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

筛选
英文 中文
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
Association between mitochondrial DNA genotype and sperm motility in humans. 人类线粒体 DNA 基因型与精子活力之间的关系。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-06-24 DOI: 10.1080/24701394.2024.2361609
Xueyou Song, Xiaoning Hong, Zilong Wang, Fuding Lu, Changze Song, Xinkun Wang, Xiaoyong Zhan, Jiaying Yu, Jiawen Zhai, Jiang Li, Xi Xiang, Xujun Xuan
{"title":"Association between mitochondrial DNA genotype and sperm motility in humans.","authors":"Xueyou Song, Xiaoning Hong, Zilong Wang, Fuding Lu, Changze Song, Xinkun Wang, Xiaoyong Zhan, Jiaying Yu, Jiawen Zhai, Jiang Li, Xi Xiang, Xujun Xuan","doi":"10.1080/24701394.2024.2361609","DOIUrl":"https://doi.org/10.1080/24701394.2024.2361609","url":null,"abstract":"<p><p>The relationship between genetic alterations in mitochondrial DNA (mtDNA) and progressive motility (PR) and rapid progressive motility (grade A) of ejaculated human spermatozoa remains unclear. In this study, we explored the association between human mtDNA genotype and sperm PR and grade A by analyzing mtDNA copy number, loci, haplogroup, rearrangement, deletions, and duplications and sperm motility parameters. Human sperm mtDNA copy number, loci and haplogroups were not associated with human sperm motility PR or A grade. However, the cumulative frequency of human sperm mtDNA rearrangements (including deletions and duplications) in participants with high PR and grade A ratio was higher than in participants with low PR and grade A ratio. Additional studies are needed to understand the relationship between mtDNA genotypes, including deletions and duplications, and human sperm motility.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443882","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
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 : 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 <i>Ligia italica</i> (Crustacea, Isopoda) from Tunisia.","authors":"Nermine Laifi-Necibi, Nabil Amor, Paolo Merella, Osama Badri Mohammed, Lamia Medini","doi":"10.1080/24701394.2024.2363350","DOIUrl":"https://doi.org/10.1080/24701394.2024.2363350","url":null,"abstract":"<p><p>Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus <i>Ligia</i> (Crustacea, Isopoda). Herein the diversity of the Italian sea slater <i>Ligia italica</i> 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 <i>L. italica</i> dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that <i>L. italica</i> constitute a cryptic species complex. Divergence among different <i>L. italica</i> 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 <i>Wolbachia</i> bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of <i>Ligia italica</i>. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in <i>Ligia italica</i> in Mediterranean.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","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
Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample. 利用扩大的类群样本进行膜翅目(昆虫)线粒体基因组重排和系统发生组学研究。
Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis Pub Date : 2024-05-16 DOI: 10.1080/24701394.2024.2345663
Nan Song, Shujun Wei, Miaomiao Wang
{"title":"Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample.","authors":"Nan Song, Shujun Wei, Miaomiao Wang","doi":"10.1080/24701394.2024.2345663","DOIUrl":"https://doi.org/10.1080/24701394.2024.2345663","url":null,"abstract":"The order Hymenoptera is one of the most species-rich insect orders, with more than 150,000 described extant species. Many hymenopteran insects have very different mitochondrial genome (mitogenome) organizations compared to the putative ancestral organization of insects. In this study, we sequenced 18 mitogenomes of representatives in the order Hymenoptera to increase taxonomic sampling. A total of 475 species were used in phylogenetic analyses, including 18 new mitogenomes and 457 existing mitogenomes. Using a site-heterogeneous model, Bayesian's inference from amino acid data yielded more resolved relationships among Hymenoptera than maximum-likelihood analysis and coalescent-based species analyses. The monophyly of Symphyta was not supported. The Xyeloidea was the earliest branching clade in the Hymenoptera. The Orussoidea was closely related to Apocrita. Within Apocrita, the Parasitoida was non-monophyletic. The monophyly of most Parasitoida superfamilies received strong support. The Proctotrupomorpha clade was supported in Bayesian's analysis. The Apoidea was monophyletic when excluding Ampulex compressa from consideration. The superfamilies Vespoidea and Chrysidoidea were found to be non-monophyletic. Comparisons of mitochondrial gene order revealed a higher frequency of gene rearrangement among lineages with a parasitoid lifestyle, particularly prominent in Chalcidoidea. The degree of gene rearrangement ranked second in specific taxa of Cynipoidea and Ichneumonoidea.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":" 1241","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141127257","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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信