Incomplete Sampling Research Articles

Anurocampa (Lepidoptera: Notodontidae): two new species, systematics and immature stages.

Notodontidae (Lepidoptera, Noctuoidea) comprise over 4,000 described species distributed worldwide, among which nearly half are restricted to the Neotropics. Morphology of adults and immatures of Notodontidae have been broadly investigated and many larval, pupal, and adult characters were found to be synapomorphies of subfamilies and tribes. Despite this, the current classification of Notodontidae remains unsettled as most recent classification systems are contradictory due to reliance on incomplete global sampling and, many taxa, especially in the Neotropics, are still informally classified as incertae sedis. Anurocampa Herrich-Shäffer was recently treated as an incertae sedis genus, and immature and adult characters may provide further evidence for its systematic position among the Notodontidae. With this goal in mind, the present study describes the immature stages of Anurocampa mingens Herrich-Shäffer from Brazil and describes two new species in the genus from Costa Rica based on morphology and mitochondrial DNA: Anurocampa markhastingsi Chacón and St Laurent sp. nov. and Anurocampa abelardochaconi Chacón and St Laurent sp. nov. and discusses the systematic position of Anurocampa.

Quantifying and estimating ecological network diversity based on incomplete sampling data.

An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyse network sampling data. The proposed method integrates the following four inference procedures: (i) assessment of sample completeness of networks; (ii) asymptotic analysis via estimating the true network diversity; (iii) non-asymptotic analysis based on standardizing sample completeness via rarefaction and extrapolation with network diversity; and (iv) estimation of the degree of unevenness or specialization in networks based on standardized diversity. Interaction data between European trees and saproxylic beetles are used to illustrate the proposed procedures. The software iNEXT.link has been developed to facilitate all computations and graphics. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Effects of incomplete sampling on macroinvertebrate secondary production estimates in a forested headwater stream

Estimates of secondary production depend on the efficiency of sampling methods in capturing abundances and body lengths of the entire macroinvertebrate community. The efficiency of common sampling methods in fulfilling these criteria is poorly understood. We compared the effects of a Surber sampler (250 µm mesh size) and a Freeze corer in capturing abundance, biomass, and secondary production of macroinvertebrates in a forested headwater stream. We then examined how the use of nets with different mesh sizes could affect estimates of secondary production. Macroinvertebrate abundance was three times lower, and biomass was three times higher with the Surber than with the Freeze corer. Neither method captured the entire length distribution, and incomplete sampling of body lengths and abundance resulted in underestimating total secondary production by 48% (Surber) and 49% (Freeze corer). We estimated that reducing the mesh size from 250 to 100 µm would reduce the underestimation of production from ~ 48 to ~ 12% due to the inclusion of smaller individuals. Our results improve the efficiency of common sampling methods, allowing a reliable quantification of the role of macroinvertebrates in stream ecosystem functioning.

Rapid monitoring of ecological persistence

Effective conservation of ecological communities requires accurate and up-to-date information about whether species are persisting or declining to extinction. The persistence of an ecological community is supported by its underlying network of species interactions. While the persistence of the network supporting the whole community is the most relevant scale for conservation, in practice, only small subsets of these networks can be monitored. There is therefore an urgent need to establish links between the small snapshots of data conservationists can collect, and the "big picture" conclusions about ecosystem health demanded by policymakers, scientists, and societies. Here, we show that the persistence of small subnetworks (motifs) in isolation-that is, their persistence when considered separately from the larger network of which they are a part-is a reliable probabilistic indicator of the persistence of the network as a whole. Our methods show that it is easier to detect if an ecological community is not persistent than if it is persistent, allowing for rapid detection of extinction risk in endangered systems. Our results also justify the common practice of predicting ecological persistence from incomplete surveys by simulating the population dynamics of sampled subnetworks. Empirically, we show that our theoretical predictions are supported by data on invaded networks in restored and unrestored areas, even in the presence of environmental variability. Our work suggests that coordinated action to aggregate information from incomplete sampling can provide a means to rapidly assess the persistence of entire ecological networks and the expected success of restoration strategies.

