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Li Q, Jiang P, Li M, Du J, Sun J, Chen N, Wu Y, Chang Q, Hu C. Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae). Curr Issues Mol Biol 2024; 46:6186-6198. [PMID: 38921040 PMCID: PMC11202466 DOI: 10.3390/cimb46060369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
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Affiliation(s)
- Quanheng Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Peiyue Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Mingxuan Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jingjing Du
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jianxiang Sun
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Nuo Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Yu Wu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
- Analytical and Testing Center, Nanjing Normal University, Nanjing 210046, China
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Langmore NE, Grealy A, Noh HJ, Medina I, Skeels A, Grant J, Murray KD, Kilner RM, Holleley CE. Coevolution with hosts underpins speciation in brood-parasitic cuckoos. Science 2024; 384:1030-1036. [PMID: 38815013 DOI: 10.1126/science.adj3210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Coevolution between interacting species is thought to increase biodiversity, but evidence linking microevolutionary processes to macroevolutionary patterns is scarce. We leveraged two decades of behavioral research coupled with historical DNA analysis to reveal that coevolution with hosts underpins speciation in brood-parasitic bronze-cuckoos. At a macroevolutionary scale, we show that highly virulent brood-parasitic taxa have higher speciation rates and are more likely to speciate in sympatry than less-virulent and nonparasitic relatives. We reveal the microevolutionary process underlying speciation: Hosts reject cuckoo nestlings, which selects for mimetic cuckoo nestling morphology. Where cuckoos exploit multiple hosts, selection for mimicry drives genetic and phenotypic divergence corresponding to host preference, even in sympatry. Our work elucidates perhaps the most common, but poorly characterized, evolutionary process driving biological diversification.
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Affiliation(s)
- N E Langmore
- Research School of Biology, Australian National University, Canberra, Australia
| | - A Grealy
- Research School of Biology, Australian National University, Canberra, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
| | - H-J Noh
- Research School of Biology, Australian National University, Canberra, Australia
| | - I Medina
- School of Biosciences, The University of Melbourne, Melbourne, Australia
| | - A Skeels
- Research School of Biology, Australian National University, Canberra, Australia
| | - J Grant
- Research School of Biology, Australian National University, Canberra, Australia
| | - K D Murray
- Research School of Biology, Australian National University, Canberra, Australia
| | - R M Kilner
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - C E Holleley
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
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Kanakachari M, Chatterjee RN, Reddy MR, Dange M, Bhattacharya TK. Indian Red Jungle fowl reveals a genetic relationship with South East Asian Red Jungle fowl and Indian native chicken breeds as evidenced through whole mitochondrial genome sequences. Front Genet 2023; 14:1083976. [PMID: 37621706 PMCID: PMC10445952 DOI: 10.3389/fgene.2023.1083976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure. Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breeds were divided into six significant clades, namely A, B, C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic. Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds.
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Affiliation(s)
- M. Kanakachari
- ICAR-Directorate of Poultry Research, Hyderabad, India
- EVA.4 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | | | - M. R. Reddy
- ICAR-Directorate of Poultry Research, Hyderabad, India
| | - M. Dange
- ICAR-Directorate of Poultry Research, Hyderabad, India
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4
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Zhang L, Xia T, Gao X, Yang X, Sun G, Zhao C, Liu G, Zhang H. Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila. Genes (Basel) 2023; 14:1205. [PMID: 37372385 DOI: 10.3390/genes14061205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. FST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Guangshuai Liu
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
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Souza TO, Luna LW, Araripe J, Silva WADEGE, Rego PSDO. Peripheral isolation and demographic stability are reflected in the genetic diversity of the populations of the Helmeted Manakin: a bird endemic to the gallery forests. AN ACAD BRAS CIENC 2022; 94:e20201206. [PMID: 36541971 DOI: 10.1590/0001-3765202220201206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
The Cerrado encompasses a complex network of hydrographic basins, which is responsible for the formation and maintenance of the riparian and gallery forests. Alterations in the vegetation resulting from the paleoclimatic changes that occurred during the Pleistocene influenced the current distribution of these humid forests. To understand of the evolutionary dynamics of this landscape on the population structure of the associated organisms, we studied the population genetics of the Antilophia galeata (Pipridae), a bird endemic to the gallery forests of the Cerrado. For this, we evaluated the variability of the mitochondrial control region of 71 A. galeata specimens from 18 localities distributed throughout the Cerrado. The results indicated the existence of significant substructure among the populations located in the peripheral areas of the Cerrado, in comparison with the populations found in the central portion, reflecting historical changes in the environment. We also found high levels of diversity in all the populations, while the analysis of the demographic history revealed a scenario of stability. Overall, then, these findings indicate that the historical modifications of the gallery forest distribution may have been most accentuated in the peripheral zones, with a greater stability and connectivity persisting in the central portion of the biome.
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Affiliation(s)
- Thainara O Souza
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil
| | - Leilton W Luna
- Universidade Federal do Pará, Departamento de Zoologia, Museu Paraense Emílio Goeldi, Avenida Perimetral, 1901/1907, 66040-170 Belém, PA, Brazil
| | - Juliana Araripe
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal
| | - Weber A DE G E Silva
- Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Avenida Pintor João Figueiredo - SESC - Iparana, 61627-250 Caucaia, CE, Brazil
| | - Péricles S DO Rego
- Universidade Federal do Pará, Instituto de Estudos Costeiros, Laboratório de Genética e Conservação, Rua Leandro Ribeiro s/n, 68600-000 Bragança, PA, Brazil.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal
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Kim JI, Do TD, Yeo Y, Kim CB. Comparative analysis of complete mitochondrial genomes of three Trichoglossus species (Psittaciformes: Psittacidae). Mol Biol Rep 2022; 49:9121-9127. [PMID: 35941414 DOI: 10.1007/s11033-022-07791-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The genus Trichoglossus belongs to the family Psittacidae and includes fourteen species distributed worldwide. According to the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species, most Trichoglossus species have shown a decreasing population trend recently. In particular, Trichoglossus forsteni is listed as "Endangered" in the IUCN Red List of Threatened Species. Moreover, Trichoglossus haematodus and Trichoglossus moluccanus are one of the most traded and illegally traded parrots. However, only a few genetic studies have been conducted regarding the conservation of this genus. METHODS AND RESULTS In the present study, complete mitochondrial genomes of three species (T. forsteni, T. haematodus, and T. moluccanus) were sequenced and compared with Trichoglossus rubritorquis, species whose mitochondrial genome is already reported. Results indicate that the complete mitochondrial genomes of the three species were similar in length (17,906 bp for T. haematodus to 17,909 bp for T. forsteni). Furthermore, the organization and order of these three mitochondrial genomes were identical, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two control regions (CRs) categorized into three domains containing nine conserved motifs. In addition, the genus Trichoglossus formed a well-supported monophyletic lineage. CONCLUSIONS The results of this study may be useful for future genetic studies toward the conservation of the genus Trichoglossus.
