Friday, 3 December 2021

Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements

When we were assembling the 10x Genomics linked read assemblies of several rock wallabies, one of them broke the lab record for Supernova assembly quality.

10x linked reads are a bit of a dead technology now, but genomes made with them are still useful and generating insights. One example is the first rock wallaby we assembled, as a (very small) part of a team that used the draft 10x genome assembly for Petrogale penicillata as a reference to investigate chromosomal rearrangements, published online today in Molecular Biology and Evolution, one of my favourite journals.


Potter P, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ & Moritz C (accepted): Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Molecular Biology and Evolution msab333 https://doi.org/10.1093/molbev/msab333

Abstract

Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.

Thursday, 2 December 2021

EdwardsLab at Australasian Evolution Society #AUSEVO2021

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…