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Tarasov, S.

Publications and source records attributed to Tarasov, S..

At least 19 recordsLinked to original sources

An integrated semantic publishing workflow for taxonomy: a review of the Afrotropical dung beetle genus Amietina (Coleoptera: Scarabaeinae)

Taxonomic studies generate large amount of descriptive information, yet species treatments are usually written directly as natural-language text. This approach makes the underlying phenotypic information difficult to extract, reuse computationally, and maintain consistently across studies. We present an integrated workflow connecting Phenoscript, GitHub, and Overleaf. Species descriptions are written semantically in Phenoscript using biological ontologies, making their phenotypic content computable and reusable; they are then stored and version-controlled in GitHub and synchronized with an Overleaf manuscript, where human-readable descriptions are rendered directly for publication. The workflow reduces repetitive copying and formatting, preserves revision history, and promotes the production of FAIR phenotypic and taxonomic data. We apply this workflow to the African dung beetle genus Amietina Cambefort, 1981 (Coleoptera: Scarabaeinae: Onthophagini), and describe four new species from Tanzania---A. bondarevi n. sp., A. grebennikovi n. sp., A. mazumbaiensis n. sp., and A. praedicta n. sp.---bringing the total number of recognized species to eight. We also provide new distributional records, present an updated identification key, and discuss microendemism in Amietina across the Eastern Arc Mountains.

zoology↗

Phylogenomics resolves a 200-year-old puzzle: a revised tribal classification of Afro-Eurasian dung beetles (Coleoptera: Scarabaeinae)

BackgroundThe tribal classification of scarab dung beetles (Coleoptera: Scarabaeinae) is currently largely incomplete due to the lack of robust phylogenetic evidence supporting the assignment of many Afro-Eurasian and American genera to tribes. MethodsWe used ultraconserved elements (UCEs) to infer phylogenetic relationships across most Afro-Eurasian dung beetle lineages, including 25 of the 27 extant genera currently incertae sedis. ResultsWe recovered full support for the monophyly of previously recognised tribes and for several phylogenetically and morphologically clearly delimited new tribal-level clades, allowing us to propose a complete tribal classification for all Afro-Eurasian dung beetle genera. Thirteen new tribes are described and diagnosed: Aphengoecini trib. nov., Bohepilissini trib. nov., Catharsiini trib. nov., Chalconotini trib. nov., Circelliini trib. nov., Dwesasilvasedini trib. nov., Haroldiini trib. nov., Heliocoprini trib. nov., Janssensantini trib. nov., Macroderini trib. nov., Nesovinsoniini trib. nov., Pycnopanelini trib. nov. and Tanzanolini trib. nov. The tribe Coprini sensu novo is redefined as comprising three subtribes: Coprina, Onychothecina subtrib. nov. and Pedariina subtrib. nov. The tribe Odontolomini is downranked to a subtribe of Endroedyolini sensu novo, becoming Endroedyolini Odontolomina stat. nov. The tribe Onthophagini sensu novo is redefined and divided into three subtribes: Helictopleurina stat. nov., Oniticellina stat. nov. and Onthophagina; the remaining former subtribes of Oniticellini (Attavicinina, Drepanocerina and Liatongina) are synonymised with Oniticellina; the subtribe Alloscelina of Onthophagini is synonymised with Onthophagina (syn. nov.). The tribe Panelini stat. rev. and sensu novo, comprising the single genus Panelus, is revalidated and redefined. Updated morphological diagnoses of Elassocanthonini, Gymnopleurini, Onitini and Scarabaeini are provided. The genus Phaedotrogus is synonymised with Haroldius (Haroldiini) (syn. nov.). An identification key to all Afro-Eurasian dung beetle tribes is provided. DiscussionOur results establish a robust phylogenetic framework and revised tribal classification for Afro-Eurasian Scarabaeinae dung beetles, providing a foundation for future taxonomic, comparative and macroevolutionary research.

zoology↗

Winners and Losers Among European Arthropods over the Last Half Century of Global Change

