Search Results (48)

Previous phylogeographic study of the root vole (Alexandromys oeconomus) revealed four mitochondrial cytochrome b lineages—North and Central European, North (=Central) Asian and Beringian. Three of them were studied in detail, while the North Asian lineage, which occupies the most extensive territory and is considered to be the place of origin for the species, was understudied. In the framework of the current study, we obtained 95 new sequences (34 localities) from the wide territory of Northern Asia and in total, examined 940 specimens from 181 localities throughout the species’ distribution range. The North Asian lineage was found to be more diverse than the Beringian and the European lineages. Southern Siberia and especially the Altai–Sayan region displayed the highest haplotype and nucleotide diversity, suggesting the region’s role as a genetic diversity hotspot. We suppose that the expansion of the North Asian lineage started from Western Transbaikalia. Its representatives colonised the territory from the Urals to the northern shore of the Okhotsk Sea, and then spread in the opposite direction, to Southern Siberia. As a result, a mixture of haplogroups is observed in the Altai–Sayan region. According to the BEAST analysis calibrated with the first A. oeconomus records, the MRCA of North Asian and Beringian lineages is dated back to ~0.82 Mya, and the first divergence within the North Asian lineage may have occurred ~0.6 Mya. When compared with colonisation times of other representatives of the Arvicolinae subfamily, our dating seems to be overestimated. In this regard, molecular data for dated fossil remains of the root vole are essential for subsequent studies. Full article

Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutionary dynamics of aMPV/B. Nested RT-PCR targeting the G gene revealed a positivity rate of 34.13% (57/167). Phylogenetic and Median-joining network analyses of sequenced amplicons identified two distinct Thai lineages: one genetically similar to vaccine strains and another of unknown origin. Divergence time analysis using a Bayesian framework estimated the time to the most recent common ancestor (tMRCA) of these lineages around 2006, with further sub-lineage diversification occurring around 2009 and 2016. These findings suggest that the circulating Thai aMPV/B strains likely stem from limited introduction events followed by local evolution. Lineage-specific amino acid substitutions within the G gene were identified, which may affect antigenic properties and immune recognition. This study highlights the molecular heterogeneity and ongoing diversification of aMPV/B in Thailand and underscores the need for sustained genomic surveillance and regionally tailored vaccination strategies. Full article

Deep learning techniques play a crucial role in medical image segmentation for diagnostic purposes, with traditional convolutional neural networks (CNNs) and emerging transformers having achieved satisfactory results. CNN-based methods focus on extracting the local features of an image, which are beneficial for handling image details and textural features. However, the receptive fields of CNNs are relatively small, resulting in poor performance when processing images with long-range dependencies. Conversely, transformer-based methods are effective in handling global information; however, they suffer from significant computational complexity arising from the building of long-range dependencies. Additionally, they lack the ability to perceive image details and adopt channel features. These problems can result in unclear image segmentation and blurred boundaries. Accordingly, in this study, a multiscale recombined channel attention (MRCA) module is proposed, which can simultaneously extract both global and local features and has the capability of exploring channel features during feature fusion. Specifically, the proposed MRCA first employs multibranch extraction of image features and performs operations such as blocking, shifting, and aggregating the image at different scales. This step enables the model to recognize multiscale information locally and globally. Feature selection is then performed to enhance the predictive capability of the model. Finally, features from different branches are connected and recombined across channels to complete the feature fusion. Benefiting from fully exploring the channel features, an MRCA-based U-Net (MRCA-UNet) framework is proposed for medical image segmentation. Experiments conducted on the Synapse multi-organ segmentation (Synapse) dataset and the International Skin Imaging Collaboration (ISIC-2018) dataset demonstrate the competitive segmentation performance of the proposed MRCA-UNet, achieving an average Dice Similarity Coefficient (DSC) of 81.61% and a Hausdorff Distance (HD) of 23.36 on Synapse and an Accuracy of 95.94% on ISIC-2018. Full article

