Immunogenetics, Journal Year: 2023, Volume and Issue: 76(1), P. 37 - 50
Published: Dec. 20, 2023
Language: Английский
Peer Community Journal, Journal Year: 2025, Volume and Issue: 5
Published: Jan. 24, 2025
Language: Английский
Citations
1
Experimental Cell Research, Journal Year: 2025, Volume and Issue: unknown, P. 114466 - 114466
Published: Feb. 1, 2025
Language: Английский
Citations
1
Peer Community Journal, Journal Year: 2024, Volume and Issue: 4
Published: March 5, 2024
We present here a high-quality genome assembly of the brown hare (Lepus europaeus Pallas), based on fibroblast cell line male specimen from Liperi, Eastern Finland. This represents first Finnish contribution to European Reference Genome Atlas pilot effort generate reference genomes for biodiversity. The was assembled using 25X PacBio HiFi sequencing data and scaffolded utilizing Hi-C chromosome structure capture approach. After manual curation, length 2,930,972,003 bp with N50 scaffold 125.8 Mb. 93.16% could be assigned 25 identified chromosomes (23 autosomes plus X Y), matching published karyotype. were numbered according size. has high degree completeness BUSCO score (mammalia_odb10 database), Complete: 96.1% [Single copy: 93.1%, Duplicated: 3.0%], Fragmented 0.8%, Missing 2.9%. mitochondrial sequenced separately. final annotated 30,833 genes which 21,467 code polypeptide. is particularly interesting as this species readily hybridizes mountain timidus L.) at contact zone in northern Eurasia, producing fertile offspring resulting gene flow between two species. In addition providing useful comparison population studies, can offer insight into chromosomal evolution among Glires general Lagomorpha particular. also demonstrates that not acquired karyotypic changes during culture.
Language: Английский
Citations
4
Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown
Published: April 30, 2025
Language: Английский
Citations
0
Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown
Published: Jan. 23, 2025
ABSTRACT How genetic variation contributes to adaptation at different environments is a central focus in evolutionary biology. However, most free‐living species still lack comprehensive understanding of the primary molecular mechanisms adaptation. Here, we characterised targets selection associated with drastically aquatic environments—humic and clear water—in common freshwater fish, Eurasian perch ( Perca fluviatilis ). By using whole‐genome sequencing (WGS) on large population dataset n = 42 populations) analysing 873,788 SNPs, our aim was uncover novel confirm known footprints selection. We compared individual pooled WGS, developed approach, termed dynamic outlier slicing, assess how choice outlier‐calling stringency influences functional Gene Ontology (GO) enrichment. integrating genome‐environment association (GEA) analysis allele frequency‐based approaches, estimated composite signals (CSS) identified 2679 SNPs distributed across 324 genomic regions, involving 468 genes. Dynamic slicing robust enrichment five annotation categories (upstream, downstream, synonymous, 5′UTR 3′UTR) highlighting crucial role regulatory elements adaptive evolution. Furthermore, GO analyses revealed strong functions gated channel activity, transmembrane transporter activity ion emphasising importance osmoregulation balance maintenance. Our findings demonstrate that despite substantial random drift divergence, WGS high number pools enabled identification both humic water environments, providing evidence widespread anticipate method will enable more thorough exploration divergence diverse range species.
Language: Английский
Citations
0
Journal of Zoology, Journal Year: 2023, Volume and Issue: 320(3), P. 214 - 225
Published: April 24, 2023
Abstract As a glacial relict species, mountain hares are adapted to cold and snowy conditions. Conversely, European originate from the grasslands of Middle East spread there throughout low‐lying agricultural areas Europe. Mountain generally occur allopatrically, however, sympatry occurs in some areas. In sympatric areas, introgressive hybridisation poses threat Alpine hare by reducing its genetic integrity. Introgressed individuals can be found both species but far more frequent than hares. The ecology hybrids is poorly known these species. To examine populations Alps with particular focus on occurrence their hybrids, we performed molecular analysis faecal samples collected four study South Tyrol for three winters compared habitat associations genotyped samples. We recorded 150 (i.e. 14 25 111 hares). Four introgressed were at levels consistent F2 whereas others showed an older interspecific gene flow. that hybrid faeces tended lower elevations those higher hare. frequency decreased as proportion grassland increased was positively correlated dwarf shrub heaths. No effect vegetation type hybrids. Our results support widely raised concerns hare, generalist, strong competitor ecosystem time global climate change.
