Abstract
BackgroundDNA barcoding of non-avian reptiles based on the cytochrome oxidase subunit I (COI) gene is still in a very early stage, mainly due to technical problems. Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar.Methodology/Principal FindingsRepresentatives of the majority of Madagascan non-avian reptile species (including Squamata and Testudines) were sampled and successfully DNA barcoded. The new primer pair achieved a constantly high success rate (72.7–100%) for most squamates. More than 250 species of reptiles (out of the 393 described ones; representing around 64% of the known diversity of species) were barcoded. The average interspecific genetic distance within families ranged from a low of 13.4% in the Boidae to a high of 29.8% in the Gekkonidae. Using the average genetic divergence between sister species as a threshold, 41–48 new candidate (undescribed) species were identified. Simulations were used to evaluate the performance of DNA barcoding as a function of completeness of taxon sampling and fragment length. Compared with available multi-gene phylogenies, DNA barcoding correctly assigned most samples to species, genus and family with high confidence and the analysis of fewer taxa resulted in an increased number of well supported lineages. Shorter marker-lengths generally decreased the number of well supported nodes, but even mini-barcodes of 100 bp correctly assigned many samples to genus and family.Conclusions/SignificanceThe new protocols might help to promote DNA barcoding of reptiles and the established library of reference DNA barcodes will facilitate the molecular identification of Madagascan reptiles. Our results might be useful to easily recognize undescribed diversity (i.e. novel taxa), to resolve taxonomic problems, and to monitor the international pet trade without specialized expert knowledge.
Highlights
The elementary question how many species of eukaryotic organisms live on Earth has in the past decades led to remarkable controversies [1,2,3,4,5]
Similar to a long standing practice in microbiology [20], a short DNA sequence of a standard marker is used for species identification—in animals typically the mitochondrial gene for cytochrome oxidase subunit I (COI)
DNA barcodes for Madagascan reptiles Using the new primer pair, we produced COI sequences for the majority of the Madagascan species of reptiles
Summary
The elementary question how many species of eukaryotic organisms live on Earth has in the past decades led to remarkable controversies [1,2,3,4,5]. Similar to a long standing practice in microbiology [20], a short DNA sequence of a standard marker is used for species identification—in animals typically the mitochondrial gene for cytochrome oxidase subunit I (COI). This molecular survey method has been applied in a number of vertebrate taxa (e.g. birds: [21,22]; fish: [23]) and invertebrates (e.g. spiders: [24], Lepidoptera: [25,26,27], marine invertebrates: [28], and Heteroptera: [29]). Using a newly developed set of reptile-specific primers for COI we present the first comprehensive study targeting the entire reptile fauna of the fourth-largest island in the world, the biodiversity hotspot of Madagascar
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