Whole-chromosome hitchhiking driven by a male-killing endosymbiont.

Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences

Population genomics of speciation and admixture

The application of population genomics to the understanding of speciation has led to the emerging field of speciation genomics. This has brought new insight into how divergence builds up within the genome during speciation and is also revealing the extent to which species can continue to exchange genetic material despite reproductive barriers. It is also providing powerful new approaches for linking genotype to phenotype in admixed populations. In this chapter, we give an overview of some of the methods that have been used and some of the novel insights gained. We also outline some of the pitfalls of the most commonly used methods and possible problems with interpretation of the results

A Genomic Perspective on the Generation and Maintenance of Genetic Diversity in Herbivorous Insects

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects

An overview of arthropod genomics, mitogenomics, and the evolutionary origins of the arthropod proteome

Arthropods represent the largest majority of animal biodiversity and include organisms of economic interest and key model species. It is thus unsurprising that the genome of an arthropod, the fruit fly Drosophila melanogaster, was among the very first to be sequenced (Adams et al. 2000) and that to date, about 21 Drosophila genomes as well as a variety of other arthropod genomes have been sequenced. Despite this promising start, current sampling is biased towards economically relevant species, and a suitable close outgroup to the arthropods, which is necessary to polarise genomic studies, is still missing. Among the suitable outgroups to the Arthropoda, the Nematoda represent one of the largest components of the extant animal biomass, and their economic importance is comparable to that of the more biodiverse arthropods. As with the Arthropoda, the importance of the nematodes is reflected in the fact that the very first animal genome to be sequenced was that of the nematode Caenorhabditis elegans (The C. elegans genome consortium 1998). Despite the nematodes being phylogenetically close to the arthropods (Aguinaldo et al. 1997; Copley et al. 2004; Dopazo and Dopazo 2005; Philippe et al. 2005; Irimia et al. 2007; Roy and Irimia 2008; Dunn et al. 2008; Belinky et al. 2010; Hejnol et al. 2009; Holton and Pisani 2010), this group is composed of highly derived species, both genetically and morphologically. Accordingly, their genomes are unlikely to be of great utility in understanding arthropod genome evolution. Some genomic data (mostly in the form of transcriptomes) are now available for other smaller ecdysozoan phyla, and some genomes (Priapulida and Tardigrada) are on the horizon. Nonetheless, enough genomic information is now available for the Arthropoda (Table 3.1) to justify an investigation into the evolution of their genome. Such an analysis, however, is intimately dependent on the availability of a robust phylogenetic background, and to a lesser extent, robust divergence times for the nodes in the background phylogen