Groups Of Taxa Research Articles

New data on the taxonomy and distribution of subfamily Polycestinae (Coleoptera: Buprestidae) in Bulgaria

Data on the distribution of 13 species group taxa of subfamily Polycestinae in Bulgaria are presented. Taxonomic notes about two species, Acmaeodera (Acmaeotethya) octodecimguttata and Acmaeodera (Acmaeotethya) degener, which allow their differentiation, are also given.

Interactome and evolutionary conservation of Dictyostelid small GTPases and their direct regulators

ABSTRACT GTP binding proteins known as small GTPases make up one of the largest groups of regulatory proteins and control almost all functions of living cells. Their activity is under, respectively, positive and negative regulation by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which together with their upstream regulators and the downstream targets of the small GTPases form formidable signalling networks. While genomics has revealed the large size of the GTPase, GEF and GAP repertoires, only a small fraction of their interactions and functions have yet been experimentally explored. Dictyostelid social amoebas have been particularly useful in unravelling the roles of many proteins in the Rac-Rho and Ras-Rap families of GTPases in directional cell migration and regulation of the actin cytoskeleton. Genomes and cell-type specific and developmental transcriptomes are available for Dictyostelium species that span the 0.5 billion years of evolution of the group from their unicellular ancestors. In this work, we identified all GTPases, GEFs and GAPs from genomes representative of the four major taxon groups and investigated their phylogenetic relationships and evolutionary conservation and changes in their functional domain architecture and in their developmental and cell-type specific expression. We performed a hierarchical cluster analysis of the expression profiles of the ~2000 analysed genes to identify putative interacting sets of GTPases, GEFs and GAPs, which highlight sets known to interact experimentally and many novel combinations. This work represents a valuable resource for research into all fields of cellular regulation.

Summer plankton of high mountain Lake Dzhulukul (Altai, Russia) in August 2020

The summer phytoplankton composition of high mountain Lake Dzhulukul located in Altai Mountainsat the source of Chulyshman River was studied in August 2020. Under the electron microscopic examination of thephytoplankton samples algae from four taxa groups – Chrysophyta, Bacillariophyta, Chlorophyta and Euglenophyta wererevealed, that has been supplemented the list of algae for the lake. Stomatocysts of chrysophycean algae various in shapeand structure have been revealed firstly for the lake algaflora.

Comparative Floral Micromorphology in Mimosa sect. Calothamnos (Fabaceae)

The genus Mimosa L. is well known for its high morphological variability and the presence of taxonomic complexes—groups of taxa that are not adequately circumscribed and are therefore in continuous revision. For this study, we analyzed flowers from 28 different taxa in Mimosa sect. Calothamnos Barneby and five vegetatively similar taxa from Mimosa sect. Mimosa. We observed three calyx shapes and four (glabrous or pubescent) calyx border types, as well as describe glandular trichomes on the calyx border for the first time in section Calothamnos. While the corolla exhibits only two shape types, trichomes on the corolla are much more diverse, as we found one simple and 11 branched trichome types in diverse orientations and dispositions. Given the taxonomic value of trichomes and profuse terminology in different families, we focused on the detailed description of their micromorphology, type, and shape, finding morphological differences between trichome types, which is an easy way to adequately compare them between even unrelated taxa. Our results using trichome types on the corolla are consistent with the original differentiation of sections Calothamnos and Mimosa. Flower micromorphology also provides characters to distinguish species, groups of species, and varieties within section Calothamnos and could be useful in a future taxonomic treatment of the section. We also found that some floral features, such as inflorescence color and stamen fusion, are associated with the characters used in this study.

Characterization of the complete mitochondrial genome of the scale worm, Eunoe nodosa (Phyllodocida; Polynoidae) from the Beaufort Sea

To increase the mitogenome data available for robust phylogeny, we sequenced the complete mitochondrial DNA of the scale worm Eunoe nodosa (Sars, 1861) in the family Polynoidae of the order Phyllodocida. The complete mitogenome has 15,366 bp and has 28.9% A, 13.2% C, 19.0% G, and 38.8% T. Using MITOS and tRNAscan-SE, we identified the 13 typical protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding region. Phylogenomic analysis based on 27 in-group taxa belonging to five families of the subclass Errantia show congruence with the published phylogenetic relationship within the Polynoidae, in which E. nodosa lies in the clade of shallow water species.

