2.5.4 Phylogenetic Analysis:
To assess the phylogenetic relationship, we construct two phylogenies
(One for sampled species and other representing MHC class I sequences of
related passerines plus sampled species) using Bayesian inference. We
find the GTR+T nucleotide substitution model [52] that fits our data
using MrModeltest [35] through the Akaike Information Criterion
(AICc) [53]. Bayesian Markov chain Monte Carlo (MCMC) was run for
two million generations and sampling every 1,000 generations to
ascertain when log Likelihood reached stationary phase. The phylogenetic
tree was summarized in MrBayes v3.1.2 [54] and the first 25% of the
tree as burn‐in was removed. Fig tree was used for visualization of the
consensus tree. Exploration of relation between sampled species and
related avian species, we conducted a maximum likelihood (ML) analysis
with MEGA 7.0 [55]. The data were analyzed with the T92+G model. We
conducted 1000 bootstrap replicates to estimate the support. Values
greater than 75% were indicated in the ML phylogenetic trees. The
species covered are mainly fromPasseridae,
Acrocephalidae,
Paridae, Motacillidae,
Muscicapidae,
Hirundinidae,
Phylloscopidae,
Fringillidae,
Cardinalidae, Sturnidae .
Representative sequences from samples species and other selected for
phylogenetic analysis were summarized in (See Table S3) with respective
studied reference from GenBank.
To further identify allelic lineages among sampled species and related
avian species, we conducted the Neighbor-Net algorithm in SplitsTree
4.14.8. Neighbor-Net networks were based on uncorrected P-distances and
carried out 1000 bootstrap replicates to estimate nodal support. Nodal
support values (> 75%) were displayed.