high hopes for his post-Schuchert development. Yes, paraphyletic groups are much more interesting than the monophyletic dead-ends called clades, although Phil of course refuses to call them groups. When Phil and some colleagues published a paper in Nature on the Cambrian fossil embryo Markuelia (again showing me wrong on a central issue), it caught the eye of Marco Stampanoni, a physicist who works at the Swiss Light Source (SLS) synchrotron near Zu¨ rich, in Switzerland. Marco had been developing methods of X-ray microtomography, using SLS beamlines. He contacted Phil with a proposal to collaborate, and Phil contacted me. Now, our collaboration based on this revolutionary technique, with Phil at the forefront, has opened our eyes to a huge amount of information to which we did not have access only a few years ago. Taphonomy is like the weather, people speak about it, but few do anything about it. But if you neglect it, you are in deep peril. Phil is much more concerned about taphonomy than most colleagues I know, and he does something about it. He started a project with embryologist Rudy Raff to determine how bacteria go about decomposing embryos in ways such that they are upgraded to exquisite fossils. He is engaging many colleagues, post-docs and students in the investigation of these processes and their end results. As a result, we are gaining insight into how bacteria can invade, devour and faithfully replicate intracellular features, and how different populations of bacteria play different roles in the process. An intriguing observation has emerged from Phil’s taphonomic work with Mark Purnell. Taphonomic degradation tends to bring about a stemward slippage of taxa in their apparent phylogenetic relationships, on account of sequential disappearance of preserved apomorphies. The general significance of this observation has still to be tested, but its potential importance for the phylogenetic analysis of fossils is obvious. Phil is leading an amazingly diverse and successful program in paleontology at the University of Bristol, permeated by his holistic approach and addressing everything from organismbased paleontology to molecular biology. Molecular, organismic, orgiastic paleontology—that’s the realm of Phil Donoghue. Mr. President, please hand the Schuchert Award for 2010 over to Phil. He thoroughly deserves it.

