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20 results for “functional trait analysis”
Seasonal trends in leaf level physiological parameters, obtained through gas exchange, reflectance spectroscopy and, functional trait analysis
This data package contains leaf level gas exchange, reflectance spectroscopy, and functional trait measurements collected in six common deciduous tree species across the full 2021 growth season (May -October) at the Black Rock Forest in Cornwall, New York, USA. Branches were sampled predawn using the shotgun method of branch retrieval, and re-cut under water to preserve hydraulic function before transport to the lab. Gas exchange data included in this package are stomatal response curves (irradiance response) which can be used to estimate stomatal slope and intercept. Spectroscopic data are full-range (350 – 2500 nm) leaf reflectance spectra collected on all leaves sampled for gas exchange and traits. Leaf level trait measurements include leaf mass per area (LMA), leaf dry matter content (LDMC), elemental nitrogen and carbon expressed on a per mass basis, and fitted values of Asat, Vcmax, and Rdark scaled to a reference temperature of 25C. Data from these three data tables (stomatal responce, spectra, leaf traits) can be cross referenced using the unique SampleID. Additional data tables include stomatal anatomy (stomatal density, length, and width of the guard cells), hydraulic properties estimated from pressure volume curves (relative water deficit at the turgor loss point), and predawn water potential for all sampled branches. Site level data includes the dGPS location of each sampled tree, its species, and DBH. Each tabular data file (*.csv) is accompanied by a data description (*_dd.csv) which includes relevant metadata (unit, definition, data type). Copies of all raw instrument output (spectroradiometer, LICOR, pressure chamber) and included as .zip files.
Data from: Provenance variation in functional traits of European forest trees: Meta-analysis reveals effects of taxa and age despite critical research gaps
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Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
<p>Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-CT imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared to Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.</p>
FUNCTIONAL ANALYSIS OF GENES FOR REPRODUCTIVE TRAITS IN PIGS: FROM GWAS TO POST-GWAS
<p>Reproductive traits, such as number of teats, uniformity and litter size, are essential for animal breeding programs due to the importance for the production chain, since they influence the maternal ability of sow and can affect the number of weaned piglets. Our objective was to identify candidate genes associated with reproductive traits in pigs, using GWAS data, from a systematic review combined with sequencing data, to build networks of biological processes and Gene-TFs (transcription factors networks from the identified genes in order to highlight the most candidate genes for litter size, uniformity and number of teats. In the systematic review only peer-reviewed articles were used, with descriptors related to the evaluated traits, and selected based on eligibility criteria. Fourteen papers were selected and classified into groups for functional analysis of gene networks with 2077 candidate genes identified. After combining with the list of genes presenting known structural variants in the 5'UTR and/or coding region, 306 genes remained to be used to build the networks of biological processes and TFs gene networks, highlighting processes associated with litter size (e.g., ionotropic glutamate receptor signaling pathway and blastocyte growth) and teats number (e.g., growth hormone receptor, regulation of the BMP - Bone Morphogenetic Proteins signaling pathway and blood vessel proliferation). Three most candidate genes for litter size trait (<em>GRID2</em>and <em>PALB2</em>) and six most candidate genes (<em>GHR, IFT80,</em> <em>FSTL3, SKOR1, SMURF1</em> and <em>AKT3</em>) for teats number were prioritized. TF associated with candidate genes were also identified for litter size (<em>PALB2</em> and <em>GRID2</em>) and teat number (<em>RIN, LTBP2</em> and <em>COL6A6</em>). Thus, it is suggested that the genes and TFs presented in this study may play an important role in the traits studied, being important for genetic studies and animal breeding. The highlighted genes may bring new considerations to the current knowledge of the genetic architecture of these traits, since the markers associated with these genes can be assigned higher weights in genomic selection and validated in specific populations.</p>
Why the long teeth? Morphometric analysis suggests different selective pressures on functional occlusal traits in Plio-Pleistocene African suids
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Data from: Trait-based functional dietary analysis provides a better insight into the foraging ecology of bats
1. The degree of trophic specialization determines the ability of predators to cope with changing foraging conditions, but in predators that prey on hundreds of species it is challenging to assess, especially when prey identity varies among predator individuals and across space and time. 2. Here, we test the hypothesis that a bat species foraging on flying insects like moths will show ample flexibility in trophic niche, and this irrespective of phylogenetic relationships among moths, so as to cope with a high diversity of prey types that vary across seasons. We predict that individual bats will show functional dietary differences consistent with energetic requirements and hunting skills. 3. We used DNA metabarcoding to determine the diet of 126 Mediterranean horseshoe bats (Rhinolophus euryale) from two different sites during three seasons. Simultaneously, we measured moth availability and characterized the traits of 290 moth taxa. Next, we explored the relationship between phylogeny and traits of all consumed and available moth taxa. Finally, we assessed the relationship between individual traits of bats and traits related to prey profitability, for which we used the RLQ and fourth-corner statistical techniques. 4. Seasonality was the main factor explaining the functional dietary variation in adult bats, with moths consumed irrespective of their phylogenetic relationships. While adults consumed moths with a broad range in wing loading, body mass and echolocation detection ability, juveniles consumed slower, smaller and lighter moths, which suggests that young individuals may undergo some fitness gain and/or psychomotor learning process during which they would acquire more effective foraging skills. 5. Our approach revealed a degree of functional flexibility in the trophic niche previously unknown for an insectivorous bat. R. euryale consumed a wide variety of moth taxa differing in profitability throughout seasons and between ontogenetic stages. We showed the validity of trait-based approaches to gain new insights in the trophic specialization of predators consuming hundreds of species of prey.
