title: 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.
authors.affiliation: Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia. Electronic address: fabriciusmaia@gmail.com.
authors.forename: Fabricius M C B
authors.initials: FMCB
authors.lastname: Domingos
authors.affiliation: Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, DF, Brazil.
authors.forename: Guarino R
authors.initials: GR
authors.lastname: Colli
authors.affiliation: Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Lemmon
authors.affiliation: Department of Biological Sciences, Florida State University, Tallahassee, FL 32306-4295, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia.
authors.forename: Luciano B
authors.initials: LB
authors.lastname: Beheregaray
mesh_terms: D000818:Animals; D001938:Brazil; D017753:Ecosystem; D014644:Genetic Variation; D005828:Genetics, Population; D023281:Genomics; D005843:Geography; D008116:Lizards / Q000235:genetics*; D010802:Phylogeny; D013045:Species Specificity
keywords: Anchored hybrid enrichment; BPP; Bayesian species delimitation; Cryptic species; Neotropics; Phylogeography