Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献

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Characterization, comparative phylogenetic, and gene transfer studies of Rosa chinensis var. spontanea organelle genomes.
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-02-20 DOI: 10.1080/24701394.2025.2460826
Zhe Hou, Zhengzhi Jiang, Jincui Wu, Ping Shen, Changbing Huang
{"title":"Characterization, comparative phylogenetic, and gene transfer studies of <i>Rosa chinensis</i> var. spontanea organelle genomes.","authors":"Zhe Hou, Zhengzhi Jiang, Jincui Wu, Ping Shen, Changbing Huang","doi":"10.1080/24701394.2025.2460826","DOIUrl":"https://doi.org/10.1080/24701394.2025.2460826","url":null,"abstract":"<p><p><i>Rosa chinensis</i> var. <i>spontanea</i>, an important horticultural species, holds high ornamental value. To investigate the phylogenetic relationships and organelle genome data of <i>R. chinensis</i> var. <i>spontanea</i> and its related species, the organelle genomes were constructed and sequenced in this study. The complete mitochondrial genome consists of a linear DNA molecule with a length of 270,143 base pairs and contains 55 genes. The whole chloroplast genome harbors 131 annotated genes. There are 39 and 54 simple sequence repeats (SSRs) in the mitochondrial and chloroplast genomes of <i>R. chinensis</i> var. <i>spontanea</i>, respectively. The phylogenetic tree of the mitochondrial genome indicates that <i>R. chinensis</i> var. <i>spontanea</i> is related to <i>R. chinensis</i>. The codon usage biases of one mitochondrial gene and nine chloroplast genes in Rosaceae were affected by mutation, while those of other genes have undergone selection. Overall, our findings suggest that the information within the organelle genomes can be utilized for constructing molecular markers, conducting genetic evolution research, and interpreting the phylogenetics of plants. The results of this study will contribute to a more in - depth investigation of the population genetics and evolution of Rosaceae.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of single nucleotide variants in the mitochondrial genome of healthy mice and humans. 健康小鼠和人类线粒体基因组单核苷酸变异的检测。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-12-12 DOI: 10.1080/24701394.2024.2439421
Alfredo Varela-Echavarría, Kenya L Contreras-Ramírez, Carlos Lozano-Flores, Maribel Hernández-Rosales
{"title":"Detection of single nucleotide variants in the mitochondrial genome of healthy mice and humans.","authors":"Alfredo Varela-Echavarría, Kenya L Contreras-Ramírez, Carlos Lozano-Flores, Maribel Hernández-Rosales","doi":"10.1080/24701394.2024.2439421","DOIUrl":"https://doi.org/10.1080/24701394.2024.2439421","url":null,"abstract":"<p><p>Single nucleotide mutations in the mitochondrial genome are linked to aging in humans, primates, and rodents and cause neuromuscular diseases in humans. Load of mitochondrial variants in healthy tissues, however, is little known. Employing an unbiased detection method with no prior enzymatic amplification, we observed that the mitochondrial genome of embryonic, adult, and aged mouse brain from two different strains contains a diversity of single nucleotide variants with no age-related increase in abundance. We also observed de novo variants in single oocytes and adult liver arising at 5x10<sup>-5</sup> and 8x10<sup>-6</sup> substitutions per base pair per generation, respectively. Moreover, we found variants in human placenta of healthy donors that may reach up to 66% of all mitochondrial genome copies. Increase in the heteroplasmy of the variants observed in healthy mouse and human tissues and of those arisen de novo at high frequency in mice may lead to mitochondrial dysfunction and disease.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats' species (Felidae: Machairodontinae). 当古生物学与基因组学相遇:两种剑齿猫物种(Felidae: macharodontinae)的完整线粒体基因组。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-12-07 DOI: 10.1080/24701394.2024.2439433
Igor Henrique Rodrigues-Oliveira, Iuri Batista da Silva, Renan Rodrigues Rocha, Rafael Augusto Silva Soares, Fabiano Bezerra Menegidio, Caroline Garcia, Rubens Pasa, Karine Frehner Kavalco