Inferring the Rate of Technosignatures from 60 yr of Nondetection

For about the last 60 yr the search for extraterrestrial intelligence has been monitoring the sky for evidence of remotely detectable technological life beyond Earth, with no positive results to date. While the lack of detection can be attributed to the highly incomplete sampling of the search space, technological emissions may be actually rare enough that we are living in a time when none cross the Earth. Here we explore the latter possibility and derive the likelihood of the Earth not being crossed by signals for at least the last 60 yr to infer upper bounds on their rate of emission. Under the assumption that technological emitters are distributed uniformly in the Milky Way and that they generate technoemissions at a constant rate, we find less than about one to five emissions generated per century with 95% credible level. This implies optimistic waiting times until the next crossing event of no less than 60–1800 yr with a 50% probability. A significant fraction of highly directional signals increases the emission rates’ upper bounds, but without systematically changing the waiting time. Although these probabilistic bounds are derived from a specific model and their validity depends on the model’s assumptions, they are nevertheless quite robust against weak time dependences of the emission rate or nonuniform spatial distributions of the emitters. Our results provide therefore a benchmark for assessing the lack of detection and may serve as a basis to form optimal strategies for the search for extraterrestrial intelligence.

Quantitative Dual-Energy Imaging of Bone Marrow Edema Using Multisource Cone-Beam CT with Model-Based Decomposition.

We investigated the feasibility of dual-energy (DE) detection of bone marrow edema (BME) using a dedicated extremity cone-beam CT (CBCT) with a unique three-source x-ray unit. The sources can be operated at different energies to enable single-scan DE acquisitions. However, they are arranged parallel to the axis of rotation, resulting in incomplete sampling and precluding the application of DE projection-domain decompositions (PDD) for beam-hardening reduction. Therefore, we propose a novel combination of a model-based "one-step" DE two-material decomposition followed by a constrained image-domain change-of-basis to obtain virtual non-calcium (VNCa) images for BME detection. DE projections were obtained using an "alternating-kV" protocol by operating the peripheral two sources of the CBCT system at low-energy (60 kV, 0.105 mAs/frame) and the central source at high-energy (100 kV, 0.028 mAs/frame), for a total of 600 frames over 216° of gantry rotation. Projections were processed with detector lag, glare and fast Monte Carlo (MC)-based iterative scatter corrections. Model-based material decomposition (MBMD) was then implemented to obtain aluminum (Al) and polyethylene (PE) volume fraction images with minimal beam-hardening. Statistical ray weights in MBMD were modified to account for regions with highly oblique sampling by the peripheral sources. To generate the VNCa maps, image-domain decomposition (IDD) constrained by the volume conservation principle (VCP) was performed to convert the Al and PE MBMD images into volume fractions of water, fat and cortical bone. Accuracy of BME detection was evaluated using physical phantom data acquired on the multi-source extremity CBCT scanner. The proposed framework estimated the volume of BME with ~10% error. The MC-based scatter corrections and the modified MBMD ray weights were essential to achieve such performance - the error without MC scatter corrections was >30%, whereas the uniformity of estimated VNCa images was 3x improved using the modified weights compared to the conventional weights. The proposed DE decomposition framework was able to overcome challenges of high scatter and incomplete sampling to achieve BME detection on a CBCT system with axially-distributed x-ray sources.

Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty.

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H2 ']) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co-occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host-parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%-10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

A waterfowl seed‐dispersal network from the Neotropical region is nested and modular

AbstractSeed dispersal by vertebrates is fundamental for the persistence of plant species, forming networks of interactions that are often nested and modular. Networks involving angiosperms and frugivorous birds are relatively well‐studied in the Neotropical region, but there are no previous studies of networks involving waterbirds. Here, we describe the structure of a Neotropical waterfowl seed‐dispersal network and identify the species that have an important role for the network structure. We used information on 40 plant taxa found in fecal samples of five common waterfowl species to calculate the nestedness (NODF), weighted nestedness (WNODF), modularity, and weighted modularity of the network. We found that the network was nested, with yellow‐billed teal showing the highest contribution both to nestedness and weighted nestedness. Twenty‐four plant species contributed positively to weighted nestedness, with Salzmann's mille graines presenting the highest influence both to nestedness and weighted nestedness. The network was modular, but the weighted modularity was not significant. These results need to be considered with caution due to incomplete interaction sampling for two species. Ringed teal, Brazilian teal, and yellow‐billed teal were considered hub modular species. Among plants, beak sedges and water snowflake were considered modular hub species, while Salzmann's mille graines and spikerush were network connectors. The structure of this Neotropical waterbird seed‐dispersal network differed from the only previous waterfowl network study, from Europe, which found similar level of nestedness but no significant modularity. We include several possible explanations for this discrepancy and identified priorities for future research into waterbird–plant interaction networks.Abstract in Portuguese is available with online material.

