DOI: 10.5061/dryad.w3r2280sk
title: On the genetic architecture of rapidly adapting and convergent life history traits in guppies

description: The genetic basis of traits shapes and constrains how adaptation proceeds
 in nature; rapid adaptation can be facilitated by polygenic traits, which
 subsequently provide multiple, redundant, genetic routes to adaptive
 phenotypes, reducing re-use of the same genes (genetic convergence). Guppy
 life history traits evolve rapidly and convergently among natural high-
 (HP) and low-predation (LP) environments in northern Trinidad. This system
 has been studied extensively at the phenotypic level, but little is known
 about the underlying genetic architecture. Here, we use an F2 QTL design
 to examine the genetic basis of seven (five female, two male) guppy life
 history phenotypes to assess whether the genetic architecture of these
 traits reflects theoretical predictions. We use RAD-sequencing data
 (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform
 linkage mapping, estimates of genome-wide and per-chromosome heritability
 (multi-locus associations), and QTL ma pping (single-locus associations).
 Our results are consistent with architectures of many-loci of small effect
 for male age and size at maturity and female interbrood period. Male trait
 associations are clustered on specific chromosomes, but female interbrood
 period exhibits a weak genome-wide signal suggesting a potentially highly
 polygenic component. Offspring weight and female size at maturity are also
 associated with a single significant QTL each. These results suggest rapid
 phenotypic evolution of guppies may be facilitated by polygenic trait
 architectures, but these could fuel redundancy and limit gene re-use
 across populations, in agreement with an absence of strong signatures of
 genetic convergence from recent population genomic analyses of wild HP-LP
 guppies.
description: Sequencing data was derived through RAD-sequencing of four F2
 cross families (F0s and F2s sequenced). Phenotype data
 was derived by phenotyping lab-reared individuals according to the methods
 in Whiting et al. 2022. The linkage map was made using
 LepMap3.
description: This repository contains data associated with the study "On
 the genetic architecture of rapidly adapting and convergent life history
 traits in guppies" by Whiting et al. 2022 Included
 are four data files:   * `guppy_LH_qtl_RAD_snps.vcf.gz`
 - 16,539 RADseq genotypes for 661 individual guppies from four F2 crosses.
 This is the primary SNP data for this study, from which all marker sets
 are derived.   *
 `qtl_female_phenotypes_clean_with_litters.csv` - Phenotypes for
 females   * `qtl_male_phenotypes_clean.csv` -
 Phenotypes for males   *
 `linkage_map_guppy_LH_final.txt` - Final linkage map used
 Notes: * Female phenotypes include age at
 first brood (days), size at first brood (mm), first brood size (number of
 offspring), interbrood interval (days), and dry offspring weight (grams)
 of brood 1 and brood 2 (only offspring weight from the first brood was
 used due to correlation/redundancy of these two phenotypes).
 * Dry offspring weight was calculated as the average weight of an
 individual, so (total dry brood weight)/(brood size) *
 Male phenotpyes include age at maturity (days), and size (mm) and weight
 (grams) at maturity (only size was used for analyses due to high
 correlation between size and weight). * In each .csv,
 the "ID" column corresponds to the number in the middle of the
 IDs of the VCF file, for e.g. "09_556.sorted.rg" in the VCF
 corresponds to ID 556. * Missing data is the male and
 female files are denoted as NA. These are individuals that were sequenced
 but weren't phenotyped, and were excluded from QTL analyses as
 described in the manuscript. * The linkage map includes
 the original marker number "marker" (1-16539, corresponding to
 order in VCF); the cM position on lepmap-derived linkage groups
 "cM"; the original VCF mapped position in bp "mapped";
 the original chromosome from the vcf "original_chr"; the
 lepmap-derived linkage group "LG"; and a column called
 "trim" that was used to trim the full linkage map ends but can
 be ignored. * Regarding the linkage map, lepmap orders
 LGs according to the number of markers mapped to it, but this is not the
 same as the original chromosome orders in the guppy genome. For e.g. chr2
 is the largest chromosome, and as such has the most markers, making it
 "LG1". These were manually changed to match the order of
 chromosomes in the genome during analyses. Additional
 associated data and analysis scripts can be found in the github
 repository:
 https://github.com/JimWhiting91/guppy_LH_QTL (archived with
 Zenodo doi:10.5281/zenodo.5938562)