Taxonomic Terms Research Articles

Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.

When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and interpret. Therefore, it is useful to have an automated way of collapsing large phylogenetic trees according to a taxonomic term decided by the user (family, class, or order, for instance), in order to highlight the minimal set of sequences that should be used to recapitulate the full history of the gene/gene family being studied at that taxonomic level, that can be refined using additional software. Here we present the Phylogenetic Tree Collapser (PTC) program (https://github.com/pegi3s/phylogenetic-tree-collapser), a flexible tool for automated tree collapsing using taxonomic information, that can be easily used by researchers without a background in informatics, since it only requires the installation of Docker, Podman or Singularity. The utility of PTC is demonstrated by addressing the evolution of the ascorbic acid synthesis pathway in insects. A Docker image is available at Docker Hub (https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser) with PTC installed and ready-to-run.

Beyond a Lush Life: Representation and Performativity at America's [Only] Queer Jazz Festival

Beyond a Lush Life: Representation and Performativity at America's [Only] Queer Jazz Festival

Complete chloroplast genome sequences of Phlomis fruticosa and Phlomoides strigosa and comparative analysis of the genus Phlomis sensu lato (Lamiaceae).

The taxonomic terms "Phlomis" and "Phlomoides" had been used to describe two sections within the genus Phlomis belonging to the Lamiaceae family. Recently, phylogenetic analyses using molecular markers showed that Phlomis and Phlomoides formed two monophyletic clades, and thus they are generally accepted as separate genera. In this study, we assembled the complete chloroplast genome of Phlomis fruticosa, which is the first reported chloroplast genome belonging to Phlomis genus, as well as the complete chloroplast genome of Phlomoides strigosa belonging to Phlomoides genus. The results showed that the length of chloroplast genome was 151,639 bp (Phlomis fruticosa) and 152,432 bp (Phlomoides strigosa), with conserved large single copy regions, small single copy regions, and inverted repeat regions. 121 genes in Phlomis fruticosa and 120 genes in Phlomoides strigosa were annotated. The chloroplast genomes of Phlomis fruticosa, Phlomoides strigosa, and three reported Phlomoides species, as well as those of 51 species from the Lamiaceae family, which covered 12 subfamilies, were subjected to phylogenetic analyses. The Phlomis and Phlomoides species were split into two groups, which were well supported by both maximum likelihood and Bayesian inference tree analyses. Our study provided further evidence to recognize Phlomis and Phlomoides as independent genera.

Meta-analysis of community composition patterns of halophyte and xerophyte rhizosphere associated bacteria

In plant roots, prokaryote-plant interactions have been extensively studied worldwide, demonstrating their importance for plant survival and growth, through the exploitation of microbial metabolic processes, such as nitrogen fixation and Extracellular Polymeric Substances (EPS). Climatic and edaphological forces structure the soil bacterial pool from which plants acquire a large share of their rhizosphere microbiome. As halophyte and xerophyte plants are subject to extreme environmental conditions, prokaryote-root interactions could be pivotal for plant establishment and survival, even more under the imminent scenario of climate change and increased water scarcity; yet, we have a limited understanding on large-scale geographical patterns of root-microbe communities in arid environments. Here, we used a meta-analysis approach to compare prokaryotic community composition associated to the rhizospheres of halophytes and xerophytes from ‘arid’ environments, representing 13 angiosperm plant species from five countries (Mexico, Namibia, Pakistan, Tunisia and USA), using a Qiime2 pipeline. In taxonomic terms, rhizosphere prokaryotic communities are diverse and include cosmopolitan classes like Alphaproteobacteria, Bacilli, and Gammaproteobacteria, as well as some site-specific groups like haline-thriving Haloarchaea, and PAUC43f which was found only in Pakistan samples. Alpha (ACE, Faith PD y Shannon) and beta (Jaccard) diversity estimates suggested that the main factors modeling microbial communities are host plant family, plant ecological strategy and the abiotic environment (bioclimatic variables, soil pH and total exchangeable bases). Furthermore, life history strategy (deciduous vs. perennial) is not significant for these communities' structure. Thus, this work presents an early sketch on the macro-geographical patterns driving rhizosphere microbiomes in arid environments.

