Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis

The populations of the loggerhead turtles, Caretta caretta, 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...

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...

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...

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...

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...

Mitochondrial DNA is a valuable tool for population genetics and evolutionary studies in a wide range of organisms. With advancements in sequencing techniques, it's now possible to gain deeper insights into this molecule. By understanding how many genes there are, how they're organized within the molecule, identifying the presence of spacers, and analyzing the composition of the D-Loop, we can better grasp the rearrangements that play a crucial role in the evolutionary dynamics of mitochondrial DNA. Additionally, phylogenetic analyses benefit significantly from having access to a larger pool of mtDNA genes...

The Rüppell's fox ( Vulpes rueppellii ) inhabits desert regions across North Africa, the Arabian Peninsula and southwestern Asia. Its phylogenetic relationship with other fox species, especially within the phylogeographic context of its sister species, V. vulpes , remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of V. rueppellii , analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the V...

We investigated the vulnerable fish species Schizothorax argentatus Kessler, 1874, using low-coverage whole genome sequencing data. The assembled 16,587 bp mitochondrial genome has a nucleotide composition of A = 29.8%, T = 25.3%, G = 17.9%, and C = 27.0%, containing 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes with a gene arrangement identical to other cofamilial species. Phylogenetic analyses of 71 schizothoracine fishes suggest a close relationship between S...

Opsarius siangi sp. nov., a previously undocumented species, has been identified from Siang River, Pasighat, Arunachal Pradesh, India. This newly described species is distinguished by a suite of unique morphological characteristics, notably including a complete lateral line, consisting of 65-77 scales, 32-39 pre-dorsal scales, 12-15 scales positioned between dorsal fin origin and lateral line, presence of two pairs of barbels, body depth ranging from 18.80% to 27.42% of standard length and a distinct pattern of 8-15 vertical bars adorning the body...

We analyzed the mitochondrial DNA of Gekko hokouensis collected from the Izu Islands (maybe an introduced population) and the Nansei Islands (native population), both in Japan. A molecular phylogenetic analysis suggested that G. hokouensis of Japan belongs to a cryptic monophyletic group different from that of the currently discovered sample of China. Furthermore, the Japanese clade of G. hokouensis is differentiated into two subclades (Clade 1 and Clade 2 in this article). In the Nansei Islands, these two subclades form a complicated nested-distribution pattern and do not coexist on any of the islands, whereas both clades appear to coexist in the Izu Islands...

A total of 241 mitochondrial genomes were assembled and annotated from the SRA database to reconstruct a mtDNA genome phylogeny for the genus Drosophila , the family Drosophilidae, and close relatives. The resulting mtDNA genome phylogeny is largely congruent with previous higher-level analyses of Drosophila species with the exception of the relationships between the melanogaster, montium, anannassae, saltans and obscura groups. Although relationships within these species groups are congruent between nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is different when compared to earlier studies...

Lamiophlomis rotata , the only species within the genus Lamiophlomis (family Labiatae), exhibits a broad geographical distribution in elevated highland areas in Qinghai-Tibetan Plateau and possesses significant therapeutic properties. Numerous chemical compositions and putative phylogenetic affiliations of this species have been documented in prior research. Nevertheless, there is a scarcity of accessible publications regarding the genomic data of L. rotata , particularly its chloroplast genome. This dearth of knowledge hampers the comprehensive investigation of its phylogenetic placement within the Labiatae family...

The nine endemic species of the genus Schizothorax from the Yarlung Zangbo River, Tibet comprise a putative cyprinid species flock. In this study, the effectiveness of the COI DNA barcode for Schizothoracinae species identification was verified by using 45 COI sequences covering nine species in four genera of Schizothoracinae fishes. The average Kimura two parameter (K2P) genetic distances within and among species were 0.13% and 8.57%, respectively. The results revealed that most of the species were clearly discriminated by their estimated genetic distances and monophyletic clustering in a maximum likelihood tree...

The Pangani catchment of Northern Tanzania harbours the critically endangered endemic tilapias of the genus Oreochromis . The introduction of non-native congenerics and consequent hybridization complicates taxa identification and phylogeny based on morphological systematics. We therefore morphologically and molecularly identified these tilapias and delimited their Molecular Operational Taxonomic Units (MOTUs) based on Cytochrome Oxidase Subunit I (CO1) gene for future management and conservation. A total of 132 indigenous and introduced tilapia specimens were morphologically identified, barcoded using the CO1 gene and delimited by Kimura 2 Parameter distance approaches, Automatic Barcode Gap Discovery (ABGD), Neighbour Joining (NJ) tree and haplotype analysis...

The giant trevallies ( Caranx ignobilis ) is a globally important fish species that is at risk from overexploitation. In this study, 150  C. ignobilis from six provinces in the Philippines were collected for genetic analyses. For each province, five representative specimens of C. ignobilis were subjected to DNA barcoding and revealed high interspecific K2P distances of 9.58% and 17.29% when compared to other species of Caranx and Carangoides , respectively. On the other hand, all 150  C. ignobilis specimens were subjected to population genetic analysis using the mitochondrial cytochrome b region...

We developed species-specific primers of five microcrustacean preys, Ceriodaphnia richardi , Diaphanosoma cf . brevireme , Daphnia gessneri, Simocephalus serrulatus, Thermocyclops decipiens and Mesocyclops sp., to analyze food-web interactions involving their two insect predators Rheumatobates crassifemur and Martarega uruguayensis distributed in a tropical shallow lake. We designed internal primers of the COI gene (177-282 bp), and tested them, by means of PCR, for specificity and sensitivity. In our tests for specificity, all primers successfully amplified the DNA target but were species-specific failing to amplify the biomarker from any of the other species tested, even in a mixed DNA sample, including predators' DNA...

The starfish Asterias amurensis is a marine pest native to the northwestern Pacific and has successfully invaded southern Australia. Asterias amurensis have caused substantial environmental and economic impacts in both native and non-native regions. However, little information is available about the genetic features of its native populations, especially for those in North China. Here we sequenced the complete mitochondrial genomes of five individuals from different locations in China and compared their characteristics with three mitogenomes available from Japan...

The chilhuil sea catfish ( Bagre panamensis ) is an ecologically relevant species contributing to the structure, organization, and functioning of the ecosystems it inhabits. Also, it is an important artisanal fishery resource in the Mexican Pacific coast. This study aimed to determine the genetic diversity, population structure, and historical demography of B. panamensis in the Mexican Pacific. The mitochondrial DNA was amplified from two distinct regions, r16S and COI, resulting in an 1142 bp of the concatenated genes...

The Serra Spanish mackerel, Scomberomorus brasiliensis , is one of the most important fishery resources in the western tropical Atlantic, including northern and eastern Brazil. Despite its economic importance, few genetic markers have been sequenced in this species, and little is known of its population genetics. The present study evaluated the genetic variability of 110 individuals, representing three distinct Brazilian populations (Macapá, Fortaleza and Paranaguá), based on a segment of the mitochondrial Control Region...

The Spiny Butterfly Ray, Gymnura altavela , is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, Gymnura altavela is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of G. altavela sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if G...