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  • 1.
    Cibois, Alice
    et al.
    Nat Hist Museum Geneva, CP 6434, CH-1211 Geneva 6, Switzerland.
    Gelang, Magnus
    Goteborgs Nat Hist Museum, Gothenburg, Sweden.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China;Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden.
    Pasquet, Eric
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat, UMR7205,Evolut,Biodiversite,CNRS,MNHN,UPMC,EPHE, Paris, France;Sorbonne Univ, Museum Natl Hist Nat, UMS MNHN, CNRS 2700,OMSI, Paris, France.
    Fjeldsa, Jon
    Nat Hist Museum Denmark, Ctr Macroecol Evolut & Climate, Zool Museum, Copenhagen, Denmark.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Vertebrate Zool, Mol Systemat Lab, Stockholm, Sweden.
    Olsson, Urban
    Univ Gothenburg, Dept Zool, Gothenburg, Sweden.
    Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy2018In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 47, no 4, p. 428-440Article in journal (Refereed)
    Abstract [en]

    DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and song babblers), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (jungle babblers) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A-D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T.fairbanki and T.cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the song babblers (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid-Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.

  • 2.
    Fuchs, Jerome
    et al.
    Sorbonne Univ, UPMC, CNRS,EPHE, UMR7205,Inst Systemat,Evolut,Biodiversite,MNHN, CP 51,57 Rue Cuvier, F-75231 Paris 05, France.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden;Chinese Acad Sci, Inst Zool, Key Lab Zool Syst & Evolut, Beijing, Peoples R China.
    Yosef, Reuven
    Ben Gurion Univ Negev, Elat, Israel.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Miocene diversification of an open-habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae)2019In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 48, no 5, p. 571-588Article in journal (Refereed)
    Abstract [en]

    Diversification of avifaunas associated with savannah and steppes appears to correlate with open habitats becoming available, starting in the Miocene. Few comparative analyses exist for families for which all species are predominantly adapted to these habitats. One such group is Laniidae (Passeriformes), which are small- to medium-sized predatory passerines known for their distinctive behaviour of impaling prey. We used multispecies coalescent-based and concatenation methods to provide the first complete species-level phylogeny for this group, as well as an estimate of the timing of diversification. Our analyses indicate that Laniidae as currently delimited is not monophyletic, as the genus Eurocephalus is not closely related to the remaining species. The two species currently assigned to the monotypic genera Urolestes and Corvinella are part of the same clade as the Lanius species, and we propose that they are included in the genus Lanius, making Laniidae monogeneric. The initial diversification of the clade is inferred to have occurred very rapidly, starting about 7.2-9.1 million years ago, timing depending on calibration method, but in either case coinciding with the expansion of C4 grasses. An African origin is inferred in the biogeographic analysis. In the redefined Laniidae, cooperative breeding is inferred to be restricted to a single clade, characterized by gregarious behaviour and rallying. Migratory behaviour evolved multiple times within the family.

  • 3. Goicoechea, Noemi
    et al.
    De La Riva, Ignacio
    Padial, Jose M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Recovering phylogenetic signal from frog mating calls2010In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 39, no 2, p. 141-154Article in journal (Refereed)
    Abstract [en]

