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. 2025 Aug 25;10(9):878–883. doi: 10.1080/23802359.2025.2549750

Characterization of the mitochondrial genome and phylogenetic position of the Varied Solitaire Myadestes coloratus (Passeriformes: Turdidae)

Jorge L Garzon a,b,*,✉, Celestino Aguilar c,d,*, Kristin Saltonstall b, Carlos F Arias b, Catherine B Viverette e, Luis F De León f
PMCID: PMC12381985  PMID: 40880614

Abstract

The Varied Solitaire (Myadestes coloratus Nelson, 1912) is a near-threatened bird species, endemic to the highlands of eastern Panama and the Colombian border. In this study, we report the complete mitochondrial genome of M. coloratus. The mitogenome exhibits a typical avian structure with a slight AT bias and a control region. Phylogenetic analysis confirms the close relationship between M. coloratus and other thrush (Turdidae) species, including the extinct M. myadestinus. This data is crucial for future research on the evolutionary history and population genetics of M. Coloratus. These findings are particularly relevant as the species is increasingly threatened by human expansion.

Keywords: Mitogenome, neotropical birds, Panama, endemic, Solitario Variado

Introduction

Myadestes coloratus Nelson, 1912, commonly known as the Varied Solitaire, is an endemic thrush (Turdidae) found in the highlands between eastern Panama and the border with Colombia (Ridgely and Gwynne 1989; Collar 2020). This region is crucial for the conservation of several endemic bird species and subspecies, which are restricted to forests above 600 m in elevation (Renjifo et al. 2017; Aguilar et al. 2025; Garzon and De León 2025). Unfortunately, these habitats are increasingly threatened by deforestation and human expansion, likely leading to the decline of several animal populations in the region (Batista et al. 2020). Consequently, M. coloratus has been classified as near-threatened by the IUCN Red List (IUCN 2021).

However, limited genetic information on M. coloratus is currently available, likely due to its restricted range and remote habitat (Garzon 2021). While one complete mitochondrial genome exists for the genus, from the now-extinct Hawaiian M. myadestinus (IUCN 2016; Anmarkrud and Lifjeld 2017), no complete mitogenome has been reported for any Neotropical species of Myadestes. For M. coloratus, only partial sequences of ATP8/6, COX1, Cytb, and ND2 genes are available (Miller et al. 2007). This paucity of data limits understanding of the species’ evolutionary history and conservation status (De León et al. 2023; Aguilar et al. 2025). Here, we sequence and annotate the complete mitochondrial genome of M. coloratus, to support future research on its phylogenetic history, population structure, as well as conservation efforts.

Materials and methods

DNA was extracted from a tissue of a deceased individual of M. coloratus previously collected in Serranía de Majé, Cerro Chucantí (8.811069 N, −78.457869 W) on 26 January 2006, under the permit DNAPVS-01-2006 from the Authority of the Environment (ANAM). The specimen was identified as M. coloratus based in diagnostic morphological features described in A Guide to the Birds of Panama: with Costa Rica, Nicaragua, and Honduras (Ridgely and Gwynne 1989), including its distinctive black facial mask, ashy-gray underparts and tawny-rufous upper part with olivaceus (Figure 1). The orange beak and legs supported the identification. The individual was an adult, confirmed by its fully developed definitive plumage. The voucher is deposited at the Smithsonian Tropical Research Institute Bird-Tissue Collection, Naos Island, Panama (María F. Castillo is the contact person: castillomf@si.edu) under the ID number GMS1933.

Figure 1.

Figure 1.

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Reference photograph of Varied Solitaire (M. coloratus). The species is characterized by its black facial mask extending from the bill to mid-eye level, dark ashy gray head and underparts, and tawny-rusty rufous upper parts with olivaceous tones. Its beak and legs are orange (Ridgely and Gwyne 1989). Photo taken by Jorge L. Garzón in Cerro Chucantí, Darién, Panamá (8.80147 N, −78.46095 W).

The mitochondrial genome was assembled from reads obtained from hybrid capture libraries originally prepared for ultra-conserved element loci (UCEs: (Faircloth et al. 2012). In brief, total DNA was extracted using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, California, USA) following the manufacturer’s protocol, with DNA quality evaluated via nanodrop and Qubit 3 fluorometry. Libraries were paired-end sequenced (2 × 150 bp) on an Illumina HiSeq (Illumina, San Diego, CA, USA) at the Arbor BioScience laboratories (Michigan, USA). After quality control and trimming using FastQC and Illumiprocessor (Faircloth 2013), de novo assembly was performed using Unicycler v. 0.5.0 (Wick et al. 2017). Through BLAST (Altschul et al. 1990) analysis, we identified one large contig sequence that matched the mitochondrial genome M. coloratus. The sequence was annotated using MitoAnnotator (Iwasaki et al. 2013) and MITOS2 (Bernt et al. 2013), with final curation in Geneious Prime v. 2024.2 (Kearse et al. 2012).

To establish the phylogenetic framework of the reported mitogenome, we downloaded published mitogenomes of Turdidae from NCBI. We also used one published mitogenome of Passer montanus as an outgroup. The nucleotide sequences of the 13 PCGs from each mitogenome were extracted manually using Geneious, aligned using MAFFT (Katoh and Standley 2013), and concatenated using Geneious Prime 2024. Phylogenetic analysis with maximum likelihood (ML) was then performed using IQ-TREE2 (Minh et al. 2020) under the best-fit model GTR+I + G4 determined using ModelFinder (Kalyaanamoorthy et al. 2017) and 1000 bootstrap replicates. Finally, we used FigTree 1.4.4 (Rambaut and Drummond 2012) to visualize the resulting phylogenetic tree.

Results

The complete mitochondrial genome of M. coloratus (Figure 2) was recovered for individual GMS1933, and the consensus sequence length was 16,783 bp with a mean coverage of 19×. The depth of the mitogenome coverage map is shown in the Supplementary Figure S1. The complete genome sequence had been deposited in GenBank under the accession number PQ872305. The base composition of mitochondrial DNA (mtDNA) showed that the percentage of A + T (53.7%) was slightly higher than G + C (46.3%). The complete mtDNA sequence contained 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), and a control region. The 13 PCGs encoded ND1, ND2, COX1, COX2, ATP8, ATP6, COX3, ND3, ND4L, ND4, ND5, CYTB, and ND6, respectively. Of the 13 PCGs, 12 utilized ATG as the start codon, whereas COX1 started with GTG. Six PCGs ended with TAA (CYTB, COX2, ATP8, ATP6, ND3, and ND4L), two ended with AGG (ND1 and COX1), one with AGA (ND5), one with TAG (ND6), and the other three ended with incomplete TA-/T– (ND2, ND4, and COXIII) stop codons. The 22 tRNA genes ranged in size from 66 bp encoding tRNA-Ser1 to 76 bp encoding tRNA-Ser2. The 12S and 16S rRNA genes were 983 bp and 1600 bp, respectively. The non-coding control region (CR) was located between tRNA-Glu and tRNA-Phe (Figure 2).

Figure 2.

Figure 2.

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Assembly and annotation of the M. coloratus mitochondrial genome. Green-colored bars represent coding sequences for protein-coding genes, red bars represent rRNA genes, magenta bars represent tRNA genes, and gray bars represent control regions. The direction of transcription is indicated by the orientation of the gene arrows. The inner blue line represents GC content across the mitogenome. The mitogenome assembly was visualized using Geneious Prime v. 2023.2.1 software.

Phylogenetic analysis placed M. coloratus as a sister taxon of the only other member of Myadestes in the analysis, the extinct M. myadestinus, with 100% bootstrap support (Figure 3). Similarly, the genus Myadestes was placed as a sister group of the other thrushes (i.e. Turdus, Geokichla, Catharus, and Zoothera) with high bootstrap support (Figure 3).

Figure 3.

Figure 3.

