Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea.

ABSTRACT: We explored single nucleotide polymorphism (SNP) variation in candidate genes for bud burst from Quercus petraea populations sampled along gradients of latitude and altitude in Western Europe. SNP diversity was monitored for 106 candidate genes, in 758 individuals from 32 natural populations. We investigated whether SNP variation reflected the clinal pattern of bud burst observed in common garden experiments. We used different methods to detect imprints of natural selection (FST outlier, clinal variation at allelic frequencies, association tests) and compared the results obtained for the two gradients. FST outlier SNPs were found in 15 genes, 5 of which were common to both gradients. The type of selection differed between the two gradients (directional or balancing) for 3 of these 5. Clinal variations were observed for six SNPs, and one cline was conserved across both gradients. Association tests between the phenotypic or breeding values of trees and SNP genotypes identified 14 significant associations, involving 12 genes. The results of outlier detection on the basis of population differentiation or clinal variation were not very consistent with the results of association tests. The discrepancies between these approaches may reflect the different hierarchical levels of selection considered (inter- and intrapopulation selection). Finally, we obtained evidence for convergent selection (similar for gradients) and clinal variation for a few genes, suggesting that comparisons between parallel gradients could be used to screen for major candidate genes responding to natural selection in trees.

SUBMITTER: Alberto FJ

PROVIDER: S-EPMC3781976 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients.

Project description:A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel method that accommodates variation in rates of species turnover along gradients and between different gradients, to compare environmental and spatial controls on the floras of two regions with contrasting evolutionary and climatic histories: southwest Australia and northern Europe. We find stronger signals of climate history in the northern European flora and demonstrate that variation in rates of species turnover is persistent across regions, taxa and different gradients. Such variation may represent an important but often overlooked component of biodiversity that complicates comparisons of distance-decay relationships and underscores the importance of using methods that accommodate the curvilinear relationships expected when modelling beta diversity. Determining how rates of species turnover vary along and between gradients is relevant to understanding the sensitivity of ecological systems to environmental change.

| S-EPMC3757964 | biostudies-literature

Signatures of natural selection in a foundation tree along Mediterranean climatic gradients.

Project description:Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean-type climates (MTC). Forest management that enhance forests' resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South-west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype-association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (FST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.

| S-EPMC9305101 | biostudies-literature

Limits to adaptation along environmental gradients.

Project description:Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.

| S-EPMC4443383 | biostudies-literature

Light and competition gradients fail to explain the coexistence of shade-tolerant Fagus sylvatica and shade-intermediate Quercus petraea seedlings.

Project description:The coexistence of forest tree species has often been linked to differences among species in terms of their response to light availability during the regeneration stage. From this perspective, species coexistence results from growth-growth or mortality-growth trade-offs along spatial light gradients. Experimental evidence of growth-growth trade-offs in natural conditions is sparse due to various confounding factors that potentially hinder the relationship. This study examined growth hierarchies along light gradients between two tree species with contrasting shade tolerance by controlling potential confounding factors such as seedling size, seedling status, seedling density and species composition.Natural regenerated shade-tolerant Fagus sylvatica and shade-intermediate Quercus petraea seedlings were used, and growth rankings over a 4-year period were compared in 8- to 10-year-old tree seedlings.No rank reversal occurs between the two species along the light gradient, or along the density, mixture or seedling size gradients. The shade-tolerant species was always the more competitive of the two. Pronounced effects of initial size on seedling growth were observed, whereas the effects of light and competition by neighbours were of secondary importance. The paramount effect of size, which results from the asymmetric nature of interseedling competition, gives a strong advantage to tall seedlings over the long term.This study extends previous efforts to identify potential drivers of rank reversals in young tree mixtures. It does not support the classical assumption that spatial heterogeneity in canopy opening explains the coexistence of the two species studied. It suggests that spatial variation in local size hierarchies among seedlings that may be caused by seedling emergence time or seedling initial performance is the main driver of the dynamics of these mixed stands.

| S-EPMC3806531 | biostudies-other

Quercus petraea

Project description:Quercus petraea SeqCapBis targeted sequencing

| PRJNA918844 | ENA

Quercus petraea

Project description:GenTree Quercus petraea Exome capture

| PRJNA602467 | ENA

Quercus petraea

Project description:Identification of miRNA involved in dormancy regulation in oaks.

| PRJNA361225 | ENA

Quercus petraea

Project description:Quercus petraea Genome sequencing

| PRJNA1121268 | ENA

Quercus petraea

Project description:Quercus petraea overview

| PRJNA705777 | ENA

Natural and sexual selection drive multivariate phenotypic divergence along climatic gradients in an invasive fish.

Project description:Invasive species that rapidly spread throughout novel distribution ranges are prime models to investigate climate-driven phenotypic diversification on a contemporary scale. Previous studies on adaptive diversification along latitudinal gradients in fish have mainly considered body size and reported either increased or decreased body size towards higher latitudes (i.e. Bergmann's rule). Our study is the first to investigate phenotypic divergence in multiple traits, including sexually selected traits (size and shape of the male copulatory organ, the gonopodium) of invasive Gambusia affinis in China. We studied body size, life history traits and morphological variation across populations spanning 17 degrees of latitude and 16 degrees of longitude. Even though we found phenotypic variation along climatic gradients to be strongest in naturally selected traits, some sexually selected traits also showed systematic gradual divergence. For example, males from southern populations possessed wider gonopodia with increased armament. Generally, males and females diverged in response to different components of climatic gradients (latitudinal or longitudinal variation) and in different trait suites. We discuss that not only temperature regimes, but also indirect effects of increased resource and mate competition (as a function of different extrinsic overwinter mortality rates) alter the selective landscape along climatic gradients.

| S-EPMC6057953 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data