Single nucleotide polymorphisms reveal a genetic cline across the north‐east Atlantic and enable powerful population assignment in the European lobster

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon ( Salmo salar ). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.

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Genome-wide association studies using single-nucleotide polymorphisms versus haplotypes: an empirical comparison with data from the North American Rheumatoid Arthritis Consortium

BMC Proceedings ◽

10.1186/1753-6561-3-s7-s35 ◽

2009 ◽

Vol 3 (Suppl 7) ◽

pp. S35 ◽

Cited By ~ 20

Author(s):

Heejung Shim ◽

Hyonho Chun ◽

Corinne D Engelman ◽

Bret A Payseur

Keyword(s):

Rheumatoid Arthritis ◽

Single Nucleotide Polymorphisms ◽

Association Studies ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Empirical Comparison ◽

Single Nucleotide ◽

The North ◽

Genome Wide

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Mycobacterium tuberculosis isolates belonging to katG gyrA group 2 are associated with clustered cases of tuberculosis in Italian patients

Journal of Medical Microbiology ◽

10.1099/jmm.0.05471-0 ◽

2004 ◽

Vol 53 (2) ◽

pp. 155-159 ◽

Cited By ~ 6

Author(s):

L. Dolzani ◽

M. Rosato ◽

B. Sartori ◽

E. Banfi ◽

C. Lagatolla ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Local Population ◽

Rflp Analysis ◽

Nucleotide Polymorphisms ◽

Transmitted Infection ◽

Single Nucleotide ◽

North East ◽

The North ◽

Group 2 ◽

Group 1

Fifty-one consecutive isolates of Mycobacterium tuberculosis, collected during a 2-year period in the north-east of Italy, were subjected to IS6110-RFLP analysis to detect the presence of clusters and assigned to one of the three genotypic groups delineated by single nucleotide polymorphisms in the genes katG and gyrA. All the isolates collected from the local population belonged to group 2 or 3, while group 1 isolates were found only in specimens collected from African immigrants. Clustered cases of tuberculosis, which are likely to be related to recently transmitted infection, were found to be significantly associated with katG gyrA group 2. In the local situation, strains belonging to this group may therefore present a higher risk of transmission.

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Study of single nucleotide polymorphisms of tumour necrosis factors and HSP genes in nasopharyngeal carcinoma in North East India

Tumor Biology ◽

10.1007/s13277-015-3767-6 ◽

2015 ◽

Vol 37 (1) ◽

pp. 271-281 ◽

Cited By ~ 5

Author(s):

Meena Lakhanpal ◽

Laishram Chandreshwor Singh ◽

Tashnin Rahman ◽

Jagnnath Sharma ◽

M. Madhumangal Singh ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Single Nucleotide Polymorphisms ◽

Tumour Necrosis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

North East India ◽

North East ◽

Hsp Genes

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Single Nucleotide Polymorphisms Are Suitable For Assessing The Success of Restocking Efforts of The European Lobster (Homarus Gammarus, L.)

10.21203/rs.3.rs-292738/v1 ◽

2021 ◽

Author(s):

Pierre De Wit ◽

Linda Svanberg ◽

Isabel Casties ◽

Susanne P Eriksson ◽

Kristina Sundell ◽

...

Keyword(s):

Dna Marker ◽

Nucleotide Polymorphisms ◽

Population Assignment ◽

Single Nucleotide ◽

Swedish West Coast ◽

European Lobster ◽

Homarus Gammarus ◽

Snp Panel ◽

First Time ◽

A Current

Abstract The European lobster (Homarus gammarus) forms the base of an important fishery along the coasts of Europe. However, stocks have been in decline for many years, prompting new regulations in the fishery and also restocking efforts. An important feature of any restocking effort is the assessment of success in the number of released juveniles that stay and become adult over time. Here, we tested the power of a SNP DNA marker panel developed for population assignment to correctly infer parentage on the maternal side of lobster larvae, in the absence of known fathers, using lobsters included in a current restocking effort on the Swedish west coast. We also examined the power to reconstruct the unknown paternal genotypes, and examined the number of fathers for each larval clutch. We found that the 96-SNP panel, despite only containing 78 informative markers, allowed us to assign all larvae to the correct mother. Furthermore, with 10 genotyped larvae or more, confident paternal genotypes could be reconstructed. We also found that 15 out of 17 clutches were full siblings, whereas two clutches had two fathers. To our knowledge, this is the first time a SNP panel of this size has been used to assess parentage in a crustacean restocking effort. Our conclusion is that the panel works well, and that it could be an important tool for the assessment of restocking success of H. gammarus in the future.

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