FROM GENES TO SPECIES: ECOLOGICAL SPECIATION WITH GENE FLOW IN \u3cem\u3eNEODIPRION PINETUM\u3c/em\u3e AND \u3cem\u3eN. LECONTEI\u3c/em\u3e

My dissertation focuses on how differences accumulate across the genome during ecological speciation with geneflow. To do this I used two species of Neodiprionpine sawflies, which are plant-feeding hymenopterans with high host specificity. I used experimental crosses to measure both intrinsic and extrinsic postzygotic isolation and to understand the contribution of specific traits to reproductive isolation. Despite substantial genetic divergence and haploid males in which all recessive incompatibilities should be expressed, I found surprisingly little evidence of intrinsic postzygotic isolation. Recombination in hybrid males may reconstitute viable genotypes and counteract the effects of haploidy in males. Nevertheless, hybrids have drastically reduced fitness due to intermediate host-use traits causing strong extrinsic postzygotic isolation. Together, these results suggest that divergent selection on host-use traits is the primary driver of speciation in these, and likely other, plant-feeding insects. Next, I performed a QTL mapping study of the traits under divergent selection that contribute to extrinsic postzygotic isolation to understand how genetic architecture can constrain or promote speciation and adaptation. I found that opposing dominance between host-choice and host-use traits composes the genetic basis of the earlier detected extrinsic postzygotic isolation. This opposing dominance is part of a growing body of work showing that trait mismatch and not hybrid intermediacy is typically how extrinsic postzygotic isolation is formed. My fourth chapter focuses on how haplodiploid sex determination shapes how populations accumulate differences across the genome during speciation. Using a combination of demographic analysis of pine sawflies, population genetic simulations, and a meta-analysis, I found that compared to diploids, haplodiploids have predictably higher and more variable differentiation across the genome when they diverge in the presence of gene flow. Overall, Neodiprion sawflies present a great opportunity to better understand the genetics of adaptation and speciation

Oviposition Traits Generate Extrinsic Postzygotic Isolation Between Two Pine Sawfly Species

Background: Although empirical data indicate that ecological speciation is prevalent in nature, the relative importance of different forms of reproductive isolation and the traits generating reproductive isolation remain unclear. To address these questions, we examined a pair of ecologically divergent pine-sawfly species: while Neodiprion pinetum specializes on a thin-needled pine (Pinus strobus), N. lecontei utilizes thicker-needled pines. We hypothesized that extrinsic postzygotic isolation is generated by oviposition traits. To test this hypothesis, we assayed ovipositor morphology, oviposition behavior, and host-dependent oviposition success in both species and in F1 and backcross females. Results: Compared to N. lecontei, N. pinetum females preferred P. strobus more strongly, had smaller ovipositors, and laid fewer eggs per needle. Additionally, we observed host- and trait-dependent reductions in oviposition success in F1 and backcross females. Hybrid females that had pinetum-like host preference (P. strobus) and lecontei-like oviposition traits (morphology and egg pattern) fared especially poorly. Conclusions: Together, these data indicate that maladaptive combinations of oviposition traits in hybrids contribute to extrinsic postzygotic isolation between N. lecontei and N. pinetum, suggesting that oviposition traits may be an important driver of divergence in phytophagous insects

Contribution of Genetic Background, Traditional Risk Factors, and HIV-Related Factors to Coronary Artery Disease Events in HIV-Positive Persons

We show in human immunodeficiency virus-positive persons that the coronary artery disease effect of an unfavorable genetic background is comparable to previous studies in the general population, and comparable in size to traditional risk factors and antiretroviral regimens known to increase cardiovascular ris

Host_ Needle_Width

This folder contains the data from the "Host needle width" section of the manuscript. It includes both mature and seedling measurement

BC_Oviposition_success

This folder contains the data for the "Impact of oviposition traits on BCL oviposition success" section of the manuscript. It includes ovipositor landmark coordinates, ovipositor size measurements, oviposition pattern, and associated oviposition success for N. lecontei backcross females

Interspecific_cross

This folder contains the data for the "cross oviposition behavior and success" section of the manuscript. It includes oviposition willingness, oviposition preference, and oviposition success for the interspecific crosses

Parental_Ovipositor_Morphology

This folder contains the data for the "Ovipositor Morphology" section of the manuscript. It includes the landmark coordinates and ovipositor size measurements for N. lecontei and N. pinetu

Faster-haplodiploid evolution under divergence-with-gene-flow: Simulations and empirical data from pine-feeding hymenopterans

Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid “genomes” (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. As long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a “faster-haplodiploid effect”) in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide single nucleotide polymorphism data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/172284/1/mec16410.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/172284/2/mec16410_am.pd

Parental_Oviposition_Behavior

This folder contains the data for the "oviposition behavior" section of the manuscript. It includes oviposition willingness, oviposition preference, Average number of eggs per needle, preslit presence, and egg spacing for N. lecontei and N. pinetu

Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants

Here, by sequencing viruses from individuals in multiple households, Bendall et al. find that SARS-CoV-2 transmission bottleneck does not vary between individuals infected with pre-variant lineages and those infected with highly transmissible Alpha, Delta, or Omicron variants, suggesting these tight bottlenecks will limit the spread of new mutations