  • 20.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Presentation of the 2010 Paleontological Society Medal to Bruce Runnegar.2011Ingår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Journal of Paleontology, Vol. 85, nr 5, s. 1012-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ladies and gentlemen, friends and colleagues, the 2010 Paleontological Society Medal is awarded to Professor Bruce Runnegar of the University of California at Los Angeles. Preparing for this presentation, I got hold of a list of Bruce’s invited lectures, given during the past ten years. There are 86 titles on almost as many subjects. I will mention what these presentations were about, so you can get an impression of this Renaissance mind: Carbon isotopes and ocean evolution; Precambrian–Cambrian stratigraphy; Molecular evolution and the fossil record; Ediacaran organisms; Life on Mars; Oxygen and metazoan evolution; Orbital dynamics of the Earth–Moon system; Snowball Earth; Multiplated mollusks; Mass-independent fractionation of sulfur; Biomineralization; The Cambrian Explosion; Geobiology in the Archean; Cross-calibration of geological and astronomical time scales; Origins of biological complexity; Astrobiology of the Earth; Astrobiology of everything else; The Acraman impact of the Ediacaran; Biosignatures in ancient rocks; Microbial metabolism in the Early Archean. Now, most people can waffle about almost anything. A good teacher can read up on such topics and deliver useful lectures on them to students. But, as you will know if you are the least bit familiar with Bruce’s work, these are nearly all topics in fields where he has made startlingly innovative and pioneering contributions. Some would say that his most important contributions are missing from this list, such as molecular paleobiology, for example, or—if you prefer more tangible fossils—the systematics and evolution of Cambrian and Permian mollusks. But what is represented on the list is sufficient to document several brilliant careers in science: Bruce broke new ground in understanding the biomineralization processes of early mollusks by working with natural phosphatic replicas of the now vanished crystals of various species of calcium carbonate. He published a seminal set of papers on the evolution of the earliest mollusks, together with his longtime friend John Pojeta. And, as a leader of the astrobiology movement, Bruce has not only inspired everyone to start looking at life in a universal context, he has also brought his visions to life as Director of NASA’s Astrobiology Institute. It was in this context that Bruce was formally transformed from a U.S.-based Aussie to a full-fledged Australian– American (which is, I think, the politically correct term). In reference to molecular paleontology, I have some personal recollections. Bruce and I both have backgrounds as editors of paleontological journals. Bruce founded and for several years edited the successful Australasian journal Alcheringa, which is still going strong. Some of my first interactions with Bruce occurred in the 1970s, when he submitted manuscripts to Lethaia, of which I was an editor. One of my early forays was to question the number of authors of one of these manuscripts. I knew that no less than five authors of a single paper was excessive and confronted Bruce with this. It may have been the first time I really annoyed him, as he politely told me not to forget to turn my brain on, next time I wrote to him. Well, recently I saw an article in Nature with 230 authors, at which point it finally became clear to me that Bruce was ahead of his time. But back in those times I was a wee bit miffed, so when Bruce sent me a manuscript in which he estimated geological ages of major animal lineages using molecular clock techniques, I knew I could get my revenge. I sent the paper out for review by the sharpest molecular biologists of the day, smugly expecting to receive patronizing comments about paleontologists who should stick to their snail shells rather than pretending to be real scientists. No such luck. The reviews that came in were extravagant in their praise of the paper. Published in 1982, it predated by almost 15 years the avalanche of contributions that later came out on this topic. As usual, Bruce was ahead of the pack, but when others reached the spot where he had stood 15 years earlier, he wasn’t there anymore. Discrepancies between molecular and fossil data for a while seemed insurmountable, not to mention the discrepancies between different sets of molecular data and different sorts of analyses. But Bruce had inspired a bright set of younger biologists and paleontologists to refine their calculations. When the dust settled, one of those with whom Bruce had shared his spark, Kevin Peterson, was able to show that there is no significant conflict between the dates provided by fossils and by molecules. But I mentioned molecular paleontology. In 1986, Bruce published a seminal paper with just that title. In it he expressed his credo, thus: ‘‘palaeontologists should use all available sources of information to understand the evolution of life and its effect on the planet.’’ These are not empty words; they present a formidable challenge. Like all splendid visions, they stake out a direction rather than a goal. That it is possible to pursue this vision we see from the example set by this year’s Schuchert Award winner, Phil Donoghue, who together with Kevin Peterson and Roger Summons wrote a stimulating twenty-first century follow-up to Bruce’s earlier paper. But the foremost example is Bruce Runnegar himself. Here is a taste of the way in which his productive mind works. In 1982, Bruce used the anatomy and hypothesized physiology of the Ediacaran fossil Dickinsonia to estimate constraints for ambient oxygen levels in the Ediacaran atmosphere. This paper is much cited, and geochemists are only now catching up with him, developing geochemical proxies to test the hypothesis that a rising oxygen level was a trigger for the Cambrian Explosion, or, as Bruce so aptly put it, that one ‘‘ingredient, as in most explosives, may well have been a strong oxidising agent.’’ Finally, consider another example. In 1998, Bruce published a cladistic analysis of glaciogenic sediments, testing and corroborating the hypothesis that there were only two major Neoproterozoic glaciations, a result that still seems to stand. Who but Bruce would have thought of such a preposterous idea, using cladistics to resolve a stratigraphical conundrum? Bruce Runnegar has, over the years, formed collegial bonds with many scientists. The many younger people inspired by him include Phil Donoghue, now standing on Bruce’s shoulders. Bruce himself has stood on the shoulders of other giants, as he is quick to acknowledge. But, like Sir Isaac Newton, he has no reason to be bashful about his success, and I don’t think he is. The Paleontological Society Medal was really made for Bruce Runnegar, so please, Mr. President, give it to him!

  • 21.
    Bengtson, Stefan
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Rasmussen, Birger
    Curtin University.
    Ivarsson, Magnus
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Muhling, Janet
    Curtin University.
    Broman, Curt
    Stockholm University.
    Marone, Federica
    Stampanoni, Marco
    Bekker, Andrey
    University of California Riverside.
    Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt.2017Ingår i: Nature Ecology & Evolution, ISSN 2397-334X, Vol. 1, nr 6, s. 1-6, artikel-id 0141Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces. Filaments branch and anastomose, touch and entangle each other. They are indistinguishable from mycelial fossils found in similar deep-biosphere habitats in the Phanerozoic, where they are attributed to fungi on the basis of chemical and morphological similarities to living fungi. The Ongeluk fossils, however, are two to three times older than current age estimates of the fungal clade. Unless they represent an unknown branch of fungus-like organisms, the fossils imply that the fungal clade is considerably older than previously thought, and that fungal origin and early evolution may lie in the oceanic deep biosphere rather than on land. The Ongeluk discovery suggests that life has inhabited submarine volcanics for more than 2.4 billion years.

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  • 22.
    Bengtson, Stefan
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Sallstedt, Therese
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Belivanova, Veneta
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Whitehouse, Martin
    Naturhistoriska riksmuseet, Enheten för geovetenskap.
    Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae2017Ingår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 15, nr 3, s. 1-38, artikel-id e2000735Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.

