Biology subjects

Löytynoja, A.

Publications and source records attributed to Löytynoja, A..

8 recordsLinked to original sources

bioRxiv2026

Contemporary hybridization and localized genomic differentiation between grey seal subspecies

Grey seals are divided into two subspecies, Halichoerus grypus grypus in the Baltic Sea and H. grypus atlantica in the North Atlantic Ocean. Historically, intense hunting caused local extinctions of grey seals across their range and promoted geographical isolation of the subspecies. However, recent population recovery and recolonization have renewed their overlap in a contact zone in Danish and Swedish waters. Here, using whole-genome sequencing data from 119 individuals, we investigate the demographic history of grey seals, the divergence of the subspecies, and genomic signatures of local adaptation and potential hybridization in the contact zone. We estimate that divergence began approximately 10,000 years ago, with gene flow ceasing 2000 years ago. We detect peaks of high genetic differentiation near genes with putative functions in osmo- and thermoregulation, consistent with salinity and temperature differences between the Baltic Sea and the North Atlantic. As evidence of the geographic isolation breaking up, we report a hybrid individual in the southwest Baltic contact zone, with Baltic maternal and Atlantic paternal ancestry, and identify a migrant of Baltic origin in the North Sea. Our study illustrates how local environmental variation and long-term hunting pressure have contributed to divergence between mammal subspecies over a short evolutionary timescale, with recent population recovery, recolonization and hybridization reshaping gene flow dynamics. Broadly, our work emphasizes the importance of studying evolutionary processes amid anthropogenic influences, including both disturbances and conservation successes, where demographic fluctuations, range shifts, altered gene flow, and adaptation to changing environments interact in complex, potentially consequential ways.

evolutionary biology↗

bioRxiv2023

Sex chromosome turnover in hybridizing stickleback lineages

Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. We first identified an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses. We then verified this region as the SDR in most other WL populations and demonstrated an ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosomes replace the older and heteromorphic LG12 sex chromosomes. The results provide a rare glimpse of ongoing sex chromosome turnover and indicate possible existence of additional but yet undiscovered sex chromosome diversity in Pungitius sticklebacks. TeaserEvolutionarily young sex chromosomes replace the older ones in the hybrid zone of European Pungitius stickleback lineages.

evolutionary biology↗

bioRxiv2022

Low heritability of crossover rate in wild sticklebacks

Crossover rate is mostly studied with domesticated or lab-reared populations and little is known about its genetic variation in the wild. We studied the variation and genetic underpinnings of crossover rate in outbred wild nine- (Pungitius pungitius) and three-spined (Gasterosteus aculeatus) sticklebacks. In both species, the crossover rate of females exceeded that of males as did also its repeatability (RFemales =0.21-0.33, RMales=0.026-0.11), implying individual differences of crossover rate in females, but no or less so in males. However, in both species and sexes additive genetic variance and heritability of crossover rate were effectively zero. A review of the previously reported repeatability and heritability estimates revealed that the repeatabilities in stickleback females were moderately high, whereas those in males were very low. Genome-wide association analyses recovered a few candidate regions possibly involved with control of crossover rate. The low additive genetic variance of crossover rate in wild sticklebacks suggest limited evolvability of crossover rate.

evolutionary biology↗

bioRxiv2022

Fragmented habitat compensates for the adverse effects of genetic bottleneck

In the face of human-caused biodiversity crisis, understanding the theoretical basis of conservation efforts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat shape is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, by whole-genome sequencing 105 individuals and additional individuals from three other ringed seal subspecies. We analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of a genetic bottleneck with prevalent homozygosity in Saimaa ringed seals, we found evidence for population structure mirroring the subregions of the lake. Highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact, genome-wide analyses showed that the subpopulations had retained unique variation and largely complementary patterns of homozygosity. Integration of genetic analyses in conservation decisions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.

evolutionary biology↗

bioRxiv2021

Drastic mutations can be hidden in short-read mapping: thousands of mutation clusters in human genome are explained by short-range template switching

Variation within human genomes is unevenly distributed, and variants show spatial clustering. DNA- replication-related template switching is a poorly known mutational mechanism capable of causing major chromosomal rearrangements as well as creating short inverted sequence copies that appear as local mutation clusters in sequence comparisons. I reanalyzed haplotype-resolved genome assemblies representing 25 human populations and multinucleotide variants aggregated from 140,000 human sequencing experiments. Local template switching could explain thousands of complex mutation clusters across the human genome, the loci segregating within and between populations. I developed computational tools for identification of template switch events using both short-read sequencing data and genotype data, and for genotyping candidate loci using short-read data. The characteristics of template-switch mutations complicate their detection and, worryingly, widely used analysis pipelines for short-read sequencing data, normally capable of identifying single nucleotide changes, were found to miss template-switch mutations of tens of base pairs, potentially invalidating medical genetic studies searching for a causative allele behind genetic diseases. Combined with the massive sequencing data now available for humans, the novel tools described here enable building catalogs of affected loci and studying the cellular mechanisms behind template switching in both healthy organisms and disease.

genomics↗

bioRxiv2020

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

We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. 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). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.

genomics↗

bioRxiv2020

We shall meet again - Genomics of historical admixture in the sea

We studied the impact of genetic introgression in evolution and on evolutionary studies with whole-genome data from two divergent lineages of sticklebacks. Our results reveal that the hybrid zone between the lineages ranges across the entire Baltic Sea and parts of the North Sea with the foreign ancestry decreasing with increasing distance to the source population. Introgression has also penetrated currently isolated freshwater populations. We identified footprints of selection on regions enriched for introgressed variants, suggesting that some of the introgression has been adaptive. However, the levels of introgression were in general negatively correlated with the recombination rate, suggesting that the introgression has been largely neutral and adaptive ancestral standing variation likely had a more important role in shaping the genomic landscape. Our results further suggest that overlooked introgression can mislead analyses of local adaptation and phylogenetic affinities, highlighting the importance of accounting for introgression in studies of local adaptation.

genomics↗

bioRxiv2018

Mechanistic insights into the evolution of DUF26-containing proteins in land plants

Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation in plants. Here we infer the evolutionary history of a representative protein family, the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 first appeared in secreted proteins. Domain duplications and rearrangements led to the emergence of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). While the DUF26 itself is specific to land plants, structural analyses of Arabidopsis PDLP5 and PDLP8 ectodomains revealed strong similarity to fungal lectins. Therefore, we propose that DUF26-containing proteins constitute a novel group of plant carbohydrate-binding proteins. Following their appearance, CRKs expanded both through tandem duplications and preferential retention of duplicates in whole genome duplication events, whereas PDLPs evolved according to the dosage balance hypothesis. Based on our findings, we suggest that the main mechanism of expansion in new gene families is small-scale duplication, whereas genome fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.

plant biology↗