Look out for some interesting talks by Edwards Lab members at this year’s Australasian Evolution Society 2021 conference, starting today:
Thursday 2nd December: 3-minute talks | 1130-1230
Kelton Cheung - Analysis of mitochondrial DNA reveals significant genetic diversity in invasive Australian cane toads
Kelton Cheung, Mark Richardson, Richard Edwards & Lee Ann Rollins
Mitochondrial DNA haplotype patterns across the native and invaded ranges can reveal the history and evolutionary trajectory of invasions. The invasion of Australia by the cane toad (Rhinella marina) has accelerated as it expanded westward. Despite this success, previous studies reported no mitochondrial genetic diversity in Australia. Here, we assembled a complete mitochondrial reference genome and haplotyped toads (N=119) from the native range and two introduced populations (Hawai’i and Australia), using whole genome and RNA-seq data. The complete R. marina mitochondrial genome consists of 18,152 base pairs with no significant gene arrangement as compared to other bufonid species. Although native range genetic diversity was much higher than that of the introduced ranges, we identified 29 haplotypes in Australia. While we did find evidence of founder effects following introduction, our results suggest there is significant genetic diversity within Australia, which may assist adaptation and invasion success in this species.
Thursday 2nd December: Selection 1 | 1415-1430
Katarina Stuart - A genetic perspective on rapid adaptation in the globally invasive European starling (Sturnus vulgaris)
Abstract coming soon…
Thursday 2nd December: Biogeography and phylogenetics | 1530-1545
Richard Edwards - DepthKopy: copy number prediction using single-copy long-read depth profiles
Richard J Edwards, Stephanie H Chen, Katarina C Stuart, Mark M Tanaka & Jason G Bragg
Gene duplication, followed by functional divergence of gene copies, is a fundamental component of genetic adaption and the evolution of novelty. Increasingly, evolutionary studies make use of the ever-expanding number of high-quality genome assemblies to characterise patterns of gene gain and loss. However, even reference genomes of the highest quality can experience assembly errors at tandemly repeated gene loci, resulting in incorrect inference of gene duplication patterns. Here, we present DepthKopy (https://github.com/slimsuite/depthkopy), which estimates the copy number for a gene, region or sequence of interest, using an estimate of single-copy sequencing depth derived from complete BUSCO genes. This is useful for identifying haplotigs, and collapsed repeat regions during genome assembly curation. Critically, for evolutionary studies of gene families, DepthKopy can identify genes for which the number of genes in the assembly does not seem to match the genome.
Friday 3rd December: Climate change and temperature | 1330-1345
Collin Ahrens - Genomic constraints of drought adaptation
Abstract coming soon…