{"title":"When paleontology meets genomics: complete mitochondrial genomes of two saber-toothed cats' species (Felidae: Machairodontinae).","authors":"Igor Henrique Rodrigues-Oliveira, Iuri Batista da Silva, Renan Rodrigues Rocha, Rafael Augusto Silva Soares, Fabiano Bezerra Menegidio, Caroline Garcia, Rubens Pasa, Karine Frehner Kavalco","doi":"10.1080/24701394.2024.2439433","DOIUrl":"https://doi.org/10.1080/24701394.2024.2439433","url":null,"abstract":"<p><p>Within the Machairodontinae subfamily, commonly referred to as saber-toothed cats, it is worth noting that only two species, namely <i>Homotherium latidens</i>, recognized as the scimitar-toothed cat, and <i>Smilodon populator</i>, renowned as the saber-toothed tiger, possess partial mitochondrial genomes accessible in the NCBI database. These sequences, however, do not include the mitogenome control region (mtDNA control region) and have several gaps in their genes, including protein-coding genes (PCGs) that are widely used in phylogenetic analysis. In this study, we aimed to obtain a complete assembly of the mitogenomes of these two species from next-generation sequencing data available at NCBI's SRA. The <i>de novo</i> assemblies showed complete mitogenomes with 17,323bp (<i>H. latidens</i>) and 16,769 bp (<i>S. populator</i>), both with 13 PCGs, 22tRNAs, two rRNAs and the mtDNA control region, with all genes following the standard order and position of most vertebrate mitogenomes. Despite being generally very similar to previous studies, our phylogeny and molecular dating reveals an earliest divergence between North American and North Sea <i>H. latidens</i> specimens which may be related to an Early Pleistocene migration across Beringia.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic diversity, population genetic structure and demographic history of the Ribbontail stingray Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) along the Tanzanian coastline. 坦桑尼亚海岸线带尾黄貂鱼 Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) 的遗传多样性、种群遗传结构和人口历史。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-11-18 DOI: 10.1080/24701394.2024.2427841
Alex Nehemia
{"title":"Genetic diversity, population genetic structure and demographic history of the Ribbontail stingray <i>Taeniura lymma</i> (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) along the Tanzanian coastline.","authors":"Alex Nehemia","doi":"10.1080/24701394.2024.2427841","DOIUrl":"https://doi.org/10.1080/24701394.2024.2427841","url":null,"abstract":"<p><p>The Ribbontail stingray <i>Taeniura lymma</i> is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of <i>T. lymma</i> collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species' genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall F<sub>ST</sub> = 0.09, <i>p</i> < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Population genetic structure of the bottlenose dolphin in the Turkish waters based on mtDNA sequences with implications for the Black Sea subspecies Tursiops truncatus ponticus. 基于 mtDNA 序列的土耳其水域瓶鼻海豚种群遗传结构及其对黑海亚种 Tursiops truncatus ponticus 的影响。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-11-13 DOI: 10.1080/24701394.2024.2427216
Arda M Tonay, Begüm Uzun, Ayhan Dede, Erdem Danyer, Işıl Aytemiz Danyer, Ayaka Amaha Öztürk, Frederick I Archer, Bayram Öztürk, Raşit Bilgin
{"title":"Population genetic structure of the bottlenose dolphin in the Turkish waters based on mtDNA sequences with implications for the Black Sea subspecies <i>Tursiops truncatus ponticus</i>.","authors":"Arda M Tonay, Begüm Uzun, Ayhan Dede, Erdem Danyer, Işıl Aytemiz Danyer, Ayaka Amaha Öztürk, Frederick I Archer, Bayram Öztürk, Raşit Bilgin","doi":"10.1080/24701394.2024.2427216","DOIUrl":"10.1080/24701394.2024.2427216","url":null,"abstract":"<p><p>The bottlenose dolphin is a widely distributed species found in temperate waters, including the Mediterranean and Black Seas. The Black Sea population is recognized as a distinct subspecies, <i>Tursiops truncatus ponticus</i>, due to genetic and morphological differences. This study analyzed mitochondrial DNA (mtDNA) sequences of 73 bottlenose dolphin samples collected between 1999 and 2016 along the Turkish Black Sea coast, Turkish Straits System (TSS), Aegean, and Mediterranean Seas revealing 14 haplotypes, eight of which are reported here for the first time.