Significance The molecular basis of morphological and physiological adaptations in snakes is largely unknown. Here, we study these phenotypes using the genome of the Burmese python ( Python molurus bivittatus ), a model for extreme phenotypic plasticity and metabolic adaptation. We discovered massive rapid changes in gene expression that coordinate major changes in organ size and function after feeding. Many significantly responsive genes are associated with metabolism, development, and mammalian diseases. A striking number of genes experienced positive selection in ancestral snakes. Such genes were related to metabolism, development, lungs, eyes, heart, kidney, and skeletal structure—all highly modified features in snakes. Snake phenotypic novelty seems to be driven by the system-wide coordination of protein adaptation, gene expression, and changes in genome structure.

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline.

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Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting geneflow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at geneflow within and between populations with rearrangements. We found that geneflow was present between individuals with chromosome rearrangements within populations, but there was no geneflow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting included coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems. A community using snakes as model systemsSnakes are gaining importance as model systems for a diversity of research. They are valued models for studying extreme physiological and morphological plasticity, evolutionary ecology, molecular evolution, developmental biology, and venom evolution. Despite the importance of snakes as models for basic and biomedical research, there is little known about the genomes of snakes, and there are minimal genomic resources currently available. These limitations, however, will soon be lifted as numerous groups are making progress in establishing complete snake genomes and genomic resources, thereby enabling numerous new areas of research utilizing snakes.The first Snake Genomics and Integrative Biology meeting was held October 5-8, 2011 in Vail, Colorado USA to bring together an international collection of researchers from diverse backgrounds that share a common interest in snake genomics and comparative biology. A core aim of the meeting was to showcase ongoing and potential projects that utilize (or aim to utilize) snake genomic and transcriptomic data for integrative and comparative biology. The meeting was organized around the goals of catalyzing collaborative research, identifying shared interests in research and data collection, and coordinating among research groups to maximize scientific impact, collaboration, fundability,

Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.

Sex chromosomes are mostly conserved, but in some cases are variable within species. Varanids are known for conserved sex chromosomes, but there are differences in the size of the W chromosome among species representing varying stages of sex chromosome evolution. We tested for homology of the ZW sex chromosome system in varanids with size differences among four species from two lineages in Australia, the dwarf lineage Odatria and the sand goanna lineage Gouldii, with a combined genomic and cytogenetic approach. We found that while DNA sequences of the sex chromosomes are conserved, a mutation on an enlarged autosomal microchromosome is homologous with the W in some isolated populations of V. acanthurus and V. citrinus from the Odatria lineage. The enlarged microchromosome was unpaired in all individuals tested and is likely an unbalanced segmental duplication translocated from the W to another microchromosome. We also found evidence of an ancient balanced duplication that is also homologous to the W and to the telomeric region of chromosome 2. We conclude the most parsimonious explanation is that the duplicated region likely originated on chromosome 2. We also demonstrated that genes and related DNA sequences have likely originated on an autosome, translocated to the W, accumulated repeats and amplified on the W and then duplicated and translocated to another autosomal microchromosome. Given the role of these duplications as important evolutionary drivers of speciation in other taxa, our findings provide broader insight into the evolutionary pathway leading to rapid chromosomal and genic divergence of species.