Contemporary Problems of Ecology, Год журнала: 2024, Номер 17(6), С. 781 - 798
Опубликована: Дек. 1, 2024
Язык: Английский
Contemporary Problems of Ecology, Год журнала: 2024, Номер 17(6), С. 781 - 798
Опубликована: Дек. 1, 2024
Язык: Английский
BMC Genomics, Год журнала: 2025, Номер 26(1)
Опубликована: Фев. 5, 2025
Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model
Язык: Английский
Процитировано
1Aquatic Conservation Marine and Freshwater Ecosystems, Год журнала: 2023, Номер 33(12), С. 1460 - 1476
Опубликована: Сен. 19, 2023
Abstract Extinctions occur naturally in all environments, but rates have accelerated rapidly during the Anthropocene, especially fresh water. Despite supporting many fish species of conservation importance, there has never been a formal assessment their extinction risks Britain, which impeded inclusion relevant legislation and policy. This study therefore used International Union for Conservation Nature (IUCN) Red List Threatened Species™ Categories Criteria to conduct first systematic threats facing native freshwater diadromous fishes Britain. In addition, national assessments were produced England, Scotland Wales, reflecting level at environmental policy decisions are taken Seven categorized as being threatened with regional level, European eel Anguilla anguilla allis shad Alosa alosa classified Critically Endangered, Atlantic salmon Salmo salar , vendace Coregonus albula whitefish lavaretus Arctic charr Salvelinus alpinus twaite fallax Vulnerable. burbot Lota lota was Regionally Extinct, ferox trout Data Deficient, 25 Least Concern. sturgeon Acipenser sturio houting oxyrinchus although probably native, qualified only vagrants water, so Not Applicable. The provide objective baselines against future changes can be determined, key evidence base support management habitats It is recommended that repeated every 10 years, would enable status, effectiveness policies where targeted interventions may required examined using Index.
Язык: Английский
Процитировано
9BMC Genomic Data, Год журнала: 2025, Номер 26(1)
Опубликована: Март 25, 2025
Abstract Objectives European whitefish ( Coregonus lavaretus L .) is a freshwater salmonid that inhabits cold regions of central and north Europe Siberia. It an important aquaculture species in Finland, selectively bred since 1999. The breeding programme has applied genomic selection uses SNP markers phenotypic data to improve traits such as growth, product quality, fish health. Salmonids are known for chromosomal rearrangements, the current C. reference genome based on individual from Switzerland may deviate Finnish one. Therefore, we have assembled whitefish. This allows us better assess genetic basis enhance accuracy selection. Data description was sequenced using combination Illumina PacBio technologies wtbg2 HiRise software. assembly size 2.94 Gb comprises 6,706 scaffolds with scaffold N50 1.36 Mb.
Язык: Английский
Процитировано
0Evolutionary Applications, Год журнала: 2021, Номер 14(10), С. 2470 - 2489
Опубликована: Июнь 11, 2021
Identifying the molecular mechanisms facilitating adaptation to new environments is a key question in evolutionary biology, especially face of current rapid and human-induced changes. Translocations have become an important tool for species conservation, but attendant small population sizes ecological pressures might affect phenotypic genotypic variation trajectories dramatically unknown ways. In Scotland, European whitefish (
Язык: Английский
Процитировано
20Scottish Geographical Journal, Год журнала: 2023, Номер 139(3-4), С. 445 - 465
Опубликована: Июль 18, 2023
Ice coverage not only affects the climate and landscape of geographical regions but has impacted species composition, fragmentation isolation populations, colonisation routes post-glaciation. Major advancements in generating genetic data applying sophisticated analyses to accurately model demographic history animal plant allowed evolutionary biologists novel insights. Meanwhile, physical geographers have made major reconstructing glacial history. However, information flow between geographic fields on this topic remains limited; consequently, studies contemporary biodiversity tend be vague about role history, while is rarely leveraged when discussing historical glaciation. In review, we bring together current knowledge changing patterns ice British Isles from maximum extent British-Irish sheet (BIIS) ca. 27 ka through end large-scale at start Holocene period 11.5 ka. We do so then highlight how glaciation affected composition during time subsequent temperate flora fauna variation seen them.