The greening ashore.

More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.

NeoBat Interactions: A data set of bat-plant interactions in the Neotropics.

Data papers and open databases have revolutionized contemporary science, as they provide the long-needed incentive to collaborate in large international teams and make natural history information widely available. Nevertheless, most data papers have focused on species occurrence or abundance, whereas interactions have received much less attention. To help fill this gap, we have compiled a georeferenced data set of interactions between 93 bat species of the family Phyllostomidae (Chiroptera) and 501 plant species of 68 families. Data came from 169 studies published between 1957 and 2007 covering the entire Neotropical Region, with most records from Brazil (34.5% of all study sites), Costa Rica (16%), and Mexico (14%). Our data set includes 2571 records of frugivory (75.1% of all records) and nectarivory (24.9%). The best represented bat genera are Artibeus (28% of all records), Carollia (24%), Sturnira (10.1%), and Glossophaga (8.8%). Carollia perspicillata (187), Artibeus lituratus (125), Artibeus jamaicensis (94), Glossophaga soricina (86), and Artibeus planirostris (74) were the bat species with the broadest diets recorded based on the number of plant species. Among the plants, the best represented families were Moraceae (17%), Piperaceae (15.4%), Urticaceae (9.2%), and Solanaceae (9%). Plants of the genera Cecropia (46), Ficus (42), Piper (40), Solanum (31), and Vismia (27) exhibited the largest number of interactions. These data are stored as arrays (records, sites, and studies) organized by logical keys and rich metadata, which helped to compile the information on different ecological and geographic scales, according to how they should be used. Our data set on bat-plant interactions is by far the most extensive, both in geographic and taxonomic terms, and includes abiotic information of study sites, as well as ecological information of plants and bats. It has already facilitated several studies and we hope it will stimulate novel analyses and syntheses, in addition to pointing out important gaps in knowledge. Data are provided under the Creative Commons Attribution 4.0 International License. Please cite this paper when the data are used in any kind of publication related to research, outreach, and teaching activities.

PHYLOGENETIC PROCESSES IN EUROPEAN AND ASIAN PIG POPULATIONS

As a result of evolution, a gradual change in the hereditary structure of a species, not only the number of genes changes, but also their properties, frequency, and direction of variability. Changes in gene frequencies occurring over a relatively small period of time belong to microevolution. The breeding process in pig breeding is the microevolutionary processes originating from the ancestral forms of Sus scrofa to the modern specialized breeds of pigs. Genetic monitoring of the genetic systems of blood groups makes it possible to assess the genetic structure and processes occurring in populations. The microevolutionary process of transformation of wild ancestral forms over the last 10-12 thousand years from transitional forms of local aboriginal to factory breeds has occurred with significant genetic and phenotypic transformations in animal populations. In this connection, it is important to clarify the correct understanding of the terms 'population' and 'breed'. Naturally, any breed is a population, but not any population is not a breed, especially since both population and population as taxonomic terms have different interpretations. In the first place, a distinction must be made between wild populations, in which microevolution takes place only by means of natural selection, and breed populations, in the development of which artificial selection was involved as a fundamental factor in microevolution. Depending on the level of methods and forms of selection, we have to distinguish local indigenous populations (e.g., Kakhetian and Mangali breeds) and basic factory breeds (Large White, Berkshire, Landrace, Duroc, etc.), which have been created for decades and centuries. The concept of a breed is closely linked to the size of the reproductive population and the range of distribution. According to FAO, in 2006 there were some 730 breeds and lines of pigs worldwide, most of which are bred in China and Europe, and 270 of which are regarded as rare breeds. At the same time, 58 breeds (25 regional and 33 international) are registered as common, i.e. occurring in more than one country. Five international breeds are now widely distributed: Large White (117 countries), Duroc (93 countries), Landrace (91 countries), Hampshire (54 countries) and Petren (35 countries).

