Browsing by Author "Sullivan, Kevin A.M. (TTU)"
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Item Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats(2018) Platt, Roy N. (TTU); Faircloth, Brant C.; Sullivan, Kevin A.M. (TTU); Kieran, Troy J.; Glenn, Travis C.; Vandewege, Michael W. (TTU); Lee, Thomas E.; Baker, Robert J. (TTU); Stevens, Richard D. (TTU); Ray, David A. (TTU)The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution.Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the NewWorld, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.Item Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths(2019) Ray, David A. (TTU); Grimshaw, Jenna R. (TTU); Halsey, Michaela K. (TTU); Korstian, Jennifer M. (TTU); Osmanski, Austin B. (TTU); Sullivan, Kevin A.M. (TTU); Wolf, Kristen A. (TTU); Reddy, Harsith (TTU); Foley, Nicole (TTU); Stevens, Richard D. (TTU); Knisbacher, Binyamin A.; Levy, Orr; Counterman, Brian; Edelman, Nathaniel B.; Mallet, James; Schaack, SarahTransposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.Item Six reference-quality genomes reveal evolution of bat adaptations(2020) Jebb, David; Huang, Zixia; Pippel, Martin; Hughes, Graham M.; Lavrichenko, Ksenia; Devanna, Paolo; Winkler, Sylke; Jermiin, Lars S.; Skirmuntt, Emilia C.; Katzourakis, Aris; Burkitt-Gray, Lucy; Ray, David A. (TTU); Sullivan, Kevin A.M. (TTU); Roscito, Juliana G.; Kirilenko, Bogdan M.; Dávalos, Liliana M.; Corthals, Angelique P.; Power, Megan L.; Jones, Gareth; Ransome, Roger D.; Dechmann, Dina K.N.; Locatelli, Andrea G.; Puechmaille, Sébastien J.; Fedrigo, Olivier; Jarvis, Erich D.; Hiller, Michael; Vernes, Sonja C.; Myers, Eugene W.; Teeling, Emma C.Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.Item Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice(2017) Sullivan, Kevin A.M. (TTU); Platt, Roy N. (TTU); Bradley, Robert D. (TTU); Ray, David A. (TTU)Background Recent phylogenies of deer mice, genus Peromyscus, have relied heavily on mitochondrial markers. These markers provided resolution at and below the level of species groups, but relationships among species groups and Peromyscus affiliated genera have received little support. Here, we present the mitochondrial genomes of 14 rodents and infer the phylogeny of Peromyscus and related taxa. Results Our analyses support results from previous molecular phylogenies, but also yield support for several previously unsupported nodes throughout the Peromyscus tree. Our results also confirm several instances of paraphyly within the clade and suggest additional taxonomic work will be required to clarify some relationships. Conclusions Our findings greatly enhance our understanding of the evolution of Peromyscus providing support for previously unsupported relationships. However, the results also highlight the need to address paraphyly that may exist in this clade.