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Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation. [ABSTRACT FROM AUTHOR]

Tri-axial accelerometers (ACTs) are becoming increasingly common in studies of animal behavior wherein direct observation of subjects in nature is constrained or impossible. ACTs are small (< 1 g) piezo-electric (spring-like) sensors that measure three-dimensional acceleration (upward, downward, and side-to-side) derived from subject motion. When leveraged with advanced machine learning techniques, these data can enable precise automated classification of a wide range of movement-mediated behaviors. Until recently, ACTs were largely reserved for larger-bodied organisms or those most amenable to the temporary external attachment of devices. Ongoing ACT miniaturization has now expanded the breadth of organisms amenable to these methods. This project aims to expand on a recently developed framework for ACT monitoring in wild-ranging snakes, a group that has been mostly overlooked in biologging applications. We have completed extensive captive ACT validation trials with timber rattlesnakes (Crotalus horridus) and have used these datasets in the training and testing of robust classification models of foraging behaviors, i.e. strike and swallowing of prey items. Using AcceleRater, a free online service available to the community, we trained, tested and compared linear SVM, decision tree, and random forest classification models for strike, movement, and stillness using a window size of 0.4 seconds. Separate linear SVM, decision tree and random forest models were trained, tested, and compared with a window size of three seconds for swallowing behaviors. Following validation of these models, we translated this method to the field with a population of C. horridus in the lower Piedmont of middle Georgia to evaluate the efficacy of externally attached ACTs for remote and continuous monitoring of predatory behaviors by wild-ranging vipers., Acknowledgements Georgia College & State University Recommended Citation Authors Morgan L. Thompson, Georgia College & State University Follow Richard H. Adams, Georgia College & State University Follow Anna F. Tipton, [...]

The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates. Key words: comparative genomics, microsatellite seeding, repeat elements, tandem repeats, simple sequence repeats. La dynamique evolutive des sequences simples repetees (SSR ou microsatellites) au sein des vertebres demeure largement non-documentee et mal connue. Dans ce travail, les auteurs ont analyse l'abondance et revolution des microsatellites chez 71 genomes de vertebres. Les abondances de microsatellites les plus grandes ont ete rencontrees au sein des genomes des poissons dotes de nageoires a rayons, des reptiles a ecailles et des mammiferes, tandis que les genomes des crocodiliens, des tortues et des oiseaux presentaient le moins de microsatellites. Les auteurs ont employe des methodes comparatives pour inferer les taux de changements evolutifs en matiere d'abondance des microsatellites parmi les vertebres et pour mettre en evidence des lignages qui ont connu des taux exceptionnellement eleves ou faibles. Globalement, la majeure partie de la variation en matiere de contenu, d'abondance et de taux d'evolution des microsatellites a ete observee au sein des grands groupes de reptiles, et pourtant, les auteurs ont note que certains clades tres distants (p. ex. les reptiles a ecailles et les mammiferes) presentaient des compositions genomiques semblables en matiere de microsatellites. Les reptiles archosauromorphes (tortues, crocodiliens et oiseaux) affichaient une teneur reduite en microsatellites et les plus faibles taux evolutifs au sein des microsatellites, tandis que les genomes des reptiles a ecailles avaient des taux parmi les plus eleves. Des variations substantielles limitees a certaines branches specifiques ont egalement ete observees chez les primates, les monotremes, les rongeurs, les serpents et les poissons. Ensemble, ces resultats appuient l'hypothese de multiples changements importants dans le paysage des microsatellites chez les vertebres. [Traduit par la Redaction] Mots-cles: genomique comparee, ensemencement de microsatellites, elements repetes, repetitions en tandem, sequences simples repetees., Introduction Microsatellites, also known as simple sequence repeats (SSRs), are 2-6 base pair (bp) nucleotide motifs that are tandemly repeated to form larger DNA stretches usually between 20 and 100 [...]

