Bayesian Inference Trees Research Articles

Mitochondrial genome of Euchirus longimanus (Coleoptera: Scarabaeidae) and phylogenetic relationship of Euchirini

The long-armed scarab beetles, a charismatic group within the small tribe Euchirini, are characterized by their large body sizes and distinctly elongated forelegs in males. While mitochondrial genomes have been sequenced for two of the included genera, Cheirotonus and Propomacrus, the type genus of the tribe, Euchirus, remains unexplored. It will provide valuable insights into the phylogenetic position and internal relationships of the Euchirini to investigate the mitochondrial genome of Euchirus and conduct phylogenetic analyses. In this study, it presents the first mitochondrial genome of Euchirus longimanus. The length of the mitochondrial genome of Euchirus longimanus is 16,591 bp. We analyzed its genes arrangement, base composition, codon usage frequency, and constructed phylogenetic trees based on the nucleic acid sequences of 13 protein-coding genes. The phylogenetic results are consistent with previous studies, confirming the phylogenetic position of Euchirini within the paraphyletic Melolonthinae. Notably, we firstly elucidate the phylogenetic relationship among all three genera: Propomacrus + (Cheirotonus + Euchirus), supported by robust values in Bayesian inference (BI) analysis. However, the maximum likelihood (ML) tree shows weaker support for the internal node of Euchirini and exhibits distinct topological variations compared to the BI tree, suggesting the potential paraphyly of Cheirotonus with the inclusion of Euchirus longimanus. These findings highlight the importance of including additional species of Euchirus and Cheirotonus in the future phylogenetic investigations to achieve a comprehensive understanding of their evolutionary relationships.

Two new species of the genus Anilocra Leach, 1818 (Isopoda: Cymothoidae) parasitic on reef fishes from the western Pacific.

Anilocra harazakii sp. nov. and Anilocra boucheti sp. nov. are described from specimens collected from Pterocaesio marri (Caesionidae) in the northern Ryukyu Islands, Japan and Myripristis kuntee (Holocentridae) off Madang, Papua New Guinea, respectively. Anilocra harazakii sp. nov. is characterized by the combination of the following characters in the female: the elongate narrow body dorsally vaulted; the pleonite 1 concealed by the pereonite 7; the uropod extending that of the angled pleotelson, and its endopod longer than the exopod; and the dactyli of only pereopods 2 and 3 with one nodule on anterior margins. Anilocra boucheti sp. nov. is characterized by the following: body with convex lateral margins; almost part of the pleonite 1 not concealed by the pereonite 7; pleonite 5 with posterolateral acute angle strongly produced; coxa 3 clearly smaller than coxae 1 and 2; the uropod not extending past the posterior margin of the pleotelson with the tip of one of the rami not exceeding the other; and the dactyli of pereopods 1-4 without nodules. Furthermore, the coloration, i.e., the orange body with black margins, of A. boucheti sp. nov. is unique. Bayesian inference tree using partial mitochondrial cytochrome c oxidase subunit I (COI) genes supported the monophyletic clade composed of the members of the genus Anilocra including the two new species. Since the wounds caused by A. harazakii sp. nov. are often hemorrhagic, the isopod might have severe negative effects on the host.