Widespread concern over arthropod declines has raised questions about how global change is reshaping biodiversity, yet large-scale responses within the group remain poorly understood. Here, we analyse 50 years (1970-2019) of European arthropod occurrence data to quantify distributional changes across more than 700 species within 11 taxonomic groups. Using occupancy-detection models that account for imperfect detection, we compare time-only and environmentally mediated trends, including changes to temperature, precipitation, and agricultural and urban land cover. We find no universal signal of decline; responses are highly heterogeneous, revealing distinct winners and losers both within and among groups. Climate variables, particularly temperature and precipitation, are the strongest predictors of change, while agricultural intensification is broadly negative and urbanisation produces group-specific effects. Trait analyses indicate that warm- and dry-affiliated species and larger-bodied arthropods generally fare better. These results show that recent European arthropod change is dominated by redistribution rather than uniform collapse, with important implications for conservation and monitoring under ongoing global change.

ecology↗

Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy

Proteasome function depends on a network of transient interactions that remain structurally and functionally unresolved. We developed PhIX-MS (Photo-induced In situ Crosslinking-Mass Spectrometry), a structural proteomics workflow that stabilizes transient interactions in cells by UV-activated crosslinking to capture topological information. Applying PhIX-MS with cryo-electron microscopy (cryo-EM), we mapped redox sensor TXNL1 at the proteasome regulatory particle (RP), placing its PITH domain above deubiquitinase RPN11 and resolving its dynamic thioredoxin domain near RPN2/PSMD1 and RPN13/ADRM1, ideally located to reduce substrates prior to proteolysis. We also resolved chaperone PSMD5 bound to RP without the proteolytic core particle (CP) where its C-terminus inserts into the ATPase pore blocking CP binding. PhIX-MS and AlphaFold modeling tether ubiquitin ligase UBE3C/Hul5 along the RP placing its catalytic site above the RPN11 active site, enabling their coupled activities. Our integrative approach enables the localization of native, low-affinity protein interactions and is broadly applicable to dynamic macromolecular assemblies.

cell biology↗

Angulin-1/LSR inhibition transiently disrupts the blood-tumor barrier to enhance doxil permeability and impair malignant glioma progression

The blood-tumor barrier (BTB) prevents effective central nervous system (CNS) drug delivery, especially in malignant gliomas. Brain endothelium predominates the BTB and connects through bicellular and tricellular tight junctions (TJ). Angulin-1/LSR, is a highly expressed endothelial tricellular TJ. Our studies explore the role of Angubindin-1, an Angulin-1/LSR binder, to disrupt tricellular TJ integrity, increase drug entry and hamper glioma progression. Using rat brain endothelial cells (RBMVEC) we tracked Angulin-1/LSR localization and expression to the membrane; binding tightest to Angubindin-1 2-8 hours post-treatment (p < 0.05). Angubindin-1 dose-dependently reduced bicellular and tricellular TJs 1-4 hours post treatment (p < 0.05), returning to baseline by 24 hours (p < 0.05). In human and rat-derived glioma cells, Angubindin-1 transiently reduced Angulin-1/LSR expression between 2-8 hours (p < 0.05), with return to baseline by 24 hours (p < 0.001). Silenced Angulin-1/LSR expression on endothelium resulted in decreased mRNA levels of bicellular (occludin, claudin-5, ZO-1) and tricellular (tricellulin/MARVELD2, angulin-1/LSR) TJs compared to control (p < 0.01). Angubindin-1 treatment also inhibited efflux transporter P-gp in both RBMVECs and glioma cells with high P-gp expression only. Orthotopic rat glioma models were treated with Doxil (3 mg/kg), Angubindin-1 (10 mg/kg), or combination to evaluate BTB permeability/drug accumulation, and overall survival. Combination therapy enhanced Doxil tumor accumulation by 20% (p < 0.001), reduced tumor volume by day 14 (77.5% vs. 81.6%, p < 0.05), and significantly extended survival compared to Doxil alone (24 days vs. 18 days, p < 0.0001). These findings demonstrate the effects of tricellular tight junction inhibition on disrupting the BTB, enhancing CNS drug delivery, and improving rodent glioma survival. SignificanceThis study demonstrates that Angubindin-1, a targeted modulator of tricellular tight junction protein Angulin-1/LSR, transiently disrupts BTB integrity to enhance chemotherapy delivery and prolong survival in glioma-bearing rats. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/667901v1_ufig1.gif" ALT="Figure 1"> View larger version (76K): org.highwire.dtl.DTLVardef@b1b46corg.highwire.dtl.DTLVardef@bc552dorg.highwire.dtl.DTLVardef@7c1a74org.highwire.dtl.DTLVardef@1ace101_HPS_FORMAT_FIGEXP M_FIG C_FIG Angubindin-1 targets both bicellular tight junctions and the tricellular tight junction protein, Angulin-1/LSR, in brain endothelial and glioma cells leading to transient disruption of the blood-tumor barrier (BTB) and inhibition of P-glycoprotein towards enhanced Doxil penetration and reduced tumor burden.