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Affiliation(s)
- Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
- Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong, Vietnam
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea.
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Yang C, Du X, Liu Y, Yuan H, Wang Q, Hou X, Gong H, Wang Y, Huang Y, Li X, Ye H. Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications. Zookeys 2022; 1109:49-65. [PMID: 36762344 PMCID: PMC9848870 DOI: 10.3897/zookeys.1109.81125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/21/2022] [Indexed: 11/12/2022] Open
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 Dendronanthusindicus, 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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Affiliation(s)
- Chao Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina,Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Xiaojuan Du
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Yuxin Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Hao Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina,School of Basic Medical Sciences, Xi’an Medical University, Xi’an, ChinaXi’an Medical UniversityXi’anChina
| | - Qingxiong Wang
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Xiang Hou
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Huisheng Gong
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Yan Wang
- Shaanxi Institute of Zoology, Xi’an 710032, ChinaShaanxi Normal UniversityXi’anChina
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
| | - Haiyan Ye
- College of Life Sciences, Shaanxi Normal University, Xi’an 710062, ChinaShaanxi Institute of ZoologyXi’anChina
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Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana. Animals (Basel) 2022; 12:ani12101250. [PMID: 35625095 PMCID: PMC9137629 DOI: 10.3390/ani12101250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana. Abstract The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.
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Chen W, Miao K, Wang J, Wang H, Sun W, Yuan S, Luo S, Hu C, Chang Q. Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris. PeerJ 2022; 10:e13268. [PMID: 35462767 PMCID: PMC9022639 DOI: 10.7717/peerj.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Background The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved. Methods Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. Results We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.
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Affiliation(s)
- Wan Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China,Jiangsu Open University (The City Vocational College of Jiangsu), College of Environment and Ecology, Nanjing, Jiangsu, China
| | - Keer Miao
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Junqi Wang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hao Wang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wan Sun
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Sijia Yuan
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Site Luo
- School of Life Science, Xiamen University, Xiamen, Guangdong, China
| | - Chaochao Hu
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China,Nanjing Normal University, Analytical and Testing Center, Nanjing, Jiangsu, China
| | - Qing Chang
- School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
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Kundu S, Alam I, Maheswaran G, Tyagi K, Kumar V. Complete Mitochondrial Genome of Great Frigatebird (Fregata minor): Phylogenetic Position and Gene Rearrangement. Biochem Genet 2021; 60:1177-1188. [PMID: 34800202 DOI: 10.1007/s10528-021-10156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022]
Abstract
The complete mitogenome sequence of the Great Frigatebird, Fregata minor was sequenced for the first time in this study. The mitogenome (16,899 bp) comprises of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The mitogenome was AT-rich (55.60%) with 11 overlapping and 18 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. A maximum-likelihood phylogeny of concatenated PCGs resulted in a well-resolved phylogeny of all the species of Suliformes and illuminates the sister relationship of F. minor with F. magnificens. The present mitogenome-based phylogeny clearly enlightens the evolutionary position of Suliformes and Pelecaniformes species. Unique tandem repeats were identified in both F. minor and F. magnificens, which can be employed as a species-specific marker. To illuminate the population structure of this migratory seabirds, the present study advocate more sampling and the generation of additional molecular data to clarify their genetic diversity. The present study also rejects an earlier hypothesis on the mitochondrial gene order of Suliformes and corroborated the typical avian gene order in frigatebirds.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India
| | - Imran Alam
- Bird Section, Zoological Survey of India, Kolkata, 700053, India
| | | | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, 700053, India.
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Torres L, Pante E, González‐Solís J, Viricel A, Ribout C, Zino F, MacKin W, Precheur C, Tourmetz J, Calabrese L, Militão T, Zango L, Shirihai H, Bretagnolle V. Sea surface temperature, rather than land mass or geographic distance, may drive genetic differentiation in a species complex of highly dispersive seabirds. Ecol Evol 2021; 11:14960-14976. [PMID: 34765153 PMCID: PMC8571584 DOI: 10.1002/ece3.8180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 06/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Seabirds, particularly Procellariiformes, are highly mobile organisms with a great capacity for long dispersal, though simultaneously showing high philopatry, two conflicting life-history traits that may lead to contrasted patterns of genetic population structure. Landmasses were suggested to explain differentiation patterns observed in seabirds, but philopatry, isolation by distance, segregation between breeding and nonbreeding zones, and oceanographic conditions (sea surface temperatures) may also contribute to differentiation patterns. To our knowledge, no study has simultaneously contrasted the multiple factors contributing to the diversification of seabird species, especially in the gray zone of speciation. We conducted a multilocus phylogeographic study on a widespread seabird species complex, the little shearwater complex, showing highly homogeneous morphology, which led to considerable taxonomic debate. We sequenced three mitochondrial and six nuclear markers on all extant populations from the Atlantic (lherminieri) and Indian Oceans (bailloni), that is, five nominal lineages from 13 populations, along with one population from the eastern Pacific Ocean (representing the dichrous lineage). We found sharp differentiation among populations separated by the African continent with both mitochondrial and nuclear markers, while only mitochondrial markers allowed characterizing the five nominal lineages. No differentiation could be detected within these five lineages, questioning the strong level of philopatry showed by these shearwaters. Finally, we propose that Atlantic populations likely originated from the Indian Ocean. Within the Atlantic, a stepping-stone process accounts for the current distribution. Based on our divergence time estimates, we suggest that the observed pattern of differentiation mostly resulted from historical and current variation in sea surface temperatures.
