Publications by authors named "Fedosov Alexander"
The exon capture approach allows for sequencing a large number of loci to reconstruct phylogenetic relationships at varying taxonomic levels. In order to efficiently recover the targeted loci, the probes designed to capture the exons need to be genetically sufficiently similar to bind to the DNA, with a proposed limit of 10% of divergence. However, this threshold has never been tested with a specific protocol.
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- Venom systems have evolved multiple times across different plant and animal species and show variation based on factors like evolutionary history and diet.
- Marine cone snails (genus Conus) are a key model for studying these variations due to their diverse species and significant dietary shifts.
- Research on the venom genes of 42 cone snail species shows that changes from eating worms to fish lead to unique venom compositions that enhance potency, highlighting how prey choice influences venom characteristics.
Article Synopsis
- - DNA barcoding is crucial for identifying new species and understanding biodiversity; it's especially useful for classifying species using single-locus DNA sequences.
- - Various tools have been created for species delimitation, but many were not initially user-friendly, despite their common goal of identifying distinct species.
- - Recently, a standardized format called SPART has been introduced for sharing species partition data, and this chapter outlines protocols for using two specific bioinformatics tools, ASAP and LIMES, for species analysis.
Article Synopsis
- * Traditional species differentiation relies on morphological traits, but molecular methods are becoming essential for cryptic species.
- * The chapter presents protocols for the bioinformatics tool MolD, which helps identify diagnostic nucleotide combinations to improve DNA-based taxa differentiation.
Article Synopsis
- - The availability of user-friendly software for analyzing DNA barcodes is limited, often requiring complex procedures and manual formatting to perform basic functions like detecting gaps and calculating distance matrices.
- - The iTaxoTools project aims to create user-friendly solutions to enhance the workflow in alpha-taxonomy, focusing on improving the tool TaxI2 for analyzing DNA barcodes.
- - This chapter offers detailed protocols for using TaxI2, which can calculate genetic distances using various methods and format input data easily, while providing tools for comparing sequences against reference datasets and interpreting the results.
Article Synopsis
- - Venomous organisms have evolved toxins independently over 101 times, resulting in over 200,000 species that produce millions of toxins, making them significant for bioprospecting and genetic study.
- - RNA-seq is commonly used to analyze toxin repertoires, but current methods face challenges due to their reliance on similarity-based mapping, which doesn’t effectively utilize structural features of toxins.
- - DeTox is a new user-friendly tool that integrates structural and similarity-based approaches for toxin research, improving toxin identification in diverse organisms and easing the analysis process for those with less experience.
Article Synopsis
- - Neogastropoda is a diverse order of over 15,000 marine species that are significant for both ecological functions and the economies of coastal regions, but their evolutionary relationships are complex and poorly understood due to a dense "bush" in their evolutionary tree.
- - The study utilized various phylogenetic methods and a comprehensive dataset of 1,817 genetic loci from 112 taxa to analyze relationships within Neogastropoda, confirming the monophyly of several superfamilies while revealing that some currently recognized groups are paraphyletic.
- - Three major uncertainties were identified in the phylogenetic relationships, particularly concerning the placement of the Cancellariidae family, which could hint at deeper evolutionary interventions,
Article Synopsis
- In phylogenomic studies, taxon sampling often relies on known species, leading to the risk of missing out on undocumented diversity, particularly in groups like the Turridae, a family of venomous snails.* -
- Researchers developed a comprehensive sampling strategy that identified 201 species hypotheses using over 3,000 cox-1 barcode sequences, with nearly 50% of these potentially representing new or cryptic species.* -
- Their findings reveal the genus Gemmula is polyphyletic, containing up to 10 lineages, and emphasize the importance of blind and exploratory sampling to reduce biases in future phylogenomic research.*
Article Synopsis
- Venomous marine gastropods, particularly cone snails of the family Conidae, are highly diversified predators due to their complex venoms, which are valuable for studying neuropeptides and molecular evolution.
- Current research reveals that traditionally understood roles of venom production may involve not just the venom gland, but also other secretory glands (salivary and accessory salivary glands) that have not been fully explored.
- A detailed transcriptome analysis of Conus virgo highlights unique venom-related transcripts in the salivary and accessory glands, suggesting these tissues contribute to venom composition and warrant further functional studies to clarify their specific roles.
Article Synopsis
- The Neogastropoda includes over 15,000 marine predator species, but their evolutionary relationships and classification are largely unclear.
- Researchers created a new molecular phylogeny using mitochondrial genomes and transcriptomic data from various neogastropod families, leading to the analysis of 113 taxa with multiple evolutionary models to construct phylogenetic trees.
- Despite revealing new relationships and insights, the study notes that key taxa are missing and suggests that alternative methods, like reduced-genome strategies, might be necessary for a complete understanding of neogastropod phylogeny.
Article Synopsis
- * Extensive tissue loss from tumor removal in this area needs immediate reconstruction to protect vital structures and prevent exposure to the environment.
- * A multidisciplinary approach was used in a recent operation, involving three specialized surgical teams working together, which allowed for simultaneous tumor removal and reconstruction using advanced techniques like free fibular flaps and dental implants.
Article Synopsis
- Venoms from marine cone snails are important for biomedical research due to their neuropeptides known as conotoxins, which have various applications.
- Some gastropods have developed similar venom-producing glands, particularly within the genus being studied, leading to the production of complex venoms termed vexitoxins.
- Research shows that vexitoxins share similarities with conotoxins in structure and function, suggesting a closer evolutionary relationship and offering insights into the evolution of venoms in these species.
Article Synopsis
- A new software program called "mold" has been developed to identify diagnostic nucleotide combinations (DNCs) that provide formal diagnoses for specific taxa.
