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  • 51.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evaluation of methods for single hair DNA amplification2007In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, no 4, p. 977-981Article in journal (Refereed)
    Abstract [en]

    Because of the low amount of DNA in single hairs, it may be difficult to obtain reliable genotypes for forensic and conservation genetics studies. We therefore compared different methods for reliably genotyping single hair samples. Our results indicate that preliminary whole genome amplification can increase the likelihood of successfully genotyping a single hair compared to other commonly used protocols. The difference between the methods is small for single locus comparisons, but it becomes more important in multi-locus comparisons. The economic and time costs of the whole genome amplification may prevent its large-scale use in non-invasive monitoring programs. Nevertheless, it may be a very useful approach for the analysis of especially valuable samples.

  • 52.
    Björnerfeldt, Susanne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Relaxation of selective constraint on dog mitochondrial DNA following domestication2006In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 16, no 8, p. 990-994Article in journal (Refereed)
    Abstract [en]

    The domestication of dogs caused a dramatic change in their way of life compared with that of their ancestor, the gray wolf. We hypothesize that this new life style changed the selective forces that acted upon the species, which in turn had an effect on the dog's genome. We sequenced the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. Here we show that dogs have accumulated nonsynonymous changes in mitochondrial genes at a faster rate than wolves, leading to elevated levels of variation in their proteins. This suggests that a major consequence of domestication in dogs was a general relaxation of selective constraint on their mitochondrial genome. If this change also affected other parts of the dog genome, it could have facilitated the generation of novel functional genetic diversity. This diversity could thus have contributed raw material upon which artificial selection has shaped modern breeds and may therefore be an important source of the extreme phenotypic variation present in modern-day dogs.

  • 53. Bond, Brian C
    et al.
    Virley, David J
    Cairns, Nigel J
    Hunter, A Jackie
    Moore, Gary B T
    Moss, Stephen J
    Mudge, Anne W
    Walsh, Frank S
    Jazin, Elena
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Preece, Paul
    The quantification of gene expression in an animal model of brain ischaemia using TaqMan real-time RT-PCR.2002In: Brain Res Mol Brain Res, ISSN 0169-328X, Vol. 106, no 1-2, p. 101-16Article in journal (Other scientific)
  • 54.
    Borge, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genetics and the Origin of Two Flycatcher Species2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, different genetic tools are used to investigate pre- and postzygotic barriers to gene exchange and their role in speciation in the pied flycatcher (Ficedula hypoleuca) and the collared flycatcher (F. albicollis). This species complex consists of four genetically distinct clades that apparently diverged in allopatry (I). Sequencing of introns from autosomal and Z-linked genes from the two species reveals signs of selection on the Z-chromosome. Sexual selection acting on Z-linked genes might explain this pattern (II). By using large-scale genotyping of single nucleotide polymorphisms (SNPs), introgression is observed at autosomal- but not Z-linked loci, mostly from the pied- to the collared flycatcher. Male plumage characters and genes involved in hybrid fitness are largely mapped to the Z-chromosome (III). By studying mate choice of female hybrids I show that there is a link between female preferences and the Z chromosome (IV). The rate of introgression in island versus clinal hybrid zones is consistent with regional differences in hybrid fertility. Asymmetric gene flow from allopatry on the islands may oppose reinforcement, leading to introgression and a partial breakdown of postzygotic isolation. Adaptive introgression may explain the high rate of introgression observed at one of the genetic markers (V). For late breeding female collared flycatchers it appears to be adaptive to use pied flycatchers as social fathers but conspecific males as genetic fathers. Additionally, females in mixed species pairs may reduce hybridization costs by producing an excess of male hybrid offspring that are more fertile than females (VI).

    In conclusion, the Z-chromosome appears to play a major role in flycatcher speciation. Sexual selection and reinforcement are important mechanisms in the divergence of these birds. However, gene flow from allopatry, introgression of adaptive genes and adaptive hetrospecific pairing by late breeding collared flycatcher females may work in the opposite direction.