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Affiliation(s)
- Lucas Torres
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Eric Pante
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Jacob González‐Solís
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | - Amélia Viricel
- Laboratoire LIENSsUMR 7266CNRS ‐ La Rochelle UniversitéLa RochelleFrance
| | - Cécile Ribout
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
| | | | - Will MacKin
- 3913 Sterling Ridge LnDurhamNorth CarolinaUSA
| | | | - Julie Tourmetz
- Société d'Etudes Ornithologiques de La RéunionSaint AndréFrance
| | - Licia Calabrese
- Island Conservation SocietyMahéSeychelles
- Faculty of Business & Sustainable DevelopmentIsland Biodiversity & Conservation CenterUniversity of SeychellesMahéSeychelles
| | - Teresa Militão
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | - Laura Zango
- Department de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA)Institut de Recerca de la Biodiversitat (IRBio)Universitat de BarcelonaBarcelonaSpain
| | | | - Vincent Bretagnolle
- Centre d'Etudes Biologiques de ChizéUMR 7372CNRS ‐ La Rochelle UniversitéBeauvoir sur NiortFrance
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12
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De Panis D, Lambertucci SA, Wiemeyer G, Dopazo H, Almeida FC, Mazzoni CJ, Gut M, Gut I, Padró J. Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures. Sci Rep 2021; 11:17109. [PMID: 34429448 PMCID: PMC8384887 DOI: 10.1038/s41598-021-96080-6] [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: 05/25/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
The evolution of large vultures linked to mountainous habitats was accompanied by extreme physiological and behavioral specializations for energetically efficient flights. However, little is known on the genetic traits associated with the evolution of these obligate soaring scavengers. Mitochondrial DNA plays a vital role in regulating oxidative stress and energy production, and hence may be an important target of selection for flight performance. Herein, we characterized the first mitogenomes of the Andean and California condors, the world's heaviest flying birds and the only living representatives of the Vultur and Gymnogyps genus. We reconstructed the phylogenetic relationships and evaluated possible footprints of convergent evolution associated to the life-history traits and distributional range of vultures. Our phylogenomic analyses supported the independent evolution of vultures, with the origin of Cathartidae in the early Paleogene (~ 61 Mya), and estimated the radiation of extant condors during the late Miocene (~ 11 Mya). Selection analyses indicated that vultures exhibit signals of relaxation of purifying selection relative to other accipitrimorph raptors, possibly indicating the degeneration of flapping flight ability. Overall, our results suggest that the extreme specialization of vultures for efficient soaring flight has compensated the evolution of large body sizes mitigating the selection pressure on mtDNA.
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Affiliation(s)
- D. De Panis
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina ,grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - S. A. Lambertucci
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
| | - G. Wiemeyer
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina ,Ecoparque Buenos Aires-Argentina, República de la India 3000, 1425 Ciudad Autónoma de Buenos Aires, Argentina ,Fundación Cabure-Í, Mcal Antonio Sucre 2842, 1428 Ciudad Autónoma de Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Present Address: Hospital Escuela, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, 1427 Ciudad Autónoma de Buenos Aires, Argentina
| | - H. Dopazo
- grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - F. C. Almeida
- grid.7345.50000 0001 0056 1981Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires-CONICET, Intendente Güiraldes 2160, 1428 Ciudad Autónoma de Buenos Aires, Argentina
| | - C. J. Mazzoni
- grid.511553.6Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - M. Gut
- grid.11478.3bCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - I. Gut
- grid.11478.3bCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - J. Padró
- grid.412234.20000 0001 2112 473XGrupo de Investigaciones en Biología de la Conservación, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
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13
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Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes. Int J Mol Sci 2021; 22:ijms22041811. [PMID: 33670420 PMCID: PMC7918261 DOI: 10.3390/ijms22041811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 01/06/2023] Open
Abstract
Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.
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14
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Kundu S, Tyagi K, Alam I, Maheswaran G, Kumar V, Chandra K. Complete mitochondrial genome of Chroicocephalus brunnicephalus from India: phylogeny with other Larids. Mitochondrial DNA B Resour 2021; 6:339-343. [PMID: 33659671 PMCID: PMC7872550 DOI: 10.1080/23802359.2020.1866448] [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: 08/19/2020] [Accepted: 12/13/2020] [Indexed: 11/14/2022] Open
Abstract
The complete mitogenome sequence of the brown-headed gull, Chroicocephalus brunnicephalus was determined in this study. The 16,771 bp genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The decoded mitogenome was AT-rich (54.77%) with nine overlapping and 17 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. Further, the usual termination codons (AGG, TAG, TAA, and AGA) were used by 11 PCGs except for cox3 and nad4. The concatenated PCGs based Bayesian phylogeny clearly discriminates all the Laridae species and reflects the sister relationship of C. brunnicephalus with C. ridibundus. The present mitogenome-based phylogeny was congruent with the earlier hypothesis and confirmed the evolutionary position of the brown-headed gull as masked species. The generated mitogenome of C. brunnicephalus is almost identical to the previously generated mitogenome from China except for two base pairs in CR. To visualize the population structure of this migratory species, we propose more sampling from different geographical locations and the generation of additional molecular data to clarify the reality.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Imran Alam
- Bird Section, Zoological Survey of India, Kolkata, India
| | | | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- Bird Section, Zoological Survey of India, Kolkata, India
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15
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Kim JI, Do TD, Choi Y, Yeo Y, Kim CB. Characterization and Comparative Analysis of Complete Mitogenomes of Three Cacatua Parrots (Psittaciformes: Cacatuidae). Genes (Basel) 2021; 12:genes12020209. [PMID: 33572592 PMCID: PMC7910981 DOI: 10.3390/genes12020209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cacatua alba, Cacatua galerita, and Cacatua goffiniana are parrots of the family Cacatuidae. Wild populations of these species are declining with C. alba listed by the International Union for the Conservation of Nature and Natural Resources (IUCN) as Endangered. In this study, complete mitogenomes were sequenced for a comparative analysis among the Cacatua species, and a detailed analysis of the control region. Mitogenome lengths of C. alba,C. galerita, and C. goffiniana were 18,894, 18,900, and 19,084 bp, respectively. They included 13 protein coding genes, two ribosomal RNA genes, 24 transfer RNA genes, three degenerated genes, and two control regions. Ten conserved motifs were found in three domains within each of the two control regions. For an evolution of duplicated control regions of Cacatua, domain I and the 3′ end of domain III experienced an independent evolution, while domain II and most of the regions of domain III was subjected to a concerted evolution. Based on a phylogenetic analysis of 37 mitochondrial genes, the genus Cacatua formed a well-supported, monophyletic, crown group within the Cacatuidae. Molecular dating results showed that Cacatua diverged from other genera of Cacatuinae in the middle of Miocene.
