Bayesian estimation of species richness from quadrat sampling data in the presence of prior information

We consider the problem of estimating the number of species of an animal community. It is assumed that it is possible to draw up a list of species liable to be present in this community. Data are collected from quadrat sampling. Models considered in this article separate the assumptions related to the experimental protocol and those related to the spatial distribution of species in the quadrats. Our parameterization enables us to incorporate prior information on the presence, detectability, and spatial density of species. Moreover, we elaborate procedures to build the prior distributions on these parameters from information furnished by external data. A simulation study is carried out to examine the influence of different priors on the performances of our estimator. We illustrate our approach by estimating the number of nesting bird species in a forest.     

Estimating the Occupancy Rate of Spatially Rare or Hard to Detect Species: A Conditional Approach

Summary We consider the problem of estimating the occupancy rate of a target species in a region divided in spatial units (called quadrats); this quantity being defined as the proportion of quadrats occupied by this species. We mainly focus on spatially rare or hard to detect species that are typically detected in very few quadrats, and for which estimating the occupancy rate (with an acceptable precision) is problematic. We develop a conditional approach for estimating the quantity of interest; we condition on the presence of the target species in the region of study. We show that conditioning makes identifiable the occurrence and detectability parameters, regardless of the number of visits made in the sampled quadrats. Compared with an unconditional approach, it proves to be complementary, in that this allows us to deal with biological questions that cannot be addressed by the former. Two Bayesian analyses of the data are performed: one is noninformative, and the other takes advantage of the fact that some prior information on detectability is available. It emerges that taking such a prior into account significantly improves the precision of the estimate when the target species has been detected in few quadrats and is known to be easily detectable.     

Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.     

Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod

Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway–located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.     

生物群落多样性的测度方法 V.生物群落物种数目的估计方法

群落的物种数目,即物种丰富度,是最古老、同时也是最基本的一个多样性概念,从对它的估计中可以得到关于物种灭绝速率方面的信息,这对生物多样性保护是非常重要的。已经提出了很多方法来估计群落中的物种数目,这些方法可以分为两大类,即基于理论抽样的方法和基于数据分析的方法。前者包括经典估计方法和贝叶斯估计方法;后者包括对数正态分布的积分方法、再抽样方法和种－面积曲线的外推方法。发现：（１）有些方法适用于动物群落,如大多数基于理论抽样的方法;有些方法则适用于植物群落,如大多数基于数据分析的方法;（２）这些方法还没有经过全面而系统地比较;（３）还没有一个普遍认为比较好的方法。因此,建议采用野外调查与模拟研究相结合的方法对各种估计方法进行系统地评价。     

Metabarcoding a diverse arthropod mock community

Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.     

Aliens in caves: the global dimension of biological invasions in subterranean ecosystems

Alien species are a significant threat to natural ecosystems and human economies. Despite global efforts to address this challenge, the documented number of alien species is rapidly increasing worldwide. However, the magnitude of the impact of alien species may vary significantly across habitats. For example, some habitats are naturally less prone to biological invasions due to stringent abiotic and biotic characteristics, selecting for a limited number of introduced species possessing traits closely related to the native organisms. Subterranean ecosystems are quintessential examples of habitats with strong environmental filters (e.g. lack of light and scarcity of food), driving convergent adaptations in species that have successfully adapted to life in darkness. Despite these stringent environmental constraints, the number of records of alien species in subterranean ecosystems has increased in recent decades, but the relevant literature remains largely fragmented and mostly anecdotal. Therefore, even though caves are generally considered very fragile ecosystems, their susceptibility to impacts by alien species remains untested other than for some very specific cases. We provide the first systematic literature survey to synthesise available knowledge on alien species in subterranean ecosystems globally. This review is supported by a database summarising the available literature, aiming to identify gaps in the distribution and spread of alien invertebrate species in subterranean habitats, and laying the foundations for future management practices and interventions. First, we quantitatively assessed the current knowledge of alien species in subterranean ecosystems to shed light on broader questions about taxonomic biases, geographical patterns, modes of dispersal, pathways for introductions and potential impacts. Secondly, we collected species-specific traits for each recorded alien species and tested whether subterranean habitats act as ecological filters for their establishment, favouring organisms with pre-adaptive traits suitable for subterranean life. We found information on the presence of 246 subterranean alien species belonging to 18 different classes. The dominant alien species were invertebrates, especially insects and arachnids. Most species were reported in terrestrial subterranean habitats from all continents except Antarctica. Palaearctic and Nearctic biogeographic regions represented the main source of alien species. The main routes of introductions into the recipient country are linked to commercial activities (84.3% of cases for which there was information available). Negative impacts have been documented for a small number of case studies (22.7%), mostly related to increased competition with native species. For a limited number of case studies (6.1%), management strategies were reported but the effectiveness of these interventions has rarely been quantified. Accordingly, information on costs is very limited. Approximately half of the species in our database can be considered established in subterranean habitats. According to our results, the presence of suitable traits grants access to the stringent environmental filter posed by subterranean environments, facilitating establishment in the new habitat. We recommend that future studies deepen the understanding of invasiveness into subterranean habitats, raising public and scientific community awareness of preserving these fragile ecosystems.     

