Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes

Yakimowski SB, Barrett SCH

Date Published: June 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.gs7k6

 

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Title Clonality.Sagittaria.Sexclones
Description For 11 dioecious populations there is a worksheet with SSR data formatted for GenAlEx; each dioecious populations is named “d popname”. To the right of the raw data worksheet is an output sheet “MS”. On the left is the orginal GenAlEx output – the important column is ‘Label’ which labels samples with identical multilocus genotypes with the same label. To the right the data is sorted by sample ID and the sex phenotype is provided for each sample for which sex phenotype was observed in the field. Below this sex phenotypes (f, h, m) are tallied for calculation of phenotypic sex ratio.
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Title SexCloneSummary
Description This file summarizes the sex of each clone from Clonality.Sagittaria.Sexclones.xls. Within each population’s worksheet each line represents a clone for which sex phenotype is known. Genotypic sex ratio is calculated based on these assignments. The final column “Clone.Size.Area” is the estimate of area covered (m2) by each clone (calculated by GenAlEx, see Clonality.Sagittaria.SexclonesArea.xls).
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Title SexCloneSummary
Description This file summarizes phenotypic and genotypic sex ratio for 11 dioecious populations. It is used for the R analysis of correlation between phenotypic and genotypic sex ratio. Popn – population code. Lat – Latitude in degrees N. Long – Longitude in degrees W. Ph.Num.f – number of ramets phenotyped as female (in field). Ph.Num.h - number of ramets phenotyped as hermaphrodite (in field). Ph.Num.m - number of ramets phenotyped as male (in field). Ph.Num.hm - number of ramets phenotyped as hermaphrodite or male (in field). Ph.Num.fh - number of ramets phenotyped as female of hermaphrodite (in field). Ph.Total – total number of ramets sex phenotyped (in field). Ph.Freq.f - proportion of ramets phenotyped as female (in field). Ph.Freq.h - proportion of ramets phenotyped as hermaphrodite (in field). Ph.Freq.m - proportion of ramets phenotyped as male (in field). G.Num.f - number of female multilocus genotypes. G.Num.h - number of hermaphrodite multilocus genotypes. G.Num.m - number of male multilocus genotypes. G.Total – total number of multilocus genotypes with known sex phenotype. G.Freq.f - proportion of multilocus genotypes female. G.Freq.h - proportion of multilocus genotypes hermaphrodite. G.freq.m - proportion of multilocus genotypes male. Gcorr.Num.f.corr - number of female multilocus genotypes (corrected for by scoring error / mutations). G.Num.m.corr - number of male multilocus genotypes (corrected for by scoring error / mutations). G.Total.corr – total number of multilocus genotypes (corrected for by scoring error / mutations). G.Freq.f.corr - proportion of multilocus genotypes female (corrected for by scoring error / mutations). G.freq.m.corr – proportion of multilocus genotypes male (corrected for by scoring error / mutations).
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Title CloneSize_FvsM
Description Input file for R analysis – comparison of clone size between female and male clones in 11 dioecious populations. Each line contains information on a single multilocus genotype. Popn – population ID. Clone.ID. Clone.Sex. Clone.Size.Num – number of ramets assigned to the multilocus genotype. Clone.Size.NumNot – number of ramets assayed not assigned to this multilocus genotype . Total.Clone.Num – total number ramets assayed in population. Clone.Size.Ppn – proportion of ramets assigned to multilocus genotype
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Title CloneSize_byClone_GenoDive_flw
Description Input file for R analysis – comparison of clone size between female and male clones in 11 dioecious populations. Each line contains information on a single multilocus genotype. This data file was made following clone assignments corrected for scoring errors / mutations (GenoDive). Popn – population ID. Threshold – threshold genetic distance (GenoDive, see Supplement 3) . ind. Clones. Clone.Sex. Clone.Size.Num - number of ramets assigned to the multilocus genotype . Clone.Size.NumNot - number of ramets assayed not assigned to this multilocus genotype. Total.Clone.Num - total number ramets assayed in population. Clone.Size.Ppn - proportion of ramets assigned to multilocus genotype
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Title Clonality.Sagittaria.SexclonesArea
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Title CloneArea_FvsM
Description Input file for R analysis of clone size by sex. Each line is a multilocus genotype. Popn – population code. Lat – Latitude in degrees N. Long – Longitude in degrees W. Clone.ID. Clone.Sex. Clone.Size.Num – number of ramets assigned to the multilocus genotype. Clone.Size.Area-no1s - area (m2) of each multilocus genotype for which more than 1 ramet was assigned; ramets with unique genotypes are NA. Clone.Size.Area-all - area (m2) of each multilocus genotype; single ramets with unique genotypes were assigned a value of 0.1
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Title CloneFlwFreq
Downloaded 1 time