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Affiliation(s)
- Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yisoo Choi
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
| | - Yonggu Yeo
- Conservation and Health Center, Seoul Zoo, Gwacheon 13829, Korea;
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea; (J.-I.K.); (T.D.D.); (Y.C.)
- Correspondence: ; Tel.: +82-2-2287-5288
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16
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Structural variation and phylogenetic relationship of Geospiza magnirostris based on mitochondrial control region. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00669-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Sarkar I, Dey P, Sharma SK, Ray SD, Kochiganti VHS, Singh R, Pramod P, Singh RP. Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family. Sci Rep 2020; 10:16202. [PMID: 33004841 PMCID: PMC7530654 DOI: 10.1038/s41598-020-72674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 08/24/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
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Affiliation(s)
- Indrani Sarkar
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Prateek Dey
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Sanjeev Kumar Sharma
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India.
| | - Swapna Devi Ray
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | | | - Renu Singh
- Central Avian Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Padmanabhan Pramod
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India
| | - Ram Pratap Singh
- National Avian Forensic Laboratory, Sálim Ali Centre for Ornithology and Natural History, Anaikatty, Coimbatore, Tamil Nadu, 641108, India.
- Department of Life Science, Central University of South Bihar, Gaya, Bihar, 824236, India.
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18
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Complete mtDNA genome of Otus sunia (Aves, Strigidae) and the relaxation of selective constrains on Strigiformes mtDNA following evolution. Genomics 2020; 112:3815-3825. [DOI: 10.1016/j.ygeno.2020.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/10/2020] [Accepted: 02/28/2020] [Indexed: 11/17/2022]
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19
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Bernacki LE, Kilpatrick CW. Structural Variation of the Turtle Mitochondrial Control Region. J Mol Evol 2020; 88:618-640. [PMID: 32808073 DOI: 10.1007/s00239-020-09962-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022]
Abstract
The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.
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Affiliation(s)
- Lucas E Bernacki
- Department of Sciences, Saint Joseph's College, Mercy Hall, Rm 122, 278 Whites Bridge Road, Standish, ME, 04084, USA.
- Department of Biology, University of Vermont, Burlington, VT, USA.
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20
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Kundu S, Kumar V, Tyagi K, Chandra K. The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny. PLoS One 2020; 15:e0225233. [PMID: 32324729 PMCID: PMC7179895 DOI: 10.1371/journal.pone.0225233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/08/2020] [Indexed: 12/02/2022] Open
Abstract
The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.
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Affiliation(s)
- Shantanu Kundu
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Molecular Systematics Division, Centre for DNA Taxonomy, Zoological Survey of India, Kolkata, India
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21
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Zhu K, Gao Y, Yuan P, Cao P, Ying X, Tao H, Liu B. The complete mitochondrial genome of ostorhinchus fleurieu (kurtiformes: Apogonidae) and phylogenetic studies of apogoninae. Mitochondrial DNA B Resour 2019; 4:3691-3692. [PMID: 33366146 PMCID: PMC7707501 DOI: 10.1080/23802359.2019.1679681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
The complete mitochondrial genome of Ostorhinchus fleurieu was first determined, which was 16,521 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region and one origin of replication on the light-strand. The overall base composition included C(29.2%), A(26.7%), T(26.7%) and G(17.4%). Moreover, the 13 PCGs encoded 3800 amino acids in total, twelve of which used the initiation codon ATG except for COI started with GTG. Most of them ended with complete stop codon, whereas three protein-coding genes (COII, ND4 and Cytb) used incomplete stop codon and represented as T. The phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Apogoninae, which could be a useful basis for management of this species.
