Marine phytoplankton play essential roles in global primary production and biogeochemical cycles. Yet, the evolutionary genetic underpinnings of phytoplankton adaptation to complex marine and coastal environments, where many environmental variables fluctuate and interact, remain unclear. We combined population genomics with experimental transcriptomics to investigate the genomic basis underlying a natural evolutionary experime...

The scale of the Deepwater Horizon disaster was and is unprecedented: geographic extent, pollutant amount, countermeasure scope, and of most relevance to this Research Topic issue, range of ecotypes affected. These ecotypes include coastal/nearshore, continental shelf, deep benthic, and open-ocean domains, the last of which is the subject of this synthesis. The open-ocean ecotype comprises ~90% of the volume of the Gulf of Mex...

Natural populations often exist in spatially diverse environments and may experience variation in the strength and targets of natural selection across their ranges. Drosophila provides an excellent opportunity to study the effects of spatially varying selection in natural populations, as both Drosophila melanogaster and Drosophila simulans live across a wide range of environments in North America. Here, we characterize pattern...

Inversion polymorphisms are responsible for many ecologically important phenotypes and are often found under balancing selection. However, the same features that ensure their large role in local adaptation—especially reduced recombination between alternate arrangements—mean that uncovering the precise loci within inversions that control these phenotypes is unachievable using standard mapping approaches. Here, we take advantage...

Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree–species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider durin...

Because they are considered rare, balanced polymorphisms are often discounted as crucial constituents of genome‐wide variation in sequence diversity. Despite its perceived rarity, however, long‐term balancing selection can elevate genetic diversity and significantly affect observed divergence between species. Here, we discuss how ancestral balanced polymorphisms can be “sieved” by the speciation process, which sorts them unequ...

Gene flow can impede the evolution of reproductive isolating barriers between species. Reinforcement is the process by which prezygotic reproductive isolation evolves in sympatry due to selection to decrease costly hybridization. It is known that reinforcement can be prevented by too much gene flow, but we still do not know how often have prezygotic barriers evolved in the presence of gene flow or how much gene flow can occur...

Little is known about the physiological responses and genetic mutations associated with reproductive isolation between species, especially for postmating prezygotic isolating barriers. Here, we examine changes in gene expression that accompany the expression of ‘unilateral incompatibility’ ( UI )—a postmating prezygotic barrier in which fertilization is prevented by gamete rejection in the reproductive tract [in this case of p...

Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next‐generation sequencing data sets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the si...

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al . ( Science , 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex...

The metaphor of ‘genomic islands of speciation’ was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower lev...

Divergent selection based on aquatic larval ecology is a likely factor in the recent isolation of two broadly sympatric and morphologically identical African mosquito species, the malaria vectors Anopheles gambiae and An. coluzzii . Population‐based genome scans have revealed numerous candidate regions of recent positive selection, but have provided few clues as to the genetic mechanisms underlying behavioural and physiologica...

The African malaria mosquito Anopheles gambiae is polymorphic for chromosomal inversion 2La, whose frequency strongly correlates with degree of aridity across environmental gradients. Recent physiological studies have associated 2La with resistance to desiccation in adults and thermal stress in larvae, consistent with its proposed role in aridity tolerance. However, the genetic basis of these traits remains unknown. To identif...

Populations of the malaria mosquito, Anopheles gambiae , are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high‐density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in nea...

A speciation process is ongoing in the primary vector of malaria in Africa, Anopheles gambiae . Assortatively mating incipient species known as the M and S forms differentially exploit larval breeding sites associated with different ecological settings. However, some ongoing gene flow between M and S limits significant genomic differentiation mainly to small centromere‐proximal regions on chromosomes X and 2L, termed ‘speciati...