Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献_第2页

Complete chloroplast genomes of five Aegilops aucheri Boiss. accessions having different geographical origins. 5种紫叶藻叶绿体全基因组的研究。具有不同地理来源的加入。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-04-01 Epub Date: 2025-03-12 DOI: 10.1080/24701394.2025.2476401

Azat R Kuluev, Rustam T Matniyazov, Bulat R Kuluev, Dmitry A Chemeris, Alexey V Chemeris

{"title":"Complete chloroplast genomes of five Aegilops aucheri Boiss. accessions having different geographical origins.","authors":"Azat R Kuluev, Rustam T Matniyazov, Bulat R Kuluev, Dmitry A Chemeris, Alexey V Chemeris","doi":"10.1080/24701394.2025.2476401","DOIUrl":"10.1080/24701394.2025.2476401","url":null,"abstract":"The subject of this study is Aegilops aucheri Boiss. 1844: a member of the section Sitopsis, subsection Truncata. This species is infrequently included in phylogenetic studies and is commonly regarded as a heterotypic synonym of Aegilops speltoides Tausch. The aim of this study was to detect genetic differences between Ae. aucheri and Ae. speltoides using the phylogenetic signal retrieved from chloroplast genomes. Plastomes of five Ae. aucheri accessions from different geographical locations were sequenced, annotated, and subjected to a phylogenetic analysis. Plastome sizes were found to range between 135,666 and 135,668 bp in Ae. aucheri. Comparative analysis of the chloroplast genome sequences from five Ae. aucheri accessions revealed single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) relative to the Ae. speltoides plastome. To gain a more comprehensive understanding of the genetic divergence within the Truncata subsection, sequencing the nuclear genome of Ae. aucheri and comparing it to that of Ae. speltoides is essential.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"119-125"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618016","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 : 2025-04-01 Epub 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":"10.1080/24701394.2024.2427206","url":null,"abstract":"We sequenced and assembled mitochondrial genomes of three tenthredinid sawflies (Euura poecilonota, E. striata, and Dolerus timidus) 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 E. poecilonota, D. timidus, and E. striata 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 trnQ, which is on the minus strand in Euura and the plus strand in Dolerus. Using published tenthredinid genome data, we show that control region lengths are often underestimated.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"84-92"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","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

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 : 2025-04-01 Epub Date: 2024-09-27 DOI: 10.1080/24701394.2024.2409067

Sandra Ludwig, Lais Amorim, Ana C Barcelos, Paula R Guimarães, Sarah M Vargas

引用次数: 0

The complete mitochondrial genome of the grasshopper Chorthippus dubius (Zub.) (Orthoptera: Acrididae: Gomphocerinae): detailed characterization and phylogenetic position. 蝗虫Chorthippus dubius （Zub.）线粒体全基因组（直翅目：蝗科：Gomphocerinae）的详细特征和系统发育定位。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-04-01 Epub Date: 2024-12-30 DOI: 10.1080/24701394.2024.2446772

Xiaoli Liu, Yun Fu, Jizhuang Liu, Xinxin Li, Yuan Li, Di Meng, Yang Hu, Tao Sun

{"title":"The complete mitochondrial genome of the grasshopper Chorthippus dubius (Zub.) (Orthoptera: Acrididae: Gomphocerinae): detailed characterization and phylogenetic position.","authors":"Xiaoli Liu, Yun Fu, Jizhuang Liu, Xinxin Li, Yuan Li, Di Meng, Yang Hu, Tao Sun","doi":"10.1080/24701394.2024.2446772","DOIUrl":"https://doi.org/10.1080/24701394.2024.2446772","url":null,"abstract":"Chorthippus dubius (Zub.) is one of the dominant grasshopper species. The limited data on Ch. dubius (Zub.) has impeded further understanding of its genetic characteristics and molecular detection. In this study, we analyzed the mitogenome of Ch. dubius (Zub.), which was 15,561 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and an AT-rich region. The entire mtDNA exhibited a strong AT bias, with an overall A+T content of 74.8%. The relative synonymous codon usage (RSCU) analysis revealed UUA (L) as the most frequently used codon. All the PCGs evolved under purifying selection (Ka/Ks <0.5), with ATP8 gene exhibited the highest Ka/Ks ratio. Maximum likelihood (ML) and Bayesian inference (BI) analyses reconstructed two topologically similar phylogenetic trees, and supported the monophly of the six subfamilies in Acrididae. Our results indicated two stable clades of the six subfamilies, with Oedipodinae emerging as the ancestral taxon and being sister group to the remaining taxa. In the alternative phylogenetic lineage, the remaining five subfamilies clustered the following relationship: Gomphocernae + (Acridinae + (Calliptaminae + (Melanoplinae + Oxyinae))). Both phylogenetic trees exhibited a closer relationship between Chorthippus dubius (Zub.) and Chorthippus aethalinus, members from the same genus.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"35 3-4","pages":"111-118"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055101","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 : 2025-04-01 Epub 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":"10.1080/24701394.2024.2416179","url":null,"abstract":"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, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, 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.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"75-83"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","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

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 : 2025-04-01 Epub 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":"10.1080/24701394.2024.2439433","url":null,"abstract":"Within the Machairodontinae subfamily, commonly referred to as saber-toothed cats, it is worth noting that only two species, namely Homotherium latidens, recognized as the scimitar-toothed cat, and Smilodon populator, 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 de novo assemblies showed complete mitogenomes with 17,323bp (H. latidens) and 16,769 bp (S. populator), 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 H. latidens specimens which may be related to an Early Pleistocene migration across Beringia.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"102-110"},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","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

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 : 2025-01-01 Epub 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":"10.1080/24701394.2024.2416173","url":null,"abstract":"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.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"23-33"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","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

DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia. DNA 条形码揭示了突尼斯海蛞蝓 Ligia italica（甲壳纲，等足目）中的隐秘物种。

Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2025-01-01 Epub Date: 2024-06-20 DOI: 10.1080/24701394.2024.2363350

Nermine Laifi-Necibi, Nabil Amor, Paolo Merella, Osama Badri Mohammed, Lamia Medini

{"title":"DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia.","authors":"Nermine Laifi-Necibi, Nabil Amor, Paolo Merella, Osama Badri Mohammed, Lamia Medini","doi":"10.1080/24701394.2024.2363350","DOIUrl":"10.1080/24701394.2024.2363350","url":null,"abstract":"Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428491","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 : 2025-01-01 Epub 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 Tursiops truncatus ponticus.","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":"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, Tursiops truncatus ponticus, 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.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.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.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"34-43"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","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

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 : 2025-01-01 Epub Date: 2024-06-21 DOI: 10.1080/24701394.2024.2368570

Amnuay Jondeung, Nuntachai Boonjorn

{"title":"Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand.","authors":"Amnuay Jondeung, Nuntachai Boonjorn","doi":"10.1080/24701394.2024.2368570","DOIUrl":"10.1080/24701394.2024.2368570","url":null,"abstract":"The short mackerel Rastrelliger brachysoma (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 (h) 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 D and Fu's FS 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.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"12-22"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","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