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  • 23.
    Benoit, Julien
    et al.
    University of the Witwatersrand.
    Kruger, Ashley
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Swedish Museum of Natural History.
    Jirah, Sifelani
    University of the Witwatersrand.
    Fernandez, Vincent
    University of the Witwatersrand.
    Rubidge, Bruce
    University of the Witwatersrand.
    Palaeoneurology and palaeobiology of the dinocephalian Anteosaurus magnificus2021Ingår i: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 66, s. 29-39Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dinocephalians (Therapsida), some of the earliest amniotes to have evolved large body size, include the carnivorous Anteosauria and mostly herbivorous Tapinocephalia. Whilst the palaeoneurology of the Tapinocephalia has been investigated in Moschognathus whaitsi, that of the Anteosauria remains completely unknown. Here we used X-ray micro-Computed Tomography to study, for the first time, the palaeoneurology of Anteosaurus magnificus. Compared to Moschognathus, we reconstruct Anteosaurus as an agile terrestrial predator based on the enlarged fossa for the floccular lobe of the cerebellum and semicircular canals of the inner ear. A major difference between the two genera resides in the orientation of the braincase, as indicated by the angle between the long axis of the skull and the plane of the lateral semicircular canal. This angle is 25° in Anteosaurus, whereas it is 65° in Moschognathus, which suggests that the braincase of the latter was remodelled as an adaptation to head-butting. This is consistent with less cranial pachyostosis and the retention of a large canine in Anteosauria, which suggests that dentition may have been used for intraspecific fighting and display in addition to trophic interactions. The evolution of a thick skull, horns, and bosses in tapinocephalids parallels the evolutionary reduction of the canine, which lead to a shift of the agonistic function from the mouth to the skull roof, as observed in extant social ungulates. Similarly, tapinocephalians may have developed complex social behaviour.

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  • 24.
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Enheten för zoologi.
    A bee-fly's host, Facebook, and DNA Barcoding.2016Ingår i: Barcode Bulletin, Vol. 7, nr 2, s. 8-9Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 25.
    Bergsten, Johannes
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Nilsson, Lars G R
    Bukontaite, Rasa
    Naturhistoriska riksmuseet, Enheten för zoologi. Stockholm University.
    Åkerjordfly, Agrotis exclamationis, identifierad som värdart för svävflugan Villa hottentotta med hjälp av DNA streckkodning (Diptera: Bombyliidae).2015Ingår i: Entomologisk Tidskrift, ISSN 0013-886X, Vol. 136, nr 4, s. 121-130Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this study we identify Agrotis exclamationis (Linnaeus, 1758) as a host species for the bee y Villa hottentotta (Linnaeus, 1758) in Sweden. Host use and speci city for bee y species are generally very poorly known, why the hatching of a bee y of the genus Villa from an unknown Noctuid pupa caught our attention. The parasitized Noctuid pupa was found in a garden in Staffanstorp, Skåne (Sweden), in May 2015 and kept in a jar to hatch. The bee y hatched in June leaving two empty exuviae in the jar. DNA was extracted sepa- rately from both excuviae to identify the y and the host using DNA Barcoding. A 600+ bp long sequence of the gene Cytochrome oxidase subunit 1 was sequenced for both samples and queried against the reference library BOLD (www.boldsystems.org). The Noctuid host pupa was unambiguously identi ed as the common Noctuid species Agrotis exclamationis. The sequence was identical to the most common haplotype over much of Europe. The bee y pupa was identi ed as Villa hottentotta, the most common Villa species in Sweden. This added a new Noctuid species to the list of known hosts for V. hottentotta which also includes several other Noctuid genera as well as a Geometrid moth. Belonging to the sand chamber group of bee ies where the female scatter the eggs on the ground while hovering, the active host-seeking rst instar planidium larvae bene ts from having a wide host range to potentially encounter in the substrate zone. 

  • 26. Bergstrom, Anders
    et al.
    Frantz, Laurent
    Schmidt, Ryan
    Ersmark, Erik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Lin, Audrey T.
    Stora, Jan
    Sjogren, Karl-Goran
    Anthony, David
    Antipina, Ekaterina
    Amiri, Sarieh
    Bar-Oz, Guy
    Bazaliiskii, Vladimir I.
    Bulatovic, Jelena
    Brown, Dorcas
    Carmagnini, Alberto
    Davy, Tom
    Fedorov, Sergey
    Fiore, Ivana
    Fulton, Deirdre
    Germonpre, Mietje
    Haile, James
    Irving-Pease, Evan K.
    Jamieson, Alexandra
    Janssens, Luc
    Kirillova, Irina
    Horwitz, Liora Kolska
    Kuzmanovic-Cvetkovic, Julka
    Kuzmin, Yaroslav
    Losey, Robert J.
    Dizdar, Daria Loznjak
    Mashkour, Marjan
    Novak, Mario
    Onar, Vedat
    Orton, David
    Pasaric, Maja
    Radivojevic, Miljana
    Rajkovic, Dragana
    Roberts, Benjamin
    Ryan, Hannah
    Sablin, Mikhail
    Shidlovskiy, Fedor
    Stojanovic, Ivana
    Tagliacozzo, Antonio
    Trantalidou, Katerina
    Ullen, Inga
    Villaluenga, Aritza
    Wapnish, Paula
    Dobney, Keith
    Gotherstrom, Anders
    Linderholm, Anna
    Dalen, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pinhasi, Ron
    Larson, Greger
    Skoglund, Pontus
    Origins and genetic legacy of prehistoric dogs2020Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 370, nr 6516, s. 557-563Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

