DOI: 10.5061/dryad.ns1rn8q13
title: Data from: Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species

description: The evolution of postzygotic isolation is thought to be a key step in
 maintaining species boundaries upon secondary contact, yet the dynamics
 and persistence of hybrid incompatibilities in naturally hybridizing
 species are not well understood. Here, we explore these issues using
 genetic mapping in three independent populations of recombinant inbred
 lines between naturally hybridizing monkeyflowers Mimulus guttatus and M.
 nasutus from the sympatric Catherine Creek population. We discover that
 the three M. guttatus founders differ dramatically in admixture history,
 with nearly a quarter of one founder’s genome introgressed from M.
 nasutus. Comparative genetic mapping in the three RIL populations reveals
 three new putative inversions, each one segregating among the M. guttatus
 founders, two due to admixture. We find strong, genome-wide transmission
 ratio distortion in all RILs, but patterns are highly variable among the
 three populations. At least some of this distortion appears to be
 explained by epistatic selection favoring parental genotypes, but tests of
 inter-chromosomal linkage disequilibrium also reveal multiple candidate
 Dobzhansky-Muller incompatibilities. We also map several genetic loci for
 hybrid pollen viability, including two interacting pairs that coincide
 with peaks of distortion. Remarkably, even with this limited sample of
 three M. guttatus lines, we discover abundant segregating variation for
 hybrid incompatibilities with M. nasutus, suggesting this population
 harbors diverse contributors to postzygotic isolation. Moreover, even with
 substantial admixture, hybrid incompatibilities between Mimulus species
 persist, suggesting postzygotic isolation might be a potent force in
 maintaining species barriers in this system. 
description: # Postzygotic barriers persist despite ongoing introgression in
 hybridizing *Mimulus* species
 Using inbred lines of
 *Mimulus guttatus* and *M. nasutus* derived from the sympatric site
 Catherine Creek (CAC), we produced three Recombinant Inbred Line (RIL)
 populations from crosses between a common *M. nasutus* maternal parent
 CAC9 and the *M. guttatus* paternal parents CAC110, CAC162, and CAC415.
 Dataset includes genetic and phenotypic (male and female fertility) data
 for these RIL individuals. ## Description of the data and file structure
 Male_Fertility: Raw male fertility data for each RIL individual (Plant) in
 each RIL population (RIL_pop), including the number of darkly stained
 (Viable) and unstained (Inviable) pollen grains counted from a haphazardly
 selected group of ≥100, after staining with lactophenol-aniline blue
 stain, and the proportion of pollen grains which were viable (PropV).
 Because each row represents pollen collected from a separate flower, each
 RIL individual is referenced in multiple rows. Female_Fertility: Raw
 female fertility data for each experimental cross made between RIL
 individuals by pollinating the emasculated maternal parent (M_Parent) with
 pollen from the paternal parent (P_Parent), including the number of mature
 seeds produced by each hand pollination (Seeds_per_Fruit) during either of
 the two growouts (Year). During the 2018 growout multiple fruits of the
 same cross were collected together, making Seeds_per_Fruit an average over
 1 or more fruits, during the 2022 growout each fruit was collected
 separately, so each row represents the number of seeds contained in a
 single fruit. As such each cross from 2018 is represented by a single row,
 while each cross from 2022 is represented by 1 or more rows, depending on
 the number of hand pollinations performed. Data is also grouped by the RIL
 population of the maternal and paternal plants (Cross_Group), for example
 a CAC110 RIL plant pollinated by a CAC162 RIL plant is in cross group 1x2,
 a CAC162 RIL plant pollinated by a CAC415 RIL plant is in cross group 2x3,
 etc. CAC110 RILs QTL Mapping: Files used as inputs for QTL mapping (r/QTL)
 in CAC110 RILs * CAC110RILs_Genos_Min_for_rQTL: Genotype matrix used in
 r/QTL containing genotypes for each CAC110 RIL individual (id) at each
 50kb windowed marker (AA: Homozygous *M. guttatus* alleles, BB: Homozygous
 *M. nasutus* alleles, - : Missing data). Markers are named based on the
 starting position of the window they represent, for example window
 Chr_01_350000 consists of position 350,000 - 400,000 on chromosome 1.
 Linkage map information including linkage group number, and map position
 in cM is included beneath each marker. * CAC110RILs_PropV_Ave: Average
 proportion of viable pollen grains across all counted flowers (AvePropV)
 and the logit transformation of those proportions (LogitAvePropV) for each
 CAC110 RIL individual (id). * CAC110RILs_FemaleSter_Ave: Calculated least
 square means of female fertility (FemaleSter), using seeds per fruit as a
 proxy, from a linear mixed model including maternal parent genotype (fixed
 effect), average pollen viability of the paternal parent (fixed effect), a
 unique RIX identifier nested within RIX cross type (random effect), and
 the year that the cross was made (random effect), and the square root
 transformation of those values (SqRootFemaleSter) for each CAC110 RIL
 individual (id). CAC162 RILs QTL Mapping: Files used as inputs for QTL
 mapping (r/QTL) in CAC162 RILs * CAC162RILs_Genos_Min_for_rQTL: Genotype
 matrix used in r/QTL containing genotypes for each CAC162 RIL individual
 (id) at each 50kb windowed marker (AA: Homozygous *M. guttatus* alleles,
 BB: Homozygous *M. nasutus* alleles, - : Missing data). Markers are named
 based on the starting position of the window they represent. Linkage map
 information including linkage group number, and map position in cM is
 included beneath each marker. * CAC162RILs_PropV_Ave: Average proportion
 of viable pollen grains across all counted flowers (AvePropV) and the
 logit transformation of those proportions (LogitAvePropV) for each CAC162
 RIL individual (id). * CAC162RILs_FemaleSter_Ave: Calculated least square
 means of female fertility (FemaleSter), using seeds per fruit as a proxy,
 from a linear mixed model including maternal parent genotype (fixed
 effect), average pollen viability of the paternal parent (fixed effect), a
 unique RIX identifier nested within RIX cross type (random effect), and
 the year that the cross was made (random effect), and the square root
 transformation of those values (SqRootFemaleSter) for each CAC162 RIL
 individual (id). CAC415 RILs QTL Mapping: Files used as inputs for QTL
 mapping (r/QTL) in CAC415 RILs * CAC415RILs_Genos_Min_for_rQTL: Genotype
 matrix used in r/QTL containing genotypes for each CAC415 RIL individual
 (id) at each 50kb windowed marker (AA: Homozygous *M. guttatus* alleles,
 BB: Homozygous *M. nasutus* alleles, - : Missing data). Markers are named
 based on the starting position of the window they represent. Linkage map
 information including linkage group number, and map position in cM is
 included beneath each marker. * CAC415RILs_PropV_Ave: Average proportion
 of viable pollen grains across all counted flowers (AvePropV) and the
 logit transformation of those proportions (LogitAvePropV) for each CAC415
 RIL individual (id). * CAC415RILs_FemaleSter_Ave: Calculated least square
 means of female fertility (FemaleSter), using seeds per fruit as a proxy,
 from a linear mixed model including maternal parent genotype (fixed
 effect), average pollen viability of the paternal parent (fixed effect), a
 unique RIX identifier nested within RIX cross type (random effect), and
 the year that the cross was made (random effect), and the square root
 transformation of those values (SqRootFemaleSter) for each CAC415 RIL
 individual (id).