Polychaetes as surrogates for marine biodiversity: lower taxonomic resolution and indicator groups

Due to conservation needs, reliable rapid-assessment methods for mapping of biodiversity are needed. One approach is to use surrogates, i.e. quantities that correlate strongly with the number of species, but are easier to obtain. The purpose of this paper is to test two polychaete surrogates, one for higher taxa and one for indicator groups, that will facilitate prediction of species richness in marine soft-bottom communities. Soft sediment is an important habitat which covers most of the ocean bottom. Data on polychaetes from the North Atlantic were used since polychaetes are often numerically dominant in the benthic assemblages, both with regard to the number of species and their abundance. In the polychaete assemblages along the Norwegian coast, richness at the genus, family and order level were significantly, linearly correlated to total species richness (r 0.92). Polychaetes in the order Terebellida were found to be a good indicator of polychaete species richness and to a lesser extent also of whole benthic assemblages. The group Terebellida is potentially well suited as an indicator group, since it contains long-lived, large species that are easy to sort from the sediment and it is well defined taxonomically. Although promising as proxies for species richness in marine biodiversity studies, the use of lower taxonomic resolution and indicator groups requires further investigations in more local areas where there are conservation issues.     

Natural regeneration and biodiversity: a global meta‐analysis and implications for spatial planning

Natural regeneration offers a cheaper alternative to active reforestation and has the potential to become the predominant way of restoring degraded tropical landscapes at large‐scale. We conducted a meta‐analysis for tropical regions and quantified the relationships between both ecological and socioeconomic factors and biodiversity responses in naturally regenerating areas. Biogeographic realms, past disturbance, and the human development index (HDI) were used as explanatory variables for biodiversity responses. In addition, we present a case study of large‐scale natural regeneration in the Brazilian Atlantic Forest and identify areas where different forms of restoration would be most suitable. Using our dataset for tropical regions, we showed that natural regeneration was predominantly reported within: the Neotropical realm; areas that were intensively disturbed; and countries with medium HDI. We also found that biodiversity in regenerating forests was more similar to the values found in old growth forests in: countries with either low, high, or very high HDI; less biodiverse realms; and areas of less intensive past disturbance. Our case study from Brazil showed that the level of forest gain resulting from environmental legislation, in particular the Brazilian Forest Code, has been reduced, but remains substantial. Complementary market incentives and financial mechanisms to promote large‐scale natural regeneration in human‐modified agricultural landscapes are also needed. Our analysis provides insights into the factors that promote or limit the recovery of biodiversity in naturally regenerating areas, and aids to identify areas with higher potential for natural regeneration.     

The effects of livestock grazing on biodiversity are multi‐trophic: a meta‐analysis

Anthropogenic disturbance has generated a significant loss of biodiversity worldwide and grazing by domestic herbivores is a contributing disturbance. Although the effects of grazing on plants are commonly explored, here we address the potential multi‐trophic effects on animal biodiversity (e.g. herbivores, pollinators and predators). We conducted a meta‐analysis on 109 independent studies that tested the response of animals or plants to livestock grazing relative to livestock excluded. Across all animals, livestock exclusion increased abundance and diversity, but these effects were greatest for trophic levels directly dependent on plants, such as herbivores and pollinators. Detritivores were the only trophic level whose abundance decreased with livestock exclusion. We also found that the number of years since livestock was excluded influenced the community and that the effects of grazer exclusion on animal diversity were strongest in temperate climates. These findings synthesise the effects of livestock grazing beyond plants and demonstrate the indirect impacts of livestock grazing on multiple trophic levels in the animal community. We identified the potentially long‐term impacts that livestock grazing can have on lower trophic levels and consequences for biological conservation. We also highlight the potentially inevitable cost to global biodiversity from livestock grazing that must be balanced against socio‐economic benefits.     

