10.5061/DRYAD.NB526
Dowle, Eddy J.
Massey University
Morgan-Richards, Mary
Massey University
Brescia, Fabrice
Axe 2 ‘Diversités biologique et fonctionnelle des Ecosystèmes’; Institut
Agronomique néo-Calédonien (IAC); Port-Laguerre BP73 98890 Païta New
Caledonia
Trewick, Steve A.
Massey University
Data from: Correlation of shell phenotype and local environment suggests a
role for natural selection in the evolution of Placostylus snails
Dryad
dataset
2015
<20 million years
Placostylus
Climate Response
Ecotypes
Contemporary Evolution
2015-07-02T16:07:04Z
2015-07-02T16:07:04Z
en
https://doi.org/10.1111/mec.13302
5384713605 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 etcSpreadsheet 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 samplesSetUpSpreadSheet.xlsxMorphometric
DataMorphometric Dataset. Coordinates and Species/Population/Code
classifiersPlacoAllinSlidV2.txtND2 Sequences Placostylus Aligned100
individuals ND2 sequence. Codes match spreadsheetND2Placo.phyND2 assembled
GeneAssembly of placostylus mtDNA reads. Covers ND2, CO1, ND4,
ND3,COX3ND2assembledGene.fastaMain SNP file STRUCTURE formatDataset of
3764 SNP structure file. Population information included in second
column.MainDataSetSTRUCTUREfile.txtNon Neutral SNP file STRUCTURE
formatResults from Bayescan non-neutral SNP loci detected. Population ID
included in STRUCTURE fileNonNeutralSNPstructure.txtEnvironmental
DataEnvironmental Data for populations used on correlation
analysisEnvirodatagrandTerreOvAlldatapops.csvLargest SNP dataset
statistics results from Stacksparameters 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.zipSTACKS dataset statistics dataset Number 2parameters
set -m 8 –N 2 –M 4 –n 3 -t. This dataset required SNP occur across all
populations at any coverageArchive.zipStructure file for sympatric
populationsSTRUCTURE file for sympatric
populationsstructureSYMPATRICpopNOSINGLESp2r5sym.txtSTACKS dataset
statistics for sympatric datasetStacks raw statistics for sympatric
datasetArchive.zipSTACKS dataset statistics dataset Number 3Raw 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 calledArchive.zipIndex_E part 1 Raw RAD readsRaw RAD reads. Barcodes
and Codes can be found in SpreadsheetArchive.zipIndex e part 2 Raw RAD
readsSee spread sheet for individual details. De multiplexed Index E part
2.Archive 2.zipIndex_F part 1 Raw RAD readsIndex_F part 1 raw RAD reads.
Codes correlate to spreadsheet.Archive.zipIndex_F part 2 Raw RAD
readsIndex_F part 2 Raw RAD reads. Codes and barcodes located in
spreadsheetArchive 2.zipIndex_G part 1 Raw RAD readsIndex_G part 1 Raw RAD
reads. Codes in spreadsheet.Archive.zipIndex_G part 2 Raw RAD readsIndex_G
part 2 Raw RAD reads. Codes in spreadsheetArchive 2.zipIndex_H part 1 Raw
RAD readsIndex_H part 1 Raw RAD reads. Codes in
SpreadsheetArchive.zipIndex_H part 2 Raw RAD readsIndex_H part 2 Raw RAD
reads. Codes in SpreadsheetArchive 2.zipIndex_I part 1 Raw RAD
readsIndex_I part 1 Raw RAD reads. Codes in spreadsheetArchive.zipIndex_I
part 2 Raw RAD readsIndex_I part 2 Raw RAD reads. Codes in
spreadsheetArchive 2.zipForward Read Genomic DNAForward Read used to
assembled partial mtDNA genome of Placostylus. Sample from Mépouiri.
Sequenced HiSeq120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-142_1.fq.gzReverse
Read Genomic DNAReverse Read. Genomic DNA
placostylus120223_I238_FCC0HH4ACXX_L5_SZAXPI005962-142_2.trimmed.paired.fq.gzRaxMLTreeBSTRAPplacoND2Raw tree file from RaxML of ND2 genePlacostylus Morphometric Data Better explainedSee 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
New Caledonia