Higher-level Taxa Research Articles

Morphological disparity and structural performance of the dromaeosaurid skull informs ecology and evolutionary history

Non-avialan theropod dinosaurs had diverse ecologies and varied skull morphologies. Previous studies of theropod cranial morphology mostly focused on higher-level taxa or characteristics associated with herbivory. To better understand morphological disparity and function within carnivorous theropod families, here we focus on the Dromaeosauridae, ‘raptors’ traditionally seen as agile carnivorous hunters.We applied 2D geometric morphometrics to quantify skull shape, performed mechanical advantage analysis to assess the efficiency of bite force transfer, and performed finite element analysis to examine strain distribution in the skull during biting. We find that dromaeosaurid skull morphology was less disparate than most non-avialan theropod groups. Their skulls show a continuum of form between those that are tall and short and those that are flat and long. We hypothesise that this narrower morphological disparity indicates developmental constraint on skull shape, as observed in some mammalian families. Mechanical advantage indicates that Dromaeosaurus albertensis and Deinonychus antirrhopus were adapted for relatively high bite forces, while Halszkaraptor escuilliei was adapted for high bite speed, and other dromaeosaurids for intermediate bite forces and speeds. Finite element analysis indicates regions of high strain are consistent within dromaeosaurid families but differ between them. Average strain levels do not follow any phylogenetic pattern, possibly due to ecological convergence between distantly-related taxa.Combining our new morphofunctional data with a re-evaluation of previous evidence, we find piscivorous reconstructions of Halszkaraptor escuilliei to be unlikely, and instead suggest an invertivorous diet and possible adaptations for feeding in murky water or other low-visibility conditions. We support Deinonychus antirrhopus as being adapted for taking large vertebrate prey, but we find that its skull is relatively less resistant to bite forces than other dromaeosaurids. Given the recovery of high bite force resistance for Velociraptor mongoliensis, which is believed to have regularly engaged in scavenging behaviour, we suggest that higher bite force resistance in a dromaeosaurid taxon may reflect a greater reliance on scavenging rather than fresh kills.Comparisons to the troodontid Gobivenator mongoliensis suggest that a gracile rostrum like that of Velociraptor mongoliensis is ancestral to their closest common ancestor (Deinonychosauria) and the robust rostra of Dromaeosaurus albertensis and Deinonychus antirrhopus are a derived condition. Gobivenator mongoliensis also displays a higher jaw mechanical advantage and lower resistance to bite force than the examined dromaeosaurids, but given the hypothesised ecological divergence of troodontids from dromaeosaurids it is unclear which group, if either, represents the ancestral condition. Future work extending sampling to troodontids would therefore be invaluable and provide much needed context to the origin of skull form and function in early birds. This study illustrates how skull shape and functional metrics can discern non-avialan theropod ecology at lower taxonomic levels and identify variants of carnivorous feeding.

Dissimilarity among Species and Higher Taxa of Amphibians in a Hotspot of Biodiversity and Endemism in the Neotropics

The Mexican Republic ranks fifth in the world in terms of amphibian diversity, and within Mexico, the state of Oaxaca has the greatest amphibian richness and endemism. Unfortunately, various factors, such as land use change and global warming, have caused a global crisis that threatens the conservation of this class. In the face of these threats, an analysis of beta diversity provides information that can be applied to conservation strategies, since its study reveals the spatial scaling of diversity loss and clarifies the mechanisms of regional diversity maintenance. In this work, we analyzed the beta diversity at the species and higher taxa level (order, family, subfamily, genus and species) for the amphibians of Oaxaca and their replacement components and the differences in richness for anurans and caudates separately between physiographic subprovinces. Very high beta diversity was recorded, with higher diversity occurring among caudates (0.92) than among anurans (0.84). Species replacement was the component that most contributed to this result, and the subprovinces with substantial environmental differences had the most dissimilar amphibian communities. The results of this study show the need to implement conservation strategies in subprovinces with high amphibian richness and endemism levels, following the example of Sierra Madre de Oaxaca (SMO), where local communities have developed conservation actions in most of the territory.

A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems

Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.