    List of papers
    1. Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
    Open this publication in new window or tab >>Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
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    2001 In: Molecular Ecology, Vol. 10, p. 737-749Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91245 (URN)
    Available from: 2004-01-07 Created: 2004-01-07Bibliographically approved
    2. Recurrent selective sweeps on the Z chromosome characterize the evolutionary history of two closely related flycatcher species (Ficedula hypoleuca and F. albicollis)
    Open this publication in new window or tab >>Recurrent selective sweeps on the Z chromosome characterize the evolutionary history of two closely related flycatcher species (Ficedula hypoleuca and F. albicollis)
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91246 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2010-01-13Bibliographically approved
    3. Sex chromosome evolution and speciation in Ficedula flycatchers
    Open this publication in new window or tab >>Sex chromosome evolution and speciation in Ficedula flycatchers
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    2003 In: Proceedings of the Royal Society of London: Biological Sciences, Vol. 270, p. 53-59Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91247 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2012-02-29
    4. Paternally determined species recognition in female flycathcer hybrids
    Open this publication in new window or tab >>Paternally determined species recognition in female flycathcer hybrids
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    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91248 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2010-01-13Bibliographically approved
    5. Rate of introgression in island versus clinal hybrid zones of Ficedula flycatchers are consistent with regional differences in hybrid fertility
    Open this publication in new window or tab >>Rate of introgression in island versus clinal hybrid zones of Ficedula flycatchers are consistent with regional differences in hybrid fertility
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91249 (URN)
    Available from: 2004-01-07 Created: 2004-01-07 Last updated: 2012-02-29
    6. Hybridization and adaptive mate choice in flycatchers
    Open this publication in new window or tab >>Hybridization and adaptive mate choice in flycatchers
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    2001 In: Nature, Vol. 411, p. 45-50Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91250 (URN)
    Available from: 2004-01-07 Created: 2004-01-07Bibliographically approved
  • 55.
    Brandström, Miakel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias2008In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 18, no 6, p. 881-887Article in journal (Refereed)
    Abstract [en]

    Studies of microsatellites evolution based on marker data almost inherently suffer from an ascertainment bias because there is selection for the most mutable and polymorphic loci during marker development. To circumvent this bias we took advantage of whole-genome shotgun sequence data from three unrelated chicken individuals that, when aligned to the genome reference sequence, give sequence information on two chromosomes from about one-fourth (375,000) of all microsatellite loci containing di- through pentanucleotide repeat motifs in the chicken genome. Polymorphism is seen at loci with as few as five repeat units, and the proportion of dimorphic loci then increases to 50% for sequences with similar to 10 repeat units, to reach a maximum of 75%-80% for sequences with 15 or more repeat units. For any given repeat length, polymorphism increases with decreasing GC content of repeat motifs for dinucleotides, nonhairpin-forming trinucleotides, and tetranucleotides. For trinucleotide repeats which are likely to form hairpin structures, polymorphism increases with increasing GC content, indicating that the relative stability of hairpins affects the rate of replication slippage. For any given repeat length, polymorphism is significantly lower for imperfect compared to perfect repeats and repeat interruptions occur in >15% of loci. However, interruptions are not randomly distributed within repeat arrays but are preferentially located toward the ends. There is negative correlation between microsatellite abundance and single nucleotide polymorphism ( SNP) density, providing large-scale genomic support for the hypothesis that equilibrium microsatellite distributions are governed by a balance between rate of replication slippage and rate of point mutation.

  • 56.
    Brandström, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Bagshaw, Andrew T.
    Gemmell, Neil J.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The relationship between microsatellite polymorphism and recombination hot spots in the human genome2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 12, p. 2579-2587Article in journal (Refereed)
    Abstract [en]

    Although previous studies have failed to detect an association between microsatellite polymorphism and broadscale recombination rates in the human genome, there are several possible reasons why such a relationship could exist. For instance, there might be a direct link if recombination is mutagenic to microsatellite sequences or if polymorphic microsatellites act as recombination signals. Alternatively, recombination could exert an indirect effect by uncoupling of natural selection at linked loci, promoting polymorphism. As recombination is concentrated in narrow hotspot regions in the human genome, we investigated the relationship between microsatellite polymorphism and recombination hot spots. By using data from a common allele frequency database, we found several polymorphism estimates to be similar for hot spots and the genomic average. However, this is likely explained by an ascertainment bias because markers with high polymorphism information content are usually selected for genotyping in human populations and pedigrees. In contrast, by using an unbiased set of shotgun sequence data, we found an excess of microsatellite polymorphism in recombination hot spots of 14%. However, when other genomic variables are taken into account in a generalized model and using wavelet analysis, the effect is no longer detectable and the only firm predictor of microsatellite polymorphism is the incidence of SNPs and indels. One possible neutral explanation to these observations is that there is a common denominator affecting the local rate of mutation in unique as well as in repetitive DNA, for example, base composition.

  • 57.
    Bremdal, K T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Seddon, J M
    MHC promoter polymorphism in grey wolves and domestic dogs.2006In: Tissue Antigens, no 67, p. 466-Article in journal (Refereed)
  • 58.
    Brohede, J.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Arnheim, N.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Single molecule analysis of the hypermutable tetranucleotide rpeat locus D21S1245 through sperm genotyping:: A heterogeneous pattern of mutation but no clear male age effect.2004In: Molecular Biology and Evolution, no 21, p. 58-64Article in journal (Refereed)
  • 59. Buckley, Michael
    et al.
    Anderung, Cecilia
    Penkman, Kirsty
    Raney, Brian J.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Thomas-Oates, Jane
    Collins, Matthew J.
    Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites 2008In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 35, no 6, p. 1756-1764Article in journal (Refereed)
    Abstract [en]

