DOI: 10.5061/dryad.qbzkh18v7
title: SNP reports of Cylindropuntia species from Dartseq used for population genetics analysis

description: Dioecy, the separation of sexes, is found in 6% of flowering plants. One
 widely known hypothesis suggests that it is an adaptation to mitigate
 inbreeding. A contrary hypothesis suggests that dioecy is an evolutionary
 dead-end. However, contrasting patterns emerged from population genetic
 studies that compared the genetic diversity between dioecy vs
 hermaphroditic species. Specifically, in Silene it was shown that
 dioecious species possess higher genetic diversity than hermaphroditic
 species, challenging the dead-end hypothesis. To evaluate whether dioecy
 is indeed advantageous, further studies are needed in systems with diverse
 sexual systems such as the genus Cylindropuntia (Cactaceae). It
 encompasses species with sexual separation observed solely in polyploids.
 Notably, these polyploids (C. wolfii and C. chuckwallensis) share similar
 ploidy, flower colors, and geographic proximity raising speculation about
 their shared ancestry. Moreover C. wolfii has been reported to have a low
 seed production highlighting the need to assess the reproductive
 strategies of the species. Our first goal was to compare the genetic
 diversity patterns among species with different sexual systems within the
 genus Cylindropuntia (Cactaceae). Our second goal was to investigate
 genetic shared ancestry among the polyploid species. As C. wolfii is
 struggling to sexually reproduce our third objective was to investigate
 whether it is dominated by clonal reproduction diversity parameters and
 population structure. The clonality of C. wolfii was assessed using a
 combination of field survey and genetic analysis. The pattern of genetic
 diversity in species with diverse sexual systems did not support the
 dead-end hypothesis. The field survey of C. wolfii revealed no seed
 recruitment but the genetic analysis on the current adult plants showed
 low signs of clonality suggesting that this species has recently shifted
 to clonal reproduction. Results showed that overall, this genus had low
 genetic diversity and high differentiation implying that it is vulnerable
 to environmental threats.
description: # SNP reports of Cylindropuntia species from Dartseq used for population
 genetics analysis
 [https://doi.org/10.5061/dryad.qbzkh18v7](https://doi.org/10.5061/dryad.qbzkh18v7) ## Description of the data and file structure This dataset was generated using DArTseq, a reduced-representation sequencing method, to investigate genetic diversity and population structure in Cylindropuntia species. Fragments of cacti were collected from 251 individuals and SNPs were identified to assess genetic differentiation and population connectivity. ### Files and variables File name: Report_DCylin23-8324_SNP_2.csv and Report_DCylin23-8324_SNP_3.csv\ File type: SNP File description: SNP 2 Rows Format: Each allele scored in a binary fashion ("1"=Presence and "0"=Absence). Heterozygotes are therefore scored as 1/1 (presence for both alleles/both rows) ### Metadata columns in the file: AlleleID - Unique identifier for the sequence in which the SNP marker occurs AlleleSequence - In 1 row format: the sequence of the Reference allele. In 2 rows format: the sequence of the Reference allele is in the Ref row, the sequence of the SNP allele in the SNP row AvgCountRef - The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row AvgCountSnp - The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row AvgPIC- The average of the polymorphism information content (PIC) of the Reference and SNP allele rows CallRate - The proportion of samples for which the genotype call is either "1" or "0", rather than "-"  CloneID - Unique identifier for the sequence in which the SNP marker occurs FreqHets - The proportion of samples which score as heterozygous FreqHomRef - The proportion of samples which score as homozygous for the Reference allele FreqHomSnp - The proportion of samples which score as homozygous for the SNP allele OneRatioRef - The proportion of samples for which the genotype score is "1", in the Reference allele row OneRatioSnp - The proportion of samples for which the genotype score is "1", in the SNP allele row PICRef - The polymorphism information content (PIC) for the Reference allele row PICSnp - The polymorphism information content (PIC) for the SNP allele row RepAvg - The proportion of technical replicate assay pairs for which the marker score is consistent SNP - In 2 rows format: this column is blank in the Reference row, and contains the base position and base variant details in the SNP row. In 1 row format: contains the base position and base variant details  SnpPosition - The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs TrimmedSequence - Same as the full sequence, but with removed adapters in short marker tags "-" missing data Header rows: 1 - Order number where sample belongs to - important for multi-orders reports 2 - DArT plate barcode 3 - client plate barcode 4 - well row position 5 - well column position 6 - sample comments 7 - genotype name ## Code/software Microsoft excel ## Access information NA