Description SampleNo – original sample number. Popn – population code. Lat – latitude in degrees N. Long – longitude in degrees W. Genotype. Label – clone ID. Clone.Sex. Num.Ramets.Flw - number of ramets associated with multilocus genotype observed flowering (in field). Num.Ramets - number of ramets associated with multilocus genotype. Num.Ramets.NonFlw - number of ramets associated with multilocus genotype not observed flowering (in field). (The following are same as above but NA for genotypes associated with single ramet). Num.Ramets.Flw.1. Num.Ramets.NonFlw.1. Ppn.Ramets.Flw.1. Num.Ramets – number of ramets associated with multilocus genotype. Num.Ramets.Flw – number of ramets associated with multilocus genotype observed flowering (in field) . Num.Ramets.NonFlw- number of ramets associated with multilocus genotype not observed flowering (in field). Ppn.Ramets.Flw – proportion of ramets associatied with multilocus genotype observed flowering (in field)
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Title CloneSize_byClone_GenoDive_flwfreq
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Title Clonality.Sagittaria.IDclones
Description Raw clone assignments for fine-scale sampling of 10 monoecious and 11 dioecious populations. The raw data for each population is formatted for GenAlEx; dioecious populations are labeled ‘d popname’ and monoecious populations are labeled ‘m popname’. To the right of each raw data worksheet is the GenAlEx output ‘MS’ file. From the raw output calculations of clone size are shown in columns to the right; mean for the population appears at the bottom.
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Title ClonalDiversity
Description Popn – population ID. Sex.System. Location – south (s) or north (n). Lat – latitude in degrees N. Long – longitude in degrees W. G – number of multilocus genotypes per population (raw clone assignments). G_corr - number of multilocus genotypes per population (corrected for scoring error/mutations). G_1_corr – (G_corr) minus one. N – number of ramets genotyped. G_N – G divided by N. G_1 – G minus one. N_1 – N minus one. N_1_G_1 – (N minus 1) minus (G minus 1). N_1_G_1_corr – (N_corr minus 1) minus (G_corr minus 1). R_corr - genotypic diversity corrected for scoring error / mutations, R - genotypic diversity (calculated from raw data)
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Title Psex-correction
Description Modified output from GenClone. Column “Psex(Fis)” shows Psex for each clone, corrected by Fis. Column L “Num.ramets” shows the number of ramets associated with the multilocus genotype. Column O “Corr.num.ramets.w1s.Int” shows the number of ramets associated with the multilocus genotype, corrected by Psex. Rows highlighted in this column show a decrease from column L of at least 1. Only 4 rows (clones) show this: (CTP-ON) row 4, row 14, (TRL-ON) row 130, row 136. Only the relevant populations showing any Psex values <0.05 are shown in this file.
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Title CloneArea_MvsD
Description Input file (for R) for analysis of clone area between monoecious and dioecious populations. Popn – populations ID . Sex.System – M for monoecious, D for dioecious . Lat – latitude in degrees N. Long – latitude in degrees W. Clone.Genotype – genotype ID. Area – area of genotype in metres-squared.
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Title Spatial_MvsD
Description Popn – population ID. Sex.System = M for monoecious, D for dioecious. Lat – latitude in degrees N. Long – longitude in degrees W. Clonal.subrange – mean clonal subrange calculated by GenClone. Ac – Aggregation index (GenClone). P.Ac – P value associated with Ac. Total.Locations – total number of spatial locations surveyed in field. Num.Occupied – number of spatial locations occupied by a ramet. Num.Not.Occupied – number of spatial location not occupied by a ramet. Ppn.Occupied – proportion of spatial positions surveyed occupied by a ramet
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Title InputFiles
Description Self extracting Stuffin folder of input files (.txt) for each monoecious and dioecious population for GenClone analysis. Data consists of SSR genotype data and spatial positions of each sample.
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Title GenoDive
Downloaded 2 times
Description Self extracting stuffit folder of input files formatting for GenoDive. One file for each monoecious population. For each dioecious population there is one file for the fine-scale samples, plus one file (population name + 'f" for flowering) that contains fine-scale plus extra flowering samples. PDFs of genetic distance threshold choice are also in this folder.
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Title GenCloneFiles
Description Self-extracting stuff-it folder with GenClone output files for each monoecious and dioecious population (separate folder for each population).
Download GenCloneFiles.sea (2.719 Mb)
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Title MvsD_Analyses
Description Word document with R script and output of analyses comparing genotypic diversity, clone size, and clone area between moneocious and dioecious populations.
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Title Dioecious_Analyses
Description Analysis in R of phenotypic vs. genotypic sex ratio; comparison of size, area and flowering frequency of female vs. male clones in 11 dioecious populations.
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When using this data, please cite the original publication:

Yakimowski SB, Barrett SCH (2014) Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes. Molecular Ecology 23(12): 2914-2928. http://dx.doi.org/10.1111/mec.12791

Additionally, please cite the Dryad data package:

Yakimowski SB, Barrett SCH (2014) Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gs7k6
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