cell biology↗

A review of Sisyphini Dung Beetles (Coleoptera: Scarabaeinae) endemic to Mauritius: insights from subfossil evidence and phylogenetic analysis

Five indigenous species of Scarabaeinae are known from Mauritius island, classified into two genera: the monotypic Nesovinsonia Martinez & Pereira, 1958 and Nesosisyphus Vinson, 1946. This study conducts a taxonomic review of the latter genus Nesosisyphus, and evaluates its recent extinction using historical and new occurrence records, subfossils, and niche modeling. We provide the first molecular phylogeny and evaluate the evolutionary relationships of Nesosisyphus by comparing two different phylogenetic trees: the first, based on a Ultraconserved Elements (UCEs hereafter) dataset, and the second one, on three loci (28S, 16S, COI). We identify five Mauritian Nesosisyphus species, including a new extinct one, Nesosisyphus draco sp. n., from a 4,000 yr old subfossil. We diagnose, illustrate, and provide an updated key to all the sisyphine species from Mauritius, as well as the occurrence map. Our niche modeling analysis reveals a broader past distribution range for Mauritian sisyphines, now confined to small, disjunct forest patches due to extensive forest contraction and local extinctions.

evolutionary biology↗

Untangling the Evolutionary Dynamics of the Phenome in Megadiverse Hymenoptera

How complex phenotypes evolve across the Tree of Life remains poorly understood because phenotypic evolution unfolds across multiple hierarchical and developmental scales. Hymenoptera (ants, wasps, and bees) represent one of the largest animal radiations (>150,000 species), yet the origin of their remarkable phenotypic diversity remains unclear. Here, we reconstruct the evolution of the hymenopteran skeletomuscular phenome and analyze its dynamics across anatomical hierarchies and developmental stages. We show that hymenopteran adaptive radiation was a phenome-wide process facilitated by evolutionary decoupling between adults and larvae and the semi-independent evolution of adult anatomical systems. Phenotypic and lineage diversification was driven not simply by key innovations or elevated phenomic rates, but by the partitioning of evolutionary innovation across anatomical systems, generating a broader repertoire of adaptive solutions. These findings extend the classical view of adaptive radiation from individual key innovations to phenome-wide reorganization.

evolutionary biology↗

From museum drawer to tree: historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections

Although several methods exist for extracting and sequencing historical DNA originating from drypreserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol ([~] {euro}10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprise enigmatic dung beetle genera (Nesosisyphus, Onychotechus and Helictopleurus) that varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus, was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny suggested the reclassification of Onychotechus (previously incertae sedis) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v1 HighlightsO_LIWe combined custom low-cost archival DNA extractions and Ultraconserved Element phylogenomics C_LIO_LIDNA from rare museum specimens of enigmatic dung beetles revealed their phylogenetic connections C_LIO_LIGenomic data was obtained from the holotype of a potentially extinct monoinsular endemic species C_LIO_LIGenomic data allowed a rare and enigmatic species of previously unknown affinity to be classified C_LIO_LIThe morphology of museum specimens remained intact following non-destructive DNA extraction C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/564347v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@34aad0org.highwire.dtl.DTLVardef@1ba597dorg.highwire.dtl.DTLVardef@1493c2dorg.highwire.dtl.DTLVardef@10dd2eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology-informed phylogenetic methods