Holocarpic oomycete parasites of red algae are not Olpidiopsis, but neither are they all Pontisma or Sirolpidium (Oomycota)

Oomycetes are ubiquitous heterotrophs of considerable economic and ecological importance. Lately their diversity in marine environments has been shown to be greatly underappreciated and many lineages of intracellular holocarpic parasites, infecting micro- and macro-algae, remain to be fully described taxonomically. Among them, pathogens of marine red algae have been studied extensively as they infect important seaweed crops. Throughout the 20th century, most intracellular, holocarpic biotrophic oomycetes that infect red algae have been assigned to the genus Olpidiopsis Cornu. However, 18S rRNA sequencing of Olpidiopsis saprolegniae, the species considered the generitype for Olpidiopsis, suggests that this genus is not closely related to the marine pathogens and that the latter requires a nomenclatural update. Here, we compile and reanalyze all recently published 18S rRNA sequence data for marine holocarpic oomycetes, with a particular focus on holocarpic pathogens of red algae. Their taxonomy has been revised twice over the past four years, with suggestions to transfer them first into the genus Pontisma and then Sirolpidium, and into a monogeneric order, Pontismatales. We show however, that previously published topologies and the proposed taxa Pontisma, Sirolpidium, and Pontismatales are unsupported. We highlight that name changes that are unfounded and premature create confusion in interested parties, especially concerning pathogens of marine red algae that infect important seaweed crops. We thus propose that the names of these holocarpic biotrophic parasites of red algae are retained temporarily, until a supported topology is produced with more genetic markers to enable the circumscription of species and higher-level taxa.

Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes.

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.

Diversity of planktonic pro- and microeukaryotes in water bodies of the Volga-Don basin during the period of cyanobacterial bloom according to metabarcoding data

The first data on the phylogenetic diversity of planktonic communities of pro- and microeukaryotes in different types of water bodies of the Volga-Don basin during the period of cyanobacterial bloom are presented. Aphanizomenon flos-aquae/Dolichospermum flos-aquae blooms were found mainly in the Kuibyshev Reservoir; Planktothrix agardhii bloom was observed in floodplain lakes of the majority of investigated rivers. Bloom of Raphidiopsis raciborskii was found in a lake on the Volga River terrace, and in a pond in the floodplain of the Samara River Anabaenopsis dominated anong Cyanobacteria. Among heterotrophic prokaryotes, Proteobacteria, Bacteroidota, Verrucomicrobiota, Planctomycetota and Actinobacteriota predominate in the number of sequences, and among protists - Ciliophora, Gyrista (mainly Chrysophyceae), Cryptista and Myzozoa. During the period of cyanobacterial bloom, the contributions of Proteobacteria (especially, Burkholderiales and Pseudomonadales) and Actinobacteriota slightly decrease, while Myzozoa, on the contrary, increase. Monodominant blooms of various species of cyanobacteria significantly change the composition and structure of microbial communities, both at the OTUs and higher taxa levels. The plankton of the pond with Anabaenopsis bloom is most peculiar. Communities with blooms of P. agardhii, R. raciborskii and A. flos-aquae/D. flos-aquae are more similar to each other.

Community structure of abyssal macrobenthos of the South and equatorial Atlantic Ocean - Identifying patterns and environmental controls

The DIVA (Latitudinal Gradients of Deep-sea BiodDIVersity in the Atlantic) expeditions studied benthic biodiversity of the abyssal Equatorial and South Atlantic as part of the Census of the Diversity of Abyssal Marine Life (CeDAMar), the abyssal component of the ten-year programme Census of Marine Life (2000–2010). Three expeditions were carried out from RV Meteor between 2000 and 2009. Samples were taken along a latitudinal gradient spanning the Cape, Angola, and Guinea basins in the SE Atlantic and the Argentine and Brazilian basins in the SW Atlantic. The objectives of this study were to analyse patterns of epi- and suprabenthic macrofaunal density and composition at higher taxon level from epibenthic sledge (EBS) taken during the DIVA sampling campaigns and how they relate to differences in environmental conditions. In particular, the different oceanic basins are characterized by variation in surface primary productivity, sedimentary properties, and depth. We expected this difference to be reflected in the structure of the abyssal benthic communities. Consistent with this hypothesis, we found significant differences in macrofauna density between different deep-sea basins, mainly related to food availability. However, only subtle differences in community composition were observed. We found that stations in close proximity to one another showed great variability in both macrofaunal density and composition. We conclude that smaller spatial scale sampling should be paired with higher taxonomic resolution analyses of macrofaunal samples to better understand the factors contributing to variations of macrobenthic communities in the deep sea.