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Affiliation(s)
- Kehua Zhu
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- Key Laboratory of Informatization of Habitat Monitoring and Fishery Resource Conservation Research in the East China Sea of Zhejiang Province, Zhejiang Ocean University, Zhoushan, China
| | - Yuanpei Gao
- Key Laboratory of Aquatic Products Processing of Zhejiang Province, Department of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Pengxiang Yuan
- Key Laboratory of Aquatic Products Processing of Zhejiang Province, Department of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Pinglin Cao
- Key Laboratory of Informatization of Habitat Monitoring and Fishery Resource Conservation Research in the East China Sea of Zhejiang Province, Zhejiang Ocean University, Zhoushan, China
| | - Xiaoguo Ying
- Key Laboratory of Aquatic Products Processing of Zhejiang Province, Department of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Hengcong Tao
- Key Laboratory of Aquatic Products Processing of Zhejiang Province, Department of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
- Key Laboratory of Informatization of Habitat Monitoring and Fishery Resource Conservation Research in the East China Sea of Zhejiang Province, Zhejiang Ocean University, Zhoushan, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Kundu S, Kumar V, Tyagi K, Chakraborty R, Chandra K. The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis. Ecol Evol 2019; 9:10854-10868. [PMID: 31624586 PMCID: PMC6787814 DOI: 10.1002/ece3.5606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/24/2019] [Accepted: 08/07/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Vikas Kumar
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kaomud Tyagi
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Rajasree Chakraborty
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
| | - Kailash Chandra
- Centre for DNA TaxonomyMolecular Systematics DivisionZoological Survey of IndiaKolkataIndia
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Jiang L, Peng L, Tang M, You Z, Zhang M, West A, Ruan Q, Chen W, Merilä J. Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses. Ecol Evol 2019; 9:8813-8828. [PMID: 31410282 PMCID: PMC6686361 DOI: 10.1002/ece3.5433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/12/2022] Open
Abstract
This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Liqing Peng
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Tang
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Andrea West
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
| | - Wei Chen
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and TechnologyMianyang Normal UniversityMianyangSichuanChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangSichuanChina
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty Biological & Environmental SciencesUniversity of HelsinkiHelsinkiFinland
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Gutiérrez‐Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, Cadena CD. Molecular and morphological differentiation among Torrent Duck (
Merganetta armata
) populations in the Andes. ZOOL SCR 2019. [DOI: 10.1111/zsc.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natalia Gutiérrez‐Pinto
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- School of Biological Sciences University of Nebraska Lincoln Nebraska
| | - Kevin G. McCracken
- Department of Biology University of Miami Coral Gables Florida
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences Miami Florida
- Institute of Arctic Biology University of Alaska Museum Fairbanks Alaska
- Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks Alaska
| | - Pablo Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET) Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CONICET‐CCT Mendoza) Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
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25
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Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses. Int J Biol Macromol 2019; 133:683-692. [DOI: 10.1016/j.ijbiomac.2019.04.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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Kulikova IV, Zhuravlev YN, Korobitsyn IG, Nemkova GA, McCracken KG, Peters JL. Holarctic phylogeographic structure of Eurasian wigeon (Mareca penelope). Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Eurasian wigeon (Mareca penelope) is one of the most numerous migrant species of waterfowl in the Palearctic. Annually, significant part of the world’s wigeon population makes seasonal flights over distances from tens to thousands or more kilometers. According to different estimates based on banding data, five geographic populations of the species were described in the Palearctic. However, distinct borders between the populations have not been identified. At the same time, no phylogeographic studies have been carried out for the complete native range of wigeon so far. In addition to the fundamental importance of such a study, knowledge of the genetic structure of populations is necessary for the development of measures to increase the number of and preserve this valuable game species. The aim of our work was a phylogeographic analysis of the wigeon across its vast native range in the Palearctic including ducks wintering in North America. We examined genetic diversity and differentiation of wigeon populations identified with banding data, phylogenetic relationships of mtDNA haplotypes and demographic history of populations and species as a whole by sequencing a 661 base-pair 5’-fragment of the mitochondrial control region from 195 individual ducks collected throughout the Palearctic and Nearctic. Genetic diversity was high in all studied populations. A reconstruction of haplotypes phylogeny revealed the absence of geographic structure in the data. Nonetheless, analysis of molecular variance (AMOVA) identified two groups of populations: EuropeanSiberian and East Asian. The former included wigeons from Europe, Siberia and the Atlantic coast of North America, and the latter comprised ducks from Russian Far East, Kamchatka Peninsula, Chukotka Autonomous District, the Aleutian Islands, Alaska, and the Pacific coast of North America.
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Affiliation(s)
- I. V. Kulikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | - Y. N. Zhuravlev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | | | - G. A. Nemkova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS
| | - K. G. McCracken
- Department of Biology, University of Miami; Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami; Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
| | - J. L. Peters
- Department of Biological Sciences, Wright State University
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Kundu S, Kumar V, Tyagi K, Chakraborty R, Singha D, Rahaman I, Pakrashi A, Chandra K. Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae. Sci Rep 2018; 8:17378. [PMID: 30478342 PMCID: PMC6255766 DOI: 10.1038/s41598-018-35822-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/09/2018] [Indexed: 11/08/2022] Open
Abstract
The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.
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Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India.
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Iftikar Rahaman
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, M-Block, New Alipore, Kolkata, 700 053, West Bengal, India
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Lima NCB, Soares AER, Almeida LGDP, Costa IRD, Sato FM, Schneider P, Aleixo A, Schneider MP, Santos FR, Mello CV, Miyaki C, Vasconcelos ATR, Prosdocimi F. Comparative mitogenomic analyses of Amazona parrots and Psittaciformes. Genet Mol Biol 2018; 41:593-604. [PMID: 30235395 PMCID: PMC6136379 DOI: 10.1590/1678-4685-gmb-2017-0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.
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Affiliation(s)
- Nicholas Costa Barroso Lima
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.,Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | | | | | - Igor Rodrigues da Costa
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Midori Sato
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Patricia Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Belém, PA, Brazil
| | - Maria Paula Schneider
- Departamento de Genética, Centro de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fabrício R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Cristina Miyaki
- Laboratório de Genética e Evolução Molecular de Aves, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
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The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes. Genes Genomics 2018; 40:151-165. [PMID: 29892923 DOI: 10.1007/s13258-017-0617-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772 bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.
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Warzecha J, Fornal A, Oczkowicz M, Bugno-Poniewierska M. A molecular characteristic of the Anatidae mitochondrial control region – a review. ANNALS OF ANIMAL SCIENCE 2018. [DOI: 10.1515/aoas-2017-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Mitochondrial DNA (mtDNA) is a molecular tool that is very effective in genetic research, including phylogenetic analysis. The non-coding region is the most variable fragment of mtDNA, showing variability in length and nucleobase composition and containing three domains: two hypervariable peripheral regions and the conserved domain (D-loop) in the middle. The Anseriformes are amongst the best studied avian groups, including approximately 150 species and containing geese, swans, ducks (Anatidae), the Magpie goose (Anseranatidae) and screamers (Anhimidae). The most numerous family is the Anatidae, appearing in close relationships within the phylogenetic branches of the species. There are differences between the non-coding region of the Anatidae in comparison to other avian control regions. In the article presented below the control region sequences and the phylogeny of the Anatidae were reviewed.
