Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura

 

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Title PCR primer sequences for markers used
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Description Primer 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.
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Title Recombination rates, Diversity, and Divergence Measures
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Description Data 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.
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Title Raw Data Used in Analysis of Recombination Rate with Maternal Age
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Description This 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.
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When using this data, please cite the original publication:

Manzano-Winkler B, McGaugh SE, Noor MAF (2013) How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura. PLoS ONE 8(8): e71582. http://dx.doi.org/10.1371/journal.pone.0071582

Additionally, please cite the Dryad data package:

Manzano-Winkler B, McGaugh SE, Noor MAF (2013) Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2r730
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