Host-microbiome interactions in apical periodontitis: The endodontic microbiome in relation to circulatory immunologic markers.

To explore microbial differences in the endodontic infection of teeth with primary or secondary apical periodontitis (AP), with or without symptomatology. Additionally, to investigate if these differences are depicted in immunologic markers in blood. Twenty-nine teeth with primary or secondary AP were extracted and cryo-pulverized. Blood was drawn from the subjects at three different time-points before and three time-points after the extraction in a time period of four months. The V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq. The microbial profiles were ordinated using principal component analysis and tested for differences between groups with permutational multivariate analysis of variance using the Bray-Curtis distance. If significantly different, the microbial profiles were further analysed using the LDA effect size (LEfSe) biomarker discovery tool. A broad panel of inflammatory mediators in blood was examined longitudinally in all subjects during the six visits with mixed models. The Spearman correlation between these mediators and the zOTUs was calculated, and significant correlations (p < .05) were used as input for significant analysis of microarrays (SAM) using MeV. After subsampling, the 467 zOTUs were classified into 9 phyla and 99 genera or higher level taxa. The predominant genus in the entire sample set was Fusobacterium with a relative abundance of 12.3%, followed by Prevotella (9.9%), Actinomyces (7.7%) and Streptococcus (6.7%). The microbiomes of the endodontic infections were significantly associated with endodontic status (primary/secondary infection; p=.015) as well as with the presence or absence of pain (p=.011). There was also a difference in the concentration of inflammatory mediators, namely, C-reactive protein, Interleukin (IL)-8, IL-10, IL-12p70, RANKL and TNF-α, depending on the existence of pain. In addition, the presence of specific bacteria (zOTUs) was correlated, positively or negatively, with the expression of several circulating inflammatory markers. The microbial profiles and the concentration-time relationship of systemic inflammatory mediators of primary endodontic infection differed from those of secondary, and of symptomatic from those of asymptomatic cases. The fingerprint of associations between the immunological and microbiological profiles differed between asymptomatic and symptomatic patients.

Incisor enamel microstructure of West Indian caviomorph hystricognathous rodents (Octodontoidea and Chinchilloidea)

Analysis of the incisor enamel microstructure of extinct and extant West Indian caviomorph rodents emphasizes a clear microstructural distinction between the Echimyidae (Capromyinae and Heteropsomyinae) among Octodontoidea and the “Heptaxodontidae”, whose phylogenetic affinities are debated. All capromyines and heteropsomyines have a pattern of enamel characterized by a rectangular crystallite arrangement, which is biomechanically strongest in limiting crack propagation most efficiently (subtype [Sbt.] 3 of multiserial Hunter-Schreger bands [HSBs]). This enamel condition is exclusive to all mainland octodontoids. In stark contrast, “heptaxodontids” sampled here exhibit much less derived enamel subtypes of multiserial HSBs, with parallel to acute angular crystallite arrangement (Sbt. 1 [Clidomys], Sbt. 1–2 [Elasmodontomys], and low acute Sbt. 2 [Amblyrhiza]), less well adapted for prevention of crack propagation. The incisor enamel microstructure of Amblyrhiza and Clidomys is consistent with a chinchilloid assignment, as reflected by the anatomy of their auditory region and their unusual dental pattern. For Elasmodontomys, the primitive condition of its incisor enamel is difficult to reconcile with its highly nested phylogenetic position within the Octodontoidea clade (among the Capromyinae), as recently inferred from aDNA analyses. The different enamel patterns among extinct and extant West Indian caviomorphs indicate distinct high-level taxonomic groups, but restricted to the Octochinchilloi (Octodontoidea and Chinchilloidea) among Caviomorpha. The great diversity of caviomorphs on the Caribbean islands resulted from intra-archipelago diversification through time, but their high-level phylogenetic diversity can only be explained by distinct sources, implying de facto multiple (potentially time-staggered) natural colonizations of the West Indies. The chinchilloid-compatible enamel and dental pattern characterizing Borikenomys from lower Oligocene deposits in Puerto Rico strongly suggest a link with some of the recently-extinct “heptaxodontids”, which would substantiate their much greater antiquity in the Caribbean islands.