Язык: Английский
Процитировано
7International Journal of Limnology, Год журнала: 2024, Номер 60, С. 5 - 5
Опубликована: Янв. 1, 2024
Over the past centuries, coregonines have been exposed to a range of stressors that led extinctions, extirpations, and speciation reversals. Given some populations remain at risk fishery managers begun restoring where they extirpated, we reviewed primary gray literature describe diversity coregonine restoration or conservation actions previously used. Although stocking hatchery-reared fish has commonly used for supplementing existing fisheries, considered efforts only with specifically goals. Likewise, conservation-driven translocation were not widespread, except in United Kingdom creation refuge supplement distribution declining stocks. Habitat occurred more broadly included improving spawning habitat, connectivity, nutrient concentrations. harvest regulations are regulate found fewer examples protected areas outright closures. Finally, interactions invasive species can be considerable stressor, yet relatively few control undertaken direct benefit coregonines. In conclusion, our review prior Coregonid symposia revealed limited emphasis on relative traditional approaches ( e.g. , supplementation stock assessment) studying life history genetics. Ideally, by providing this broad strategies, future management will from learning about greater potential could locally applied.
Язык: Английский
Процитировано
2Evolution Letters, Год журнала: 2024, Номер 8(5), С. 706 - 718
Опубликована: Июнь 19, 2024
Reciprocal effects of adaptive radiations on the evolution interspecific interactions, like parasitism, remain barely explored. We test whether recent European whitefish (
Язык: Английский
Процитировано
2Journal of Evolutionary Biology, Год журнала: 2021, Номер 34(12), С. 1954 - 1969
Опубликована: Окт. 17, 2021
Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion contemporary biodiversity complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish on mainland Europe, but Britain it has only seven native populations, all of which are found the western extremes island. origins colonization routes into unknown likely contributed to genetic patterns regional uniqueness. Here, we used up 25,751 genome-wide polymorphic loci reconstruct history discern demographic evolutionary forces underpinning divergence between British populations. Overall, lower diversity Scottish populations high differentiation (FST = 0.433-0.712) from English/Welsh other Differentiation was elevated rather than particular genomic regions. Demographic modelling supported Scotland northern refugia separate route for southern refugia, with these two groups having been separated more ca. 50 Ky. We cyto-nuclear discordance at scale, clustering closely Baltic population mtDNA analysis not nuclear data, Norwegian Alpine displaying same haplotype being distantly related tree. These findings suggest neutral processes, primarily drift regionally distinct pre-glacial histories, important drivers whitefish. This sheds new light establishment freshwater fauna after last glacial maximum.
Язык: Английский
Процитировано
11bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown
Опубликована: Окт. 4, 2023
Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model
Язык: Английский
Процитировано
1Research Square (Research Square), Год журнала: 2024, Номер unknown
Опубликована: Фев. 16, 2024
Abstract Background Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data used automate the bioinformatic analysis. application optimization demonstrated on European whitefish data. Results DdRAD generation designed reliable estimation relatedness and is scalable up 384 samples. GBS sequencing yielded approximately one million reads each around 100 assessed Optimizing various strategies create de-novo reference genome variant calling (mock reference) showed that using three samples outperformed other building with single or very large number Adjustments most pipeline tuning parameters had limited impact high-quality data, except identity criterion merging mock clusters. For species, over 15k variants based were obtained comparable results ones called an existing genome. Repeatability analysis high concordance replicates, particularly in bovine while repeatability did not exceed earlier observations. Conclusions proposed cost-effective ddRAD strategy, coupled bioinformatics workflow, enables broad adoption across diverse farmed species. While beneficial, obligatory. integration Snakemake streamlines usage computer clusters supports customization. This user-friendly solution facilitates both model
Язык: Английский
Процитировано
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