    The small mineral-binding bone protein, osteocalcin, has been applied in a number of studies on ancient bone due to predictions of its long-term stability. However, the intact protein has not been shown to survive in ancient bone devoid of DNA, which is a much more phylogenetically informative biomolecule. In this investigation, the survival of osteocalcin is directly compared to the amplification of mtDNA in a set of 34 archaeological samples from four sites throughout Europe. We also present unpublished osteocalcin sequences of seven mammalian species in addition to the 19 published sequences to highlight phylogenetic limitations of this protein. The results indicate that the intact osteocalcin molecule survives less in archaeological samples than mtDNA and is more subject to the temperature of the archaeological site. Amino acid analyses show the persistence of the dominant protein collagen in samples that failed both osteocalcin and mtDNA analyses. The implications these findings present for biomolecular species identification in archaeological and palaeontological material are that, although proteins do survive beyond ancient DNA, osteocalcin does not appear to be the most ideal target

  • 60. Burger, J.
    et al.
    Rosendahl, W.
    Loriell, O.
    Hemmer, H.
    Eriksson, T.
    Götherström, A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hiller, J.
    Coillins, M.
    Wess, T.
    Alt, K.W.
    Molecular phylogeny of the extinct cave lion Pathera leo spelaea.2004In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, no 30, p. 841-849Article in journal (Refereed)
  • 61.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Preece, Paul
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies2000In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 10, no 8, p. 1219-29Article in journal (Refereed)
    Abstract [en]

    Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. Comparison of the relative mRNA levels between two groups of samples with different time postmortem revealed unchanged relative expression levels for most genes. Only CYP26A1 mRNA levels showed a significant decrease with prolonged time postmortem (p = 0.00004). Also, there was a general decrease in measured mRNA levels for all genes in autopsies compared to biopsies; however, on comparing mRNA levels after adjusting with reference genes, no significant differences were found between mRNA levels in autopsies and biopsies. This observation indicates that studies of postmortem material can be performed to reveal the relative in vivo mRNA levels of genes. Power calculations were done to determine the number of individuals necessary to detect differences in mRNA levels of 1.5-fold to tenfold using the strategy described here. This analysis showed that samples from at least 50 individuals per group, patients and controls, are required for high-resolution ( approximately twofold changes) differential expression screenings in the human brain. Experiments done on ten individuals per group will result in a resolution of approximately fivefold changes in expression levels. In general, the sensitivity and resolution of any differential expression study will depend on the sample size used and the between-individual variability of the genes analyzed.

  • 62.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Sundberg, Rolf
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Decrease of serotonin receptor 2C in schizophrenia brains identified by high-resolution mRNA expression analysis2003In: Biological Psychiatry, ISSN 0006-3223, E-ISSN 1873-2402, Vol. 54, no 11, p. 1212-1221Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: RNA expression profiling can provide hints for the selection of candidate susceptibility genes, for formulation of hypotheses about the development of a disease, and/or for selection of candidate gene targets for novel drug development. We measured messenger RNA expression levels of 16 candidate genes in brain samples from 55 schizophrenia patients and 55 controls. This is the largest sample so far used to identify genes differentially expressed in schizophrenia brains. METHODS: We used a sensitive real-time polymerase chain reaction methodology and a novel statistical approach, including the development of a linear model of analysis of covariance type. RESULTS: We found two genes differentially expressed: monoamine oxidase B was significantly increased in schizophrenia brain (p =.001), whereas one of the serotonin receptor genes, serotonin receptor 2C, was significantly decreased (p =.001). Other genes, previously proposed to be differentially expressed in schizophrenia brain, were invariant in our analysis. CONCLUSIONS:The differential expression of serotonin receptor 2C is particularly relevant for the development of new atypical antipsychotic drugs. The strategy presented here is useful to evaluate hypothesizes for the development of the disease proposed by other investigators.

  • 63.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McCarthy, Shane
    Andersson, Björn
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Serotonin receptor 2C (HTR2C) and schizophrenia: effect of medication and genetic variants on expression levelsManuscript (Other academic)
  • 64.
    Castensson, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Åberg, Karolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    McCarthy, Shane
    Saetre, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Andersson, Björn
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Serotonin Receptor 2C (HTR2C) and Schizophrenia: Examination of Possible Medication and Genetic Influences on Expression Levels2005In: American Journal of Medical Genetics, ISSN 0148-7299, E-ISSN 1096-8628, Vol. 134B, p. 84-89Article in journal (Refereed)
    Abstract [en]

    The serotonin receptor 2C (HTR2C) gene is of interest in schizophrenia due to its involvement in regulation of dopamine activity in the prefrontal cortex. We have previously reported a decreased expression of HTR2C mRNA levels in the prefrontal cortex of schizophrenia patients. The variability in mRNA expression levels is evaluated here more closely in relation to promoter haplotypes and neuroleptic treatment received by the patients. The decrease in HTR2C mRNA was present in neuroleptic treated individuals and in patients untreated at death, indicating that the lower expression is not a short-term medication effect. Three promoter polymorphisms were used to construct haplotypes. No SNP displayed genotypic or haplotypic association with the disease. Gene expression of HTR2C was not affected by haplotype and the expression decrease in schizophrenia patients was similar in all haplotype combinations (diplotypes). We conclude that the decrease in HTR2C expression in schizophrenia may be related to the disease mechanism rather than to drug treatment. The disease related changes in HTR2C expression are not related to the promoter variants typed in our sample, but could be due to other regulatory variants or trans-acting factors.

