determine whether apoptosis spread up the thin tube in a diffusive fashion, with propagation slowing as apoptosis proceeded, or at a constant velocity as expected for trigger waves
The hypothesis here is that: a diffusive apoptotic wave will slow down over the course of time while apoptosis propagated by trigger waves will maintain a steady speed during progression.
The scanning or probing movements have also been hypothesized to help recognize object features.
The movements that these electric fish use allows for the recongition of an object's features. Evidence from Heiligenberg's stimulation show that when electric fish bend their tails it increases the spatial contrast and makes it easier to distinguish an object's features. While Bacher's 3-D model showed that fish's tail bending help show a clear difference between the object's location and its shape . The BEM stimulation showed that electric fish control their movement in order to regulate their electrosensory system input by demonstrating a stable image of the rostral body which is thought to help the fish to distinguish features. - Michelle Gomez-Guevara
We used maximum entropy models [MaxEnt (17)] to infer the contributions of 11 bioclimatic variables to the distribution of each SNP allele (table S3) (16) and tested whether fitness-associated alleles occupy specific climate spaces relative to genomic controls
The authors hypothesized that high fitness alleles would be associated with climate as they were the basis of local adaptation. A maximum entropy model is a way of modelling species geographic distributions with presence-only data. This means that the researcher only needs to input where the species are known to be and not where they are known not to be as this data is rarely available. This model was used to identify whether 11 climatic factors affected the distribution of the alleles.
To identify potential candidate genes for local adaptation, we searched for fitness-associated SNPs in the top 0.05% (with minor allele frequency >8% to exclude rare deleterious mutations) that also appeared in the top 0.5% of allele climate differentiation and in the top 5% of global iEH
The final analysis conducted in this paper is an attempt to identify the genes that have been vital for local adaptation in Arabidopsis populations. To do this the authors identified alleles that were present in the top 0.05% of alleles strongly correlated with plant fitness, strongly correlated with climatic factors and underwent strong selection.
whether the candidate genes present in 10,000–base pair (10-kbp) windows surrounding the associated SNPs were enriched for a particular subset of the Gene Ontology (GO slim) annotations
The authors wanted to understand what the gene functions were for the alleles that were identified as involved in local adaptation. To do this they compared the genes they identified with a large database of gene functions call the GO slim annotations
determining whether local selection in different environments more commonly acted upon alternate alleles of the same loci, or if entirely different loci were found among different environments.
The authors were interested to find out whether local adaptation in different populations often occurred at the same genetic site or occurred in many different sites.
We also tested whether fitness-associated SNPs were involved in recent selective sweeps by computing the integrated extended haplotype homozygosity (iEH) around each SNP
A selective sweep occurs when a new beneficial allele rapidly spreads through a population due to selection.
The authors were interested to know if local adaptation is based on selective sweeps or alleles that are already present in a population.
To do this the authors assessed the extended haplotype homozygosity around each allele involved in local adaptation. This method evaluates whether the alleles surrounding the allele of interest have been largely preserved. If they have then this suggests the allele of interest underwent a selective sweep which lead to the conservation of the surrounding alleles.
We therefore tested whether the global frequency of the alleles associated with high fitness was different relative to genomic controls
The authors wanted to understand whether the genetic basis of local adaptation was a few beneficial genes that become common in a population or whether it was based on the removal of locally deleterious genes. They did this by comparing the frequency of the alleles involved in local adaptation to genomic controls that were not involved in local adaptation.
limited by sample size in Finland (16) as well as by the sparse sample of local ecotypes available for our sites in Finland and Spain
In Finland fewer plants could be planted in the common garden experiments and fewer Arabidopsis populations naturally occur nearby. Smaller sample sizes reduce the likelihood of identifying statistically significant results. The authors suggest that the results may have been significant if they had been able to increase the sample sizes in Finland.
We tested whether alleles associated with high fitness in a given site were more locally abundant than genomic controls, as expected if they contributed to the local adaptation of that population
In order for the researchers to investigate the genetic basis of local adaptation they first need to prove that the populations are locally adapted.
Therefore, the first hypothesis they test is that alleles that increase plants fitness in a certain location are more likely to be abundant in that location than anywhere else. Whereas genomic controls, alleles not necessary for increased fitness, will be not be abundant in one area compared to another.
For each fitness trait in each of the four field sites, we defined a set of associated SNPs corresponding to the 0.05% of the SNPs that explained the most variance (around 100 per GWAS; figs. S2 and S3)
0.05% of all SNPs were selected as being important for explaining differences in survival and reproduction between populations. The genes that contained these SNPs are hypothesized to be important for local adaptation. These SNPs are used in the study as genetic markers to identify genetic differences in local adaptation in the populations studied.
genome-wide association study (GWAS) for survival and silique number using 213,248 single-nucleotide polymorphisms (SNPs)
The authors used a genome wide association study to identify links between plant survival (and reproduction) and single nucleotide polymorphisms (SNPs).
SNPs are mutations in DNA where one base- A, T, C or G -has been changed.
If a SNP is identified as linked to survival or reproduction then the gene that contained the SNP can be identified. Therefore, genes associated with reproduction and survival can be identified.
we grew a geographically diverse set of ecotypes (inbred lines derived from natural populations) across their native range, in replicated common garden experiments in four European field sites
In order to show that Arabidopsis populations are locally adapted the authors used common garden experiments. In this experimental set up the effect of environment is tested by moving species from their native environment into one common environment.
It is hypothesized that if populations are locally adapted then the population that normally grows in an environment similar to the common one will have a higher survival rate. For instance, plants that naturally grow in a Mediterranean environment will be more likely to survive in Spain than plants that normally grow in the much colder climate of Finland.
We control for the same variables as described in Model 6 of Table 1.
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