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Affiliation(s)
- Joanna Warzecha
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice n. Kraków , Poland
| | - Agnieszka Fornal
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice n. Kraków , Poland
| | - Maria Oczkowicz
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice n. Kraków , Poland
| | - Monika Bugno-Poniewierska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083 Balice n. Kraków , Poland
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32
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Huang Z, Ke D. Organization and variation of the Tetraonidae (Aves: Galliformes) mitochondrial DNA control region. Mitochondrial DNA B Resour 2017; 2:568-570. [PMID: 33490466 PMCID: PMC7800250 DOI: 10.1080/23802359.2017.1361345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji’an, Jiangxi, China
| | - Dianhua Ke
- School of Life Sciences, Jinggangshan University, Ji’an, Jiangxi, China
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Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong. Heredity (Edinb) 2017; 119:360-370. [PMID: 28792491 DOI: 10.1038/hdy.2017.47] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 11/08/2022] Open
Abstract
The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant ΦST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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Hu C, Zhang C, Sun L, Zhang Y, Xie W, Zhang B, Chang Q. The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes. PLoS One 2017; 12:e0175244. [PMID: 28384231 PMCID: PMC5383286 DOI: 10.1371/journal.pone.0175244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/22/2017] [Indexed: 11/18/2022] Open
Abstract
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.
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Affiliation(s)
- Chaochao Hu
- Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Lei Sun
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, United States of America
| | - Yi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Wenli Xie
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui, People's Republic of China
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China
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Zhang HL, Ye F. Comparative Mitogenomic Analyses of Praying Mantises (Dictyoptera, Mantodea): Origin and Evolution of Unusual Intergenic Gaps. Int J Biol Sci 2017; 13:367-382. [PMID: 28367101 PMCID: PMC5370444 DOI: 10.7150/ijbs.17035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/20/2016] [Indexed: 11/23/2022] Open
Abstract
Praying mantises are a diverse group of predatory insects. Although some Mantodea mitogenomes have been reported, a comprehensive comparative and evolutionary genomic study is lacking for this group. In the present study, four new mitogenomes were sequenced, annotated, and compared to the previously published mitogenomes of other Mantodea species. Most Mantodea mitogenomes share a typical set of mitochondrial genes and a putative control region (CR). Additionally, and most intriguingly, another large non-coding region (LNC) was detected between trnM and ND2 in all six Paramantini mitogenomes examined. The main section in this common region of Paramantini may have initially originated from the corresponding control region for each species, whereas sequence differences between the LNCs and CRs and phylogenetic analyses indicate that LNC and CR are largely independently evolving. Namely, the LNC (the duplicated CR) may have subsequently degenerated during evolution. Furthermore, evidence suggests that special intergenic gaps have been introduced in some species through gene rearrangement and duplication. These gaps are actually the original abutting sequences of migrated or duplicated genes. Some gaps (G5 and G6) are homologous to the 5' and 3' surrounding regions of the duplicated gene in the original gene order, and another specific gap (G7) has tandem repeats. We analysed the phylogenetic relationships of fifteen Mantodea species using 37 concatenated mitochondrial genes and detected several synapomorphies unique to species in some clades.
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Affiliation(s)
- Hong-Li Zhang
- School of Life Sciences, Datong University, Datong 037009, China
| | - Fei Ye
- College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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Wen L, Liao F. Complete mitochondrial genome of Pycnonotus xanthorrhous (Passeriformes, Pycnonotidae) and phylogenetic consideration. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Huang Z, Shen Y, Ma Y. Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:867-871. [PMID: 27549748 DOI: 10.1080/24701394.2016.1199023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The control region is the major noncoding segment of animal mitochondrial DNA. To infer the structure and variation of Fringillidae mitochondrial DNA control region, the entire control region sequences of 25 species were analyzed. The length of the control region sequences was very conserved (1230 ± 18) and can be separated into three domains. The frequency of both substitutions and gaps was highest in the third domain and lowest in the central region. The control region has the same flanking gene order from tRNAGlu to tRNAPhe. Genetic distances between species ranged from 1.80% (between Carduelis pinus and Carduelis spinus) to 25.34% (between Carduelis sinica and Coccothraustes vespertinus). The average genetic distances among the species within the genera varied from 5.11% (Leucosticte) to 14.31% (Carpodacus). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain III is the most variable of the three domains among all the genera. The control region of Fringillidae contains a putative TAS element and the highly conserved CSB-1, and F, E, D, C boxes. However, neither CSB-2 nor CSB-3 could be unambiguously identified in the Fringillidae. The maximum likelihood method was used to construct a phylogenetic tree. Control region analysis demonstrated that some currently recognized genera may be polyphyletic, including Carpodacus, Carduelis and Serinus.
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Affiliation(s)
- Zuhao Huang
- a School of Life Sciences, Jinggangshan University , Ji'an , China
| | - Yamin Shen
- a School of Life Sciences, Jinggangshan University , Ji'an , China
| | - Yurong Ma
- a School of Life Sciences, Jinggangshan University , Ji'an , China
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Rahman MM, Yoon KB, Kim JY, Hussin MZ, Park YC. Complete mitochondrial genome sequence of the Indian pipistrellePipistrellus coromandra(Vespertilioninae). Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1150877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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40
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Hao RC, Wang GH, Yang GZ, Zan LS. The complete mitochondrial genome sequence of Zebrias crossolepis (pleuronectiformes: soleidae) and Acrossocheilus monticola (cypriniformes: cyprinidae) and phylogenetic studies. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4326-4327. [PMID: 26463086 DOI: 10.3109/19401736.2015.1089485] [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
In this study, two complete mitogenome sequences of Zebrias crossolepis and Acrossocheilus monticola were determined and the phylogenetic relationship were constructed based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes. The length of the complete mitogenome sequence are 16 775 bp and 16 605 bp in Z. crossolepis and A. monticola, respectively, both containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.3% A, 26.3% T, 30.0% C, 15.5% G, with a slight AT bias (54.6%) in Z. crossolepis, while 31.4% A, 24.5% T, 28.2% C, 15.9% G, with an slight AT bias (55.9%) in A. monticola. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while ND4 and Cytb in Z. crossolepis and COII, ND4, and Cytb in A. monticola use an incomplete stop codon T. These results are expected to provide useful molecular data for species identification and further phylogenetic studies.