  • 27. Bergstrom, Anders
    et al.
    Stanton, David WG
    Taron, Ulrike H
    Frantz, Laurent
    Sinding, Mikkel-Holger S
    Ersmark, Erik
    Pfrengle, Saskia
    Cassatt-Johnstone, Molly
    Lebrasseur, Ophelie
    Girdland-Flink, Linus
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Grey wolf genomic history reveals a dual ancestry of dogs2022Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 607, s. 313-320Artikel i tidskrift (Refereegranskat)
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  • 28. Bieker, Vanessa C
    et al.
    Battlay, Paul
    Petersen, Bent
    Sun, Xin
    Wilson, Jonathan
    Brealey, Jaelle C
    Bretagnolle, François
    Nurkowski, Kristin
    Lee, Chris
    Barreiro, Fátima Sánchez
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Uncovering the genomic basis of an extraordinary plant invasion2022Ingår i: Science Advances, E-ISSN 2375-2548, Vol. 8, nr 34Artikel i tidskrift (Refereegranskat)
  • 29.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Ehrlén, Johan
    Persson, Christin
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Family affiliation, sexratio and sporophyte frequency in unisexual mosses2014Ingår i: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 174, s. 163-172Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Patterns of sex expression and sex ratios are key features of the life histories of organisms. Bryophytes are the only haploid-dominant land plants. In contrast with seed plants, more than half of bryophyte species are dioecious, with rare sexual expression and sporophyte formation and a commonly female-biased sex ratio. We asked whether variation in sex expression, sex ratio and sporophyte frequency in ten dioecious pleurocarpous wetland mosses of two different families was best explained by assuming that character states  evolved: (1) in ancestors within the respective families or (2) at the species level as a response to recent habitat conditions. Lasso regression shrinkage identified relationships between family membership and sex ratio and sporophyte frequency, whereas environmental conditions were not correlated with any investigated reproductive trait. Sex ratio and sporophyte frequency were correlated with each other. Our results suggest that ancestry is more important than the current environment in explaining reproductive patterns at and above the species level in the studied wetland mosses, and that mechanisms controlling sex ratio and sporophyte frequency are phylogenetically conserved. Obviously, ancestry should be considered in the study of reproductive character state variation in plants.

  • 30.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Infraspecific sex ratio variation and its predictors in mosses – the case of the wetland moss Drepanocladus lycopodioides2015Ingår i: Botany 2015. Science and Plants for People. Abstracts. / [ed] Anonymous, 2015Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    Sex ratio variation is a common but unexplained phenomenon of many species with chromosomal sex determination, including many bryophytes. Expressed sex ratio variation could be related to environmental conditions in a few mosses investigated to date. However, many bryophyte populations are non-fertile during their entire life cycle and intraspecific genetic sex ratio variation remains highly unexplored in natural populations. Drepanocladus lycopodioides, a pleurocarpous wetland moss with a distribution largely confined to Western Eurasia, rarely to occasionally forms sexual organs. It belongs to the majority of bryophytes that exhibits a female bias in expressed sex ratio. We applied a novel approach to sex individual shoots irrespective of their reproductive state using a specifically designed female-targeting molecular marker. We demonstrated that the bias in sex expression corresponds to a genetic female bias in the European adult population. Here, we investigated three regional populations of D. lycopodioides in its core distribution area. We asked whether haplotype diversity (H), sex expression (SE), genetic sex ratios, and sporophyte frequency varied within and among regions, whether these characteristics were related with each other, and / or to environmental parameters. Levels of H differed among regions and were positively related to habitat patch size. H was unequally partitioned between the sexes and was associated with estimated regional sporophyte frequency. Recorded plot-wise sporophyte frequency was generally very low in all regions. Overall genetic sex ratio was female-biased in all regions. Sex expression and genetic sex ratio varied strongly within regions (SE 0 –75%), with 27% of the plots lacking sex organs and 78% of the plots one-sexed, but differences among regions were non-significant. While no sex expression occurred in habitats deeper than 25cm, genetic sex ratio was not related to the measured environmental parameters.

  • 31.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Males Are Not Shy in the Wetland Moss Drepanocladus lycopodioides2013Ingår i: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 174, nr 5, s. 733-739Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Premise of research. Maintenance of dioecious and monoecious sexual systems at nearly equal frequencies, infrequent sexual expression, and distinctly female-skewed sex ratios among the dioecious species are reproductive characteristics of bryophytes, which are otherwise unusual among embryophytes. Most sex ratio assessments to date have relied on gametophytes forming sexual organs, and how these reflect genetic genders is largely unresolved.

