DOI: 10.5061/dryad.q573n5tpk
title: Data from: Divergent dynamics of sexual and habitat isolation at the transition between stick insect populations and species

description: Speciation is often viewed as a continuum along which populations diverge
 until they become reproductively-isolated species. However, such
 divergence may be heterogeneous, proceeding in `fits and bursts',
 rather than being uniform and gradual. We show in Timema stick insects
 that one form of reproductive isolation indeed evolves non-uniformly
 across this continuum, whereas another does not. Specifically, we use
 thousands of host-preference and mating trials to study habitat and sexual
 isolation among 42 pairs of taxa spanning a range of genomic
 differentiation and divergence time. We find that the evolution of habitat
 isolation is uncoupled from genomic differentiation within species, but
 accumulates linearly with it between species. In contrast, sexual
 isolation accumulates linearly across the speciation continuum. The
 results show different evolutionary dynamics for different components of
 reproductive isolation, indicate sudden transitions between phases of
 speciation, and highlight a special relevance for species status in the
 evolution of reproductive isolation.
description: Host preference was assayed using previously published protocols.
 Each evening, individual stick insects were placed in a 500-milliliter
 plastic cup with ~15 cm cuttings of two different host-plant species. The
 cups were covered with mosquito mesh and left overnight. In the morning we
 scored which of the two plant species the stick insect was resting upon
 (trials where neither was chosen were excluded). These experiments tested
 field-caught individuals within a few days of collection. Habitat
 isolation was estimated as the degree of divergence between taxon pairs in
 host-plant feeding preference. This was estimated by assigning one of the
 two host species used in each assay as the `reference host' and then
 calculating the absolute value of: (proportion of trials in which taxon 1
 of the pair picked the reference host) - (the proportion of trials in
 which taxon 2 of the pair picked the reference host). Note that the
 assignment of a reference host is totally arbitrary as the degree of
 divergence in preference is identical no matter which host species is
 picked as the reference.  Mating preference was assayed
 using previously published protocols. One adult male and one adult female
 were placed in a standard 10 cm petri dish. Each pair was observed for one
 hour and scored as having mated or not (<em>Timema</em> have
 an extended copulation period that is unambiguous and easy to observe).
 Trials were conducted using the four mating combinations possible for each
 population pair (male population 1 x female population 1, male population
 2 x female population 2; between-population trials: male population 1 x
 female population 2, male population 2 x female population 1). The same
 protocol was applied to within- and between-species trials. These
 experiments largely tested field-caught individuals that were captured as
 virgin sub-adults and reared to sexual-maturity on the host upon which
 they were collected, in plastic containers where the sexes were kept
 separate to ensure virgin status of the individuals tested.  Using the
 results of these mating trials, we quantified sexual isolation as one
 minus the frequency of matings for heterospecific (or between population)
 divided by the frequency of matings for homospecific (or within
 population) pairs, respectively.  We obtained nuclear
 DNA sequence for an anonymous nuclear gene, Tc_nuc235 using primer pairs
 developed for <em>T. cristinae</em>: Tc_nuc235F =
 ATCCTGGAATTCACGCACTTAC and Tc_nuc235R = CTTACCCTTCTCCAAAATGTCG. DNA
 sequences were then obtained using Sanger sequencing, and trimmed and
 edited to retain 500 bps of high-quality data.
 Phylogenetic divergence time estimates were extracted from a
 published, time-calibrated Bayesian phylogenetic tree (see https://doi.org/10.5061/dryad.nq67q). Demographic inferences were based on a re-alignment and analysis of the same previously published genotyping-by-sequencing data.
description: # Data from: Divergent dynamics of sexual and habitat isolation at the
 transition between stick insect populations and species --- This dataset
 comprises measures of habitat isolation and sexual isolation from
 experiments, aligned DNA sequences, divergence time estimates, and variant
 (SNP) data for multiple species of *Timema* stick insects. ## Description
 of the data and file structure Ten files are included in this dataset. The
 format of each is described below: TimemaNucDNA.nex = DNA sequence
 alignment. This is a nexus format alignment file for an anonymous nuclear
 gene, Tc_nuc235. HostRIDat.csv = csv file with host (habitat) isolation
 data. This file contains the raw data used to compute habitat isolation,
 along with associated metadata on the taxon pair types, species and
 population IDs and hosts tested. The key data are in the columns labeled
 PctPick1 and PctPick2, these give the percentage of individuals choosing a
 given host plant species from each of the two test populations (species).
 The file also includes estimates of nuclear DNA sequence divergence
 (nucDNA) and Fst based on genotyping-by-sequencing data (GBS).
 CountData.csv = csv file with the sexual isolation data. This file
 contains the raw data used to compute sexual isolation. Pair numbers
 (Pair) in this file match the pair numbers in HostRIDat.csv, and thereby
 provide metadata on species IDs, etc. The key data give the number (nF1M1,
 nF1M2, nF2M1, nF2M2) of tests of each mating pair type (F and M denote
 female and male and 1 vs 2 denote species number) and the number of tests
 of each type where mating occurred (yF1M1, yF1M2, yF2M1, yF2M2).
 divtimes.pairs.100kmreads_10kdepth_20QS_85cov_phylob.4runs.tsv = tab
 separated file with phylogenetic divergence time estimates. This file
 contains summaries of the posterior distribution for the divergence time
 between each pair of taxa (denoted pop1 and pop2), including the posterior
 median (div.median) and lower and upper bounds of the highest posterior
 density (HPD) interval. filtered2x_timema_chum_variants.vcf.gz =
 compressed variant (SNP) file in VCFv4.2 format. This is the filtered vcf
 file for *Timema chumash* with 17,574 SNPs and 358 individuals.
 filtered2x_timema_cris_variants.vcf.gz = compressed variant (SNP) file in
 VCFv4.2 format. This is the filtered vcf file for *Timema cristinae* with
 205 individuals. filtered2x_timema_curi_variants.vcf.gz = compressed
 variant (SNP) file in VCFv4.2 format. This is the filtered vcf file for
 *Timema curi* with 27,289 SNPs and 85 individuals.
 filtered2x_timema_knul_variants.vcf.gz = compressed variant (SNP) file in
 VCFv4.2 format. This is the filtered vcf file for *Timema knulli* with
 78,404 SNPs and 76 individuals. filtered2x_timema_podu_variants.vcf.gz =
 compressed variant (SNP) file in VCFv4.2 format. This is the filtered vcf
 file for *Timema podura* with 14,433 SNPs and 244 individuals.
 filtered2x_timema_popp_variants.vcf.gz = compressed variant (SNP) file in
 VCFv4.2 format. This is the filtered vcf file for *Timema poppensis* with
 35,010 SNPs and 116 individuals. ## Sharing/Access information Links to
 other publicly accessible locations of the data: * The raw
 genotyping-by-sequencing data that were reanalyzed here are available from
 the NCBI SRA ([Accession =
 PRJNA356405](https://www.ncbi.nlm.nih.gov/bioproject/356405)).