  • 65.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Species Limits, and Evolutionary History of Glassfrogs2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Recognizing the mechanisms of speciation and the limits of species is essential to understand the origin of biodiversity and how to conserve it. The general aims of my investigations during my doctoral studies were two-fold: to study evolutionary patterns and processes, and to provide specific and superspecific taxonomic classifications that try to reflect evolutionary history. I have focused my research on anurans in their biodiversity hotspot, the American Tropics.

    I have used morphological, behavioral (mating calls), and genetic (DNA sequences) characters to study species boundaries between frogs of the genus Pristimantis and the family Centrolenidae (glassfrogs). The results show that the exclusive use of single lines of evidence or the application of arbitrary thresholds impair and bias our ability to recognize new species and limit the possibility to understand evolutionary processes. Only an integrative approach combining every source of evidence provides the necessary feedback to discover all species and test their identity by comparing independent sets of data. This approach further allows identifying those species that probably represent stable comparative units (well supported species hypotheses) and to flag taxa that require further assessment.

    Phylogenetic reconstructions based on seven nuclear and mitochondrial genes for about 100 species of glassfrogs revealed that previous hypotheses of relationships were mislead by rampant convergent evolution at the phenotypic level. None of the previously suggested classifications fit with the reconstructed evolutionary history. Consequently, we proposed a new classification consistent with this phylogeny.

    I also studied the tempo and mode of diversification among glassfrogs. Based on sequences from ten genes in 87 species, I estimated species divergence times, age-range correlation between sister species, and reconstructed ancestral areas and dispersal/vicariance events. The results revealed a complex model of diversification where geographical isolation seems to be the dominant scenario for speciation and only clades of altitudinal generalists have been able to spread across the Neotropical rainforests.

    List of papers
    1. Deciphering the products of evolution at the species level: the need for an integrative taxonomy
    Open this publication in new window or tab >>Deciphering the products of evolution at the species level: the need for an integrative taxonomy
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    2009 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 4, p. 431-447Article in journal (Refereed) Published
    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.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100912 (URN)10.1111/j.1463-6409.2008.00381.x (DOI)000267130400005 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    2. Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana Shield
    Open this publication in new window or tab >>Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana Shield
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    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-100913 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2010-01-14
    3. Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes
    Open this publication in new window or tab >>Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes
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    2008 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 2, p. 574-595Article, review/survey (Refereed) Published
    Abstract [en]

    Glassfrogs (family Centrolenidae) represent an exceptionally diverse group among Neotropical anurans, but their evolutionary relationships never have been assessed from a molecular perspective. Mitochondrial and nuclear markers were used to develop a novel hypothesis of centrolenid phylogeny. Ingroup sampling included 100 terminals, with 78 (53%) of the named species in the family, representing most of the phenotypic diversity described for the group. Thirty-five species representing taxa traditionally associated with glassfrogs were used as outgroups. Gene sampling consisted of complete or partial sequences of three mitochondrial (12S, 16S, ND1) and three nuclear markers (c-myc exon 2, RAG1, POMC) for a total of ∼4362 bp. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and combined datasets. The separate analysis of mitochondrial and nuclear datasets allowed us to clarify the relationships within glassfrogs; also, we corroborate the sister-group relationship between Allophryne ruthveni and glassfrogs. The new phylogeny differs significantly from all previous morphology-based hypotheses of relationships, and shows that hypotheses based on few traits are likely to misrepresent evolutionary history. Traits previously hypothesized as unambiguous synapomorphies are shown to be homoplastic, and all genera in the current taxonomy (Centrolene, Cochranella, Hyalinobatrachium, Nymphargus) are found to be poly- or paraphyletic. The new topology implies a South American origin of glassfrogs and reveals allopatric speciation as the most important speciation mechanism. The phylogeny profoundly affects the traditional interpretations of glassfrog taxonomy, character evolution, and biogeography-topics that now require more extensive evaluation in future studies.