</p><p><p>The haplotype network shows two main nodes with star-like sub-networks, but no apparent geographic pattern. The lack of geographical groupings of haplotypes indicates the high mobility of the species within the sampled area. The northern Black Sea bottlenose dolphins (NBS) appear to be genetically differentiated from those in the southwestern Black Sea (SBS), Mediterranean, and Atlantic Ocean, but not from the TSS and Aegean Sea populations. Besides, SBS bottlenose dolphins were differentiated only from those in the western Mediterranean (WM) and the Atlantic. Therefore, NBS and SBS bottlenose dolphins should at least be categorized as different populations. However, contrary to some previous studies there was no evidence supporting the classification of Black Sea bottlenose dolphins as a separate subspecies.</p><p><p>The TSS differs only from the Atlantic and the Aegean, and functions like a migratory 'melting pot' for surrounding populations. Despite the largest sample size, NBS bottlenose dolphins exhibited the lowest haplotype and nucleotide diversity. This low genetic diversity and potential isolation from adjacent populations highlight the need for prioritizing the conservation of NBS bottlenose dolphins.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Large mitochondrial genomes in tenthredinid sawflies (Hymenoptera, Tenthredinidae). 第十缙类锯蝇(膜翅目,第十缙科)的大型线粒体基因组。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-11-11 DOI: 10.1080/24701394.2024.2427206
Suvi Olli, Nok Ting Lam, Siri Hiljanen, Taru Kettunen, Laura Haikonen, Heidi-Mari Hyvönen, Angelika Kiebler, Ida Köngäs, Saana Minkkinen, Veera Pöykiö, Ville Sannikka, Ronja Vesa, Gerrit Wehrenberg, Stefan Prost, Marko Prous
{"title":"Large mitochondrial genomes in tenthredinid sawflies (Hymenoptera, Tenthredinidae).","authors":"Suvi Olli, Nok Ting Lam, Siri Hiljanen, Taru Kettunen, Laura Haikonen, Heidi-Mari Hyvönen, Angelika Kiebler, Ida Köngäs, Saana Minkkinen, Veera Pöykiö, Ville Sannikka, Ronja Vesa, Gerrit Wehrenberg, Stefan Prost, Marko Prous","doi":"10.1080/24701394.2024.2427206","DOIUrl":"https://doi.org/10.1080/24701394.2024.2427206","url":null,"abstract":"<p><p>We sequenced and assembled mitochondrial genomes of three tenthredinid sawflies (<i>Euura poecilonota</i>, <i>E. striata</i>, and <i>Dolerus timidus</i>) using Oxford Nanopore Technologies' MinION. The Canu assembler produced circular assemblies (23,000-40,000 bp). Still, errors were found in the highly repetitive non-coding control region because of the fragmented DNA which led to no reads spanning the complete control region, preventing its reliable assembly. Based on the non-repetitive coding region's sequencing coverage, we estimate the lengths of mitochondrial genomes of <i>E. poecilonota</i>, <i>D. timidus</i>, and <i>E. striata</i> to be about 30,000 bp, 31,000 bp, and 37,000 bp and control region to be 15,000 bp, 16,000 bp, and 22,000 bp respectively. All standard bilaterian mitochondrial genes are in the same order and orientation, except <i>trnQ</i>, which is on the minus strand in <i>Euura</i> and the plus strand in <i>Dolerus</i>. Using published tenthredinid genome data, we show that control region lengths are often underestimated.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New mitochondrial gene order arrangements and evolutionary implications in the class Octocorallia. 八带目新的线粒体基因顺序排列及其对进化的影响。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-10-21 DOI: 10.1080/24701394.2024.2416173
Angelo Poliseno, Andrea M Quattrini, Yee Wah Lau, Stacy Pirro, James D Reimer, Catherine S McFadden
{"title":"New mitochondrial gene order arrangements and evolutionary implications in the class Octocorallia.","authors":"Angelo Poliseno, Andrea M Quattrini, Yee Wah Lau, Stacy Pirro, James D Reimer, Catherine S McFadden","doi":"10.1080/24701394.2024.2416173","DOIUrl":"https://doi.org/10.1080/24701394.2024.2416173","url":null,"abstract":"<p><p>The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date, seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole class Octocorallia, have been often overlooked. Here, we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from 7 to 14 and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT and GC skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, inverted transpositions and transpositions. Furthermore, gene order rearrangement events were restricted only to some regions of the tree. Overall, different rearrangement events arose independently and from the ancestral and most common gene order, instead of being derived from other rearranged orders. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini). 鼯鼠(Pteromyini)和树松鼠(Sciurini)线粒体蛋白编码基因的选择压力比较分析。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-10-17 DOI: 10.1080/24701394.2024.2416179
