Large Taxonomic Groups Research Articles

From dinosaurs to birds: paleomacroecological analysis of the body size inversion in the maniraptor lineage

Large taxonomic groups, distributed over vast geological periods, may exhibit wide patterns of morphological variation, such as variation in body size and complexity of living beings. Some studies seek to determine whether these trends of increasing or decreasing size and complexity result from persistent directional forces (e.g., natural selection) or from non-directional (random) trends produced by constraint limits. These mechanisms have been characterized as "active or directed" and "passive" trend processes, respectively. Understanding these variation patterns allows assessing hypotheses within a paleomacroecological context, such as Cope's Rule, which suggests that lineages with longer evolutionary time spans tend to increase in size. This pattern has been demonstrated in various groups of fossil vertebrates, such as dinosaurs. However, the Maniraptora lineage (ancestral to groups that gave rise to birds) seems to exhibit an inverted pattern, with a reduction in body size in recent lineages. Tests indicate that this asymmetry in size evolution can be explained by passive or active trends, i.e., random size variation or directional selection. In this case, an "Inverted Cope's Rule" could indicate directional selection for size reduction in the Maniraptora lineage towards the derivation of birds. Body size and time distribution vectors will be derived for each lineage, evaluating the general trend of size variation. If asymmetry in size evolution is observed, a Subclade Test will be conducted to assess if a specific subclade repeats the asymmetric distribution pattern. The goal of this project is to assess active and/or passive trends related to body size variation in Maniraptora dinosaurs, using fossil data from the Paleobiology Database and the Natural History Museum Database.

A new species of winter noctuid moth (Lepidoptera, Noctuidae, Xyleninae) from Zhejiang, China, with a key to species of the genus.

The tribe Xylenini is one of the main large taxonomic groups known as Winter Noctuidae. A new species of the genus Antivaleria Sugi, 1980, Antivaleriaronkayorum Zhang & Wang, sp. nov. is described and illustrated from Zhejiang Prov., China. The species resembles Antivaleriaperegovitsi Ronkay et al., 2010, but differs in wing pattern, foot-like cucullus and special shape of harpe. A key to the Antivaleria species is presented. The holotype is deposited in the Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou.

Response of invertebrate populations of steppe and floodplain meadows to emissions from the Karabash copper smelter

Based on the data of 2014, the response of invertebrate communities in floodplain and steppe meadows to emissions from the Karabash Copper Smelter (the main pollutants are SO2 and heavy metals) was assessed. When approaching the smelter, the phytomass of forbs decreases (2–7 times) and the proportion of graminoids increases (from 36–45 to 53–85%) in the phytocenoses of both meadow types. The abundance of invertebrates changes similarly in meadows of both types: the total abundance decreases (by 1.4–2.9 times), while the abundance of all trophic and most of the large taxonomic groups does not change. The taxonomic structure of invertebrates in floodplain meadows changes only in the impact zone, whereas in the steppe meadows – already in the buffer zone. This result partially confirms the hypothesis put forward that the response to pollution in floodplain meadow communities is less pronounced than in steppe meadow communities.

Complementing model species with model clades.

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.

Endoparasitofauna of Altai mountain sheep (Ovis ammon ammon), Siberian mountain goats (Capra sibirica) and small cattle of the Saylyugemsky National Park, Altai Republic

The theriofaunal list of wild bovids of the South-Eastern Altai includes the Altai mountain sheep (Ovis ammon ammon), as well as the Siberian mountain goat (Capra sibirica). The predominant types of farm animals in the Altai Republic are goats and sheep. Parasite fauna and the interchange between wild bovids and small cattle in these areas is not well understood. Samples were taken by employees of the Sailyugemsky National Park. At the department, V.L. Yakimov, ovoscopic and larvoscopic research methods were carried out. The calculation of the average number of eggs was carried out using a VIGIS counting chamber (VNIIP named after K.I. Skryabin). According to the results obtained, an analysis of cross-invasion was carried out. In wild bovids from 120 samples studied and in small cattle from 31 samples, endoparasites belonging to four large taxonomic groups were found: protists, trematodes, cestodes, and nematodes. In wild bovids from the group of nematodes, invasion with eggs of the genus Trichuris was established, according to morphological and morphometric characteristics, eggs of the ascarid type were found, eggs of nematodes of the order Strongylida, the genus Marshallagia, Nematodirella, Nematodirus spp., as well as larvae of the genus Protostrongylus were also found. From the group of trematodes, eggs of the species Hasstilesia ovis, as well as Dicrocoelium sp. From the group of cestodes, eggs of the genus Moniezia sp. From the group of protists, oocysts of the genus Eimeria spp. In small cattle, in contrast to wild bovids, nematodes of the genus Strongyloides sp. The number of cases of detection in small cattle of the nematode of the genus Protostrongylus sp. significantly lower than in wild bovids, and eggs of the strongylid type were more common. Also, no eggs of the trematode of the genus Dicrocoelium sp. Otherwise, the endoparasite fauna was similar to wild bovids. This study will help to compile a complete picture of the parasite fauna and cross-invasion of wild bovids and small cattle.

