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3 results for “Ecological indirect effect”
Relyea, R. A. 2000. Trait-mediated indirect effects in larval anurans: Reversing competition with the threat of predation. Ecology 81:2278-2289.
Ecologists recently have been focusing on the role that trait-mediated indirect effects can have on community structure and composition. To date, this work has primarily focused on the effects of predator-induced behavioral plasticity on communities. However, predator-induced morphological plasticity, which has been documented in many taxa, might also lead to trait-mediated indirect effects. Here, I examined how predators altered the behavior and morphology of larval wood frogs (Rana sylvatica) and leopard frogs (R. pipiens) and how these phenotypic changes altered the outcome of competition between the two species. Competition in the absence of caged predators was asymmetric; when reared separately, leopard frogs grew more than wood frogs, but when competing (without predators), wood frogs grew faster than leopard frogs. The presence of caged predators reversed the outcome of competition between the two anuran prey. In the presence of larval dragonflies (Anax spp.) or caged mudminnows (Umbra limi), leopard frogs grew faster than wood frogs while total tadpole biomass production remained unchanged. Thus, there was a predator-mediated indirect effect. Because predators alter both the behavior and morphology of larval anurans and both of these traits are known to affect resource consumption and growth, both are potential mechanisms to explain the change in competitive outcome. Changes in behavior were not related to changes in growth, but changes in morphology (specifically mouth width and tail length) were related to changes in growth. When competitors were added (without predators), wood frogs increased their mouth width by 10% and their tail length by 3%, while leopard frogs increased their mouth width by 5% and did not change their tail length. The greater increase in mouth width for wood frogs should increase their forage intake, since tadpoles feed by scraping periphyton; the importance of a 3% longer tail in competitive ability is unknown. The presence of the p
Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana
<p><em>This folder contains data & code used for the study "Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana"</em></p> <p>All data analyzed in the study are stored in the folder "data":</p> <ul> <li>"pheno_file.csv": the main phenotypic file corresponding to the experiment with paired plants used to estimate Indirect Genetic Effects.</li> <li>"pheno_file_single_plants.csv": phenotypic file with measurements of plant biomasses in the absence of competition (single plants)</li> <li>"call_method_75_TAIR9.csv": genomic data (SNPs) for each accession from the RegMap panel (ref [1])</li> <li>"Data_geo_RegMap_accessions.csv": geographic localization of each accession from the RegMap panel (ref [2])</li> <li>"igeGWAS_scores.csv": Genome-Wide Association Study (GWAS) results reporting for each SNP from the RegMap panel the p-value and estimated effect sizes of their direct and indirect genetic effects</li> <li>"1001_accessions_info.csv": geographic localization and admixture group for each accession from the 1001 genomes project (ref [3])</li> <li>"snp_data_all_samples.txt": allelic value of each accession from the 1001 genomes project at the eleven top SNPs associated with IGE</li> <li>"sample_names.txt": names of accessions listed in the file "snp_data_all_samples.txt"</li> <li>"climatic_data.csv": climatic data for each accessions from the 1001 genomes project (ref [4])</li> <li>"candidate_genes_all.csv": list of all genes (and associated GO terms) with a non-synonymous, nonsense, or frameshift mutation in close proximity (distance < half LD decay distance) and high linkage (r2>0.5) with a SNP significantly associated with IGE</li> <li>"genes.coord.bed": list of all genes in a +- 500 kb around top IGE SNPs and their coordinates</li> <li>"AllGenes_fst.GeneID.txt": pairwise Fst computed between each pair of admixture groups, for all genes annotated in the genome of A. thaliana</li> </ul> <p>"ABBA_BABA" subfolder contains ABBA_BABA statistics computed for each individual chromosome (Chr1-Chr5) using genomic windows of 20 kb with at least 250 SNPs per windows. ABBA-BABA statistics were computed using custom python scripts from https://github.com/simonhmartin/genomics_general</p> <p><br> "GEA" subfolder contains Genome-Environment Association results, with one file per chromosome x climatic variable. Climatique variable are indexed, following the order listed in the file "Climatic_variables.txt" within the subfolder "GEA". GEA analysis were run with the gemma program: https://github.com/genetics-statistics/GEMMA.</p> <p><br> "LD_IGE_SNPs" subfolders contains the list of SNPs located at +- 2Mb of a significant IGE SNP (one file per IGE SNP, named "SNPalias_LDSimplified.csv") and their linkage (r2) with the IGE SNP. It also contains the file "LD_windows_sizes.csv" with the half LD decay distances for all significant IGE SNP.</p> <p>All analysis performed to produce the tables and figures presented in the study (main manuscript & supplementary information) were done with the R script "Arabidopsis_IGE_analysis.R", which uses "manhattan_custom.R" as a source function to produce custom manhattan plots.</p> <p> </p> <p><strong>REFERENCES:</strong></p> <p>[1] Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjálmsson BJ, et al. 2012. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212–216.</p> <p>[2] Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. 2011. Source verification of mis-identified Arabidopsis thaliana accessions. The Plant Journal 67: 554–566.</p> <p>[3] 1001 Genomes Consortium. 2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491.</p> <p>[4] Ferrero-Serrano Á, Assmann SM. 2019. Phenotypic and genome-wide association with the local environment of Arabidopsis. Nature Ecology & Evolution 3: 274–285.</p>
Data from: Wildfire disturbance and ecological cascades: teasing apart the direct and indirect effects of fire on tick populations
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