Nuclear DNA-based phylogenetic analysis of Neocinnamomum species

AbstractNeocinnamomum plants are evergreen shrubs or small trees belonging to the Neocinnamomeae tribe of the Lauraceae family. Their seeds are rich in fatty acids, and their leaves are often used in traditional Chinese medicine. Presently, only a few studies have been performed on Neocinnamomum plants; therefore, the genome-based phylogeny among Neocinnamomum species has not been determined, which limits the germplasm innovation of this genus. In this study, by the Illumina (next-generation sequencing) and third-generation sequencing technologies, the whole genomes of seven Neocinnamomum species samples were sequenced, their nuclear DNA (nrDNA) sequences were assembled and characterized, and their phylogeny was reconstructed. The results revealed four hypervariable regions (i.e. transcribed spacer regions) in the nrDNA sequences, among which the highest degree of variation was observed in the external transcribed spacer (ETS) region localized behind the 26S gene. A total of 27 insertions/deletions and 184 single-nucleotide polymorphisms, both localized mainly in the ETS and internal transcribed spacer regions, were identified. Phylogenetic trees were constructed based on the nrDNA sequences using the maximum likelihood (ML) and Bayesian inference (BI) methods with Caryodaphnopsis henryi as the outgroup. The ML tree divided the seven Neocinnamomum species into four clades. Clade I consisted of Neocinnamomum caudatum var. macrocarpum and Neocinnamomum caudatum, clade II included Neocinnamomum delavayi and Neocinnamomum mekongense, clade III included Neocinnamomum fargesii and a branch species of N. delavayi and clade IV included Neocinnamomum lecomtei, constituting a monophyletic and basal group. The BI tree shared the same topological structure as the ML tree, and all the support values of the BI tree were one except for that of one Neocinnamomum species (0.98). The results of this study provide new evidence regarding the phylogenetic evolution of the Neocinnamomum plants.

DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia

BackgroundDNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.MethodsGenomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.ResultsThe DNA barcodes successfully distinguished most morphologically distinct species (> 80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32–13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa.ConclusionsThe findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.Graphical abstract

Polyclonal Burkholderia cepacia complex outbreak caused by contaminated chlorhexidine gluconate solution

Background:Burkholderia cepacia complex is an opportunistic environmental pathogen that has been linked to nosocomial outbreaks. We describe an outbreak of bacteremia caused by Burkholderia cenocepacia from a contaminated chlorhexidine gluconate solution. Methods: The hospital infection control team carried out an outbreak investigation on February 21, 2021, when 3 adult hemodialysis patients developed B. cenocepacia bacteremia. Patient demographics and clinical profile were reviewed retrospectively. Potential sources of infection were identified, and environmental screening was performed in several units. Processes of catheter care in the hemodialysis unit were reviewed. Water samples from the hemodialysis unit, and samples of solutions used in patient care were sent for culture. Isolates from patients and from environmental samples were sent for 16S rRNA gene sequencing to determine genetic relatedness. Results: In total, 16 patients, 8 of whom were male, developed B. cenocepacia bacteremia during the investigated period. The median age was 68 years (range, 19–83), and 15 of 16 had at least 1 comorbidity. All patients used a central venous catheter (CVC) for hemodialysis, and 11 (70%) of these 16 were temporary. Chlorhexidine gluconate solution was routinely used as part of CVC care and 1 bottle was shared among 4 hemodialysis stations. On suspicion of contamination, all identified chlorhexidine bottles were recalled on February 26, 2021, and random samples from 15 opened and 19 unopened bottles were sent for culture from the following units: hemodialysis (n = 2), ICU (n = 14), wards (n = 6), and 4 each from transplant surgery, and delivery suites. O0f 34 sampled bottles, 17 grew B. cenocepacia: 8 opened and 9 unopened bottles. The Bayesian inference tree (Fig. 1) supports the hypothesis that patient samples and the samples from the chlorhexidine solutions were most probably related to each other based on the 16S rRNA sequences. However, the individual identities of the specific sample sequences could not be determined using the analyzed region of the gene, possibly due to low quality of the sequences received. No new cases of B. cenocepacia were identified after recall of the chlorhexidine solution, and the outbreak was deemed resolved on March 24, 2021. Conclusions: Medical solutions routinely used in patient care can cause outbreaks and should be suspected as a potential source of infection by infection control teams.Disclosures: None

Complete mitochondrial genomes of Gritzenko's charr Salvelinus gritzenkoi and Miyabe charr Salvelinus malma miyabei and their interpretation regarding intraspecific taxonomy.