    Methodology. For the European wetland moss Drepanocladus lycopodioides, we ask whether the adult expressed sex ratio is more strongly female biased than the “true” population sex ratio based on genetically male and female plants, i.e., whether males exhibit a lower sex expression rate than females (shy males). We assess expressed sex ratio on the basis of sex expression in individually scored herbarium specimens. We directly and on a large geographic scale assess nonexpressed sex ratio, for the second time in a moss, by sexing individual shoots from nonexpressing specimens using a molecular sex marker.

    Pivotal results. On the basis of the female and male frequencies in these two data sets and the overall proportion of expressing specimens, we estimate the European population sex ratio as 2.6 : 1 (female to male). All three sex ratios are significantly female skewed and do not significantly differ from each other, indicating that there is no gender difference in sex expression rates.

    Conclusions. These results and previous data for Drepanocladus trifarius show that males are not shy in the two wetland mosses of markedly different habitats.

  • 32.
    Bisang, Irene
    et al.
    Naturhistoriska riksmuseet, Enheten för botanik.
    Hedenäs, Lars
    Naturhistoriska riksmuseet, Enheten för botanik.
    Mass occurrence of springtails on a moss cushion – what are they doing?2015Ingår i: Melting Pot, Swedish Museum of Natural History, Abstracts: https://vega.nrm.se/vanstermenyn/forskningochsamlingar/meltingpot/2015.9654.html, 2015Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    The motile spermatozoids of bryophytes can swim up to a few centimetres. They require free water to fertilize the egg of the female organs, which sit on plants separate from the males in more than 50% of the species. When the sex organs are produced on different plants, this presents a serious obstacle to successful fertilization. The problems are overcome by a variety of mechanisms. Some of the more spectacular include spermatozoid transport up to at least several decimetres by water movement, by water drops spread from splash-cups surrounding the male organs up to two meters, by ejection up to15 centimetres into the air, or by having dwarf males that grow directly on the female plants. Here we report on another special kind of spermatozoid transfer that we came across during fieldwork in 2014, namely by micro-arthropods. Bryophyte fertilization mediated by animals was suggested more than a century ago, and was recently shown to occur in experimental settings. However, our observation is likely one of the first made directly in nature.

     

     

  • 33. Black, Andrew B.
    et al.
    Jansen, Justin J.F.
    Frahnert, Sylke
    Johansson, Ulf S.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Provisional identification of historical grasswren(Amytornis: Maluridae) specimens in European collectionsdraws attention to the incomplete phylogeny of the group2019Ingår i: Bulletin of the British Ornithologists' Club, ISSN 0007-1595, Vol. 139, nr 3, s. 228-237Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The phylogeny and systematics of grasswrens Amytornis species areincompletely resolved, in particular for three widely distributed members ofthe genus. In part this is a consequence of the dispersal to European and NorthAmerican collections of early specimens of now extinct populations. We describethree historical grasswren specimens from museums in Berlin and Stockholm, all ofwhich represent taxa for which phylogenetic and / or other data are incomplete. Wefurther identify other specimens that might contribute towards greater resolutionof grasswren phylogeny.

  • 34. Boeskorov, G G
    et al.
    Plotnikov, V V
    Protopopov, A V
    Baryshnikov, G F
    Fosse, P
    Dalen, L
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Stanton, D W G
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Pavlov, I S
    Suzuki, N
    Tikhonov, A N
    The Preliminary Analysis of Cave Lion Cubs Panthera spelaea (Goldfuss, 1810) from the Permafrost of Siberia2021Ingår i: Quaternary, E-ISSN 2571-550X, Vol. 4, nr 3Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 35. Braga, Mariana P.
    et al.
    Janz, Niklas
    Department of Zoology Stockholm University Stockholm Sweden.
    Nylin, Sören
    Department of Zoology Stockholm University Stockholm Sweden.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Landis, Michael J.
    Department of Biology Washington University in St. Louis St. Louis MO USA.
    Phylogenetic reconstruction of ancestral ecological networks through time for pierid butterflies and their host plants2021Ingår i: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 24, nr 10, s. 2134-2145Artikel i tidskrift (Refereegranskat)
  • 36. Braga, Mariana P.
    et al.
    Landis, Michael J.
    Nylin, Sören
    Janz, Niklas
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Bayesian Inference of Ancestral Host–Parasite Interactions under a Phylogenetic Model of Host Repertoire Evolution2020Ingår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 69, s. 1149-1162Artikel i tidskrift (Refereegranskat)
  • 37. Brealey, Jaelle C
    et al.
    Leitão, Henrique G
    van der Valk, Tom
    Xu, Wenbo
    Bougiouri, Katia
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Guschanski, Katerina
    Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome2020Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, nr 10, s. 3003-3022Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