Biodiversity in cities needs space: a meta‐analysis of factors determining intra‐urban biodiversity variation

Understanding varying levels of biodiversity within cities is pivotal to protect it in the face of global urbanisation. In the early stages of urban ecology studies on intra‐urban biodiversity focused on the urban–rural gradient, representing a broad generalisation of features of the urban landscape. Increasingly, studies classify the urban landscape in more detail, quantifying separately the effects of individual urban features on biodiversity levels. However, while separate factors influencing biodiversity variation among cities worldwide have recently been analysed, a global analysis on the factors influencing biodiversity levels within cities is still lacking. We here present the first meta‐analysis on intra‐urban biodiversity variation across a large variety of taxonomic groups of 75 cities worldwide. Our results show that patch area and corridors have the strongest positive effects on biodiversity, complemented by vegetation structure. Local, biotic and management habitat variables were significantly more important than landscape, abiotic or design variables. Large sites greater than 50 ha are necessary to prevent a rapid loss of area‐sensitive species. This indicates that, despite positive impacts of biodiversity‐friendly management, increasing the area of habitat patches and creating a network of corridors is the most important strategy to maintain high levels of urban biodiversity.     

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.     

National biodiversity risk assessment: a composite multivariate and index approach

Due to the shortage of financial resources for international conservation assistance, the setting of priorities for this assistance is an important issue. A national biodiversity risk assessment index (NABRAI) is constructed to quantify national conservation performances and identify nation states of critical conservation concern. The index, which contains measures of biodiversity stock, flow and response measures, attempts to overcome several weaknesses present in other models used to prioritize nations for conservation assistance. Multivariate analyses of the index as well as economic and biodiversity resources reveal significant positive correlations between the NABRAI values and population density as well as land area exposed to high disturbance intensity. The combination of the multivariate analyses and the interpretation of NABRAI values allows for prioritization of biodiversity risk among the global community and can thus serve as an indicator of current priorities for policy makers. The present study also suggests two methods to incorporate a better understanding of biodiversity risk in models of conservation priorities; by including a wider range of variables and by developing a theoretical foundation for the relationship between the categories of variables used in the model.     

How quantitative is metabarcoding: A meta‐analytical approach

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.     

Interactions between climate and habitat loss effects on biodiversity: a systematic review and meta‐analysis

Climate change and habitat loss are both key threatening processes driving the global loss in biodiversity. Yet little is known about their synergistic effects on biological populations due to the complexity underlying both processes. If the combined effects of habitat loss and climate change are greater than the effects of each threat individually, current conservation management strategies may be inefficient and at worst ineffective. Therefore, there is a pressing need to identify whether interacting effects between climate change and habitat loss exist and, if so, quantify the magnitude of their impact. In this article, we present a meta‐analysis of studies that quantify the effect of habitat loss on biological populations and examine whether the magnitude of these effects depends on current climatic conditions and historical rates of climate change. We examined 1319 papers on habitat loss and fragmentation, identified from the past 20 years, representing a range of taxa, landscapes, land‐uses, geographic locations and climatic conditions. We find that current climate and climate change are important factors determining the negative effects of habitat loss on species density and/or diversity. The most important determinant of habitat loss and fragmentation effects, averaged across species and geographic regions, was current maximum temperature, with mean precipitation change over the last 100 years of secondary importance. Habitat loss and fragmentation effects were greatest in areas with high maximum temperatures. Conversely, they were lowest in areas where average rainfall has increased over time. To our knowledge, this is the first study to conduct a global terrestrial analysis of existing data to quantify and test for interacting effects between current climate, climatic change and habitat loss on biological populations. Understanding the synergistic effects between climate change and other threatening processes has critical implications for our ability to support and incorporate climate change adaptation measures into policy development and management response.     

Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta‐analytic review

Comparative analyses aim to explain interspecific variation in phenotype among taxa. In this context, phylogenetic approaches are generally applied to control for similarity due to common descent, because such phylogenetic relationships can produce spurious similarity in phenotypes (known as phylogenetic inertia or bias). On the other hand, these analyses largely ignore potential biases due to within‐species variation. Phylogenetic comparative studies inherently assume that species‐specific means from intraspecific samples of modest sample size are biologically meaningful. However, within‐species variation is often significant, because measurement errors, within‐ and between‐individual variation, seasonal fluctuations, and differences among populations can all reduce the repeatability of a trait. Although simulations revealed that low repeatability can increase the type I error in a phylogenetic study, researchers only exercise great care in accounting for similarity in phenotype due to common phylogenetic descent, while problems posed by intraspecific variation are usually neglected. A meta‐analysis of 194 comparative analyses all adjusting for similarity due to common phylogenetic descent revealed that only a few studies reported intraspecific repeatabilities, and hardly any considered or partially dealt with errors arising from intraspecific variation. This is intriguing, because the meta‐analytic data suggest that the effect of heterogeneous sampling can be as important as phylogenetic bias, and thus they should be equally controlled in comparative studies. We provide recommendations about how to handle such effects of heterogeneous sampling.     

