Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature.

No abstract

The molecular mechanisms underlying major phenotypic changes that have evolved repeatedly in nature are generally unknown. Pelvic loss in different natural populations of threespine stickleback fish has occurred by regulatory mutations deleting a tissue-specific enhancer of the Pituitary homeobox transcription factor 1 (Pitx1) gene. The high prevalence of deletion mutations at Pitx1 may be influenced by inherent structural features of the locus. Although Pitx1 null mutations are lethal in laboratory animals, Pitx1 regulatory mutations show molecular signatures of positive selection in pelvic-reduced populations. These studies illustrate how major expression and morphological changes can arise by single mutational leaps in natural populations, producing new adaptive alleles via recurrent regulatory alterations in a key developmental control gene.

Sexual antagonism, or conflict between the sexes, has been proposed as a driving force in both sex chromosome turnover and speciation. Although closely related species often have different sex chromosome systems, it is unknown whether sex chromosome turnover contributes to the evolution of reproductive isolation between species. In this study, we show that a newly evolved sex chromosome harbours genes that contribute to speciation in threespine stickleback fish (Gasterosteus aculeatus). We first identified a neo-sex chromosome system found only in one member of a sympatric species pair in Japan. We then performed genetic linkage mapping of male-specific traits important for reproductive isolation between the Japanese species pair. The neo-X chromosome harbours loci for male courtship display traits that contribute to behavioural isolation, while the ancestral X chromosome contains loci for both behavioural isolation and hybrid male sterility. Our work not only provides strong evidence for a large-X effect on reproductive isolation in a vertebrate system, but also provides direct evidence that a young neo-X chromosome contributes to reproductive isolation between closely related species. Our data suggest that sex chromosome turnover might play a greater role in speciation than previously appreciated.

Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Though this process is a major generator of biodiversity, its genetic basis remains poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but that depend on the ecological context.

Summary Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine–freshwater species-pairs, and a small number of benthic–limnetic species-pairs found within single lakes [1]. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine–freshwater or benthic–limnetic species-pairs. Surveying 34 global populations with 1159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detect large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine–freshwater and benthic–limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic–limnetic species-pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants, and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species-pairs.

Explaining consistent variation in the behaviour of individuals in terms of personality differences is one of the cornerstones of understanding human behaviour but is seldom discussed in behavioural ecology for fear of invoking anthropomorphism. Recently, however, interest has begun to focus on identifying personality traits in animals and examining their possible evolutionary consequences. One major axis used to define personality traits is the shyness-boldness continuum. We examined boldness in an in situ experiment using fish from eight populations of the poeciliid Brachyraphis episcopi (also referred to as Brachyrhaphis episcopi). Fish from high-and low-predation regions within four streams that run independently into the Panama Canal were tested. Boldness scores were strongly influenced by standard length and the relative level of predation pressure in the rivers. In all four rivers, fish from high-predation areas were bolder than those from low-predation areas. Fish became increasingly shy as they grew. Animals are expected to titrate energy intake closely with predation risk and hundreds of studies support this notion (reviewed in Lima 1998). For example, when a risky patch had four times the amount of food available than a low-risk patch, fish accepted the higher risk in return for a higher foraging reward (Pitcher et al. 1988). Not all individuals in a population solve the problem in the same way, however. In laboratory assays of foraging behaviour under predation risk, there is a continuum of responses within a population of prey species, from complete recklessness to complete predator avoidance (Fraser & Huntingford 1986). These behavioural extremes correspond closely to the shyness-boldness spectrum, recognizable psychological states that exist in a diverse suite of taxa, from crustaceans to humans (Wilson et al. 1994; Gosling 2001). Although many studies have concentrated on the heritability of individual differences in temperament (Goddard & Bilharz 1985), this range of responses is also determined by life experiences (van Gestel & van Broeckhoven 2003), and, as such, should be influenced by environmental variables during ontogeny. While the two mechanisms are by no means mutually exclusive, the manner in which the environment shapes and maintains shyness-boldness traits over both evolutionary and ontogenetic timeframes has received little attention from behavioural ecologists. Comparative analyses are frequently used to address potential differences in animal behaviour caused by variable exposure to selection pressures that result from the occupation of different environments (Kamil & Balda 1990). Testing populations of the same species that occupy different habitats allows us to examine how the environment affects the determination of personality traits while minimizing the possible confounds of phylogeny.

Changing the taxonomic scale of a biotic-assemblage dataset influences our ability to detect ecological patterns. In bioassessments, a test-site’s biological community is compared against a benchmark to indicate ecosystem condition, but the taxonomic resolution needed to judge impairment reliably is the subject of much scientific debate. This paper reviews taxonomic sufficiency for freshwater benthic-macroinvertebrate bioassessments. Three main issues are discussed: (1) the ecological significance of different taxonomic aggregations; (2) trade-offs involving taxonomic detail and information content versus money, time, expertise, and data quality; and (3) sampling- and analytical-method-specific factors affecting taxonomic sufficiency. Although Species should be the default taxonomic level for bioassessments, taxonomic sufficiency is chiefly determined by a study’s purpose, and pragmatism often dictates reduced detail. When a taxonomic-minimalism approach is necessary, a quantitative criterion for taxonomic sufficiency should be specified; this criterion should be based on an optimization of cost-benefit trade-offs associated with different taxonomic scales. Mixed-level aggregations, as well as morpho-species and ecological-trait classifications should be considered in this optimization process. Looking to the future, closer ties between taxonomists and bioassessment researchers would benefit both of their disciplines. Such coordination would provide the autoecological information and better diagnostic tools (such as keys and molecular methods) needed for biomonitoring, and better (and more widespread) biomonitoring would fuel taxonomy’s resurgence.