Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus).

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex.

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Phylogeography of montane dragons could shed light on the history of forests and diversification processes on Sumatra.

Biogeographical evidence, both, for and against the "regional endemism paradigm" hypothesis has been uncovered across the Greater Sunda Region (Sundaland) of Southeast Asia. Additionally, there are competing hypotheses regarding how Pleistocene forests may have impacted biological patterns and processes in Sumatra. Using montane agamid lizards from Sumatra, we derived and analyzed a phylogenetic dataset, genetic divergence estimates, and contemporary distributional patterns among species. We tested whether (1) Sumatra's highland Draconinae diversification fits the regional endemism paradigm hypothesis and (2) Draconinae phylogeography provides biological evidence for Pleistocene forest extent at various points in history. Our results suggest in situ diversification was the main driver behind montane Draconinae lizard diversification in Sumatra, rejecting the "regional endemism paradigm". Contemporary distribution of endemic species and their genetic relationships may potentially provide biologicalevidence for determining more precise elevational lower limits of montane forests during the Pleistocene epoch. Our data suggests montane forests did not retreat more than 700-750 m during glacial maxima because lower retreating forests would have become interconnected, allowing for widespread dispersal, exchange of gene flow and sympatric distributions contemporarily. To the contrary, our divergence estimates show that cloud forest dragons have been isolated for millions of years, suggesting there may have been a continuous disconnect between some areas, predating the Pleistocene. There may also be other ecological and evolutionary factors that impacted Draconinae distributions, such as competition, making this an excellent system for testing questions regarding montane biogeography. Additionally, we provide the first phylogeny for a wide range of Sundaland agamid species and identify some biogeographic pressures that may have triggered montane Draconinae diversification in Sumatra.

Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae).

New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity and prominence as model systems, surprisingly little is known about species boundaries and phylogenetic relationships within Micrurus, which has substantially hindered meaningful analyses of their evolutionary history. Here we use mitochondrial genes together with thousands of nuclear genomic loci obtained via ddRADseq to study the phylogenetic relationships and population genomics of a subclade of the genus Micrurus: The M. diastema species complex. Our results indicate that prior species and species-group inferences based on morphology and color pattern have grossly misguided taxonomy, and that the M. diastema complex is not monophyletic. Based on our analyses of molecular data, we infer the phylogenetic relationships among species and populations, and provide a revised taxonomy for the group. Two non-sister species-complexes with similar color patterns are recognized, the M. distans and the M. diastema complexes, the first being basal to the monadal Micrurus and the second encompassing most North American monadal taxa. We examined all 13 species, and their respective subspecies, for a total of 24 recognized taxa in the M. diastema species complex. Our analyses suggest a reduction to 10 species, with no subspecific designations warranted, to be a more likely estimate of species diversity, namely, M. apiatus, M. browni, M. diastema, M. distans, M. ephippifer, M. fulvius, M. michoacanensis, M. oliveri, M. tener, and one undescribed species.

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

Complex geological processes often drive biotic diversification on islands. The islands of Sumatra and Java have experienced dramatic historical changes, including isolation by marine incursions followed by periodic connectivity with the rest of Sundaland across highland connections. To determine how this geological history influenced island invasions, we investigated the colonization history and diversification of bent-toed geckos (genus Cyrtodactylus) on Sumatra and west Java. We used mitochondrial and nuclear sequence data to explore species boundaries, estimate phylogenetic relationships and divergence times, and to reconstruct ancestral range evolution. We found that Sumatran and Javan Cyrtodactylus were closely related to species from the Thai-Malay Peninsula, rather than from Borneo, and that Cyrtodactylus most likely dispersed to Sumatra three times during the late Oligocene and early Miocene. Similarly, Cyrtodactylus invaded west Java from Sumatra once in the early Miocene. Our results suggest that despite isolation by marine incursions during much of the Miocene, Cyrtodactylus dispersed to and from Sumatra and west Java likely via land bridges, and that in situ diversification occurred several times on Sumatra.

The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis).

A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use genome-wide SNP data and coalescent species delimitation to explore lineage relationships within several North American whipsnake species, test the species status of several lineages, and test the effect of missing data on species delimitation. We find support for the elevation of several previously recognized subspecies to full species status, and formally elevate two species. This study demonstrates the power of molecular data and model-based delimitation methods to identify evolutionary relationships, and finds that missing data have little impact on the outcome of delimitation analyses.

Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java.

Geological and climatological processes can drive the synchronous diversification of co-distributed species. The islands of Sumatra and Java have experienced complex geological and climatological histories, including extensive sea-level changes and the formation of valleys between northern, central, and southern components of the Barisan Mountain Range, which may have promoted diversification of their resident species. We investigate diversification on these islands using 13 species of the parachuting frog genus Rhacophorus. We use both mitochondrial and nuclear sequence data, along with genome-wide SNPs to estimate phylogenetic structure and divergence times, and to test for synchronous diversification. We find support for synchronous divergence among sister-species pairs from Sumatra and Java ∼9 Ma, as well as of populations of four co-distributed taxa on Sumatra ∼5.6 Ma. We found that sister species diverged in allopatry on Sumatra and conclude that divergence on Sumatra and Java was affected by sea-level fluctuations that promoted isolation in allopatry.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes.

