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Mo R, Zhu D, Sun J, Yuan Q, Guo F, Duan Y. Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna ( Passeriformes, Sittidae). Heliyon 2024; 10:e30513. [PMID: 38765151 PMCID: PMC11098796 DOI: 10.1016/j.heliyon.2024.e30513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).
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Affiliation(s)
- Ruixin Mo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Dong Zhu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Jing Sun
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
| | - Feng Guo
- Administration of Zixi Mountain Provincial Nature Reserve, Chuxiong, 675008, China
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
- College of Forestry, Southwest Forestry University, Kunming, Yunnan, 650224, China
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Yuan Q, Guo Q, Cao J, Luo X, Duan Y. Description of the Three Complete Mitochondrial Genomes of Sitta (S. himalayensis, S. nagaensis, and S. yunnanensis) and Phylogenetic Relationship (Aves: Sittidae). Genes (Basel) 2023; 14:genes14030589. [PMID: 36980861 PMCID: PMC10047972 DOI: 10.3390/genes14030589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis, S. nagaensis, and S. yunnanensis), which were 16,822–16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister group of Troglodytidae, and the genus Sitta can be divided into three major clades. We demonstrated the phylogenetic relationships within the genus Sitta (S. carolinensis + ((S. villosa + S. yunnanensis) + (S. himalayensis + (S. europaea + S. nagaensis)))).
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Affiliation(s)
- Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Qiang Guo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jing Cao
- Administration of Zixi Mountain Provincial Nature Reserve, Chuxiong 675000, China
| | - Xu Luo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, China
- Correspondence: authors: (X.L.); (Y.D.)
| | - Yubao Duan
- Department of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
- Correspondence: authors: (X.L.); (Y.D.)
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Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications. Animals (Basel) 2022; 13:ani13010096. [PMID: 36611705 PMCID: PMC9817927 DOI: 10.3390/ani13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.
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Aguilar C, Miller MJ, Loaiza JR, Krahe R, De León LF. Mitogenomics of Central American weakly-electric fishes. Gene 2019; 686:164-170. [PMID: 30453071 DOI: 10.1016/j.gene.2018.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/05/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022]
Abstract
Electric fishes are a diverse group of freshwater organisms with the ability to generate electric organ discharges (EODs) that are used for communication and electrolocation. This group (ca. 200 species) has originated in South America, and six species colonized the Central American Isthmus. Here, we assembled the complete mitochondrial genomes (mitogenomes) for three Central American electric fishes (i.e. Sternopygus dariensis, Brachyhypopomus occidentalis, and Apteronotus rostratus), and, based on these data, explored their phylogenetic position among Gymnotiformes. The three mitogenomes show the same gene order, as reported for other fishes, with a size ranging from 16,631 to 17,093 bp. We uncovered a novel 60 bp intergenic spacer (IGS) located between the COII and tRNALys genes, which appears to be unique to the Apteronotidae. Furthermore, phylogenetic relationships supported the traditional monophyly of Gymnotiformes, with the three species positioned within their respective family. In addition, the genus Apteronotus belongs to the early diverging lineage of the order. Finally, we found high sequence divergence (13%) between our B. occidentalis specimen and a sequence previously reported in GenBank, suggesting that the prior mitogenome of B. occidentalis represents a different South American species. Indeed, phylogenetic analyses using Cytochrome b gene across the genus placed the previously reported individual within B. bennetti. Our study provides novel mitogenome resources that will advance our understanding of the diversity and phylogenetic history of Neotropical fishes.
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Affiliation(s)
- Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panama, Panama; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panama, Panama
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jose R Loaiza
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panama, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panama, Panama
| | - Rüdiger Krahe
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panama, Panama; Department of Biology, University of Massachusetts Boston, Boston, MA, USA.
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Meimberg H, Schachtler C, Curto M, Husemann M, Habel JC. A new amplicon based approach of whole mitogenome sequencing for phylogenetic and phylogeographic analysis: An example of East African white-eyes (Aves, Zosteropidae). Mol Phylogenet Evol 2016; 102:74-85. [DOI: 10.1016/j.ympev.2016.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 01/14/2023]
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Pegan TM, Rumelt RB, Dzielski SA, Ferraro MM, Flesher LE, Young N, Class Freeman A, Freeman BG. Asymmetric Response of Costa Rican White-Breasted Wood-Wrens (Henicorhina leucosticta) to Vocalizations from Allopatric Populations. PLoS One 2015; 10:e0144949. [PMID: 26671001 PMCID: PMC4679390 DOI: 10.1371/journal.pone.0144949] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/25/2015] [Indexed: 11/25/2022] Open
Abstract
Divergence in song between allopatric populations can contribute to premating reproductive isolation in territorial birds. Song divergence is typically measured by quantifying divergence in vocal traits using audio recordings, but field playback experiments provide a more direct way to behaviorally measure song divergence between allopatric populations. The White-breasted Wood-Wren (Henicorhina leucosticta; hereafter “WBWW”) is an abundant Neotropical species with four mitochondrial clades (in Central America, the Darién, the Chocó and the Amazon) that are deeply divergent (~5–16% sequence divergence). We assessed the possibility that the WBWW as currently defined may represent multiple biological species by conducting both statistical analysis of vocal characters and field playback experiments within three clades (Central America, Chocó and Amazon). Our analysis of vocal traits revealed that Central American songs overlapped in acoustic space with Chocó songs, indicating vocal similarity between these two populations, but that Central American songs were largely divergent from Amazonian songs. Playback experiments in the Caribbean lowlands of Costa Rica revealed that Central American WBWWs typically responded aggressively to songs from the Chocó population but did not respond to playback of songs from the Amazonian population, echoing the results of the vocal trait analysis. This marked difference in behavioral response demonstrates that the songs of Central American and Amazonian WBWWs (but not Central American and Chocó WBWWs) have diverged sufficiently that Central American WBWWs no longer recognize song from Amazonian WBWWs as a signal to elicit territorial defense. This suggests that significant premating reproductive isolation has evolved between these two populations, at least from the perspective of the Central American population, and is consistent with the possibility that Central American and Amazonian populations represent distinct biological species. We conclude by advocating for the further use of field playback experiments to assess premating reproductive isolation (and species limits) between allopatric songbird populations, a situation where behavioral systematics can answer questions that phylogenetic systematics cannot.
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Affiliation(s)
- Teresa M Pegan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Reid B Rumelt
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Sarah A Dzielski
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Mary Margaret Ferraro
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Lauren E Flesher
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Nathaniel Young
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | | | - Benjamin G Freeman
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
- Cornell Laboratory of Ornithology, Ithaca, NY, United States of America
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López K, Angeli C, Aguilar C, Loaiza JR, De León LF, McMillan WO, Miller MJ. Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3451-3. [PMID: 26367084 DOI: 10.3109/19401736.2015.1066344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.
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Affiliation(s)
- Krisangel López
- a Department of Biology , Villanova University , Villanova , PA , USA
| | - Cody Angeli
- a Department of Biology , Villanova University , Villanova , PA , USA
| | - Celestino Aguilar
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and.,c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| | - Jose R Loaiza
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and
| | - Luis Fernando De León
- b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and
| | - W Owen McMillan
- c Smithsonian Tropical Research Institute , Panamá , República de Panamá
| | - Matthew J Miller
- a Department of Biology , Villanova University , Villanova , PA , USA .,b Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP) , Panamá , República de Panamá , and.,c Smithsonian Tropical Research Institute , Panamá , República de Panamá
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