The ubiquitous cellular heterogeneity underlying many organism-level phenotypes raises questions about what factors drive this heterogeneity and how these complex heterogeneous systems evolve. Here, we use single-cell expression data from a Prairie rattlesnake (Crotalus viridis) venom gland to evaluate hypotheses for signaling networks underlying snake venom regulation and the degree to which different venom gene families have evolutionarily recruited distinct regulatory architectures. Our findings suggest that snake venom regulatory systems have evolutionarily co-opted trans -regulatory factors from extracellular signal-regulated kinase and unfolded protein response pathways that specifically coordinate expression of distinct venom toxins in a phased sequence across a single population of secretory cells. This pattern of co-option results in extensive cell-to-cell variation in venom gene expression, even between tandemly duplicated paralogs, suggesting this regulatory architecture has evolved to circumvent cellular constraints. While the exact nature of such constraints remains an open question, we propose that such regulatory heterogeneity may circumvent steric constraints on chromatin, cellular physiological constraints (e.g. endoplasmic reticulum stress or negative protein–protein interactions), or a combination of these. Regardless of the precise nature of these constraints, this example suggests that, in some cases, dynamic cellular constraints may impose previously unappreciated secondary constraints on the evolution of gene regulatory networks that favors heterogeneous expression. [ABSTRACT FROM AUTHOR]

Few studies have examined the impact of international migration and remittances on poverty in the developing world. This paper fills this lacuna by constructing and analyzing a new data set on international migration, remittances, inequality, and poverty from 71 developing countries. The results show that both international migration and remittances significantly reduce the level, depth, and severity of poverty in the developing world. After instrumenting for the possible endogeneity of international migration, and controlling for various factors, results suggest that, on average, a 10% increase in the share of international migrants in a country's population will lead to a 2.1% decline in the share of people living on less than $1.00 per person per day. After instrumenting for the possible endogeneity of international remittances, a similar 10% increase in per capita official international remittances will lead to a 3.5% decline in the share of people living in poverty. Key words--international migration, remittances, poverty

This paper uses a new data set of 126 intervals from 60 developing countries to analyze the growth elasticity of poverty, that is, how much does poverty decline in percentage terms with a given percentage rise in economic growth. The data set is both broader in coverage and more selective in terms of quality controls than those used in the past. The study finds that while economic growth does reduce poverty in developing countries, the rate of poverty reduction depends very much on how economic growth is defined. Controlling for changes in income inequality, when economic growth is measured by changes in survey mean income (consumption), the growth elasticity of poverty (excluding Eastern Europe and Central Asia) is -2.79; that is, a 10% increase in the survey mean will reduce poverty ($1.00/person/day) by 27.9%. But, when growth is measured by changes in GDP per capita, the growth elasticity of poverty is a statistically insignificant -2.27, which is lower than has previously been estimated. Key words--poverty, inequality, economic growth, growth elasticity of poverty

This paper uses crosscountry data and country-case studies to analyze trends in poverty, inequality and economic growth in the Middle East and North Africa (MENA) region. Compared to other regions, the MENA region has a low incidence of poverty and income inequality. Two factors account for this situation: international migration/remittances and public sector (government) employment. Since the early 1980s international migration to the Persian Gulf and Europe has helped boost the incomes of the poor in the Middle East. At the same time, many MENA countries have used government employment as a means of keeping people employed and out of poverty. Regression analysis of crosscountry data shows that both of these factors have a statistically significant impact on reducing the level and depth of poverty in the MENA region. Key words--Middle East, poverty, income distribution, migration, remittances, government, employment

Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared with macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here, we analyze Hi-C sequencing data from multiple vertebrate lineages and show that microchromosomes exhibit consistently high degrees of interchromosomal interaction (particularly with other microchromosomes), appear to be colocalized to a common central nuclear territory, and are comprised of a higher proportion of open chromatin than macrochromosomes. These findings highlight an unappreciated level of diversity in vertebrate genome structure and function, and raise important questions regarding the evolutionary origins and ramifications of microchromosomes and the genes that they house. [ABSTRACT FROM AUTHOR]

Neither Jason Byassee ('Dinosaurs in the garden') nor Amy Frykholm ('God in evolution') focuses on what I see as the principal challenge of Darwinism (Feb. 12). What was distinctive about [...]

Convergent evolution is often documented in organisms inhabiting isolated environments with distinct ecological conditions and similar selective regimes. Several Central America islands harbor dwarf Boa populations that are characterized by distinct differences in growth, mass, and craniofacial morphology, which are linked to the shared arboreal and feast-famine ecology of these island populations. Using high-density RADseq data, we inferred three dwarf island populations with independent origins and demonstrate that selection, along with genetic drift, has produced both divergent and convergent molecular evolution across island populations. Leveraging whole-genome resequencing data for 20 individuals and a newly annotated Boa genome, we identify four genes with evidence of phenotypically relevant protein-coding variation that differentiate island and mainland populations. The known roles of these genes involved in body growth (PTPRS , DMGDH , and ARSB), circulating fat and cholesterol levels (MYLIP), and craniofacial development (DMGDH and ARSB) in mammals link patterns of molecular evolution with the unique phenotypes of these island forms. Our results provide an important genome-wide example for quantifying expectations of selection and convergence in closely related populations. We also find evidence at several genomic loci that selection may be a prominent force of evolutionary change—even for small island populations for which drift is predicted to dominate. Overall, while phenotypically convergent island populations show relatively few loci under strong selection, infrequent patterns of molecular convergence are still apparent and implicate genes with strong connections to convergent phenotypes. [ABSTRACT FROM AUTHOR]