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions

Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.

Importance of the morphological plasticity of Cervus elaphus in the biochronology of the Middle and Late Pleistocene of the Italian peninsula

The species Cervus elaphus is characterised by its significant and very swift ability to adapt to the broad woodland-related range of environments in the northern hemisphere, as can be seen by the large number of distinct populations and living subspecies. From studies on the phenotypic plasticity and adaptative capability of living populations of red deer, we can hypothesise that environmental conditions influenced the spread and the evolution of the species, especially in changing landscapes like those of the Italian peninsula during the Middle and Late Pleistocene. In fact, Cervus elaphus occurs on the Italian peninsula from the Middle Pleistocene, a period characterised by a particularly wide variety of environments determined by changeable palaeoclimatic and palaeogeographical conditions that are in all cases more significant in the late Middle Pleistocene and in the Late Pleistocene. If we observe the various fossil subspecies and apply the principle that present features like phenotypic plasticity are important keys to understanding the past, we must reconsider the Pleistocene red deer in evolutionary and taxonomic terms. This reappraisal also provides new data on the biochronological importance of the various red deer subspecies widespread in Italy during the Middle and Late Pleistocene.

Revival of Philozoon Geddes for host-specialized dinoflagellates, ‘zooxanthellae’, in animals from coastal temperate zones of northern and southern hemispheres

ABSTRACT The dinoflagellate family Symbiodiniaceae comprises numerous genera and species with large differences in diversity, ecology and geographic distribution. An evolutionarily divergent lineage common in temperate symbiotic cnidarians and designated in the literature by several informal names including ‘temperate–A’, AI, Phylotype A´ (A-prime) and ‘Mediterranean A’, is here assigned to the genus Philozoon. This genus was proposed by Geddes (1882) in one of the earliest papers that recognized ‘yellow cells’ as distinct biological entities separate from their animal and protist hosts. Using phylogenetic data from nuclear (rDNA), chloroplast (cp23S) and mitochondrial genes (cob and cox1), as well as morphology (cell size), ecological traits (host affinity) and geographic distributions, we emend the genus Philozoon Geddes and two of its species, P. medusarum and P. actiniarum, and describe six new species. Each symbiont species exhibits high host fidelity for particular species of sea anemone, soft coral, stony coral and a rhizostome jellyfish. Philozoon is most closely related to Symbiodinium (formerly Clade A), but, unlike its tropical counterpart, occurs in hosts in shallow temperate marine habitats in northern and southern hemispheres including the Mediterranean Sea, north-eastern Atlantic Ocean, eastern Australia, New Zealand and Chile. The existence of a species-diverse lineage adapted to cnidarian hosts living in high latitude habitats with inherently wide fluctuations in temperature calls further attention to the ecological and biogeographic reach of the Symbiodiniaceae. HIGHLIGHTS A dinoflagellate genus symbiotic with temperate invertebrates is characterized and named using a discarded taxonomic term revived from the golden age of Natural Historians. The work highlights how animal–algal mutualisms are evolved to thrive under a broad range of environmental conditions.

El holobionte/hologenoma como nivel de selección: Una aproximación a la evolución de los consorcios de múltiples especies

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs (which entity acts as an interactor), and the question of the level at which reproduction occurs (which entity acts as a replicator or reproducer). In recent years, biologists and philosophers have discussed a new aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome (holobionts/hologenomes) may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms.

