Multiple data sources and freely available code is critical when investigating species distributions and diversity: a response to Knouft (2018)

A recent comment from Knouft ( 2018 ) has suggested that our original article (Dallas et al. 2017 ) was an ‘inappropriate application of biodiversity data’. Here, we affirm our results, and address the more general point about biodiversity data use.     

Biodiversity monitoring,earth observations and the ecology of scale

Human activity and land‐use change are dramatically altering the sizes, geographical distributions and functioning of biological populations worldwide, with tremendous consequences for human well‐being. Yet our ability to measure, monitor and forecast biodiversity change – crucial to addressing it – remains limited. Biodiversity monitoring systems are being developed to improve this capacity by deriving metrics of change from an array of in situ data (e.g. field plots or species occurrence records) and Earth observations (EO; e.g. satellite or airborne imagery). However, there are few ecologically based frameworks for integrating these data into meaningful metrics of biodiversity change. Here, I describe how concepts of pattern and scale in ecology could be used to design such a framework. I review three core topics: the role of scale in measuring and modelling biodiversity patterns with EO, scale‐dependent challenges linking in situ and EO data and opportunities to apply concepts of pattern and scale to EO to improve biodiversity mapping. From this analysis emerges an actionable approach for measuring, monitoring and forecasting biodiversity change, highlighting key opportunities to establish EO as the backbone of global‐scale, science‐driven conservation.     

Botanical information in the Italian Biodiversity Network: One year of data aggregation and future perspectives

Since its formal institution in May 2012, the Italian Biodiversity Network is aggregating data from several research centres, for a total of ca. 1.5 million records. Botanical data made ca. 50% of the total, and range from primary biodiversity data to ecological, morpho-anatomical and taxonomical information. However, this is only a small portion of the total amount of botanical data which could be aggregated and exposed to the scientific community, professionals and citizens. In this paper we present the current status of data aggregation of the Network and its impact on digitalisation of biodiversity data, research, conservation and environmental management and education in Italy.     

Integrating conservation and development: incorporating vulnerability into biodiversity-assessment of areas

Protection of regional biodiversity requires that priority for protection of individual areas be based on both the contribution the area can make to representing overall biodiversity and the degree to which the area, in the absence of action, is vulnerable to loss of its biodiversity. Attempts to apply these criteria together largely have been ad hoc. A solution to this problem is presented for environmental surrogate data, based on environmental diversity (ED). ED uses a standard ecological continuum model to link environmental pattern to species-level biodiversity, so that a set of areas can be characterized by its relative expected biodiversity. This allows explicit incorporation of estimates of area-vulnerability, interpreted as the relative probability that any member species will not persist, into biodiversity assessments. The contribution of a given area to regional expected biodiversity is influenced not only by its own vulnerability value, but also by the vulnerability of other areas. Increasing the degree of protection of any area (reducing its vulnerability) will increase expected biodiversity: however, expected regional biodiversity sometimes may be maximized when limited resources for protection are directed to an area with lower vulnerability rather than to one with higher vulnerability.The allocation of land uses in a region need not be viewed as an all-or-nothing assignment of protection. The effect of a particular management regime on the biodiversity of a given area can be equated with some consequent degree of vulnerability; viewed positively, a management regime that offers some degree of biodiversity protection can make a measurable contribution to the protection of the biodiversity of a region.     

Downscaling land‐use data to provide global 30″ estimates of five land‐use classes

Land‐use change is one of the biggest threats to biodiversity globally. The effects of land use on biodiversity manifest primarily at local scales which are not captured by the coarse spatial grain of current global land‐use mapping. Assessments of land‐use impacts on biodiversity across large spatial extents require data at a similar spatial grain to the ecological processes they are assessing. Here, we develop a method for statistically downscaling mapped land‐use data that combines generalized additive modeling and constrained optimization. This method was applied to the 0.5° Land‐use Harmonization data for the year 2005 to produce global 30″ (approx. 1 km²) estimates of five land‐use classes: primary habitat, secondary habitat, cropland, pasture, and urban. The original dataset was partitioned into 61 bio‐realms (unique combinations of biome and biogeographical realm) and downscaled using relationships with fine‐grained climate, land cover, landform, and anthropogenic influence layers. The downscaled land‐use data were validated using the PREDICTS database and the geoWiki global cropland dataset. Application of the new method to all 61 bio‐realms produced global fine‐grained layers from the 2005 time step of the Land‐use Harmonization dataset. Coarse‐scaled proportions of land use estimated from these data compared well with those estimated in the original datasets (mean R²: 0.68 ± 0.19). Validation with the PREDICTS database showed the new downscaled land‐use layers improved discrimination of all five classes at PREDICTS sites (P < 0.0001 in all cases). Additional validation of the downscaled cropping layer with the geoWiki layer showed an R² improvement of 0.12 compared with the Land‐use Harmonization data. The downscaling method presented here produced the first global land‐use dataset at a spatial grain relevant to ecological processes that drive changes in biodiversity over space and time. Integrating these data with biodiversity measures will enable the reporting of land‐use impacts on biodiversity at a finer resolution than previously possible. Furthermore, the general method presented here could be useful to others wishing to downscale similarly constrained coarse‐resolution data for other environmental variables.     

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata,Ciliophora)

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN‐BC proposes to populate The Ciliate Guide, an online database, with biodiversity‐related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.     

