Groups Of Taxa Research Articles

SurvBal: compositional microbiome balances for survival outcomes.

Identification of balances of bacterial taxa in relation to continuous and dichotomous outcomes is an increasingly frequent analytic objective in microbiome profiling experiments. SurvBal enables the selection of balances in relation to censored survival or time-to-event outcomes which are of considerable interest in many biomedical studies. The most commonly used survival models-the Cox proportional hazards and parametric survival models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e. the ratio of the geometric means of two groups of taxa's relative abundances. The SurvBal R package and Shiny app can be accessed at https://github.com/yinglia/SurvBal and https://yinglistats.shinyapps.io/shinyapp-survbal/.

Utilizing a Dashboard for Efficient Biodiversity Data Overview and Gap-Filling Effort

Taiwan Biodiversity Information Facility has been leading the effort to integrate and mobilize biodiversity data nationally. We recently accomplished the integration of local databases and successfully developed a data portal that efficiently links to the most comprehensive biodiversity database in Taiwan: the Taiwan Biodiversity Information Alliance Data Portal. However, we identified an emerging challenge following this development. Preliminary analyses have revealed several gaps in the current dataset, impeding robust data use. For instance, land data dominates over sea data, and bird records are more abundant than those of other taxonomic groups. In our endeavour to enhance national biodiversity data coverage, we are actively exploring methodologies to address these existing data gaps. Here, we broadly define data gap as the absence of required data or information for use. Our primary objective is to empower users to identify these gaps, thereby facilitating efficient, informed survey planning and eventually filling these gaps. For this purpose, we are evaluating the effectiveness of a user-friendly dashboard, tailored for biodiversity survey planning in Taiwan. We developed and deployed a R Shiny dashboard*1 that provides users with insightful data visualizations that highlight spatial, temporal, and taxonomical data overviews. It also offers customizable filtering options, such as by major taxon groups and habitat types, for easy viewing. Additionally, the dashboard includes a download function, so users can access spatial and taxon gap information in their survey planning efforts. After deploying the dashboard, we conducted user interviews to collect feedback aimed at refining its usability and effectiveness. In addition to helping survey planning, we anticipate that this tool will also aid data users in promptly assessing data integrity within the national biodiversity data portal, thereby enabling them to identify potential data gaps and biases that may affect subsequent use. Through this presentation, we aim to share our experience in developing an interactive dashboard tailored for public use. Preliminary results had indicated that the dashboard highlighted some visible data gaps and biases, particularly in underrepresented areas such as marine habitats and less-studied taxonomic groups. Additionally, user interviews revealed a demand for a feature that provides single species data overviews, suggesting a potential area for further development to enhance the tool's utility. Some challenges remain, such as the need to enhance data granularity and user interface usability. Future work will focus on incorporating more real-time data integration and expanding the range of customizable filters. We believe these efforts will further empower users in Taiwan to conduct more informed and efficient biodiversity surveys, ultimately supporting research and policy-making to address critical biodiversity data gaps.

A morphology-based phylogeny of the diatoms formerly assigned to the Orthoseiraceae (Bacillariophyta): phylogenetic relationships, character analysis and classification

