DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae)

Abstract

The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra-and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.

Cryptic Diversity, but to What Extent? Discordance Between Single-Locus Species Delimitation Methods Within Mainland Anoles (Squamata: Dactyloidae) of Northern Central America

“…DNA barcoding has been applied to numerous vertebrate (e.g., Hebert et al, 2004; Álvarez-Castañeda et al, 2011; Mendoza et al, 2016; Ramirez et al, 2017; Barman et al, 2018) and invertebrate (e.g., Barrett and Hebert, 2005; Moura et al, 2011; Barco et al, 2016; Jin et al, 2018) taxa, but the barcoding of herpetofauna largely has lagged behind. The initiation of the “ColdCode” campaign (Murphy et al, 2013) has led to a more concentrated effort to provide reference libraries for reptiles and amphibians, including those focused on specific taxa (e.g., Dang et al, 2015; Liu et al, 2015) and broad-scale regional assessments (e.g., Nagy et al, 2012; Guarnizo et al, 2015; Hawlitscheck et al, 2016; Vasconcelos et al, 2016; Deichmann et al, 2017).…”

Molecular species delimitation in the primitively segmented spider genusHeptathelaendemic to Japanese islands

“…Furthermore, a clear cut-off DNA barcode gap between intra-and interspecific genetic distances, which are used as a threshold to delimit species boundaries (e.g., Barrett and Hebert, 2005;Hebert et al, 2004;Meyer and Paulay, 2005;Weigand et al, 2011), may be elusive. Instead, substantial overlap is often detected between intra-and interspecific divergences in diverse taxonomic groups (Čandek and Kuntner, 2015;Dang et al, 2016;Hickerson et al, 2006;Kvist, 2016;Meier et al, 2006;Meyer and Paulay, 2005). Because of this challenge, researchers have developed other single-locus, distancebased species delimitation methods, including the automatic barcode gap discovery (ABGD) algorithm (Puillandre et al, 2012).…”

Characteristics Evaluation of a Barcode Sequence of Two Limnonectes (Anura) Sympatric Populations from Kendari, Southeast Sulawesi

“…Finding mean of variations intra-species is 0.26%, range 0.04-1.09%, while mean inter-species 32 fold greater at 8,22% with range 3.42-12.67%. Anura, also shows a low genetic distance, ie 0.00 to 0.19 inter-species and 0.015 to 0.334 intra-species 29 . Estupiñán et al 42 also got similar results on Eutropical Anura, while 18 found higher intra-species variation than inter-species variation in parasitoids (Hymenoptera), Paramaecium 22 and green lacewings 38 .…”

“…Nuclear genes develop slower than mitochondrial genes 4,32,[39][40][41][42] . Furthermore, it is known that genes in the mitochondrial genome develop at different rates and the COI gene develops faster than other genes and interspecies variation more than intra-species variation so the COI gene was used as an animal barcode 10,29 and has been widely used in some animal taxa as a means of species identity or evolutionary change estimation.…”

“…In addition, 93% of the total 2130 DNA barcode specimens were diagnostic of geometric moths in Europe. There were several evolutionary studies and molecular identification has been carried out using the COI gene, ranging from invertebrates to vertebrates, namely: Parasitoids Hymenopteran [16][17][18] , Diptera 19,20 , In worms (Ancylostoma ceynalicum) 21 , Paramaecium 22 , Trypanosoma 23 , Coleoptera 24 , Ciliata 25 , fish in Taiwan 26 , gourami fish 27 , tree frogs of several amphibians 28,29 , Mammalians [30][31][32] .…”