1. Reconstructing ancestral states for discrete characters is essential for understanding trait evolution in organisms. However, most existing methods are limited to individual characters and often overlook the hierarchical and interactive nature of traits. Recent advances in phylogenetics now offer the possibility of integrating knowledge from anatomy ontologies to reconstruct multiple discrete character histories. However, practical applications that fully harness the potential of these new approaches are still lacking. 2. This paper introduces ontophylo, an R package that extends the PARAMO pipeline to address these limitations. Ontophylo enables the reconstruction of phenotypic entities composed of amalgamated characters, such as entire phenomes or anatomical regions. It offers three new applications: (1) reconstructing evolutionary rates of amalgamated characters using phylogenetic non-homogeneous Poisson process (pNHPP), allowing for rate variation and shifts over time and phylogeny; (2) explicit reconstruction of morphospace dynamics; and (3) direct visualization of evolutionary rates and statistics on vector images of organisms. Ontophylo incorporates ontological knowledge to facilitate these applications. 3. Benchmarking confirms the accuracy of pNHPP in estimating character rates under different evolutionary scenarios, and example applications demonstrate the utility of ontophylo in studying morphological evolution in Hymenoptera using simulated data. 4. Ontophylo is easily integrated with other ontologyoriented and general-purpose R packages and offers new opportunities to examine morphological evolution on a phenomic level using new and legacy data.

evolutionary biology↗

rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits

O_LIOrganismal anatomy is a complex hierarchical system of interconnected anatomical entities often producing dependencies among multiple morphological characters. Ontologies provide a formalized and computable framework for representing and incorporating prior biological knowledge about anatomical dependencies in models of trait evolution. Further, ontologies offer new opportunities for assembling and working with semantic representations of morphological data. C_LIO_LIIn this work we present a new R package--rphenoscate--that enables incorporating ontological knowledge in evolutionary analyses and exploring semantic patterns of morphological data. In conjunction with rphenoscape it also allows for assembling synthetic phylogenetic character matrices from semantic phenotypes of morphological data. We showcase the new package functionalities with three data sets from bees and fishes. C_LIO_LIWe demonstrate that ontology knowledge can be employed to automatically set up ontologyinformed evolutionary models that account for trait dependencies in the context of stochastic character mapping. We also demonstrate how ontology annotations can be explored to interrogate patterns of morphological evolution. Finally, we demonstrate that synthetic character matrices assembled from semantic phenotypes retain most of the phylogenetic information of the original data set. C_LIO_LIOntologies will become an increasingly important tool not only for enabling prior anatomical knowledge to be integrated into phylogenetic methods but also to make morphological data FAIR compliant--a critical component of the ongoing phenomics revolution. Our new package offers key advancements toward this goal. C_LI

evolutionary biology↗

To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.

evolutionary biology↗

Metagenomics reveals that Dung Beetles (Coleoptera: Scarabaeinae) broadly feed on Reptile dung and could feed on that of Dinosaurs

According to traditional views, the evolution of dung beetles (Coleoptera: Scarabaeinae) and their feeding habits are largely attributed to mammal dung. In this paper, we challenge this view and provide evidence that many dung beetle communities are actually associated with the dung of reptiles and birds (= Sauropsida). In turn, this indicates that sauropsid dung may have played a crucial evolutionary role that was previously underestimated. We argue that it is physiologically realistic to consider that coprophagy in dung beetles could have evolved during the Cretaceous in response to the massive amount of dung produced by dinosaurs. Furthermore, we demonstrate that sauropsid dung may be one of the major factors driving the emergence of insular dung beetle communities across the globe. We support our findings with amplicon-metagenomic analyses, trapping experiments, and meta-analysis of the published literature.

evolutionary biology↗

Resolving ubiquitous model congruence in phylogenetics and its application for studying macroevolution

