Flinders University
DataFiles_Mssplendida_Rainforest_Riverscape.zip (15.92 MB)


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posted on 2023-03-14, 04:11 authored by Katie GatesKatie Gates, Jonathan SandovalJonathan Sandoval, Chris BrauerChris Brauer, Peter Unmack, Martin Laporte, Louis Bernatchez, Luciano B. Beheregaray


"Environmental selection, rather than neutral processes, best explain patterns of diversity in a tropical rainforest fish"


Katie Gates, 

Jonathan Sandoval-Castillo, 

Chris J. Brauer, 

Peter J. Unmack, 

Martin Laporte, 

Louis Bernatchez, 

Luciano B. Beheregaray


Luciano Beheregaray (luciano.beheregaray@flinders.edu.au) 


#1: "MSSplendida_Sampling_And_Environmental_Data.csv"

- Comma-delimited spreadsheet containing location-specific sampling and environmental data for Melanotaenia splendida splendida*

- Fields include:

Date (sampling date)

Location (sampling location)

Code (sampling location code used for individual IDs in other data files)

Catchment (river drainage of sampling location)

Latitude (latitude of sampling location)

Longitude (longitude of sampling location)

Collected n (sample size of collected individuals)

Final n (DNA) (sample size of final SNP dataset)

Final n (Morpho) (sample size of final morphometric dataset)

Final n (GxPxE) (sample size of overlapping datasets used for genotype x phenotype x environment analysis)

STRANNTEMP (average annual mean temperature (decrees celsius))

STRANNRAIN (average annual mean rainfall (mm))

RUNSUMMERMEAN (average summer mean runoff (ML))

RDI (river disturbance index (index: 0-1))

ASPECT (stream segment aspect (degrees))

STRDENSITY (stream density; total length of upstream segments calculated for the segment pour-point (km/km^2))

*NOTE: Additional metadata describing the environmental data can be accessed at http://www.ga.gov.au/scientific-topics/water/national-surface-water-information

#2: "MSSplendida_Full_SNP_Dataset.vcf"

- VCF file containing the 14,540 SNP genotypes identified for 210 Melanotaenia splendida splendida individuals, used as a basis for all downstream genomic analyses

- A description of data fields can be accessed at https://samtools.github.io/hts-specs/VCFv4.2.pdf

#3: "MSSplendida_Morphometric_Landmarks_And_Size.csv"

- Comma-delimited spreadsheet containing coordinates (x,y) for 18 morphometric landmarks, as well as centroid size, for individuals used in geometric morphometric and GxPxE analyses 


#1: "RDA_GEA"

- Folder containing R code and input files for genotype-environment association (GEA) RDA

#2: "RDA_PEA"

- Folder containing R code and input files for phenotype-environment association (PEA) RDA

#3: "RDA_GxPxE"

- Folder containing R code and input files for genotype-phenotype-environment association (GxPxE) RDA


Australian Research Council (DP150102903 and FT130101068)

Royal Society of South Australia for the Advancement of Science

Flinders University Student Association Development Grant


Primary contact