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Research Article
Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications
expand article infoChao Yang§, Xiaojuan Du, Yuxin Liu, Hao Yuan|, Qingxiong Wang§, Xiang Hou§, Huisheng Gong§, Yan Wang§, Yuan Huang, Xuejuan Li, Haiyan Ye
‡ Shaanxi Normal University, Xi’an, China
§ Shaanxi Institute of Zoology, Xi’an, China
| Xi’an Medical University, Xi’an, China
Open Access

Abstract

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.

Keywords

Comparative analysis, mitogenome, phylogeny

Introduction

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).

Passeriformes comprises 6533 currently described species (Gill et al. 2020). The genus Motacilla belongs to Motacillidae (Passeriformes) and contains 12 species (Alström et al. 2003; del Hoyo et al. 2004), which show striking plumage pattern variation (Harris et al. 2018). Motacilla flava Linnaeus, 1758 is a small, insectivorous oscine (Ödeen and Björklund 2003) and is closely related to M. alba Linnaeus, 1758, distributed in the Palearctic (Dong and Zhang 2011). Some mitochondrial fragments, such as nad2 and CR of M. alba (Li et al. 2016b), have been used to study the phylogeography and population history of Motacilla. Additionally, some mitochondrial genes, such as nad2 (Suppl. material 1: Fig.S1A; Dong et al. 2016) and cytb (Suppl. material 1: Fig. S1B; Zhang et al. 2016), have been used to study the phylogenetic relationships of Motacilla. However, the phylogenetic position of some Motacilla species is still controversial. For example, M. alba has been reported to form a sister group with M. madaraspatensis Gmelin, 1789 (Suppl. material 1: Fig. S1A, Dong et al. 2016), but it has also been grouped with M. cinerea Tunstall, 1771 (Suppl. material 1: Fig. S1B; Zhang et al. 2016). In addition, phylogenetic results reconstructed from genome-wide SNPs (Suppl. material 1: Fig. S1C, Harris et al. 2018) have some incongruence with those based on mitochondrial genes or mitogenomes (Suppl. material 1: Fig. S1A, B, D; Dong et al. 2016; Zhang et al. 2016; Gao et al. 2019).

Figure 1. 

Gene map of four newly sequenced mitogenomes. Notes: tRNAs are abbreviated with a single letter; mitochondrial genes encoded by the J- and N-strands, indicated in bold, are located outside and inside of the circle, respectively.

An increasing number of avian mitogenome sequences are being generated with high-throughput sequencing technology (Morinha et al. 2016; Yang et al. 2018), facilitating the identification of mitogenomic characteristics such as gene order and base composition through the comparison of mitogenomes. However, the limited Motacilla mitogenomic sequences available from the GenBank database restricts the exploration of mitogenome features in this genus. For example, recent studies of Motacilla (Dong et al. 2016; Zhang et al. 2016; Harris et al. 2018; Gao et al. 2019) have focused on the phylogenetic relationships within this genus but have not conducted further comparative analyses among mitogenomes. In the present study, we obtained complete mitogenome sequences of M. flava, M. cinerea, M. alba, and Dendronanthus indicus Gmelin, 1789, performed comparative analyses and generated phylogenies (Subspecies differentiation was not discussed here). The new mitogenome data not only may help us understand the mitogenomic characteristics of Motacilla but also provide a basis for exploring phylogenetic relationships.

Methods

Specimen collection

Muscle samples were collected from the following species: M. flava (from China, Shaanxi Province, Hongjiannao in 2013); M. cinerea (from China, Shaanxi Province, Feng County in 2017); and M. alba and D. indicus (from China, Shaanxi Province, Lantian in 2018). All specimens of muscle samples were preserved in 100% ethanol and stored at -20 °C at the Shaanxi Institute of Zoology, Shaanxi Province, China.

Mitogenome sequencing, assembly and annotation

The mitogenome of M. flava was sequenced by Genesky Biotechnologies Inc., Shanghai, China, using the Illumina HiSeq2000 platform, while those of M. cinerea, M. alba and D. indicus were sequenced at Biomarker Technologies Inc., Beijing, China, using the Illumina Xten platform and a 150 bp paired-end strategy. Genomic DNA was extracted using a DNeasy kit and fragmented using ultrasonic methods to prepare a small-inserted-fragment library. The library data were obtained via Bridge PCR and Illumina paired-end sequencing.

