Subset Of Taxa Research Articles

The nature of 'jaws': a new predatory representative of Provora and the ultrastructure of nibbling protists.

The recently discovered Provora supergroup has primarily been examined to determine their phylogenomic position in the eukaryotic tree. Their morphology is more poorly studied, and here we focus on their cellular organization and how it compares with that of other supergroups. These small eukaryovorous flagellates exhibit several ultrastructural features that are also found in a subset of taxa from a wide variety of deep-branching lineages (Stramenopiles, Alveolata, Hemimastigophora, Malawimonadidae, Discoba and Metamonada), including vesicles beneath the plasmalemma, two opposing vanes on the flagella, a ventral feeding groove and a fibrillar system resembling the excavate type. Additionally, we identified four main microtubular roots (r1-r4) and a singlet root between r1 and r2, which support the strong feeding apparatus resembling 'jaws'. Their unique extrusive organelles (ampulosomes) have a similar organization to Hemimastigophora extrusomes, but most of their cell characteristics most closely resemble features of the TSAR + Haptista grouping. We also describe a new species, Nibbleromonas piranha sp. nov., and highlight features of its feeding behaviour, which can be so aggressive as to result in cannibalism.

Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSCquartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study.

Terrestriality across the primate order: A review and analysis of ground use in primates.

Terrestriality is relatively rare in the predominantly arboreal primate order. How frequently, and when, terrestriality appears in primate evolution, and the factors that influence this behavior, are not well understood. To investigate this, we compiled data describing terrestriality in 515 extant nonhuman primate taxa. We describe the geographic and phylogenetic distribution of terrestriality, including an ancestral state reconstruction estimating the frequency and timing of evolutionary transitions to terrestriality. We review hypotheses concerning the evolution of primate terrestriality and test these using data we collected pertaining to characteristics including body mass and diet, and ecological factors including forest structure, food availability, weather, and predation pressure. Using Bayesian analyses, we find body mass and normalized difference vegetation index are the most reliable predictors of terrestriality. When considering subsets of taxa, we find ecological factors such as forest height and rainfall, and not body mass, are the most reliable predictors of terrestriality for platyrrhines and lemurs.

Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon-environment relationships.

Changes in phosphorus concentrations affect periphytic diatom composition in streams, yet we rarely observe strong relationships between diatom richness and phosphorus. In contrast, changes in conductivity are strongly associated with differences in both diatom composition and richness. We hypothesised that we could better understand the mechanisms that control the phosphorus-richness relationship by examining relationships between phosphorus and the occurrence of individual diatom taxa, comparing these with relationships between conductivity and taxon occurrence, and documenting how niche breadths of taxa affect richness patterns. We estimated relationships between phosphorus and taxon occurrence using DNA metabarcoding data of diatoms collected from 1,811 sites distributed across the conterminous U.S.A. and contrasted patterns in these relationships with those between conductivity and taxon occurrence. The distribution of taxon optima for phosphorus was bimodal, with most optima located at either the maximum or minimum observed phosphorus concentration. The distribution of taxon optima for conductivity was unimodal. Niche breadths of taxa for phosphorus and for conductivity both generally increased with optimum values. The distribution of conductivity optima gave rise to a prominent hump-shaped relationship between richness and conductivity. The relationship between richness and phosphorus was also slightly hump-shaped, but this relationship would not be expected from the bimodal distribution of optima. Instead, we determined that broad niche breadths caused the hump-shaped relationship between richness and phosphorus. Our results highlight the nuanced effects that increased P loadings exert on diatom assemblages in rivers and streams and identify reasons that weak relationships between taxon richness and increased phosphorus have been observed. These findings allow us to better describe how excess phosphorus and subsets of taxa and their niche breadths contribute to patterns of taxa richness in diatom assemblages, and to improve the tools used to manage phosphorus pollution.

CleanSURFACES® intervention reduces microbial activity on surfaces in a senior care facility.