Molecular phylogeny and evolution of Calaphidinae (Hemiptera: Aphididae).

Calaphidinae is the second-largest subfamily in the family Aphididae. Despite their species diversity and some taxonomic controversy, no phylogenetic studies have been conducted on them thus far. Herein, we report the first molecular phylogeny of Calaphidinae and two related lineages, Phyllaphidinae and Saltusaphidinae, based on five genes (3418 bp) for 126 taxa. Maximum parsimony, maximum-likelihood and Bayesian inference phylogenetic analyses were performed on the multilocus dataset. Divergence time estimation, biogeographical reconstruction, ancestral host plant reconstruction and PhyloType analyses were performed to identify evolutionary trends in Calaphidinae. Our phylogenetic results lead to several conclusions: Phyllaphidinae is a sister group to Calaphidinae s.l.; Calaphidinae is paraphyletic with respect to the former "Saltusaphidinae"; the ingroup clade was subdivided into nine newly recognized lineages; and three subtribes of Calaphidinae (Monaphidina, Calaphdina and Panaphidina) and many genera were not recovered as monophyletic. A new classification is proposed with eight tribal divisions that reflect our phylogenetic results, including three new tribes (Pterocallidini trib.n., Pseudochromaphidini trib.n. and Shivaphidini trib.n.) and three new statuses (Saltusaphidini stat.n., Therioaphidini stat.n. and Myzocallidini stat.n.). The ancestral reconstruction results imply that the ingroup taxa's common ancestor originated in the Eastern Palaearctic and might have fed on Fagaceae in the Late Cretaceous. Later, multiple host shifts and an expanding geographical distribution led to the current species diversity of Calaphidinae. Our reconstructions suggest that species diversification cannot solely be explained by speciation via host shifts and that geographical isolation probably also played a key role. Our results provide new insight into the natural classification and history of the host plant associations and biogeography of Calaphidinae s.l.

Species and genera in Aleurodiscus sensu lato as viewed from the Southern Hemisphere

ABSTRACT Phylogenetic relationships of 12 species in Aleurodiscus sensu lato (Stereaceae, Russulales) described from the Patagonian forests of Chile and Argentina were investigated based on sequences of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and the D1–D2 domains of nuc 28S rDNA (28S). A new genus and a new species are presented, and 10 new combinations proposed. The genus Gloeosoma is shown to be phylogenetically well supported and morphologically circumscribed; it includes G. vitellinum (type species), G. mirabile, comb. nov., G. zealandicum, comb. nov., and Gloeosoma decorticans, sp. nov., which is newly described from Chile. The new genus Stereodiscus is proposed to accommodate a group of taxa characterized by an austral distribution and morphologically by smooth, thin-walled, amyloid basidiospores and a lack of gloeocystidia and acanthocystidia; three species develop Stereum-like basidiomata and two species present discoid ones. The new genus includes the species formerly known as Aleurodiscus antarcticus, A. limonisporus, A. parmuliformis, A. patagonicus, and A. triviale. Specimens of Stereodiscus parmuliformis (A. parmuliformis) from New Zealand (where it was originally described) and southern Chile are shown to be phylogenetically conspecific, which confirms its presence in Patagonia. Gloeosoma and Stereodiscus are shown to be distantly related to Aleurodiscus s. str. and other genera in Stereaceae. The new combinations Aleurocystidiellum bernicchiae, Aleurocystidiellum hallenbergii, and Acanthobasidium quilae are proposed based on morphology and phylogenetic analyses, and Aleurodiscus cerussatus is shown to be a cryptic species complex.