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Affiliation(s)
- Rong-Chao Hao
- a College of Animal Science and Technology, Hebei North University , Zhangjiakou , China and
| | - Guo-Hua Wang
- a College of Animal Science and Technology, Hebei North University , Zhangjiakou , China and
| | - Guo-Zhong Yang
- a College of Animal Science and Technology, Hebei North University , Zhangjiakou , China and
| | - Lin-Sen Zan
- b College of Animal Science and Technology, Northwest A&F University , Yangling , China
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Weston KA, Robertson BC. Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris). Mol Ecol 2015; 24:4778-94. [DOI: 10.1111/mec.13349] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 11/28/2022]
Affiliation(s)
- K. A. Weston
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - B. C. Robertson
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
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Eberhard JR, Wright TF. Rearrangement and evolution of mitochondrial genomes in parrots. Mol Phylogenet Evol 2015; 94:34-46. [PMID: 26291569 DOI: 10.1016/j.ympev.2015.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/15/2015] [Accepted: 08/11/2015] [Indexed: 12/27/2022]
Abstract
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.
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Affiliation(s)
- Jessica R Eberhard
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Timothy F Wright
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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Rutkowski R, Krupiński D, Kitowski I, Popović D, Gryczyńska A, Molak M, Dulisz B, Poprach K, Müller S, Müller R, Gierach KD. Genetic structure and diversity of breeding Montagu’s harrier (Circus pygargus) in Europe. EUR J WILDLIFE RES 2015. [DOI: 10.1007/s10344-015-0943-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yoon KB, Cho CU, Park YC. The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes). Gene 2015; 572:227-36. [PMID: 26165451 DOI: 10.1016/j.gene.2015.07.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 06/20/2015] [Accepted: 07/07/2015] [Indexed: 01/22/2023]
Abstract
The complete mitogenome of Chroicocephalus saundersi was characterized and compared with the 6 published Charadriiformes mitogenomes. The mitogenome of C. saundersi is a closed circular molecule 16,739 bp in size, and contains 37 genes and a control region. The AT and GC skews are positive and negative, respectively, and in agreement with those of the other Charadriiformes mitogenomes. The mitogenome of C. saundersi contains 3 start codons (ATG, GTG, and ATT), 4 stop codons (TAA, TAG, AGG, and AGA), and an incomplete stop codon (T-) in 13 PCGs. A codon usage analysis of all available Charadriiformes mitogenomes showed that the ATG (78%) and TAA (50.5%) were the most common start codon and stop codon, respectively. An unusual start codon, ATT, is commonly found in the ND3s of Charadriiformes mitogenomes, whereas the more common start codons, ATC and ATA, are rarely found. In all the Laridae species, one extra cytosine was inserted at position 174 in ND3. The control region of C. saundersi is 1180-bp long, with a nucleotide composition of 30.2% A, 28.6% T, 27.3% C, and 14.0% G. Variable numbers of tandem repeats (VNTRs) with nine copies of the 10 bp repeat sequence (AACAACAAAC) are found within the CSB domain of the control region. The ML/BI analyses, based on the amino acids of the 13 mitochondrial PCGs, strongly support the monophyly of the order Charadriiformes, with the suborder Lari considered sister to the Scolopaci, which is in turn a sister group to the suborder Charadrii.
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Affiliation(s)
- Kwang Bae Yoon
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Chea Un Cho
- Species Restoration Technology Institute, Korea National Park Service, Inje 252-829, Republic of Korea
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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Yang C, Lian T, Wang QX, Huang Y, Xiao H. Structural characteristics of the Relict Gull (Larus relictus) mitochondrial DNA control region and its comparison to other Laridae. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2487-91. [PMID: 26016878 DOI: 10.3109/19401736.2015.1033711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The structure of the mitochondrial DNA control region in the Relict Gull (Larus relictus) was predicted and compared with data from the National Center for Biotechnology Information (NCBI) on five other gulls. The results showed that the control regions of the six gulls comprise three domains. Sequences of CSB-1-like (domain I) and CSB-1 (domain III) in L. relictus have the highest similarity with those in the other five gulls. The insertion fragments are located in downstream domain I of L. ridibundus, L. brunnicephalus, and L. saundersi. Seven conserved sequence boxes (additional box, F-box, E-box, D-box, C-box, bird-similarity-box, and B-box) are located in domain II in all six gulls. It is suggested that the CSB-2/3 sequence, the origin of H-strand replication, and bidirectional light- and heavy-strand transcription promoters in domain III of L. relictus have some distinguishing features to those of other gulls. Some repeat units are contained in the 3' end of the control region in the five gulls; however, no repeat units are found in the sequence CAAACAACAAA in L. relictus. The distribution of nucleotide diversity analysis will provide the useful information on the selected DNA fragment within the control region for genetic analyses among gulls.