How much of morphological variability in pollen from genus Rubus L. might be explained by climate variability

The aim of this study was to assess the influence of 19 climatic factors during flowering periods and taxonomic proximity on the morphological features of the pollen from the genus Rubus L., which comprises numerous species, often with small ranges of natural occurrence.. It was hypothesized that the pollen morphology would be driven more by the effects of taxonomic proximity than by climatic variables, due to the conservatism of the pollen features, connected with a shared evolutionary history. The analyses revealed that climatic variability can explain an additional 2.5% to 14.0% of pollen morphology. The majority of the modelled pollen features were not correlated with the bioclimatic factors studied, except for the P/E ratio, which was positively correlated, and E, which was negatively correlated with PC3. However, most of the variability was explained by random effects connected with the taxonomic affiliation of the studied species to the genus Rubus L., which is very difficult in taxonomic terms. The study, therefore, showed how much additional interspecific variability in pollen morphology might be explained by the climatic variability of the species distributions.

Correlation between physical and chemical parameters of water and biotic indices: The case study the White Drin River basin, Kosovo

The major impacts on aquatic ecosystems worldwide caused by land use lead to changes in their natural conditions and limitation of water use for various needs. This paper presents the results of the study of the physical and chemical parame-ters and macroinvertebrate assemblage in the White Drin River (or: the Drim River, Alb. the Drini i Bardhë River) basin, the largest in Kosovo. Macroinvertebrate sampled at 11 sites in the river resulted in 5946 collected benthic organisms, which in taxonomic terms belong to 12 orders and 51 families. Of the total number of organisms, 72.28% were Insects, 25.39% Amphipoda crustaceans and 2.33% were Annelide worms and Mollusk. The used biotic indices Biological Moni-toring Working Party (BMWP), Ephemeroptera, Plecoptera, and Trichoptera (EPT), average score per taxon (ASPT) and Stroud Water Research Center (SWRC) classify water quality in excellent category in the sampling site S1 near the source of the White Drin River, whereas in other sampling sites, as a result of pollution, water quality varies on category II–IV. The Pearson's correlation analyses shown that the physical and chemical parameters affect the water quality and the com-position of macroinvertebrates. Our results show that the parameters that adversely affect the BMWP, EPT and ASPT bio-tic indices as well as the Shannon–Wiener, Mergalef and Menhinik diversity indices are: pH, electrical conductivity (EC), total suspended solids (TSS), nitrates (NO3–) and chlorides (Cl–). We can conclude that the anthropogenic impact on White Drin basin affects the physical, chemical and biological parameters of the water therefore these parameters should be con-stantly included in Biomonitoring and Management plans for water resources in Kosovo.

Regional Development in Poland in Taxonomic Terms

Regional development is a complex economic category and a commonly used term today, yet it is vaguely defined and, therefore, interpreted implicitly and understood intuitively. From a statistical point of view, this concept, on account of its imprecision and ambiguity, is a kind of multidimensional characteristic which may be measured, though not conclusively. Due to the lack of a universal set of diagnostic variables adopted in taxonomic analyses, the quantitative approach to the examined research area, which is in most cases presented descriptively, poses the main problem. The objectives of the article are to rank the provinces of Poland in terms of regional development in the years 2006–2018 and to assess the similarity of results over time. The research study is based on linear ordering methods within the scope of multidimensional statistical analysis. The results of the conducted analyses allowed us to rank the provinces of Poland in terms of regional development in the years 2006–2018 and to assess the similarity of the results over time. The results of the analysis indicate a clear stabilization of high ranked positions during the examined period, last places are generally taken by the same regions. This situation may indicate an increase or at least strengthening of the disproportions between the most and least developed regions in Poland. Theoretical considerations presented in the article as well as the empirical results of our own research may provoke more detailed discussion on the subject.

Farming system shapes traits and composition of spider assemblages in Mediterranean cherry orchards.

