A need for continued collecting of avian voucher specimens in Africa: why blood is not enough

Bates, John M.; Bowie, Rauri C. K.; Willard, David E.; Voelker, Gary; Kahindo, Charles

doi:10.2989/00306520409485442

Cited by 25 publications

(20 citation statements)

References 12 publications

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“…One obvious possibility is that the phylogenetic position of one of the C. trifasciata clades is actually based on numts. After all, we have strong evidence that numts do exist in these animals , and the similarity of our phylogenetic pattern to some that are thought to be based on numts (i.e., Sorenson and Quinn 1998;Bates et al 2004) motivated our thorough sequencing effort to investigate this possibility. Using our long-range PCR strategy, we consistently recovered identical sequences from clade ''B'' individuals from multiple PCR reactions of different large fragments.…”

Section: Discussionmentioning

confidence: 95%

Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

Spinks

Shaffer

2006

Conserv Genet

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Asian box turtles (genus Cuora, family Geoemydidae) comprise a clade of 12 aquatic and semiaquatic nominate species distributed across southern China and Southeast Asia. Over the last two decades, turtles throughout Asia have been harvested at an unsustainable rate to satisfy demands for food, traditional Chinese medicine, and the pet trade. Consequently, all species of Cuora were recently placed on the IUCN Red List, nine are currently listed as critically endangered by the IUCN, and all species are listed in Appendix II of CITES. We compiled a 67-specimen mitochondrial (~1,650 base pairs (bp) from two mitochondrial genes) and a 40-specimen nuclear-plus-mitochondrial (~3,900 bp total, three nuclear introns plus an additional~860 bp mitochondrial gene fragment) DNA data set to reconstruct the phylogeny of Cuora species and to assess genetic diversity and species boundaries for several of the most problematic taxa. Our sampling included 23 C. trifasciata, 17 C. zhoui and 1-4 individuals of the remaining 10 species of Cuora. Maximum likelihood, maximum parsimony and Bayesian analyses all recovered similar, well resolved trees. Within the Cuora clade, mitochondrial and nuclear sequence data indicated that both C. zhoui and C. mccordi represent old lineages with little or no history of interspecific gene flow, suggesting that they are good genealogical species.Based on mtDNA, Cuora pani was paraphyletic and C. trifasciata was composed of two highly divergent lineages that were not each other's closest relatives; both cases of non-monophyly were due to a mtDNA sequence that was widespread and identical in C. aurocapitata, C. pani and C. trifasciata. However, when combined with nuclear DNA results, our data indicate that C. trifasciata is a single, monophyletic taxon, and that mitochondrial introgression and nuclear-mitochondrial pseudogenes have led to a complex pattern of mitochondrial gene relationships that does not reflect species-level histories. Our results imply that captive ''assurance colonies'' of both C. trifasciata and C. pani should be genotyped to identify pure, non-hybrid members of both taxa, and we recommend that introgressed and pure taxa be managed as independent entities until the full evolutionary histories of these critically endangered turtles are resolved.

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Section: Discussionmentioning

confidence: 95%

Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

Spinks

Shaffer

2006

Conserv Genet

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“…Genetic comparisons among individuals are valid when made between orthologous (like with like) pieces of DNA not paralogous ones (like with unlike). Bates et al (2004) show how erroneous biogeographical conclusions could have appeared had the presence of paralogs not been detected. An even clearer example is a report of DNA allegedly from the time of dinosaurs but which turned out to be paralogs of the gene in question that were essentially contaminants from humans (see Woodward et al 1994;and Hedges and Schweitzer 1995)!…”

Section: New Methodologies Drive New Collectionsmentioning

confidence: 97%

“…The use of blood samples is more complicated, and the risks of using blood as a source of mtDNA have often been explained (see Bates et al 2004). Avian red blood-cells are nucleated and so multiple nuclear DNA copies, or paralogs, can exist of target mtDNA, which is rare in blood anyway.…”

Section: New Methodologies Drive New Collectionsmentioning

confidence: 99%

“…This complements Gill's (2006) inventory and analysis of 10 Australian and four New Zealand bird collections, which together comprise some 500 000 specimens. I address the vulnerability of collections at a time of variable and increasingly uncertain institutional support and touch on the scientific need for voucher specimens (especially in molecular genetics studies; Bates et al 2004;Peterson et al 2007) and the need for carefully and ethically conducted scientific collecting of birds (Remsen 1995). If has not already been dispelled, I also hope to dispel the whimsical image shown in Fig.…”

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confidence: 99%

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Museum collections in ornithology: today's record of avian biodiversity for tomorrow's world

Joseph¹

2011

Emu - Austral Ornithology

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“…I expected that MSB's specimen growth in the last 25 years has widened MSB's scope such that a higher proportion of non-NM specimens were loaned recently in comparison to past years. The popularity of molecular studies has increased over time, and more researchers are collecting specimen parts rather than whole vouchers for vertebrate groups (Bates et al 2004). Therefore, I expected to observe a decrease in traditional specimens (skins and skeletons) loaned.…”

Section: Predictionsmentioning

confidence: 99%

Tracking changes in natural history collections utilization: A case study at the Museum of Southwestern Biology at the University of New Mexico

Abrahamson

2015

Collection Forum

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Abstract.-Natural history collections (NHCs) are used in many fields of study, but general knowledge regarding their uses is poor. Because of this, funding and support for NHCs frequently fluctuate. One way in which collections professionals can illustrate a collection's contribution to a variety of fields is based on the collection's history of use. Tracking NHC utilization through time can increase NHC value to others outside of the collection, allow for the analysis of changes in specimen-based research trends, and assist in effective collection management. This case study focuses on NHC usage records held by the Museum of Southwestern Biology (MSB), a currently growing university collection used in many research fields, and presents methods for quantifying collections utilization through time. Through an exploration of these data, this paper illustrates MSB's growth and changes in research produced over time and offers explanations for the changes observed. Last, this study provides suggestions for how collections professionals can most greatly benefit from considering NHC records as a data source. Understanding NHC usage from "the collection's perspective" provides a new way for NHC professionals to understand NHCs' value in the context of the research it supports and demonstrates the importance of this key infrastructure to a broader audience.

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A need for continued collecting of avian voucher specimens in Africa: why blood is not enough

Cited by 25 publications

References 12 publications

Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

Museum collections in ornithology: today's record of avian biodiversity for tomorrow's world

Tracking changes in natural history collections utilization: A case study at the Museum of Southwestern Biology at the University of New Mexico

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