Biology subjects

Kliver, S.

Publications and source records attributed to Kliver, S..

8 recordsLinked to original sources

bioRxiv2026

Convergent molecular changes in populations of two pipefish species in the Baltic Sea

While studies of molecular convergence typically focus on species that independently evolved similar phenotypes, similar questions can be asked among populations of different species adapting to the same environment. Here, we study the Baltic Sea environmental gradient and two co-distributed, ecologically similar, but distantly related pipefish species, the broadnosed pipefish (Syngnathus typhle) and the straightnose pipefish (Nerophis ophidion), to test whether independent colonization of the Baltic Sea led to similar population structure and caused convergence at different genomic levels. Using a new diploid genome for S. typhle and whole-genome resequencing data (N=99 for S. typhle; N=81 for N. ophidion) across seven locations from France to Finland, we identified stronger population structure in S. typhle than in N. ophidion, while both species showed differentiation between North Atlantic, Danish Straits, and Baltic Sea populations. Genetic diversity was lower in Baltic populations, particularly in S. typhle. Cross-species comparisons of Baltic populations revealed contrasting chromosome-level patterns of genomic differentiation, with differentiation spread across the genome in S. typhle but concentrated in specific chromosomal regions in N. ophidion. Nonetheless, we identified multiple orthologous genes and SNPs showing convergent differentiation in the Baltic populations of both species, including genes related to metabolism, immunity, and regulatory functions. Overall, we identified molecular convergence at the gene and nucleotide level between Baltic populations of distantly related pipefish species, while convergence was limited at broader genomic scales. These findings suggest that similar environmental pressures can repeatedly target specific genetic elements even when genomic backgrounds and population structures differ.

evolutionary biology↗

bioRxiv2026

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.

evolutionary biology↗

bioRxiv2026

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

The extinct giant deer (Megaloceros giganteus) was one of the most striking megafaunal species of the Late Quaternary, distinguished by its enormous palmated antlers reaching up to 3.5 m across, the largest known among both living and extinct cervids. Despite its iconic status, little is known about its genomic history prior to extinction [~]8 thousand years ago (kya). We generated the first nuclear palaeogenomes for Megaloceros, represented by nine individuals from Germany ([~]40 kya) and Ireland ([~]11 kya), mapped to a new chromosome-level reference genome of the fallow deer (Dama dama). Phylogenomic analyses placed Megaloceros as sister to Dama (divergence [~]3.5 Ma) and revealed evidence of gene flow with ancestral Cervus lineages. Population analyses identified clear differentiation between German and Irish lineages, with higher genetic diversity in the German individuals. Two genes under strong positive selection, BNIPL and SLC10A7, are associated with apoptosis regulation and skeletal development/bone mineralisation, respectively, and may relate to the species large body and antler size. Demographic reconstructions indicate a long-term decline in effective population size, extremely low heterozygosity, little evidence of extensive runs of homozygosity, and an elevated burden of predicted deleterious alleles. Together, these results suggest that Megaloceros entered the terminal Pleistocene in a genomically fragile state, offering new insight into the biology and evolutionary legacy of one of the largest and most distinctive cervids that ever lived.

evolutionary biology↗

bioRxiv2025

Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae)

The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (M. zibellina zibellina), the Ural pine marten (M. martes uralensis), and the Far East yellow-throated marten (M. flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39-2.45 Gbp, N50 values of 137-145 Mbp, and high BUSCO scores (93.6-96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n=38 and 2n=40, respectively). Annotation predicted ~20,000 protein-coding genes per genome, of which >90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

genomics↗

bioRxiv2025

Genomics of sable (Martes zibellina) x pine marten (Martes martes) hybridization

The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed hybrids beyond F1, but details remained unclear due to low-resolution methods. Both species were hunted for centuries, but anthropogenic pressures during the 20th-century caused severe bottlenecks in the sable followed by hunting bans and large-scale reintroduction programs across much of its range, including the sympatric zone, potentially affecting hybridization. We resequenced 30 individuals from most of the sables range and Eastern part of pine martens. Among samples, we found a broad spectrum of hybrid types with mosaic recombinant chromosomes that confirm hybrid fertility and indicate crossover is not suppressed in kidases. This necessitates re-evaluation of previous research, as we detected notable discrepancies between STR-based ancestry and whole-genome analysis. In pine martens, we revealed mitochondrial DNA introgression from sables, indicating displacement of native pine marten mitochondrial sequences. Pine marten heterozygosity is relatively low ([~]0.5-0.6 hetSNPs/kbp) while sable diversity ([~]1.5-1.8 hetSNPs/kbp) is unexpectedly high for a species with its demographic history, likely reflecting successful reintroduction programs. We dated species divergence at 1.52 (CI: 1.05-2.06) Mya and identified candidate genes associated with ecological, morphological, and dietary differences, as well as hybrid fertility issues. This study is the first to elucidate marten hybridization at the whole-genome level, opening new research directions for understanding hybridization among Holarctic martens, the genetic consequences of reintroduction programs, and comparative adaptomics.

genomics↗

bioRxiv2025

Comparative genomics and phylogenomics of the Mustelinae lineage (Mustelidae, Carnivora)

Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from ten species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter-and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the ancestral karyotype of Mustela (2n=44) and the Mustelinae (2n=42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.

evolutionary biology↗

bioRxiv2021

Genome assembly of the tayra (Eira barbara, Mustelidae) and comparative genomic analysis reveal adaptive genetic variation in the subfamily Guloninae

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined contributed substantially to the identification of candidate loci. This strongly argues for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

evolutionary biology↗

bioRxiv2017

Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn graph approach, due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous genes, repeats, variable microsatellite loci and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single copy orthologs from 10 other mammals. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

evolutionary biology↗