There were 15,149,744 paired-end raw reads of M. flava, of which 47,390 reads were used for mitogenome assembly, with average coverage of 417.1X. There were 20,702,440 paired-end raw reads of M. cinerea, with clean data 6.92 G. A total of 261,229 reads were used for mitogenome assembly, with average coverage of 2256.2X. There were 7,868,047 raw reads in M. alba, with 7,860,296 reads with clean data, and 8,430,436 raw reads of D. indicus, with 8,420,710 reads with clean data.

The raw data from M. flava, M. cinerea and M. alba were quality trimmed with CLC Genomics Workbench 9.5.2 (CLC bio, Aarhus, Denmark) using the default parameters. Mitogenome assembly was performed in MITOBIM 1.8 (Hahn et al. 2013), with M. alba (GenBank: NC029229) as a reference. The mitogenomic sequences of D. indicus were assembled using MitoZ 2.4 (Meng et al. 2019). Mitochondrial PCGs were identified using Geneious 11.1.3 (Kearse et al. 2012) by searching for open reading frames and employing the M. alba mitogenome (GenBank: NC029229) as a reference. Most tRNAs were identified using tRNAscan-SE 1.21 (Lowe and Eddy 1997), with secondary structures used as references. The remaining tRNAs, rRNAs and CRs were identified by comparison with other Motacilla species. Each mitochondrial gene was confirmed by alignment with the corresponding homologous genes from other Motacilla species available in GenBank. The secondary structures of rrnS and rrnL were generated using the mitogenomic rRNAs of Remiz consobrinus as a reference (Gao et al. 2013).

Comparative analysis and phylogenetic reconstruction

The six mitogenomes (M. flava, M. cinerea and M. alba mitogenomes from collected specimens combined with M. tschutschensis, M. alba and M. cinerea genomes from GenBank) were used for comparative analysis. A mitogenome of M. lugens (KU246035/NC_029703) was excluded because this has been shown to represent a chimera (Sangster and Luksenburg 2021). The nucleotide compositions of the mitogenomes and different datasets were calculated using Geneious 11.1.3 (Kearse et al. 2012). Nucleotide bias was calculated using the formulas AT-skew = (A−T)/(A+T) and GC-skew = (G−C)/(G+C) (Perna and Kocher 1995). Relative synonymous codon usage (RSCU) was calculated with MEGA 11 (Tamura et al. 2021).

A total of 90 mitogenomes of Passeriformes were used to reconstruct phylogenetic relationships; the included mitogenomes came from 12 taxonomic families with Aethopyga gouldiae (Nectariniidae) used as an outgroup (Suppl. material 7: Table S1). Each mitochondrial gene was aligned individually using MUSCLE in MEGA 11 (Tamura et al. 2021), starting with the alignment of PCGs to amino acid sequences. One mitogenomic dataset (mtDNA) was used for phylogenetic analysis, which included the nucleotide sequences of 13 PCGs, two rRNAs and 22 tRNAs, with a length of 15,722 bp. The best models of GTR+F+R5 for maximum likelihood (ML) analysis and GTR+F+I+G4 for Bayesian inference (BI) analysis were assessed in ModelFinder (Kalyaanamoorthy et al. 2017) using the Bayesian information criterion (BIC) in PhyloSuite 1.2.1 (Zhang et al. 2020). Phylogenetic relationships were analyzed using ML phylogenies with IQ-TREE 1.6.8 (Nguyen et al. 2015) with 1000 bootstrap replicates. The BI phylogeny was analysed with MrBayes 3.2.7 (Ronquist et al. 2012). Two independent runs with four simultaneous Markov chains were run for 5,000,000 generations and were sampled every 100 generations. The first 25% of generations were discarded as burn-in. The effective sample size (ESS) values were estimated in Tracer 1.7 (Rambaut et al. 2018), with ESS values > 200.

Results and discussion

Mitogenomic structure and organization

The obtained complete mitogenomes of M. flava, M. cinerea, M. alba and D. indicus ranged from 16,831 bp to 16,870 bp in length and each contained 37 genes and a noncoding region (CR) (Fig. 1). The complete mitogenome sequences were submitted to GenBank (MW929088MW929091). Four gene arrangements have been identified among the Passeriformes mitogenomes sequenced to date (Caparroz et al. 2018; Mackiewicz et al. 2019). The gene order cytb-trnT-trnP-nad6-trnE-CR-trnF-rrnS is found in the mitogenomes of three Motacilla species and D. indicus, which is consistent with the order observed in most Passeriformes species (Mackiewicz et al. 2019). The major strand (J-strand) encodes 12 PCGs and two rRNAs as well as trnF, trnV, trnL(uur), trnI, trnM, trnW, trnD, trnK, trnG, trnR, the HSL cluster [trnH, trnS(agy), trnL(cun)] and trnT (Fig. 1). The lengths of the intergenic spacers range from 1–23 bp in the three Motacilla mitogenomes and 1–18 bp in D. indicus, with the longest intergenic spacer being located between the trnP and nad6 genes.

Comparative analysis of Motacilla mitogenomes

The gene orders and nucleotide compositions of the six sampled Motacilla mitogenomes were generally similar. For instance, the A+T content ranges from 53.5% to 53.9%, which was slightly higher than the G+C contents. 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).

Protein-coding genes

The A+T contents of the 13 PCGs excluding stop codons ranged from 52.4% to 52.9% in sampled Motacilla mitogenomes (Suppl. material 8: Table S2). The highest A+T content was found at the second codon position in all Motacilla mitogenomes. Obvious T-skew was recovered at the second codon position, while the most significant A-skew was found at the third codon position. The three codon positions showed different degrees of C-skew, which was most obvious at the third codon position.

The first and last codons of the PCGs of Motacilla were compared (Suppl. material 9: Table S3). Twelve of the 13 PCGs started with an ATG codon, while nad3 started with ATT. The start codons were conserved in the six mitogenomes. The termination codons of the PCGs included TAA, TAG, AGG, AGA, TA and T, which are conserved among PCGs with the exception of cox2, cox3 and nad2. The incomplete T termination codons found in cox3 and nad4 have also been reported in other avian mitogenomes (Ma et al. 2014; Li et al. 2015; Eberhard and Wright 2016).

RSCU analysis indicated that among all PCGs, codons including A or C at the third position were frequently overused relative to other synonymous codons (Fig. 2). The codon usage among Motacilla species was found to be conserved, with CUA (L), CGA (R) and UCC(S) representing the most frequently used codons.

Figure 2. 

RSCU analysis of the PCGs of six mitogenomes from the genus Motacilla. Note a M. alba b M. cinerea c M. flava d M. tschutschensis e M. alba (MN356232) f M. cinerea (NC_027933).

RNA genes

Similar to other avian mitogenomes, rrnS was found to be located between trnF and trnV, and rrnL was located between trnV and trnL(uur). The length of rrnS was 975 bp in M. alba (MN356232) and 973 bp in the other Motacilla mitogenomes, while the length of rrnL was 1595 bp in all Motacilla species. The A+T content was slightly greater than the G+C content in the rRNA genes, ranging from 52.2% to 52.3% in rrnS and 55.2% to 55.4% in rrnL, and both rRNA genes exhibited A-skew and C-skew (Suppl. material 8: Table S2).

The rrnS included three domains and 47 helices in M. flava (Suppl. material 2: Fig. S2), while rrnL included six domains and 60 helices (Suppl. material 3: Fig. S3). Most of the identified sequences and secondary structures were conserved compared with those of other Motacilla rRNAs. In addition, most of the stems of the rRNA secondary structures were similar to those found in other Passeriformes mitogenomes. For example, stems 21 and 47 of rrnS and 15 and 40 of rrnL were consistent with those found in R. consobrinus (Gao et al. 2013).

A total of eight tRNAs (trnQ, trnA, trnN, trnC, trnY, trnS(ucn), trnP and trnE) were located on the N-strand, while the remaining 14 tRNAs were located on the J-strand (Fig. 1). The lengths of the 22 tRNAs in each Motacilla species ranged from 66 to 75 bp. The A+T content ranged from 58.3% to 58.6% in the tRNAs, which exhibited A-skew and G-skew (Suppl. material 8: Table S2).

Twenty-one of the 22 tRNAs of M. flava were folded into a clover-leaf-like secondary structure, with the exception of trnS(agy), lacking a dihydrouridine (DHU) stem (Suppl. material 4: Fig. S4), which is considered to be a typical feature of metazoan mitogenomes (Wolstenholme 1992). Comparisons among Motacilla tRNAs showed that the most conserved tRNAs were trnL(UUR), trnM, trnW, trnA, trnC, trnH, trnL(CUN), trnT, trnP and trnE (Suppl. material 4: Fig. S4), which contained the same nucleotides. Some mismatched base pairs found in Motacilla were similar to those observed in some other Passeriformes species (Pyrgilauda ruficollis, Ma et al. 2014; R. consobrinus, Gao et al. 2013), such as the C-C pair located in the acceptor stem of trnL(uur) and the anticodon stem of trnG, A-A in the TφC stem of trnD, and U-U in the anticodon stem of trnG.

Control region

The CR was located between the trnE and trnF genes and were 1243–1250 bp in length. The average A+T content was 56.2% among all sampled Motacilla mitogenomes, which was slightly higher than that of G+C. The CRs showed a tendency toward T-skew and C-skew (Suppl. material 8: Table S2), with C-skew being more obvious. This C-skew was consistent with findings in other reported avian CRs (e.g., Huang et al. 2017).

The CR regulates the replication of the H strand and the transcription of all mitochondrial genes (Clayton 1992) and can be divided into three domains: extended termination-associated sequence (ETAS) domain I, central conserved domain II, and conserved sequence block (CSB) domain III (Sbisà et al. 1997; Randi and Lucchini 1998; Ruokonen and Kvist 2002). Among the three domains of the CR, domain I showed slight A-skew and obvious C-skew, domain II showed a tendency toward T-skew and C-skew, and domain III exhibited A-skew and a highly significant C-skew (Suppl. material 8: Table S2).

The proportions of variable sites among the three domains were 3.6%, 2.4% and 9.0%, respectively. Thus, most variation was found in domain III, similar to the findings of previous studies (Ruokonen and Kvist 2002; Huang et al. 2017). A poly-C sequence was found near the 5’ end of CR domain I in M. flava, with a sequence of CCCCCCCCCCTTCCCCCCCC, and this sequence was relatively conserved in the sampled mitogenome CRs (Suppl. material 5: Fig. S5). Within the M. flava CR sequence, boxes F, E, D, C, B and a bird similarity box in domain II were identified. The F, E, D and C boxes were similar to those found in other avian mitogenomes (Suppl. material 5: Fig. S5; Huang et al. 2017). Among these boxes, the F-box, bird similarity box and B-box were fully conserved among sampled mitogenomic sequences. Domain III contained CSB1, whose sequence was similar to that found in other birds (Huang et al. 2017). However, it was difficult to identify sequences corresponding to OH, CSB2, CSB3 and bidirectional LSP/HSP promoters found in other birds (Li et al. 2015), which might play important roles in mitogenome replication. Furthermore, tandem repeat sequences in CRs are found in many avian mitogenomes (Yang et al. 2018). However, none of the sampled Motacilla CRs contained tandem repeats.

Phylogenetic analysis

The ML and BI phylogenetic trees were reconstructed using the mtDNA dataset, showing consistent topological results among Motacillidae (Fig. 3 and Suppl. material 6: Fig. S6). The analyses supported the monophyly of Motacillidae with 100% bootstrap support and posterior probabilities of 1.0. Among the three sampled genera among Motacillidae (Anthus, Dendronanthus and Motacilla), Anthus was sister to D. indicus and Motacilla. The monophyly of Motacilla was also recovered, with D. indicus forming a sister group with Motacilla.

Figure 3. 

Phylogenetic results based on the maximum likelihood method using the mtDNA dataset.

Within Motacilla, the following phylogenetic relationships were recovered: (((M. flava+M. tschutschensis)+M. alba)+M. cinerea), similar to previous studies (Suppl. material 1: Fig. S1A; Dong et al. 2016; Suppl. material 1: Fig. S1D; Gao et al. 2019). Motacilla cinerea was in the basal position within Motacilla, and M. flava showed a closer relationship with M. tschutschensis. However, M. alba showed a closer relationship with M. cinerea (Suppl. material 1: Fig. S1B; Zhang et al. 2016), while M. cinerea presented a closer phylogenetic relationship with M. flava (Suppl. material 1: Fig. S1C; Harris et al. 2018). These differences might be due to the different data types, dataset sizes and sampling strategies involved. 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.

Conclusions

The complete mitogenomes of Motacilla flava, M. cinerea, M. alba and Dendronanthus indicus were sequenced and were shown to present the typical genome organization and gene order found in other Passeriformes mitogenomes. We focused on comparative analyses of the six mitogenomes to identify the mitogenomic characteristics of the genus Motacilla, such as the base composition, codon usage and RNA secondary structures. The complete mitogenomes showed a tendency toward A-skew and C-skew. Most PCGs start with typical ATG codons and terminated with TAA codons. All tRNAs could be folded into classic clover-leaf structures except for trnS(agy), which lacked a DHU arm. In addition, 90 mitogenomes of Passeriformes were used to build the tree of phylogenetic relationships. The phylogenetic tree supported the monophyly of Motacillidae. Within Motacilla, the phylogenetic topology of (((M. flava+M. tschutschensis)+M. alba)+M. cinerea) was recovered.

Acknowledgements

We would like to thank Liliang Lin for kindly providing us with results of data analyses. This work was supported by the National Natural Science Foundation of China (Grant No. 31601846 and 31801993), Natural Science Foundation of Shaanxi Province, China (Grant No. 2017JQ3014 and 2020JM-270), China Postdoctoral Science Foundation (Grant No. 2016M602760), Fundamental Research Funds for the Central Universities, China (Grant No. GK202003052 and GK202103068), Projects of the Department of Science and Technology of Shaanxi Province, China (Grant No. 2019NY-089 and 2018ZDXM-NY-071), and the First Wildlife Resource Survey Project of Xi’an (Grant No. XCZX2015-0297-3). The complete mitogenomes of Motacilla flava, M. cinerea, M. alba and Dendronanthus indicus are openly available on GenBank at https://www.ncbi.nlm.nih.gov/nuccore, with accession No. MW929088-MW929091. CY, XD and XL analyzed the data and wrote the manuscript. CY, YH, XL and YH participated in the design of the experiments. XD, XD, YL, HY, QW, XH, HG and YW helped to improve the manuscript. All authors read and approved the final manuscript.

References

  • Alström P, Mild K, Zetterström B (2003) Pipits and Wagtails of Europe, Asia and North America: identification and systematics. Christopher Helm, London.
  • Cai T, Cibois A, Alström P, Moyle RG, Kennedy JD, Shao S, Zhang R, Irestedt M, Ericson PGP, Gelang M, Qu YH, Lei FM, Fjeldså J (2019) Near-complete phylogeny and taxonomic revision of the world’s babblers (Aves: Passeriformes). Molecular Phylogenetics and Evolution 130: 346–356. https://doi.org/10.1016/j.ympev.2018.10.010
  • Campillo LC, Burns KJ, Moyle RG, Manthey JD (2019) Mitochondrial genomes of the bird genus Piranga: Rates of sequence evolution, and discordance between mitochondrial and nuclear markers. Mitochondrial DNA. Part B, Resources 4(2): 2566–2569. https://doi.org/10.1080/23802359.2019.1637286
  • Caparroz R, Rocha AV, Cabanne GS, Tubaro P, Aleixo A, Lemmon EM, Lemmon AR (2018) Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes. Molecular Biology Reports 45(3): 279–285. https://doi.org/10.1007/s11033-018-4160-5
  • del Hoyo J, Elliott A, Christie D (2004) Handbook of the Birds of the World (Volume 9): Cotingas to Pipits and Wagtails. Lynx Edicions, Barcelona.
  • Dong L, Zhang YY (2011) Theoretical backgrounds and recent advances in avian molecular phylogeography. Acta Ecologica Sinica 31(14): 4082–4093.
  • Dong XY, Pan T, Kang X, Zhang YN, Sun XN, Qian LF (2016) Complete mitochondrial genome of Motacilla alba and implications for Motacillidae taxonomy. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis 27(6): 4675–4676. https://doi.org/10.3109/19401736.2015.1106497
  • Gao RR, Huang Y, Lei FM (2013) Sequencing and analysis of the complete mitochondrial genome of Remiz consobrinus. Zoological Research 34(3): 228–237.
  • Gao XD, Xu DJ, Xia T, Dou HS, Sha WL, Zhang HH (2019) The complete mitochondrial genome of Eastern Yellow Wagtail (Motacilla tschutschensis). Mitochondrial DNA. Part B, Resources 4(2): 3486–3487. https://doi.org/10.1080/23802359.2019.1674737
  • Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-A baiting and iterative mapping approach. Nucleic Acids Research 41(13): e129. https://doi.org/10.1093/nar/gkt371
  • Harris RB, Alström P, Ödeen A, Leaché AD (2018) Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla). Molecular Phylogenetics and Evolution 120: 183–195. https://doi.org/10.1016/j.ympev.2017.11.020
  • Hassanin A, Léger N, Deutsch J (2005) Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa and consequences for phylogenetic inferences. Systematic Biology 54(2): 277–298. https://doi.org/10.1080/10635150590947843
  • Huang ZH, Shen YM, Ma YR (2017) Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis 28(6): 867–871. https://doi.org/10.1080/24701394.2016.1199023
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods 14(6): 587–589. https://doi.org/10.1038/nmeth.4285
  • Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L (2010) Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). Genetics and Molecular Research 9(2): 1234–1249. https://doi.org/10.4238/vol9-2gmr853
  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton B, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England) 28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
  • Li XJ, Huang Y, Lei FM (2015) Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes). BMC Genomics 16(1): е42. https://doi.org/10.1186/s12864-015-1234-9
  • Li XJ, Lin LL, Cui AM, Bai J, Wang XY, Xin C, Zhang Z, Yang C, Gao RR, Huang Y, Lei FM (2016a) Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments. Molecular Phylogenetics and Evolution 104: 14–20. https://doi.org/10.1016/j.ympev.2016.07.022
  • Li XL, Dong F, Lei FM, Alström P, Zhang R, Ödeen A, Fjeldså J, Ericson PGP, Zou FS, Yang XJ (2016b) Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of white wagtail Motacilla alba (Aves: Passeriformes). Journal of Avian Biology 47(2): 263–274. https://doi.org/10.1111/jav.00826
  • Lowe TM, Eddy SR (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25(5): 955–964. https://doi.org/10.1093/nar/25.5.955
  • Ma YG, Huang Y, Lei FM (2014) Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome. Zoological Research 35(2): 81–91. https://doi.org/10.3109/19401736.2014.984179
  • Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D (2019) Resolving phylogenetic relationships within Passeriformes based on mitochondrial genes and inferring the evolution of their mitogenomes in terms of duplications. Genome Biology and Evolution 11(10): 2824–2849. https://doi.org/10.1093/gbe/evz209
  • Meng GL, Li YY, Yang CT, Liu SL (2019) MitoZ: A toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research 47(11): e63. https://doi.org/10.1093/nar/gkz173
  • Morinha F, Clemente C, Cabral JA, Lewicka MM, Travassos P, Carvalho D, Dávila JA, Santos M, Blanco G, Bastos E (2016) Next-generation sequencing and comparative analysis of Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus (Passeriformes: Corvidae) mitochondrial genomes. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis 27(3): 2278–2281.
  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32(1): 268–274. https://doi.org/10.1093/molbev/msu300
  • Ödeen A, Björklund M (2003) Dynamics in the evolution of sexual traits: Losses and gains, radiation and convergence in yellow wagtails (Motacilla flava). Molecular Ecology 12(8): 2113–2130. https://doi.org/10.1046/j.1365-294X.2003.01883.x
  • Perna NT, Kocher TD (1995) Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution 41(3): 353–358. https://doi.org/10.1007/BF01215182
  • Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67(5): 901–904. https://doi.org/10.1093/sysbio/syy032
  • Randi E, Lucchini V (1998) Organization and evolution of the mitochondrial DNA control region in the avian genus Alectoris. Journal of Molecular Evolution 47(4): 449–462. https://doi.org/10.1007/PL00006402
  • Ronquist F, Teslenko M, van Haeseler Haeseler P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539–542. https://doi.org/10.1093/sysbio/sys029
  • Sangster G, Luksenburg JA (2021) Sharp increase of problematic mitogenomes of birds: causes, effects and remedies. Genome Biology Evolution 13(9): evab210. https://doi.org/10.1093/gbe/evab210
  • Sbisà E, Tanzariello F, Reyes A, Pesole G, Saccone C (1997) Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications. Gene 205(1–2): 125–140. https://doi.org/10.1016/S0378-1119(97)00404-6
  • Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Phylogenetics and Evolution 38(7): 3022–3027. https://doi.org/10.1093/molbev/msab120
  • Yang C, Yang MX, Wang QX, Lu YC, Li XJ (2018) The complete mitogenome of Falco amurensis (Falconiformes, Falconidae), and a comparative analysis of genus Falco. Zoological Science 35(4): 367–372. https://doi.org/10.2108/zs170182
  • Zhang Z, Qian LF, Wang YP, Zhang BW (2016) The complete mitochondrial genome of Motacilla cinerea (Passeriformes: Motacillidae). Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis 27(5): 3680–3681. https://doi.org/10.3109/19401736.2015.1079853
  • Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT (2020) PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources 20(1): 348–355. https://doi.org/10.1111/1755-0998.13096

Supplementary materials

Supplementary material 1 

Figure S1

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Phylogenetic hypotheses of previous studies. a: Dong et al. (2016); b: Zhang et al. (2016); c: Harris et al. (2018); d: Gao et al. (2019).

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (342.70 kb)
Supplementary material 2 

Figure S2

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Secondary structures of rrnS of M. flava. Note: differences within the six mitogenomes from the genus Motacilla are indicated by filled grey circles.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (2.64 MB)
Supplementary material 3 

Figure S3

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Secondary structures of rrnL of M. flava. Note: differences within the six mitogenomes from the genus Motacilla are indicated by filled grey circles.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (1.95 MB)
Supplementary material 4 

Figure S4

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Secondary structures of tRNAs of M. flava. Note: differences within the six mitogenomes from the genus Motacilla are indicated by filled grey circles.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (1.57 MB)
Supplementary material 5 

Figure S5

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Control region structures of M. flava. Note: differences within the six mitogenomes from the genus Motacilla are indicated with filled circles.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (64.20 kb)
Supplementary material 6 

Figure S6

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Image.

Explanation note: Maximum likelihood and Bayesian inference phylogenetic results based on the mtDNA dataset, corresponding to Fig. 3. Note: a: ML tree, b: BI tree.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (496.14 kb)
Supplementary material 7 

Table S1

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Doc file.

Explanation note: Mitogenome sequences employed for reconstructing phylogenetic trees.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (86.50 kb)
Supplementary material 8 

Table S2

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Doc file.

Explanation note: Nucleotide composition and bias of six mitogenomes of the genus Motacilla. Notes: Stop codons of protein-coding genes were excluded; AT-skew=[A-T]/[A+T], GC-skew=[G-C]/[G+C]. The sequenced mitogenome species in this study are shown in the bold format.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (53.00 kb)
Supplementary material 9 

Table S3

Chao Yang, Xiaojuan Du, Yuxin Liu, Hao Yuan, Qingxiong Wang, Xiang Hou, Huisheng Gong, Yan Wang, Yuan Huang, Xuejuan Li, Haiyan Ye

Data type: Doc file.

Explanation note: Initial and terminal codons of protein-coding genes in the six mitogenomes from the genus Motacilla. Notes: The sequenced mitogenome species in this study are shown in the bold format.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (37.00 kb)