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

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. Theoverall mean conspecific, congeneric and confamillial genetic distances based on the K2P model were 0.54%, 5.32% and 13.29% respectively. All taxa had a mean K2P distance < 2% and 90% (n = 10), were clearly delimited by the ABGD method. The NJ tree delimited tilapia taxa commensurate to the genetic distances depicted by DNA barcoding. However, DNA barcoding and NJ tree coherently failed to discriminate the morphologically distinct allopatric Oreochromis jipe and Oreochromis hunteri taxa. Moreover, the two methods depicted lack of monophyly in Oreochromis korogwe MOTUs implying that the taxon could consist of at least one MOTU. We conclude that the integration of morphological-based taxonomy and DNA barcoding among ichthyofaunal taxa herein will be invaluable in conservation and management of native tilapias in Pangani basin.

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. In this study, we present a comprehensive analysis of the plastid genome of L. rotata. The plastid genome has a length of 151,837 base pairs (bp) and a GC content of 38.5%. Within this genome, a total of 135 genes were identified, including 90 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. By employing phylogenetic analysis, the taxonomic position of L. rotata within the family Labiatae is elucidated, highlighting a close relationship between the genus Lamiophlomis and the genus Phlomis. Notably, extensive genetic variations were uncovered between L. rotata and other Phlomis species. This study could provide significant insights for understanding the phylogenetic relationships of taxa within Labiatae.

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. Monophyly of known species groups within the genus Drosophila are highly supported and, as in previous work, the genera Lordiphosa, Hirtodrosophila, Zaprionus and Scaptomya are all imbedded within the genus Drosophila. Incongruence and partitioned support analyses indicate that DNA sequences are better at resolving the phylogeny than their translated protein sequences. Such analyses also indicate that genes on the minus strand of the circular molecule (Lrrna, Srrna, ND4, ND4L and ND5) provide most of the support for the overall phylogenetic hypothesis.

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. The two clades exhibit high genetic diversity in the Nansei islands, which are the source population. Surprisingly, it has been revealed that high genetic diversity has also been maintained in the Izu Islands, which are the introduced population, in each clade. AMOVA has also revealed that the genetic differentiation between the populations in the Izu Islands and the Nansei Islands was not significant in each clade. These results suggest that the population of the Izu Islands is now in secondary contact between two clades by multiple migrations from various regions of the Nansei Islands.

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. In the studied population of C. ignobilis, 33 unique haplotypes were observed, and the population exhibited high haplotype (h = 0.831) and nucleotide (π=0.930%) diversity. Pairwise F_ST values between the six study sites indicated limited genetic differentiation among the studied populations. The limited genetic differentiation may be due to the oceanic currents in the Philippines facilitating larval dispersal as observed in the results of the Lagrangian dispersion model. Data from neutrality tests, mismatch distribution, and Bayesian skyline plot revealed that the population may have undergone demographic expansion. This study provides valuable genetic information on C. ignobilis that can be used for formulating sustainable fishery management strategies.

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. However, insignificant genetic distances were noticed in two reportedly valid species: Schizothorax molesworthi and S. integrilabiatus (0.1%), and the monophyly of S. macropogon could not be recovered in the schizothoracine group. The fishes of S.curilabiatus living in the lower course of Yalung Zangbo River were clustered together with three species from the upper course, which is inconsistent with the geographical distribution of the populations.

Pleistocene climatic changes have played a major role in the evolution of Brazilian Atlantic Forest and South America biodiversity but their impacts on the genetic structure of widely distributed species remain unclear. Here, we investigate mitochondrial DNA (mtDNA) diversity in 21 geographical populations of Drosophila sturtevanti, Nucleotide sequences of the cytochrome C oxidase subunits I and II genes (COI and COII, respectively) from 163 individuals, showed a significant north-south structure, in spite of an overall low level of variation. The haplotypes clustered in three groups that showed strong correlations with geographical and climatic variables, suggesting that local adaptations might have contributed to differentiation within the species. Coalescent-based analyses indicated that the three clusters have differentiated nearly ∼17.000 years ago, suggesting a major role for Pleistocene changes in shaping current day distributions and differentiation of widespread Neotropical species.

Genetic diversity, genetic structure, and demographic history of the endemic and endangered cyprinid species Alburnus tarichi based on samples from 17 populations consisting of resident and potamodromous specimens from the Lake Van basin in eastern Turkey were analyzed using two mitochondrial DNA markers. A. tarichi populations in the Lake Van basin are genetically heterogeneous, as indicated by the high haplotype and low nucleotide diversity of 1233 bp of the 16S rRNA marker (44 haplotypes; 70 polymorphic sites, haploid diversity (H_d) = 0.9130, π = 0.0032) and 1140 bp of the cyt b marker (47 haplotypes; 82 polymorphic sites, H_d = 0.9339, π = 0.0057). Clades were separated by average sequence divergences of 1.94% (II vs. III), 1.80% (I vs. III), and 0.66% (I vs. II). Based on these clades, AMOVA analysis revealed that 80.76% of the total variation occurred among populations, 10.74% occurred within populations, and only 8.50% occurred between populations within groups for the concatenated 16S rRNA-cyt b sequences. Pairwise F_ST values varied from 0.0167 to 0.9705 for the concatenated 16S rRNA-cyt b dataset, emphasizing the high genetic variation among populations. The time since the endemic tarek populations split from their last common ancestor has been dated to 5.647 Ma (95% highest posterior density: 4.183-7.011 Ma) in the Messinian Stage. Recent population expansion for tarek populations has been determined by neutrality tests and mismatch distribution analyses. The results of this study provide valuable information on the genetic population structure, conservation, and management of this species.