Salvelinus is one the most species-rich genera of salmonids (Salmoniformes: Salmonidae), and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new charr species. However, current reference databases contain limited mitochondrial genome information on narrow-ranged, endemic charrs with disputable origin and systematic status. More comprehensive mitochondrial genome-based phylogenetics will help enhance understanding of the relationship and delineate charr species. In the present study, the complete mitochondrial genomes of three taxa (S. gritzenkoi, S malma miyabei, and S. curilus) were sequenced (PCR and Sanger dideoxy sequencing) and compared with those of other charr species whose mitochondrial genomes are already reported. Results indicate that the mitochondrial genomes of the three taxa were similar in length (16,652bp and 16,653bp for S. curilus and S. malma miyabei, to 16,658bp for S. gritzenkoi). Analyses of nucleotide composition showed that the newly sequenced five mitochondrial genomes skewed strongly towards high AT (54.4%) content, which is typical of Salvelinus. No large deletions and insertions were found in the mitochondrial genomes, including samples from isolated populations. Heteroplasmy associated with single-nucleotide substitution in the ND1 gene was found in one case (S. gritzenkoi). In maximum likelihood and Bayesian inference trees, S. gritzenkoi and S malma miyabei were clustered with S. curilus with strong branch support. Our results provide the basis for a possible reclassification of S. gritzenkoi to S. curilus. The results of this study may be useful for future genetic studies on charrs of the genus Salvelinus toward the in-depth phylogenetic study and proper assessment of the conservation status of the disputed taxa.

Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

BackgroundThe genus Amaranthus L. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species’ complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank).ResultsComparative analysis of the dioecious Amaranthus species’ plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported.ConclusionsOur study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced.

The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea.

Capniidae are a family of stoneflies, also known as snow flies, who emerge in winter. The phylogeny of Capniidae is widely accepted to be based on morphological analysis. Until now, only five Capniidae mitochondrial genomes have been sequenced so far. In addition, sampling is required to determine an accurate phylogenetic association because the generic classification of this family is still controversial and needs to be investigated further. In this study, the first mitogenome of genus Isocapnia was sequenced with a length of 16,200 bp and contained 37 genes, including a control region, two rRNAs, 22 tRNAs, and 13 PCGs, respectively. Twelve PCGs originated with the common start codon ATN (ATG, ATA, or ATT), while nad5 used GTG. Eleven PCGs had TAN (TAA or TAG) as their last codon; however, cox1 and nad5 had T as their final codon due to a shortened termination codon. All tRNA genes demonstrated the cloverleaf structure, which is distinctive for metazoans excluding the tRNASer1 (AGN) that missed the dihydrouridine arm. A Phylogenetic analysis of the superfamily Nemouroidea was constructed using thirteen PCGs from 32 formerly sequenced Plecoptera species. The Bayesian inference and maximum likelihood phylogeny tree structures derived similar results across the thirteen PCGs. Our findings strongly supported Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). Ultimately, the best well-supported generic phylogenetic relationship within Capniidae is as follows; (Isocapnia + (Capnia + Zwicknia) + (Apteroperla + Mesocapnia)). These findings will enable us to better understand the evolutionary relationships within the superfamily Nemouroidea and the generic classification and mitogenome structure of the family Capniidae.

The complete mitochondrial genome of Pardosa pusiola (Araneae, Lycosidae) and its phylogenetic implications

AbstractThe mitochondrial genome (mitogenome) is useful for identification and phylogenetic analyses among arthropods, but there are no sufficient mitogenome data for wolf spiders. To enrich the mitogenome database of wolf spiders, the complete mitogenome of Pardosa pusiola was sequenced by high‐throughput sequencing. It is 14,284 bp, comprising 13 protein‐coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). It represents a high bias toward A and T nucleotides with an A + T content of 76.49%. The mitogenome exhibited a negative AT skew (−0.13) and a positive GC skew (0.32). Most PCGs started with ATN codons and ended with TAA, TAG, or an incomplete T. In addition, most tRNAs had aberrant secondary structures with the absence of DHU arm or TΨC arm. Analysis performed with CREx software demonstrated that large‐scale rearrangements of tRNAs were observed in the mitogenome of P. pusiola as compared with the putative ancestral mitogenome. The Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees based on the 13 PCGs of 25 spiders had the same topology, which could be presented as (Araneidae + (Agelenidae + (Dictynidae + Desidae)) + (Salticidae + (Thomisidae + (Oxyopidae + (Pisauridae + Lycosidae))))). This study offers a useful genetic resource for the taxonomy and phylogeny of spiders.

First Report with Molecular Confirmation of the Colonial Sphenopid Palythoa mutuki (Cnidaria: Anthozoa: Zoantharia: Sphenopidae) Forming Massive Colonies in Southern Jeju Island, Korea

As the global sea surface water temperature increases due to climate change, some zooxanthellate species have extended their habitat range to higher latitudes. Palythoa species, a colonial zooxanthellate cnidarian, is one such example of a range-extending animal. Recently, massive colonies of zoantharians that appeared to be of Palythoa spp. were discovered in a subtidal area of southern Jeju Island. Because a zoantharian-dominated ecosystem could indicate an unhealthy status, the documentation of its occurrence and species identification are crucial for subsequent studies. In this study, we report and confirm the presence of massive Palythoa colonies in Taeheung and Topyeong, off the southern coast of Jeju Island, using in situ underwater images and identify the species by sequencing the internal transcribed spacer rDNA. The resulting Bayesian inference tree clearly demonstrates that the massive colonies consist of Palythoa mutuki and are closely related to P. mutuki collected from the Ryukyu Archipelago in southern Japan. These records provide evidence of the northward expansion of subtropical and tropical marine organisms.

DNA barcoding of the genus Alburnoides Jeitteles, 1861 (Actinopterygii, Cyprinidae) from Anatolia, Turkey

The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides. Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance (A. tzanevi and A. velioglui) and minimum nearest-neighbour distance (A. freyhofi and A. kurui) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species (A. coskuncelebii and A. emineae) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.

Divergence time of mites of the family Laelapidae based on mitochondrial barcoding region.

Using the mitochondrial barcoding region to correlate research with 58 species in 19 genera of the family Laelapidae with the aim of determining the origin, phylogenetic relationships, and biogeographic historical distribution characteristics of mites in the family Laelapidae. Phylogenetic trees were obtained using Bayesian inference (BI) and Maximum-likelihood (ML) methods, based on three fossil records calibrated as molecular clock nodes, to estimate the divergence time of mites in the family Laelapidae as well as to apply Dispersal-Extinction-Cladogenesis (DEC) analyses to obtain biogeographic history inferences. The result showed species of the genera Hyperlaelaps and Haemolaelaps and some species of the genus Androlaelaps in the family Laelapidae were divided into clades of the genus Laelaps in both the BI and ML trees. Divergence time estimates and biogeographic history analysis revealed that the family Laelapidae likely diverged from other taxa during the Middle Jurassic (ca. 156.73 Mya), with Asia considered the most likely ancestral region for the family Laelapidae. Species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The results suggest that some genera in the family Laelapidae need to be re-defined or new genera need to be established; the Late Cretaceous to Late Neogene warm period would have promoted the divergence and expansion of species in the family Laelapidae. The divergence and dispersal of the family Laelapidae species is most likely a joint response to the continued northward drift of the Indian plate away from the Gondwana paleo-continent and gradually closer to Asia during the Late Cretaceous and the geological activity of the Tibetan Plateau during the Cenozoic Tertiary. The results strengthen our understanding of the origin and evolution of species in the family Laelapidae.

Cryptic diversity in a gastrointestinal acanthocephalan of New World primates from Costa Rica

Prosthenorchis elegans is a worm of the family Archiacanthocephala that infects non-human primates in the Americas, producing an intestinal pathology that may compromise the life of its hosts. Squirrel monkeys, Saimiri oerstedii citrinellus, were found with P. elegans in Costa Rica. Histopathological analysis revealed a severe pyogranulomatous response composed by macrophages, neutrophils, eosinophils, fibroblasts and lymphocytes. Morphological worm analyses revealed 36 hooks in the proboscis distributed in six rows; and total body, hook and lemnisci length were compatible to the original descriptions of P. elegans. In addition, phylogenetic, haplotype network and genetic distance analyses were done on cytochrome oxidase subunit 1, cox1, sequences obtained from the collected specimens. Sequences obtained herein clustered separately with high posterior probabilities in a Bayesian Inference tree and showed 8.12% nucleotide differences when compared to P. elegans from Colombia. This high divergence was confirmed in the TCS network that separated Colombian and Costa Rican sequences by 32 mutational steps, a genetic distance PCA which separated sequences from both geographical locations by 89.5% and an FST value of 0.655, indicating the presence of cryptic diversity in P. elegans. Additional studies from specimens collected from other definitive hosts and geographical locations are required to better understand the biodiversity of this species.

Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea).

The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.

Spatial Versus Nonspatial Variance in Fecal Indicator Bacteria Differs Within and Between Ponds

Surface water environments are inherently heterogenous, and little is known about variation in microbial water quality between locations. This study sought to understand how microbial water quality differs within and between Virginia ponds. Grab samples were collected twice per week from 30 sampling sites across nine Virginia ponds (n = 600). Samples (100 mL) were enumerated for total coliform (TC) and Escherichia coli (EC) levels, and physicochemical, weather, and environmental data were collected. Bayesian models of coregionalization were used to quantify the variance in TC and EC levels attributable to spatial (e.g., site, pond) versus nonspatial (e.g., date, pH) sources. Mixed-effects Bayesian regressions and conditional inference trees were used to characterize relationships between data and TC or EC levels. Analyses were performed separately for each pond with ≥3 sampling sites (5 intrapond) while one interpond model was developed using data from all sampling sites and all ponds. More variance in TC levels were attributable to spatial opposed to nonspatial sources for the interpond model (variance ratio [VR] = 1.55) while intrapond models were pond dependent (VR: 0.65–18.89). For EC levels, more variance was attributable to spatial sources in the interpond model (VR = 1.62), compared to all intrapond models (VR < 1.0) suggesting that more variance is attributable to nonspatial factors within individual ponds and spatial factors when multiple ponds are considered. Within each pond, TC and EC levels were spatially independent for sites 56–87 m apart, indicating that different sites within the same pond represent different water quality for risk management. Rainfall was positively and pH negatively associated with TC and EC levels in both inter- and intrapond models. For all other factors, the direction and strength of associations varied. Factors driving microbial dynamics in ponds appear to be pond-specific and differ depending on the spatial scale considered.

Retrospective genomic analysis of the first Lumpy skin disease virus outbreak in China (2019).

Lumpy skin disease caused by Lumpy skin disease virus (LSDV) is a severe systemic disease affecting cattle and other ruminants. Lumpy skin disease was first reported in northwest China in August 2019 and has severely threatened the cattle breeding industry in China. However, there have been limited genomic studies of LSDV from the first outbreak and its subsequent epidemics. This study aims to characterize the comparative genomic evolution of the LSDV strain from the first outbreak in China. The etiological agent was isolated in a Madin-Darby bovine kidney cell culture and subsequently identified by PCR and Sanger sequencing of six selected genes. The genome sequence was determined using Illumina sequencing and analyzed through genome alignment and phylogenetic tree. The results showed that all six genes were successfully amplified and genetically clustered into LSDV. The virus presented the highest homology to strain China/GD01/2020, which shared 100% identities among 150 open reading frames (ORFs), and 97.1-99.7% identities among additional 6 ORFs. Bayesian inference tree analysis revealed that the virus shared a common ancestor with LSDV strains from China and Vietnam. The study provides an additional genomic data for LSDV tracking and control in China and neighboring countries.