Using hierarchical text classification to investigate the utility of machine learning in automating online analyses of wildlife exploitation

Expanding digital data sources, including social media, online news articles and blogs, provide an opportunity to understand better the context and intensity of human-nature interactions, such as wildlife exploitation. However, online searches encompassing large taxonomic groups can generate vast datasets, which can be overwhelming to filter for relevant content without the use of automated tools. The variety of machine learning models available to researchers, and the need for manually labelled training data with an even balance of labels, can make applying these tools challenging. Here, we implement and evaluate a hierarchical text classification pipeline which brings together three binary classification tasks with increasingly specific relevancy criteria. Crucially, the hierarchical approach facilitates the filtering and structuring of a large dataset, of which relevant sources make up a small proportion. Using this pipeline, we also investigate how the accuracy with which text classifiers identify relevant and irrelevant texts is influenced by the use of different models, training datasets, and the classification task. To evaluate our methods, we collected data from Facebook, Twitter, Google and Bing search engines, with the aim of identifying sources documenting the hunting and persecution of bats (Chiroptera). Overall, the ‘state-of-the-art’ transformer-based models were able to identify relevant texts with an average accuracy of 90%, with some classifiers achieving accuracy of >95%. Whilst this demonstrates that application of more advanced models can lead to improved accuracy, comparable performance was achieved by simpler models when applied to longer documents and less ambiguous classification tasks. Hence, the benefits from using more computationally expensive models are dependent on the classification context. We also found that stratification of training data, according to the presence of key search terms, improved classification accuracy for less frequent topics within datasets, and therefore improves the applicability of classifiers to future data collection. Overall, whilst our findings reinforce the usefulness of automated tools for facilitating online analyses in conservation and ecology, they also highlight that the effectiveness and appropriateness of such tools is determined by the nature and volume of data collected, the complexity of the classification task, and the computational resources available to researchers.

Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales

ABSTRACT Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the “true” reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.

Existence Of A Latent Developmental Program: Revisiting The Universal Genome Model Of Evolution Of Metazoa

Abstract In 2007, I published a hypothesis about mechanisms of evolution of large taxonomic groups of the Kingdom Animalia, which was based on advances in paleontology genome analysis, genetics and embryology that are difficult to understand within Darwinian intuition. According to this model that I called a Universal Genome hypothesis: (a) the Universal Genome that encodes major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular common ancestral organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar gene sets, are nonetheless very morphologically distinct because each utilize specific combinations of developmental programs. A highly counterintuitive prediction of this idea, which strictly dissociates it from the classical evolutionary model, is that latent developmental programs should exist in genomes of lower Metazoan taxa. These latent programs control the development of organs and other morphologies that would emerge in evolutionary higher taxa. Potentially such programs could be activated by mutations or application of signaling molecules, and thus be revealed in lower taxa. A paper on the embryology of fins published in the Cell journal provides an evidence for existence of such a latent developmental program. Here I comment of this discovery and its implication in our understanding of evolution.

Lessons from linking bio- and ecological traits to stoichiometric traits in stream macroinvertebrates.

Ecologists rely on various functional traits when investigating the functioning of ecological systems and its responses to global changes. Changing nutrient levels, for example, can affect taxa expressing different trait combinations in various ways, e.g., favoring small, fast-growing species under high phosphorus conditions. Stoichiometric traits, describing the elemental composition of organism body tissues, can help in understanding the mechanisms behind such functional shifts. So far, mainly life-history traits have been related to body stoichiometry (e.g., the growth rate hypothesis) on a limited number of taxa, and there is little knowledge of the general link between stoichiometric and other functional traits on a taxonomically large scale. Here, we highlight this link in the freshwater macroinvertebrates, testing predictions from underlying trait-based and Ecological Stoichiometry Theory (EST) in >200 taxa belonging to eight larger taxonomic groups. We applied a series of multivariate analyses on six of their stoichiometric traits (%C, %N, %P, C:N, C:P, and N:P) and 23 biological and ecological traits. We found significant relationships between stoichiometric traits and other types of traits when analyzing single-trait and multi-trait profiles. Patterns found within traits related to organism development or nutrient cycling were in line with our assumptions based on EST, e.g., traits describing predators were associated with high %N; traits suggesting a fast development (small maximum body size and high molting frequency) with high %P. Associations between ecological traits and body stoichiometry could be explained by the longitudinal stream gradient: Taxa preferring headwater habitats (i.e., high altitude, coarse substrate, and cold temperature) exhibited high %N and %P. Demonstrating the link between stoichiometric and both bio- and ecological traits on a large diversity of taxa underlines the potential of integrating stoichiometric traits into ecological analyses to improve our understanding of taxonomic and functional responses of communities-and ecosystems-to changing environmental conditions worldwide.

The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms

BackgroundCACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown.ResultsApplication of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. This approach yielded knowledge regarding: (i) the coexistence of two CACTA transposons subtypes in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv)) identification of captured satDNA arrays. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions.ConclusionsOur study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in the genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with the proposed novel functional features of structural-different CACTA elements can impact evolutionary trajectory of the host genome.

The influence of Bt cotton cultivation on the structure and functions of the soil bacterial community by soil metagenomics

Bt cotton successfully controlled major devastating pests in cotton，such as Helicoverpa armigera and Spodoptera exigua, and led to a drastic decrease in insecticide use in cotton fields, and it has been grown commercially worldwide. However, Bt cotton cultivation left Bt toxin residues in the soil, resulting in a response by its microbiome that caused potential environmental risks. In this research, the metagenomics analysis was performed to investigate the structure and functions of the soil bacterial community in the Bt cotton field from the Binzhou, Shandong province of China, where the Bt cotton has been cultivated for over fifteen years. Analysis of the function genes proved that the receptors of Bt toxins were absent in the soil bacteria and Bt toxins failed to target the soil bacteria. The microbiome structure and function were highly influenced by Bt cotton cultivation, however, no significant change in the total abundance of the bacteria was observed. Proteobacteria was the largest taxonomic group in the soil bacterial (42–52%) and its abundance was significantly increased after Bt cotton cultivation. The increase of Proteobacteria abundance resulted in an increase in ABC transporters gene abundance, indicating the improved ability of detoxification metabolism over Bt cotton cultivation. Xanthomonadales could be a biomarker of the Bt cotton group, whose abundance was significantly increased to contribute to the increase of the genes abundance in ABC transporters. The abundance of apoptosis genes was significantly decreased, and it might be related to the increase of Proteobacteria abundance by Bt cotton cultivation. In addition, Myxococcales was responsible for carotenoid biosynthesis, whoes genes abundance was significantly decreased due to the decrease of Myxococcales abundance by Bt cotton cultivation. These changes in soil bacterial community structure and functions indicate the influence by Bt cotton cultivation, leading to an understanding of the bacteria colonization patterns due to successive years of Bt cotton cultivation. These research results should be significant for the rational risk assessment of Bt cotton cultivation.

A unique microbiome in a highly polluted and alkalic lake in a seasonally frozen area.

Highly polluted waters profoundly promoted microbial activities and vice versa. Although microbial community structures and bioprocesses in polluted environments have been fully investigated, they are rarely uncovered in abandoned and highly polluted aquatic environment, especially in a seasonally frozen area. East Lake had been polluted by surrounding paper mills and dairy plants from the 1960s to the early 2000s. Under low biodegradability (BOD5/COD ratio<0.2) and alkalic (pH>9) conditions, a unique microbiome was discovered in East lake. Proteobacteria was the largest taxonomic group in the microbial community, covering almost half of the top-100 genera. Among them, seven genera are sulfate-reducing bacteria, including Desulfuromusa, Desulfuromonas, Desulfobulbus, Desulfocapsa, Desulfurivibrio, Desulfatiglans, and Desulfomicrobium. Functional analysis revealed abundant predicted functional genes for the respiration of sulfur compounds and sulfate respiration. Great vertical variations were found to both microbial community structures and predicted functions. This work provides unique evidence for future microbiome studies of nutrient-rich, alkalic, and seasonally frozen water habitats.

A coherent biogeographical framework for Old World Neogene and Pleistocene mammals

AbstractIn order to understand mammalian evolution and compute a wide range of biodiversity indices, we commonly use the ‘bioregion’, a spatial division adapted to ecological and evolutionary constraints. While commonly conducted by neontologists, the establishment of bioregions in palaeontology is generally a secondary analysis, shaped on subjective time scales and areas specific to the investigated questions and groups. This heterogeneity, coupled with the scale‐dependency of biodiversity indices, prevents the clear identification of macroecological and macroevolutionary trends for large taxonomic groups like extinct mammals. Here we tackle this issue by providing a coherent framework for Neogene and Pleistocene mammals of the Old World following two steps: (1) a temporal scale adapted to mammalian evolutionary history (i.e. evolutionary fauna) is defined by poly‐cohort analysis; (2) bioregions are then computed for each evolutionary fauna by clustering, ordination and intermediate approaches at multiples spatial scales (i.e. continental to regional) for Eurasia and Africa. Additionally, providing a coherent framework for a wide range of mammalian datasets, our results show: (1) the synchronous emergence and fall of five mammalian evolutionary faunas identified at chronological scales varying from the epoch to the geological stage; (2) a transition from a longitudinal to a latitudinal biogeographical structuring between the Miocene and Pliocene, especially in Europe; (3) the long‐term affinity of southern Asian with African faunas, in sharp contrast with the modern Palaearctic bioregion extension; and (4) the establishment of a vast Mediterranean bioregion from fragmented areas in the Late Miocene to its full extent in the Pleistocene.

Benthic macroinvertebrates assemblages of glacial-fed (Bheri) and rain-fed (Babai) rivers in western Nepal in the wake of proposedinter-basin water transfer.

BackgroundBenthic macroinvertebrates, encompassing large taxonomic groups of invertebrate organisms, are important components of aquatic ecosystems and play crucial roles in aquatic food webs. These organisms are also extensively used in water quality assessments as bioindicators for a range of stressors. Inter-basin water transfer (IBWT) is the transfer of water from a donor basin to a recipient basin and such transfers have both beneficial as well as adverse environmental and socio-economic impacts. This study attempts to generate baseline information on macroinvertebrates assemblages in glacial-fed (Bheri) and rain-fed (Babai) rivers of west Nepal, where Nepal’s first ever inter-basin transfer is in progress and the data can be used to assess the impact of inter-basin water transfer on water quality and aquatic biodiversity after completion.New informationThe dataset includes the records on the taxonomic diversity of macroinvertebrate in the Bheri and the Babai River systems. A total of 56 families of macroinvertebrates belonging to eight classes and four phyla were observed. A significant variation between the glacial-fed and rain-fed and seasons were observed reflecting different ecological zones and abiotic variables in the rivers and their catchments. Hydropsychidae and Baetidae were reported to be the most abundant taxa in the Bheri River system, whereas Gyrinidae, Physidae, Chironomidae and Hydropsychidae were most abundant taxa in the Babai River system.

Influence of different Eucalyptus hybrids on soil macrofauna.

The present work aimed to evaluate the influence of different eucalyptus hybrids on the edaphic macrofauna community. It is hypothesized that the density and diversity of edaphic fauna are influenced by the quantity and quality of the litter deposited by the different hybrids on the soil surface. The study area is in the city of Vitória da Conquista (BA) and consists of seven eucalyptus hybrids, one from sexual reproduction (seminal) and six from asexual (clonal) reproduction. Sampling of the soil macrofauna was performed by the Tropical Soil Biology and Fertility method. All visible invertebrates were collected and identified at the level of large taxonomic groups. The relative density, group richness, and diversity index were calculated. Hybrids did not influence the total density and richness of the soil macrofauna. However, it was possible to observe changes in litter accumulation and composition, and as a result in the diversity indexes and in the presence or absence of macrofauna groups. Among the studied hybrids, those from Eucalyptus urophylla (seminal, 1335 and 1249) promote greater macrofauna diversity and favor the occurrence of detritivores organisms, suggesting the occurrence of better quality and more palatable litter for the edaphic fauna.