ABSTRACT A formal cladistic analysis of the morphological features of taxa assigned to the Orthoseiraceae, including Phycavernosa, Guarreraea and species of the genus Orthoseira is developed for 35 taxa based on 16 characters along with two Melosira species and four biddulphioid species as ingroup taxa as well as Leptocylindrus danicus as the outgroup. A consensus tree of 266 843 most parsimonious topologies suggests that the Orthoseiraceae is monophyletic, and that Guarreraea plus all former species of Orthoseira represent a monophyletic group. This analysis of morphological data did not provide support for the members of the Orthoseiraceae being more closely related to melosiroid or biddulphioid diatoms. Relationships within the monophyletic orthoseiracean group are detailed. Due to the exclusion of the generitype of Orthoseira not possessing carinoportulae which are central tube processes, one of the diagnostic features of the former Orthoseiraceae, other taxon names are described and recognized herein. We recognize and describe a new order, the Liparogyrales, based on the genus Liparogyra for taxa that were previously assigned to Orthoseira. Two families, the Phycavernosaceae, comprising the genus Phycavernosa, and the Liparogyraceae, comprising Guarreraea and taxa formerly assigned to Orthoseira, are described. The genus Liparogyra is composed of three subgenera: the subgenus Liparogyra, the subgenus Porocyclia, and the subgenus Insularis which are diagnosed by synapomorphic features. Based on our analysis, the genus Stephanosira appears to lack synapomorphies. Liparogyra, Porocyclia and Stephanosira had previously been described as genera by Ehrenberg. Guarreraea and one newly proposed genus are also included in the Liparogyraceae. Several other lineages are aphyletic, due to them either being monotypic or without diagnostic features. Thus, a total of 29 species in five genera are recognized within the newly described order and two newly described families. Eighteen new combinations are proposed for the transfer of taxa from Orthoseira to other genera. Homoplasy amongst some of the character states is discussed.

Key role of plankton species and nutrients on biomagnification of PAHs in the micro-food chain: A case study in plateau reservoirs of Guizhou, China

There is considerable inconsistency in results pertaining to the biomagnification of PAHs in aquatic systems. Zooplankton specifically play an important role controlling the fate and distribution of organic contaminants up the food chain, particularly in large plateau reservoirs. However, it remains largely unknown how secondary factors affect the magnification of organic compounds in zooplankton. The present study assessed plankton species and nutrients affecting the trophic transfer of PAHs through the micro-food chain in plateau reservoirs, Guizhou Province China. Results show soluble ∑PAHs range from 99.9 – 147.3 ng L-1, and concentrations of ∑PAHs in zooplankton range from 1003.2 - 22441.3, with a mean of 4460.7 ng g-1 dw. Trophic magnification factors (TMFs) > 1 show biomagnifications of PAHs from phytoplankton to zooplankton. The main mechanisms for trophic magnification > 1 are 1) small Copepoda, Cladocera and Rotifera are prey for larger N. schmackeri and P. tunguidus, and 2) the δ15N and TLs of zooplankton are increasing with the increasing nutrients TN, NO3- and CODMn. As a result, log PAHs concentrations in zooplankton are positively correlated with the trophic levels (TLs) of zooplankton, and log BAFs of the PAHs in zooplankton are increasing with increasing TLs and log Kow. Temperature further enhances TMFs and biomagnifications of PAHs as noted by temperature related reductions in δ15N. There are also available soluble PAHs in the water column which are assimilated with increasing phytoplankton biomass within the taxa groups, diatoms, dinoflagellates and chlorophytes. Notable TMFs of PAHs in zooplankton in Guizhou plateau reservoirs are not significantly affected by phytoplankton and zooplankton biomass dilutions. The present study demonstrates the important roles of species selection, nutrients and temperature in the environmental fate of PAHs in freshwaters.

Aerial eDNA contributes vital information for fungal biodiversity assessment

Abstract Fungal diversity drives key processes in terrestrial ecosystems, but remains challenging to measure in the field and to monitor over time. In particular, we lack methods capable of describing both the regional biotas and fungal related conservation values, such as habitats for rare and threatened fungi. Environmental DNA (eDNA) could serve this purpose, once its validity to capture fungal assemblage properties is established. Using three approaches (full‐season eDNA sampling from air, snapshot visual surveys, and eDNA sampling from dead wood), we present the first comparative assessment of fungal diversity at forest stand scale. The focus was on two well‐known fungal groups (lichens and wood inhabiting basidiomycetes) in old hemiboreal forests. Aerial eDNA revealed regional‐scale cryptic diversity not detected in visual surveys, particularly among lichens and including species of conservation concern. However, at the local population scale, both aerial eDNA and eDNA sampled from dead wood often missed visually detected species. In particular, eDNA sampled from dead wood performed only as a supplementary source of species data. The methods differed in detecting the spatial covariance of wood fungal and lichen diversity, with the combined (most complete) dataset indicating the strongest congruence. Synthesis and applications. Neither eDNA approaches nor visual surveys were able to detect full diversity of local fungi and all species of specific conservation value. However, there is clear merit in combined use of these methods, particularly in pairing aerial eDNA with visual observation‐based surveys on selected taxon groups. This approach can be especially valuable in fungal groups that have challenging taxonomy, inhabit partly inaccessible microhabitats, or have overall high diversity (such as lichens).

