Using Transposable Elements as Tools to Better Understand Evolution at the Genomic Level

Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not uncommon for 50% of the genome to be derived from TEs, yet they remain an underutilized tool for tracking evolutionary change. With the increasing number of publicly funded genome projects and affordable access to next-generation sequencing platforms, it is important to demonstrate the role TEs may play in helping us understand evolutionary patterns. The research presented herein utilizes TEs to investigate such patterns at the genomic, specific, and generic levels in three distinct ways. First at the genomic level, an analysis of the historical TE activity within the thirteen-lined ground squirrel (Spermophilus tridecemlineatus) shows that non-LTR retrotransposon activity has been declining for the past ~26 million years and appears to have ceased ~5 million years ago. Since most mammals, and all other rodents studied to date, have active TEs the extinction event in S. tridecemlineatus makes it a valuable model for understanding the factors driving TE activity and extinction. Second, we examined TEs as factors impacting genomic and species diversity. We found that DNA transposon insertions in Eptesicus fuscus, appear to have been exapted as miRNAs. When placed within a phylogenetic context a burst of transposon-driven, miRNA origination and the vespertilionid species radiation occurred simultaneously ~30 million years ago. This observation implies that lineage specific TEs could generate lineage specific regulatory pathways, and consequently lineage specific phenotypic differences. Finally, we utilized TEs to investigate their phylogenetic potential at the level of genus. In particular a method was developed that identified, over 670 thousand Ves SINE insertions in seven species of Myotis for use in future phylogenetic studies. Our method was able to accurately identify insertions in taxa for which no reference genome was available and was confirmed using traditional PCR and Sanger sequencing methods. By identifying polymorphic Ves insertions, it may be possible to resolve the phylogeny of one of the largest species radiations in mammals

A Prolegomenon to the Systematics of South American Cottontail Rabbits (Mammalia, Lagomorpha, Leporidae: Sylvilagus): Designation of a Neotype for S. brasiliensis (Linnaeus, 1758), and Restoration of S. andinus (Thomas, 1897) and S. tapetillus Thomas, 1913.

A critical issue with species names derived from Linnaeus’ 10th edition of the Systema Naturae is the lack of holotypes, which in many instances has led to taxonomic confusion and uncertainty, as well as an unstable taxonomy. In the particular case of the South American cottontail, currently known as Sylvilagus brasiliensis, Linnaeus listed the type locality as “America Meridionali,” or South America. As a result, S. brasiliensis was ascribed a widespread distribution in North and South America, over an area estimated as approximately 1.09 × 107 Km2, and containing upwards of 37 named subspecies.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/136089/1/MP205.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136089/2/MP205_SupplementaryFigs.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136089/3/MP205_Appendix1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/136089/4/MP205_Appendix 2.xlsxDescription of MP205.pdf : Main ArticleDescription of MP205_SupplementaryFigs.pdf : Additional FiguresDescription of MP205_Appendix1.pdf : Dataset - MapsDescription of MP205_Appendix 2.xlsx : Datase

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead