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

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. 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.

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.

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 F_S 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.

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.

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.

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. This wealth of genetic information allows for the establishment of evolutionary relationships with greater accuracy than ever before, providing a more robust framework than analyses based on a limited number of genes. Studies on mitogenomes belonging to the family Formicidae have proven promising, enabling the identification of gene rearrangements and enhancing our understanding of the internal relationships within the group. Despite this, the number of mitogenomes available for the subfamily Ponerinae is still limited, and here we present for the first time the complete mitogenome of Odontomachus. Our data reveal a gene duplication event in Formicidae, the first involving trnV, and new gene arrangements involving the trnM-trnI-trnQ and trnW-trnC-trnY clusters, suggesting a possible synapomorphy for the genus. Our phylogenetic analysis using the PCGs available for Formicidae supports the monophyly of the subfamily Ponerinae and sheds light on the relationship between Odontomachus and Pachycondyla.

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. rueppellii mitogenome, obtaining identical sequences except for the incompletely assembled tandem-repeat region within the D-loop. The mitogenome displayed an identical organization, number and length of genes as V. vulpes. We found high support for clustering of both known subclades of V. rueppellii within the Palearctic clade of V. vulpes, rendering the latter species paraphyletic, consistent with previous analyses of shorter mtDNA fragments. More work is needed for a full understanding of the evolutionary drivers and consequences of hybridization in foxes.

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. argentatus and Schizothorax eurystomus, sharing a common ancestor with Schizothorax pseudoaksaiensis. Our study supports dividing extant schizothoracine fishes into two tribes, Schizothoracini and Schizopygopsini. The estimated time to most recent common ancestor (t_MRCA) and their distribution imply geological and climatic events during the Miocene around the Qinghai-Tibet Plateau as significant evolutionary drivers explaining the diversification of main clades in schizothoracine fishes.

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. A comprehensive genetic analysis was conducted by scrutinizing 78 Cytochrome oxidase I (COI) sequences extracted from Chedrinae fishes, with particular focus on Opsarius and Barilius genera. Phylogenetic analysis revealed that O. siangi sp. nov. occupies a distinctive clade, displaying close affinity with O. shacra. Intraspecific K2P genetic divergence, assessed at 0.02, falls well within established species delineation thresholds, while interspecific divergence in comparison to O. shacra was recorded at 0.112. Complementary species delimitation methodologies, including BIN and bPTP, further underscore taxonomic uniqueness of O. siangi sp. nov., within Chedrinae family. This description enriches our understanding of biodiversity within Siang River ecosystem and underscores the merit of employing multi-pronged approaches in taxonomic investigations.