  • 38.
    Bukontaite, Rasa
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi. Stockholm University.
    Miller, Kelly
    University of New Mexico.
    Bergsten, Johannes
    Naturhistoriska riksmuseet, Enheten för zoologi.
    The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae).2014Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 14, nr 5, s. 1-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background

    Aciliini presently includes 69 species of medium-sized water beetles distributed on all continents except Antarctica. The pattern of distribution with several genera confined to different continents of the Southern Hemisphere raises the yet untested hypothesis of a Gondwana vicariance origin. The monophyly of Aciliini has been questioned with regard to Eretini, and there are competing hypotheses about the intergeneric relationship in the tribe. This study is the first comprehensive phylogenetic analysis focused on the tribe Aciliini and it is based on eight gene fragments. The aims of the present study are: 1) to test the monophyly of Aciliini and clarify the position of the tribe Eretini and to resolve the relationship among genera within Aciliini, 2) to calibrate the divergence times within Aciliini and test different biogeographical scenarios, and 3) to evaluate the utility of the gene CAD for phylogenetic analysis in Dytiscidae.

    Results

    Our analyses confirm monophyly of Aciliini with Eretini as its sister group. Each of six genera which have multiple species are also supported as monophyletic. The origin of the tribe is firmly based in the Southern Hemisphere with the arrangement of Neotropical and Afrotropical taxa as the most basal clades suggesting a Gondwana vicariance origin. However, the uncertainty as to whether a fossil can be used as a stem-or crowngroup calibration point for Acilius influenced the result: as crowngroup calibration, the 95% HPD interval for the basal nodes included the geological age estimate for the Gondwana break-up, but as a stem group calibration the basal nodes were too young. Our study suggests CAD to be the most informative marker between 15 and 50 Ma. Notably, the 2000 bp CAD fragment analyzed alone fully resolved the tree with high support.

    Conclusions

    1) Molecular data confirmed Aciliini as a monophyletic group. 2) Bayesian optimizations of the biogeographical history are consistent with an influence of Gondwana break-up history, but were dependent on the calibration method. 3) The evaluation using a method of phylogenetic signal per base pair indicated Wnt and CAD as the most informative of our sampled genes.

    Ladda ner fulltext (pdf)
    Bukontaite_etal_2014_BMC_Evol_Biol
  • 39. Cahill, James A
    et al.
    Stirling, Ian
    Kistler, Logan
    Salamzade, Rauf
    Ersmark, Erik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. 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.2015Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArtikel i tidskrift (Refereegranskat)
    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.

  • 40.
    Caputo, A
    et al.
    Stockholm University.
    Nylander, Johan A A
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. NBIS.
    Foster, R A
    Stockholm University.
    The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration2019Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 366, nr 2, artikel-id fny297Artikel i tidskrift (Refereegranskat)
  • 41.
    Cardoni, Simone
    et al.
    Department of Agricultural and Forestry Science (DAFNE) Università degli studi della Tuscia Viterbo 01100 Italy.
    Piredda, Roberta
    Department of Veterinary Medicine University of Bari ‘Aldo Moro’ Valenzano 70010 Italy.
    Denk, Thomas
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Grimm, Guido W.
    Unaffiliated, Orléans France.
    Papageorgiou, Aristotelis C.
    Department of Molecular Biology and Genetics Democritus University of Thrace Alexandroupolis Greece.
    Schulze, Ernst‐Detlef
    Max‐Planck Institute for Biogeochemistry Jena 07701 Germany.
    Scoppola, Anna
    Department of Agricultural and Forestry Science (DAFNE) Università degli studi della Tuscia Viterbo 01100 Italy.
    Salehi Shanjani, Parvin
    Natural Resources Gene Bank, Research Institute of Forests and Rangelands Agricultural Research, Education and Extension Organization Tehran Iran.
    Suyama, Yoshihisa
    Graduate School of Agricultural Science Tohoku University Osaki Miyagi 989‐6711 Japan.
    Tomaru, Nobuhiro
    Graduate School of Bioagricultural Sciences Nagoya University Nagoya Aichi 464‐8601 Japan.
    Worth, James R. P.
    Ecological Genetics Laboratory Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki 305‐8687 Japan.
    Cosimo Simeone, Marco
    Department of Agricultural and Forestry Science (DAFNE) Università degli studi della Tuscia Viterbo 01100 Italy.
    5S‐IGS rDNA in wind‐pollinated trees ( Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species2021Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 109, nr 4, s. 909-926Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Standard models of plant speciation assume strictly dichotomous genealogies in which a species, theancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionaryhistories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata – F.sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect acomplex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.