Feiyun Tu, Yaqin Qiao, Wenjing Zhao, Tong Wu
{"title":"Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini).","authors":"Feiyun Tu, Yaqin Qiao, Wenjing Zhao, Tong Wu","doi":"10.1080/24701394.2024.2416179","DOIUrl":"https://doi.org/10.1080/24701394.2024.2416179","url":null,"abstract":"<p><p>Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, <i>ATP8</i> exhibited the highest dN/dS values, while <i>COX1</i> showed the lowest. The background selection ratio (ω<sub>2</sub>) values for six genes (<i>ND1</i>, <i>ND2</i>, <i>ND4</i>, <i>ATP6</i>, <i>ND5</i>, and <i>COX3</i>) in Pteromyini were lower than the foreground selection ratio (ω<sub>0</sub>) values observed in Sciurini. A RELAX analysis revealed that <i>CYTB</i>, <i>ND4</i>, <i>ATP6</i>, and <i>COX3</i> genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in <i>CYTB</i> and <i>ATP6</i>, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Inferring the origin of new D-loop haplotypes of loggerhead sea turtles (Testudinata: Cheloniidae) from the Southwest Atlantic lineage. 从西南大西洋系推断蠵海龟(Testudinata: Cheloniidae)新 D-环单倍型的起源。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-09-27 DOI: 10.1080/24701394.2024.2409067
Sandra Ludwig, Lais Amorim, Ana C Barcelos, Paula R Guimarães, Sarah M Vargas
{"title":"Inferring the origin of new D-loop haplotypes of loggerhead sea turtles (Testudinata: Cheloniidae) from the Southwest Atlantic lineage.","authors":"Sandra Ludwig, Lais Amorim, Ana C Barcelos, Paula R Guimarães, Sarah M Vargas","doi":"10.1080/24701394.2024.2409067","DOIUrl":"https://doi.org/10.1080/24701394.2024.2409067","url":null,"abstract":"<p><p>The populations of the loggerhead turtles, <i>Caretta caretta,</i> present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals' origins and the inference of their lineage.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand. 泰国湾短鲭鱼的种群遗传结构和人口历史。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-06-21 DOI: 10.1080/24701394.2024.2368570
Amnuay Jondeung, Nuntachai Boonjorn
{"title":"Population genetic structure and demographic history of short mackerel, <i>Rastrelliger brachysoma</i>, in the Gulf of Thailand.","authors":"Amnuay Jondeung, Nuntachai Boonjorn","doi":"10.1080/24701394.2024.2368570","DOIUrl":"https://doi.org/10.1080/24701394.2024.2368570","url":null,"abstract":"<p><p>The short mackerel <i>Rastrelliger brachysoma</i> (Bleeker 1851) is an important fish in the Gulf of Thailand (GoT). The biology of this species has been intensively studied, but its genetic diversity is little known. The genetic diversity, population genetic structure, and demographic history of this species in the GoT were studied using complete mt control region sequences. The CR sequences of 455 mackerel samples collected from 23 localities at four fishing grounds revealed 333 haplotypes with haplotype diversity (<i>h</i>) per population, ranging between 0.8933 and 1.000, with an average of 0.9781. In turn, the nucleotide diversity (µ) ranged between 0.0119 ± 0.0060 and 0.0333 ± 0.0174, with an average of 0.0220 ± 0.00059.A haplotype network analysis showed that all sequences segregated into two subgroups named, clade I and clade II. Two clades were separated by 26 mutational steps. Each clade formed star-like clusters with many haplotypes derived from a common haplotype. Moreover, an analysis of molecular variance (AMOVA) revealed no significant differences among the studied localities, suggesting the presence of a single population in the GoT. Pairwise differences between samples from different fishing regions also indicated no population structure. Both Tajima's <i>D</i> and Fu's <i>F</i><sub>S</sub> statistics were highly significant for the two clades but nonsignificant for the entire population according to a mismatch distribution analysis. These results confirmed that both clades experienced demographic expansion. The estimated expansion times for clade I and clade II were 1,542.307 years (1.5423 ka BP) and 7,602.541 (7.6025 ka BP) years, respectively.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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