National Fish and Wildlife Forensic Laboratory

Oregon City, OR, United States

National Fish and Wildlife Forensic Laboratory

Oregon City, OR, United States
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Finch K.,Oregon State University | Espinoza E.,National Fish and Wildlife Forensic Laboratory | Andrew Jones F.,Oregon State University | Andrew Jones F.,Smithsonian Tropical Research Institute | Cronn R.,U.S. Department of Agriculture
Applications in Plant Sciences | Year: 2017

Premise of the study: We investigated whether wood metabolite profiles from direct analysis in real time (time-of-flight) mass spectrometry (DART-TOFMS) could be used to determine the geographic origin of Douglas-fir wood cores originating from two regions in western Oregon, USA. Methods: Three annual ring mass spectra were obtained from 188 adult Douglas-fir trees, and these were analyzed using random forest models to determine whether samples could be classified to geographic origin, growth year, or growth year and geographic origin. Specific wood molecules that contributed to geographic discrimination were identified. Results: Douglas-fir mass spectra could be differentiated into two geographic classes with an accuracy between 70% and 76%. Classification models could not accurately classify sample mass spectra based on growth year. Thirty-two molecules were identified as key for classifying western Oregon Douglas-fir wood cores to geographic origin. Discussion: DART-TOFMS is capable of detecting minute but regionally informative differences in wood molecules over a small geographic scale, and these differences made it possible to predict the geographic origin of Douglas-fir wood with moderate accuracy. Studies involving DART-TOFMS, alone and in combination with other technologies, will be relevant for identifying the geographic origin of illegally harvested wood. © 2017 Finch et al. Published by the Botanical Society of America.


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.


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.


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.


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.


Fain S.R.,National Fish and Wildlife Forensic Laboratory | Straughan D.J.,National Fish and Wildlife Forensic Laboratory | Taylor B.F.,National Fish and Wildlife Forensic Laboratory
Conservation Genetics | Year: 2010

Conflicting interpretations of the influence of coyote hybridization on wolf recovery in the western Great Lakes (WGL) states have stemmed from disagreement over the systematics of North American wolves. Questions regarding their recovery status have resulted. We addressed these issues with phylogenetic and admixture analysis of DNA profiles of western wolves, WGL states wolves and Wisconsin coyotes developed from autosome and Y-chromosome microsatellites and mitochondrial DNA control region sequence. Hybridization was assessed by comparing the haplotypes exhibited by sympatric wolves and coyotes. Genetic variability and connectivity were also examined. These analyses support the recognition of Canis lycaon as a unique species of North American wolf present in the WGL states and found evidence of hybridization between C. lupus and C. lycaon but no evidence of recent hybridization with sympatric coyotes. The recolonized WGL states wolves are genetically similar to historical wolves from the region and should be considered restored. © 2010 US Government.


McClure P.J.,National Fish and Wildlife Forensic Laboratory | Chavarria G.D.,National Fish and Wildlife Forensic Laboratory | Espinoza E.,National Fish and Wildlife Forensic Laboratory
Rapid Communications in Mass Spectrometry | Year: 2015

Rationale: The genus Dalbergia includes approximately 250 species worldwide. Of these, 58 species are of economic importance and listed under CITES. Identification of illegal transnational timber trade is a challenge because logs or boards lack the typical descriptors used for species identification such as leaves and flowers; therefore, frequently the lowest taxonomic determination of these tree byproducts is genus. In this study, we explore the use of Direct Analysis in Real Time (DART) Time-Of-Flight Mass Spectrometry (TOFMS) in making species determinations of protected Dalbergia trees from Africa, Madagascar, and Asia. Methods: Metabolic profiles were collected using DART TOFMS from the heartwood of seven species and the sapwood of 17 species of Dalbergia. Also included in this study are 85 Dalbergia heartwood samples from Madagascar that were only identified to genus. In all, 21 species comprising 235 specimens were analyzed, the metabolic chemotypes were interpreted, and the spectra were analyzed using chemometric tools. Results: Dalbergia cochinchinensis and Dalbergia spp. from Madagascar (both CITES Appendix II) could be differentiated from each other and from the non-protected Dalbergia latifolia and Dalbergia melanoxylon. Conclusions: DART TOFMS is a valuable high-throughput tool useful for making phytochemical classifications of Dalbergia spp. The data produced allows the protected Dalbergias from Madagascar to be distinguished and can differentiate closely related rosewood trees. Published in 2015. This article is a U.S. Government work and is in the public domain in the USA. Copyright © 2015 John Wiley & Sons, Ltd.