As one of the top public health challenges outlined by the Centers for Disease Control (CDC), estimates report that hospital acquired infections (HAIs) claim the lives of 99,000 Americans and cost healthcare providers over $28 billion each year. In addition to underlying conditions related to age, elderly patients in long-term care facilities are at an elevated risk of acquiring HAIs. A large percentage of HAIs is attributable to contaminated surfaces and medical devices. To that end, this study utilized a metatranscriptomic sequencing workflow (CSI-Dx™) to profile active microbial communities from surfaces in the HJ Heinz Community Living Center, a long-term care facility in the Veterans Affairs Pittsburgh Health Care System. Swabs were collected from high-touch surfaces (Keyboard, Ledge, Workstation on Wheels, Worksurfaces) before (Baseline) and after cleanSURFACES® were installed at 4 timepoints (Day 1, Day 7, Day 14, and Day 30). Microbial richness was significantly reduced after cleanSURFACES® intervention (Wilcoxon test with Holm correction, p=0.000179). Beta diversity results revealed distinct clustering between Baseline and Post-intervention samples (Adonis, p<0.001). Reduction in bacterial (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis) and fungal (Malassezia restricta, Candida albicans, Candida glabrata, and Candida orthopsilosis) expression of opportunistic pathogens was observed. Additionally, a subset of taxa (Corynebacterium, Cutibacterium acnes, and Ralstonia pickettii) was present in specific Post-intervention timepoints and surface types. This study revealed decreased microbial activity, highlighting the potential for the combinatorial application of cleanSURFACES® and regular decontamination practices to reduce the prevalence of microbes causing HAIs.

Living and dead bivalves are congruent surrogates for whole benthic macroinvertebrate communities in Puget Sound

To integrate paleoecological data with the “whole fauna” data used in biological monitoring, analyses usually must focus on the subset of taxa that are inherently preservable, for example by virtue of biomineralized hardparts, and those skeletal remains must also be identifiable in fragmentary or otherwise imperfect condition, thus perhaps coarsening analytical resolution to the genus or family level. Here we evaluate the ability of readily preserved bivalves to reflect patterns of compositional variation from the entire infaunal macroinvertebrate fauna as typically sampled by agencies in ocean monitoring, using data from ten long-established subtidal stations in Puget Sound, Washington State. Similarity in compositional variation among these stations was assessed for five taxonomic subsets (the whole fauna, polychaetes, malacostracans, living bivalves, dead bivalves) at four levels of taxonomic resolution (species, genera, families, orders) evaluated under four numerical transformations of the original count data (proportional abundance, square root- and fourth root-transformation, presence-absence). Using the original matrix of species-level proportional abundances of the whole fauna as a benchmark of “compositional variation,” we find that living and dead bivalves had nearly identical potential to serve as surrogates of the whole fauna; they were further offset from the whole fauna than was the polychaete subset (which dominates the whole fauna), but were far superior as surrogates than malacostracans. Genus- and family-level data were consistently strong surrogates of species-level data for most taxonomic subsets, and correlations declined for all subsets with increasing severity of data transformation, although this effect lessened for subsets with high community evenness. The strong congruence of death assemblages with living bivalves, which are themselves effective surrogates of compositional variation in the whole fauna, is encouraging for using bivalve dead-shell assemblages to complement conventional monitoring data, notwithstanding strong natural environmental gradients with potential to bias shell preservation.

Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast.