Turbo sazae, a commercially and ecologically significant marine gastropod traditionally found in Jeju Island and the southern coast of Korea, is experiencing a reported northward expansion into the East Sea, likely influenced by rising seawater temperatures. This study provides preliminary genetic insights into the genetic structure and connectivity of T. sazae populations between Jeju and the East Sea using mitochondrial COI sequences. Samples from 6 geographically distinct locations were analyzed, with three cloned replicates generated to enhance sequence reliability. Genetic diversity, haplotype distribution, and population differentiation were then assessed. Our analysis reveals potential genetic connectivity between Jeju and East Sea populations, possibly driven by larval dispersal via the Kuroshio and Tsushima Currents, highlighted by the predominance of shared haplotype EJ1 (60.0% in Jeju, 50.0% in East Sea). Bayesian phylogenetic analysis estimated the time to the most recent common ancestor (MRCA) between Jeju and East Sea populations at approximately 9.7 to 23.3 million years ago, indicating ancient divergence rather than very recent separation. Pairwise FST values and AMOVA results showed generally low levels of genetic differentiation. Given the small sample sizes and use of a single mitochondrial marker, these findings should be interpreted cautiously as preliminary evidence. Nevertheless, this study highlights the need for continued genetic monitoring of T. sazae populations under climate-driven range shifts and provides a foundation for future research incorporating broader genomic approaches. Full article

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen. Full article

Background: Polydactylus macrochir (Günther; 1867) is a member of the family Polynemidae. The placement of Polynemidae among teleosts has varied over the years. Methods: Therefore, in this study, we sequenced the complete mitochondrial genome of P. macrochir, analyzed the characterization of the mitochondrial genome, and investigated the phylogenetic relationships of Polynemidae. Results: The length of the P. macrochir mitogenome was 16,738 bp, with a typical order. Nucleotide composition analysis showed that the P. macrochir mitogenome was AT-biased (54.15%), and the PCGs tended to use A and C rather than T and G at the third codon. All the PCGs started with the regular codon ATG, except for cox1, which started with GTG. The termination codon varied across the PCGs. It was shown that the ka/ks ratios of all the PCGs were less than one. Phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, indicated that eight threadfins formed a well-supported monophyletic cluster. Polynemidae and Sphyraenidae clustered together as a monophyletic group. According to TimeTree analyses, the most recent common ancestor (MRCA) of Polynemidae was traced back to about 52.81 million years ago (MYA), while six species within Polynemidae diverged from 11.70 MYA to 20.05 MYA. Conclusions: The present study provides valuable mitochondrial information for the classification of P. macrochir and new insights into the phylogenetic relationships of Polynemidae. Full article

The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world’s population at risk. This increase is attributed to several factors, including urbanization, climate change, and global travel, which facilitate the spread of both the virus and its mosquito vectors. While dengue is primarily associated with tropical regions, outbreaks in temperate areas are becoming increasingly common due to the spread of Aedes albopictus, a competent vector for DENV that can adapt to cooler climates. This study investigates the molecular dynamics and geographic evolution of DENV type 1 (DENV-1) strains isolated from 13 patients during an autochthonous outbreak in Lombardy, Northern Italy, between August and September 2023. Additionally, Aedes albopictus mosquitoes were collected from a neighboring area to assess their potential role in the outbreak. A metagenomic approach was used to recover DENV-1 consensus sequences from clinical samples. Genotype classification and phylogenetic analyses were performed using Bayesian methods and a comprehensive dataset of DENV-1 sequences from other countries. The Italian autochthonous strains clustered with South American strains collected between 2020 and 2023, specifically those belonging to genotype V, subtype D. Bayesian analysis estimated a mean evolutionary substitution rate of 8.234 × 10⁻⁴ substitutions per site per year (95% HPD interval: 7.1448 × 10⁻⁴–9.3343 × 10⁻⁴), with the time to the most recent common ancestor (tMRCA) dating back to 1972 (95% HPD interval: 1968–1976). These findings suggest the likely introduction of the virus into the region from endemic areas in South America, followed by local transmission. This study offers valuable insights into the dynamics of the DENV-1 outbreak in Lombardy, underscoring the importance of genomic surveillance in monitoring viral spread and evolution. The findings emphasize the critical need for enhanced molecular and entomological surveillance to detect and respond to emerging autochthonous DENV cases in temperate regions where competent vectors, such as Aedes albopictus, are present. Public health strategies should prioritize integrated vector management, real-time genomic monitoring, and awareness campaigns to mitigate the risk of future outbreaks. These measures are essential to address the growing threat posed by the geographic expansion of the dengue virus. Full article