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

Spatio-temporal variability (up- and down-stream and three seasons) of response patterns of macroinvertebrates to commonly applied low-head concrete weirs under reclaimed water intervention in urban river restoration

Understanding how aquatic communities respond to various structures is important for assessing ecological effectiveness, developing theory and guiding sustainable river restoration. However, there is still minimal understanding on spatio-temporal variability of response patterns of macroinvertebrates to commonly applied low-head concrete weirs and reclaimed water in urban river restoration. Our results showed that the presence of above two structures and their interactions sometimes produce varying distribution of macroinvertebrate before and after each structure in different seasons. At higher taxa level, it is not a bad choice to utilize various structures and their composite construction to increase biological heterogeneity, to reduce costs and risk of failure, and to improve reasonably designed structures for recovery aquatic communities. Reclaimed water mainly played three major functions, sustaining more taxa; reversing the relationship of values between up and down weir on a 150 m reach-scale; maintaining macroinvertebrates indexes on a 1500 m reach-scale. These results could highlight ongoing challenges in designing structures to meet multiple goals. For stakeholders, the recommendations of this study are most suitable for river restoration focused on improving diversity of specific aquatic groups. Although case-specific, the results are analyzed within a wider framework to emphasize the importance of using various structures and composite construction in river restoration, the significance of extensive and repeated post-restoration monitoring to explore project effectiveness and provide valuable insights to river restoration.

The rising threat of climate change for arthropods from Earth's cold regions: Taxonomic rather than native status drives species sensitivity.

Polar and alpine regions are changing rapidly with global climate change. Yet, the impacts on biodiversity, especially on the invertebrate ectotherms which are dominant in these areas, remain poorly understood. Short‐term extreme temperature events, which are growing in frequency, are expected to have profound impacts on high‐latitude ectotherms, with native species being less resilient than their alien counterparts. Here, we examined in the laboratory the effects of short periodic exposures to thermal extremes on survival responses of seven native and two non‐native invertebrates from the sub‐Antarctic Islands. We found that survival of dipterans was significantly reduced under warming exposures, on average having median lethal times (LT50) of about 30 days in control conditions, which declined to about 20 days when exposed to daily short‐term maxima of 24°C. Conversely, coleopterans were either not, or were less, affected by the climatic scenarios applied, with predicted LT50 as high as 65 days under the warmest condition (daily exposures at 28°C for 2 h). The native spider Myro kerguelensis was characterized by an intermediate sensitivity when subjected to short‐term daily heat maxima. Our results unexpectedly revealed a taxonomic influence, with physiological sensitivity to heat differing between higher level taxa, but not between native and non‐native species representing the same higher taxon. The survival of a non‐native carabid beetle under the experimentally imposed conditions was very high, but similar to that of native beetles, while native and non‐native flies also exhibited very similar sensitivity to warming. As dipterans are a major element of diversity of sub‐Antarctic, Arctic and other cold ecosystems, such observations suggest that the increased occurrence of extreme, short‐term, thermal events could lead to large‐scale restructuring of key terrestrial ecosystem components both in ecosystems protected from and those exposed to the additional impacts of biological invasions.

Nest site selection and breeding ecology of the red-billed blue magpie Urocissa erythrorhyncha in central China

Abstract While knowledge on birds’ breeding ecology is essential for understanding avian adaptation and managing conservation, it is poorly studied for many species, even for some common species. The knowledge of the natural history of the red-billed blue magpie (Urocissa erythrorhyncha), a species widely distributed in China and Southeast Asia, is sketchy. Here we present detailed data of nest site selection and the breeding ecology of red-billed blue magpie in central China, and of the effects of nest predation and brood parasitism on reproductive strategies. Most nests were built on Phyllostachys sulphurea and Quercus acutissima. Breeding season ranged from March to August. The first egg was laid between early April and late July. The incubation period lasted 15 days and the nestling period, 18 days. Average clutch size was 4.6 eggs, and brood size at fledging was 3.3 young. Overall, 43.8% of nesting attempts successfully produced at least one fledged young. Nest predation and brood parasitism were the two main reasons for fledging failure, which mainly occurred after April. Correspondingly, U. erythrorhyncha showed a tendency to build nests higher up and have a smaller clutch size in late stages of the breeding season. This study provides the first reliable and comprehensive information on the reproductive parameters of U. erythrorhyncha, which will lay a foundation for further understanding this species’ biology and opens up an avenue for large-scale comparative studies of the Urocissa genus or higher-level taxa.