Data from: Trait-based functional dietary analysis provides a better insight into the foraging ecology of bats
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A meta-analysis of natural selection on plant functional traits
<p>A common assumption in plant physiological ecology is that variation in functional traits reflects the adaptation of organisms to their abiotic environment. This assumption can be tested by estimating natural selection as the relationship between a functional trait and a fitness component (i.e. survival or reproduction) within a population. To understand how natural selection operates on plant functional traits, we compiled directional selection gradients (<i>β</i><span><span></span></span>), which estimate direct selection, and differentials (<i>S</i><span><span></span></span>), which estimate both direct and indirect selection, from studies conducted in manipulated and unmanipulated environments. We found that relative to manipulating biotic factors, manipulating abiotic factors had a ~5.7´ larger effect on <i>β </i><span><span></span></span>and a ~16´ larger effect on <i>S</i><span><span></span></span>, suggesting that functional traits primarily evolve in response to the abiotic environment. We found that the strength of selection on functional traits <i>(</i><span></span><i>β</i><i>)</i><span><span></span></span> did not vary with trait type, performance/fitness component, or measurement context (i.e. common garden vs. natural population). However, the direction of selection did differ between some trait types: <i>β</i><span><span></span></span> was positive for plant size traits, but negative for phenology traits. Lastly, we found that the absolute value of selection differentials (<span></span><i>S</i><span><span></span></span>) was ~2´ larger than the absolute value of selection gradients (<span></span><i>β</i><span><span></span></span>), indicating that there was indirect selection on functional traits. Overall, our meta-analysis illustrates that natural selection on plant functional traits is common, and that estimates of selection on these traits in experimentally manipulated environments can be used effectively to test hypotheses about the causes of adaptation.</p>
Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted
A plant's growth rate is seen as a central element of its ecological strategy, and as determined by its traits.Yet the literature is inconsistent about the empirical correlation between functional traits and growth, casting doubt on the capacity of some prominent traits to influence growth rate. We propose that traits should influence growth in a way that depends on the size of individual plants. We outline mechanisms and hypotheses based on new theoretical work, and test these predictions in tree species using a meta-analysis of 103 studies (> 500 correlations) for five traits (specific leaf area, wood density, maximum height, seed mass and maximum assimilation rate).We also recorded data for 14 other traits commonly used in the trait literature.To capture the effects of plant size, we tested for a shift in the direction of correlation between growth rates and each trait across three ontogenetic stages: seedling,sapling and adult. Results were consistent with predictions, although there were some limitations arising from unequal numbers of observation across ontogenetic stages.Specific leaf area was correlated with relative growth rate in seedlings but not in adult plants.Correlations of growth with wood density were not affected by ontogenetic stage. Seed mass, assimilation rate and maximum height were correlated with relative growth rate only in one ontogenetic stage category: seedlings,seedlings and adults,respectively. Although we were able to confirm several of our theoretical predictions,major knowledge gaps still exist in the trait literature.For example,for one third of the traits considered,the majority (> 75%) of reported correlations with growth came from the same ontogenetic stage. Synthesis: We show for some traits, how trait-growth correlations change in a predictable way with plant size.Our understanding of plant strategies should shift away from describing species as having a fixed growth strategy throughout their life (on a continuous axis from slow to fast growth), in favour of a size-dependent growth trajectories.
Raw data associated to the paper "Analysis of species pair associations combined with functional traits reveals the effects of environmental filtering and biotic interactions in an unmanaged temperate forest"
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Effects of blood cell traits on cardiovascular morpho-functional phenotypes: Evidence from Mendelian randomization analysis
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Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted
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A meta-analysis of natural selection on plant functional traits
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Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ChIP-Seq]
GEO Series GSE106372. Branchiostoma lanceolatum. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits
GEO Series GSE106431. Branchiostoma lanceolatum; Danio rerio; Oryzias latipes. 217 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [ATAC-Seq]
GEO Series GSE106428. Branchiostoma lanceolatum; Oryzias latipes; Danio rerio. 29 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA-Seq]
GEO Series GSE106430. Branchiostoma lanceolatum; Danio rerio; Oryzias latipes. 81 samples. Type: Expression profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of ptychodera and the origin of vertebrate genomic traits
GEO Series GSE189808. Xenopus tropicalis; Ptychodera flava. 18 samples. Type: Expression profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [CAGE]
GEO Series GSE106429. Branchiostoma lanceolatum. 7 samples. Type: Expression profiling by high throughput sequencing.
Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [4C-seq]
GEO Series GSE115945. Danio rerio. 83 samples. Type: Other.
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