DOI: 10.5281/zenodo.13225943
title: Sequencing data from: Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula

description: Premise: Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.Methods: We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.Results: Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species.Conclusions: Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida.
description: Fresh leaf samples of 120 plants were collected from 20 locations across the species range (Figure 1; Appendix S1: Table S1) and dried in silica gel. We extracted DNA from 100 mg of each dried sample using the Qiagen DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). DNA quality and concentration were evaluated using GelRed 1.5% agarose gels (Sigma‐Aldrich, St. Louis, MO, USA) and a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).

Genomic DNA was converted into nextRAD sequencing libraries (SNPsaurus LLC, Eugene, OR, USA) as described by Russello et al. (2015). Briefly, DNA was fragmented with Nextera reagent (Illumina, San Diego, CA, USA), which also ligates short adapter sequences to the ends of the fragments. The reaction was scaled to fragment 20 ng of DNA, and 50ng of DNA was added to compensate for DNA degradation and to increase the number of fragments. The DNA was amplified for 27 cycles at 74°C. The libraries were sequenced on a HiSeq. 4000 150bp single‐end line (University of Oregon, Eugene, OR, USA). The data set was enriched with 40 raw sequences of Y. valida (NCBI SRA: SRR11514779) and 40 of Y. capensis (NCBI SRA: SRR11514778) from Arteaga et al. (2020) that were generated for previous population genetic analyses using the same extraction and sequencing protocols described here, thus representing a consistent data set across analyses.

In order of use (described in the article Methods): FastQC, MultiQC, BBTools, Stacks, GBS_SNP_filter.sh, Plink 1.9, ADMIXTURE, R, iTOL 6, GENODIVE (or VCFtools, Genepop, Arlequin), PGDSpider, pixy, PCAdapt, LFMM, δaδi, δaδi_pipeline, Stacks_pipeline, easySFS, Bowtie, Samtools, ANGSD, seqtk, RAxML-ng, BEAST, and MAFFT.