The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus , Crotalus viridis , Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically. [ABSTRACT FROM AUTHOR]

Summary Here, we present PhyloWGA , an open source R package for conducting phylogenetic analysis and investigation of whole genome data. Availabilityand implementation Available at Github (https://github.com/radamsRHA/PhyloWGA). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Invasive species provide powerful in situ experimental systems for studying evolution in response to selective pressures in novel habitats. While research has shown that phenotypic evolution can occur rapidly in nature, few examples exist of genomewide adaptation on short "ecological" timescales. Burmese pythons (Python molurus bivittatus) have become a successful and impactful invasive species in Florida over the last 30 years despite major freeze events that caused high python mortality. We sampled Florida Burmese pythons before and after a major freeze event in 2010 and found evidence for directional selection in genomic regions enriched for genes associated with thermosensation, behaviour and physiology. Several of these genes are linked to regenerative organ growth, an adaptive response that modulates organ size and function with feeding and fasting in pythons. Independent histological and functional genomic data sets provide additional layers of support for a contemporary shift in invasive Burmese python physiology. In the Florida population, a shift towards maintaining an active digestive system may be driven by the fitness benefits of maintaining higher metabolic rates and body temperature during freeze events. Our results suggest that a synergistic interaction between ecological and climatic selection pressures has driven adaptation in Florida Burmese pythons, demonstrating the often‐overlooked potential of rapid adaptation to influence the success of invasive species. [ABSTRACT FROM AUTHOR]

Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25-73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny. [ABSTRACT FROM AUTHOR]

Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake ( Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater-than-expected overlap between genes linked to lineage-specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome-scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize. [ABSTRACT FROM AUTHOR]

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 bisulphite sequencing and AFLP-based approaches. However, existing methods are sometimes difficult to apply to non-traditional model organisms that lack genomic resources (bisulphite sequencing), and can fail to be economical and readily scalable to diverse research questions because of reliance on traditional Sanger sequencing ( AFLP approaches)., Here we develop a reduced-representation library-based approach that is scalable and economical to quantitatively compare patterns of genomewide methylation. This approach shares substantial similarity to the now widely used double digest restriction-site associated DNA sequencing-based method (dd RADseq), except that it utilizes a methylation-sensitive restriction enzyme. This method therefore identifies changes in the genomic methylation state of cytosine (to 5-methylcytosine; 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., 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., Applications of this general method are broad and diverse and include the analysis of epigenetic shifts in both experimental and natural study systems. [ABSTRACT FROM AUTHOR]

Snakes provide a unique and valuable model system for studying the extremes of physiological remodeling because of the ability of some species to rapidly upregulate organ form and function upon feeding. The predominant model species used to study such extreme responses has been the Burmese python because of the extreme nature of postfeeding response in this species. We analyzed the Burmese python intestine across a time series, before, during, and after feeding to understand the patterns and timing of changes in gene expression and their relationship to changes in intestinal form and function upon feeding. Our results indicate that 2,000 genes show significant changes in expression in the small intestine following feeding, including genes involved in intestinal morphology and function (e.g., hydrolases, microvillus proteins, trafficking and transport proteins), as well as genes involved in cell division and apoptosis. Extensive changes in gene expression occur surprisingly rapidly, within the first 6 h of feeding, coincide with changes in intestinal morphology, and effectively return to prefeeding levels within 10 days. Collectively, our results provide an unprecedented portrait of parallel changes in gene expression and intestinal morphology and physiology on a scale that is extreme both in the magnitude of changes, as well as in the incredibly short time frame of these changes, with up- and downregulation of expression and function occurring in the span of 10 days. Our results also identify conserved vertebrate signaling pathways that modulate these responses, which may suggest pathways for therapeutic modulation of intestinal function in humans. [ABSTRACT FROM AUTHOR]