Browsing by Author "Vandewege, Michael W. (TTU)"
Now showing 1 - 3 of 3
- Results Per Page
- Sort Options
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 Gene turnover and diversificationof the α-and β-GlobinGene families in sauropsid vertebrates(2018) Hoffmann, Federico G.; Vandewege, Michael W. (TTU); Storz, Jay F.; Opazo, Juan C.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 thanmammals 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 familieswithin and among themajor 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 thatwere present inthe common ancestor of tetrapods. In the β-globin gene cluster,which was translocated to a newchromosomal 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, allmajor groups ofamniotes possess unique repertoires ofembryonic and postnatally expressed β-typeglobingenes that diversifiedindependently ineachlineage.These independentlyderived β-typeglobinsdescend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.Item Positive selection and gene expression analyses from salivary glands reveal discrete adaptations within the ecologically diverse bat family phyllostomidae(2020) Vandewege, Michael W. (TTU); Sotero-Caio, Cibele G. (TTU); Phillips, Caleb D. (TTU)The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.