Fig 1.
Family-level phylogenetic relationships of Charadriiformes.
(A) based on RAG-1 [12], (B) based on 14 mitochondrial genes [8], (C) based on 3 mitochondrial genes and 3 nuclear genes [11], and (D) based on 3 mitochondrial genes and 1 nuclear gene [13].
Table 1.
List of the complete mitogenomes sequences included in this study.
Fig 2.
Circular map of the mitochondrial genome of Gallinago stenura.
Fig 3.
The A + T content in Charadriiformes mitogenomes.
Each point represents a species.
Table 2.
Nucleotide composition of mitochondrial genomes in Charadriiformes.
Fig 4.
The AT skew and GC skew in Charadriiformes mitogenomes.
Each point represents a species.
Table 3.
The mutational information and average distances among Charadriiformes calculated by gene.
Fig 5.
Evolutionary rates of 13 protein-coding genes in Charadriiformes mitogenomes.
The Y-axis provides the substitution rate of mitochondrial gene. Synonymous nucleotide substitutions per synonymous site (Ks) and nonsynonymous nucleotide substitutions per nonsynonymous site (Ka) are calculated using Dnasp, and dN/dS is calculated using DataMonkey.
Fig 6.
The usage of start and stop codons in the 13 mitochondrial protein-coding genes of the order Charadriiformes.
All genes are shown in the order of occurrence in the mitochondrial genome starting from ND1.
Fig 7.
Organization of the control region in Charadriiformes mitochondrial genomes.
The location and copy number of tandem repeats are shown by oval with Arabic numerals inside. Non-repeat regions are indicated by square box. L: Length.
Fig 8.
The phylogenetic trees of Charadriiformes based on the 13 mitochondrial protein-coding genes, 12S and 16S dataset using BI and ML methods.
Branch lengths and topologies were obtained using Bayesian inference analysis, and the numbers above each branches are the posterior probabilities and ML bootstrap support.
Fig 9.
The phylogenetic trees of Charadriiformes based on the concatenated 12 mitochondrial protein-coding genes using BI and ML methods.
Branch lengths and topologies were obtained using Bayesian inference analysis. Asterisks indicate bootstrap values of 100% and posterior probability of 1.