Browsing by Subject "INVERSIONS"

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  • Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjorn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Regular, Paul; Fairweather, Robert; Bradbury, Ian R. (2019)
    Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.
  • Jonassen, Marius; Välisuo, Ilona; Vihma, Timo; Uotila, Petteri; Makshtas, Alexander; Launiainen, Jouko (2019)
    Surface layer and upper-air in situ observations from two research vessel cruises and an ice station in the Weddell Sea from 1992 and 1996 are used to validate four current atmospheric reanalysis products: ERA-Interim, CFSR, JRA-55, and MERRA-2. Three of the observation data sets were not available for assimilation, providing a rare opportunity to validate the reanalyses in the otherwise datasparse region of the Antarctic against independent data. All four reanalyses produce 2 m temperatures warmer than the observations, and the biases vary from +2.0 K in CFSR to +2.8 K in MERRA-2. All four reanalyses are generally too warm also higher up in the atmospheric boundary layer (ABL), with biases up to +1.4 K (ERA-Interim). Cloud fractions are relatively poorly reproduced by the reanalyses, MERRA-2 and JRA-55 having the strongest positive and negative biases of about +30 % and -17 %, respectively. Skill scores of the error statistics reveal that ERA-Interim compares generally the most favorably against both the surface layer and the upper-air observations. CFSR compares the second best and JRA-55 and MERRA-2 have the least favorable scores. The ABL warm bias is consistent with previous evaluation studies in high latitudes, where more recent observations have been applied. As the amount of observations has varied depending on the decade, season, and region, the consistency of the warm bias suggests a need to improve the modeling systems, including data assimilation as well as ABL and surface parameterizations.
  • Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjørn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Wringe, Brendan; Fairweather, Robert; Bradbury, Ian R. (2020)
    Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.