SNP reports of Cylindropuntia species from Dartseq used for population genetics analysis
Data files
Apr 03, 2025 version files 270.11 MB
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README.md
3.45 KB
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Report_DCylin23-8324_SNP_2.csv
236.23 MB
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Report_DCylin23-8324_SNP_3.csv
33.87 MB
Abstract
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.
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