Relaxed risk of predation drives parallel evolution of stickleback behaviour

The occurrence of similar phenotypes in multiple independent populations (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at the genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviours between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioural traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that habitat divergence in behaviour is aligned with the response to relaxation of predation pressure. Finally, we show that this alignment is found across multiple pairs of populations, and that the relaxation of predation pressure has likely driven parallel evolution of behaviour in this species.

Species-environment relationships of fish and map-based variables in small boreal streams: linkages with climate change and bioassessment

Species-environment relationships were studied between the occurrence of 13 fish and lamprey species and 9 mainly map-based environmental variables of Finnish boreal small streams. A self-organizing map (SOM) analysis showed strong relationships between the fish species and environmental variables in a single model (explained variance 55.9%). Besides basic environmental variables such as altitude, catchment size, and mean temperature, landcover variables were also explored. A logistic regression analysis indicated that the occurrence probability of brown trout, Salmo trutta L., decreased with an increasing percentage of peatland ditch drainage in the upper catchment. Ninespine stickleback, Pungitius pungitius (L.), and three-spined stickleback, Gasterosteus aculeatus L., seemed to benefit from urban areas in the upper catchment. Discovered relationships between fish species occurrence and land-use attributes are encouraging for the development of fish-based bioassessment for small streams. The presented ordination of the fish species in the mean temperature gradient will help in predicting fish community responses to climate change.

Population structure limits parallel evolution

Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e. parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically co-distributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbours less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2996 vs. 379 SNPs located within 26 vs nine genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, regions involved in freshwater adaptation in P. pungitius were younger, and often associated with reduced diversity. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.

Effects of crossover interference on genomic recombination landscape

Crossovers in meiosis increase genetic variability in gamete pool by breaking existing and creating new haplotypes, resulting in novel combinations of alleles. Frequencies of crossovers are known to differ between sexes in many species, but possible sex differences in localization of crossovers have seldom been studied in detail. Here, we address several long-standing questions regarding frequency and distribution of crossovers, with aid of in-depth analyses of ultra-dense sex-specific linkage maps of nine-spined (Pungitius pungitius) and three-spined (Gasterosteus aculeatus) sticklebacks. We observe that males have typically one crossover per chromosome, independently of the chromosome length, whereas in females the number of crossovers increases with the chromosome length, being typically more than two. We show that these differences largely explain more uniform crossover distribution of females and the fact that females have crossovers closer to the centromere. Furthermore, highly constrained crossover localization reveals that the relationship between linkage and genetic distance varies inside the chromosome. Our analyses show that recombination rate is highly heritable in females (h^2=0.56-0.65), and thus, able to evolve in response to selection. Similar results for the two species that diverged 26 million years ago suggest that our findings are general, at least in the context of stickleback fishes.

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin

Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.

New gains with a slimmer genome – An automated approach to improve reference genome assemblies

The utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome. Although the reference genomes have improved, it is evident that the assemblies could still be refined, especially in non-model study organisms. Here, we describe an integrative approach to improve contiguity and haploidy of a reference genome assembly. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.7 Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus).

Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis , whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

No evidence for individual recognition in threespine or ninespine sticklebacks ( Gasterosteus aculeatus or Pungitius pungitius )

Recognition plays an important role in the formation and organization of animal groups. Many animals are capable of class-level recognition, discriminating, for example, on the basis of species, kinship or familiarity. Individual recognition requires that animals recognize distinct cues, and learn to associate these with the specific individual from which they are derived. In this study, we asked whether sticklebacks ( Gasterosteus aculeatus and Pungitius pungitius ) were capable of learning to recognize individual conspecifics. We have used these fish as model organisms for studying selective social learning, and demonstrating a capacity for individual recognition in these species would provide an exciting opportunity for studying how biases for copying specific individuals shape the dynamics of information transmission. To test for individual recognition, we trained subjects to associate green illumination with the provision of a food reward close to one of two conspecifics, and, for comparison, one of two physical landmarks. Both species were capable of recognizing the rewarded landmark, but neither showed a preference for associating with the rewarded conspecific. Our study provides no evidence for individual recognition in either species. We speculate that the fission–fusion structure of their social groups may not favour a capacity for individual recognition.