The regulation of flowering time is a highly coordinative process that involves the interplay of multiple genes. The FLOWERING LOCUS D (FD) gene is one of those important players. In this study, we identified and characterized FD genes in bamboo, a plant with the unique monocarpy flowering phenomenon. An angiosperm-wide FD gene family analysis demonstrated that unlike the most recent common ancestor (MRCA) of angiosperms, which had only one FD gene, five FD copies were present in the MRCA of Poaceae, and the same gene copy number was retained in the MRCA of the Bambusoideae subfamily. Further analysis of the Poaceae FD gene family revealed five distinctive clades resulted from four duplication events, with two of these events being specific to the Bambusoideae subfamily. High levels of conservation were observed in the gene structure and amino acid composition of structural domain among the FD genes across bamboos and their close relatives, indicating functional conservation. Furthermore, gene expression profiling indicated that FD gene expression in bamboo closely resemble the expression patterns of their homologs in rice. Additionally, overexpression of two bamboo genes (Phy.ed_05093.t1 and Phy.ed_14669.t1) in Arabidopsis resulted in an early flowering phenotype, demonstrating their involvement in the regulation of the flowering process in plants. Our findings provide a comprehensive resource for understanding the evolution, structure, expression, and function of FD genes in Poaceae and Bambusoideae. Full article

The Brazilian Amazon region is a highly endemic area for hepatitis Delta and has areas that are difficult to access. Understanding the dynamics of HDV transmission in these remote locations is important for elucidating the routes of infection. To investigate this, a molecular analysis of HDV was conducted to assess the spatio-temporal dynamics of HDV cases. Between 2010 and 2023, 35 patients were recruited from the Viral Hepatitis Outpatient Clinic in Rondônia, Brazil. Conventional PCR was used to amplify the complete HDV genome followed by nucleotide sequencing via the Sanger method. The HDV genotype was determined using maximum likelihood phylogenetic reconstruction. A Skygrid coalescent approach with a Relaxed Random Walk phylogeographic model was used for the spatio-temporal analysis. Most individuals were males (21/35), with a median age of 39 years. HDV-3 was identified in all samples (35/35; 100%). The tMRCA was estimated to be 1824, with a substitution rate of 8.2 × 10⁻⁴ substitutions/site/year. The results suggest that HDV likely entered Brazil around 1820, in the state of Amazonas, subsequently spreading to Acre and Rondônia. Notable migration events were observed starting from 2010. This study suggests that HDV-3 has a complex evolutionary history spanning over two centuries, with intricate transmission routes in different locations in Brazil. Full article

Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species’ mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26–27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20–68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae. Full article

Dengue virus (DENV) is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of São Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we sequenced 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for serotype 1, for genotype V and its main lineages. Within the last ten years, there have been at least three introductions of genotype V in Araraquara, distributed in two main lineages (L Ia and L Ib, and L II). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding the emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region. Full article

As the proportion of non-enterovirus 71 and non-coxsackievirus A16 which proportion of composition in the hand, foot, and mouth pathogenic spectrum gradually increases worldwide, the attention paid to other enteroviruses has increased. As a member of the species enterovirus A, coxsackievirus A14 (CVA14) has been epidemic around the world until now since it has been isolated. However, studies on CVA14 are poor and the effective population size, evolutionary dynamics, and recombination patterns of CVA14 are not well understood. In this study, 15 CVA14 strains were isolated from HFMD patients in mainland China from 2009 to 2019, and the complete sequences of CVA14 in GenBank as research objects were analyzed. CVA14 was divided into seven genotypes A-G based on an average nucleotide difference of the full-length VP1 coding region of more than 15%. Compared with the CVA14 prototype strain, the 15 CVA14 strains showed 84.0–84.7% nucleotide identity in the complete genome and 96.9–97.6% amino acid identity in the encoding region. Phylodynamic analysis based on 15 CVA14 strains and 22 full-length VP1 sequences in GenBank showed a mean substitution rate of 5.35 × 10⁻³ substitutions/site/year (95% HPD: 4.03–6.89 × 10⁻³) and the most recent common ancestor (tMRCA) of CVA14 dates back to 1942 (95% HPD: 1930–1950). The Bayesian skyline showed that the effective population size had experienced a decrease–increase–decrease fluctuation since 2004. The phylogeographic analysis indicated two and three possible migration paths in the world and mainland China, respectively. Four recombination patterns with others of species enterovirus A were observed in 15 CVA14 strains, among which coxsackievirus A2 (CVA2), coxsackievirus A4 (CVA4), coxsackievirus A6 (CVA6), coxsackievirus A8 (CVA8), and coxsackievirus A12 (CVA12) may act as recombinant donors in multiple regions. This study has filled the gap in the molecular epidemiological characteristics of CVA14, enriched the global CVA14 sequence database, and laid the epidemiological foundation for the future study of CVA14 worldwide. Full article