Habitat properties, including crop type, farming system, management practices, or topographic features such as the hillside aspect, may act as environmental filters that select organisms sharing traits compatible with those conditions. The more environmentally-friendly management practices implemented in organic farming seem to benefit a range of taxa, but the extent of those benefits is not well understood. In cherry orchards of the Jerte Valley (Extremadura, western Spain), we explored the response of spider assemblages to the farming system (organic and conventional) and the hillside aspect (sunny or shady) from a taxonomical, behavioral, and morphological perspective. Spiders from both the canopy and soil surface were collected and identified to family. According to their foraging strategy, spiders were sorted in guilds and, for a selected family in each guild, body size was measured on each captured individual. Spider traits and composition were determined by local factors derived from farming system, and by climate conditions associated to the hillside aspect. In taxonomical terms, spiders benefit from organic farming and by the shady aspect. However, from a behavioral perspective, spiders with different foraging strategies exhibit strong variations in their response to the evaluated factors. From a morphological perspective, body size within guilds is differently conditioned by management practices that constitute conditioning disturbance events for each guild, resulting in selecting small individuals. The observed differences in taxonomical, behavioral, and morphological responses of spider communities to habitat properties highlight the importance of examining their assemblages from different perspectives when assessing how they respond to changes in management practices and topographic features.

Current phylogeny of Rhodospirillaceae: A multi-approach study

Rhodospirillaceae represents a major family of the class alphaproteobacteria that includes an increasing number of functionally diverse taxa. The aim of this work is to evaluate the present phylogenetic diversity of the Rhodospirillaceae, which includes several metagenome-assembled genomes of uncultivated bacteria, as well as cultivated bacteria that were previously classified in different families. Various methodological approaches have been followed to discern the phylogenetic diversity of the taxa associated with the Rhodospirillaceae, which are grouped in three major sub-divisions and several other taxonomic entities that are currently confined to the genus rank. These genera include Tistrella, Elstera, Dongia and Ferrovibrio among cultivated organisms and alphaproteobacteria bacterium 41–28 among uncultivated bacteria. Overall, this study adds at least 11 genera and over 40 species to the current set of taxa belonging to the Rhodospirillaceae, a taxonomic term that clearly requires amendment. We propose to re-classify all taxa associated with the Rhodospirillaceae family under the new order, Diaforabacterales ord. nov. (from the Greek word for diversity, διάφορα). This study also uncovers the likely root of Rhodospirillaceae among recently reported metagenome-assembled genomes of uncultivated marine and groundwater bacteria.

Морфологічні особливості насінин деяких видів роду Epipactis Zinn. (Orchidaceae Juss.) флори України

The investigation of macro- and micromorphological peculiarities of seeds of four species of genus Epipactis (Orchidaceae) of Ukrainian flora were carried out. The genus Epipactis is difficult in the in in taxonomic terms and for its representatives are characterized by polymorphism of morphological features of vegetative and generative organs of plants and ability of species to hybridize. The aim of the research was to perform a comparative morphological study of seeds of E. helleborine, E. albensis, E. palustris, E. purpurata and to determine carpological features that could more accurately identify species at the stage of fruiting. A high degree of variation in the shape of the seeds in different populations within the species and overlap of most quantitative carpological characteristics of studied species are noted. There were no significant differences in micromorphological features of the structure of the testa at species or population level. The reticulate surface of the testa is characteristic of all species, the cells of testa are mostly elongated, penta-hexagonal, individual cells almost isodiametric-pentagonal. From the micropillary to the chalasal end, a noticeable change in the shape and size of the seed coat cells is not observed. There are no intercellular spaces, the anticlinal walls of adjacent cells are intergrown and the boundaries between them become invisible. The outer periclinal walls have a single, mainly longitudinal thin ribbed thickenings. Anticlinal cell walls are thick, dense, smooth. The longitudinal Anticlinal walls are almost straight, transverse - straight or sometimes curved in some cells. Epicuticular deposits on the periclinal walls are absent. It is concluded that the use of macro and micromorphological characteristics of seeds of these species for clearer diagnosis at the stage of fruiting is low informative.