How to describe a new species in zoology and avoid mistakes

Abstract Taxonomy is the science of discovering, naming, describing, diagnosing, identifying, and classifying different kinds of taxa, from species to families. It lays the foundation for all of the biological sciences. The rapid increase in both taxonomic descriptions and malpractice in recent decades indicates a need for consistency in the procedure and quality of taxonomic research publications dealing with recognition of new taxa, name changes, and nomenclatural acts. Indeed, there are numerous examples in the recent literature of taxonomic works that fall short of the basic procedures and minimum standards required for naming new species according to the mandatory provisions and recommendations of the International Code of Zoological Nomenclature, accepted standards of taxonomic best practice, and journal editorial policy. Here, we provide practical guidelines of the procedure and key elements required to name, describe, and publish a new animal species or revise the taxonomic status of a species. We then discuss some of the common pitfalls that should be avoided. Mistakes commonly made include failure to read the Code, to review the primary taxonomic literature, to examine type material, to construct the taxon name correctly, to explicitly establish the new taxon, to provide adequate typification, to clearly differentiate the new taxon, to register the publication of the new taxon name in ZooBank, or to publish the name of the new taxon in a manner that is compliant with the Code. We provide some examples of these mistakes, mainly from butterflies (Insecta: Lepidoptera: Papilionoidea) and, to some extent, reptiles because these taxon groups seem to have an unusually high level of poor taxonomic practice.

Quantifying the effects of fragmentation of connectivity networks of deep‐sea vulnerable marine ecosystems

AbstractAimProtection of vulnerable marine ecosystems (VMEs) in the high seas has focussed on identifying concentrations of indicator species and prohibiting the operation of bottom‐contact fishing gears where those occur in significant concentrations. Most such species have planktonic larvae and depend on dispersal networks for inter‐generational persistence. Yet, connectivity amongst patches of VME has seldom been considered when spatial management measures are introduced. Here, the relative importance of individual patches for the maintenance of their connectivity networks is evaluated, and a prioritization scheme for management action is proposed. Effective conservation measures should maintain approximately natural network configurations whenever possible.LocationGrand Bank and Flemish Cap, Northwest Atlantic Ocean.Methods3‐D Lagrangian particle tracking was used to model larval dispersal connections between known patches of each of seven groups of benthic invertebrate taxa, previously recognized as indicators of VME. Connectivity networks were constructed and the effects of habitat loss simulated by systematic removal of whole patches, to determine the importance of each patch to connectivity within its respective network.ResultsThe various patches differed widely in their contributions to network connectivity. Each taxon group had both some patches that, if removed from the network, would result in a major decline in connectedness but also several which could be lost with negligible consequences for the remainder.Main ConclusionsWhile protecting each patch of VME has conservation value, the wide variation in connectedness shows that some patches are much more critical than others to the long‐term persistence of the taxa, providing a foundation for prioritization of conservation actions.