Approximately 30–50% of hereditary breast and ovarian cancer (HBOC) is due to the presence of germline pathogenic variants in the BRCA1 (OMIM 113705) and BRCA2 (OMIM 600185) onco-suppressor genes, which are involved in DNA damage response. Women who carry pathogenic BRCA1 variants are particularly likely to develop breast cancer (BC) and ovarian cancer (OC), with a 45–79 percent and 39–48 percent chance, respectively. The BRCA1 c.4096+1G>A variant has been frequently ascertained in Tuscany, Italy, and it has also been detected in other Italian regions and other countries. Its pathogenetic status has been repeatedly changed from a variant of uncertain significance, to pathogenic, to likely pathogenic. In our study, 48 subjects (38 of whom are carriers) from 27 families were genotyped with the Illumina OncoArray Infinium platform (533,531 SNPs); a 20 Mb region (24.6 cM) around BRCA1, including 4130 SNPs (21 inside BRCA1) was selected for haplotype analysis. We used a phylogenetic method to estimate the time to the most recent common ancestor (MRCA) of BRCA1 c.4096+1G>A founder pathogenic variant. This analysis suggests that the MRCA lived about 155 generations ago—around 3000 years ago. Full article

HoBi-like pestivirus (HoBiPeV), classified under Pestivirus H species, is an emerging cattle pathogen of high economic impact. However, the origin and evolution of HoBiPeV are not very clear due to a lack of full genomic sequences from diverse clades. This study aimed to determine full-genome sequences of HoBiPeV strains of three novel clades (c, d and e) and perform full-genome-based genetic and evolutionary analyses. Bayesian phylogenetic analyses herein confirmed the existence and independent evolution of four main HoBiPeV clades (a, c, d and e) globally, with genetic divergence ranging from 13.0% to 18.2%. Our Bayesian molecular clock estimates revealed that HoBiPeV most likely originated in India, with a dated tMRCA of 1938 (1762–2000), evidencing a more recent origin of HoBiPeV. The evolution rate of HoBiPeV was estimated to be 2.133 × 10⁻³ subs/site/year at full-genome level but varied widely among individual genes. Selection pressure analyses identified most of the positively selected sites in E2. Additionally, 21.8% of the ORF codon sites were found under strong episodic diversifying selection, providing first evidence of negative selection in HoBiPeV evolution. No recombination event was evident for HoBiPeV-c, d and e strains. These findings provide new insights into HoBiPeV origin and evolutionary history for better understanding the epidemiology and host–pathogen interactions and stimulate vaccine research. Full article

Almost all published rooting and dating studies on SARS-CoV-2 assumed that (1) evolutionary rate does not change over time although different lineages can have different evolutionary rates (uncorrelated relaxed clock), and (2) a zoonotic transmission occurred in Wuhan and the culprit was immediately captured, so that only the SARS-CoV-2 genomes obtained in 2019 and the first few months of 2020 (resulting from the first wave of the global expansion from Wuhan) are sufficient for dating the common ancestor. Empirical data contradict the first assumption. The second assumption is not warranted because mounting evidence suggests the presence of early SARS-CoV-2 lineages cocirculating with the Wuhan strains. Large trees with SARS-CoV-2 genomes beyond the first few months are needed to increase the likelihood of finding SARS-CoV-2 lineages that might have originated at the same time as (or even before) those early Wuhan strains. I extended a previously published rapid rooting method to model evolutionary rate as a linear function instead of a constant. This substantially improves the dating of the common ancestor of sampled SARS-CoV-2 genomes. Based on two large trees with 83,688 and 970,777 high-quality and full-length SARS-CoV-2 genomes that contain complete sample collection dates, the common ancestor was dated to 12 June 2019 and 7 July 2019 with the two trees, respectively. The two data sets would give dramatically different or even absurd estimates if the rate was treated as a constant. The large trees were also crucial for overcoming the high rate-heterogeneity among different viral lineages. The improved method was implemented in the software TRAD. Full article