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Berlin Brandenburg

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  • 1
    Language: English
    In: Science, 2012, Vol.336(6079), pp.344-347
    Description: Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data...
    Keywords: Medicin Och Hälsovetenskap ; Klinisk Medicin ; Neurologi ; Medical And Health Sciences ; Clinical Medicine ; Neurology ; Medicin Och Hälsovetenskap ; Klinisk Medicin ; Kirurgi ; Medical And Health Sciences ; Clinical Medicine ; Surgery
    ISSN: 1095-9203
    ISSN: 00368075
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  • 2
    Language: English
    In: Mitochondrial DNA Part A, 03 May 2016, Vol.27(3), pp.1887-1889
    Description: We report the first complete mitochondrial genome (mitogenome) of an invasive Ponto-Caspian goby, Ponticola kessleri (bighead goby, Günther 1891). Ion Torrent PGM sequencing of total DNA from two individuals yielded a contig of 16,971 bp, with overlapping ends located in the repetitive control...
    Keywords: Bighead Goby ; High Throughput Sequencing ; Invasive ; Mitochondrial Genome ; Ponticola Kessleri ; Rhine ; Anatomy & Physiology
    ISSN: 2470-1394
    E-ISSN: 2470-1408
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  • 3
    Language: English
    In: BMC Genomics, 2015, Vol. 16
    Description: Background: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. Results: The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Conclusions: Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.
    Keywords: Arctic Fox ; Vulpes Lagopus ; Red Fox ; Vulpes Vulpes ; Transcriptome ; Positive Selection ; Arctic Adaptation ; Natural Sciences ; Biological Sciences ; Evolutionary Biology ; Naturvetenskap ; Biologiska Vetenskaper ; Evolutionsbiologi ; Genetics ; Genetik
    ISSN: 1471-2164
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  • 4
    In: Molecular Biology and Evolution, 2014, Vol. 31(8), pp.2004-2017
    Description: Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.
    Keywords: Species Tree ; Introgressive Hybridization ; Ursidae ; Phylogenetic Network ; Coalescence ; Multi - Locus Analyses
    ISSN: 0737-4038
    E-ISSN: 1537-1719
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  • 5
    In: Molecular Ecology Resources, May 2013, Vol.13(3), pp.362-368
    Description: We report a new approach for molecular sex identification of extant and bears. Two Y‐specific fragments ( and ) and one X‐specific fragment () are amplified in a multiplex PCR, yielding a double test for male‐specific amplification and an internal positive control. The primers were designed and tested to be bear‐specific, thereby minimizing the risk of cross‐amplification in other species including humans. The high sensitivity and small amplicon sizes (100, 124, 160 base pairs) facilitate analysis of non‐invasively obtained DNA material. DNA from tissue and blood as well as from 30 non‐invasively collected hair and faeces yielded clear and easily interpretable results. The fragments were detected both by standard gel electrophoresis and automated capillary electrophoresis.
    Keywords: Bears ; Molecular Sexing ; Multiplex Pcr ; Non‐Invasive ; Ursidae ; Ursus Arctos
    ISSN: 1755-098X
    E-ISSN: 1755-0998
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  • 6
    Language: English
    In: Science (New York, N.Y.), 29 March 2013, Vol.339(6127), pp.1522
    Description: Nakagome et al. reanalyzed some of our data and assert that we cannot refute the mitochondrial DNA-based scenario for polar bear evolution. Their single-locus test statistic is strongly affected by introgression and incomplete lineage sorting, whereas our multilocus approaches are better suited to recover the true species relationships. Indeed, our sister-lineage model receives high support in a Bayesian model comparison.
