The efficacy of an allometric growth model to correct for ontogenetic body size variation has been known for decades, yet this method remains relatively obscure and rarely applied. We optimize the implementation of this method through a newly developed and easy-to-use R package GroupStruct and further extend its application from intraspecific to interspecific datasets. Using empirical examples, we show that different size correction methods (i.e., ratios, residuals, and allometry) can result in vastly different conclusions. Our results demonstrate that choosing the appropriate size correction method is crucial as it can have significant impacts on downstream analyses and has the potential to alter biological interpretations.

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 344 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group.

Although body size correction and inferential statistics have been used in morphological studies for many decades, their applications are far from being ubiquitous. We performed a meta-analysis to quantify the extent of taxonomic papers that performed body size correction and implemented a statistical hypothesis testing framework during the analysis of morphological data. Our results indicate that in most papers, neither of these analyses were performed but instead, cursory comparisons of descriptive statistics were presented. With the development of numerous freely available and powerful statistical programs such as R, we find it prudent to outline a standardized and statistically defensible framework to enhance the workflow of morphological analyses in taxonomic studies. This 5-step approach can be applied to meristic and mensural data across a wide range of taxonomic groups. We include an easy-to-use companion R script to facilitate the implementation of this workflow. Our proposed framework is not rooted in phylogenetic or evolutionary theory and hence, should not be used in place of explicit species delimitation techniques. Nevertheless, it can be incorporated into a more robust integrative taxonomic framework and is particularly useful for identifying diagnostic characters for species diagnoses.

Twelve new karst-adapted species of the gekkonid genus Cyrtodactylus Gray are described from the Shan Hills and Salween River Basin of Myanmar. Three species occur in rocky habitats along karst ridges and nine species are microendemics restricted to isolated karst caves and towers. This high, localized diversity underscores the archipelago-like nature and microendemism associated with karst habitat-islands. Eleven of the 12 new species are not related to other Indo-Burmese species and form four monophyletic species groups nested within a larger Indo-Chinese clade of Southeast Asian species. Phylogenetic relationships and distributions indicate Cyrtodactylus originated in the Himalayan uplands and dispersed westward through Myanmar with subsequent invasions back into eastern and southern Myanmar. These new species highlight the understudied nature of karst biodiversity in general and karst herpetology in particular. Extensive karst ecosystems throughout the massive Shan Plateau of eastern Myanmar remain largely unexplored and are likely to harbour tens—if not hundreds—of undiscovered species. The unique and complex structure of understudied limestone ecosystems throughout Southeast Asia are habitats in which amphibians and reptiles have specialized, speciated and become endemic. In an age of biodiversity crisis, managing and conserving these ecosystems throughout Southeast Asia should be given greater priority. A key to the species of Cyrtodactylus of Myanmar is provided.

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independently over time in different lineages. The gekkonid genusCyrtodactylusis just such a lineage with approximately 300 species that range from South Asia to Melanesia and occupy a vast array of habitats. Ancestral state reconstructions using a stochastic character mapping analysis of nine different habitat preferences were employed across a phylogeny composed of 76% of the known species ofCyrtodactylus. This was done in order to ascertain which habitat preference is the ancestral condition and from that condition, the transition frequency to more derived habitat preferences. The results indicate that a general habitat preference is the ancestral condition forCyrtodactylusand the frequency of transitioning from a general habitat preference to anything more specialized occurs approximately four times more often than the reverse. Species showing extreme morphological and/or ecological specializations generally do not give rise to species bearing other habitat preferences. The evolution of different habitat preferences is generally restricted to clades that tend to occur in specific geographic regions. The largest radiations in the genus occur in rocky habitats (granite and karst), indicating that the transition from a general habitat preference to a granite or karst‐dwelling life style may be ecologically uncomplicated. Two large, unrelated clades of karst‐associated species are centered in northern Indochina and the largest clade of granite‐associated species occurs on the Thai‐Malay Peninsula. Smaller, independent radiations of clades bearing other habitat preferences occur throughout the tree and across the broad distribution of the genus. With the exception of a general habitat preference, the data show that karst‐associated species far out‐number all others (29.6% vs. 0.4%–10.2%, respectively) and the common reference to karstic regions as “imperiled arcs of biodiversity” is not only misleading but potentially dangerous. Karstic regions are not simply refugia harboring the remnants of local biodiversity but are foci of speciation thatcontinueto generate the most speciose, independent, radiations across the genus. Unfortunately, karstic landscapes are some of the most imperiled and least protected habitats on the planet and these data continue to underscore the urgent need for their conservation.