Opechona chloroscombri and Opechona corkumi n. sp. (Digenea: Lepocreadiidae) from the Northern Gulf of Mexico with Phylogenetic Analysis Based on 28S RDNA

This study investigated the identity of 2 lepocreadiid digenean species belonging in the genus Opechona Looss, 1907 that infect littoral fishes of the northern Gulf of Mexico. Opechona chloroscombriNahhas and Cable, 1964, a species previously known only from the Caribbean Sea and the Atlantic Ocean off Brazil, is reported herein from the Atlantic bumper, Chloroscombrus chrysurus (L.), in the northern Gulf of Mexico. A second species infects the gulf butterfish, Peprilus burti Fowler, and the American harvestfish, Peprilus paru (L.), and it is described as a new species that occurs in coastal waters of the north-central and northeastern Gulf of Mexico. Metacercariae infecting the mesoglea of pelagic jellyfishes (Bougainvillia carolinensis [McCady], Chrysaora quinquecirrha [Desor], and Stomolophus meleagris Agassiz) and pelagic comb jellies (Mnemiopsis leidyi Agassiz and Beroe ovata Bruguière) were collected that resemble the new species but require further study to identify. Newly generated sequence fragments (28S rDNA) from both species of Opechona plus 2 other lepocreadiids collected during the study were aligned with publicly available sequences from 18 other lepocreadiids, 6 species of Aephnidiogenidae Yamaguti, 1934, and 2 species of Gorgocephalidae Manter, 1966. The alignment was subjected to Bayesian inference analysis rooted using a gorgocephalid. The resulting tree estimated the positions of both Opechona spp. as being unresolved within a group of taxa that included all available species of Opechona plus available species from the morphologically similar genera ProdistomumLinton, 1910, Preptetos Pritchard, 1960, and Clavogalea Bray, 1985. Although relatively similar in morphology, the 2 studied species of Opechona were surprisingly not closely related. Opechona cablei (Stunkard, 1980) Bray and Gibson, 1990 is herein considered to be a junior synonym of Opechona pyriformis (Linton, 1900) Bray and Gibson, 1990.

Applying Biodiversity Metrics as Surrogates to a Habitat Conservation Plan

Unabated urbanization has led to environmental degradation and subsequent biodiversity loss across the globe. As an outcome of unmitigated land use, multi-jurisdictional agencies have developed land use plans that attempt to protect threatened or endangered species across selected areas by which some trade-offs between harm to species and additional conservation approaches are allowed among the partnering organizations. Typical conservation plans can be created to focus on single or multiple species, and although they may protect a species or groups of species, they may not account for biodiversity or its protection across the given area. We applied an approach that clustered deductive habitat models for terrestrial vertebrates into metrics that serve as surrogates for biodiversity and relate to ecosystem services. In order to evaluate this process, we collaborated with the partnering agencies who are creating a Multi-Species Habitat Conservation Plan in southern California and compared it to the entire Mojave Desert Ecoregion. We focused on total terrestrial vertebrate species richness and taxon groupings representing amphibians, birds, mammals, and reptiles, and two special status species using the Normalized Index of Biodiversity (NIB). The conservation planning area had a lower NIB and was less species rich than the Mojave Desert Ecoregion, but the Mojave River riparian corridor had a higher NIB and was more species-rich, and while taxon analysis varied across the geographies, this pattern generally held. Additionally, we analyzed desert tortoise (Gopherus agassizii) and desert kit fox (Vulpes macrotis arsipus) as umbrella species and determined that both species are associated with increased NIB and large numbers of species for the conservation area. Our process provided the ability to incorporate value-added surrogate information into a formal land use planning process and used a metric, NIB, which allowed comparison of the various planning areas and geographic units. Although this process has been applied to Apple Valley, CA, and other geographies within the U.S., the approach has practical application for other global biodiversity initiatives.

A Dirichlet Autoregressive Model for the Analysis of Microbiota Time-Series Data

Growing interest in understanding microbiota dynamics has motivated the development of different strategies to model microbiota time series data. However, all of them must tackle the fact that the available data are high-dimensional, posing strong statistical and computational challenges. In order to address this challenge, we propose a Dirichlet autoregressive model with time-varying parameters, which can be directly adapted to explain the effect of groups of taxa, thus reducing the number of parameters estimated by maximum likelihood. A strategy has been implemented which speeds up this estimation. The usefulness of the proposed model is illustrated by application to a case study.