Mosses and vascular plants show diverging diversity patterns along a latitudinal gradient in boreal bogs and fens

AbstractQuestionsThe latitudinal biodiversity gradient; i.e., the increase in biodiversity towards the equator, is one of the most prominent biodiversity patterns. Nevertheless, many questions remain to be answered about the influence of multiple environmental factors on the latitudinal biodiversity gradient, especially for mosses, and the functional diversity of mosses and vascular plants. This study aims at evaluating the influence of latitude, climate, environmental variables, and habitat types (bog vs fen) on taxonomic and functional diversity (α‐diversity and β‐diversity) and the composition of vascular plant and moss species.Location49° N to 55° N in Northwestern Quebec, Canada.TaxonMosses, vascular plants.MethodsWe used a database containing 376 phytosociological plots (400 m2) sampled in boreal peatlands located along a 600‐km latitudinal gradient. We evaluated changes in α‐diversity and β‐diversity in response to latitude, longitude, climate, and local abiotic variables for both taxonomic groups using linear mixed effect models. We evaluated the effects of these variables on taxonomic and functional composition using variance partitioning by redundancy analysis.ResultsMoss diversity increased with latitude, although the effects were masked by environmental variables, whereas vascular plant diversity decreased with latitude in fens and did not vary with latitude in bogs. We observed a decrease in taxonomic and functional uniqueness with latitude. Moss and vascular plant taxonomic and functional composition were primarily structured by contrasting local conditions in bogs and fens, whereas climatic variations along the latitudinal gradient played a secondary role.ConclusionsOur results highlight the contrasting biodiversity patterns in both peatland types and the importance of local habitat conditions in structuring vascular plant and moss diversity. These patterns varied depending on the diversity indicator used, as α‐ and β‐diversity and functional and taxonomic diversity were often decoupled. Future studies should therefore include more than one diversity indicator and consider the differences between ecosystems and taxon groups.

Biogeographical patterns of species richness in stream diatoms from southwestern South America.

The latitudinal diversity gradient (LDG) hypothesis has been validated for many taxon groups, but so far, stream diatoms have not conformed to this pattern. Research on diatoms that includes data from South America is lacking, and our study aims to address this knowledge gap. Previous studies have successfully explained stream diatom species richness by considering niche dimensionality of physicochemical variables. Moreover, in southwestern South America, the observed biogeographical pattern differs from LDG and has been shown to be determined by historical factors. We used a dataset comprising 373 records of stream diatom communities located between 35° S and 52° S latitude, southwestern South America. The dataset included physicochemical river water variables, climate data, and ice sheet cover from the Last Glacial Maximum. We explored geographical patterns of diatom species richness and evaluated 12 different causal mechanisms, including climate-related theories, physicochemical and climatical exploratory analyses, historical factors, and niche dimensionality. A metacommunity analysis was conducted to evaluate the possible nested structure due to historical factors. We observed an increase in diatom species richness from south to north. Models containing both physicochemical and climatic predictors explained the highest proportion of variation in the data. Silica, which was correlated with latitude, and flow velocity, which did not show any spatial pattern, were the most important predictors. Historical factors and nested structure did not play any role. Contrary to what has been reported in the literature, we found no support for climate-related explanations of species richness. Instead, theories related to niche dimensionality and local factors provided better explanations, consistent with previous related research. We suggest that the increase in diatom richness in the north of our study region is due to a higher nutrient supply in these rivers, rather than a due to larger species pool in the area.

How do different modalities of land use practices impact the environmental features and macroinvertebrates? An assessment of mountain streams from Patagonia, Argentina