    Few studies have tried to analyse the phylogenetic information contained in frog mating calls. While some of those studies suggest that sexual selection deletes any phylogenetic signal, others indicate that frog calls do retain phylogenetic informative characters. Discordant results can be the outcome of disparate rates of character evolution and evolutionary plasticity of call characters in different groups of frogs, but also the result of applying different coding methods. No study to date has compared the relative performance of different coding methods in detecting phylogenetic signal in calls, hampering thus potential consilience between previous results. In this study, we analyse the strength of phylogenetic signal in 10 mating call characters of 11 related species of frogs belonging to three genera of Andean and Amazonian frogs (Anura: Terrarana: Strabomantidae). We use six quantitative characters (number of notes per call, note length, call length, number of pulses per note, fundamental frequency and dominant frequency) and four qualitative ones (presence/absence of: pseudopulses, frequency modulation in notes, amplitude modulation in notes and amplitude modulation in pulses). We code quantitative characters using four different coding and scaling methods: (i) gap-coding, (ii) fixed-scale, (iii) step-matrix gap-weighting with between-characters scaling, and (iv) step-matrix gap-weighting with between-states scaling. All four coding methods indicate that frog calls contain phylogenetic information. These results suggest that divergent selection on frog mating calls may not always be strong enough to eliminate phylogenetic signal. However, coding methods strongly affect the amount of recoverable information. Step-matrix gap-weighting with between-characters scaling and gap-coding are suggested as the best methods available for coding quantitative characters of frog calls. Also, our results indicate that the arbitrariness in selecting character states and the method for scaling transitions weights, rather than the number of character states, is what potentially biases phylogenetic analyses with quantitative characters.

  • 4. HOGLUND, J
    et al.
    THULIN, J
    THE EXTERNAL MORPHOLOGY OF THE PARASITIC COPEPOD HOLOBOMOLOCHUS-CONFUSUS (STOCK)1988In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 17, no 4, p. 371-379Article in journal (Refereed)
  • 5.
    Koblmuller, Stephan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Duftner, Nina
    Sefc, M
    Aigner, Ursula
    Rogetzer, Martina
    Sturmbauer, Christian
    Phylogeographic structure and gene flow in the scale-eating cichlid Perissodus microlepis (Teleostei, Perciformes, Cichlidae) in southern Lake Tanganyika2009In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 3, p. 257-268Article in journal (Refereed)
    Abstract [en]

    One of the most fragmented habitats in freshwater lakes is the rocky littoral zone, where the already richly structured habitat is frequently interspersed with more pronounced barriers such as sandy bays, river estuaries and deep slopes. Although habitat fragmentation generally constrains the dispersal of specialized rock-dwelling species, patterns of population structure vary in sympatric taxa due to species-specific traits. In the present study, we examine the phylogeographic and population genetic structure of Perissodus microlepis, a presumptively highly mobile scale-eating cichlid fish endemic to Lake Tanganyika with a lake-wide distribution in the rocky littoral zone and no obvious geographical colour variation. Analysis of the mitochondrial DNA of six populations in the southern end of the lake suggests isolation by distance along rocky shoreline. Across a large muddy bay, a phylogeographic break indicates that environmental barriers restrict gene flow even in this highly mobile species. Restricted dispersal across the bay is not necessarily a consequence of an intrinsic propensity to avoid sand, but may be connected with the association between P. microlepis and other rock-dwelling fish, which the scale-eaters mimic and intermingle in order to be able to approach other fish to rip off scales from their bodies.

  • 6. Koehler, Joern
    et al.
    Koscinski, Daria
    Padial, José M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Chaparro, Juan C.
    Handford, Paul
    Lougheed, Stephen C.
    De la Riva, Ignacio
    Systematics of Andean gladiator frogs of the Hypsiboas pulchellus species group (Anura, Hylidae)2010In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 39, no 6, p. 572-590Article in journal (Refereed)
    Abstract [en]

    We revisit the taxonomic status of Andean species and populations of frogs of the Hypsiboas pulchellus group using multiple lines of evidence potentially indicative of evolutionary lineage divergence in anurans: differences in qualitative morphological or bioacoustic character states, no overlap in quantitative characters of advertisement calls, and monophyly of gene genealogies. We found qualitative and quantitative morphological characters to be extremely variable among species and populations of the group and thus of very limited use in assessing lineage divergence. In contrast, phylogenetic analyses based on 16S rRNA and cytochrome b sequences resolved highly supported clades that are in concordance with bioacoustic differences. The results support the specific distinctness of most nominal species recognized in the group, including the Bolivian Hypsiboas balzani and Hypsiboas callipleura, two species that were considered to be synonymous, and revealed the presence of an undescribed species from southern Peru, which is here described as Hypsiboas gladiator sp. n. In contrast, Hypsiboas andinus and Hypsiboas riojanus were mutually paraphyletic, and showed no differences in morphology and acoustic characters. Consequently, we regard the former as a junior synonym of the latter. However, we discovered that populations of H. riojanus from central Bolivia exhibit some degree of genetic differentiation and advertisement call differences with respect to Argentine populations, but sampling of these Bolivian populations is too sparse to draw taxonomic conclusions. Our phylogenetic results support the hypothesis that ancestral lineages of the Andean H. pulchellus group experienced successive splitting events along a latitudinal gradient from north to south.

