• Assessing the Architecture of Drosophila mojavensis Locomotor Evolution with Bulk Segregant Analysis

      Benowitz, Kyle M; Coleman, Joshua M; Matzkin, Luciano M; Univ Arizona, Dept Entomol; Univ Arizona, Dept Ecol & Evolutionary Biol; Univ Arizona, BIO5 Inst (GENETICS SOCIETY AMERICA, 2019-05)
      Behavior is frequently predicted to be especially important for evolution in novel environments. If these predictions are accurate, there might be particular patterns of genetic architecture associated with recently diverged behaviors. Specifically, it has been predicted that behaviors linked to population divergence should be underpinned by a few genes of relatively large effect, compared to architectures of intrapopulation behavioral variation, which is considered to be highly polygenic. More mapping studies of behavioral variation between recently diverged populations are needed to continue assessing the generality of these predictions. Here, we used a bulk segregant mapping approach to dissect the genetic architecture of a locomotor trait that has evolved between two populations of the cactophilic fly Drosophila mojavensis We created an F8 mapping population of 1,500 individuals from advanced intercross lines and sequenced the 10% of individuals with the highest and lowest levels of locomotor activity. Using three alternative statistical approaches, we found strong evidence for two relatively large-effect QTL that is localized in a region homologous to a region of densely packed behavior loci in Drosophila melanogaster, suggesting that clustering of behavior genes may display relatively deep evolutionary conservation. Broadly, our data are most consistent with a polygenic architecture, though with several loci explaining a high proportion of variation in comparison to similar behavioral traits. We further note the presence of several antagonistic QTL linked to locomotion and discuss these results in light of theories regarding behavioral evolution and the effect size and direction of QTL for diverging traits in general.
    • A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

      Nelson, A. D. L.; Forsythe, E. S.; Devisetty, U. K.; Clausen, D. S.; Haug-Batzell, A. K.; Meldrum, A. M. R.; Frank, M. R.; Lyons, E.; Beilstein, M. A.; Univ Arizona, Dept Chem & Biochem; et al. (GENETICS SOCIETY AMERICA, 2016-07-20)
      Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of >5000 lincRNA loci from A. thaliana. From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.
    • Mutations in a Novel Cadherin Gene Associated with Bt Resistance in Helicoverpa zea

      Fritz, Megan L; Nunziata, Schyler O; Guo, Rong; Tabashnik, Bruce E; Carrière, Yves; Univ Arizona, Dept Entomol (GENETICS SOCIETY AMERICA, 2020-05-01)
      Transgenic corn and cotton produce crystalline (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt) that are toxic to lepidopteran larvae. Helicoverpa zea, a key pest of corn and cotton in the U.S., has evolved widespread resistance to these proteins produced in Bt corn and cotton. While the genomic targets of Cry selection and the mutations that produce resistant phenotypes are known in other lepidopteran species, little is known about how selection by Cry proteins shape the genome of H. zea We scanned the genomes of Cry1Ac-selected and unselected H. zea lines, and identified twelve genes on five scaffolds that differed between lines, including cadherin-86C (cad-86C), a gene from a family that is involved in Cry1A resistance in other lepidopterans. Although this gene was expressed in the H. zea larval midgut, the protein it encodes has only 17 to 22% identity with cadherin proteins from other species previously reported to be involved in Bt resistance. An analysis of midgut-expressed cDNAs showed significant between-line differences in the frequencies of putative nonsynonymous substitutions (both SNPs and indels). Our results indicate that cad-86C is a likely target of Cry1Ac selection in H. zea It remains unclear, however, whether genomic changes at this locus directly disrupt midgut binding of Cry1Ac and cause Bt resistance, or indirectly enhance fitness of H. zea in the presence of Cry1Ac by some other mechanism. Future work should investigate phenotypic effects of these nonsynonymous substitutions and their impact on fitness of H. zea larvae that ingest Cry1Ac.
    • De Novo Assembly and Annotation from Parental and F-1 Puma Genomes of the Florida Panther Genetic Restoration Program

      Ochoa, Alexander; Onorato, David P; Fitak, Robert R; Roelke-Parker, Melody E; Culver, Melanie; Univ Arizona, Sch Nat Resources & Environm (GENETICS SOCIETY AMERICA, 2019-11-05)
      In the mid-1990s, the population size of Florida panthers became so small that many individuals manifested traits associated with inbreeding depression (e.g., heart defects, cryptorchidism, high pathogen-parasite load). To mitigate these effects, pumas from Texas were introduced into South Florida to augment genetic variation in Florida panthers. In this study, we report a de novo puma genome assembly and annotation after resequencing 10 individual genomes from partial Florida-Texas-F1 trios. The final genome assembly consisted of ∼2.6 Gb and 20,561 functionally annotated protein-coding genes. Foremost, expanded gene families were associated with neuronal and embryological development, whereas contracted gene families were associated with olfactory receptors. Despite the latter, we characterized 17 positively selected genes related to the refinement of multiple sensory perceptions, most notably to visual capabilities. Furthermore, genes under positive selection were enriched for the targeting of proteins to the endoplasmic reticulum, degradation of mRNAs, and transcription of viral genomes. Nearly half (48.5%) of ∼6.2 million SNPs analyzed in the total sample set contained putative unique Texas alleles. Most of these alleles were likely inherited to subsequent F1 Florida panthers, as these individuals manifested a threefold increase in observed heterozygosity with respect to their immediate, canonical Florida panther predecessors. Demographic simulations were consistent with a recent colonization event in North America by a small number of founders from South America during the last glacial period. In conclusion, we provide an extensive set of genomic resources for pumas and elucidate the genomic effects of genetic rescue on this iconic conservation success story.