Genes, Transposable Elements, and Small RNAs: Studying the Evolution of Diverse Genomic Components

The evolution of genes and genomes has attracted great interest. The research presented here is an examination of genomes at three distinct levels, protein evolution, gene family evolution, and TE content regulation. First at a genetic level, I conducted an analysis of the salivary androgen-binding proteins (ABPs). I focused on comparing patterns of molecular evolution between the Abpa gene expressed in the submaxillary glands of species of New World and Old World muroids and found that in both sets of rodents, the Abpa gene expressed in the submaxillary glands appear to be evolving under sexual selection, suggesting ABP might play a similar biological role in both systems. Thus, ABP could be involved with mate recognition and species isolation in New World as well as Old World muroids. Second I examined the largest gene family in vertebrate olfactory receptors (ORs) among birds and reptiles. I found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the lizard to over 1000 in turtles. My results suggest that different sauropsid lineages have highly divergent OR repertoire compositions. These differences suggest that varying rates of gene birth and death, together with selection related to diverse natural histories, have shaped the unique OR repertoires observed across sauropsid lineages. Lastly, I studied the interactions between transposable elements (TEs) and PIWI-interacting RNAs (piRNAs) among laurasiatherian mammals. piRNAs are predominantly expressed in germlines and reduce TE expression and risks associated with their mobilization. I found that within TE types, families that are the most highly transcribed appear to elicit the strongest ping-pong response. This was most evident among LINEs, but the relationships between expression and PPE was more complex among SINEs. I also found that the abundance of insertions within piRNAs clusters strongly correlated with genome insertions and there was little evidence to suggest that piRNA clusters regulated TE silencing. In summary, the piRNA response is efficient at protecting the genome against TE mobility, particularly LINEs, and can have an evolutionary impact on the TE composition of a genome

Gene Turnover and Diversification of the α- and β- Globin Gene Families in Sauropsid Vertebrates

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here,we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster,which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globingenes that diversified independently in each lineage.These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids

Harvard Personal Genome Project: lessons from participatory public research

Background: Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants

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

Gene Turnover and Diversification of the α- and β- Globin Gene Families in Sauropsid Vertebrates

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here,we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and β-globin gene clusters. In the α-globin gene cluster,which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the β-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed β-type globingenes that diversified independently in each lineage.These independently derived β-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids

Magnitude of the freshwater turtle exports from the US: long term trends and early effects of newly implemented harvest management regimes.

Unregulated commercial harvest remains a major threat for turtles across the globe. Due to continuing demand from Asian markets, a significant number of turtles are exported from the United States of America (US). Beginning in 2007, several southeastern states in the US implemented restrictions on the commercial harvest of turtles, in order to address the unsustainable take. We have summarized freshwater turtle exports from the US between 2002 and 2012 and demonstrated that the magnitude of turtle exports from the US remained high although the exports decreased throughout the decade. Louisiana and California were the major exporters. The majority of exports were captive bred, and from two genera, Pseudemys and Trachemys. We review the changes over the decade and speculate that the increase in export of wild turtles out of Louisiana after 2007 could be a consequence of strict regulations in surrounding states (e.g., Alabama, Florida). We suggest that if wild turtle protection is a goal for conservation efforts, then these states should work together to develop comprehensive regulation reforms pertaining to the harvest of wild turtles

Proportion of freshwater turtles exported from the US in the period from 2002–2012, partitioned by the exporting state (A), and an overview of state regulations in the southeast US (B), the region with the further conservation concern regarding freshwater turtles.

<p>Four states (Louisiana, California, Texas, and Florida) account for 96% of all exports. On the other hand, Louisiana, Arkansas, and Mississippi still allow unlimited take while Alabama and Florida banned commercial harvest from all water bodies and therefore represent two states with the strictest laws regarding commercial turtle harvest.</p

Number of native freshwater turtles (y-axis) exported from Louisiana, California, Texas, and Florida from 2002–2012 (x-axis).

<p>Louisiana and California accounted for 96% of the overall export from the US. Texas and Florida accounted for 2% each of the overall export from the US.</p