    Keywords
    Anura, Biogeography, Centrolenidae, Evolution, Homoplasy, Monophyly, Neotropics, Phylogeny, Speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100914 (URN)10.1016/j.ympev.2008.04.012 (DOI)000258556100016 ()18515151 (PubMedID)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    4. Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni
    Open this publication in new window or tab >>Phylogenetic systematics of Glassfrogs (Amphibia: Centrolenidae) and their sister taxon Allophryne ruthveni
    Show others...
    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2100, p. 1-97Article, review/survey (Refereed) Published
    Abstract [en]

    Based on a molecular phylogeny, a new phylogenetic taxonomy that is compatible with both the International Code of Zoological Nomenclature (ICZN) and the PhyloCode is proposed for Glassfrogs and their sister taxon, Allophryne ruthveni. The arrangement presented herein emphasizes the recognition of clades having (i) significant statistical support and congruence among phylogenetic estimation methods (i.e., parsimony, maximum likelihood, and Bayesian inference criteria), (ii) congruence among genetic markers, and (iii) morphological and/or behavioral distinctiveness. Also, when previously recognized groups are recovered as monophyletic or nearly monophyletic, we propose taxa that minimize the number of name changes required to make these groups monophyletic, preserving the names and contents of previous classifications (i.e., nomenclatural stability). The evolutionary proximity of Centrolenidae and Allophrynidae is recognized by combining these families into an unraked taxon, Allocentroleniae-a proposal that maintains the traditional names and species contents of Centrolenidae and Allophrynidae. We arrange centrolenid diversity in two subfamilies: Centroleninae and Hyalinobatrachinae. Within Centroleninae, the diagnosis and species content of the genera Centrolene, Cochranella, and Nymphargus are modified; Teratohyla is resurrected and modified, and Chimerella, Espadarana, Rulyrana, Sachatamia, and Vitreorana are proposed as new genera. The other subfamily, Hyalinobatrachinae, contains the new genus Celsiella and a modified Hyalinobatrachium that fully corresponds to the former fleischmanni Group. Additionally, the genus Ikakogi is described. Ikakogi could not be assigned with confidence to either subfamily and it is placed as incertae sedis in Centrolenidae. The data at hand suggest that Ikakogi tayrona is a lineage as old as the subfamilies Hyalinobatrachinae and Centroleninae. The revised taxonomy differs markedly from previous arrangements, which were based on phenetics and few morphological characters. Most of the genera defined herein are confined to distinct biogeographic regions, highlighting the importance of geography in the speciation of Glassfrogs. The principal limitation of this proposal is that it is based on an incomplete sampling of taxa (54% of the recognized Glassfrogs). Although diagnoses are based on phenotypic traits, there are several cases (16% of all species) in which the allocation of species is ambiguous because of morphological homoplasy and the lack of molecular data. Finally, in an attempt to facilitate species identification, comparison, and generic placement, we provide photographs for most (similar to 96%) of the recognized centrolenid species.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100915 (URN)000266232500001 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    5. Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)
    Open this publication in new window or tab >>Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-100916 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2010-01-14
    6. A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela
    Open this publication in new window or tab >>A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela
    2007 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1441, p. 51-62Article in journal (Refereed) Published
    Abstract [en]

    We describe a new species of Hyalinobatrachium from Serran a de Perija, Estado de Zulia, Venezuela. The new species is placed in the Hyalinobatrachium fleischmanni group and can be differentiated from all other species of Hyalinobatrachium by having small enamelled glands on the lower part of the upper lip and on the skin covering the jaw, iris with a horizontal dark band that connects the pupil with the lateral edges of the eye, marked ulnar and tarsal white enamelled folds, extensive webbing between fingers and between toes, white pericardium and an advertisement call formed by a high-pitched single note composed of two parts: a group of modulated pulses increasing in frequency followed by a long and modulated sound at a constant frequency.

    Keywords
    Andes, biogeography, colombia, glass frogs, hyalinobatrachium tatayoi, taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-15723 (URN)000245487700004 ()
    Available from: 2008-05-19 Created: 2008-05-19 Last updated: 2017-12-08Bibliographically approved
    7. Glassfrogs (Anura: Centrolenidae) of Kaieteur National Park, Guyana, with notes on the distribution and taxonomy of some species of the family in the Guiana Shield
    Open this publication in new window or tab >>Glassfrogs (Anura: Centrolenidae) of Kaieteur National Park, Guyana, with notes on the distribution and taxonomy of some species of the family in the Guiana Shield
    2008 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1680, p. 25-53Article in journal (Refereed) Published
    Abstract [en]

    We provide new distribution records and discuss the taxonomy of three species of Glassfrogs from the Guiana Shield: Centrolene gorzulai, Cochranella helenae, and Hyalinobatrachium taylori. These three species were collected in Kaieteur National Park in west-central Guyana. Taxonomic changes were based on morphological, bioacoustic and genetic ( a fragment of the mitochondrial ribosomal gene 16S) comparisons. We consider Centrolene papillahallicum to be a junior synonym of C. gorzulai. We assign the Venezuelan population of Cochranella oyampiensis to Co. helenae and describe the phenotypic variation of this taxon. We refine the description of Cochranella oyampiensis and transfer it to the Co. spinosa species group. We propose the new name Cochranella helenae Group for those species of Cochranella assigned to the former Co. oyampiensis Group. We report the first record of Cochranella midas for French Guiana, and the first record of Hyalinobatrachium nouraguense, new emendation, for Suriname.