Characteristics and Determinants of Endemic Plant Taxa in the Gabonese Area of Endemism

Endemism is one of the most important concepts in biogeography and is often used to guide biodiversity conservation, yet our understanding of the determinants of endemism in many biodiverse tropical regions is limited. This is true for western Central Africa, a region with one of the highest levels of plant diversity in tropical Africa, where endemism is poorly documented. This study examines the Gabonese Area of Endemism (GAE) and explores the main characteristics and determinants of its vascular plant endemism with regard to taxonomy, growth form, habitat, distribution, and range size. We compiled a comprehensive, verified specimen database of vascular plant taxa restricted to the GAE, comprising 19,876 occurrences of 1145 species and infraspecific taxa, and we characterized the habitat and habit for each taxon. We then calculated the proportion of taxa in the regional flora that are endemic to the GAE. A Wilcoxon rank-sum test was used to investigate range size among endemic taxa exhibiting different growth forms, and Fisher exact tests were used to explore the association between their habit and habitat, and to test the distribution of these attributes among higher-level taxa and growth forms compared to patterns in the regional flora as a whole. We found that endemic taxa represent ca. 13% of the GAE flora, and that the rate of endemism varies considerably among taxonomic groups and growth forms. Endemism is highest among shrubs (22%) and lowest in herbs (8%), especially monocotyledons (e.g., 5% among Poales). Most endemic taxa grow preferentially in forest habitats, the dominant vegetation type of the region. Endemic trees, which structure forest ecosystems, have significantly larger ranges than endemic herbs, climbers, and shrubs. About 17% of the flora of Gabon is endemic or subendemic to the country. Our results show that the dispersal capacity of taxa and the biogeographical history of the region appear to be critical factors in explaining differences in the rate of endemism among growth forms and taxonomic groups. Our findings also highlight the benefits of carefully building a comprehensive and verified database for studying rare and range-restricted plants, and they underscore the necessity to strengthen botanical exploration throughout western Central Africa in order to develop improved and better-informed conservation strategies.

Phylogenetic definitions for 25 higher-level clade names of birds

Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic data. However, the nomenclature of higher-level taxa has not become more stable, due to the lack of regulation of taxon names above the level of superfamily by the ICZN, and the usage of rank-based nomenclature, which is not tied to clades in a phylogeny. Lack of regulation and the instability of rank-based nomenclature impede effective communication among systematists. We review support for higher-level avian clades using a set of 10 phylogenomic data sets, and identify clades that are supported by congruency of at least four of these. We provide formal definitions of the names of these clades based on the rules of the recently published PhyloCode. The names of 25 clades are here defined using minimum-crown-clade (n ​= ​23), minimum-clade (n ​= ​1) and maximum-crown-clade (n ​= ​1) definitions. Five new names are introduced here: Dinocrypturi, Pteroclimesites, Musophagotides, Phaethoquornithes and Pelecanes. We also review diagnostic apomorphies of the relevant clades, and identify known synonyms and homonyms. By establishing a formal link between higher-level taxon names and well-supported phylogenetic hypotheses, our phylogenetic definitions will provide a solid basis for the stabilization of avian higher-level nomenclature.

Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns.