- The program also introduces a more reliable type of DNA diagnosis called "redundant DNC" (rDNC), which factors in unsampled genetic diversity, improving the reliability of taxonomic descriptions.
Article Synopsis
- Marine gastropods known as cone snails exhibit a vast diversity of venomous compounds, which are of interest for biomedical research, yet their venom composition remains underexplored in many species.
- The study involved profiling the venom transcriptomes of two specific genera of cone snails for the first time, while leveraging data from two additional lineages to identify shared toxin clusters based on genetic regions.
- The researchers discovered numerous putative toxins and unexpected distributions of rare gene superfamilies, illustrating the importance of a phylogenetic approach in understanding venom evolution and complexity within the Conidae family.
Article Synopsis
- The study presents the complete mitochondrial genome sequence of a Caribbean gastropod species that typically inhabits sunken wood at deep ocean depths.
- This mitochondrial genome is 15,321 base pairs long, featuring a specific percentage of nucleotides: 29.2% Adenine (A), 41.8% Thymine (T), 12.0% Cytosine (C), and 17.0% Guanine (G).
- Phylogenetic analysis shows that this species belongs to the superfamily Turbinelloidea, which diverged early in the Neogastropod evolution and is closely related to several other superfamilies within the group.
Article Synopsis
- * The study characterizes a specific peptide from Drilliidae venom, named cdg14a, which is small and rich in disulfide bonds, and shows effects on mouse behavior, causing increased excitability in certain nerve cells.
- * Findings indicate that cdg14a could influence specific potassium channels, highlighting the potential of Drilliidae venoms as a source for developing new therapeutic agents targeting ion channels in the nervous system.
Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense, and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized.
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- The text discusses a unique cone snail genus that is crucial for studying venom evolution and diversity due to its distinct genetic relationship within the Conidae family.
- Researchers analyzed venom components from two species, identifying 137 components in one and 82 in the other, with only four overlapping between them.
- The findings highlight a low diversity of conotoxins and specific types of insulin, suggesting these snails have a limited diet consisting mainly of worms or mollusks, making their venom different from other cone snails in the family.
Article Synopsis
- High Throughput Sequencing (HTS) has transformed phylogenetics but remains costly and complex, especially for non-model taxa, with 74% of published trees in 2018 still relying on traditional Sanger sequencing.
- The study focused on sequencing 32 transcriptomes from the marine mollusk family Turridae to assess various genetic loci for reconstructing phylogenies, comparing their robustness and accuracy.
- The findings suggest that while full mitogenomes are cost-effective, they may introduce biases, and it is recommended to include a mix of commonly used phylogenetic loci when designing data capture strategies.
Article Synopsis
- The study investigates how diversification occurs in predatory sea snails from the Terebridae family, focusing on factors like shell size and larval ecology.
- A new molecular phylogeny indicates that the Terebridae family has seen an increase in diversification rates since around 25 million years ago, with shell size and depth range playing significant roles in this process.
- Interestingly, the presence of venom glands did not significantly impact species diversification, suggesting that environmental factors were more influential in the evolutionary history of these marine invertebrates.
Article Synopsis
- Species delimitation in poorly known groups typically uses single gene (COI) methods, whereas well-studied groups often employ multi-gene (multilocus) approaches.
- In this study, researchers applied both methods to the Xenuroturris/Iotyrris complex, a group of venomous marine snails, analyzing sequences and constructing a phylogenetic tree.
- The combined results led to refined species hypotheses, revealing one new species, Iotyrris conotaxis n. sp., and demonstrating the effectiveness of integrating both monolocus and multilocus data for species delimitation.
Article Synopsis
- The study utilized transcriptome-based exon capture methods to analyze phylogenetic relationships among diverse venomous marine snails (Conoidea), targeting 850 protein-coding genes from around 120 samples, leading to a more resolved evolutionary tree.
- Although the capture was mostly successful, some samples had lower efficiency due to issues with DNA quality and targeting divergent lineages, recovering an average of 75.4% of proteins.
- The findings provided insights into the evolution of Conoidea, illustrating that anatomy changes over time are linked to diversification rates influenced by radula types, while losses of the venom gland had no significant impact on these rates.
Article Synopsis
- The Conus genus contains about 700 species of venomous marine cone snails, which are effective predators of other sea creatures, with their earliest fossils dating back to about 55 million years ago.
- Research focused on two closely related species, Conus andremenezi and Conus praecellens, revealed a vast diversity in their toxin genes, with 196 and 250 unique sequences found in their venom glands respectively.
- The study suggests that while the overall patterns of toxin gene families remain similar across species, changes in individual toxin sequences indicate recent speciation events and adaptations to ecological interactions.
Article Synopsis
- A new type of insulin was discovered in the venom of a specific fish-hunting cone snail, Conus geographus, and similar types of insulins were found in other cone snails that hunt worms and snails.
- These venom insulins form a rapidly diversifying gene family, adapting quickly to different prey and the snails' own predators and competitors.
- In contrast, the traditional signaling insulin in cone snails is highly conserved, showing slow evolution to target a stable internal receptor, illustrating different evolutionary pressures on internal versus venom insulins.
Article Synopsis
- The cone snails (Conus) evolved from worm-preying ancestors to develop eight distinct lineages that hunt fish, with a focus on the interplay of behavior and venom in this transition.
- The article outlines three unique fish-hunting strategies—'taser-and-tether', 'net-engulfment', and 'strike-and-stalk'—each linked to specific groups of venom components that influence prey behavior.
- Analysis of these hunting strategies, their associated toxins, and the radular tooth structure reveals that fish-hunting behavior evolved independently at least twice, showcasing a strong relationship between evolutionary changes in behavior, anatomy, and physiology.