    Keywords
    Centrolenid frogs, Centrolene gorzulai, Centrolene papillahallicum, Cochranella ametarsia, Cochranella helenae, Cochranella midas, Cochranella oyampiensis, French Guiana, Hyalinobatrachium mondolfii, Hyalinobatrachium ouraguense, Hyalinobatrachium taylori, mitochondrial DNA, Suriname
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100917 (URN)000252281700002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    8. Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae)
    Open this publication in new window or tab >>Comments on the distribution, taxonomy and advertisement call of the Guyanan glass frog Hyalinobatrachium ignioculus (Anura: Centrolenidae)
    2008 (English)In: Salamandra, ISSN 0036-3375, Vol. 44, no 4, p. 235-240Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-100918 (URN)
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2009-09-18Bibliographically approved
    9. Taxonomic identity of Cochranella petersi Goin, 1961 and Centrolenella ametarsia Flores, 1987
    Open this publication in new window or tab >>Taxonomic identity of Cochranella petersi Goin, 1961 and Centrolenella ametarsia Flores, 1987
    2008 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1815, p. 25-34Article in journal (Refereed) Published
    Abstract [en]

    We assess the taxonomic status of Hyalinobatrachium petersi and Cochranella ametarsia based on the examination oftype material and recently collected specimens. We conclude that the material assigned to them is morphologically undistinguishablefrom two previously described species (Cochranella pulverata and Cochranella oyampiensis, respectively) and, therefore, are junior synonyms.

    Keywords
    Centrolenidae, ametarsia, Cochranella, Hyalinobatrachium, oyampiensis, petersi, pulverata, Synonymy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100919 (URN)000257321200002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    10. Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)
    Open this publication in new window or tab >>Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)
    2008 (English)In: Herpetologica, ISSN 0018-0831, E-ISSN 1938-5099, Vol. 64, no 4, p. 472-484Article in journal (Refereed) Published
    Abstract [en]

    Hyalinobatrachium orientale has a complex taxonomic history suggesting that more than one species could be under this name. In this review, we try to clarify the current taxonomic status of this species by means of morphological, bioacoustic, and mitochondrial DNA sequence comparisons of specimens from Tobago Island and the Venezuelan Cordillera de la Costa (Oriental Sector, Cordillera del Litoral and Cordillera del Interior). Our data support the resurrection of Hyalinobatrachium orocostale, restricted to the Cordillera del Interior. Additionally, specimens from Cordillera del Litoral and Oriental Sector do not form a monophyletic group; hence, we define as Hyalinobatrachium sp. the populations from Cordillera del Litoral and H. orientale sensu stricto the populations from the Oriental Sector. Preliminary bioacoustic and morphological analyses indicate that the populations from Tobago are conspecific with Hyalinobatrachium orientale sensu stricto.

    Keywords
    Cordillera de la Costa, Cryptic species, Glassfrogs, Mitochondrial DNA, Taxonomy, Tobago, Venezuela
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100920 (URN)10.1655/07-049R2.1 (DOI)000264060900007 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    11. Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
    Open this publication in new window or tab >>Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy
    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 1980, p. 16-28Article in journal (Refereed) Published
    Abstract [en]

    We evaluate the hypothesis of Centrolene lema as a species distinct from C. gorzulae using morphological, bioacousticand genetic comparisons. Our results show that there are no consistent differences in any of these three areas; hence, wepresent C. lema as a synonym of C. gorzulae. Additionally we provide new data on the distribution and ecology of thespecies.

    Keywords
    Bioacoustics, Centrolene gorzulae, Centrolenid frogs, Distribution, Glassfrogs, Guiana Shield, Guyana, mitochondrial DNA, Synonym, Venezuela
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100921 (URN)000262632400002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
    12. A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area
    Open this publication in new window or tab >>A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area
    Show others...
    2009 (English)In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2143, p. 24-44Article in journal (Refereed) Published
    Abstract [en]

    We describe a new species of Hyalinobatrachium from the Amazonian   slopes of the Andes in Peru and Bolivia on the basis of morphological,   bioacoustic and genetic characteristics. Hyalinobatrachium carlesvilai   sp. nov. can be distinguished from other species of Hyalinobatrachium   by the combination of the following characters: (1) truncate snout in   dorsal and lateral view; (2) white pericardium; (3) enameled dorsal,   tarsal and cloacal folds; (4) hand webbing formula III 2(-) -1(+) IV;   (5) iris cream; (6) advertisement call consisting of a single,   frequency-modulated note with a pulsed section followed by a tonal   section. The new species had been previously identified as   Hyalinobatrachium munozorum and H. bergeri. The advertisement call of   the new species was previously assigned to H. bergeri. Here we describe   the previously unknown call of Hyalinobatrachium bergeri. Additionally,   we study the taxonomic status of H. lemur and H. pellucidum and place   the former as synonym of the later. We extend the distribution of H. pellucidum to Departamento Cusco in southern Peru.