Foliose species of the genus Ulva are notoriously difficult to identify due to their variable morphological characteristics and high phenotypic plasticity. We reassessed the taxonomic status of several distromatic foliose Ulva spp., morphologically related to Ulva rigida, using DNA barcoding with the chloroplastic tufA and rbcL (for a subset of taxa) genes for 339 selected attached Ulva specimens collected from three intertidal rocky sites. Two of the collection sites were in Brittany and one site was in Vendée, along the Atlantic coast of France. Molecular analyses included several museum specimens and the holotype of Ulva armoricana Dion, Reviers & Coat. We identified five different tufA haplotypes using a combination of phylogenetic analysis, with the support of several recently sequenced holotypes and lectotypes, and a species delimitation method based on hierarchical clustering. Four haplotypes were supported by validly named species: Ulva australis Areschoug, Ulva fenestrata Postels & Ruprecht, Ulva lacinulata (Kützing) Wittrock and U. rigida C. Agardh. The later was additionally investigated using rbcL. The fifth haplotype represented exact sequence matches to an unnamed species from European Atlantic coasts. Our results support: (1) the synonymy of both U. rigida sensu Bliding non C. Agardh and U. armoricana with U. lacinulata. This finding is based on current genetic analysis of tufA from the U. armoricana holotype and recent molecular characterization of the lectotype of U. laetevirens, which is synonymous to U. australis, (2) the presence of U. australis as a misidentified introduced species in Brittany, and (3) the presence of U. fenestrata and U. rigida in southern Brittany. The taxonomic history of each species is discussed, highlighting issues within distromatic foliose taxa of the genus Ulva and the need to genetically characterize all its available type specimens.

On the quartet distance given partial information

AbstractLet be an arbitrary phylogenetic tree with leaves. It is well known that the average quartet distance between two assignments of taxa to the leaves of is . However, a longstanding conjecture of Bandelt and Dress asserts that is also themaximumquartet distance between two assignments. While Alon, Naves, and Sudakov have shown this indeed holds for caterpillar trees, the general case of the conjecture is still unresolved. A natural extension is when partial information is given: the two assignments are known to coincide on a given subset of taxa. The partial information setting is biologically relevant as the location of some taxa (species) in the phylogenetic tree may be known, and for other taxa it might not be known. What can we then say about the average and maximum quartet distance in this more general setting? Surprisingly, even determining theaveragequartet distance becomes a nontrivial task in the partial information setting and determining the maximum quartet distance is even more challenging, as these turn out to be dependent on the structure of . In this paper we prove nontrivial asymptotic bounds that are sometimes tight for the average quartet distance in the partial information setting. We also show that the Bandelt and Dress conjecture does not generally hold under the partial information setting. Specifically, we prove that there are cases where the average and maximum quartet distance substantially differ.

SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

BackgroundThe aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. There is still a lack of knowledge surrounding the importance and functionality of the teleost gut microbiome in fish nutrition. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host’s microbial communities. Several in vitro gut models targeted at monogastric vertebrates are now in operation. Here, we report the development of an Atlantic salmon gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum, and midgut) and associated microbial communities.ResultsThe gut model was established in a series of linked bioreactors seeded with biological material derived from farmed adult marine-phase salmon. We first aimed to achieve a stable microbiome composition representative of founding microbial communities derived from Atlantic salmon. Then, in biological triplicate, the response of the in vitro system to two distinct dietary formulations (fishmeal and fishmeal free) was compared to a parallel in vivo trial over 40 days. Metabarcoding based on 16S rDNA sequencing qPCR, ammoniacal nitrogen, and volatile fatty acid measurements were undertaken to survey the microbial community dynamics and function. SalmoSim microbiomes were indistinguishable (p = 0.230) from their founding inocula at 20 days and the most abundant genera (e.g., Psycrobacter, Staphylococcus, Pseudomonas) proliferated within SalmoSim (OTUs accounting for 98% of all reads shared with founding communities). Real salmon and SalmoSim responded similarly to the introduction of novel feed, with majority of the taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa (e.g., a small fraction of Psychrobacter) was differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acid profiles were not significantly different in SalmoSim pre- and post-feed switch.ConclusionBy establishing stable and representative salmon gut communities, this study represents an important step in the development of an in vitro gut system as a tool for the improvement of fish nutrition and welfare. The steps of the system development described in this paper can be used as guidelines to develop various other systems representing other fish species. These systems, including SalmoSim, aim to be utilised as a prescreening tool for new feed ingredients and additives, as well as being used to study antimicrobial resistance and transfer and fundamental ecological processes that underpin microbiome dynamics and assembly.8JdHojFsA4Kj53z48mRJ2PVideo abstract

Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa.

Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Among these methods, comparisons of topologies obtained from plastid markers with those from a few nuclear sequences are favored, even though they restrict in-depth studies of hybridization and polyploidization. The genus Rosa encompasses c. 150 species widely distributed throughout the northern hemisphere and represents a challenging taxonomic group in which hybridization and polyploidization are prominent. Our main objective was to develop a general framework that would take patterns of reticulation into account in the study of the phylogenetic relationships among Rosa species. Using amplicon sequencing, we targeted allele variation in the nuclear genome as well as haploid sequences in the chloroplast genome. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization using a maximum pseudo-likelihood approach on taxon subsets. Our diploid-first approach followed by hybrid and polyploid grafting resolved most of the evolutionary relationships among Rosa subgenera, sections, and selected species. Based on these results, we provide new directions for a future revision of the infrageneric classification in Rosa. The stepwise strategy proposed here can be used to reconstruct the phylogenetic relationships of other challenging taxonomic groups with large numbers of hybrid and polyploid taxa. [Amplicon sequencing; interspecific hybridization; polyploid detection; reticulate evolution.].

Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

BackgroundEven when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates.ResultsWe built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth.ConclusionsDomain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.

Coral microbiome changes over the day–night cycle

Coral-associated microbiomes play important roles in host health and metabolism. It is therefore critical to understand the factors that shape microbiome taxonomic composition and function. Little is known about the stability of coral microbiomes over hourly fluctuations in environmental conditions. For parameters such as temperature and pH, the magnitude of day–night fluctuations can exceed those observed in mean values over seasons, especially on shallow reefs. Such short-term heterogeneity can affect longer term trends, possibly by influencing the extent to which corals acclimate to stress and increase resilience. This study examined diel dynamics of microbiomes (Bacteria and Archaea) in three species of stony coral (Porites lutea, Porites cylindrica, and Pocillopora damicornis) from a shallow reef in Mo’orea (French Polynesia). We assessed microbiome composition and relative transcriptional activity by analyzing 16S rRNA gene and transcript sequences from six timepoints over 48 h for each species. Both the composition and transcription of microbiome members changed significantly over the diel cycle. Most changes did not exhibit clear diel periodicity but were instead stochastic, a pattern potentially influenced also by microspatial variation within a coral colony. However, a subset of taxa, notably the dinoflagellate-associated bacterium Porticoccus and bacteria of the ubiquitous coral-associated Endozoicomonas genus, exhibited cyclic changes in relative frequency over the 2 d sampling period in the DNA dataset of Porites lutea. These patterns raise the possibility that ecological functions of the microbiome may vary substantially over hourly timescales, notably between day and night. Further studies are needed to compare temporal change in the coral microbiome with that due to other factors, such as spatial distance within and among colonies.

Suitability of surgically implanted 8‐mm passive integrated transponder tags for small‐bodied fishes

Innovative tools that benefit conservation are critical as freshwater fishes are lost at unprecedented rates. Mark-recapture methods can characterize population demographics and life-history traits of diverse fishes, but suitable techniques for tagging for individual recognition of small-bodied fishes are rare. Passive integrated transponder (PIT) tag technology may facilitate the tagging of small fishes and early life stages of larger species. However, relatively little research has evaluated the suitability of these small (8.4 × 1.4 mm) tags for many groups of small fishes. Tag loss (retention and survival) and growth of individuals implanted with PIT tags relative to control and sham treatments were compared for eight fishes of differing morphologies. Additionally, the utility of cyanoacrylate to improve tag retention was tested on a subset of taxa. Fish of each species were equally divided and randomly assigned to one of three treatment groups (handled [control], surgical incision [sham], or surgical incision and PIT tag implantation [PIT]). During the 42-d study period, mortalities and expelled tags were counted daily and growth was measured weekly. Researchers can generally expect little tag loss and uncompromised growth rates for a variety of small-bodied fishes; however, initial fish length was related to the magnitude of physiological effects for some taxa (i.e., blacknose dace Rhinichthys atratulus, johnny darter Etheostoma nigrum, juvenile white sucker Catostomus commersonii). Relatively poor survival (<80%) was observed for two benthic species: johnny darter and blacknose dace, often when incision wounds became inflamed before healing. Prevalent tag loss for johnny darter, tadpole madtom Noturus gyrinus, and a dorsal-laterally compressed cyprinid can be reduced by closing the wounds with cyanoacrylate, but with substantially increased mortality rates. This research demonstrates the broad applicability of PIT tagging technology for ecological studies of small-bodied fishes and alleviates many concerns when surgically implanting tags into several fishes.

Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands

Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.

Bryophytes at the Western Limits of Canada's Great Lakes Forest: Floristic Patterns and Conservation Implications

The Great Lakes–St. Lawrence Forest Region in Canada occupies a narrow band of mixed forest from the Gaspe Peninsula to southeastern Manitoba. The westernmost extent of this forest region in Manitoba is expected to support at least some of the bryophyte species that occur further east within the climatic and vegetation boundaries of the region. However, very few bryophytes have been reported from this area in Manitoba either in the scientific literature or herbaria, necessitating further investigation. This study provides the first assessment of bryophytes from mixed forests and treed swamps within the Great Lakes forest in Manitoba and relates them to physiography and habitat, including the first documented bryophytes for Buffalo Point First Nation on Lake of the Woods. Reported here are 153 bryophyte taxa, including 40 liverworts from 29 genera in 23 families, and 113 mosses from 77 genera in 31 families. Among these, 27 bryophytes (9 liverworts and 18 mosses) are new to Manitoba, and an additional 7 bryophytes (1 liverwort and 6 mosses) that previously had incomplete information or were equivocal are now confirmed for Manitoba. These findings expand substantially the provincial bryophyte flora. A further 35 bryophytes are re-discovered for Manitoba after more than 40 years since they were last reported in the literature. The surveyed flora is characterized as predominantly boreal (61.7% of taxa) in terms of world phytogeographic distributions. However, more than one quarter of taxa (27.9%) are temperate and frequently associated with habitats containing Fraxinus nigra (Black Ash) or Fraxinus pennsylvanica (Green Ash) trees. Many of the temperate taxa reported have widespread distributions in eastern North America but approach their western and/or northern distribution limits in the study area. Herein I identify bryophytes of high conservation value for Great Lakes forest in Manitoba using nested subsets of taxa. Additional documentation of bryophytes in the area is needed to help inform the conservation and management of lands that support a high diversity of Great Lakes-associated bryophytes.

No background in biology is assumed

No background in biology is assumed

Heritability and Functional Importance of the Setaria viridis Bacterial Seed Microbiome

Seed-associated bacteria represent an important reservoir of microorganisms passed onto progeny plants and have been postulated to be important for early plant development and early plant vigor. According to a few reports, some bacterial taxa seem to be transferred from seed to seed and some seed-associated microorganisms may derive from insect visits during flowering; however, the origin of seed endophytes is poorly understood. To better understand the origin, ecology, and functional role of seed bacterial endophytes, we planted Setaria viridis seeds over several generations in a sterile growth substrate. Seed microbiota of each generation were analyzed by next generation sequencing of 16S rRNA genes and seeds were characterized regarding to their germination and plant growth. Growing plants in a sterile (or highly depleted) substrate resulted in seed microbiota, which were largely less diverse and which had altered community composition, particularly at later generations, indicating that soil is an important reservoir of seed microbiota. Some taxa were inherited to the next generations seeds; however, different subsets of taxa were inherited in different seeds/seed batches and across different generations. This suggests that other factors than the host control the establishment of most seed endophytes and only few, e.g., obligate endophytes, might be consistently inherited. Furthermore, we observed a drastic decline in seed vigor and later generations were particularly affected. Overall, our results demonstrated that the supply of endophytes from external sources such as the soil/rhizosphere environment is highly important for the build-up of a healthy seed microbiome warranting early plant establishment and vigor of next generation plants.

Use of RNA and DNA to Identify Mechanisms of Bacterial Community Homogenization.

