DOI: 10.5061/dryad.4mw6m90g1
title: Data from: Long-term climatic stability drives accumulation and maintenance of divergent lineages in a temperate biodiversity hotspot

description: Anthropogenic climate change is forecast to drive regional climate
 disruption and instability across the globe. These impacts are likely to
 be exacerbated within biodiversity hotspots, both due to the greater
 potential for species loss but also to the possibility that endemic
 lineages might not have experienced significant climatic variation in the
 past, limiting their evolutionary potential to respond to rapid climate
 change. We assessed the role of climatic stability on the accumulation and
 persistence of lineages in an obligate freshwater fish group endemic to
 the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426
 genomic (ddRAD-seq) markers and species distribution modelling, we
 explored the phylogeographic history of western (Nannoperca vittata) and
 little (Nannoperca pygmaea) pygmy perches, assessing population divergence
 and phylogenetic relationships, delimiting species and estimating changes
 in species distributions from the Pliocene to 2100. We identified two deep
 phylogroups comprising three divergent clusters, which showed no
 historical connectivity since the Pliocene. We conservatively suggest
 these represent three isolated species with additional intraspecific
 structure within one widespread species. All lineages showed long-term
 patterns of isolation and persistence owing to climatic stability but with
 significant range contractions likely under future climate change. Our
 results highlighted the role of climatic stability in allowing the
 persistence of isolated lineages in the SWWA. This biodiversity hotspot is
 under compounding threat from ongoing climate change and habitat
 modification, which may further threaten previously undetected cryptic
 diversity across the region.
description: # Data from: Long-term climatic stability drives accumulation and
 maintenance of divergent freshwater fish lineages in a temperate
 biodiversity hotspot ## Contents: **WPP1_5.phy**: concatenated alignment
 of 19,426 ddRAD loci across 37 samples (including four outgroup Nannoperca
 obscura samples). Used for phylogenomic analyses.
 **WPP1_5.phy.partitions**: partition file describing ends of individual
 ddRAD loci within WPP1_5.phy: used in partitioned and gene tree
 phylogenomic analyses. **WPP1_5_2.str**: Structure file of 18,177
 putatively unlinked (one SNP per ddRAD locus) SNPs across 33 samples
 (outgroup samples not included). Used for PCoA, TreeMix, and subsamples
 for SNAPP analyses. **SubsampledVittata_LowerRes.csv**: Coordinates for
 114 Nannoperca vittata individuals derived from this study and the Atlas
 of Living Australia. Coordinates have been reduced to a single decimal
 point precision to minimise risk to species of conservation concern. Used
 as input for species distribution models.
 **WPP_CurrentEnviroRasters.tif**: Stacked rasters of nine environmental
 layers under current climatic conditions used for species distribution
 models. Layers correspond to (in order): 1. bio1 = annual mean temperature
 2. bio3 = isothermality 3. bio8 = mean temperature of wettest quarter 4.
 bio9 = mean temperature of driest quarter 5. bio11 = mean temperature of
 coldest quarter 6. bio12 = annual precipitation 7. bio14 = precipitation
 of driest month 8. bio15 = precipitation seasonality 9. elevation The full
 raster stack should be read into R using the "terra" package and
 the "rast" command: ``` WPPCurrentEnviroRasters =
 terra::rast(WPP_CurrentEnviroRasters.tif) ```