The Discovery of XY Sex Chromosomes in a \u3cem\u3eBoa\u3c/em\u3e and \u3cem\u3ePython\u3c/em\u3e

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1, 2, 3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]. Here we demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes

Precisión de los estudiantes de psicología en la estimación de la asociación

Las tablas de contingencia son un recurso frecuente para presentar información estadística en prensa e Internet, así como en documentos técnicos usados en el trabajo profesional, aunque la enseñanza actual no presta mucha importancia a este tema, suponiendo que su interpretación es sencilla. En este trabajo analizamos la percepción de la asociación y estimación de su intensidad en tablas de contingencia en una muestra de 414 estudiantes de psicología de tres universidades españolas. Se observan respuesta similares en las tres universidades, alta consistencia entre percepción subjetiva de la asociación y precisión de la estimación y mejores resultados que los obtenidos en un estudio previo de Estepa (1994) con estudiantes de Bachillerato. Sin embargo, las estrategias al realizar el juicio de asociación son mayoritariamente incorrectas y sólo influyen en la precisión del juicio en el caso de independencia en los datos. Estos problemas podrían presentarse en otros estudiantes, por lo que los profesores debieran conocerlos para tenerlos en cuenta en la enseñanza

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the \u27venom-ome\u27 and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 \u27venom-ome-specific toxins\u27 (VSTs) that showed venom-gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery

Genetic Surfing, Not Allopatric Divergence, Explains Spatial Sorting Of Mitochondrial Haplotypes In Venomous Coralsnakes

Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern-local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation-not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male-biased dispersal

<i>GppFst</i>: genomic posterior predictive simulations of <i>FST</i> and <i>dXY</i> for identifying outlier loci from population genomic data

Abstract Summary We introduce GppFst, an open source R package that generates posterior predictive distributions of FST and dx under a neutral coalescent model to identify putative targets of selection from genomic data. Availability and Implementation GppFst is available at (https://github.com/radamsRHA/GppFst). Supplementary information Supplementary data are available at Bioinformatics online. </jats:sec

Cryptic Genetic Diversity, Population Structure, And Gene Flow In The Mojave Rattlesnake (Crotalus Scutulatus)

The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene

Data from: EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing

1. Research addressing the role of epigenetics in a diversity of experimental and natural systems is rapidly accumulating. Diverse methods have been developed to study epigenetic states, including bisulfite sequencing and AFLP-based approaches. However, existing methods are sometimes difficult to apply to non-traditional model organisms that lack genomic resources (bisulfite sequencing), and can fail to be economical and readily scalable to diverse research questions because of reliance on traditional Sanger sequencing (AFLP approaches). 2. Here we develop a reduced-representation library-based approach that is scalable and economical to quantitatively compare patterns of genome-wide methylation. This approach shares substantial similarity to the now widely used double digest restriction-site associated DNA sequencing-based method (ddRADseq), except that it utilizes a methylation-sensitive restriction enzyme. This method therefore identifies changes in the genomic methylation state of cytosine (to 5-methyl-cytosine; 5mC) by sampling loci (via next-generation sequencing) that are not methylated within a sample. We test this method to identify shifts in the epigenome of clonal water fleas (Daphnia ambigua) in response to exposure to fish predator cues, which are known to induce transgenerational changes in life history traits. 3. We found evidence for differential transgenerational responses (inferred via significant shifts in the methylation state of sampled loci) to predator cues among our treatment groups, and remarkably consistent responses within treatment groups. Our results demonstrate that this method is capable of producing highly repeatable results even without the use of a reference genome. 4. Applications of this general method are broad and diverse, and include the analysis of epigenetic shifts in both experimental and natural study systems