  • 7.
    Padial, José M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Köhler, Jörn
    Vilà, Carles
    Chaparro, Juan C.
    De la Riva, Ignacio
    Deciphering the products of evolution at the species level: the need for an integrative taxonomy2009In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 4, p. 431-447Article in journal (Refereed)
    Abstract [en]

    Progress in molecular techniques together with the incorporation of phylogenetic analyses of DNA into taxonomy have caused an increase in the number of species' discoveries in groups with morphological characters that are difficult to study or in those containing polytypic species. But some emerged criticisms plead for a taxonomic conservatism grounded either on the requirement of providing evidences of morphological distinctiveness or reproductive barriers to erect new species names. In a case study of taxonomic research on Neotropical frogs, we combine several lines of evidence (morphological characters, prezygotic reproductive isolation and phylogenetic analyses of mitochondrial DNA) to test the status of 15 nominal species and to assess the degree of agreement of the different lines of evidence. Our study reveals that morphology alone is not sufficient to uncover all species, as there is no other single line of evidence independently. Full congruence between lines of evidence is restricted to only four out of the 15 species. Five species show congruence of two lines of evidence, whereas the remaining six are supported by only one. The use of divergence in morphological characters seems to be the most conservative approach to delineate species boundaries because it does not allow the identification of some sibling reciprocally monophyletic species differing in their advertisement calls. The separate analysis of differences in advertisement calls (evidence of reproductive isolation) or of phylogenetic data alone also shows limitations, because they do not support some morphological species. Our study shows that only an integrative approach combining all sources of evidence provides the necessary feedback to evaluate the taxonomic status of existing species and to detect putative new ones. Furthermore, the application of integrative taxonomy enables the identification of hypotheses about the existence of species that will probably be rejected or changed, and those that can be expected to persist.

  • 8.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves2016In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 45, p. 50-62Article, review/survey (Refereed)
    Abstract [en]

    Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous-Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy.

  • 9.
    Wallberg, Andreas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Curini-Galletti, Marco
    Ahmadzadeh, Afsaneh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Jondelius, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Dismissal of Acoelomorpha: Acoela and Nemertodermatida are separate early bilaterian clades2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 5, p. 509-523Article in journal (Refereed)
    Abstract [en]

    We used new 18S and 28S rRNA sequences analysed with parsimony, maximum likelihood and Bayesian methods of phylogenetic reconstruction to show that Nemertodermatida, generally classified as the sister group of Acoela within the recently proposed Phylum Acoelomorpha, are a separate basal bilaterian lineage. We used several analytical approaches to control for possible long branch attraction (LBA) artefacts in our results. Parsimony and the model based phylogenetic reconstruction methods that incorporate 'corrections' for substitution rate heterogenities yielded concordant results. When putative long branch taxa were experimentally removed the resulting topologies were consistent with our total evidence analysis. Deletion of fast-evolving nucleotide sites decreased resolution and clade support, but did not support a topology conflicting with the total evidence analysis. Establishment of Acoela and Nemertodermatida as two early lineages facilitates reconstruction of ancestral bilaterian features. The ancestor of extant Bilateria was a small, benthic direct developer without coelom or a planktonic larval stage. The previously proposed Phylum Acoelomorpha is dismissed as paraphyletic.

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