Short Communication Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species

Abstract

ABSTRACT. Bats are important flagship species for biodiversity research; however, diversity in Southeast Asia is considerably underestimated in the current checklists and field guides. Incorporation of DNA barcoding into surveys has revealed numerous species-level taxa overlooked by conventional methods. Inclusion of these taxa in inventories provides a more informative record of diversity, but is problematic as these species lack formal description. We investigated how frequently documented, but undescribed, bat taxa are encountered in Peninsular Malaysia. We discuss whether a barcode library provides a means of recognizing and recording these taxa across biodiversity inventories. Tissue was sampled from bats trapped at Pasir Raja, Dungun Terengganu, Peninsular Malaysia. The DNA was extracted and the COI barcode region amplified and sequenced. We identified 9 species-level taxa within our samples, based on analysis of the DNA barcodes. Six specimens matched to four previously Short Communication 921©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (1): 920-925 (2014) DNA barcoding bat biodiversity in Malaysia documented taxa considered candidate species but currently lacking formal taxonomic status. This study confirms the high diversity of bats within Peninsular Malaysia (9 species in 13 samples) and demonstrates how DNA barcoding allows for inventory and documentation of known taxa lacking formal taxonomic status.

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

“…For example, Rattus (under BIN BOLD:AAB2208) detected from blowfly-derived DNA, cage traps, and scat collection likely represents Rattus "sp. R3" (Pages et al 2010), a classic "dark taxon" (see Wilson et al 2014) whereby it has not yet been formally described and is likely to be reported as R. andamanensis, R. argentiventer, or R. tanezumi in studies relying on visual diagnosis (Robins et al 2007;Pages et al 2010;Latinne et al 2013;Li et al 2015). The BIN associated with this taxon comprises DNA barcode members under the traditional names Rattus tanezumi, Rattus tiomanicus, Rattus rattus, Rattus sp., and Rattus sp.…”

“…Linnaean species names were assigned to our DNA barcodes (individual specimens collected from cage traps, mist nets, and scat collection) and a representative DNA metabarcode (recovered from blowfly-derived DNA) when they had sequence similarity matches of >98% to DNA barcodes with Linnaean species names (submitted by other BOLD users) in the full database of BOLD (see Wilson et al 2014). In the case of conflicts, i.e., our DNA (meta)barcodes had sequence similarity matches of >98% to database DNA barcodes with several different Linnaean species names, we assigned the Barcode Index Number (BIN) (Ratnasingham and Hebert 2013) of the matching reference DNA barcodes to our DNA (meta)-barcodes without using a species epithet.…”

“…The extracted DNA samples from hair, bat tissue, and scat samples were used for PCR in standard protocols following Wilson (2012) and Wilson et al (2014). Primers VF1d_t1 and VR1d_t1 (Ivanova et al 2012) were used for a first pass and RonM and VR1 for a second pass (Ivanova et al 2012).…”

Mercury accumulation in bats near hydroelectric reservoirs in Peninsular Malaysia

“…Note that bat species in Malaysia are often ''dark taxa'', species which have been recognized and recorded previously but which have not yet been formally described (Sing et al 2013;Wilson et al 2014), so a few of the species are referred to using non-Linnaean species names.…”

“…Sex and lifestage of the captured bats were recorded. Bats were identified in the field using morphological guides Francis 2008), but given the prevalence of cryptic bat species in Malaysia (Sing et al 2013;Wilson et al 2014) species identification was confirmed using DNA barcoding (Francis et al 2010), following standard methods used in previous studies (see Sing et al 2013;Wilson et al 2014). …”