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Phylogenetic position of Myadestes coloratus within the family Turdidae based on complete mitochondrial genomes. The phylogenetic tree was based on maximum likelihood analysis of 13 PCGs and included 22 species of Turdidae for which mitochondrial genomes were available. ML bootstrap support values ≥70% are shown along the nodes. The GenBank accession numbers are displayed after the species name. The following sequences were used: Turdus naumanni KJ834096 (Li et al. 2016), Turdus eunomus NC_028273 (Dong et al. 2018), Turdus ruficollis MT712159 (X. Zhang et al. 2021), Turdus atrogularis PQ790019 (Jiang et al. 2025), Turdus pallidus PQ249424 (direct submission), Turdus celaenops LC541445 (Yamamoto et al. 2023), Turdus kessleri MG912943 (Song et al. 2018), Turdus hortulorum KF926987 (Yan et al. 2016), Turdus mandarinus KT601060 (Peng et al. 2016), Turdus abyssinicus MT017912 (Behrends et al. 2024), Turdus migratorius KJ909198 (Keith Barker 2014), Turdus rufiventris KT346357 (Gomes de Sá et al. 2017), Turdus merula MN122910 (Margaryan et al. 2021), Turdus philomelos KC545406 (Gibb et al. 2015), Turdus eunomus NC_028273 (Dong et al. 2018), Turdus obscurus MZ424446 (direct submission), Turdus cardis NC_046948 (Sun et al. 2020), Turdus dissimilis NC_059847 (Gou et al. 2024), Geokichla sibirica MK377247 (Sun et al. 2019), Catharus fuscescens NC_051013 (Feng et al. 2020), Catharus ustulatus CM020378 (direct submission), Zoothera aurea KT340629 (Park et al. 2019), Myadestes coloratus PQ872305 (this study), Myadestes myadestinus NC_031352 (Anmarkrud and Lifjeld 2017), and Passer montanus MW495245 (Lee et al. 2021).

Discussion and conclusion

M. coloratus is a near-threatened bird species (IUCN 2021), which is endemic to eastern Panama and the border with Colombia. However, limited genetic resources are currently available for the species. We report the complete mitochondrial genome sequence of M. coloratus. The 16,783 bp mitochondrial genome showed AT content bias, typical of thrushes (Sun et al. 2016; Zhang et al. 2021). It contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis grouped M. coloratus with extinct M. myadestinus, confirming its position within Myadestes and Turdidae, which is consistent with previous studies using short fragments of mitochondrial genes (Miller et al. 2007).

Our study represents the first complete mitochondrial genome reported for any Neotropical Myadestes species and the second of the entire genus, which contains 13 species (Winkler et al. 2020). This mitogenome sequence data provides novel genetic resources for elucidating the evolutionary history of M. coloratus, as well as informing the conservation status of this threatened species within its natural habitat. Our findings also highlight the scarcity of molecular data for the genus Myadestes. Indeed, despite the genus’ broad distribution, which include the Americas and Hawaii (Bankert et al. 2009), only two species currently have available mitogenomic data. Thus, expanding sequencing efforts to include other underrepresented lineages within the genus will be crucial for future comparative studies across the genus’ range.

Supplementary Material

Supplementary materials.pdf
TMDN_A_2549750_SM7767.pdf (685.9KB, pdf)

Acknowledgments

We want to thank the Smithsonian Tropical Research Institute Cryo-collection, specially to María Fernanda Castillo, for providing access to the tissue sample used in this study.

Funding Statement

This work was supported by Secretaria Nacional de Ciencia y Tecnología de Panama [DDCCT No. 103-2022], a Short-Term Fellowship at the Smithsonian Tropical Research Institute [#5226], and the Rufford Foundation [38743-1].

Ethical statement

The original Myadestes coloratus specimen was collected in compliance with all necessary permissions, and ethical approvals through collection permits maintained by the Smithsonian Tropical Research Institute Bird-Tissue Collection. This study involved the use of a tissue sample from a Myadestes coloratus individual previously collected and deposited in a scientific collection. No new collection or fieldwork was conducted for this research. The species is classified as Near Threatened on the IUCN Red List, and this research complies with the IUCN guidelines for research involving species at risk of extinction. The study also adheres to the principles of the Convention on Biological Diversity (CBD) and the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The use of previously stored material ensured that no impact was made on wild populations.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession no. PQ872305. The associated BioProject, SRA, and BioSample numbers are PRJNA1236001, SRR32695440, and SAMN47378098, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary materials.pdf
TMDN_A_2549750_SM7767.pdf (685.9KB, pdf)

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession no. PQ872305. The associated BioProject, SRA, and BioSample numbers are PRJNA1236001, SRR32695440, and SAMN47378098, respectively.

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