Tree-aggregated predictive modeling of microbiome data

Modern high-throughput sequencing technologies provide low-cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data-driven and scalable tree-guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workflows to remove rare sequencing variants or group them by a fixed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we call trac (tree-aggregation of compositional data), learns data-adaptive taxon aggregation levels for predictive modeling, greatly reducing the need for user-defined aggregation in preprocessing while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large-scale regression problems in human gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbiome researchers gain insights into the structure and functioning of the underlying ecosystem of interest.

The Status of Flora and Fauna in the Nzoia River Drainage Basin in Western Kenya

The species richness of flora and fauna in the Nzoia River drainage basin is documented through a study of museum specimens, catalogues and databases. The catchment area and basin covers 2.2% (12900/580367 km2) of Kenya's total land area with an altitudinal range of 1140 to 4300 m and varied ecosystem and land uses. We recorded approximately 9.3% (3239/34677) of Kenya's current known species of vascular plants, invertebrates (insects and spiders), fish, amphibians, reptiles, birds and mammals. Bird species made up the highest proportion 58.3% (650/1114) of the national total followed by amphibians 37.3% (41/110), reptiles 45.0% (86/191), mammals 31.3% (122/390), vascular plants 17.9% (1251/7000), fish 6.7% (58/872) (32.2% (58/180) for freshwater fish only) and invertebrates (insects and spiders) 4.1% (1031/25000). Ninety-five species recorded in this area are endemic to Kenya and 42 globally threatened. The species recorded contribute to several ecosystem services including pest control, pollination, bio-indicators, medicine and cosmetics, building materials, ecotourism, research and education. Data available differed substantially across counties and taxon groups with gaps apparent in five counties (Bungoma, Busia, Elgeyo Marakwet, Siaya and Usain Gishu) and four taxa plants, invertebrates, fungi and bacteria where a dearth of information exists. To fill these gaps we recommend prioritisng future survey effort on taxa and counties with fewer than 10% of the total numbers of records.

Linking long-term changes of the zooplankton community to the environmental variability at the EPEA Station (Southwestern Atlantic Ocean)

A significant sea surface temperature increase has been reported for the Southwestern Atlantic Ocean between 20° S-50° S over the last decades. Zooplankton organisms are highly sensitive to temperature rise. They play a very important role in marine ecosystems by providing the main pathway of energy transfer from primary producers to consumers. Seasonal and interannual (2000-2017) variability of metazooplankton in relation to environmental changes, particularly temperature, were analyzed at the EPEA station (38° 28′ S-57° 41′ W). Copepods, appendicularians, cladocerans, chaetognaths, and lamellibranch larvae were identified and quantified. Temperature exhibited a positive interannual trend during the series, whereas the Simpson parameter showed a decreasing tendency and salinity remained almost constant. Adults, copepodites, and nauplii of small copepods belonging to Oithonidae (mostly Oithona nana) and Paracalanidae-Clausocalanidae families dominated the metazooplankton community during the study period. Three groups of taxa with different seasonal patterns of variability were clearly identified. Members of Oithonidae exhibited positive interannual trends, whereas lamellibranch larvae and Calanidae showed negative interannual trends. A direct influence of temperature anomaly on these changes is suggested as well as possible indirect effects of this anomaly upon zooplankton through different phytoplankton fractions. Under the current scenario of climate change, the maintenance of this time-series becomes crucial in order to evaluate the eventual transfer of the environmental variability to the local food webs through planktonic organisms.

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

PREMISEUniversal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost‐efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on‐target DNA molecules may fail to map to references, resulting in fewer on‐target reads for assembly, and reducing locus recovery.METHODSWe expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop‐in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user‐selected taxon groups, and to incorporate other transcriptome or protein‐coding gene data sets.RESULTSCompared to the default Angiosperms353 file, the mega353 file increased the percentage of on‐target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%.DISCUSSIONIncreasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson‐pellicle/NewTargets.