    Ladda ner fulltext (pdf)
    fulltext
  • 42.
    Celemín, Enrique
    et al.
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Autenrieth, Marijke
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Roos, Anna
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning. Swedish Museum of Natural History Stockholm Sweden.
    Pawliczka, Iwona
    Prof. Krzysztof Skóra Hel Marine Station, Faculty of Oceanography and Geography University of Gdansk Hel Poland.
    Quintela, María
    Institute of Marine Research Bergen Norway.
    Lindstrøm, Ulf
    Institute of Marine Research Tromsø Norway;UiT The Arctic University of Norway Tromsø Norway.
    Benke, Harald
    Deutsches Meeresmuseum Stralsund Germany.
    Siebert, Ursula
    Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation Büsum Germany.
    Lockyer, Christina
    Age Dynamics Kongens Lyngby Denmark.
    Berggren, Per
    School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK.
    Özturk, A. Amaha
    Marine Biology Department, Faculty of Fisheries Istanbul University Istanbul Turkey.
    Özturk, Bayram
    Marine Biology Department, Faculty of Fisheries Istanbul University Istanbul Turkey.
    Lesage, Véronique
    Fisheries and Oceans Canada Maurice Lamontagne Institute Mont‐Joli Quebec Canada.
    Tiedemann, Ralph
    University of Potsdam, Institute of Biochemistry and Biology, Evolutionary Biology & Systematic Zoology Potsdam Germany.
    Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters2023Ingår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species primarily occurring in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes broadly varying in salinity and temperature. Here, we produced 74 whole genomes at intermediate coverage to study Harbour porpoise's evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at eight localities across the North Atlantic and adjacent waters, which we used for population structure, demographic and genotype–environment association analyses. Our results suggest a genetic differentiation between three subspecies (P.p. relicta, P.p. phocoena and P.p. meridionalis), and three distinct populations within P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima's D suggest population contraction in Black Sea and Iberian porpoises, but expansion in the P.p. phocoena populations. Phylogenetic trees indicate post-glacial colonization from a southern refugium. Genotype–environment association analysis identified salinity as major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species, shows how strong environmental gradients and local adaptation may lead to population differentiation, and how neutral and adaptive markers can give different perspectives on population subdivision. The results have great conservation implications as we found inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.

    Ladda ner fulltext (pdf)
    fulltext
  • 43. Chen, Yilin
    et al.
    Ge, Deyan
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Song, Gang
    Wen, Zhixin
    Luo, Xu
    Yang, Qisen
    Lei, Fumin
    Qu, Yanhua
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Alpine burrow-sharing mammals and birds show similar population-level climate change risks2023Ingår i: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 13, nr 9, s. 990-996Artikel i tidskrift (Refereegranskat)
  • 44. Chen, Yilin
    et al.
    Jiang, Zhiyong
    Fan, Ping
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Song, Gang
    Luo, Xu
    Lei, Fumin
    Qu, Yanhua
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability2022Ingår i: Nature Communications, E-ISSN 2041-1723, Vol. 13, nr 1, artikel-id 4821Artikel i tidskrift (Refereegranskat)
  • 45.
    Cheng, Yalin
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;.
    Miller, Matthew J.
    Conservation Genetics Division, Reneco International Wildlife Consultants LLC, Abu Dhabi, United Arab Emirates;;University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775;.
    Zhang, Dezhi
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;.
    Xiong, Ying
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;.
    Hao, Yan
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;.
    Jia, Chenxi
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;.
    Cai, Tianlong
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;.
    Li, Shou-Hsien
    Department of Life Sciences, National Taiwan Normal University, Taipei 116, Taiwan, China;.
    Johansson, Ulf S.
    Naturhistoriska riksmuseet, Enheten för zoologi. Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden;.
    Liu, Yang
    State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;.
    Chang, Yongbin
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;.
    Song, Gang
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;.
    Qu, Yanhua
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;.
    Lei, Fumin
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;;College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;;Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China.
    Parallel genomic responses to historical climate change and high elevation in East Asian songbirds2021Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, nr 50Artikel i tidskrift (Refereegranskat)
  • 46.
    Chris, Mays
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Monash University.
    Bevitt, Joseph
    Australian Nuclear Science and Technology Organisation, Research Office, Lucas Heights, Australia.
    Stilwell, Jeffrey
    School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria, Australia.
    Pushing the limits of neutron tomography in palaeontology: Three-dimensional modelling of in situ resin within fossil plants2017Ingår i: Palaeontologia Electronica, ISSN 1935-3952, E-ISSN 1094-8074, Vol. 20, nr 3, s. 1-12, artikel-id 20.3.57AArtikel i tidskrift (Refereegranskat)
    Abstract [en]