Agricultural intensification is a significant process, transforming the land and modifying stream water quality and biodiversity. Land-use practices are associated with substantial changes in vegetation structure, significant inputs of nutrients, erosion, and increased sedimentation, all of which profoundly impact aquatic biota and ecosystem functioning. The effect of different agricultural practices (horticulture, extensive and intensive livestock) on stream water quality was compared in terms of physicochemical features, bacteria, habitat condition, riparian ecosystem, and macroinvertebrate variables in a temperate rural landscape (Patagonia). The main objective was to identify which variables related to land use were determinants in the configuration of biotic communities. Significantly higher values in water temperature, conductivity, nutrients, and bacteria were found at intensively developed sites than at reference ones. The quality of the habitat and the riparian ecosystem had been profoundly modified. A multidimensional scaling analysis revealed that macroinvertebrate assemblages also differed among land use categories, with the variables: total phosphorous, total nitrogen, bacteria (E. coli, mesophilic and total coliforms), water temperature, and oxygen having the highest predictive power. Macroinvertebrate metrics (richness of EPT (Ephemeroptera+Plecoptera+Trichoptera), Plecoptera, shredders and scrapers, and the percentage of scrapers and collectors) proved appropriate bioindicators for discriminating intensive land use impacts and highlighted a trend of biodiversity loss. Plecoptera richness, a taxa group with a high level of endemism, responded significantly to habitat condition degradation. These results confirm that the intensification of land use leads to increased nutrient levels and suppressed aquatic-terrestrial interactions involved in the provision of allochthonous detrital input, shade, and habitat structure for larval stages and adults. The Habitat Condition Index appears to be a useful tool for rapid stream assessment and providing early warnings. Several ecological services are threatened in these Patagonian agroecosystems. Restoring riverbank heterogeneity and improving management practices that ameliorate nutrient and sediment inputs are crucial to enhance biodiversity.

Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives.

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C.eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C.cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Priority areas for the establishment of genetic reserves to actively protect key crop wild relative species in Italy

Crop Wild Relatives (CWR) are wild plant taxa genetically close to a crop. Being a precious source of genetic variability and of traits for crop improvement, CWR have a high socio-economic value and are identified among the main plant genetic resources. Alarming enough, the inter- and intraspecific diversity, as well as their habitat diversity, is under threat of irremediable loss. Italy is the second richest country in Europe in terms of plant species number; applying the taxon group concept 5712 have been recently identified as CWR. The aims of the present research are to identify the best sites for: i) the institution of genetic reserves to actively protect CWR species of the key crop genera as Allium, Brassica and Triticum and ii) performing new collection missions to reach adequate ex situ conservation of target species. Georeferenced data were retrieved from different online databases. CAPFITOGEN tools were initially used to develop an ecogeographic land characterisation map (ELC) of Italy. Geographical distribution data were assembled for 379 populations of 18 CWR taxa. Results of the complementarity analysis showed that 10 protected areas provide coverage of the 46.4% of the target conservation units and include 66.7% of the priority CWR taxa investigated. Alarming enough, only 7.4% of the 379 populations are currently conserved ex situ; among the 18 ecogeographic land characterisation categories only 3 are covered by ex situ conservation. This is the first study where most suitable protected areas for the institution of genetic reserves are proposed for Italy for the protection of multiple CWR taxa of key genera; this is relevant also considering the global value of many of the related crop such as different wheat species, cabbages, rape, garlic and onion. Being already dedicated to habitat and species conservation, the identified sites are optimal candidates for the institution of genetic reserves. Results will hopefully also guide new collecting missions that are urgently needed to strength ex situ conservation of such precious genetic resources.

Vertebrates can be more important pollinators than invertebrates on islands: the case of Malva (=Lavatera) arborea L.

