Biology subjects

Kemppainen, P.

Publications and source records attributed to Kemppainen, P..

5 recordsLinked to original sources

bioRxiv2024

SLRfinder: a method to detect candidate sex-linked regions with linkage disequilibrium clustering

Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms. In contrast to conserved sex chromosomes in mammals and birds, studies of fish, amphibians, and reptiles have found highly labile sex chromosomes with newly evolved sex-linked regions (SLRs). These labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here we present SLRfinder, a method to identify candidate SLRs and labile sex chromosomes using linkage disequilibrium (LD) clustering, patterns of heterozygosity, and genetic divergence. SLRfinder does not rely on specific sequencing methods or reference genomes and does not require phenotypic sexes which may be unknown from population sampling, although sex information can be incorporated to provide additional inference on candidate SLRs. We tested SLRfinder using various published datasets and compared it to SATC, a method that identifies sex chromosomes based on the depth of coverage and also does not require phenotypic sex. Results show that SATC works better on conserved sex chromosomes (e.g., in African leopards), whereas SLRfinder outperforms SATC in analyzing labile sex chromosomes (e.g., in nine-spined sticklebacks and chum salmon). Since SLRfinder primarily relies on LD clusters, it is expected to be most sensitive to the SLRs harboring structural variants (e.g., inversion) due to strongly reduced recombination rates in heterozygotes. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.

genomics↗

bioRxiv2023

Boundary effects cause false signals of range expansions in population genomic data

Studying range expansions (REs) is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index ({psi}), are sensitive to REs and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution. Such boundary effects (BEs) are expected to affect geographic patterns in {psi} as well as genetic diversity. With simulations we show that BEs consistently cause high false positive rates in equilibrium meta-populations when testing for REs. In the simulations, the absolute value of {psi} (|{psi}|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of REs as a function of {varepsilon}=|{psi}|/FST and geographic clines in {psi}, strong evidence for REs could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards or the Indo-Australasian blacktip shark that were significant for the standard RE tests. Thus, while clinal variation in {psi} is still the most sensitive statistic to REs, in order to detect true signatures of REs in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.

evolutionary biology↗

bioRxiv2023

Heterogeneous genomic architecture of skeletal armour traits in sticklebacks

Whether populations adapt to similar selection pressures using the same underlying genetic variants depends on population history and the distribution of standing genetic variation at the metapopulation level. Studies of sticklebacks provide a case in point: when colonising and adapting to freshwater habitats, three-spined sticklebacks (Gasterosteus aculeatus; TSSs) with high gene flow tend to fix the same adaptive alleles in the same major loci, whereas nine-spined sticklebacks (Pungitius pungitius; NPSs) with limited gene flow tend to utilize a more heterogeneous set of loci. In accordance with this, we report results of quantitative trait locus (QTL) analyses using a F2 back-cross design showing that lateral plate number variation in the western European lineage of NPSs mapped to three moderate-effect QTL, contrary to one major QTL in TSSs and these QTL were different from the four previously identified QTL in the eastern European lineage of NPSs. Furthermore, several QTL were identified associated with variation in lateral plate size, and three moderate-effect QTL with body size. Together, these findings indicate that genetic underpinnings of skeletal armour variation in Pungitius sticklebacks are more polygenic and heterogenous than those in three-spined sticklebacks, indicating limited genetic parallelism underlying armour trait evolution in the family Gasterostidae.

evolutionary biology↗

bioRxiv2021

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.

evolutionary biology↗

bioRxiv2019

Oceans apart: Heterogeneous patterns of parallel evolution in sticklebacks

An important model system for the study of genomic mechanisms underlying parallel ecological adaptation in the wild is the three-spined stickleback (Gasterosteus aculeatus), which has repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies have identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes, but these are typically based on limited geographic sampling and are biased towards studies in the Eastern Pacific. We analysed population genomic data from marine and freshwater ecotypes of three-spined sticklebacks with from a comprehensive global collection of marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Our findings highlight that most signatures of parallel evolution were unique to the Eastern Pacific. Trans-oceanic marine and freshwater differentiation was only found in a very limited number of genomic regions, including three chromosomal inversions. Using both simulations and empirical data, we demonstrate that this is likely due to both the stochastic loss of freshwater-adapted alleles during founder events during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which have reduced the amount of standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the existence of highly elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is also consistent with a secondary contact scenario between marine and freshwater populations that have evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies focused on Eastern Pacific populations have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range.

evolutionary biology↗