Applications of Nematode Community Structure Research to Agricultural Production and Habitat Disturbance

Nematode communities in agricultural habitats are diverse, usually comprising tens of species and a large number of individuals. The study of nematode community structure can be approached in a number of ways which can be categorized under a synecological approach. Although the plant-parasitic species are of most obvious interest to plant hematologists, these are only a part of the nematode fauna that affects agroecosystems. The application of community structure research to investigation of those effects can help elucidate their importance. This information is not only intrinsically valuable, but it is necessary in the development of sustainable agricultural production systems.     

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

The abundance of different SSU rRNA (“16S”) gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly – from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.     

Bacterial community reconstruction using compressed sensing

Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. Our method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of all known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a simple and efficient way for identifying bacterial species compositions in biological samples. All supplementary data and the MATLAB code are available at www.broadinstitute.org/?orzuk/publications/BCS/.     

Estimation of local extinction rates when species detectability covaries with extinction probability: is it a problem?

Estimating the rate of change of the composition of communities is of direct interest to address many fundamental and applied questions in ecology. One methodological problem is that it is hard to detect all the species present in a community. Nichols et al. presented an estimator of the local extinction rate that takes into account species probability of detection, but little information is available on its performance. However, they predicted that if a covariance between species detection probability and local extinction rate exists in a community, the estimator of local extinction rate complement would be positively biased.
Here, we show, using simulations over a wide range of parameters that the estimator performs reasonably well. The bias induced by biological factors appears relatively weak. The most important factor enhancing the performance (bias and precision) of the local extinction rate complement estimator is sampling effort. Interestingly, a potentially important biological bias, such as the covariance effect, improves the estimation for small sampling efforts, without inducing a supplementary overestimation when these sampling efforts are high. In the field, all species are rarely detectable so we recommend the use of such estimators that take into account heterogeneity in species detection probability when estimating vital rates responsible for community changes.     

On molecular taxonomy: what is in a name?

Gene sequences of small portions of the genome are often used for premature detailed taxonomic changes, neglecting polyphasic taxonomy, which should also consider phenotypical characteristics. Three examples are given: (i) Recently, members of the genera Eperythrozoon and Haemobartonella have been moved, correctly so, from the Rickettsiales to the Mycoplasmatales, but were assigned to the genus Mycoplasma, mostly on the basis of 16S rRNA sequence analysis. Not only is the 16S rRNA sequence similarity between 'classical' Mycoplasma and these species of Eperythrozoon and Haemobartonella less than that between some other well-recognised bacterial genera, but their biological differences amply justify their classification in different genera of the Mycoplasmatales. Furthermore, the move creates considerable confusion, as it necessitates new names for some species, with more confusion likely to come when the 16S rRNA sequences of the type species of Eperythrozoon, a name which has priority over Mycoplasma, will be analysed. (ii) In the Rickettsiales, members of the genera Anaplasma, Ehrlichia, Cowdria, Neorickettsia and Wolhbachia are so closely related phylogenetically on the basis of 16S rRNA sequences, and for some also of groESL operon sequences, that they have recently been fused, correctly so, into one family, the Anaplasmataceae, while the tribes Ehrlichieae and Wolbachieae have been abolished. Sequence diversity within the 'classical' genus Ehrlichia has led to classifying E. phagocytophila (including E. equi and the agent of human granulocytic ehrlichiosis), E. platys and E. bovis in the genus Anaplasma, while others have been retained in Ehrlichia, which also includes Cowdria ruminantium. E. sennetsu and E. risticii have been transferred to the genus Neorickettsia. 16S rRNA and GroEL sequences of 'classical' Anaplasma and some members of 'classical' Ehrlichia do show a close relationship, but differences in citrate synthase gene sequences, the GC content of this gene, and sequences of the gene encoding the beta-subunit of RNA polymerase, not to speak of the phenotypical differences, do not justify the fusion into one genus. Because of the phylogenetical diversity in Ehrlichia it is recommended that a new genus name be created for the E. phagocytophila genogroup (and E. platys and E. bovis). (iii) One of the conclusions of studies on the phylogeny of ticks of the subfamilies Rhipicephalinae and Hyalomminae, based on nucleotide sequences from 12S rRNA, cytochrome c oxidase I, the internal transcribed spacer 2, 18S rRNA, as well as morphological characters, is that Boophilus should be considered as a subgenus of Rhipicephalus. While Boophilus and Rhipicephalus are undoubtedly close, the obviously important morphological and biological differences between the genera Rhipicephalus and Boophilus are thus overruled by similarities in the sequences of a number of genes and this leads to considerable confusion. Polyphasic taxonomy amply justifies maintaining Boophilus as a separate genus, phylogenetically near to Rhipicephalus. This note is a plea for a cautious and balanced approach to taxonomy, taking into account molecular genotypical information, as far as is possible from different genes, as well as phenotypical characteristics.     

