DOI: 10.5061/dryad.jm63xsjbq
title: Data from: Genetic and ecogeographic controls on species cohesion in Australia’s most diverse lizard radiation

description: Species vary extensively in geographic range size and climatic niche
 breadth. If range limits are primarily determined by climatic factors,
 species with broad climatic tolerances and those that track geographically
 widespread climates should have large ranges. However, large ranges might
 increase the probability of population fragmentation and adaptive
 divergence, potentially decoupling climatic niche breadth and range size.
 Conversely, ecological generalism in widespread species might lead to
 higher gene flow across climatic transitions, increasing species’ cohesion
 and thus decreasing genetic isolation-by-distance (IBD). Focusing on
 Australia’s iconic Ctenotus lizard radiation, we ask whether species range
 size scales with climatic niche breadth and the degree of population
 isolation. To this end, we infer independently evolving operational
 taxonomic units (OTUs), their geographic and climatic ranges, and the
 strength of IBD within OTUs based on genome-wide loci from 722 individuals
 spanning 75 taxa. Large-ranged OTUs were common and had broader climatic
 niches than small-ranged OTUs; thus, large ranges do not simply result
 from passive tracking of widespread climatic zones. OTUs with larger
 ranges and broader climatic niches showed relatively weaker IBD,
 suggesting that large-ranged species might possess intrinsic attributes
 that facilitate genetic cohesion across large distances and varied
 climates. By influencing population divergence and persistence, traits
 that affect species cohesion may play a central role in large-scale
 patterns of diversification and species richness.
description: <strong>Brief description of the
 methods for data collection:</strong>
 <em>Climatic data and climatic niche
 estimation</em> We generated
 2,000 random points within the range of Australian lizard and snake taxon
 and rarified these points to ensure a minimum distance of 5 km. We used
 these points to extract values of four bioclimatic variables: annual mean
 temperature, temperature seasonality, annual precipitation, and
 precipitation seasonality. We then used these data to estimate a climatic
 hypervolume for each taxon as an estimate of climatic niche breadth. As a
 metric of range size, we used the area of each taxon polygon. To estimate
 climatic niches for operational taxonomic units (OTUs) in
 <em>Ctenotus</em>, we extracted the same climatic information
 from the collection sites of individuals. We estimated each OTU’s range
 size based on the area of a convex hull defined by the outermost
 collecting sites. <em>Generation of genetic
 data</em> To delimit OTUs,
 estimate isolation-by-distance, and infer phylogenetic relationships in
 <em>Ctenotus</em>, we generated a double-digest restriction
 associated DNA (ddRAD) dataset. Briefly, genomic DNA extractions were
 digested with the restriction enzymes EcoRI and MspI, and the resulting
 fragments were tagged with individual barcodes, PCR-amplified,
 multiplexed, and sequenced on an Illumina HiSeq or NovaSeq platform. We
 used the ipyrad pipeline to de-multiplex and assign reads to individuals
 based on sequence barcodes, allowing no nucleotide mismatches from
 individual barcodes. The number of paired-end reads ranged from ~100
 thousand to ~27 million per sample, with a read length of 100 base pairs.
 Using ipyrad, we performed de novo read assembly (clustering threshold =
 0.90), aligned reads into loci, and called SNPs. A minimum Phred quality
 score (= 33), sequence coverage (= 6x), read length (= 35 bp), and maximum
 proportion of heterozygous sites per locus (= 0.5) were enforced while
 ensuring that variable sites had no more than two alleles within an
 individual (i.e., a diploid genome). To estimate OTUs and isolation-by-distance in
 <em>Ctenotus</em>, a single SNP was extracted from each locus
 to minimize sampling of linked SNPs. We then filtered out SNPs whose minor
 allele frequency was lower than 0.05. To estimate phylogenetic
 relationships, we generated in ipyrad a dataset composed of 83,083 SNPs,
 each present in at least 50% of the samples. 
description: The following information is provided: 
 Sample
 information; Filtered and assembled genetic (ddRAD)
 data; Climatic and biome data extracted from the
 localities of sampled individuals or taxon range polygons;
 Outputs from phylogenetic, genetic structure, and
 OTU delimitation analyses; Outputs and
 intermediate files generated during the estimation of geographic range
 size and climatic niche breadth for Australian squamate taxa and
 <em>Ctenotus</em> OTUs; Outputs and
 intermediate files generated during the estimation of genetic
 isolation-by-distance and expected heterozygosity for<em>
 Ctenotus</em> OTUs; Raw
 read data for the newly sequenced samples were deposited in the Sequence
 Read Archive and can be retrieved at:
 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA755251
 Please send questions to ivanprates [at]
 gmail [dot] com.