    Keywords: Biological Evolution ; Genome ; Multilocus Sequence Typing ; Ursidae -- Genetics
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 7
    Language: English
    In: BMC Evolutionary Biology, June 5, 2013, Vol.13(1)
    Description: Background Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Results Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. Conclusions The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories. Keywords: Carnivores, Divergence time estimate, Generalist, mtDNA control region, Phylogeography, Vulpes
    Keywords: Bears ; DNA Sequencing ; Mitochondrial DNA ; Gray Wolf ; Niches (Ecology)
    ISSN: 1471-2148
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  • 8
    Language: English
    In: BMC Genomics, 2017, Vol. 18
    Description: Background: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases ( kb). Results: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions: Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto- Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.
    Keywords: Mitogenome ; Genome Size ; Genome Organisation ; Phylogeny ; Gobiidae ; Salinity ; Neogobius Melanostomus ; Pomatoschistus Minutus ; Ponticola Kessleri ; Medical And Health Sciences ; Medical Biotechnology ; Medical Biotechnology (With A Focus On Cell Biology (Including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry Or Biopharmacy) ; Medicin Och Hälsovetenskap ; Medicinsk Bioteknologi ; Medicinsk Bioteknologi (Med Inriktning Mot Cellbiologi (Inklusive Stamcellsbiologi), Molekylärbiologi, Mikrobiologi, Biokemi Eller Biofarmaci)
    ISSN: 1471-2164
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  • 9
    Language: English
    In: Animal Conservation, 2016, Vol. 19(4), pp. 337-349
    Description: Projections by the Intergovernmental Panel on Climate Change (IPCC) and sea ice forecasts suggest that Arctic sea ice will decline markedly in coming decades. Expected effects on the entire ecosystem include a contraction of suitable polar bear habitat into one or few refugia. Such large-scale habitat decline and fragmentation could lead to reduced genetic diversity. Here we compare genetic variability of four vagrant polar bears that reached Iceland with that in recognized subpopulations from across the range, examining 23 autosomal microsatellites, mitochondrial control region sequences and Y-chromosomal markers. The vagrants' genotypes grouped with different genetic clusters and showed similar genetic variability at autosomal microsatellites (expected heterozygosity, allelic richness, and individual heterozygosity) as individuals in recognized subpopulations. Each vagrant carried a different mitochondrial haplotype. A likely route for polar bears to reach Iceland is via Fram Strait, a major gateway for the physical exportation of sea ice from the Arctic basin. Vagrant polar bears on Iceland likely originated from more than one recognized subpopulation, and may have been caught in sea ice export during long-distance movements to the East Greenland area. Although their potentially diverse geographic origins might suggest that these vagrants encompass much higher genetic variability than vagrants or dispersers in other regions, the four Icelandic vagrants encompassed similar genetic variability as any four randomly picked individuals from a single subpopulation or from the entire sample. We suggest that this is a consequence of the low overall genetic variability and weak range-wide genetic structuring of polar bears - few dispersers can represent a large portion of the species' gene pool. As predicted by theory and our demographic simulations, continued gene flow will be necessary to counteract loss of genetic variability in increasingly fragmented Arctic habitats. Similar considerations will be important in the management of other taxa that utilize sea ice habitats.
    Keywords: Climate Change ; Dispersal ; Genetic Variability ; Habitat Fragmentation ; Inbreeding ; Arctic Sea Ice ; Ursus Maritimus ; Polar Bear ; Natural Sciences ; Biological Sciences ; Evolutionary Biology ; Naturvetenskap ; Biologiska Vetenskaper ; Evolutionsbiologi ; Ecology ; Ekologi
    ISSN: 1367-9430
    E-ISSN: 14691795
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  • 10
    In: Ecology and Evolution, October 2019, Vol.9(19), pp.11448-11463
    Description: Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used... We explore the potential of a newly established approach that relies on Pool‐seq data to generate de novo genome assemblies in nonmodel species upon which Pool‐seq data are used to estimate population divergence and diversity. Estimates of population differentiation between sympatric brown trout () populations...
    Keywords: Genetic Diversity ; Genome Sequencing ; Population Genomics ; Salmo Trutta ; Salmonid ; Single Nucleotide Polymorphism
    ISSN: 2045-7758
    E-ISSN: 2045-7758
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