Data on taxonomic status and phylogenetic relationship of tits

The data in this paper are related to the research article entitled “Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments” (X.J. Li et al., 2016) [1]. The mitochondrial genomes and nuclear segments of tits were sequenced to analyze mitochondrial characteristics and phylogeny. In the data, the analyzed results are presented. The data holds the resulting files of mitochondrial characteristics, heterogeneity, best schemes, and trees.


a b s t r a c t
The data in this paper are related to the research article entitled "Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments" (X.J. Li et al., 2016) [1]. The mitochondrial genomes and nuclear segments of tits were sequenced to analyze mitochondrial characteristics and phylogeny. In the data, the analyzed results are presented. The data holds the resulting files of mitochondrial characteristics, heterogeneity, best schemes, and trees.
& 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). The analyses of A þT contents, conserved site percentages and P-distances, were obtained in MEGA 4.1 [2]. Sequences were aligned in Muscle [3]. The best schemes were analyzed in Partitionfinder v1.1.1 [4]. The heterogeneity was inferred with AliGROOVE [5]. The gene trees based on six datasets (one mitochondrial dataset and five nuclear segments) were constructed in RAxML 7.0.3 [6]. A species tree was obtained with employing these gene trees in ASTRAL [7]. Data format Analyzed Experimental factors

Specifications
The RY-coding method was employed for the third sites of protein-coding genes, while nuclear dataset was divided into different parts (exons and introns).

Experimental features
The phylogeny employed the best schemes inferred by PartionFinder v1.1.1 [4]. A species tree was obtained by employing gene trees in ASTRAL [7]. Data source location

Shaanxi Normal University
Data accessibility Data is with this article

Value of the data
The provided files of comparative mitochondrial characteristics of tits can be valuable to further summarize.
The files of phylogenetic relationships would help to further study the phylogeny of tits and even Passeriformes.
The provided '.tree' files can be directly used to compare with other results.

Data
In the data, Figs. 1 and 2 show base compositions and conserved site percentages of tits, respectively. Fig. 3 is the result of heterogeneity. Fig. 4 shows gene trees and a species tree. Table 1 describes the taxonomic samples. Table 2 lists the primer sequences. Table 3 is the P-distance based on mitochondrial dataset. Table 4 shows the best schemes.

Experimental design, materials and methods
This study sampled 13 individuals of tits by using Sylviparus modestus and Remiz consobrinus as outgroups. Each gene was aligned in Muscle [3] independently. The mitochondrial characteristics, including A þT contents, conserved site percentages and P-distances, were analyzed by using MEGA 4.1 [2], and the results can be found in Figs. 1 and 2 and Table 3, respectively.
Four datasets, A: the first and second sites of protein-coding genes, B: protein-coding genes with the third sites not employing RY-coding method, C: 37 mitochondrial genes with the third sites of protein-coding genes not using RY-coding method plus one control region, D: five nuclear segments, were used to analyze the heterogeneity in AliGROOVE [5], and the results can be found in Fig. 3. The best schemes were analyzed by using Partitionfinder v1.1.1 [4], and the results were in Table 4. The gene trees in Fig. 4 were constructed by using RAxML 7.0.3 [6], employing 1000 replications, and these results were used to construct a species tree by using ASTRAL [7].