    Keywords
    Bioacoustics, Centrolenid frogs, Cryptic species, Glassfrogs, Hyalinobatrachium bergeri, Hyalinobatrachium lemur, Hyalinobatrachium munozorum, Hyalinobatrachium pellucidum, mitochondrial DNA, Synonymy, Taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100922 (URN)000267615900002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
  • 66.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ayarzaguena, J.
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    A new species of Hyalinobatrachium (Centrolenidae : Anura) from Serrania de Perija, Venezuela2007In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 1441, p. 51-62Article in journal (Refereed)
    Abstract [en]

    We describe a new species of Hyalinobatrachium from Serran a de Perija, Estado de Zulia, Venezuela. The new species is placed in the Hyalinobatrachium fleischmanni group and can be differentiated from all other species of Hyalinobatrachium by having small enamelled glands on the lower part of the upper lip and on the skin covering the jaw, iris with a horizontal dark band that connects the pupil with the lateral edges of the eye, marked ulnar and tarsal white enamelled folds, extensive webbing between fingers and between toes, white pericardium and an advertisement call formed by a high-pitched single note composed of two parts: a group of modulated pulses increasing in frequency followed by a long and modulated sound at a constant frequency.

  • 67.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Guayasamin, Juan M.
    Ayarzagüena, José
    Trueb, Linda
    Vilà, Carles
    Biogeography and diversification of Neotropical glassfrogs (Anura: Centrolenidae)Manuscript (Other (popular science, discussion, etc.))
  • 68.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Guayasamin, Juan M.
    Kok, Philippe J. R.
    Species status of Centrolene lema Duellman & Señaris, 2003 (Amphibia: Centrolenidae) revealed by Integrative Taxonomy2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 1980, p. 16-28Article in journal (Refereed)
    Abstract [en]

    We evaluate the hypothesis of Centrolene lema as a species distinct from C. gorzulae using morphological, bioacousticand genetic comparisons. Our results show that there are no consistent differences in any of these three areas; hence, wepresent C. lema as a synonym of C. gorzulae. Additionally we provide new data on the distribution and ecology of thespecies.

  • 69.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Padial, José M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Chaparro, Juan C.
    Aguayo, Rodrigo
    de la Riva, Ignacio
    A new species of Hyalinobatrachium (Anura: Centrolenidae) from the Amazonian slopes of the central Andes with comments on the diversity of the genus in the area2009In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 2143, p. 24-44Article in journal (Refereed)
    Abstract [en]

    We describe a new species of Hyalinobatrachium from the Amazonian   slopes of the Andes in Peru and Bolivia on the basis of morphological,   bioacoustic and genetic characteristics. Hyalinobatrachium carlesvilai   sp. nov. can be distinguished from other species of Hyalinobatrachium   by the combination of the following characters: (1) truncate snout in   dorsal and lateral view; (2) white pericardium; (3) enameled dorsal,   tarsal and cloacal folds; (4) hand webbing formula III 2(-) -1(+) IV;   (5) iris cream; (6) advertisement call consisting of a single,   frequency-modulated note with a pulsed section followed by a tonal   section. The new species had been previously identified as   Hyalinobatrachium munozorum and H. bergeri. The advertisement call of   the new species was previously assigned to H. bergeri. Here we describe   the previously unknown call of Hyalinobatrachium bergeri. Additionally,   we study the taxonomic status of H. lemur and H. pellucidum and place   the former as synonym of the later. We extend the distribution of H. pellucidum to Departamento Cusco in southern Peru.

  • 70.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Señaris, J. Celsa
    Ayarzagüena, José
    Vilà, Carles
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Resurrection of Hyalinobatrachium orocostale and notes on the Hyalinobatrachium orientale species complex (Anura: Centrolenidae)2008In: Herpetologica, ISSN 0018-0831, E-ISSN 1938-5099, Vol. 64, no 4, p. 472-484Article in journal (Refereed)
    Abstract [en]

    Hyalinobatrachium orientale has a complex taxonomic history suggesting that more than one species could be under this name. In this review, we try to clarify the current taxonomic status of this species by means of morphological, bioacoustic, and mitochondrial DNA sequence comparisons of specimens from Tobago Island and the Venezuelan Cordillera de la Costa (Oriental Sector, Cordillera del Litoral and Cordillera del Interior). Our data support the resurrection of Hyalinobatrachium orocostale, restricted to the Cordillera del Interior. Additionally, specimens from Cordillera del Litoral and Oriental Sector do not form a monophyletic group; hence, we define as Hyalinobatrachium sp. the populations from Cordillera del Litoral and H. orientale sensu stricto the populations from the Oriental Sector. Preliminary bioacoustic and morphological analyses indicate that the populations from Tobago are conspecific with Hyalinobatrachium orientale sensu stricto.

