In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)

Abstract

The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.

Museums and cradles of diversity are geographically coincident for narrowly distributed Neotropical snakes

“…Low sampling in Amazonia (Guedes et al 2018) might account for part of the low PE, but there are still a large number of species occurring across disjunct areas; thus resulting in large ranges when estimated by alpha hulls. Cryptic diversity might play a particular role in the weak endemism of Amazonia, and additional taxonomic reviews and phylogeographic studies may reveal additional species complexes in the region (Prudente and Passos 2010, Passos et al 2016 as well in as other parts of the Neotropics (Domingos et al 2017). Thus, our results set the ground for additional studies on hypotheses concerning the impact of cryptic diversity on PE patterns in the Neotropics.…”

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

“…In recent years, the advent of high throughput DNA sequencing technology has exponentially increased our capability to obtain large scale genomic data from non-model organisms, removing previous data-related constraints, while promoting further development of new phylogenetic inference methods and model-based approaches of species delimitation (van Dijk, Auger, Jaszczyszyn, & Thermes, 2014;Ekblom & Galindo, 2011;Fujita et al, 2012). In particular, the multispecies coalescent model (MCM) is considered an excellent approach to test alternative hypotheses of lineage divergence (Knowles & Carstens, 2007;Yang & Rannala, 2010) and identify boundaries among recently diverged species using multilocus data (Domingos, Colli, Lemmon, Lemmon, & Beheregaray, 2017;Rannala & Yang, 2013;Yang, 2015). More recent developments have incorporated the possibility of combining diverse sources of information (quantitative traits and genomic data) to objectively identify independently evolving lineages into an integrative analytical framework (Edwards & Knowles, 2014;Fujita et al, 2012;Solis-Lemus, Knowles, & Ane, 2015).…”

A New Collared Lizard (Tropidurus: Tropiduridae) Endemic to the Western Bolivian Andes and Its Implications for Seasonally Dry Tropical Forests

“…Taxonomic Advances: Although morphological and morphometric conservatism and convergence in traits are known to be a common occurrence within tropidurine clades (Frost, 1992;Harvey and Gutberlet, 2000;Frost et al, 2001;Carvalho et al, 2016), a number of species with different levels of crypsis await description Domingos et al, 2017). Adding up to recent findings (Carvalho, 2016;Carvalho et al, 2016), Tropidurus azurduyae represents one more example of a conspicuous but previously overlooked taxon.…”