DOI: 10.5061/dryad.2r730
title: Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura

description: Fine scale meiotic recombination maps have uncovered a large amount of
 variation in crossover rate across the genomes of many species, and such
 variation in mammalian and yeast genomes is concentrated to &lt;5 kb
 regions of highly elevated recombination rates (10–100x the background
 rate) called “hotspots.” Drosophila exhibit substantial recombination rate
 heterogeneity across their genome, but evidence for these highly-localized
 hotspots is lacking. We assayed recombination across a 40 Kb region of
 Drosophila pseudoobscura chromosome 2, with one 20 kb interval assayed
 every 5 Kb and the adjacent 20 kb interval bisected into 10 kb pieces. We
 found that recombination events across the 40 kb stretch were relatively
 evenly distributed across each of the 5 kb and 10 kb intervals, rather
 than concentrated in a single 5 kb region. This, in combination with other
 recent work, indicates that the recombination landscape of Drosophila may
 differ from the punctate recombination pattern observed in many mammals
 and yeast. Additionally, we found no correlation of average pairwise
 nucleotide diversity and divergence with recombination rate across the 20
 kb intervals, nor any effect of maternal age in weeks on recombination
 rate in our sample.
description: PCR primer sequences for
 markers usedPrimer sequences for
 markers used in the study, including the primers brought in from the older
 McGaugh et al 2012 PLoS Biology paper. Also included are the positions of
 the markers in the sequence assembly of the second chromosome of D.
 pseudoobscura. Some markers used three primers simultaneously to
 differentiate the inbred lines in a single PCR.Primers_for_Dryad.csvRecombination rates, Diversity, and Divergence MeasuresData used to examine correlation of recombination rate with nucleotide diversity within D. pseudoobscura (measured as "pi") and divergence between D. pseudoobscura and D. miranda (measured as "Dxy"). Data are listed by position in the second chromosome sequence assembly of D. pseudoobscura. Measures are done for both four-fold degenerate synonymous sites and intergenic regions. Divergence between D. pseudoobscura and outgroup D. lowei are also included.Diversity_Divergence_Measures_for_Dryad.csvRaw Data Used in Analysis of Recombination Rate with Maternal AgeThis file has the raw data used for analysis of recombination rate with maternal age (crudely dichotomized as "young" vs. "old" as specified in the paper). Each row identifies whether a single pair of markers specified were recombinant (1) or not (0) in a single fly, so each fly studied is represented by many rows. File is large: 170,272 rows. To look for "food batch" effects, the vial from which the mother and grandmother were derived is also denoted. "Young" corresponds roughly to post-eclosion adult day 7-10 of life and day 7-17 of life for grandmother and mother (the F1 female), respectively. "Old" corresponds roughly to adult day 10-17 of life and day 17-24 of life for grandmother and mother, respectively.Age_Analysis_RawData_for_Dryad.csv