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Bidon T.,Biodiversity and Climate Research Center | Janke A.,Biodiversity and Climate Research Center | Janke A.,Goethe University Frankfurt | Fain S.R.,National Fish and Wildlife Forensic Laboratory | And 7 more authors.
Molecular Biology and Evolution | Year: 2014

Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. © 2014 The Author. Source


Kutschera V.E.,Biodiversity and Climate Research Center | Bidon T.,Biodiversity and Climate Research Center | Hailer F.,Biodiversity and Climate Research Center | Rodi J.L.,Biodiversity and Climate Research Center | And 3 more authors.
Molecular Biology and Evolution | Year: 2014

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. © The Author 2014. Source


Bidon T.,Biodiversity and Climate Research Center | Frosch C.,Senckenberg Institute | Eiken H.G.,Norwegian Institute for Agricultural And Environmental Research Bioforsk | Kutschera V.E.,Biodiversity and Climate Research Center | And 5 more authors.
Molecular Ecology Resources | Year: 2013

We report a new approach for molecular sex identification of extant Ursinae and Tremarctinae bears. Two Y-specific fragments (SMCY and 318.2) and one X-specific fragment (ZFX) 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. © 2013 Blackwell Publishing Ltd. Source


Dormontt E.E.,University of Adelaide | Boner M.,Agroisolab GmbH | Breulmann G.,International Tropical Timber Organization ITTO | Degen B.,Thunen Institute of Forest Genetics | And 13 more authors.
Biological Conservation | Year: 2015

The prosecution of illegal logging crimes is hampered by a lack of available forensic timber identification tools, both for screening of suspect material and definitive identification of illegally sourced wood. Reputable timber traders are also struggling to police their own supply chains and comply with the growing requirement for due diligence with respect to timber origins and legality. A range of scientific methods have been developed independently with the potential to provide the required identification information, but little attention has been given to how these tools can be applied synergistically to support the legal timber trade. Here we review the use of visual identification methods (wood anatomy, dendrochronology), chemical methods (mass spectrometry, near infrared spectroscopy, stable isotopes, radio-carbon), and genetic methods (DNA barcoding, population genetics/phylogeography, DNA fingerprinting) each with potential application to forensic timber identification. We further highlight where future research and development are required to identify illegal logging crimes using these methods and suggest ways in which multiple methods can be used together to answer specific identification questions. We argue that a new integrated field of forensic timber identification should be a global investment priority, for which the ongoing collection, curation and taxonomic study of appropriate reference material is a critical part. Consideration of the specific legal requirements for method development and the application of identification methodologies to criminal evidence are also imperative to achieve robust scientific support for illegal logging crime prosecutions and prevention. © 2015. Source


Espinoza E.O.,National Fish and Wildlife Forensic Laboratory | Wiemann M.C.,Center for Wood Anatomy Research | Barajas-Morales J.,National Autonomous University of Mexico | Chavarria G.D.,National Fish and Wildlife Forensic Laboratory | McClure P.J.,National Fish and Wildlife Forensic Laboratory
IAWA Journal | Year: 2015

Species identification of logs, planks, and veneers is difficult because they lack the traditional descriptors such as leaves and flowers. An additional challenge is that many transnational shipments have unreliable geographic provenance. Therefore, frequently the lowest taxonomic determination is genus, which allows unscrupulous importers to evade the endangered species laws. In this study we explore whether analysis of wood using a Direct Analysis in Real Time (DART) Time-Of-Flight Mass Spectrometer (TOFMS) can assist in making unequivocal species determinations of Dalbergia. DART TOFMS spectra were collected from the heartwood of eight species of Dalbergia and six other look-alike species. In all, fourteen species comprising of 318 specimens were analyzed and the species chemical profiles were examined by statistical analysis. Dalbergia nigra (CITES Appendix I) was differentiated from D. spruceana; D. stevensonii (Appendix II) was distinguished from D. tucurensis (Appendix III), and all the look-alike timbers could be readily distinguished. Surprisingly, D. retusa (Appendix III) could not be differentiated from D. granadillo, and we postulate that they are synonymous. We conclude that DART TOFMS spectra are useful in making species identifications of American Dalbergia species, and could be a valuable tool for the traditional wood anatomist. © 2015 by Koninklijke Brill NV, Leiden, The Netherlands. Source

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