A recent study (Louca and Pennell, 2020) spotlighted the issue of model congruence, or asymptotic unidentifiability, in time-dependent birth-death models used for reconstructing species diversification histories on phylogenetic trees. The present work investigates this issue in state-dependent speciation and extinction (SSE) models, commonly used to study trait-dependent diversification. We found that model unidentifiability is universal due to hidden states, with every SSE belonging to an infinite congruence class. Notably, any trait-independent model is congruent with trait-dependent models, raising concerns for hypothesis testing. To address this, we propose an analytical solution that resolves model selection within a congruence class. Our findings show that this type of congruence is the only one possible, and with our solution in place, model unidentifiability in SSEs becomes absolutely harmless for inference. However, model selection across congruence classes remains challenging due to extremely high false positive rates. The discovered congruence offers a clear explanation of this issue and suggests potential ways forward.

evolutionary biology↗

ontoFAST: An R package for interactive and semi-automatic annotation of characters with biological ontologies

O_LIThe commonly used Entity-Quality (EQ) syntax provides rich semantics and high granularity for annotating phenotypes and characters using ontologies. However, EQ syntax might be time inefficient if this granularity is unnecessary for downstream analysis. C_LIO_LIWe present an R package ontoFAST that aid production of fast annotations of characters and character matrices with biological ontologies. Its interactive interface allows quick and convenient tagging of character statements with necessary ontology terms. C_LIO_LIThe annotations produced in ontoFAST can be exported in csv format for downstream analysis. Additinally, OntoFAST provides: (i) functions for constructing simple queries of characters against ontologies, and (ii) helper function for exporting and visualising complex ontological hierarchies and their relationships. C_LIO_LIOntoFAST enhances data interoperability between various applications and support further integration of ontological and phylogenetic methods. Ontology tools are underrepresented in R environment and we hope that onto-FAST will stimulate their further development. C_LI

bioinformatics↗

Markov models provide many solutions for appropriate modeling of inapplicable morphological characters in phylogenetics

AO_SCPLOWBSTRACTC_SCPLOWThis paper proposes new Markov models for phylogenetic inference with anatomically dependent (inapplicable) morphological characters. The proposed models can explicitly model an anatomical dependency in which one or several characters are allowed to evolve only within a specific state of the hierarchically upstream character. The new models come up in two main types depending on the type of character hierarchy. The functions for constructing custom character hierarchies are provided in the R package rphenoscate. The performance of the new models is assessed using theory and simulations. This paper provides practical recommendations for using the new models in Bayesian phylogenetic inference with RevBayes.

evolutionary biology↗

Causal modeling refutes Hockett's hypothesis that bite configuration affects human sound evolution

Blasi et al. (Research article, 15 March 2019) argue in support of Hocketts hypothesis - that languages of hunter-gatherers are less likely to develop labiodental sounds than those of agricultural societies due to the formers heavy-wear diet that favors edge-to-edge bite, thereby decreasing likelihood of labiodental articulation. We reanalyze the data in Blasi et al. and find little to no support in favor of the Hocketts hypothesis. The negative association between labiodentals and hunter-gatherers instead appears to be an artifact of labiodental decline with increasing distance from Africa, which is a general trend of language phonemes.

evolutionary biology↗

PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of phenotypic entities that consist of ensembles of multiple discrete traits - entire organismal anatomies or organismal body regions. In this study, we provide a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies) that appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.

evolutionary biology↗

The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks

What constitutes a morphological character versus character state has been long discussed in the systematics literature but the consensus on this issue is still missing. Different methods of classifying organismal features into characters and character states can dramatically affect the results of phylogenetic analyses. Here, I show that the modular structure of the gene regulatory network (GRN) underlying trait development, and the hierarchical nature of GRN evolution, essentially remove the distinction between morphological character and character state, thus endowing the character and character state with an invariant property with respect to each other. This property allows representing the states of one character as several individual characters and vice versa. In practice, this means that a phenotype can be encoded using a set of characters or just one complex character with numerous states. The representation of a phenotype using one complex character requires a selection of an appropriate penalty for the state transitions.

evolutionary biology↗