Into the Light: Diurnality has Evolved Multiple Times in Geckos

Geckos are the only major lizard group consisting mostly of nocturnal species. Nocturnality is presumed to have evolved early in gecko evolution and geckos possess numerous adaptations to functioning in low light and at low temperatures. However, not all gecko species are nocturnal and most diurnal geckos have their own distinct adaptations to living in warmer, sunlit environments. We reconstructed the evolution of gecko activity patterns using a newly generated time-calibrated phylogeny. Our results provide the first phylogenetic analysis of temporal activity patterns in geckos and confirm an ancient origin of nocturnality at the root of the gecko tree. We identify multiple transitions to diurnality at a variety of evolutionary time scales and transitions back to nocturnality occur in several predominantly diurnal clades. The scenario presented here will be useful in reinterpreting existing hypotheses of how geckos have adapted to varying thermal and light environments. These results can also inform future research of gecko ecology, physiology, morphology and vision as it relates to changes in temporal activity patterns

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (\u3e1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups

The measure of success: geographic isolation promotes diversification in Pachydactylus geckos

Abstract Background Geckos of the genus Pachydactylus and their close relatives comprise the most species-rich clade of lizards in sub-Saharan Africa. Many explanations have been offered to explain species richness patterns of clades. In the Pachydactylus group, one possible explanation is a history of diversification via geographic isolation. If geographic isolation has played a key role in facilitating diversification, then we expect species in more species-rich subclades to have smaller ranges than species in less diverse subclades. We also expect traits promoting geographic isolation to be correlated with small geographic ranges. In order to test these expectations, we performed phylogenetic analyses and tested for correlations among body size, habitat choice, range sizes, and diversification rates in the Pachydactylus group. Results Both body size and habitat use are inferred to have shifted multiple times across the phylogeny of the Pachydactylus group, with large size and generalist habitat use being ancestral for the group. Geographic range size is correlated with both of these traits. Small-bodied species have more restricted ranges than large-bodied species, and rock-dwelling species have more restricted ranges than either terrestrial or generalist species. Rock-dwelling and small body size are also associated with higher rates of diversification, and subclades retaining ancestral conditions for these traits are less species rich than subclades in which shifts to small body size and rocky habitat use have occurred. The phylogeny also illustrates inadequacies of the current taxonomy of the group. Conclusions The results are consistent with a model in which lineages more likely to become geographically isolated diversify to a greater extent, although some patterns also resemble those expected of an adaptive radiation in which ecological divergence acts as a driver of speciation. Therefore, the Pachydactylus group may represent an intermediate between clades in which radiation is adaptive versus those in which it is non-adaptive.http://deepblue.lib.umich.edu/bitstream/2027.42/135714/1/12862_2016_Article_846.pd

Repeated Origin and Loss of Adhesive Toepads in Geckos

Geckos are well known for their extraordinary clinging abilities and many species easily scale vertical or even inverted surfaces. This ability is enabled by a complex digital adhesive mechanism (adhesive toepads) that employs van der Waals based adhesion, augmented by frictional forces. Numerous morphological traits and behaviors have evolved to facilitate deployment of the adhesive mechanism, maximize adhesive force and enable release from the substrate. The complex digital morphologies that result allow geckos to interact with their environment in a novel fashion quite differently from most other lizards. Details of toepad morphology suggest multiple gains and losses of the adhesive mechanism, but lack of a comprehensive phylogeny has hindered efforts to determine how frequently adhesive toepads have been gained and lost. Here we present a multigene phylogeny of geckos, including 107 of 118 recognized genera, and determine that adhesive toepads have been gained and lost multiple times, and remarkably, with approximately equal frequency. The most likely hypothesis suggests that adhesive toepads evolved 11 times and were lost nine times. The overall external morphology of the toepad is strikingly similar in many lineages in which it is independently derived, but lineage-specific differences are evident, particularly regarding internal anatomy, with unique morphological patterns defining each independent derivation

Uncovering karst endemism within Borneo: two new Cyrtodactylus species from Sarawak, Malaysia

