Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails

Dowle EJ, Morgan-Richards M, Brescia F, Trewick SA

Date Published: July 2, 2015

DOI: http://dx.doi.org/10.5061/dryad.nb526

 

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Title Set Up Spread Sheet-Codes Barcodes etc
Downloaded 23 times
Description Spreadsheet describing individuals species and collection location. Second sheet describes the inline barcodes and illumina index used for demultiplexing. Third sheet has Long Lat information for samples
Download SetUpSpreadSheet.xlsx (59.98 Kb)
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Title Morphometric Data
Downloaded 22 times
Description Morphometric Dataset. Coordinates and Species/Population/Code classifiers
Download PlacoAllinSlidV2.txt (259.8 Kb)
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Title ND2 Sequences Placostylus Aligned
Downloaded 3 times
Description 100 individuals ND2 sequence. Codes match spreadsheet
Download ND2Placo.phy (84.45 Kb)
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Title ND2 assembled Gene
Downloaded 6 times
Description Assembly of placostylus mtDNA reads. Covers ND2, CO1, ND4, ND3,COX3
Download ND2assembledGene.fasta (6.071 Kb)
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Title Main SNP file STRUCTURE format
Downloaded 9 times
Description Dataset of 3764 SNP structure file. Population information included in second column.
Download MainDataSetSTRUCTUREfile.txt (2.027 Mb)
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Title Non Neutral SNP file STRUCTURE format
Downloaded 6 times
Description Results from Bayescan non-neutral SNP loci detected. Population ID included in STRUCTURE file
Download NonNeutralSNPstructure.txt (29.52 Kb)
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Title Environmental Data
Downloaded 5 times
Description Environmental Data for populations used on correlation analysis
Download EnvirodatagrandTerreOvAlldatapops.csv (3.198 Kb)
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Title Largest SNP dataset statistics results from Stacks
Downloaded 36 times
Description parameters set -m 8 –N 2 –M 4 –n 3 -t. A filtered version of this dataset was used in analysis in paper. This dataset required SNPs occur across 2 populations at 90% to be called.
Download Archive 2.zip (23.06 Mb)
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Title STACKS dataset statistics dataset Number 2
Downloaded 35 times
Description parameters set -m 8 –N 2 –M 4 –n 3 -t. This dataset required SNP occur across all populations at any coverage
Download Archive.zip (22.72 Mb)
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Title Structure file for sympatric populations
Downloaded 4 times
Description STRUCTURE file for sympatric populations
Download structureSYMPATRICpopNOSINGLESp2r5sym.txt (141.6 Kb)
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Title STACKS dataset statistics for sympatric dataset
Downloaded 33 times
Description Stacks raw statistics for sympatric dataset
Download Archive.zip (10.22 Mb)
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Title STACKS dataset statistics dataset Number 3
Downloaded 39 times
Description Raw statistics for SNP dataset number 3 (settings -m 8 –N 2 –M 4 –n 3 -t). This dataset required SNPs to occur in 90% of individuals across 3 populations before being called
Download Archive.zip (10.39 Mb)
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Title Index_E part 1 Raw RAD reads
Downloaded 41 times
Description Raw RAD reads. Barcodes and Codes can be found in Spreadsheet
Download Archive.zip (180.5 Mb)
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Title Index e part 2 Raw RAD reads
Downloaded 32 times
Description See spread sheet for individual details. De multiplexed Index E part 2.
Download Archive 2.zip (441.5 Mb)
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Title Index_F part 1 Raw RAD reads
Downloaded 37 times
Description Index_F part 1 raw RAD reads. Codes correlate to spreadsheet.
Download Archive.zip (323.7 Mb)
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Title Index_F part 2 Raw RAD reads
Downloaded 35 times
Description Index_F part 2 Raw RAD reads. Codes and barcodes located in spreadsheet
Download Archive 2.zip (306.0 Mb)
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Title Index_G part 1 Raw RAD reads
Downloaded 38 times
Description Index_G part 1 Raw RAD reads. Codes in spreadsheet.
Download Archive.zip (361.4 Mb)
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Title Index_G part 2 Raw RAD reads
Downloaded 36 times
Description Index_G part 2 Raw RAD reads. Codes in spreadsheet
Download Archive 2.zip (405.8 Mb)
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Title Index_H part 1 Raw RAD reads
Downloaded 34 times
Description Index_H part 1 Raw RAD reads. Codes in Spreadsheet
Download Archive.zip (310.7 Mb)
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Title Index_H part 2 Raw RAD reads
Downloaded 34 times
Description Index_H part 2 Raw RAD reads. Codes in Spreadsheet
Download Archive 2.zip (260.8 Mb)
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Title Index_I part 1 Raw RAD reads
Downloaded 34 times
Description Index_I part 1 Raw RAD reads. Codes in spreadsheet
Download Archive.zip (341.9 Mb)
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Title Index_I part 2 Raw RAD reads
Downloaded 37 times
Description Index_I part 2 Raw RAD reads. Codes in spreadsheet
Download Archive 2.zip (337.9 Mb)
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Title Forward Read Genomic DNA
Downloaded 3 times
Description Forward Read used to assembled partial mtDNA genome of Placostylus. Sample from Mépouiri. Sequenced HiSeq
Download 120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-14...fq.gz (1.233 Gb)
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Title Reverse Read Genomic DNA
Downloaded 7 times
Description Reverse Read. Genomic DNA placostylus
Download 120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-14...fq.gz (810.9 Mb)
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Title RaxMLTreeBSTRAPplacoND2
Downloaded 5 times
Description Raw tree file from RaxML of ND2 gene
Download RaxMLTreeBSTRAPplacoND2.tree (7.163 Kb)
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Title Placostylus Morphometric Data Better explained
Downloaded 8 times
Description See comments in file for explanation. Includes the same data as the other morphological data file but is better explained. Includes Raw and Procrustes Distance co-ordinates.
Download PlacostylusMorphometricData.xlsx (285.3 Kb)
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When using this data, please cite the original publication:

Dowle EJ, Morgan-Richards M, Brescia F, Trewick SA (2015) Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails. Molecular Ecology 24(16): 4205–4221. http://dx.doi.org/10.1111/mec.13302

Additionally, please cite the Dryad data package:

Dowle EJ, Morgan-Richards M, Brescia F, Trewick SA (2015) Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nb526
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