One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae: Leptotyphlops sylvicolus Broadley & Wallach, 1997)

Abstract

We investigate the phylogeographic structure of a fossorial forest-living snake species, the forest thread snake, Leptotyphlops sylvicolus Broadley & Wallach, 1997 by sampling specimens from the Eastern Cape and KwaZulu-Natal provinces of South Africa. Phylogenetic results, using Bayesian inferences and maximum likelihood, from the combined mitochondrial sequence data (cyt b and ND4), along with population genetic analyses suggest the presence of phylogeographic breaks broadly congruent to those exhibited by other forest-living taxa. Divergence-time estimates indicate that cladogenesis within the study taxon occurred during the late Miocene climatic shifts, suggesting that cladogenesis was driven by habitat fragmentation. We further investigate the species-level divergence within L. sylvicolus by including two partial nuclear loci (PRLR and RAG1). The three species delimitation methods (ABGD, bGMYC, and STACEY), retrieved 10-12 putative species nested within the L. sylvicolus species complex. These results were corroborated by iBPP implementing molecular and morphological data in an integrative Bayesian framework. The morphological analyses exhibit large overlap among putative species but indicate differences between grassland and forest species. Due to the narrow distributions of these putative species, the results of the present study have further implications for the conservation status of the L. sylvicolus species complex and suggest that forest and grassland habitats along the east coast of South Africa may harbor significantly higher levels of diversity than currently recognized.

Barcoding of South African forest‐dwelling snails (Mollusca: Gastropoda) reveals widespread cryptic diversity

“…Our results are consistent with other studies showing that different species delimitation methods often produce different numbers of OTUs (Barnes et al, 2020;Busschau et al, 2020;Garcia-Melo et al, 2019;Prévot et al, 2013). In general, the RESL method retrieved large numbers of groupings, whereas ABGD analysis retrieved the smallest number of OTUs.…”

“…The analyses may have overestimated or underestimated the number of OTUs present in each species. The incongruence between the single-locus species delimitation analyses can be validated by the multispecies coalescence models such as STACEY (Barnes et al, 2020;Busschau et al, 2020;Murphy et al, 2015). Coalescent theory provides a framework to determine the shape and pattern of trees to identify species as evolving lineages and is consistent with the assumptions of some species concepts (Murphy et al, 2015).…”

“…Given the rapid evolution, low vagility, and low dispersal capability of land snails (Feng et al, 2011;Strong & Whelan, 2019;Thomaz et al, 1996) and that the majority of the South African fauna is in need of taxonomy and systematic revision, it is not surprising that there may be undocumented diversity. Whereas some of the recognized OTUs may represent undiscovered species, others may represent populations or evolutionarily significant units (ESUs) (Busschau et al, 2020;Gibbs, 2018).…”

Burrowing in blindsnakes: A preliminary analysis of burrowing forces and consequences for the evolution of morphology

“…Synapomorphies for this clade are cranial features comprising a venom delivery system, and this key innovation may have allowed them to diversify so suddenly and so widely (Pyron & Burbrink, 2012). The scolecophidians are comparatively species-poor with just 459 species described (see Uetz, Freed, & Hošek, 2020), although it is very likely that there are numerous cryptic species (Busschau, Conradie, & Daniels, 2021;Thomas & Hedges, 2007). The bulk of these species (60%) resides within one family, the Typhlopidae (Pyron & Wallach, 2014;Uetz et al, 2020).…”

Pseudocongruent phylogeography reflects unique responses to environmental perturbations in a biodiversity hotspot

“…Herpetological diversity in southern Africa is exceptionally high (Bates et al, 2014; Du Preez & Carruthers, 2017) and molecular systematic endeavours are constantly revealing undocumented diversity (e.g. Busschau et al, 2019, 2021; Minter et al, 2017). Phylogeographic studies on the subcontinental herpetofauna have sought to identify various environmental variables underpinning evolutionary diversity (e.g.…”