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.

Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands.

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

Mind-set interventions are a scalable treatment for academic underachievement.

The efficacy of academic-mind-set interventions has been demonstrated by small-scale, proof-of-concept interventions, generally delivered in person in one school at a time. Whether this approach could be a practical way to raise school achievement on a large scale remains unknown. We therefore delivered brief growth-mind-set and sense-of-purpose interventions through online modules to 1,594 students in 13 geographically diverse high schools. Both interventions were intended to help students persist when they experienced academic difficulty; thus, both were predicted to be most beneficial for poorly performing students. This was the case. Among students at risk of dropping out of high school (one third of the sample), each intervention raised students' semester grade point averages in core academic courses and increased the rate at which students performed satisfactorily in core courses by 6.4 percentage points. We discuss implications for the pipeline from theory to practice and for education reform.

The skull of the semi-aquatic neotropical lizard Echinosaura horrida (Gymnophthalmidae: Cercosaurinae) reveals new synapomorphies within Gymnophthalmoidea.

The rough teiid or water cork lizard (Echinosaura horrida) is a small reptile from Colombia and Ecuador placed in a genus that contains eight species and well-known phylogenetic relationships. Here we provide a detailed description and illustrations, bone by bone, of its skull, while we discussed its intraspecific variation by comparing high-resolution computed tomography data from two specimens and the variation within the genus by including previously published data from Echinosaura fischerorum. This allowed to propose putative diagnostic character states for Echinosaura horrida and synapomorphies for Echinosaura. In addition, our discussion includes broader comparisons of new character transformations of the jugal, vomer, orbitosphenoid, and hyoid. These characters are important for diagnosing clades at different levels of the Gymnophthalmoidea phylogeny.

Rampant horizontal transfer of SPIN transposons in squamate reptiles.

Transposable elements (TEs) are highly abundant in the genome and capable of mobility, two properties that make them particularly prone to transfer horizontally between organisms. Although the impact of horizontal transfer (HT) of TEs is well recognized in prokaryotes, the frequency of this phenomenon and its contribution to genome evolution in eukaryotes remain poorly appreciated. Here, we provide evidence that a DNA transposon called SPIN has colonized the genome of 17 species of reptiles representing nearly every major lineage of squamates, including 14 families of lizards, snakes, and amphisbaenians. Slot blot analyses indicate that SPIN has amplified to high copy numbers in most of these species, ranging from 2,000-28,000 copies per haploid genome. In contrast, we could not detect the presence of SPIN in any of the turtles (seven species from seven families) and crocodiles (four species) examined. Genetic distances between SPIN sequences from species belonging to different squamate families are consistently very low (average = 0.1), considering the deep evolutionary divergence of the families investigated (most are >100 My diverged). Furthermore, these distances fall below interfamilial distances calculated for two genes known to have evolved under strong functional constraint in vertebrates (RAG1, average = 0.24 and C-mos, average = 0.27). These data, combined with phylogenetic analyses, indicate that the widespread distribution of SPIN among squamates is the result of at least 13 independent events of HTs. Molecular dating and paleobiogeographical data suggest that these transfers took place during the last 50 My on at least three different continents (North America, South America and, Africa). Together, these results triple the number of known SPIN transfer events among tetrapods, provide evidence for a previously hypothesized transoceanic movement of SPIN transposons during the Cenozoic, and further underscore the role of HT in the evolution of vertebrate genomes.

Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri).

The longtailed rattlesnakes of western Mexico represent an enigmatic group of poorly known venomous snake species: Crotalus ericsmithi, C. lannomi, and C. stejnegeri. In the 120 years since their discovery, fewer than twenty individuals have been deposited in natural history collections worldwide. These three species share similar morphological traits, including a particularly long tail that has been interpreted as either an ancestral condition among rattlesnakes or as derived within the longtailed group. An understanding of the phylogenetic distinctiveness and relationships among the longtailed rattlesnakes, and their relationships to other rattlesnake groups, has previously been hampered by a dearth of comparative material and tissues for collection of DNA sequence data. Facilitated by the recent availability of tissue samples from multiple individuals of each species, we estimate the phylogenetic relationships among the longtailed rattlesnakes and their placement among other rattlesnake groups, using DNA sequence data from three mitochondrial and three nuclear gene fragments. We explore phylogenetic signal in our data using Bayesian and maximum likelihood methods, species tree analyses and hypothesis testing. Our results strongly support the monophyly of longtailed rattlesnakes and suggest the three species diverged from each other during the mid to late Pliocene or early Pleistocene (~1.5-5.6 mya). Contrary to prevailing hypotheses, we find no evidence for an early or basal divergence of the longtailed clade within the rattlesnake tree, and instead estimate that it diverged relatively recently (~6.8 mya) from its sister lineage, composed of the diamondback rattlesnakes (C. atrox group) and the prairie rattlesnakes (C. viridis group). With our added sampling of lineages and identification of previously used problematic sequences, we provide a revised hypothesis for relationships among Crotalus species, yet underscore the need for future studies and new data to deliver a well-supported robust estimate of rattlesnake relationships.