Comparative analysis of flora of the Middle Volga region

The authors took 32 local floras (LF) to study the floristic g-diversity of the Middle Volga region. Their species composition was studied on an area not exceeding 400 km 2 , which is the optimal value for this area. For such an area, the number of vascular plant species was 679 species (the maximum value is 835, the minimum is 586). This sample size is sufficient to illustrate the main taxonomic parameters. The considered local floras are geographically located within 3 zones and five subzones according to zones and types of vegetation zonation in Russia and are located within the territories of the Republics of Tatarstan, Mordovia, Chuvashia, as well as Samara, Ulyanovsk, and Penza regions. Based on the family and genera spectra, we identified groups of similar LFs using the k-means method in the R package. When analyzing the spectrum of families, the determining feature for this territory is the third place in the spectrum, which is occupied by the families Fabaceae or Rosaceae . All 32 LFs considered ranged from the Fabaceae type in the southeast to the Rosaceae type in the northerly direction. We have identified the following boundaries of qualitative changes in the floristic composition at the level of large taxonomic groups (genera and families): 1) extreme types of flora, in which the characteristics of "forest" and "steppe" are most pronounced: Rosaceae -type, characterized by a large number of species from the genus Alchemilla , as well as Potentilla and Fabaceae type, which is determined mainly by the numerical combination of the genera Astragalus and Vicia ; 2) transitional types of floras arise due to a decrease in the number of representatives of these genera. The reason for this may be anthropogenic impact, primarily deforestation; 3) the greatest differences in the composition of large taxonomic groups are observed in the southernmost local flora of the Trans-Volga region (south of Samara region).

A Collective Effort to Update the Legume Checklist

Taxonomic names are critical to the communication of biodiversity—they link data together whether it be distribution data, traits or phylogeny. Large taxonomic groups, such as many plant families, are globally distributed as is the taxonomic expertise of the family. A growing knowledge base requires collaboration to develop an up-to-date checklist as a research foundation. The legume (Fabaceae) community has a strong history of collaboration including the International Legume Database and Information Service (ILDIS), which curated the names but ILDIS is no longer up to date. In 2020, under the umbrella of the Legume Phylogeny Working Group (LPWG), a group of taxonomists began updating the legume taxonomy as part of a larger collaboration around a legume data portal. Currently the World Checklist of Vascular Plants (WCVP) is the most up-to-date reference and was used as the starting point for the project. The workflow begins with over 80 volunteer taxonomic experts updating the checklist in their specialty area. These lists are manually collated, centrally creating a consensus taxonomy with synonyms. Any taxonomic conflicts are adjudicated within the group. The checklist then undergoes a comprehensive nomenclature assessment at Royal Botanic Gardens, Kew and becomes part of the WCVP. This checklist was submitted to the Catalogue of Life Checklist Bank and is integrated as the preferred legume checklist in the GBIF taxonomic backbone. After one round of taxonomic curation, 38% of the legume names in GBIF (Global Biodiversity Information Facility), which were previously unmatched to WCVP, are now connected to GBIF names, therefore also improving the occurrence records of those species. The GBIF taxonomic backbone contains names found on herbarium specimens and in the literature, which are not currently part of the legume expert community checklist or WCVP. This list of unresolved names will be forwarded to the legume community for curation, thereby developing a cycle of data improvement. It is anticipated that after a few rounds of expert curation, the WCVP and GBIF taxonomies will converge. At each cycle, a snapshot of GBIF occurrences is taken and the improvement of the occurrences is quantified to measure the value of the expert taxonomic work. The current checklist is also available via Catalogue of Life and soon via the World Flora Online to support research. In this talk, we describe the workflow and impact of the expert curated legume taxonomy.

Insights into 6S RNA in lactic acid bacteria (LAB)

Background6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB.ResultsWe provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs.ConclusionsDespite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.

Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes

Recent studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns. We determined plastid RNA-editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read-mapping and SNP-calling software to identify RNA-editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene. We found direct evidence for 505 plastid RNA-editing sites in A. aleuticum and 509 in A. shastense, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA-editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved. Variation in the frequency of RNA editing within Adiantum implies that RNA-editing sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.

Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.