Biology subjects

Chris D. Jiggins

Publications and source records attributed to Chris D. Jiggins.

3 recordsLinked to original sources

bioRxiv2015

Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridise in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. Firstly, we whole genome sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Secondly, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Thirdly, we incorporated ~20x coverage of Pacific Biosciences sequencing and scaffolded the haploid genome using an assembly of this long read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an L50 of 2.1 Mb, an N50 of 34 and with 99% of the genome placed and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million years.

Genomics↗

bioRxiv2015

Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

Documenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterflies Heliconius melpomene and Heliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.

Evolutionary Biology↗

bioRxiv2013

Evaluating the use of ABBA-BABA statistics to locate introgressed loci

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Pattersons D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic [Formula] a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. [Formula] is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and [Formula] outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

Evolutionary Biology↗