Neotropical bats: estimating species diversity with DNA barcodes

Abstract

DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

Figure 1. A neighbour-joining tree of COI sequence divergence (K2P) in surveyed species in the family Emballonuridae.

All currently recognized species are supported by bootstrap values ≥97 (1000 replications). Triangles indicate the relative number of individuals sampled (height) and sequence divergence (width). In two cases, Saccopteryx bilineata and Cormura brevirostris (highlighted in red) deep intraspecific mitochondrial lineages are present which are strongly supported indicating the need for additional taxonomic scrutiny. The identification of intraspecific lineages can be hindered by small sample sizes from large geographic areas (e.g. Cyttarops alecto) where divergent sequences may represent independent lineages or poorly sampled intraspecific variation.

Figure 2. Allopatric and sympatric divergences of COI. Intraspecific clusters within Saccopteryx bilineata (A) are allopatric.

One cluster in Pteronotus parnellii (B) exists in Central America, while the other three have potential zones of sympatry in Guyana.

Figure 3. Neighbour joining trees of COI sequences demonstrating the diversity in the twelve most widely sampled bat species (n>60) in the DNA barcode dataset from Central and South America.

Figure 4. Geographic distribution and genetic diversity of COI for Carollia brevicauda and C. sowelli.

C. brevicauda is found in eastern Panama and South America whereas C. sowelli occurs in other parts of Central America with a potential sympatric zone in central Panama. Intraspecific variation exists within both species including additional divergent clusters.