  • 71.
    Castroviejo-Fisher, Santiago
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Vilà, Carles
    Ayarzagüena, José
    Blanc, Michel
    Ernst, Raffael
    Delimiting species boundaries using different criteria: taxonomy of Hyalinobatrachium Glassfrogs (Amphibia: Centrolenidae) from the Guiana ShieldManuscript (Other (popular science, discussion, etc.))
  • 72. Cavelier, L
    et al.
    Erikson, I
    Tammi, M
    Jalonen, P
    Lindholm, Eva
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, P
    Luthman, H
    Gyllensten, U
    MtDNA mutations in maternally inherited diabetes: presence of the 3397 ND1 mutation previously associated with Alzheimer's and Parkinson's disease2001In: Hereditas, ISSN 0018-0661, E-ISSN 1601-5223, Vol. 135, no 1, p. 65-70Article in journal (Refereed)
    Abstract [en]

    Mutations in the mitochondrial tRNA(leu) (UUR) gene have been associated with diabetes mellitus and deafness. We screened for the presence of mtDNA mutations in the tRNA(leu) (UUR) gene and adjacent ND1 sequences in 12 diabetes mellitus pedigrees with a possible maternal inheritance of the disease. One patient carried a G to A substitution at nt 3243 (tRNA(leu) (UUR) gene) in heteroplasmic state. In a second pedigree a patient had an A to G substitution at nt 3397 in the ND1 gene. All maternal relatives of the proband had the 3397 substitution in homoplasmic state. This substitution was not present in 246 nonsymptomatic Caucasian controls. The 3397 substitution changes a highly conserved methionine to a valine at aa 31 and has previously been found in Alzheimer's (AD) and Parkinson's (PD) disease patients. Substitutions in the mitochondrial ND1 gene at aa 30 and 31 have associated with a number of different diseases (e.g. AD/PD, MELAS, cardiomyopathy and diabetes mellitus, LHON, Wolfram-syndrome and maternal inherited diabetes) suggesting that changes at these two codons may be associated with very diverse pathogenic processes. In a further attempt to search for mtDNA mutations outside the tRNAleu gene associated with diabetes, the whole mtDNA genome sequence was determined for two patients with maternally inherited diabetes and deafness. Except for substitutions previously reported as polymorphisms, none of the two patients showed any non-synonymous substitutions either in homoplasmic or heteroplasmic state. These results imply that the maternal inherited diabetes and deafness in these patients must result from alterations of nuclear genes and/or environmental factors.

  • 73.
    Ceplitis, H.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Adaptive molecula evolution in HINTW, a female-specific gene in birds.2004In: Molecular Biology and Evolution, no 21, p. 249-254Article in journal (Refereed)
  • 74.
    Corl, Ammon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Davis, Alison R.
    Kuchta, Shawn R.
    Sinervo, Barry
    Selective loss of polymorphic mating types is associated with rapid phenotypic evolution during morphic speciation2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 9, p. 4254-4259Article in journal (Refereed)
    Abstract [en]

    Polymorphism may play an important role in speciation because new species could originate from the distinctive morphs observed in polymorphic populations. However, much remains to be understood about the process by which morphs found new species. To detail the steps of this mode of speciation, we studied the geographic variation and evolutionary history of a throat color polymorphism that distinguishes the "rock-paper-scissors" mating strategies of the side-blotched lizard, Uta stansburiana. We found that the polymorphism is geographically widespread and has been maintained for millions of years. However, there are many populations with reduced numbers of throat color morphs. Phylogenetic reconstruction showed that the polymorphism is ancestral, but it has been independently lost eight times, often giving rise to morphologically distinct subspecies/species. Changes to the polymorphism likely involved selection because the allele for one particular male strategy, the "sneaker" morph, has been lost in all cases. Polymorphism loss was associated with accelerated evolution of male size, female size, and sexual dimorphism, which suggests that polymorphism loss can promote rapid divergence among populations and aid species formation.

  • 75. Cruz, F.
    et al.
    Vilà, C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    The legacy of domestication: Accumulation of deleterious mutations in the dog genome2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 11, p. 2331-2336Article in journal (Refereed)
    Abstract [en]

    Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the gray wolf. We compared variation in dog and wolf genes using whole-genome single nucleotide polymorphism (SNP) data. The d(N)/d(S) ratio (omega) was around 50% greater for SNPs found in dogs than in wolves, indicating that a higher proportion of nonsynonymous alleles segregate in dogs compared with nonfunctional genetic variation. We suggest that the majority of these alleles are slightly deleterious and that two main factors may have contributed to their increase. The first is a relaxation of selective constraint due to a population bottleneck and altered breeding patterns accompanying domestication. The second is a reduction of effective population size at loci linked to those under positive selection due to Hill-Robertson interference. An increase in slightly deleterious genetic variation could contribute to the prevalence of disease in modern dog breeds.

  • 76. Dalén, L.
    et al.
    Götherström, A.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Angerbjörn, A.
    Identifying species from pieces of faeces.2004In: Conservation Genetics, ISSN 1566-0621, no 5, p. 105-111Article in journal (Refereed)
  • 77. Dalén, Love