Deconstructing molecular phylogenetic relationship among cultivated and wild Brassica species

Brassica represents an agriculturally important and diverse group of oilseed crops with a long evolutionary history. Molecular markers played an important role in understanding origin and evolution of Brassica species. In the present research, both Single Nucleotide Polymorphisms (SNPs) and Simple Sequence Repeats (SSRs) developed from Brassica juncea L. Czern. were used to find out the phylogenetic relationship between different cultivated and wild Brassica species. A total of 88 SSR and 58 SNP markers were found to be functional across 38 genotypes belonging to ten different taxon groups. The polymorphic markers were able to group the genotypes into three different clusters and showed relatedness among different genomes based on genetic distances. The transferability of these markers serve the purpose of their quick use in cultivar identification, diversity and phylogenetic analysis in those orphan crops species where no or less genomic information is available.

Rhizomal Reclassification of Living Organisms.

Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

Assessment of the efficiency of river macrophytes to detect water-column nutrient levels and other environmental conditions in Irish rivers

Macrophytes are an essential biological element of freshwater aquatic ecosystems and are well known to reflect prevailing ecological conditions in rivers. Their use as bioindicators of nutrient status in river systems is widespread yet their reliability is hotly debated. The aim of this investigation was to assess whether macrophytes are reliable indicators of nutrient levels or better applied as indicators of other non-nutrient environmental conditions. The importance of two water-column nutrients; nitrates (N) and orthophosphates (P) were assessed in terms of their influence on macrophyte species richness and diversity in relation to other non-nutrient environmental factors using 395 river plots from Ireland. Then, in this context, the efficiency of macrophytes to detect nutrient levels was assessed by selecting two macrophyte-based water quality assessment tools; the Mean Trophic Rank (MTR) and the Predictions And Classification System for river macrophytes (LEAFPACS2). Finally, the ability of phytosociological communities within these rivers to reflect trophic levels was examined using the same two water quality assessment tools. It was shown that water-column nutrients N and P have a minor influence on macrophyte richness and no significant influence on macrophyte diversity and that MTR and LEAFPACS2 were only weakly correlated with N and P levels. It was concluded that macrophytes are sensitive to environmental changes but respond to a combination of ecological factors rather than N or P alone. Therefore, this study suggests that macrophytes are not the most efficient taxon group to apply when assessing trophic changes in isolation of other non-nutrient factors.

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms.

The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3–V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.

Desalination plants do not impact the diversity or abundance of zooplankton of the Israeli coast

In order to evaluate the impact of desalination facilities on the diversity and abundance of zooplankton, the abundance and structure of the zooplankton community were sampled along the Israeli Levantine shallow coast in the vicinity of desalination facilities. Samples were collected at two sites (Hadera and Ashqelon) during different seasons over a period of 15 months from November 2016 to January 2018. Tows were conducted above bottom depths of 2–28 m with both surface and deeper tows collected during the day and night. Results show a strong seasonality in taxonomic composition and differences in abundance in different taxa groups. There were, however, no differences between day and night, surface and deeper tows, and no impact of the brine plume. Abundance estimates correspond well with other recent studies of zooplankton abundance and community composition in other regions of the Eastern Levantine. This study represents the first quantitative survey of zooplankton conducted along Israeli Levantine shallow coast.

Phylogenetic analysis places Spicaticribra within Cyclotella

A strong consensus has emerged that taxonomic classifications should be based on an underlying phylogenetic hypothesis. According to this view, named groups should be monophyletic, ensuring that a name uniquely matches the evolutionary history and biological attributes of a group of taxa. As originally conceived, the diatom genus Cyclotella is a large and morphologically diverse assemblage of taxa that we now know consists of several distantly related lineages. Considerable progress has been made in placing these lineages into different monophyletic genera. The genus Spicaticribra was originally described as monotypic and has features that suggest a close relationship to Cyclotella, but it has also retained some ancestral features that appear to differentiate it from Cyclotella. We sequenced two nuclear and two plastid genes to resolve the phylogenetic position of Spicaticribra and show that it is embedded within a clade that includes the type species of Cyclotella and, further, that maintaining Spicaticribra renders Cyclotella non-monophyletic. We transfer Spicaticribra species into Cyclotella, resolve related nomenclatural issues, and caution against using ancestral characters and character states for taxonomic classification.