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Affiliation(s)
- Chao Yang
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
| | - Ting Lian
- b Department of Bioengineering , Xi'an Vocational and Technical College , Xi'an , China , and
| | - Qing-Xiong Wang
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
| | - Yuan Huang
- c College of Life Sciences, Shaanxi Normal University , Xi'an , China
| | - Hong Xiao
- a Endangered Species Conservation Biology Research Center, Shaanxi Institute of Zoology , Xi'an , China
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Sun WL, Zhong W, Bao K, Liu HL, Ya-Han Y, Wang Z, Li GY. The complete mitochondrial genome of silver fox (Caniformia: Canidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3348-50. [PMID: 25714151 DOI: 10.3109/19401736.2015.1018216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Silver fox is color variant of Vulpes vulpes. At present, there are few studies on phylogeny of Canidae and Caniformia. In this article, we determined and described the complete mitogenome of silver fox for the first time, which is 16,723 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL) and a putative control region (CR). The overall base composition is 31.4% A, 27.9% T, 26.0% C, 14.7% G, respectively, with a AT bias (59.3%). Ten protein-coding genes use the initiation codon ATG while ND2, ND3 and ND5 use ATA. Most of them have TAA as the stop codon, except ND2 uses TAG, Cytb uses AGA, and COX3, ND3, ND4 use an incomplete stop codon TA. The information is expected to provide useful molecular data for further taxonomic and phylogenetic studies of Canidae and Caniformia.
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Affiliation(s)
- Wei-Li Sun
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Wei Zhong
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Kun Bao
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Han-Lu Liu
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Yang Ya-Han
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Zhuo Wang
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
| | - Guang-Yu Li
- a Institute of Special Animal and Plant Science, Chinese Academy of Agricultural Sciences (CAAS) , Changchun , P.R. China and.,b State Key Lab for Molecular Biology of Special Economic Animals , Changchun , P.R. China
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Liu G, Zhou L, Li B, Zhang L. The complete mitochondrial genome of Aix galericulata and Tadorna ferruginea: bearings on their phylogenetic position in the Anseriformes. PLoS One 2014; 9:e109701. [PMID: 25375111 PMCID: PMC4222781 DOI: 10.1371/journal.pone.0109701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/22/2014] [Indexed: 11/21/2022] Open
Abstract
Aix galericulata and Tadorna ferruginea are two Anatidae species representing different taxonomic groups of Anseriformes. We used a PCR-based method to determine the complete mtDNAs of both species, and estimated phylogenetic trees based on the complete mtDNA alignment of these and 14 other Anseriforme species, to clarify Anseriform phylogenetics. Phylogenetic trees were also estimated using a multiple sequence alignment of three mitochondrial genes (Cyt b, ND2, and COI) from 68 typical species in GenBank, to further clarify the phylogenetic relationships of several groups among the Anseriformes. The new mtDNAs are circular molecules, 16,651 bp (Aix galericulata) and 16,639 bp (Tadorna ferruginea) in length, containing the 37 typical genes, with an identical gene order and arrangement as those of other Anseriformes. Comparing the protein-coding genes among the mtDNAs of 16 Anseriforme species, ATG is generally the start codon, TAA is the most frequent stop codon, one of three, TAA, TAG, and T-, commonly observed. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNASer (AGY) and tRNALeu (CUN), which are missing the "DHU" arm.Phylogenetic relationships demonstrate that Aix galericula and Tadorna ferruginea are in the same group, the Tadorninae lineage, based on our analyses of complete mtDNAs and combined gene data. Molecular phylogenetic analysis suggests the 68 species of Anseriform birds be divided into three families: Anhimidae, Anatidae, and Anseranatidae. The results suggest Anatidae birds be divided into five subfamilies: Anatinae, Tadorninae, Anserinae, Oxyurinae, and Dendrocygninae. Oxyurinae and Dendrocygninae should not belong to Anserinae, but rather represent independent subfamilies. The Anatinae includes species from the tribes Mergini, Somaterini, Anatini, and Aythyini. The Anserinae includes species from the tribes Anserini and Cygnini.
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Affiliation(s)
- Gang Liu
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lizhi Zhou
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
- * E-mail:
| | - Bo Li
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
| | - Lili Zhang
- Institute of Biodiversity and Wetland Ecology, School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, P. R. China
- Anhui Biodiversity Information Center, Hefei, Anhui, P. R. China
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48
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Huang Z, Ke D. Structure and variation of the Anseriformes mitochondrial DNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:2036-9. [PMID: 25329267 DOI: 10.3109/19401736.2014.974177] [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
The control region is the major non-coding segment of animal mitochondrial DNA. To infer the structure and variation of Anseriformes mitochondrial DNA control region, the control region sequences of 52 species were analyzed. The length of the control region sequences ranged from 968 bp (Chenonetta jubata) to 1335 bp (Anseranas semipalmata) and can be separated into three domains. There is a deletion of 100-130 bp in Anatinae, compared to other groups of Anserinae. The average genetic distances among the species within the genera varied from 4.14% (Anser) to 10.58% (Cygnus). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain I is the most variable among the three domains among all the genera. Five conserved sequence boxes in the domain II of Anseriformes sequences were identified. The alignment of the Anseriformes five boxes sequences showed considerable sequence variation. CSB-1, -2 and 3 were not found in the Anseriformes. Maximum-likelihood method was used to construct a phylogenetic tree, which grouped all of the genera into four divergent clades. Anseranas + Chauna and Dendrocygna were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane.
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Affiliation(s)
- Zuhao Huang
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , P.R. China
| | - Dianhua Ke
- a School of Life Sciences, Jinggangshan University , Ji'an , Jiangxi Province , P.R. China
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Norman JA, Blackmore CJ, Rourke M, Christidis L. Effects of mitochondrial DNA rate variation on reconstruction of Pleistocene demographic history in a social avian species, Pomatostomus superciliosus. PLoS One 2014; 9:e106267. [PMID: 25181547 PMCID: PMC4152169 DOI: 10.1371/journal.pone.0106267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/04/2014] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.
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Affiliation(s)
- Janette A. Norman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Department of Genetics, University of Melbourne, Parkville, Victoria, Australia
- Museum Victoria, Melbourne, Victoria, Australia
| | - Caroline J. Blackmore
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Meaghan Rourke
- Museum Victoria, Melbourne, Victoria, Australia
- School of Science and Engineering, Deakin University, Geelong, Victoria, Australia
- New South Wales Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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