Bandlimited Signal Reconstruction From Leaky Integrate-and-Fire Encoding Using POCS

Leaky integrate-and-fire (LIF) encoding is a model of neuron transfer function in biology that has recently attracted the attention of the signal processing and neuromorphic computing communities as a technique of event-based sampling for data acquisition. While LIF enables the implementation of analog-circuit signal samplers of lower complexity and higher accuracy simultaneously, the core difficulty of this technique is the retrieval of an input from its LIF-encoded output. In this article, we study this problem in the context of bandlimited inputs, by extracting the most abstract features of an LIF encoder as a generalized nonuniform sampler. In this view, the LIF output is seen as the transformation of the input by a known linear operator. We show that the signal reconstruction method of projection onto convex sets (POCS) converges to a weighted pseudo-inverse of this operator. This allows perfect recovery under uniqueness of reconstruction, minimum-norm reconstruction under incomplete sampling, as well as a noise shaping of time quantization that outperforms standard pseudo-inversion. On the practical side, a single iteration of the POCS method can be used to improve <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">any</i> estimate whose LIF samples are not consistent with those of the input, and a rigorous discrete-time implementation of this iteration is proposed that does not require a Nyquist-rate representation of the signals.

Substantial variation in species ages among vertebrate clades

Abstract Ecological and evolutionary studies traditionally assume that species are comparable units of biodiversity. However, not only this assumption is rarely tested, but also there have been few attempts even to assess variation in most emergent, species-level traits and their corresponding underlying mechanisms. One such trait is species age, here defined as the time since the most recent common ancestor between a given species and its sister lineage. In this study, we demonstrate that different terrestrial vertebrate clades vary considerably in the age of their constituent species. In particular, species ages were youngest in mammals and birds as opposed to squamates and amphibians, although considerable variation was found within those clades as well. Sensitivity analyses showed that these results are unaffected by phylogenetic uncertainty or incomplete taxonomic sampling. Interestingly, there was little geographical correspondence in mean species age across taxa, as well as with temperature and precipitation stability over the past 21 000 years. We discuss candidate mechanisms that might explain differences in species ages among clades, and explore the implications of these findings in relation to recent advances in age-dependent speciation and extinction models of diversification.

Testing Linear Operator Constraints in Functional Response Regression with Incomplete Response Functions.

Hypothesis testing procedures are developed to assess linear operator constraints in function-on-scalar regression when incomplete functional responses are observed. The approach enables statistical inferences about the shape and other aspects of the functional regression coefficients within a unified framework encompassing three incomplete sampling scenarios: (i) partially observed response functions as curve segments over random sub-intervals of the domain; (ii) discretely observed functional responses with additive measurement errors; and (iii) the composition of former two scenarios, where partially observed response segments are observed discretely with measurement error. The latter scenario has been little explored to date, although such structured data is increasingly common in applications. For statistical inference, deviations from the constraint space are measured via integrated -distance between the model estimates from the constrained and unconstrained model spaces. Large sample properties of the proposed test procedure are established, including the consistency, asymptotic distribution and local power of the test statistic. Finite sample power and level of the proposed test are investigated in a simulation study covering a variety of scenarios. The proposed methodologies are illustrated by applications to U.S. obesity prevalence data, analyzing the functional shape of its trends over time, and motion analysis in a study of automotive ergonomics.

Minimally Incomplete Sampling and Convergence of Adaptive Play in 2 × 2 Games

Minimally Incomplete Sampling and Convergence of Adaptive Play in 2 × 2 Games

Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum

Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea, we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.

Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin.

One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns.

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 2

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 2

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 3

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 3

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. table

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. table

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 1

Effects of incomplete sampling and standardization on indices of abundance from a fishery-independent trawl survey off the Atlantic coast of the southeastern United States: Suppl. Fig. 1