scholarly journals Genetic insights into the management and conservation of Arctic charr in North Wales

2021 ◽  
Author(s):  
Samantha V. Beck ◽  
Gary R. Carvalho ◽  
Ian McCarthy ◽  
Walter Hanks ◽  
Robert Evans ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Long Term Effects ◽  
Effective Population ◽  
Isolated Populations ◽  
Anthropogenic Pressures ◽  
Southern Limit ◽  
North Wales ◽  
Native Populations

AbstractAquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (FST = 0.26 ± 0.02SD) as well as low genetic diversity (HO 0.30) compared to remaining populations (HO 0.64 ± 0.14SD). Although evidence suggests that stocking increased the effective population size of Llyn Padarn in the short term without impacting genetic diversity, the long term effects of such practices are yet to be seen. Results provide baseline data for conservation management, and highlight the need for protection of small isolated populations that are being negatively impacted by the processes of genetic drift due to escalating anthropogenic pressures. Continual monitoring of both Arctic charr and their habitats using a combination of methods will increase the likelihood that these threatened and iconic populations will persist in the future.

scholarly journals Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 899
Author(s):  
Fotis Pappas ◽  
Christos Palaiokostas
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Cost Effective ◽  
Limiting Factors ◽  
Phenotypic Traits ◽  
Production Volume ◽  
High Coverage ◽  
Genomic Relationships ◽  
Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

2019 ◽  
Vol 286 (1916) ◽  
pp. 20191989 ◽  
Author(s):  
M. C. Yates ◽  
E. Bowles ◽  
D. J. Fraser
Keyword(s):  
Genetic Diversity ◽  
Body Size ◽  
Population Size ◽  
Brook Trout ◽  
Habitat Degradation ◽  
Species Conservation ◽  
Empirical Work ◽  
Genomic Diversity ◽  
Effective Population ◽  
Isolated Populations

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size ( N e ), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N e , and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

Origin and genetic diversity of an introduced wall lizard population and its cryptic congener

2012 ◽  
Vol 33 (1) ◽  
pp. 129-140 ◽  
Author(s):  
Ulrich Schulte ◽  
Franz Gassert ◽  
Philippe Geniez ◽  
Michael Veith ◽  
Axel Hochkirch
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Effective Population ◽  
Lower Saxony ◽  
Sympatric Populations ◽  
Podarcis Muralis ◽  
Eastern Pyrenees ◽  
Native Populations ◽  
The Uk ◽  
Introduced Population

The Common Wall Lizard (Podarcis muralis) has been introduced within large parts of Central Europe, the UK and parts of North America. In an introduced population of this species in Lower Saxony, Germany, we found in addition to mtDNA haplotypes of P. muralis also haplotypes of its congener Podarcis liolepis, a species that hitherto has never been recorded outside its native range. We therefore, (1) wanted to identify the geographic origin of the founder individuals of both non-native populations, (2) test for hybridization between introduced individuals of both species in Germany and (3) compare levels of genetic diversity between native and introduced populations. We sequenced a fragment of the mitochondrial cytochrome b gene and genotyped individuals of the introduced as well as native populations of both species at eleven microsatellite loci. Our results suggest that the founders presumably stem from a region in the eastern Pyrenees, where sympatric populations of P. muralis and P. liolepis are known. No evidence for gene flow between the two species was found in the introduced population. These results are consistent with behavioural observations indicating agonistic interactions of P. muralis towards P. liolepis rather than cross-species attraction. Compared to the native populations, high levels of genetic diversity have been retained in the introduced population of both species and no evidence for a genetic bottleneck was found. The effective population size was high in P. muralis, but substantially smaller in P. liolepis.

Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Empirical Studies ◽  
Small Population ◽  
Native Plant ◽  
Effective Population ◽  
Term Survival ◽  
Inbreeding Coefficients ◽  
Native Populations ◽  
Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

scholarly journals A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr ( Salvelinus alpinus )

2021 ◽  
Author(s):  
Christos Palaiokostas ◽  
Anam Anjum ◽  
Henrik Jeuthe ◽  
Khrystyna Kurta ◽  
Fernando Lopes Pinto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Performance Traits

scholarly journals Genetic diversity and structure of native Egyptian cattle populations and French-Egyptian Cross via DNA-microsatellite

2018 ◽  
Vol 23 (1) ◽  
pp. 1
Author(s):  
Eslam Faid-Allah ◽  
E. Ghoneim ◽  
A. R. Elbetagy ◽  
M. El-Dabour
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Allelic Variation ◽  
Isolated Populations ◽  
The Third ◽  
Genetic Diversity And Structure ◽  
Ssr Primers ◽  
Native Populations ◽  
Dna Microsatellite ◽  
Dna Microsatellite Markers

This study investigates genetic diversity and structure of native Egyptian cattle populations, called Baladi, as Saidi from Southern Egypt, Menufi from Mid-Delta and their F1 crosses with the French Tarentaise breed using DNA Microsatellite markers. A total of unrelated 97 individuals were genotyped utilizing eight SSR primers (ETH10, ETH225, BM1818, BM1824, BM2113, SPS115, TGLA53 and TGLA126). All utilized SSR were found to be polymorphic. The highest and lowest numbers of alleles detected were 16 and 6 at TGLA53 and SPS115 loci, respectively. Baladi-Tarentaise crosses (Bal-Tar) had the highest number of alleles over all. The PIC values of 7 loci were higher than 0.5, indicating high allelic variation of utilized markers. Estimated PIC values were up to 0.898, 0.866 and 0.873 for TGLA53 genotyped in Saidi, Menufi and Bal-Tar, respectively. Hobs values were lower than the expected ones in the native populations accompanied with positive values for Fis and significant deviation from HWE indicating inbreeding trend in native populations. Structure analysis indicated three ancestral genetic backgrounds. The native populations share two main backgrounds in almost equal percentages, while the Bal-Tar had the third one. The three populations showed low percentage of admixture. The studied Mediterranean cattle populations that belong to Egypt and France seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations so local cattle is very similar.

Impaired Swimming Performance of Acid-exposed Arctic Charr, Salvelinus Alpinus L.

1988 ◽  
Vol 23 (2) ◽  
pp. 301-307 ◽  
Author(s):  
L.A. Hunter ◽  
E. Scherer
Keyword(s):  
Dose Response ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Swimming Performance ◽  
Control Level ◽  
Ventilation Rates

Abstract Arctic charr (Salvelinus alpinus L.) were exposed to five levels of acidity between pH 6 and pH 3.8. Swimming performance as determined by critical swimming speeds was 67.5 cm · sࢤ1 or 4.4 body lengths per second for untreated fish (pH 7.8). Performance declined sharply below pH 4.5; at pH 3.8 it was reduced by 35% after 7 days of exposure. Tailbeat frequencies and ventilation rates showed no dose-response effects. At swimming speeds between 20 and 50 cm · sࢤ1, ventilation rates at all levels of acidity were higher than at the control level.

Evolutionary genetics of small populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Evolutionary Genetic ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

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