Genomics of adaptation revealed in threespine stickleback

Natural selection is the ultimate, but not only force underlying organismal diversity. Despite this general biological insight, our understanding of how selection targets and shapes the genome during adaptation remains incomplete and is the central quest of this thesis. My main model organism is the threespine stickleback fish (Gasterosteus aculeatus). Stickleback provide an outstanding opportunity to study adaptive evolutionary change, because marine ancestors have repeatedly colonized and adapted to different freshwater environments all over the northern hemisphere since the last glacial retreat about 12,000 years ago. Besides wild populations, I also make use of lab-raised stickleback hybrids from controlled crosses for this thesis work. Thousands of genome-wide genetic polymorphisms (i.e., genetic markers) called in marine, but predominantly in distinct lake and stream stickleback populations from different geographic locations allow me to decipher the number and position of genomic targets of selection in the early phase of adaptive divergence. I find that selection acts on many loci distributed widely across the genome. On a genomic scale, the recombination landscape along chromosomes proves to be - in concert with selection - an important factor in driving heterogeneous genetic differentiation among populations. To investigate the rate of recombination across the stickleback's genome in more detail, I use an artificially crossed second-generation (F2) population. This reveals constraints in the frequency and location of detectable recombination events (i.e., cross-overs) within the genome. For example, cross-overs prove to be more frequent in chromosome peripheries than centers. This, together with selection, results in decreased within-population genetic diversity and increased between-population differentiation in the centers of chromosomes as opposed to the peripheries. Furthermore, I show that the cessation of recombination between the heterogametic sex chromosomes occurred in independent bouts. As a consequence, I find extended genomic regions distinct in their degree of degeneration between the X and Y chromosome, so called evolutionary strata. Finally, recombination reveals to be an important determinant of other aspects of a genome, such as its nucleotide composition. Integrating theoretical modeling with targeted and genome-wide sequencing, my research further demonstrates that the inference and interpretation of genomic regions exhibiting particularly high and low population differentiation is not as straightforward as commonly believed. This is because the type of genetic variation available to selection (i.e., pre-existing vs. de novo variation) as well as the mode of adaptation (i.e., divergent vs. parallel adaptation) influence the way neutral variation is shaped by selection across the genome. I demonstrate that a genomic region of high differentiation may not necessarily be indicative of divergent selection when populations adapt in parallel to similar environments from a shared pool of genetic variation. Based on several hundreds of F2 specimens reared under standardized conditions in the laboratory, I also link variation in heritable phenotypic traits to genetic variation, a research program generally referred to as quantitative trait locus (QTL) mapping. Corroborating with the results from my genome scans within and between wild populations (indicating that adaptive divergence involves many loci widespread across the genome), QTL mapping reveals that most phenotypic traits are controlled by numerous genetic loci. In general, each of these loci explains a small fraction of the entire phenotypic trait variation. I also use high resolution SNP data to infer the demographic history of several lake and stream stickleback populations from the Lake Constance watershed (Central Europe) and demonstrate that the repeated occurrence of similar stream phenotypes are, in this particular system, better explained by an evolutionary scenario of 'ecological vicariance' rather than repeated parallel divergence. I then show how selection has shaped local and broad-scale linkage, diversity and differentiation across the genome in these populations. Interestingly, I find evidence for strong divergent selection acting on large chromosomal rearrangements I had previously detected to be important for marine vs. freshwater adaptation. This finding provides a strong case for the re-use of pre-existing genetic variation in stickleback and demonstrates that the same genomic regions can be involved in adaptive divergence between disparate ecotype pairs. Overall, I come to conclude that signatures of selection are - at various physical scales - frequent within the stickleback genome. Stickleback repeatedly use pre-existing genetic variation, shared across various geographic ranges, to adapt to similar or disparate environments. Yet, there is a substantial degree of genetic non-parallelism - at least at the level of neutral markers - that goes along with parallel phenotypic evolution. My thesis emphasizes that the reliable detection and interpretation of genomic signatures of selection requires integrating many replicate study populations within a clear-cut ecological and demographic framework, as well as complementary analytical approaches. Controlled crossing experiments and theoretical modeling are key to deriving predictions about the genomics of adaptation in the wild and to facilitate our understanding of complex biological processes and patterns

Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species.

BACKGROUND Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. RESULTS Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. CONCLUSIONS Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype-phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection

Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species

Background: Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. Results Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. Conclusions: Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype–phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection

Depth-dependent abundance of Midas Cichlid fish ( Amphilophus spp: ) in two Nicaraguan crater lakes

The Midas Cichlid species complex (Amphilophus spp.) in Central America serves as a prominent model system to study sympatric speciation and parallel adaptive radiation, since small arrays of equivalent ecotype morphs have evolved independently in different crater lakes. While the taxonomy and evolutionary history of the different species are well resolved, little is known about basic ecological parameters of Midas Cichlid assemblages. Here, we use a line transect survey to investigate the depth-dependent abundance of Amphilophus spp. along the shores of two Nicaraguan crater lakes, Apoyo and Xiloá. We find a considerable higher density of Midas cichlids in Lake Xiloá as compared to Lake Apoyo, especially at the shallowest depth level. This might be due to the higher eutrophication level of Lake Xiloá and associated differences in food availability, and/or the presence of a greater diversity of niches in that lake. In any case, convergent forms evolved despite noticeable differences in size, age, eutrophication level, and carrying capacity. Further, our data provide abundance and density estimates for Midas Cichlid fish, which serve as baseline for future surveys of these ecosystems and are also relevant to past and future modeling of ecological speciatio

De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7)

Uninformative polymorphisms bias genome scans for signatures of selection

With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular.; On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a low minor allele frequency are included in the analysis. The reason is that these 'uninformative' polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artifacts in the data (PCR and sequencing errors), as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations.; We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation

Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence

Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow (‘allele-only clustering’). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate (‘locus clustering’). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation.Science, Faculty ofOther UBCZoology, Department ofReviewedFacult

A functional trade-off between trophic adaptation and parental care predicts sexual dimorphism in cichlid fish

Although sexual dimorphism is widespread in nature, its evolutionary causes often remain elusive. Here we report a case where a sex-specific conflicting functional demand related to parental care, but not to sexual selection, explains sexual dimorphism in a primarily trophic structure, the gill rakers of cichlid fishes. More specifically, we examined gill raker length in a representative set of cichlid fish species from Lake Tanganyika featuring three different parental care strategies: (i) uni-parental mouthbrooding, whereby only one parental sex incubates the eggs in the buccal cavity; (ii) bi-parental mouthbrooding, whereby both parents participate in mouthbrooding; and (iii) nest guarding without any mouthbrooding involved. As predicted from these different parental care strategies, we find sexual dimorphism in gill raker length to be present only in uni-parental mouthbrooders, but not in bi-parental mouthbrooders nor in nest guarders. Moreover, variation in the extent of sexual dimorphism among uni-parental mouthbrooders appears to be related to trophic ecology. Overall, we present a previously unrecognized scenario for the evolution of sexual dimorphism that is not related to sexual selection or initial niche divergence between sexes. Instead, sexual dimorphism in gill raker length in uni-parental mouthbrooding cichlid fish appears to be the consequence of a sex-specific functional trade-off between a trophic function present in both sexes and a reproductive function present only in the brooding sex

Natural selection: it's a many-small world after all

Understanding adaptive phenotypic change and its genetic underpinnings is a major challenge in biology. Threespine stickleback fish, experimentally exposed to divergent semi-natural environments, reveal that adaptive diversification can happen readily, affects many traits and involves numerous genetic loci across the genome