Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.

Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through nonallelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genomewide distribution of transposon insertions in a young hybrid lineage ("invasive Cottus", n = 11) and its parental species Cottus rhenanus (n = 17) and Cottus perifretum(n = 9) using a reference genome assembled from long single molecule pacbio reads. An inventory of transposable elements was reconstructed from the same data and annotated. Transposon copy numbers in the hybrid lineage increased in 120 (15.9%) out of 757 transposons studied here. The copy number increased on average by 69% (range: 10%-197%). Given the age of the hybrid lineage, this suggests that they have proliferated within a few hundred generations since admixture began. However, frequency spectra of transposon insertions revealed no increase in novel and rare insertions across assembled parts of the genome. This implies that transposons were added to repetitive regions of the genome that remain difficult to assemble. Future studies will need to evaluate whether recombination-based mechanisms rather than genomewide transposition may explain the majority of the recent transposon proliferation in the hybrid lineage. Irrespectively of the underlying mechanism, the observed overabundance in repetitive parts of the genome suggests that gene-rich regions are unlikely to be directly affected.

Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin.

Evolutionary dynamics of structural genetic variation in lineages of hybrid origin is not well explored, although structural mutations may increase in controlled hybrid crosses. We therefore tested whether structural variants accumulate in a fish of recent hybrid origin, invasive Cottus, relative to both parental species Cottus rhenanus and Cottus perifretum. Copy-number variation in exons of 10,979 genes was assessed using comparative genome hybridization arrays. Twelve genes showed significantly higher copy numbers in invasive Cottus compared to both parents. This coincided with increased expression for three genes related to vision, detoxification and muscle development, suggesting possible gene dosage effects. Copy number increases of putative transposons were assessed by comparative mapping of genomic DNA reads against a de novo assembly of 1,005 repetitive elements. In contrast to exons, copy number increases of repetitive elements were common (20.7%) in invasive Cottus, whereas decrease was very rare (0.01%). Among the increased repetitive elements, 53.8% occurred at higher numbers in C. perifretum compared to C. rhenanus, while only 1.4% were more abundant in C. rhenanus. This implies a biased mutational process that amplifies genetic material from one ancestor. To assess the frequency of de novo mutations through hybridization, we screened 64 laboratory-bred F2 offspring between the parental species for copy-number changes at five candidate loci. We found no evidence for new structural variants, indicating that they are too rare to be detected given our sampling scheme. Instead, they must have accumulated over more generations than we observed in a controlled cross.

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq.

Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence.

The design of a beautiful weapon: compensation for opposing sexual selection on a trait with two functions.

Male fiddler crabs, genus Uca, have one greatly enlarged claw with which they court females and threaten and fight other males. Longer claws are more effective signals but are thought to be less effective weapons because the relative closing force at the tip of the claw decreases with claw length. We studied claw morphology and fighting in Uca terpsichores and Uca beebei and found a mechanism that may resolve opposing selection for signaling and fighting ability. When males fought they delivered gripping forces not at the tips but at the tubercles on the inner margins of their claws' fingers. As claws grow, these tubercles remain relatively close to the apex of the gape. Consequently, the mechanical advantage that governs the forces that can be delivered at these tubercles decreases only slightly with increasing claw length allowing the claw to be an effective signal and a powerful weapon. Animal weapons are exceptionally diverse in form and detail of armature and the causes of this diversity are poorly understood. We suggest that the designs of weapons may often reflect compensatory patterns of growth and placement of armature that enhances the weapon's overall utility for multiple uses in competition for mates.

The strength of a female mate preference increases with predation risk.

When females search for mates and their perceived risk of predation increases, they less often express preferences for males that use conspicuous courtship signals, relaxing sexual selection on production of these signals. Here, we report an apparent exception to this general pattern. Courting male fiddler crabs Uca beebei sometimes build pillars of mud at the openings to their burrows in which crabs mate. Females visit several males before they choose a mate by staying and breeding in their burrows, and they preferentially visit males with pillars. Previous studies suggested that this preference is based on a visual orientation behaviour that may reduce females' risk of predation while searching for a mate. We tested this idea by determining whether the female preference for males with pillars increases with perceived predation risk. We attracted avian predators to where crabs were courting and measured the rates that sexually receptive females visited courting males with and without mud pillars. Under elevated risk, females continued to search for mates and they showed a stronger relative preference for males with pillars. Thus, when predation risk is high, females may continue to express preferences that are under natural selection because they help females avoid predation, strengthening sexual selection for use of the preferred signal.