Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate.

The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.

Combined next-generation sequencing and morphology reveal fine-scale speciation in Crocodile Skinks (Squamata: Scincidae: Tribolonotus).

Next-generation sequencing has vast potential to revolutionize the fields of phylogenetics and population genetics through its ability to collect genomic scale data sets of thousands of orthologous loci. Despite this potential, other types of data (e.g. morphology, ecology) remain important, particularly for studies endeavouring to delimit species. Here, we integrate next-generation sequencing with morphology to examine divergence between populations of Tribolonotus pseudoponceleti on the islands of Buka and Bougainville in the Solomon Archipelago. We used the Ion Torrent PGM to collect over 648 Mbp of sequence data for 12 samples, representing 1526 loci recovered from all samples, and 3342 were recovered from at least six samples. Genetic structure analyses strongly support the distinctiveness of these two populations, and Bayes factor delimitations decisively select speciation between Buka and Bougainville. Principal components and discriminant function analyses reveal concordant morphological divergence. Finally, demographic analyses via diffusion approximation and approximate Bayesian computation prefer a complex model of mid-Pleistocene divergence with migration, and a later decrease or cessation of migration and population size shift, suggesting a scenario in which migration was enabled by Pleistocene merging of these two islands, and limited when isolated by higher sea levels. Further analysis of four Sanger sequenced loci in IMa2 had limited power to distinguish among models including and excluding migration, but resulted in similar population size and divergence time estimates, although with much broader confidence intervals. This study represents a framework for how next-generation sequencing and morphological data can be combined and leveraged towards validating putative species and testing demographic scenarios for speciation.

Phylogeny and phylogeography of Mantophryne (Anura: Microhylidae) reveals cryptic diversity in New Guinea.

New Guinea is one of five high biodiversity wilderness areas, and frog diversity is exceptionally large, with more than 400 species described to date. The microhylid frog genus Mantophryne is endemic to New Guinea and consists of four species, three of which have narrow geographic distributions and a fourth, M. lateralis, with a broad range that spans the eastern half of the island. Here, we sequence 104 Mantophryne samples for three mitochondrial and three nuclear loci to reconstruct the first phylogeny of the genus and to examine spatial patterns of diversity within M. lateralis. Results indicate that the wide-ranging M. lateralis is composed of at least nine geographically separated and well-supported lineages that represent putative species. Biogeographic analysis suggests that Mantophryne evolved on the eastern Papuan peninsula with subsequent dispersal westward, as well as overwater dispersal events to the Louisiade and D'Entrecasteaux archipelagos.

The effects of sampling on delimiting species from multi-locus sequence data.

As a fundamental unit in biology, species are used in a wide variety of studies, and their delimitation impacts every subfield of the life sciences. Thus, it is of utmost importance that species are delimited in an accurate and biologically meaningful way. However, due to morphologically similar, cryptic species, and processes such as incomplete lineage sorting, this is far from a trivial task. Here, we examine the accuracy and sensitivity to sampling strategy of three recently developed methods that aim to delimit species from multi-locus DNA sequence data without a priori assignments of samples to putative species. Specifically, we simulate data at two species tree depths and a variety of sampling strategies ranging from five alleles per species and five loci to 20 alleles per species and 100 loci to test (1) Structurama, (2) Gaussian clustering, and (3) nonparametric delimitation. We find that Structurama accurately delimits even relatively recently diverged (greater than 1.5 N generations) species when sampling 10 or more loci. We also find that Gaussian clustering delimits more deeply divergent species (greater than 2.5 N generations) relatively well, but is not sufficiently sensitive to delimit more recently diverged species. Finally, we find that nonparametric delimitation performs well with 25 or more loci if gene trees are known without error, but performs poorly with estimated gene genealogies, frequently over-splitting species and mis-assigning samples. We thus suggest that Structurama represents a powerful tool for use in species delimitation. It should be noted, however, that intraspecific population structure may be delimited using this or any of the methods tested herein. We argue that other methods, such as other species delimitation methods requiring a priori putative species assignments (e.g. SpeDeSTEM, Bayesian species delimitation), and other types of data (e.g. morphological, ecological, behavioral) be incorporated in conjunction with these methods in studies attempting to delimit species.

