Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop

Lesbian, Gay, Bisexual, and Transgender Health: a Survey of Attitudes, Knowledge, Preparedness, Campus Climate, and Student Recommendations for Change in Four Midwestern Medical Schools

Medical school curricula addressing the unique healthcare needs and disparities of lesbian, gay, bisexual, and transgender (LGBT) patients are insufficient. National organizations have recommended curricular and institutional climate changes to address this problem. This study examined students’ perceived attitudes and knowledge regarding LGBT patient care and campus climate at four Midwestern US allopathic medical schools. During 2013, all medical students at the four institutions were invited to participate in the online anonymous survey. We used descriptive statistics for survey item results and qualitative methods to analyze responses to open-ended questions about curricular changes. Survey results were obtained from 34.6% of students and demonstrated that attitudes, knowledge, preparedness, and campus climate across all institutions were generally positive for LGBT patients and students. A negative correlation was found between overall campus climate and discrimination practices. Four themes emerged from students’ recommendations to improve their training, which included more clinical experiences with LGBT patients, more formal curricula on LGBT topics, establishment of safe learning environments, and addition of specific topics related to LGBT health. Due to the low prevalence of LGBT populations, reluctance to disclose sexual orientation or gender identity, and lack of LGBT-specific clinics, required experiences with LGBT patients during clinics or clerkship rotations may be more difficult in smaller urban communities in which some Midwestern medical schools are located. Potential alternatives include using multiple teaching modalities in the pre-clerkship years to expose students to LGBT-identified patients in clinical simulations and settings

Lesbian, Gay, Bisexual, and Transgender Health: a Survey of Attitudes, Knowledge, Preparedness, Campus Climate, and Student Recommendations for Change in Four Midwestern Medical Schools

Medical school curricula addressing the unique healthcare needs and disparities of lesbian, gay, bisexual, and transgender (LGBT) patients are insufficient. National organizations have recommended curricular and institutional climate changes to address this problem. This study examined students’ perceived attitudes and knowledge regarding LGBT patient care and campus climate at four Midwestern US allopathic medical schools. During 2013, all medical students at the four institutions were invited to participate in the online anonymous survey. We used descriptive statistics for survey item results and qualitative methods to analyze responses to open-ended questions about curricular changes. Survey results were obtained from 34.6% of students and demonstrated that attitudes, knowledge, preparedness, and campus climate across all institutions were generally positive for LGBT patients and students. A negative correlation was found between overall campus climate and discrimination practices. Four themes emerged from students’ recommendations to improve their training, which included more clinical experiences with LGBT patients, more formal curricula on LGBT topics, establishment of safe learning environments, and addition of specific topics related to LGBT health. Due to the low prevalence of LGBT populations, reluctance to disclose sexual orientation or gender identity, and lack of LGBT-specific clinics, required experiences with LGBT patients during clinics or clerkship rotations may be more difficult in smaller urban communities in which some Midwestern medical schools are located. Potential alternatives include using multiple teaching modalities in the pre-clerkship years to expose students to LGBT-identified patients in clinical simulations and settings

Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Theory predicts that speciation-with-gene-flow is more likely when the consequences of selection for population divergence transitions from mainly direct effects of selection acting on individual genes to a collective property of all selected genes in the genome. Thus, understanding the direct impacts of ecologically based selection, as well as the indirect effects due to correlations among loci, is critical to understanding speciation. Here, we measure the genome-wide impacts of host-associated selection between hawthorn and apple host races of Rhagoletis pomonella (Diptera: Tephritidae), a model for contemporary speciation-with-gene-flow. Allele frequency shifts of 32 455 SNPs induced in a selection experiment based on host phenology were genome wide and highly concordant with genetic divergence between co-occurring apple and hawthorn flies in nature. This striking genome-wide similarity between experimental and natural populations of R. pomonella underscores the importance of ecological selection at early stages of divergence and calls for further integration of studies of eco-evolutionary dynamics and genome divergence

VCF file for experimental and natural populations

This is the VCF file for the experimental and natural population comparisons. To test for differentiation genome wide among sympatric populations, we contrasted our apple7 and haw7 groups; for a response to selection in our experiment, we compared haw7 and haw30. Haw or apple represents the host plant from which the flies were collected; the number - 7 or 30 - represents the pre-winter warm period experienced by larvae/pupae prior to overwintering to match that found in nature on haw or apple plants. See txt file to match individual MID labels in the VCF file with the experimental group they were part of

R_pomonella_denovo_assembly

This file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details

R. pomonella Linkage Map

Linkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans