Aquatic Landscape Genomics and Environmental Effects on Genetic Variation

2019 ◽  
Vol 34 (7) ◽  
pp. 641-654 ◽  
Author(s):  
Jared A. Grummer ◽  
Luciano B. Beheregaray ◽  
Louis Bernatchez ◽  
Brian K. Hand ◽  
Gordon Luikart ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Environmental Effects ◽  
Landscape Genomics ◽  
Aquatic Landscape

scholarly journals Mhc polymorphisms fail to explain the heritability of phytohaemagglutinin-induced skin swelling in a wild passerine

2009 ◽  
Vol 5 (6) ◽  
pp. 784-787 ◽  
Author(s):  
Camille Bonneaud ◽  
Janet S. Sinsheimer ◽  
Murielle Richard ◽  
Olivier Chastel ◽  
Gabriele Sorci
Keyword(s):  
Genetic Variation ◽  
Immune Responses ◽  
Environmental Effects ◽  
Natural Populations ◽  
Wild Populations ◽  
Genetic Determinants ◽  
House Sparrows ◽  
Additive Genetic Variation ◽  
Significant Heritability ◽  
Mhc Polymorphisms

Genetic estimates of the variability of immune responses are rarely examined in natural populations because of confounding environmental effects. As a result, and because of the difficulty of pinpointing the genetic determinants of immunity, no study has to our knowledge examined the contribution of specific genes to the heritability of an immune response in wild populations. We cross-fostered nestling house sparrows to disrupt the association between genetic and environmental effects and determine the heritability of the response to a classic immunological test, the phytohaemagglutinin (PHA)-induced skin swelling. We detected significant heritability estimates of the response to PHA, of body mass and tarsus length when nestlings were 5 and 10 days old. Variation at Mhc genes, however, did not explain a significant portion of the genetic variation of nestling swelling to PHA. Our results suggest that while PHA-induced swelling is influenced by the nest of origin, the importance of additive genetic variation relative to non-additive genetic variation and the genetic factors that influence the former in wild populations still need to be identified for this trait.

scholarly journals Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

2019 ◽  
Vol 190 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Kin Onn Chan ◽  
Rafe M Brown
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Variance Partitioning ◽  
Nucleotide Polymorphisms ◽  
Landscape Genomics ◽  
Mountain Ranges ◽  
Historical Factors ◽  
Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

Genetic variation and environmental effects on agronomical and commercial quality traits in the main European market classes of dry bean

2006 ◽  
Vol 95 (2-3) ◽  
pp. 336-347 ◽  
Author(s):  
A.M. González ◽  
A.B. Monteagudo ◽  
P.A. Casquero ◽  
A.M. De Ron ◽  
M. Santalla
Keyword(s):  
Genetic Variation ◽  
Environmental Effects ◽  
European Market ◽  
Quality Traits ◽  
Dry Bean

Tocopherol Concentration in Almond Oil: Genetic Variation and Environmental Effects under Warm Conditions

2011 ◽  
Vol 59 (11) ◽  
pp. 6137-6141 ◽  
Author(s):  
Ossama Kodad ◽  
Gloria Estopañán ◽  
Teresa Juan ◽  
Ali Mamouni ◽  
Rafel Socias i Company
Keyword(s):  
Genetic Variation ◽  
Environmental Effects ◽  
Tocopherol Concentration ◽  
Almond Oil

scholarly journals The choice of the environmental covariate affects the power to detect variation in reaction norm slopes

2018 ◽  
Author(s):  
Phillip Gienapp
Keyword(s):  
Genetic Variation ◽  
Phenotypic Plasticity ◽  
Environmental Effects ◽  
Reaction Norm ◽  
Environmental Variable ◽  
Negative Results ◽  
Environmental Driver ◽  
The Mean ◽  
Evolutionary Consequences ◽  
Biased Estimates

AbstractMany traits are phenotypically plastic, i.e. the same genotype expresses different phenotypes depending on the environment. Individuals and genotypes can vary in this response to the environment and this individual (IxE) and genetic variation in reaction norm slopes (GxE) can have important ecological or evolutionary consequences. Studies on variation in plasticity often fail to show IxE or GxE; this can indicate a genuine absence or simply a lack of power. There is, however, another factor that could potentially affect the power to detect IxE or GxE: the choice of the environmental variable included in the analysis. Identifying the genuine environmental driver of phenotypic plasticity will mostly be impossible and hence only a proxy is included in the analysis. However, if this proxy is too weakly correlated with the real driver of plasticity, this will bias IxE and GxE downwards, could lead to spurious negative results and invalid conclusions. As the mean phenotype in a given environment captures all environmental effects on the phenotype, using it as ‘environment’ in the analysis should increase the power to detect IxE or GxE. Using simulations I here showed that using weakly correlated proxies indeed biased estimates downwards but that when using the environment-specific means this was not the case. Using environment-specific means as a covariate has been commonly used in animal and plant breeding but rarely used outside these fields despite its potential usefulness as ‘yardstick’ to test whether IxE or GxE is present or absent in the phenotype of interest.

Partitioning plant genetic and environmental drivers of above and belowground community assembly

2017 ◽  
Author(s):  
Matthew Barbour ◽  
Sonya Erlandson ◽  
Kabir Peay ◽  
Brendan Locke ◽  
Erik S. Jules ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Phenotypic Plasticity ◽  
Host Plant ◽  
Environmental Effects ◽  
Natural Variation ◽  
Plant Traits ◽  
Genetic Effects ◽  
Environmental Drivers ◽  
Leaf Quality ◽  
Wind Exposure

Host-plant genetic variation affects the diversity and composition of associated above and belowground communities. Most evidence supporting this view is derived from studies within a single common garden, thereby constraining the range of biotic and abiotic environmental conditions that might directly or indirectly (via phenotypic plasticity) affect communities. If natural variability in the environment renders host-plant genetic effects on associated communities unimportant, then studying the community-level consequences of genetic variation may not be warranted. We addressed this knowledge gap by planting a series of common gardens consisting of 10 different clones (genotypes) of the willow Salix hookeriana in a coastal dune ecosystem and manipulated natural variation in ant-aphid interactions (biotic) and wind exposure (abiotic) in two separate experiments. We then quantified the responses of associated species assemblages both above (foliar arthropods) and belowground (rhizosphere fungi and bacteria). In addition, we quantified plant phenotypic responses (plant growth, leaf quality, and root quality) to tease apart the effects of genetic variation, phenotypic plasticity, and direct environmental effects on associated communities. In the ant-aphid experiment, we found that willow genotype explained more variation in foliar arthropod communities than aphid additions and proximity to aphid-tending ant mounds. However, aphid additions modified willow genetic effects on arthropod community composition by attracting other aphid species to certain willow genotypes. In the wind experiment, wind exposure explained more variation than willow genotype in structuring communities of foliar arthropods and rhizosphere bacteria. Still, willow genotype had strong effect sizes on several community properties of arthropods and fungi, indicating that host-plant genetic variation remains important. Across both experiments, genetic variation in plant traits was more important than phenotypic plasticity in structuring associated communities. The relative importance of genetic variation vs. direct environmental effects though depended on the type of environmental gradient (G > E-aphid, but E-wind > G). Taken together, our results suggest that host-plant genetic variation is an important driver of above and belowground biodiversity, despite natural variation in the biotic and abiotic environment.

scholarly journals Peromyscus as a Mammalian Epigenetic Model

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Kimberly R. Shorter ◽  
Janet P. Crossland ◽  
Denessia Webb ◽  
Gabor Szalai ◽  
Michael R. Felder ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genome Sequencing ◽  
Environmental Effects ◽  
Genetic Variants ◽  
Life Histories ◽  
Coat Color ◽  
Deer Mice ◽  
Epigenetic Variation ◽  
Natural Genetic Variation ◽  
Epigenetic Effects

Deer mice (Peromyscus) offer an opportunity for studying the effects of natural genetic/epigenetic variation with several advantages over other mammalian models. These advantages include the ability to study natural genetic variation and behaviors not present in other models. Moreover, their life histories in diverse habitats are well studied. Peromyscus resources include genome sequencing in progress, a nascent genetic map, and >90,000 ESTs. Here we review epigenetic studies and relevant areas of research involving Peromyscus models. These include differences in epigenetic control between species and substance effects on behavior. We also present new data on the epigenetic effects of diet on coat-color using a Peromyscus model of agouti overexpression. We suggest that in terms of tying natural genetic variants with environmental effects in producing specific epigenetic effects, Peromyscus models have a great potential.

scholarly journals Genetic variation and environmental effects on beta-conglycinin and glycinin content in Brazilian soybean cultivars

2008 ◽  
Vol 43 (9) ◽  
pp. 1105-1114 ◽  
Author(s):  
Mercedes Concórdia Carrão-Panizzi ◽  
Prachuab Kwanyuen ◽  
Sevim Zeynep Erhan ◽  
Ivani de Oliveira Negrão Lopes
Keyword(s):  
Genetic Variation ◽  
Protein Content ◽  
Environmental Effects ◽  
Protein Fraction ◽  
Protein Fractions ◽  
Southern Brazil ◽  
Individual Protein ◽  
Central Brazil ◽  
Soybean Cultivars ◽  
Good Possibility

The objective of this work was to determine genetic and environmental effects on beta-conglycinin and glycinin content in Brazilian soybean cultivars. The concentrations of these protein fractions were analyzed by scanning densitometry after electrophoresis, in 90 Brazilian soybean cultivars sown in Ponta Grossa, PR, in 2001. The effects of the sowing location were determined in the cultivar MG/BR 46 (Conquista), sown in 16 locations of Goiás and Minas Gerais states (Central Brazil), and in the cultivar IAS 5, sown in 12 locations of Paraná and São Paulo states (Southern Brazil), in 2002 soybean season. A significant variability for beta-conglycinin (7S) and glycinin (11S) protein fractions ratio was observed among the 90 Brazilian soybean cultivars. 'MS/BRS 169' (Bacuri) and 'BR-8' (Pelotas) presented the highest and the lowest 11S/7S ratios (2.76 and 1.17, respectively). Beta-conglycinin protein fractions presented more variability than glycinin protein fractions. Grouping test classified 7S proteins in seven groups, 11S proteins in four groups, and protein fraction ratios (11S/7S) in nine groups. Significant effect of sowing locations was also observed on protein fractions contents. There is a good possibility of breeding for individual protein fractions, and their subunits, without affecting protein content.

Genetic control of some quantitative characters in upland cotton (Gossypium hirsutum L.)

1980 ◽  
Vol 94 (3) ◽  
pp. 539-543 ◽  
Author(s):  
S. S. Dhillon ◽  
T. H. Singh
Keyword(s):  
Genetic Variation ◽  
Negative Correlation ◽  
Environmental Effects ◽  
Upland Cotton ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Gossypium Hirsutum L ◽  
Significant Component ◽  
Quantitative Characters ◽  
Additive Component

SummaryThe nature of genetic variation in an intervarietal cross (J 34 × SS 167) of upland cotton was determined for seed cotton yield, number of bolls, weight of 100 seeds, ginning outturn and halo length. The materials consisted of six generations (P1, P2, F1, B1, B2 and F2) which were raised at two locations. In those cases where the additivedominance model was inadequate, models with different numbers of parameters were applied along with the six-parameter model. A consistent and high negative correlation was observed between [h] and [l], and [i] and [l] in all the models at two locations. Correlation between [d] and [i] was also consistent and negative, but its magnitude was low. Dominance and dominance × dominance, and additive × additive and dominance × dominance components were found to be antagonistic in effects to each other and the interactions observed were of duplicate type, i.e. [h] and [l] had opposite signs.The dominance component fluctuated greatly over models for a particular character at a particular location. Contrary to this the additive component was observed to be important and consistent over models at a particular location for a particular character. Also this was the only significant component involved in the inheritance of all the characters at both the locations. The expression of different components of variation was highly influenced by the environmental effects.

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