    Computed tomography is an increasingly popular technique for the non-destructivestudy of fossils. Whilst the science of X-ray computed tomography (CT) has greatlymatured since its first fossil applications in the early 1980s, the applications and limitationsof neutron tomography (NT) remain relatively unexplored in palaeontology. Thesehighest resolution neutron tomographic scans in palaeontology to date were conductedon a specimen of Austrosequoia novae-zeelandiae (Ettingshausen) Mays and Cantrillrecovered from mid-Cretaceous (Cenomanian; ~100–94 Ma) strata of the ChathamIslands, eastern Zealandia. Previously, the species has been identified with in situ fossilresin (amber); the new neutron tomographic analyses demonstrated an anomalouslyhigh neutron attenuation signal for fossil resin. The resulting data provided astrong contrast between, and distinct three-dimensional representations of the: 1) fossilresin; 2) coalified plant matter; and 3) sedimentary matrix. These data facilitated ananatomical model of endogenous resin bodies within the cone axis and bract-scalecomplexes. The types and distributions of resin bodies support a close alliance withSequoia Endlicher (Cupressaceae), a group of conifers whose extant members areonly found in the Northern Hemisphere. This study demonstrates the feasibility of NTas a means to differentiate chemically distinct organic compounds within fossils.Herein, we make specific recommendations regarding: 1) the suitability of fossil preservationstyles for NT; 2) the conservation of organic specimens with hydrogenous consolidantsand adhesives; and 3) the application of emerging methods (e.g., neutronphase contrast) for further improvements when imaging fine-detailed anatomical structures.These findings demonstrate that we are still far from reaching the conceptuallimits of NT as a means of virtually extracting fossils, or imaging their internal anatomyeven when embedded within a rock matrix.

    Ladda ner fulltext (pdf)
    Mays et al (2017) - Neutron tomography - methods - in situ resin
  • 47. Christidis, Les
    et al.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Fjeldså, Jon
    Irestedt, Martin
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Ohlson, Jan I
    The suboscine passerines2020Ingår i: The Largest Avian Radiation / [ed] Fjeldså, J., Christidis, L. & Ericson, P.G.P, Barcelona: Lynx Edicions , 2020, s. 65-65Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 48. Cockerill, Christopher A
    et al.
    Hasselgren, Malin
    Dussex, Nicolas
    Dalén, Love
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    von Seth, Johanna
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Angerbjörn, Anders
    Wallén, Johan F
    Landa, Arild
    Eide, Nina E
    Flagstad, Øystein
    Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)2022Ingår i: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 13, nr 11Artikel i tidskrift (Refereegranskat)
  • 49. Coward, Andrew
    et al.
    Mays, Chris
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Patti, Antonio
    Stilwell, Jeffrey
    O’Dell, Luke
    Viegas, Pedro
    Taphonomy and chemotaxonomy of Eocene amber from southeastern Australia2018Ingår i: Organic Geochemistry, ISSN 0146-6380, E-ISSN 1873-5290, Vol. 118, s. 103-115Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Amber is a complex, organic polymer that offers unparalleled utility as a preservation medium, providing insights into past organisms and environments. However, under specific circumstances, this information can be compromised through alteration of the amber structure. Understanding the degradation of amber in the geosphere could improve prospecting techniques and maximise the quality and validity of chemical information from altered samples. This study analysed 114 amber samples retrieved from two new Eocene Australian deposits at Strahan, Tasmania and Anglesea, Victoria using a combination of attenuated total reflectance Fourier transform infrared and solid-state 13C cross-polarised magic angle spinning nuclear magnetic resonance spectroscopy. Results identified both Class Ib polylabdanoid and Class II cadinene-based amber. The presence of Class II amber in Australia suggests one of two possibilities: (1) a local Dipterocarpaceae source, the primary producer of Class II resins, despite the absence of this family from the Australian Eocene fossil record; or (2) a local, unidentified botanical source of cadinene-based amber. A third alternative, that Class II amber was transported to Australia from Southeast Asia via ocean currents, is rejected. Taphonomic analysis revealed four mechanisms of alteration prevalent in amber across the two study regions, with evidence of oxidation and metal carboxylate formation. Both the nature and extent of these alterations were found to vary significantly between classes I and II, suggesting that amber class may play a defining role in determining the chemical pathways by which amber degrades. Of note was the high proportion of amber that exhibited no significant chemical changes despite extensive visible alteration features, suggesting the integrity of palaeobiological and palaeoenvironmental information in these samples may be preserved.

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  • 50.
    Cunningham, John A.
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. University of Bristol.
    Liu, Alexander G.
    University of Cambridge.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Donoghue, Philip C.J.
    University of Bristol.
    The origin of animals: Can molecular clocks and the fossil record be reconciled?2016Ingår i: Bioessays, ISSN 0265-9247, E-ISSN 1521-1878, Vol. 38, s. 1-12Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown-representatives of most animal phyla in the Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identificationin the fossil record. Critical assessment of both recordsmay permitbetter resolutionof the tempo and mode of early animal evolution.

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