The ecology and evolution of key innovations.

The idea of 'key innovations' has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.

Mitochondrial genome of the critically Endangered silver boa (Chilabothrus argentum; Squamata: Boidae).

We present the complete mitochondrial genome of Chilabothrus argentum, which is 17,345 bp in length, has 22 transfer ribonucleic acids (tRNAs), 2 ribosomal subunits (rRNAs), 13 protein-coding genes, an origin of the light-strand replication (OL), and two control regions (CR1, CR2). A maximum likelihood phylogenetic estimate using nine other snake mitochondrial genomes yields agreement with previous investigations into the evolutionary relationships of snakes.

Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura).

The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1 to 10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1-2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 total outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and StarBEAST2 methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all other Cyclura. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila and C. lewisi), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxa are C. nubila and C. lewisi. Cyclura collei is the sister taxon to these four species combined.

Novel Tests of the Key Innovation Hypothesis: Adhesive Toepads in Arboreal Lizards.

The evolution of key innovations-unique features that enable a lineage to interact with the environment in a novel way-may drive broad patterns of adaptive diversity. However, traditional tests of the key innovation hypothesis, those which attempt to identify the evolutionary effect of a purported key innovation by comparing patterns of diversity between lineages with and without the key trait, have been challenged on both conceptual and statistical grounds. Here, we explore alternative, untested hypotheses of the key innovation framework. In lizards, adhesive toepad structures increase grip strength on vertical and smooth surfaces such as tree trunks and leaves and have independently evolved multiple times. As such, toepads have been posited as a key innovation for the evolution of arboreality. Leveraging a habitat use data set applied to a global phylogeny of 2692 lizard species, we estimated multiple origins of toepads in three major clades and more than 100 origins of arboreality widely across the phylogeny. Our results suggest that toepads arise adaptively in arboreal lineages and are subsequently rarely lost while maintaining arboreal ecologies. Padless lineages transition away from arboreality at a higher rate than those with toepads, and high rates of invasion of arboreal niches by nonarboreal padbearing lineages provide further evidence that toepads may be a key to unlocking evolutionary access to the arboreal zone. Our results and analytical framework provide novel insights to understand and evaluate the ecological and evolutionary consequences of key innovations.[Arboreality; ecological transition; key innovation; macroevolution; phylogenetic comparative methods.].

A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar.

Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphological data, we examine lineage diversification in a cryptic radiation of Riopa skinks in Myanmar. Four species of Riopa skinks are currently recognized from Myanmar based on morphological traits, but the boundaries between three of these species, R. anguina, R. lineolata, and R. popae, are not well-defined. We find high levels of genetic diversity within these three species. Our analyses suggest that they may comprise as many as 12 independently evolving lineages, highlighting the extent to which species diversity in the region is underestimated. However, quantitative trait data suggest that these lineages have not differentiated morphologically, possibly indicating that this cryptic radiation represents non-adaptive evolution, although additional data is needed to corroborate this.

The discovery of Rock Geckos Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) in the Tanintharyi Region, Myanmar with the description of two new species.

We report the first occurrence of the Asian Rock Gecko genus Cnemaspis Strauch, 1887 from mainland Myanmar based on a series of specimens recently collected from the Tanintharyi Region. These records come from several localities in the Tanintharyi Region and fill a significant sampling gap for the genus. Molecular phylogenetic analyses using the mitochondrial gene ND2 identify two distinct clades, the first includes Cnemaspis siamensis of the Southeast Asian Cnemaspis group and the second includes two new species belonging to the South Asian Cnemaspis kandiana group. These two species are morphologically distinct and are distinguished from all other members in the C. kandiana group by a combination of character states. The first species, Cnemaspis tanintharyi sp. nov. occurs on the mainland in southern Tanintharyi and is distinguished from all congeners by the possession of keeled pectoral scales; smooth ventral scales and abdominal scales; 2-4 precloacal pores; 4-5 femoral pores on each leg; smooth subcaudal scales with the median row enlarged; coloration of the gular region beige, dark gray-brown with dark blue hueing towards throat; 15-18 subdigital lamellae on the 4th toe; and 21-23 ventral scales at midbody. The other, Cnemaspis thayawthadangyi sp. nov. is known only from the island group of Thayawthadangyi, in the Myeik Archipelago and is distinguished from all congeners by the possession of keeled pectoral scales; keeled ventral scales and abdominal scales; three precloacal pores; four femoral pores on each leg; smooth subcaudal scales, scales on median row enlarged; coloration of the gular region silver with dark-gray irregularly shaped streaks; 16-18 subdigital lamellae on the 4th toe; and 18-20 ventral scales at midbody. In addition, we address the taxonomic status of populations referred to as C. kandiana (a species now restricted to Sri Lanka) found in peninsular Thailand and provisionally assign them as C. cf. tanintharyi sp. nov. until further analysis can be conducted. Finally, we briefly discuss the biogeography of the South Asian clade of Cnemaspis.

The complete mitochondrial genome of the critically endangered Lesser Antillean iguana (Iguana delicatissima; Squamata: Iguanidae).

The Lesser Antillean iguana, Iguana delicatissima Laurenti 1768, is one of the most endangered vertebrate taxa in the West Indies. This species faces significant threats, including introgressive hybridization with the introduced congener Iguana iguana. We deploy a combination of off-target sequence capture obtained from Illumina® reads and targeted Sanger reads to assemble the mitochondrial genome of I. delicatissima. The mitogenome is 16,616 bp in length and is comprised of 13 protein-coding genes, two ribosomal subunits (rRNAs), 22 transfer RNAs, and a control region. Gene order is identical to that of congener I. iguana and other closely related taxa, absent of any tandem repeat regions. We show the phylogenetic utility of the mitogenome with a maximum-likelihood analysis, which yields a topology concordant with previous studies of iguanine taxa. We are hopeful that this genomic resource will be useful in further informing applied conservation and management for this critically endangered species.

Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data.

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).

Troublesome Trimes: Potential cryptic speciation of the Trimeresurus (Popeia) popeiorum complex (Serpentes: Crotalidae) around the Isthmus of Kra (Myanmar and Thailand).

The taxonomic identity of the Trimeresurus (Popeia) popeiorum complex from the Isthmus of Kra and to the north was investigated. Several studies over the last decade have produced several specimens and associated mtDNA sequence data for a variety of individuals of the T. popeiorum and "T. sabahi" complexes. Here, we combine four mitochondrial genes (12S, 16S, ND4, and CytB) from all available specimens in GenBank with the addition of five new specimens collected from the mainland, Tanintharyi Region of Myanmar. Maximum Likelihood and Bayesian analyses identified that T. popeiorum sensu lato is paraphyletic with two geographically distinct clades: a northern clade representing populations from northern Myanmar, Laos and northern Thailand and a southern clade representing samples from the Tanintharyi Region and adjacent west Thailand. While the two clades have considerable genetic distance, they appear to be morphologically identical, leading to the hypothesis that the southern clade represents a cryptic, undescribed species. Because they appear to be cryptic species and the limitation of only five specimens from the southern lineage, this does not permit us to formally describe the new species. In accordance to past molecular studies, we uncovered paraphyly and lack of genetic support for the validity of taxa within the T. sabahi complex. However, we suggest recognizing these populations as subspecies within T. sabahi.