Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments

Li, Xuejuan; Lu, Lin; Cui, Aiming; Bai, Jie; Wang, Xiaoyang; Xin, Chao; Zhang, Zhen; Yang, Chao; Gao, Rong; Huang, Yuan; Lei, Fumin

doi:10.1016/j.ympev.2016.07.022

Cited by 9 publications

(6 citation statements)

References 38 publications

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“…MW298528). All mitogenomes exhibited A-skew and obvious C-skew, which was consistent with findings in other birds [ 61 - 63 ]. However, a significant negative AT skew was in ND3 in Charadrius vociferous on the P-strand.…”

Section: Resultssupporting

confidence: 90%

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Qian,

Liu,

Miao

et al. 2023

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Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Methods: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of nonsynonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Results: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

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Section: Resultssupporting

confidence: 90%

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Qian,

Liu,

Miao

et al. 2023

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“…All mitogenomes showed a tendency toward A-skew and obvious C-skew (Suppl. material 8 : Table S2), which was similar to findings in other birds ( Kan et al 2010 ; Eberhard and Wright 2016 ; Li et al 2016a ).…”

Section: Results and Discussionsupporting

confidence: 89%

“…For example, the phylogenetic tree topologies obtained from the complete mitogenome are not identical to those resulting from individual mitochondrial genes in some avian taxa ( Campillo et al 2019 ). In addition, the phylogenetic relationships recovered from nuclear segment datasets are inconsistent with those recovered from mitogenomes in some aves ( Li et al 2016a ; Campillo et al 2019 ). Therefore, our results indicate that further studies are needed to address the phylogenetic relationships within Motacilla by adding more sampling and some nuclear data.…”

Section: Results and Discussionmentioning

confidence: 87%

“…In most animals, the mitochondrial genome (mitogenome) contains 13 protein-coding genes ( PCGs ), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), and one noncoding region (the control region, CR) ( Wolstenholme 1992 ; Boore 1999 ). Mitochondrial sequences are commonly used for inferring phylogeny ( Hassanin et al 2005 ), and the mitogenome has been used as an effective marker for exploring the phylogenies of some avian taxa ( Li et al 2016a ; Mackiewicz et al 2019 ; Cai et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

Yang¹,

Du²,

Yuxin³

et al. 2022

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The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M. flava, M. cinerea, M. alba and Dendronanthus indicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M. flava and M. tschutschensis showed closer relationships, and M. cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.

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“…Li et al, 2016) [1]. The mitochondrial genomes and nuclear segments of tits were sequenced to analyze mitochondrial characteristics and phylogeny.…”

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confidence: 99%

Data on taxonomic status and phylogenetic relationship of tits

Cui

et al. 2017

Data in Brief

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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.

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Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments

Cited by 9 publications

References 38 publications

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

Data on taxonomic status and phylogenetic relationship of tits

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Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments

Cited by 9 publications

References 38 publications

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

﻿Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

Data on taxonomic status and phylogenetic relationship of tits

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Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications