Divergence in allopatry provides a simple null model of speciation (Mayr, 1947). Following geographic isolation and given enough time, reproductive isolation is inevitable as incompatibilities will eventually become fixed as a result of genetic drift and/or selection (Bateson, 1909;Dobzhansky, 1937;Muller, 1942). Taxa that evolved partial reproductive isolation in allopatry may come into secondary contact as a result of range shifts and-depending on their degree of reproductive isolation and niche overlap-either form a contact zone or invade each other's range (Barton, 1985;Pigot, 2013). If allopatric divergence dominates speciation, then local alpha diversity for a given clade cannot accrue until secondary sympatry is achieved (Weir & Price, 2011). Thus, the forces that facilitate or hamper secondary sympatry and the timescale over which this occurs have profound consequences both for speciation and for the spatial distribution of species diversity. While modern ranges only provide a snapshot of the dynamic history of range shifts, understanding the

The Pleistocene glacial cycles had a profound impact on the ranges and genetic make-up of organisms. Whilst it is clear that the current contact zones between sister taxa are secondary and have formed during the last interglacial, it is unclear when the taxa involved began to diverge. Previous estimates are unreliable given the stochasticity of genetic drift and the contrasting effects of incomplete lineage sorting and gene flow on gene divergence. We use genome-wide transcriptome data to estimate divergence for 18 sister species pairs of European butterflies showing either sympatric or contact zone distributions. We find that in most cases species divergence was initiated before the Pleistocene, substantially earlier than assumed previously, and that post divergence gene flow is restricted to contact zone pairs, although they are not systematically younger than sympatric pairs. This suggests that contact zones are not limited to early stages in the speciation process, but can involve notably old taxa.

Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the two processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We present heRho, a simple composite likelihood scheme for co-estimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at two loci. We apply heRho to simulations and data from the house mouse Mus musculus castaneus, a well studied model. Our analyses show i) that the rates of crossover and gene conversion can be accurately co-estimated at the level of individual chromosomes and ii) that previous estimates of the population scaled rate of recombination ρ = 4 Ner under a pure crossover model are likely biased.

We present a genome assembly from an individual female Pieris rapae (the small white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 256 megabases in span. The majority of the assembly is scaffolded into 26 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,390 protein coding genes.

We present a genome assembly from an individual female Aglais urticae (also known as Nymphalis urticae; the small tortoiseshell; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.