Dioxin Emission Concentration Prediction Using the Selective Ensemble Algorithm Based on Bayesian Inference and Binary Tree

Dioxin Emission Concentration Prediction Using the Selective Ensemble Algorithm Based on Bayesian Inference and Binary Tree

Characterization of the complete mitochondrial genome and phylogenetic analysis of Epiverta chelonia (Coleoptera: Coccinellidae)

Epiverta chelonia (Mader 1933; Coleoptera: Coccinellidae) is an important economically and scientifically valuable insect. In this study, the first complete mitochondrial genome of E. chelonia was sequenced and characterized using next-generation sequencing techniques. The circular mitogenome of E. chelonia consists of 17,347 bp including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop). The base composition was AT-biased (75.77%). Bayesian Inference and Maximum likelihood phylogenetic trees strongly supported the monophyly of Coccinellinae. Also, E. chelonia was supported as the sister group of Subcoccinella vigintiquatuorpunctata, within Epilachninae. Thus, the E. chelonia mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich family Coccinellidae of Coleoptera.

COI gene analyses of the Daghestan pine vole (Microtus daghestanicus Shidlovsky, 1919) population from northeastern Turkey

Daghestan pine vole (Microtus daghestanicus Shidlovsky, 1919) is spread in Caucasia, Turkey and Northwestern Iran and distribution of this species is limited to Northeastern Anatolia in Turkey. Few molecular studies on M. daghestanicus have been performed so far, and it was analysed in this study with the mitochondrial cytochrome oxidase subunit I (COI) region and compared with other Terricola species (Microtus subterraneus and Microtus majori) and other Microtus species found in its distribution area (Microtus arvalis and Microtus mystacinus). For this purpose, mean genetic distance values and fixation index values were calculated. Also, Bayesian Inference tree and Median-joining network were constructed. The acquired results showed that M. daghestanicus was clearly separated in the Pleistocene Period and was closer to M subterraneus than M. majori in the subgenus Terricola.

Diversification and historical demography of Haloxylon ammodendron in relation to Pleistocene climatic oscillations in northwestern China.

The influence of aridification and climatic oscillations on the genetic diversity and evolutionary processes of organisms during the Quaternary in northwestern China is examined using Haloxylon ammodendron. Based on the variation of two cpDNA regions (trnS-trnG and trnV) and one nDNA sequence (ITS1-ITS4) in 420 individuals from 36 populations, the spatial genetic structure and demographic history of H. ammodendron in arid China is examined. Median-joining network and Bayesian inference trees enabled the identification of three diverged lineages within H. ammodendron from 24 different haplotypes and 16 ribotypes, distributed across western (Xinjiang), eastern (Gansu and Inner Mongolia) and southern (Qinghai) regions. AMOVA analysis demonstrated that more than 80% of observed genetic variation related to lineage split was based on cpDNA and nDNA variation. Allopatric divergence among the three groups was mainly triggered by geographical isolation due to Xingxingxia rock and uplift of the Qilian Mountains during the Quaternary. Local adaptive differentiation among western, eastern and southern groups occurred due to gene flow obstruction resulting from arid landscape fragmentation accompanied by local environmental heterogeneity of different geographical populations. The southern margin of the Junggar Basin and the Tengger Desert possibly served as two independent glacial refugia for H. ammodendron. The distribution of genetic variation, coupled with SDMs and LCP results, indicated that H. ammodendron probably moved northward along the Junggar Basin and westward along Tengger Desert at the end of the last glacial maximum; postglacial re-colonization was probably westward and southward along the Hexi Corridor.