Observation of suppressed viscosity in the normal state of 3He due to superfluid fluctuations.

Evidence of fluctuations in transport have long been predicted in 3He. They are expected to contribute only within 100µK of Tc and play a vital role in the theoretical modeling of ordering; they encode details about the Fermi liquid parameters, pairing symmetry, and scattering phase shifts. It is expected that they will be of crucial importance for transport probes of the topologically nontrivial features of superfluid 3He under strong confinement. Here we characterize the temperature and pressure dependence of the fluctuation signature, by monitoring the quality factor of a quartz tuning fork oscillator. We have observed a fluctuation-driven reduction in the viscosity of bulk 3He, finding data collapse consistent with the predicted theoretical behavior.

A new species of Dipsas (Serpentes, Dipsadidae) from central Panama.

A new species of Dipsas Laurenti, 1768, from Central Panama is described based on molecular analyses, hemipenial morphology, and external characters. This is the sixth species of Dipsas to be described for the country; the snake has been suspected to exist since 1977 and has not been thoroughly studied until now. Additionally, morphological comparations including scale counts are done with other species within the genus, and the current geographic distribution of Dipsastemporalis (Werner, 1909), the sister species, is updated. Finally, a key to the species of Dipsas currently known from Middle America is presented.

ResumenDescribimos una nueva especies de Dipsas Laurenti, 1768 de la región central de Panamá en base a análisis moleculares, morfología hemipenial y caracteres de morfología externa. Esta es la sexta especie del género Dipsas descrita para el país. Se sospechaba su existencia desde 1977 pero no había sido estudiada exhaustivamente hasta ahora. Adicionalmente, presentamos comparaciones morfológicas (incluyendo lepidosis) con otras especies del género y actualizamos la distribución geográfica de su especie hermana Dipsastemporalis (Werner, 1909). Finalmente, presentamos una clave para las especies de Dipsas distribuidas en Centroamérica.

Evaluation of the "rethink stress" mindset intervention: A metacognitive approach to changing mindsets.

Experimental research has demonstrated that a stress-is-enhancing mindset can be induced and can improve outcomes by presenting information on the enhancing nature of stress. However, experimental evidence, media portrayals, and personal experience about the debilitating nature of stress may challenge this mindset. Thus, the traditional approach of focusing on the more "desired" mindset without arming participants against encounters with the less desired mindsets may not be sustainable in the face of conflicting information. How might this limitation be resolved? Here, we present three randomized-controlled interventions that test the efficacy of a "metacognitive approach." In this approach, participants are given more balanced information about the nature of stress along with metacognitive information on the power of their mindsets aimed at empowering them to choose a more adaptive mindset even in the face of conflicting information. In Experiment 1, employees of a large finance company randomized to the metacognitive mindset intervention reported greater increases in stress-is-enhancing mindsets and greater improvements in self-reported measures of physical health symptoms and interpersonal-skill work performance 4 weeks later compared to a waitlist control. Experiment 2, adapted to be distributed electronically via multimedia modules, replicates the effects on stress mindset and symptoms. Experiment 3 compares the metacognitive stress mindset intervention with a more traditional stress mindset manipulation. The metacognitive approach led to greater initial increases in a stress-is-enhancing mindset relative to the traditional intervention, and these increases were sustained after exposure to contradictory information. Taken together, these results provide support for a metacognitive approach to mindset change. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Unveiling underestimated species diversity within the Central American Coralsnake, a medically important complex of venomous taxa.

Coralsnakes of the genus Micrurus are a diverse group of venomous snakes ranging from the southern United States to southern South America. Much uncertainty remains over the genus diversity, and understanding Micrurus systematics is of medical importance. In particular, the widespread Micrurus nigrocinctus spans from Mexico throughout Central America and into Colombia, with a number of described subspecies. This study provides new insights into the phylogenetic relationships within M. nigrocinctus by examining sequence data from a broad sampling of specimens from Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, and Panama. The recovered phylogenetic relationships suggest that M. nigrocinctus is a species complex originating in the Pliocene and composed of at least three distinct species-level lineages. In addition, recovery of highly divergent clades supports the elevation of some currently recognized subspecies to the full species rank while others may require synonymization.

Where and with whom does a brief social-belonging intervention promote progress in college?

A promising way to mitigate inequality is by addressing students' worries about belonging. But where and with whom is this social-belonging intervention effective? Here we report a team-science randomized controlled experiment with 26,911 students at 22 diverse institutions. Results showed that the social-belonging intervention, administered online before college (in under 30 minutes), increased the rate at which students completed the first year as full-time students, especially among students in groups that had historically progressed at lower rates. The college context also mattered: The intervention was effective only when students' groups were afforded opportunities to belong. This study develops methods for understanding how student identities and contexts interact with interventions. It also shows that a low-cost, scalable intervention generalizes its effects to 749 4-year institutions in the United States.