Phylogeny, historical biogeography and body size evolution in Pacific Island Crocodile skinks Tribolonotus (Squamata; Scincidae).

Competition heavily influences the structure of island communities, particularly in species-rich areas. If ecologically similar lineages come into contact following dispersal, selection may favor rapid evolutionary change; if constraints prevent such change, lineage extinction may result. One mechanism for relieving competition among newly sympatric species is the evolution of body size differences, such as through character displacement or size assortment. The Crocodile skinks of the genus Tribolonotus exhibit a threefold variation in body size, and several species occur in sympatry. We use 2252 bp of DNA sequence data spanning two mitochondrial (cyt b and ND2) and three nuclear (C-mos, Rhodopsin and Phosducin) gene regions to reconstruct the phylogeny of Tribolonotus, use it to examine the biogeography of the genus, and test for size assortment or character displacement. We find evidence that Tribolonotus originated on either Greater Bougainville or in New Guinea, and subsequently colonized surrounding islands via multiple colonization events. Our ancestral state reconstructions support multiple instances of parallel and independent change in body size within Tribolonotus. Additionally, we find no evidence for size assortment and conflicting evidence for character displacement, which we argue suggests that character displacement, combined with ecological differences between New Guinean species (T. gracilis and T. novaeguineae), best explains the evolution of body size in the genus Tribolonotus.

Two new species of Crocodile Skinks (Squamata: Scincidae: Tribolonotus) from the Solomon Archipelago.

We describe two new species of the scincid lizard genus Tribolonotus from the islands of Buka and Choiseul in the Solomon Archipelago, closely related to, and previously included within, T. pseudoponceleti. One species, T. parkeri sp. nov., is endemic to Buka Island and was revealed in our previous study via taxonomically focused analyses of both next-generation sequencing data and morphology. Here, we also further support the validity of this species by more taxonomically comprehensive Bayesian species delimitation of three Sanger sequenced nuclear loci. The second species, T. choiseulensis sp. nov., is endemic to Choiseul Island and was revealed by an expanded morphological data analysis. These results suggest that numerous other species found on multiple island groups in the Solomon Archipelago may similarly represent complexes of multiple, closely related species, and that the biodiversity of the region is vastly underestimated.

Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years.

Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep "tension zone," in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.

Ecological guild evolution and the discovery of the world's smallest vertebrate.

Living vertebrates vary drastically in body size, yet few taxa reach the extremely minute size of some frogs and teleost fish. Here we describe two new species of diminutive terrestrial frogs from the megadiverse hotspot island of New Guinea, one of which represents the smallest known vertebrate species, attaining an average body size of only 7.7 mm. Both new species are members of the recently described genus Paedophryne, the four species of which are all among the ten smallest known frog species, making Paedophryne the most diminutive genus of anurans. This discovery highlights intriguing ecological similarities among the numerous independent origins of diminutive anurans, suggesting that minute frogs are not mere oddities, but represent a previously unrecognized ecological guild.

A dual role for IQGAP1 in regulating exocytosis.

Polarized secretion is a tightly regulated event generated by conserved, asymmetrically localized multiprotein complexes, and the mechanism(s) underlying its temporal and spatial regulation are only beginning to emerge. Although yeast Iqg1p has been identified as a positional marker linking polarity and exocytosis cues, studies on its mammalian counterpart, IQGAP1, have focused on its role in organizing cytoskeletal architecture, for which the underlying mechanism is unclear. Here, we report that IQGAP1 associates and co-localizes with the exocyst-septin complex, and influences the localization of the exocyst and the organization of septin. We further show that activation of CDC42 GTPase abolishes this association and inhibits secretion in pancreatic beta-cells. Whereas the N-terminus of IQGAP1 binds the exocyst-septin complex, enhances secretion and abrogates the inhibition caused by CDC42 or the depletion of IQGAP1, the C-terminus, which binds CDC42, inhibits secretion. Pulse-chase experiments indicate that IQGAP1 influences protein-synthesis rates, thus regulating exocytosis. We propose and discuss a model in which IQGAP1 serves as a conformational switch to regulate exocytosis.