The human gut microbiome has been extensively studied, but its diversity scaling (changes or heterogeneities) along the digestive tract (DT) as well as their inter-individual heterogeneities have not been adequately addressed to the best of our knowledge. Here we fill the gap by applying the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR) in biogeography, by reanalyzing a dataset of over 2000 16s-rRNA microbiome samples obtained from 10 DT sites of over 200 individuals. We sketched out the biogeography “maps” for each of the 10 DT sites by cross-individual DAR analysis, and the intra-DT distribution pattern by cross-DT-site DAR analysis. Regarding the inter-individual biogeography, it was found that all DT sites have the invariant (constant) scaling parameter—all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities, which include the portions of diversity that may be absent locally but present regionally. In the case of this study, the potential diversity of each DT site covers the total diversity of the respective site from all individuals in the cohort. In terms of the genus richness, an average individual hosts approximately 20% of the population-level genus richness (total bacterial genus of a human population). In contrast, in terms of community biodiversity, the percentages of individual over population may exceed 90%. This suggests that the differences between individuals in their DT microbiomes are predominantly in the composition of bacterial species, rather than how their abundances are distributed (i.e., biodiversity). Regarding the intra-DT patterns, the scaling parameter (z) is larger—suggesting that the intra-DT biodiversity changes are larger than inter-individual changes. The higher intra-DT heterogeneity of bacteria diversity, as suggested by larger intra-DT z than the inter-individual heterogeneity, should be expected since the intra-DT heterogeneity reflects the functional differentiations of the DT tract, while the inter-individual heterogeneity (z) reflects the difference of the same DT site across individuals. On average, each DT site contains 21–36% of the genus diversity of the whole DT, and the percentages are even higher in terms of higher taxon levels.

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes.

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.

Soil microbiome predictability increases with spatial and taxonomic scale.

Soil microorganisms shape ecosystem function, yet it remains an open question whether we can predict the composition of the soil microbiome in places before observing it. Furthermore, it is unclear whether the predictability of microbial life exhibits taxonomic- and spatial-scale dependence, as it does for macrobiological communities. Here, we leverage multiple large-scale soil microbiome surveys to develop predictive models of bacterial and fungal community composition in soil, then test these models against independent soil microbial community surveys from across the continental United States. We find remarkable scale dependence in community predictability. The predictability of bacterial and fungal communities increases with the spatial scale of observation, and fungal predictability increases with taxonomic scale. These patterns suggest that there is an increasing importance of deterministic versus stochastic processes with scale, consistent with findings in plant and animal communities, suggesting a general scaling relationship across biology. Biogeochemical functional groups and high-level taxonomic groups of microorganisms were equally predictable, indicating that traits and taxonomy are both powerful lenses for understanding soil communities. By focusing on out-of-sample prediction, these findings suggest an emerging generality in our understanding of the soil microbiome, and that this understanding is fundamentally scale dependent.

Assessing accuracy and completeness of GenBank for eDNA metabarcoding: towards a reliable marine fish reference database

Environmental DNA (eDNA) metabarcoding, the process of sequencing DNA collected from the environment for producing biodiversity inventories, is increasingly being applied to assess fish diversity and distribution in marine environments. Yet, the successful application of this technique deeply relies on accurate and complete reference databases used for taxonomic assignment. The most used markers for fish eDNA metabarcoding studies are the cytochrome C oxidase subunit 1 (COI), 16S ribosomal RNA (16S), the 12S ribosomal RNA (12S) and cytochrome b (cyt b) genes, whose sequences are usually retrieved from GenBank, the largest DNA sequence database that represents a worldwide public resource for genetic studies. Thus, the completeness and accuracy of GenBank is critical to derive reliable estimations from fish eDNA metabarcoding data. Here, we have i) compiled the checklist of European marine fishes, ii) performed a gap analysis of the four genes and, within COI and 12S, also of the most used barcodes for fish, and iii) developed a workflow to detect potentially incorrect records in GenBank. We found that from the 1965 species in the checklist (1761 Actinopterygii, 189 Elasmobranchii, 9 Holocephali, 4 Petromyzonti and 2 Myxini), about 70% have sequences for COI, whereas less have sequences for 12S, 16S and cyt b (45-55%). Among the species for which COI ad 12S sequences are available, about 60% and 40% have sequences covering the most used barcodes respectively. The analysis of pairwise distances between sequences revealed pairs belonging to the same species with significantly low similarity and pairs belonging to different high level taxonomic groups (class, order) with significantly large similarity. In light of this further confirmation of presence of a substantial number of incorrect records in GenBank, we propose a method for identifying and removing spurious sequences to create reliable and accurate reference databases for eDNA metabarcoding.

An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life