Premise of the study: On islands, flowering plants tend to be more generalist in their pollination needs, as insects (the main pollinators of flowering plants) are underrepresented in these ecosystems compared to the mainland. In addition, some vertebrate species that are typically insectivorous or granivorous on the mainland are forced to broaden their diet and consume other resources such as nectar or pollen on the islands. The shrub Malva arborea, with its large and colourful flowers, attracts different groups of potential pollinators. This study aimed to compare the effectiveness of vertebrates versus insects in an insular population of M. arborea and to investigate its reproductive system. Methods: For three groups of taxa (insects, birds and lizards), we assessed the two components of pollination effectiveness: (i) the quantitative component (i.e. number of visits and number of flowers contacted) through direct observations of flowers; and (ii) the qualitative component (fruit and seed set, number and size of seeds and proportion of seedling emergence) through pollinator exclusion experiments. Key results: Vertebrates (birds and lizards) were quantitatively the most effective pollinators, followed by insects. However, when all three groups visited the flowers, fruit and seed set were higher than when any of them were excluded. We also found that M. arborea has hermaphrodite flowers and is able to reproduce by autogamy, although less efficiently than when pollinated by animals. Conclusions: Both vertebrates and insects play an important role in the reproduction of M. arborea. Although the plant does not need pollinators to produce seeds, its reproductive success increases when all pollinators are allowed to visit the flowers. Besides providing new information on M. arborea, these findings may help to better understand the role of different pollinator groups in the reproduction of other plant species, especially on islands where the co-occurrence of vertebrate and invertebrate pollination in the same plant species is usual.

The response of diatom community to small hydropower plant and fish farm

Some of the direct and indirect environmental impacts are related to the construction of fish farms (FFs) and small hydropower plants (SHPs) around the world. Diatom communities are one of the best bioindicators of various pressures like eutrophication, chemical and organic pollution. The main objective of this study was to examine the influence of SHP and FF on diatom community and water quality of the Prištavica River in Serbia. A total of 184 epilithic diatom taxa from 55 genera were identified. Sites after the FF and SHP are distinguished by the same dominant species in each season. Compared to the other sites, species diversity in summer was lower at site after SHP. In terms of spatial dynamics, four groups of taxa are distinguished. Some centric taxa were associated with sites downstream the FF and SHP. Altered physical and chemical parameters were documented at sites downstream of constructions. Water quality of the Prištavica River ranged from high to bad depending on diatom index, season, and sampling site. A greater difference in diatom index values was found at sites upstream and downstream of the FF, than at sites upstream and downstream of the SHP.

Uncovering Rotifera, Cladocera and Copepoda name length patterns for enhanced scientific communication.

The motivations for describing species are multifaceted and extend beyond the scientific disciplines, promoting public engagement and enhancing biodiversity communication. We delve into the practices of naming species of Rotifera, Diplostraca (= Cladocera) and Copepoda, underpinning the effects of time, taxon group and the lengths of genus names on the length of specific names. Our investigation revolves around a comprehensive dataset comprising 6319 names described between 1758 and 2021 of Rotifers, Cladocera and Copepoda. The overall annual average hovers around a mean length of slightly over 10 and 8 letters, respectively, for genus names and specific names, although it varied noticeably across taxa. Notably, our findings reveal no substantial temporal variation in the length of specific names over the years of description. We found a positive although not significant relationship between the length of specific and genus names, suggesting that longer genus names may influence the choice of longer specific names. We support the recommendation by the International Commission on Zoological Nomenclature and existing related publications on this topic, to prioritize short names, emphasizing the importance of concise and ultimately the use of mnemonic names assigned to zooplankton species.

Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean.

Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acquire large amounts of data (morphological, molecular) at the individual scale, making it possible to study mesozooplankton using a trait-based approach. Here, combining quantitative imaging with metabarcoding time-series data obtained in the Sargasso Sea at the Bermuda Atlantic Time-series Study (BATS) site, we showed that organisms' transparency might be an important trait to also consider regarding mesozooplankton impact on carbon export, contrary to the common assumption that just size is the master trait directing most mesozooplankton-linked processes. Three distinct communities were defined based on taxonomic composition, and succeeded one another throughout the study period, with changing levels of transparency among the community. A co-occurrences' network was built from metabarcoding data revealing six groups of taxa. These were related to changes in the functioning of the ecosystem and/or in the community's morphology. The importance of Diel Vertical Migration at BATS was confirmed by the existence of a group made of taxa known to be strong migrators. Finally, we assessed if metabarcoding can provide a quantitative approach to biomass and/or abundance of certain taxa. Knowing more about mesozooplankton diversity and its impact on ecosystem functioning would allow to better represent them in biogeochemical models.

Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder

To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3–6 and 7–12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759

Peltigera (Ascomycota) living in open and shady environments depend on different Nostoc photobionts


 
 
 Species of Peltigera (lichen-forming Ascomycota) establish obligate symbioses with several monophyletic groups (phylogroups) of Nostoc cyanobacteria. Some of these fungi are strict specialists and only associate with one Nostoc phylogroup throughout their range, while others are generalists and associate with many different Nostoc phylogroups. We sampled 20 Peltigera taxa, mostly representing the Peltigera section Peltigera, from grassland and forest habitats across Europe. Mycobionts’ identities were confirmed using fungal ITS sequences. The Nostoc cyanobionts were identified and grouped based on single nucleotide differences in the trnL region and on the phylogenetic analysis of the rbcLX region. Our data confirmed that some Peltigera species clearly prefer open habitats, while others are largely confined to shady forest habitats. The two habitat preferences are consistently paired with association with different Nostoc groups. As a specific example, two ecologically versatile species, Peltigera canina and P. didactyla, both growing in open and shady habitats, consistently associated with different groups of Nostoc when growing in different habitats. As associations between specific mycobionts and cyanobionts are influenced by habitat conditions, the diversity of both taxon groups should be considered in the context of habitat management and conservation planning.
 
 

Hotspots and Factors Influencing Vertebrate Roadkill on the Ring Changbai Mountain Scenic Road, China

The spatial aggregation patterns of wildlife-vehicle collisions are used to inform where mitigation measures are most needed. Based on 10 years of observations of vertebrate roadkill on the Ring Changbai Mountain Scenic Road, the spatial distribution characteristics of roadkill incidence were analyzed in this study. Using the field survey method to investigate roadkill incidents and their influencing factors, we applied generalized linear mixed modeling (GLMM) for model selection and constructed roadkill models for different taxa groups. The spatial distribution patterns of roadkill hotspots vary among different taxa and exhibit a unimodal or multimodal distribution. The road section along a river and with a minimal distance between the road and the water has a high incidence of roadkill. The density of roadkill for various taxa decreases as the distances from rivers, bridges, and ponds increases. However, there appears to be no correlation between the density of bird roadkill and any factors. Finally, wildlife crossing facilities and guidance measures aimed at reducing the incidence of roadkill and enhancing the selection of routes and wildlife crossing structures in the area are formulated.

Phylogenetic relationships and historical biogeography of Otus species based on mitochondrial cytochrome b gene sequence

Abstract This study analyzed mitochondrial cytochrome b gene sequences to infer Otus species’ phylogenetic relationships and historical biogeography. The researchers used Maximum Parsimony and Maximum Likelihood methods to generate the phylogenetic trees. They constructed a Bayesian MCC Chronogram Tree to determine the Otus species’ age and speciation events. Paleoclimate and paleogeology maps were also used to correlate the branching out of Otus species with geological time periods and climatic conditions. The results showed five major clusters or clades for the core taxon group (Otus) and one for the sister group (Tyto). The Bayesian tree showed seven major clades for Otus, with the first speciation occurrence dating back to 21.54 mya during the Early Miocene epoch. Most of the core taxon species speciated during the Pliocene Period, with some exceptions. The paleoclimate data indicated that Otus clades branched out during the Icehouse climate state, with the first branching out occurring during the Coolhouse climatic state. The paleogeologic data revealed that the African and American (North and South) continents were already distinct and divided by the Atlantic Ocean during the first branching out of the Otus clade. The distribution areas of Otus species were also mapped using updated Wallace’s zoogeographic realms. Overall, this study provides a better understanding of the phylogenetic history of Otus species and their diversification in relation to geological and climatic events. However, the authors caution that all phylogenetic trees, evolutionary studies, and divergence time estimates should be considered hypotheses with significant uncertainty.