An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content.

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for “food and nutrition” (n = 37), “disease and specific population” (n = 100), “data description” (n = 21), “research description” (n = 35), and “supplementary (meta) data description” (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology.

Phylogeny of the orb-weaving spider family Araneidae (Araneae: Araneoidea).

We present a new phylogeny of the spider family Araneidae based on five genes (28S, 18S, COI, H3 and 16S) for 158 taxa, identified and mainly sequenced by us. This includes 25 outgroups and 133 araneid ingroups representing the subfamilies Zygiellinae Simon, 1929, Nephilinae Simon, 1894, and the typical araneids, here informally named the "ARA Clade". The araneid genera analysed here include roughly 90% of all currently named araneid species. The ARA Clade is the primary focus of this analysis. In taxonomic terms, outgroups comprise 22 genera and 11 families, and the ingroup comprises three Zygiellinae and four Nephilinae genera, and 85 ARA Clade genera (ten new). Within the ARA Clade, we recognize ten informal groups that contain at least three genera each and are supported under Bayesian posterior probabilities (≥0.95): "Caerostrines" (Caerostris, Gnolus and Testudinaria), "Micrathenines" (Acacesia, Micrathena, Ocrepeira, Scoloderus and Verrucosa), "Eriophorines" (Acanthepeira, Alpaida, Eriophora, Parawixia and Wagneriana), "Backobourkiines" (Acroaspis, Backobourkia, Carepalxis, Novakiella, Parawixia, Plebs, Singa and three new genera), "Argiopines" (Arachnura, Acusilas, Argiope, Cyrtophora, Gea, Lariniaria and Mecynogea), "Cyrtarachnines" (Aranoethra, Cyrtarachne, Paraplectana, Pasilobus and Poecilopachys), "Mastophorines" (Celaenia, Exechocentrus and Mastophora,), "Nuctenines" (Larinia, Larinioides and Nuctenea), "Zealaraneines" (Colaranea, Cryptaranea, Paralarinia, Zealaranea and two new genera) and "Gasteracanthines" (Augusta, Acrosomoides, Austracantha, Gasteracantha, Isoxya, Macracantha, Madacantha, Parmatergus and Thelacantha). Few of these groups are currently corroborated by morphology, behaviour, natural history or biogeography. We also include the large genus Araneus, along with Aculepeira, Agalenatea, Anepsion, Araniella, Cercidia, Chorizopes, Cyclosa, Dolophones, Eriovixia, Eustala, Gibbaranea, Hingstepeira, Hypognatha, Kaira, Larinia, Mangora, Metazygia, Metepeira, Neoscona, Paraplectanoides, Perilla, Poltys, Pycnacantha, Spilasma and Telaprocera, but the placement of these genera was generally ambiguous, except for Paraplectanoides, which is strongly supported as sister to traditional Nephilinae. Araneus, Argiope, Eriophora and Larinia are polyphyletic, Araneus implying nine new taxa of genus rank, and Eriophora and Larinia two each. In Araneus and Eriophora, polyphyly was usually due to north temperate generic concepts being used as dumping grounds for species from southern hemisphere regions, e.g. South-East Asia, Australia or New Zealand. Although Araneidae is one of the better studied spider families, too little natural history and/or morphological data are available across these terminals to draw any strong evolutionary conclusions. However, the classical orb web is reconstructed as plesiomorphic for Araneidae, with a single loss in "cyrtarachnines"-"mastophorines". Web decorations (collectively known as stabilimenta) evolved perhaps five times. Sexual dimorphism generally results from female body size increase with few exceptions; dimorphic taxa are not monophyletic and revert to monomorphism in a few cases.

Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics

Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms’ diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. With de novo transcriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set of a priori parasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g., Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs’ chemical defenses by colonizing tissues with fewer alkaloids than the frog’s skin, where most toxins are stored.