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Data from: Genetic and ecogeographic controls on species cohesion in Australia’s most diverse lizard radiation

Citation

Prates, Ivan et al. (2021), Data from: Genetic and ecogeographic controls on species cohesion in Australia’s most diverse lizard radiation, Dryad, Dataset, https://doi.org/10.5061/dryad.jm63xsjbq

Abstract

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.

Methods

Brief description of the methods for data collection:

Climatic data and climatic niche estimation

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 Ctenotus, 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.

Generation of genetic data

To delimit OTUs, estimate isolation-by-distance, and infer phylogenetic relationships in Ctenotus, 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 Ctenotus, 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. 

Usage Notes

The following information is provided:

  1. Sample information;

  2. Filtered and assembled genetic (ddRAD) data;

  3. Climatic and biome data extracted from the localities of sampled individuals or taxon range polygons;

  4. Outputs from phylogenetic, genetic structure, and OTU delimitation analyses;

  5. Outputs and intermediate files generated during the estimation of geographic range size and climatic niche breadth for Australian squamate taxa and Ctenotus OTUs;

  6. Outputs and intermediate files generated during the estimation of genetic isolation-by-distance and expected heterozygosity for Ctenotus 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.

Funding

National Science Foundation, Award: DEB 1754398