The giant edible Placostylus snails of New Caledonia occur across a wide range of environmental conditions, from the dry southwest to the wetter central and northeastern regions. In large, slow-moving animals such as Placostylus, speciation could be assumed to be largely driven by allopatry and genetic drift as opposed to natural selection. We examined variation in shell morphology using geometric morphometrics and genetic structure within two species of Placostylus (P. fibratus, P. porphyrostomus), to determine the drivers of diversity in this group. Despite the current patchy distribution of snails on New Caledonia, both mtDNA and nuclear SNP data sets (>3000 loci) showed weak admixing between populations and species. Shell morphology was concordant with the genetic clusters we identified and had a strong relationship with local environment. The genetic data, in contrast to the morphological data, did not show concordance with climatic conditions, suggesting the snails are not limited in their ability to adapt to different environments. In sympatry, P. fibratus and P. porphyrostomus maintained genetic and morphological differences, suggesting a genetic basis of phenotypic variation. Convergence of shell shape was observed in two adjacent populations that are genetically isolated but experience similar habitat and climatic conditions. Conversely, some populations in contrasting environments were morphologically distinct although genetically indistinguishable. We infer that morphological divergence in the Placostylus snails of New Caledonia is mediated by adaptation to the local environment.
Set Up Spread Sheet-Codes Barcodes etc
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
SetUpSpreadSheet.xlsx
Morphometric Data
Morphometric Dataset. Coordinates and Species/Population/Code classifiers
PlacoAllinSlidV2.txt
ND2 Sequences Placostylus Aligned
100 individuals ND2 sequence. Codes match spreadsheet
ND2Placo.phy
ND2 assembled Gene
Assembly of placostylus mtDNA reads. Covers ND2, CO1, ND4, ND3,COX3
ND2assembledGene.fasta
Main SNP file STRUCTURE format
Dataset of 3764 SNP structure file. Population information included in second column.
MainDataSetSTRUCTUREfile.txt
Non Neutral SNP file STRUCTURE format
Results from Bayescan non-neutral SNP loci detected. Population ID included in STRUCTURE file
NonNeutralSNPstructure.txt
Environmental Data
Environmental Data for populations used on correlation analysis
EnvirodatagrandTerreOvAlldatapops.csv
Largest SNP dataset statistics results from Stacks
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.
Archive 2.zip
STACKS dataset statistics dataset Number 2
parameters set -m 8 –N 2 –M 4 –n 3 -t. This dataset required SNP occur across all populations at any coverage
Archive.zip
Structure file for sympatric populations
STRUCTURE file for sympatric populations
structureSYMPATRICpopNOSINGLESp2r5sym.txt
STACKS dataset statistics for sympatric dataset
Stacks raw statistics for sympatric dataset
Archive.zip
STACKS dataset statistics dataset Number 3
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
Archive.zip
Index_E part 1 Raw RAD reads
Raw RAD reads. Barcodes and Codes can be found in Spreadsheet
Archive.zip
Index e part 2 Raw RAD reads
See spread sheet for individual details. De multiplexed Index E part 2.
Archive 2.zip
Index_F part 1 Raw RAD reads
Index_F part 1 raw RAD reads. Codes correlate to spreadsheet.
Archive.zip
Index_F part 2 Raw RAD reads
Index_F part 2 Raw RAD reads. Codes and barcodes located in spreadsheet
Archive 2.zip
Index_G part 1 Raw RAD reads
Index_G part 1 Raw RAD reads. Codes in spreadsheet.
Archive.zip
Index_G part 2 Raw RAD reads
Index_G part 2 Raw RAD reads. Codes in spreadsheet
Archive 2.zip
Index_H part 1 Raw RAD reads
Index_H part 1 Raw RAD reads. Codes in Spreadsheet
Archive.zip
Index_H part 2 Raw RAD reads
Index_H part 2 Raw RAD reads. Codes in Spreadsheet
Archive 2.zip
Index_I part 1 Raw RAD reads
Index_I part 1 Raw RAD reads. Codes in spreadsheet
Archive.zip
Index_I part 2 Raw RAD reads
Index_I part 2 Raw RAD reads. Codes in spreadsheet
Archive 2.zip
Forward Read Genomic DNA
Forward Read used to assembled partial mtDNA genome of Placostylus. Sample from Mépouiri. Sequenced HiSeq
120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-142_1.fq.gz
Reverse Read Genomic DNA
Reverse Read. Genomic DNA placostylus
120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-142_2.trimmed.paired.fq.gz
RaxMLTreeBSTRAPplacoND2
Raw tree file from RaxML of ND2 gene
Placostylus Morphometric Data Better explained
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.
PlacostylusMorphometricData.xlsx