Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

Abstract

We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.

Origins and patterns of endemic diversity in two specialized lizard lineages from the Australian Monsoonal Tropics (Oedura spp.)

“…However, many recent studies of savanna and grassland lineages, especially in Australia, emphasize that unrecognized, but biogeographically significant lineages remain overlooked (e.g. Agarwal & Ramakrishnan, ; Domingos et al., ; Gehring et al., ; Guarnizo et al., ; Oliver, Couper, et al., ). This includes both distinctive relict taxa with restricted ranges such as O. murrumanu (discovered and described as part of this work), and divergent lineages that remain confounded in widespread and diverse species complexes such as O. gracilis .…”

“…Larger ranges and evidence of introgression suggest a more dynamic history of the boundary between the AMT and AAZ. Resolving unrecognized biological diversity in savannas (Gehring et al., ; Miraldo et al., ; Werneck et al., ) is essential for understanding the history of these poorly known biomes.…”

DNA barcoding assessment of genetic variation in two widespread skinks from Madagascar, Trachylepis elegans and T. gravenhorstii (Squamata: Scincidae)

“…Given the high molecular variation found especially within T. gravenhorstii (Boumans et al 2007) it might be suspected that they represent species complexes, as has been observed with other widespread Malagasy reptiles thought to occur over different ecoregions in Madagascar (e.g., Raxworthy & Nussbaum 2006;Raxworthy et al 2007;Rocha et al 2010;Florio et al 2012;Gehring et al 2012aGehring et al , 2012b.…”

Hidden diversity ofEuscorpius(Scorpiones: Euscorpiidae) in Greece revealed by multilocus species-delimitation approaches

“…In our first approach, the topology obtained from the Bayesian analysis of the concatenated mtDNA sequences only (not including redundant identical sequences of same haplotypes) was used as a guide for manually grouping taxa at different levels by searching for the threshold at which the intraclade p ‐distances in the mtDNA sequences were lower than the interclade p ‐distances (Gehring et al ., ). This approach (pDist approach) was performed using net p ‐distances as estimated in MEGA5 (Tamura et al ., ).…”