Language: Английский
Citations
8
Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(5), P. 1487 - 1503
Published: Jan. 7, 2022
Understanding the evolution of local adaptations is a central aim evolutionary biology and key for identification unique populations lineages conservation relevance. By combining RAD sequencing whole-genome sequencing, we identify genetic signatures adaptation in mountain hares (Lepus timidus) from isolated distinctive habitats its wide distribution: Ireland, Alps Fennoscandia. Demographic modelling suggested that split these occurred around 20 thousand years ago, providing opportunity to study adaptive over short timescale. Using genome-wide scans, identified extreme differentiation among distinct geographic areas overlap with area-specific selective sweeps, suggesting targets adaptation. Several candidate genes are associated traits related uniqueness different environments inhabited by three groups hares, including coat colour, ability live at high altitudes variation body size. In Irish variant ASIP, gene previously implicated introgression-driven winter colour snowshoe (L. americanus), may underlie brown coats, reinforcing repeated nature ASIP moulding seasonal colouration. Comparative genomic analyses across several hare species hares' variants appear predominantly species-specific. However, using coalescent simulations, also show instances where have been introduced via introgressive hybridization. Our shows standing variation, introgressed other species, was crucial component post-glacial dynamics species.
Language: Английский
Citations
14
Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 178, P. 107634 - 107634
Published: Oct. 5, 2022
Tardigrada is an invertebrate phylum that often constitutes a dominant micrometazoan group on glaciers worldwide. We investigated tardigrades residing in surface ice above the equilibrium line altitude (ELA) three temperate of New Zealand's Southern Alps. Morphological, morphometric and multilocus DNA analyses (CO1, 18S rRNA, 28S ITS-2) revealed two new genera comprising four species, which are formally described here: Kopakaius gen. nov. nicolae sp. Kararehius gregorii The former represented by genetically distinct phyletic lineages akin to species. According CO1, inhabits Whataroa Glacier only while remaining species occur Fox Franz Joseph Glaciers, suggesting low dispersal capabilities. Although morphological characteristics could indicate affinity with subfamily Itaquasconinae, phylogenetic analysis placed them confidently Diphasconinae. lack placoids pharynx similar some whereas dark pigmentation claw shape aligns glacier-obligate genus, Cryobiotus (subfamily Hypsibiinae), example parallel evolution. second gen be classified as Adropion-like Itaquasconinae), but differs greatly genetics (placed Diphasconinae) well morphology (e.g., septulum), exemplify deep stasis Hypsibiidae. Our results suggest glacier fragmentation during Pleistocene triggered tardigrade speciation, making it suitable model for studies allopatric divergence meiofauna.
Language: Английский
Citations
11
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: June 10, 2024
Abstract We present here a high-quality genome assembly of male mountain hare ( Lepus timidus Linnaeus), from Ilomantsi, Eastern Finland, utilizing an isolated fibroblast cell line as the source for high quality DNA and RNA. Following previously published brown reference assembly, is second Finnish pilot species European Reference Genome Atlas (ERGA) initiative, collaborative effort to generate genomes biodiversity. The was assembled using 21× PacBio HiFi sequencing data scaffolded Hi-C chromosome structure capture approach. After manual curation, primary length 2,695,305,354 bp with N50 125,755,317 bp. largest scaffold 181 Mbp 127 Mbp, contributing consisting 85 scaffolds alternate 109 scaffolds. include 23 autosomes, numbered according their size, well X Y chromosomes, matching known karyotype. Telomeric regions were on at least one end 19 chromosomes. has degree completeness based BUSCO score (mammalia_odb10 database), Complete: 95.1 % [Single copy: 92.3 %, Duplicated: 2.7 %], Fragmented 0.8 Missing 4.1 %. mitochondrial sequenced separately. meets Earth BioGenome Project criteria reference-standard assembly. Compared previous pseudo-reference L. ssp. hibernicus Bell, rabbit genome, this new represents nominate subspecies species-specific chromosomal conformation. will provide solid foundation future genomic research Lagomorpha, including insights into basis adaptations snowy cold environments. Furthermore, it opens opportunities experimental analysis gene functions.
Language: Английский
Citations
1
Conservation Genetics, Journal Year: 2022, Volume and Issue: 23(6), P. 1053 - 1062
Published: Oct. 26, 2022
Abstract Introduced non-native species can threaten native through interspecific hybridisation and genetic introgression. We assessed the prevalence of introgression between introduced European brown hare, Lepus europaeus , endemic Irish L. timidus hibernicus . Roadkill hares ( n = 56) were sequenced for a 379bp section mitochondrial DNA D-loop 474bp segment nuclear transferrin Tf ) gene. A species-specific indel in gene was present L.t. absent Excluding three from which molecular data could not be recovered, 28 (53%) 7 (13%) 18 (34%) hybrids; 5 (28%) first generation (F1) involving bidirectional crosses with mismatched mtDNA (3 ♂ x ♀ 2 ). Mixed sequences suggested 13 (72%) hybrids at least 2nd (F2) 9 (69%) possessing 4 (31%) (the latter indicative hybrid backcrossing non-native). The similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) typically unidirectional (♂ high (in association projected climate change) may favour over native. Genetic surveillance population monitoring are needed to further explore potential conservation implications Ireland.
Language: Английский
Citations
5