Diversification of bent-toed geckos (Cyrtodactylus) on Sumatra and west Java

Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation

“…5). Phylogenetic relationships in the group support multiple historical interchanges of lineages between the Thai-Malay Peninsula and Sumatra, as well as adjacent island chains (Grismer and Davis 2018;O'Connell et al 2019). The group has four potentially undescribed putative species from Sumatra-cf.…”

“…The marmoratus group (Fig. 26) is composed of at least three nominal species (two of which are analyzed here) and six potentially undescribed species (O'Connell et al 2019;Riyanto et al 2015) that range from New Guinea westward across the Lesser Sundas and Java, to parts of southern and western Sumatra (Figs. 3,27).…”

“…Additionally, incompletely informed diagnoses accompanying the descriptions of new species may contain only comparisons to distantly related species that happen to occur in the same geographic area while the appropriate comparisons to closely related species may go overlooked because they are not geographically proximate or are missing from the phylogeny. Recently however, this stumbling block was in-part removed with a mitochondrial phylogeny composed of 243 species (Grismer et al 2020a)-123 more species than the previous largest phylogeny (O'Connell et al 2019)-which for the first time, integrated dozens of species into a single tree that had never before been included in the same data set and taht generated the first phylogenetic data for several other species. In a continuing effort to mitigate these methodological limitations, a phylogeny of 310 species of Cyrtodactylus is presented here which, for the first time, places as many species as possible into a single tree consisting of 244 nominal species (79% of described species as of 20 September 2020, Uetz et al 2020) and 66 undescribed candidate species.…”

Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups

“…We used this method as the main approach to exploratory delimitation (ED) of species boundaries based on DNA barcodes and to establish OTUs due to it is frequently used in empirical studies has been and outperform OTU-picking methods (relying on simple sequence similarity thresholds) and are more robust to cases where the barcoding gap is absent [44,45]. This method is useful when multiple individuals belong to putative species are analyzed [46]. In spite previous studies have found that in some cases GMYC could lead to an overestimation of the number of species [47], paradoxically, this background makes it an appropriate method to evaluate the largest number of a priori groups in the exploratory analysis and to compare with regularly more conservative methods [10,47].…”

Evolution of habitat preference in 243 species of Bent‐toed geckos (GenusCyrtodactylusGray, 1827) with a discussion of karst habitat conservation

“…(2018), and O'Connell et al. (2019); nine finely delimited habitat preference categories as opposed to five; and a more informative statistical model (Bayesian vs. MP and ML; see below), we evaluate the evolution of habitat preference across the whole of Cyrtodactylus . With these data, we aim to (a) investigate the degree of ecological lability within Cyrtodactylus by assessing the frequency and direction of habitat preference transformations, (b) note the degree of convergent evolution in habitat preference among species and clades, (c) identify the habitats that support the largest number of species and, (d) contextualize these results in the framework of karst habitat conservation.…”