Optimal investment for enhancing social concern about biodiversity conservation: A dynamic approach

To maintain biodiversity conservation areas, we need to invest in activities, such as monitoring the condition of the ecosystem, preventing illegal exploitation, and removing harmful alien species. These require a constant supply of resources, the level of which is determined by the concern of the society about biodiversity conservation. In this paper, we study the optimal fraction of the resources to invest in activities for enhancing the social concern y(t) by environmental education, museum displays, publications, and media exposure. We search for the strategy that maximizes the time-integral of the quality of the conservation area x(t) with temporal discounting. Analyses based on dynamic programming and Pontryagin’s maximum principle show that the optimal control consists of two phases: (1) in the first phase, the social concern level approaches to the final optimal value y^∗, (2) in the second phase, resources are allocated to both activities, and the social concern level is kept constant y(t)=y^∗. If the social concern starts from a low initial level, the optimal path includes a period in which the quality of the conservation area declines temporarily, because all the resources are invested to enhance the social concern. When the support rate increases with the quality of the conservation area itself x(t) as well as with the level of social concern y(t), both variables may increase simultaneously in the second phase. We discuss the implication of the results to good management of biodiversity conservation areas.     

Design of Mini‐barcode for Catfishes for assessment of archival biodiversity

Recovery of DNA barcode sequences is often challenging from the archived specimens. However, short fragments of DNA may be recovered, which would significantly improve many unresolved taxonomic conflicts. Here, we designed a mini‐barcode for catfishes comprising several species and many cryptic taxa. We analysed a data set of 3048 publicly available COI barcode sequences representing 547 worldwide catfish species and performed 152 628 interspecies comparisons. A significantly more positively correlated interspecies distance was detected with transversion (0.78, P < 0.001) than with transition (0.70, P < 0.001). This suggested that transversions were better diagnostics for species identification. In the aligned data set, two transversion‐rich fragments (53 bp and 119 bp) were identified. Transition/transversion bias value was 1.04 in 53‐bp fragment, 1.23 in 119‐bp fragment and 1.50 in full‐length barcode. The interspecies distance with full‐length barcode was 0.212 ± 0.037, while that with 53‐bp and 119‐bp fragments was 0.325 ± 0.039 and 0.218 ± 0.045, respectively. Survey of 53‐bp fragment showed a possibility of only 1144 barcodes, while that of 119‐bp fragment showed >4 million barcodes. Thus, the 119‐bp fragment is a viable mini‐barcode for catfishes comprising >3000 extant species. Experiment with 82 archived catfishes showed successful recovery of this mini‐barcode using the designed primer. The mini‐barcode sequences showed species‐specific similarity in the range of 98‐100% with the global database. Therefore, survey of a transversion‐rich fragment within the full‐length barcode would be an ideal approach of mini‐barcode design for biodiversity assessment.     

Effects of livestock grazing on rangeland biodiversity: A meta‐analysis of grouse populations

Livestock grazing affects over 60% of the world's agricultural lands and can influence rangeland ecosystem services and the quantity and quality of wildlife habitat, resulting in changes in biodiversity. Concomitantly, livestock grazing has the potential to be detrimental to some wildlife species while benefiting other rangeland organisms. Many imperiled grouse species require rangeland landscapes that exhibit diverse vegetation structure and composition to complete their life cycle. However, because of declining populations and reduced distributions, grouse are increasingly becoming a worldwide conservation concern. Grouse, as a suite of upland gamebirds, are often considered an umbrella species for other wildlife and thus used as indicators of rangeland health. With a projected increase in demand for livestock products, better information will be required to mitigate the anthropogenic effects of livestock grazing on rangeland biodiversity. To address this need, we completed a data‐driven and systematic review of the peer‐reviewed literature to determine the current knowledge of the effects of livestock grazing on grouse populations (i.e., chick production and population indices) worldwide. Our meta‐analysis revealed an overall negative effect of livestock grazing on grouse populations. Perhaps more importantly, we identified an information void regarding the effects of livestock grazing on the majority of grouse species. Additionally, the reported indirect effects of livestock grazing on grouse species were inconclusive and more reflective of differences in the experimental design of the available studies. Future studies designed to evaluate the direct and indirect effects of livestock grazing on wildlife should document (i) livestock type, (ii) timing and frequency of grazing, (iii) duration, and (iv) stocking rate. Much of this information was lacking in the available published studies we reviewed, but is essential when making comparisons between different livestock grazing management practices and their potential impacts on rangeland biodiversity.     