Biotic homogenization, i.e., the increase in community similarity through time or space, is a commonly observed response following conversion of native ecosystems to agriculture, but our understanding of the ecological mechanisms underlying this process is limited for bacterial communities. Identifying mechanisms of bacterial community homogenization following rapid environmental change may be complicated by the fact only a minority of taxa is active at any time. Here we used RNA- and DNA-based metabarcoding to distinguish putatively active taxa in the bacterial community from inactive taxa. We asked how soil bacterial communities respond to land use change following a rapid transition from rainforest to agriculture in the Congo Basin using a chronosequence that spans from roughly 1 week following slash-and-burn to an active plantation roughly 1.5 years post-conversion. Our results indicate that the magnitude of community homogenization is larger in the RNA-inferred community than the DNA-inferred perspective. We show that as the soil environment changes, the RNA-inferred community structure tracks environmental variation and loses spatial structure. The DNA-inferred community does not respond to environmental variability to the same degree, and is instead homogenized by a subset of taxa that is shared between forest and conversion sites. Our results suggest that complementing DNA-based surveys with RNA can provide insights into the way bacterial communities respond to environmental change.

Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy

BackgroundAbsolute fast converging (AFC) phylogeny estimation methods are ones that have been proven to recover the true tree with high probability given sequences whose lengths are polynomial in the number of number of leaves in the tree (once the shortest and longest branch weights are fixed). While there has been a large literature on AFC methods, the best in terms of empirical performance was DCM_{NJ}, published in SODA 2001. The main empirical advantage of {DCM}_{NJ} over other AFC methods is its use of neighbor joining (NJ) to construct trees on smaller taxon subsets, which are then combined into a tree on the full set of species using a supertree method; in contrast, the other AFC methods in essence depend on quartet trees that are computed independently of each other, which reduces accuracy compared to neighbor joining. However, {DCM}_{NJ} is unlikely to scale to large datasets due to its reliance on supertree methods, as no current supertree methods are able to scale to large datasets with high accuracy.ResultsIn this study we present a new approach to large-scale phylogeny estimation that shares some of the features of {DCM}_{NJ} but bypasses the use of supertree methods. We prove that this new approach is AFC and uses polynomial time and space. Furthermore, we describe variations on this basic approach that can be used with leaf-disjoint constraint trees (computed using methods such as maximum likelihood) to produce other methods that are likely to provide even better accuracy. Thus, we present a new generalizable technique for large-scale tree estimation that is designed to improve scalability for phylogeny estimation methods to ultra-large datasets, and that can be used in a variety of settings (including tree estimation from unaligned sequences, and species tree estimation from gene trees).

Phylogeny and molecular species delimitation of long-nosed armadillos (Dasypus: Cingulata) supports morphology-based taxonomy

AbstractThe armadillo genus Dasypus is the most species-rich and widely distributed genus of the order Cingulata and it has a dynamic taxonomic history. Recent morphology-based studies have proposed new taxonomic arrangements, but these were not yet assessed with molecular data. The two comprehensive phylogenetic hypotheses available for the genus are conflicting and were each based on a subset of taxa, hampering a proper evaluation of species boundaries. Using a multilocus molecular dataset, based on the broadest geographic sampling of Dasypus to date, we inferred the phylogenetic relationships of all species of the genus, including the recently reinstated D. beniensis and D. pastasae. We tested recent taxonomic hypotheses using several species-delimitation approaches. Our phylogeny recovered three main lineages of long-nosed armadillos that we treat as subgenera (Hyperoambon, Muletia and Dasypus) and identified the majority of its diversification as having occurred during the Pliocene. Molecular species delimitation supported morphological evidence in assigning D. hybridus as a subspecies of D. septemcinctus and confirming the split of the D. kappleri complex into three species. Our results strongly support the recognition of Guiana Shield populations formerly assigned to D. novemcinctus as a distinct species. The phylogenetic positions of D. mazzai and D. sabanicola remain uncertain. Further investigation using faster-evolving genes and additional samples may help to clarify the relationships of these young species.