The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast

The refinement and high-throughput of protein interaction detection methods offer us a protein–protein interaction network in yeast. The challenge coming along with the network is to find better ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of visualizing the network are unsuitable because of the large number of proteins. Here, we provide a simple but information-rich approach for visualization which integrates topological and biological information. In our method, the topological information such as quasi-cliques or spoke-like modules of the network is extracted into a clustering tree, where biological information spanning from protein functional annotation to expression profile correlations can be annotated onto the representation of it. We have developed a software named PINC based on our approach. Compared with previous clustering methods, our clustering method ADJW performs well both in retaining a meaningful image of the protein interaction network as well as in enriching the image with biological information, therefore is more suitable in visualization of the network.     

In search of universal patterns in community organization: the concept of neutrality paved the way to a new approach

The recent renewal of interest in community structure was strongly stimulated by the concept of neutrality, a new view on the problem of species coexistence. In contrast to traditional approach claiming that species competing for common resources should occupy different ecological niches, the neutrality concept assumes that species can coexist if they are ecologically identical, i.e., they have similar specific (per individual) rate of population growth, probability of extinction and the rate of colonization of free space. The analysis of recent literature, full of contradictory opinions on the ideas of neutrality and niche, can be resulted in form of following questions: (1) What do we suggest when we say that "species coexist"? (2) How can we explain the usual pattern of species relative abundances in a community, the so-called "hollow curve" (the distribution of numbers of species arranged in classes of abundance)? (3) Do rare species have some advantages in comparison with abundant species? (4) Can the mechanisms implied by neutrality concept and traditional niche approach work simultaneously in the same community? Trying to answer these questions we should: (1) refuse the demand of indefinite coexistence of species although this condition was considered as necessary in classical mathematical models of competition; (2) accept that community structure depends not only on ecological processes (species dispersal, competition and others) but also on the evolutionary ones (speciation) that determine the pool of species; (3) accept that rare species have some advantages as compared with the most abundant species; (4) accept that in any real community species can coexist either occupying the different niches or approaching ecological similarity. Despite considerable progress achieved in understanding of general principles of community organization, we still don't know how to answer the question "Why are there so many kinds of animals?" that was posed by Hutchinson 50 years ago.     

Hierarchical Bayesian Estimation for the Number of Species

This paper is concerned with the estimation of the number of species in a population through a fully hierarchical Bayesian model using the Metropolis algorithm. The proposed Bayesian estimator is based on Poisson random variables with means that are distributed according to some prior distributions with unknown hyperparameters. An empirical Bayes approach is considered and compared with the fully Bayesian approach based on biological data.     

Antennal sensory organs and glands of the harlequin ladybird,Harmonia axyridis

Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae) is a sub‐cosmopolitan species. Native to Asia, it has been released during the 20th century for classical and augmentative biological control of several herbivorous insects, mostly aphids and coccids. Despite its recognized positive impact on biological control, H. axyridis is now considered among the most dangerous invasive species in Europe and in most places where it has established. This is mostly due to its ability to reduce the populations of native predatory species of the same trophic guild. When exploring a new area, H. axyridis adults use semiochemical cues to acquire information about the habitat. Presumably, these cues are perceived by the sensilla located on the antennae. Surprisingly, in spite of the huge literature existing on H. axyridis, the antennal sensory organs have been poorly characterized. Here, we used scanning and transmission electron microscopy (SEM, TEM) techniques to study H. axyridis antennae, with focus on the various types of sensilla and their distribution in male and female individuals. The presence of various classes of antennal sensilla belonging to the main types described in insects (chemoreceptors, mechanoreceptors, and thermo‐hygroreceptors) was highlighted, as well as the widespread presence of antennal glands. The investigations showed some peculiar characteristics not known in Coccinellidae, such as the concentration of sensory structures at the level of the distal part of the apical antennomere and the discovery of antennal glands associated with it. No sexual dimorphism was revealed, neither for the general structure of the antenna (similar number of antennomeres and presence of modifications), nor for the total length and width of the antenna, the relative size of the antennomeres, the types of antennal sensilla, of their distribution and abundance. The potential relevance of these sensory structures and antennal glands, reported for the first time in Coccinellidae, is discussed in the context of intra‐ and interspecific communication.     