A population‐averaged approach to diagnostic test meta‐analysis

The meta‐analysis of diagnostic accuracy studies is often of interest in screening programs for many diseases. The typical summary statistics for studies chosen for a diagnostic accuracy meta‐analysis are often two dimensional: sensitivities and specificities. The common statistical analysis approach for the meta‐analysis of diagnostic studies is based on the bivariate generalized linear‐mixed model (BGLMM), which has study‐specific interpretations. In this article, we present a population‐averaged (PA) model using generalized estimating equations (GEE) for making inference on mean specificity and sensitivity of a diagnostic test in the population represented by the meta‐analytic studies. We also derive the marginalized counterparts of the regression parameters from the BGLMM. We illustrate the proposed PA approach through two dataset examples and compare performance of estimators of the marginal regression parameters from the PA model with those of the marginalized regression parameters from the BGLMM through Monte Carlo simulation studies. Overall, both marginalized BGLMM and GEE with sandwich standard errors maintained nominal 95% confidence interval coverage levels for mean specificity and mean sensitivity in meta‐analysis of 25 of more studies even under misspecification of the covariance structure of the bivariate positive test counts for diseased and nondiseased subjects.     

Carrion fly‐derived DNA as a tool for comprehensive and cost‐effective assessment of mammalian biodiversity

Large‐scale monitoring schemes are essential in assessing global mammalian biodiversity, and in this framework, leeches have recently been promoted as an indirect source of DNA from terrestrial mammal species. Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly‐derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of Côte d'Ivoire and Madagascar for mammal DNA using multiple PCR systems and retrieved DNA sequences from a diverse set of species (22 in Côte d'Ivoire, four in Madagascar) exploiting distinct forest strata and displaying a broad range of body sizes. Deep sequencing of amplicons generated from pools of flies performed equally well as individual sequencing approaches. We conclude that the analysis of fly‐derived DNA can be implemented in a very rapid and cost‐effective manner and will give a relatively unbiased picture of local mammal diversity. Carrion flies therefore represent an extraordinary and thus far unexploited resource of mammal DNA, which will probably prove useful for future inventories of wild mammal communities.     

Hybridisation is associated with increased fecundity and size in invasive taxa: meta‐analytic support for the hybridisation‐invasion hypothesis

The hypothesis that interspecific hybridisation promotes invasiveness has received much recent attention, but tests of the hypothesis can suffer from important limitations. Here, we provide the first systematic review of studies experimentally testing the hybridisation‐invasion (H‐I) hypothesis in plants, animals and fungi. We identified 72 hybrid systems for which hybridisation has been putatively associated with invasiveness, weediness or range expansion. Within this group, 15 systems (comprising 34 studies) experimentally tested performance of hybrids vs. their parental species and met our other criteria. Both phylogenetic and non‐phylogenetic meta‐analyses demonstrated that wild hybrids were significantly more fecund and larger than their parental taxa, but did not differ in survival. Resynthesised hybrids (which typically represent earlier generations than do wild hybrids) did not consistently differ from parental species in fecundity, survival or size. Using meta‐regression, we found that fecundity increased (but survival decreased) with generation in resynthesised hybrids, suggesting that natural selection can play an important role in shaping hybrid performance – and thus invasiveness – over time. We conclude that the available evidence supports the H‐I hypothesis, with the caveat that our results are clearly driven by tests in plants, which are more numerous than tests in animals and fungi.