Wildlife managers will benefit from the more complete genomic perspectives offered by advances in genomics technologies, as population-level genetic variation has the potential to be partitioned into categories of neutral variation, putatively adaptive variation, and potentially misleading variation.
On the other hand, substrain-specific variants may have a relatively large effect on protein function and thus on associated biology and it is therefore extremely important to know this category of variation when comparing experimental results obtained with different rat substrains in different labs.
ML and BI analyses of the amino acid alignment (i.e., alignment 4) was analyzed under a WAG model of substitution considering corrections for site-to-site rate variation (gamma) with eight categories of rate variation and proportion of invariable sites.
The distributions of variations are shown in the form of a histogram and show the percentages of each category of variations before and after variation filtering.
Five categories of stress variation patterns are classified, each of which provides a criteria of choosing an optimized interlayer thickness to reduce thermal stresses.
In each analysis, 4 categories of rate variation were used.
The best likelihood trees were searched under the GTR-GAMMA model with six categories of rate variation (500 bootstrap replicates were undertaken for estimation of node support).
We utilised four categories of rate variation across the amino acid sites and 500 bootstrap replicates were generated for the estimation of node support.
We performed this inference on both untrimmed and BMGE-trimmed versions of the concatenated matrix, using a combination of NNI and SPR heuristic searches, and inferring under the LG+F model with four 'free' (--free-rates) categories of rate variation.
Nucleotide substitution models were obtained from jModeltest (version 2.1, [ 38, 39], testing 11 substitution schemes, each with 4 categories of rate variation among sites) and using the corrected AIC criterion (AICc) to find the best fitting model.
Array comparative genomic hybridization (aCGH) to detect copy number variants (CNVs) in mammalian genomes has led to a growing awareness of the potential importance of this category of sequence variation as a cause of phenotypic variation.