Lancaster C.,National Fish and Wildlife Forensic Laboratory | Espinoza E.,National Fish and Wildlife Forensic Laboratory
Rapid Communications in Mass Spectrometry | Year: 2012

RATIONALE International trade of several Dalbergia wood species is regulated by The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). In order to supplement morphological identification of these species, a rapid chemical method of analysis was developed. METHODS Using Direct Analysis in Real Time (DART) ionization coupled with Time-of-Flight (TOF) Mass Spectrometry (MS), selected Dalbergia and common trade species were analyzed. Each of the 13 wood species was classified using principal component analysis and linear discriminant analysis (LDA). These statistical data clusters served as reliable anchors for species identification of unknowns. RESULTS Analysis of 20 or more samples from the 13 species studied in this research indicates that the DART-TOFMS results are reproducible. Statistical analysis of the most abundant ions gave good classifications that were useful for identifying unknown wood samples. CONCLUSIONS DART-TOFMS and LDA analysis of 13 species of selected timber samples and the statistical classification allowed for the correct assignment of unknown wood samples. This method is rapid and can be useful when anatomical identification is difficult but needed in order to support CITES enforcement. Published 2012. This article is a US Government work and is in the public domain in the USA. © 2012 Published.


Lancaster C.,National Fish and Wildlife Forensic Laboratory | Espinoza E.,National Fish and Wildlife Forensic Laboratory
Rapid Communications in Mass Spectrometry | Year: 2012

RATIONALE Agarwood is the resinous material harvested from threatened Aquilaria species. We investigated how many protonated 2-(2-phenylethyl)chromone ions were sufficient to make an accurate identification of agarwood. Analysis of 125 reference samples was carried out by direct analysis in real time time-of-flight mass spectrometry (DART-TOFMS). The identification criteria developed were applied to commercial samples. METHODS We developed a technique that uses DART-TOFMS to detect 2-(2-phenylethyl)chromones. Additionally, we developed a set of criteria to infer the presence of Aquilaria in commercial samples of wood chips, sawdust, incense and liquids. Additionally, we examined other fragrant woods to determine if they contained a chemical profile that could be falsely identified as agarwood. RESULTS Analysis of reference and commercial samples (n = 151) established that DART-TOFMS provides reproducible mass spectra that are useful for inferring the genus of suspected agarwood samples. We identified 17 ions which were useful for authenticating agarwood. Comparison of the number of chromone ions detected by direct analyses of dry wood chips versus eluent analysis of methanol-extracted wood showed that results were similar. Lastly, analysis of 25 scented woods of other species did not give false positive results. CONCLUSIONS Reliable criteria for inferring agarwood include the presence of diagnostic ions, m/z 319.118 or 349.129, in addition to ten or more ions characteristic of 2-(2-phenylethyl)chromones. Wood anatomists challenged with difficult morphological identifications can use this tool to assist in their analyses. Published 2012. This article is a US Government work and is in the public domain in the USA. © Published 2012. This article is a US Government work and is in the public domain in the USA.


Fain S.R.,National Fish and Wildlife Forensic Laboratory | Straughan D.J.,National Fish and Wildlife Forensic Laboratory | Hamlin B.C.,National Fish and Wildlife Forensic Laboratory | Hoesch R.M.,National Fish and Wildlife Forensic Laboratory | LeMay J.P.,National Fish and Wildlife Forensic Laboratory
Conservation Genetics | Year: 2013

Caviar is among the world's most valuable wildlife products. Exploitation of sturgeon and paddlefish for the caviar trade has severely reduced abundance, and harvest of most species is regulated under CITES. International trade requires that importing nations verify the species source of caviars they receive; the US domestic trade has no such requirement. We report the results of forensic species identifications of US caviar imports from 1998 to 2008 and of US domestic market caviars from 1997 to 1998. Twelve species were identified overall and species origins were mislabeled three times as often among US domestic market caviars (14.7 %) as among imports (4.9 %). Industry practices associated with the re-packaging of caviars for domestic markets and re-export from intermediate countries have created opportunities for the co-mingling of legitimate caviars with those from illegal, unreported and unregulated sources. © 2013 Springer Science+Business Media Dordrecht (outside the USA).

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