Environmental impact studies on marine communities: Pragmatical considerations

Abstract The measurement of changes in the structure of natural marine communities is widely used for the detection and monitoring of man's impact on the sea. Such studies are almost always a compromise between the scientific ideal and political, financial and logistical constraints. This paper considers a number of these constraints, suggests some possible solutions, and discusses the consequences (in terms of loss of information) of adopting strategies which might be considered suboptimal. Identification of all organisms in a community to species level is a major time and cost constraint. Many recent studies have shown that very little information is lost by working at a taxonomic level higher than species (e.g. family or even phylum). This implies a functional coherence of species within each higher taxon. Indeed, there are theoretical reasons, and some empirical evidence, for supposing that community responses to human perturbations may be more easily detected above the noise of natural variability by working at high taxonomic levels. Many environmental impacts, for example oil spillages from tankers, are accidental and it is unusual to have the luxury of a time-series of data from the site prior to the incident. Good spatial control samples may also be difficult to obtain in a heterogeneous environment. Absolute rather than comparative measures of community degradation are valuable in this context. Methods which fall into this category include comparisons of community structure with some theoretical expectation or with empirical‘training’ data, comparing attributes of community structure that respond differently to perturbation, or identifying highly conservative properties of unperturbed communities that are modified in a predictable way by perturbation. All studies are selective with regard to which components and attributes of the biota should be investigated. The choice frequently depends on local expertise and research interests, rather than on an objective decision about what biological data are most appropriate for the problem in hand. The paper concludes by a discussion of the relative merits of the various alternatives.     

Effects of salinity gradients on benthic invertebrate and diatom communities in a German lowland river

The Lippe is a lowland river located in the Western part of Germany and has been heavily impacted by coal mining activities ever since. Although mining activities significantly decreased during the last decades, the associated discharge of salt-enriched mine water into the river still poses a persistent threat to the local benthic invertebrate and diatom communities. To analyze the effect of salt pollution on invertebrate and diatom species, biological and chemical data were compiled for this study from a publicly available database. Changes in the community composition due to increased salt concentrations were explored by Non-Metrical-Multidimensional Scaling. Indicator species and salinity thresholds for single species and communities were identified using the method TITAN (Threshold Indicator Taxa Analysis). The method is an analytical approach to detect changes in frequency and abundance of species along an environmental gradient by combining the methods of change point analysis (nCPA) and indicator species analysis. The obtained salinity preferences and individual and community thresholds were compared to the literature and existing salinity classifications. For both diatoms and benthic invertebrates, Non-Metrical-Multidimensional Scaling showed a clear split between samples of high and low salinities. Significant salinity thresholds were determined for 50 invertebrate and 58 diatom species of which 23 respectively 18 species were described as ‘reliable’ indicators according to the specifications given by Baker and King (2010). A majority of salt-tolerant indicator organisms were invasive species. For both organism groups, major changes in community composition were detected at a conductivity value exceeding 900 μS/cm. A reduction of the average salinity to below this threshold may have positive effects on the overall species richness and the persistence of sensitive taxa in the river Lippe. Individual and community thresholds may however be data-dependent to a certain degree and subjected to fluctuations considering the potential interdependencies between salinity and additional physico-chemical and environmental parameters (e.g. water temperature, lime content).     

Can species data only be appropriately used to conserve biodiversity?

Despite widely acknowledged handicaps of the species approach to identifying priority conservation areas, many workers continue to use these flawed techniques as the backbone of their analyses. Species-based approaches address only a small part of biological diversity by ignoring different levels of organisation as well as the functional linkages among these levels. These data are often biased and incomplete and are often used in preference to data dealing with higher biological levels of organisation though the latter may be readily available. Within the framework of Noss's [(1990) Conservation Biology 4: 355–364] hierarchical definition of biodiversity (and Scott etal. [(1993) Wildlife Monographs 123: 1–31] gap analysis), we propose a top-down model dealing with broad organisational levels first, and finer-scale species distributions last. Note that we do not discard the latter approach, but merely argue for its use at a stage when, in our opinion, it adds most to the value of the prioritisation exercise. The model is flexible so that additional information, particularly those related to threats to biological diversity, can be added when they are available.