The island of Borneo lies within one of the most biodiverse regions in the world. Despite this, its documented gekkonid diversity is not commensurate with other areas of Southeast Asia. The megadiverse genus Cyrtodactylus is especially un-derrepresented. Limestone-karst ecosystems, in particular, harbor many endemic Cyrtodactylus species, but only one karst-dwelling species is currently recognized from Borneo. This paper adds two additional karst-dwelling Cyrtodactylus species—C. muluensis sp. nov. and C. limajalursp. nov.—from Sarawak, Malaysia. Cyrtodactylus muluensis sp. nov. is endemic to Gunung Mulu and is distinguished from its congeners by having a precloacal groove, 31–38 ventral scales, a maximum SVL of at least 88 mm, enlarged subcaudals, 19–20 subdigital lamellae, and a banded dorsal body pattern. Cyr-todactylus limajalur sp. nov. is endemic to the Serian region and is distinguished from its congeners by having 33–42 ven-tral scales, enlarged subcaudals, a precloacal pit, a maximum SVL of at least 94 mm, 5–6 enlarged femoral scales, 19–22 subdigital lamellae, and five distinct bands on the dorsum. Both species are phylogenetically distinct and deeply divergent from all other congeners. The description of two new karst-dwelling species highlights the need to conserve karst habitats and the endemic species they harbor

A New Small-Bodied Species of Bavayia (Reptilia: Squamata: Diplodactylidae) from Southeastern New Caledonia.

v. ill. 23 cm.QuarterlyA new species of diplodactylid genus Bavayia, B. goroensis, is described from the Plaine des Lacs region of the Province Sud, New Caledonia. The new gecko is the smallest member of the Bavayia cyclura clade (49 mm snout-vent length) and, based on a molecular phylogeny, is basal within this group. It differs from other members of this group in its much smaller size, more gracile body, and lower number of precloacal pores and subdigital lamellae. The new species is known from only two locations, one of which is adjacent to extensive nickel mining operations. Because of its limited distribution and the direct and indirect threats posed by the proximity of mining to one of the populations, the species is here regarded as ‘‘Endangered.’

Molecular evidence for the taxonomic status of Hemidactylus brookii group taxa (Squamata: Gekkonidae)

Hemidactylus brookii has one of the widest distributions and, arguably, one of the most confused taxonomic histories of any gekkonid lizard. Nuclear (RAG1 and PDC) and mitochondrial (ND2, cyt b ) DNA sequence data were employed to examine relationships among a sample of putative H. brookii , including a topotypical specimen from Borneo. Two clades were recovered, one consisting of specimens from Borneo (Sarawak), Myanmar, Peninsular Malaysia and Karnataka, southwestern India, and another of specimens from Sri Lanka, Mauritius and Kerala, southwestern India. Both clades are well supported and deeply divergent from one another, whereas genetic variation within each clade is limited. None of the analytical approaches used recovered a well-supported monophyletic H. brookii sensu lato . Near uniformity of H. brookii sensu stricto in East Asia suggests that this species has spread to this region relatively recently. The name H. parvimaculatus Deraniyagala 1953 is available for the Sri Lankan clade and this form should be treated as a valid species. Existing data cannot be used to distinguish whether this species has colonized Sri Lanka from South India or vice versa. The Palghat Gap provides a candidate barrier to gene flow between H. brookii and H. parvimaculatus . Although the identity of H. brookii complex geckos in East Asia and Sri Lanka appears resolved, the situation in India and Pakistan remains complex and thorough revisionary work, coupled with phylogenetic studies, is needed to determine species boundaries in this regio

Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae:Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novelbiogeographic patterns

The gekkonid genusCyrtodactylusis a highly diverse group of lizards (280 + species), which covers an expansivegeographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies,species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionaryhistory with cascading effects on taxonomy and biogeographic inferences. We assembled the most compre-hensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel se-quences and representatives from each knownCyrtodactylusspecies on the island to validate taxonomic status,assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of crypticdiversity and revealed numerous taxonomic complications, especially within theC. consobrinus, C. malayanus,andC. pubisulcusgroups. Comparisons of pairwise genetic distances and a preliminary species delimitationanalysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-rangingspecies on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricteddistributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneointo the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derivedfrom multiple separate invasions into the geopolitical areas comprising the Philippines. Although our in-vestigation of BorneanCyrtodactylusis the most comprehensive to-date, it highlights the need for expandedtaxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeographyof BorneanCyrtodactylusis far from complete

Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns

The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280+ species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete

The fallacy of placing confidence in confidence intervals

Interval estimates – estimates of parameters that include an allowance for sampling uncertainty – have long been touted as a key component of statistical analyses. There are several kinds of interval estimates, but the most popular are confidence intervals (CIs): intervals that contain the true parameter value in some known proportion of repeated samples, on average. The width of confidence intervals is thought to index the precision of an estimate; CIs are thought to be a guide to which parameter values are plausible or reasonable; and the confidence coefficient of the interval (e.g., 95 %) is thought to index the plausibility that the true parameter is included in the interval. We show in a number of examples that CIs do not necessarily have any of these properties, and can lead to unjustified or arbitrary inferences. For this reason, we caution against relying upon confidence interval theory to justify interval estimates, and suggest that other theories of interval estimation should be used instead