Application of DNA barcodes in wildlife conservation in Tropical East Asia

Abstract

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.

Impact of urbanisation and agriculture on the diet of fruit bats

“…Taxonomic assessment of fruit bats' food resources has been restricted to observations during behavioural studies of bats which are difficult in low light conditions (Phua and Corlett 1989), or morphology-based species identification of seeds in faeces or plant remnants in masticated pellets (Tan et al 1998;Hodgkison et al 2004). One potential solution to this impediment is the use of molecular methods such as DNA barcoding (Hebert et al 2003;Wilson et al 2016) which matches short DNA sequences of standardised regions (e.g. rbcL and ITS2 for plants; CBOL 2009; Chen et al 2010) to taxonomically verified DNA sequences (Kuzmina et al 2012).…”

Can concentrations of steroid hormones in brown bear hair reveal age class?

“…In addition, hair is easy and inexpensive to store for laboratory analysis; it is simply air-dried, sealed in paper envelopes, with or without a dessicant, and stored in a cool dry location (Long et al , 2007; Kendall and McKelvey, 2008). Hair collected from wildlife has been analysed in various ways, and for various purposes, including identification of individuals based on macro- and microscopic features (Stains, 1958; de Marinis and Asprea, 2006), genetic sampling of populations based on DNA extraction from hair follicles (Woods et al , 1999; Wilson et al , 2016), endocrine system function of individuals based on steroid hormone levels in hair (Koren et al , 2002; Schell et al , 2017), migration patterns and/or dietary habits of individuals based on stable isotope levels (Hobson, 1999; Cerling et al , 2006), and contaminant exposure of individuals based on hair levels of toxicants (d’Havé et al , 2005; Hernout et al , 2016). These research pursuits have generally followed independent paths, with combined studies being relatively uncommon, although several recent studies have combined genetic, endocrine and/or stable isotope analyses of hair to address issues relevant to methodology (Sergiel et al , 2017) and ecology (Bryan et al , 2013; Lafferty et al , 2015).…”

PipeCraft: Flexible open‐source toolkit for bioinformatics analysis of custom high‐throughput amplicon sequencing data

“…Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ) is commonly used to identify selected groups of micro‐ and macro‐organisms based on a single or a few taxonomic markers in combination. Information about the distribution of organisms is often used in environmental (Tedersoo et al., ; Wilson, Sing, Lee, & Wee, ) and palaeoecological surveys (Capo et al., ; Epp et al., ), monitoring diseases (Lohan, Fleischer, Carney, Holzer, & Ruiz, ), forensics (Pechal et al., ), etc.…”