Diversity patterns in grasslands along a landscape gradient in northwestern France

Abstract. Several measures of biodiversity were calculated (species richness SR, species diversity H', species evenness J', mean similarity, mosaic diversity and factorial diversity) in vascular plant communities along a landscape gradient in the Seine valley, Normandy, France. For these communities, we also recorded environmental and management data. Species and environmental data were analysed simultaneously by Canonical Correspondence Analysis (CCA) in order to study their relationships. CCA identifies one main landscape gradient linked to a set of highly linked ecological factors. Three community types were identified along this gradient: calcicolous communities on chalk slopes, mesophilous communities on colluvium and hydrophilous communities on alluviums. The measures of biodiversity between these groups and their variations along the landscape gradient indicate similar patterns for H', J' and SR. Between‐community biodiversity measures allow consideration of the distribution of species among communities in the landscape. Factorial diversity accounts for the organisation of the communities with reference to the basic mechanisms of species coexistence. Affinity analysis (similarity and mosaic diversity) measures the compositional pattern diversity, which is the function of the variation in species richness. We discuss the indicative versus the predictive value of these measures of biodiversity as regards ecological factors and processes and their application for conservation purposes.     

黄河下游农业景观中不同生境类型地表节肢动物优势类群

生物多样性是连接景观异质性与生态系统服务的桥梁。在区域尺度上,以指示类群代替地表节肢动物类群,可以有效的开展生物多样性的保护工作。但是,在黄河下游农业景观中,关于地表节肢动物指示类群的研究报道较少。以黄河下游农业景观中4种生境类型(农田、林地、树篱和沟渠)为研究样地,且在农田生境中划分不同尺度(尺度1,3.6 hm2、尺度2,14 hm2和尺度3,28 hm2),通过调查不同生境中地表节肢动物分布及其多样性,结合地表节肢动物优势类群的辨识,分析了优势类群和地表节肢动物多样性的相关性,确定了研究区内地表节肢动物多样性的指示类群。结果发现:研究区内地表节肢动物优势类群为膜翅目、鞘翅目和蜘蛛目。树篱和林地生境的地表节肢动物多样性指示类群是膜翅目,农田生境中地表节肢动物多样性指示类群是鞘翅目,沟渠生境中地表节肢动物多样性指示类群是蜘蛛目。农田生境中优势类群间无相关性(P0.05);林地、沟渠和树篱生境中鞘翅目与蜘蛛目之间存在显著正相关(P0.01);林地和沟渠生境中,鞘翅目与膜翅目之间存在正相关(P0.05)。在农田生境中优势类群之间的相关性存在尺度依赖性,随着空间尺度的增大,相关性有一定的增强。在尺度2和尺度3上膜翅目和鞘翅目均存在正相关(P0.05),并且随着尺度增加而呈上升趋势。研究表明,黄河下游农业景观中不同生境类型地表节肢动物多样性的指示类群差别较大,其中树篱和林地生境具有较高的相似性,而农田生境地表节肢动物优势类群相关性存在尺度依赖性。在黄河下游农业景观中,以优势类群多样性代替地表节肢动物类群的多样性,可以在条件不足、时间紧迫的情况下更加有效的开展生物多样性的保护工作。     

Tree biodiversity in protected and logged Bornean tropical rain forests and its measurement by satellite remote sensing

Aim Conservation activities have increasingly focused on issues at the level of the landscape but are constrained by limited data and knowledge relating to biodiversity at this scale. Satellite remote sensing has considerable, but under‐exploited, potential as a source of information on biodiversity at the landscape level. Remote sensing has generally been used to assess biodiversity indirectly, using approaches that often fail to fully exploit the information content of the imagery and typically only with regard to the species richness component of biodiversity. The aim of this paper was to assess the potential of remote sensing as a source of information on the richness, evenness and composition of tree species in a tropical rain forest. Location The test site was a c. 225 km² region centred on the Danum Valley Field Centre, Borneo. This test site contained regions of undisturbed and differentially logged rain forest. Methods Data on tree biodiversity had been acquired for fifty‐two sample plots by standard field survey methods and were used to derive summary indices of biodiversity for seedlings, saplings and mature trees. Differences between logged and unlogged sites were evaluated by comparison of the indices and species accumulation curves. A Landsat Thematic Mapper (TM) image of the site acquired close to the date of the field survey was obtained and rigorously pre‐processed. Feedforward neural networks were used to derive predictions of biodiversity indices from the imagery. A Kohonen self organizing map neural network was used to ordinate the field data to derive classes of forest defined by relative similarity in species composition. The separability of the defined classes in the Landsat TM image was evaluated with a discriminant analysis. Results Analyses of the field data revealed considerable variation in the biodiversity of seedlings, saplings and trees at the site, associated, in part, with differences in logging activities. This variation in biodiversity was manifest in the remotely sensed data. The analyses indicated an ability to (1) predict biodiversity indices, with the highest correlation between predicted and actual index observed for evenness described by Shannon entropy (r = 0.546), but especially to (2) classify nine forest classes defined on the basis of similarity in tree species composition (accuracy 95.8%). Main conclusions Logging activities impacted on biodiversity and the resulting variation in biodiversity was reflected in the remotely sensed imagery. Using methods that exploit more fully the information content of the imagery than those used in other previous studies, a richer representation of biodiversity may be derived. This representation includes estimates of key summary indices of biodiversity, notably richness and evenness, as well as information on species composition. The results indicate that remotely sensed data may be used as a source of information on biodiversity at the landscape scale that may be used to inform conservation science and management.     

Funding begets biodiversity

Aim Effective conservation of biodiversity relies on an unbiased knowledge of its distribution. Conservation priority assessments are typically based on the levels of species richness, endemism and threat. Areas identified as important receive the majority of conservation investments, often facilitating further research that results in more species discoveries. Here, we test whether there is circularity between funding and perceived biodiversity, which may reinforce the conservation status of areas already perceived to be important while other areas with less initial funding may remain overlooked. Location Eastern Arc Mountains, Tanzania. Methods We analysed time series data (1980–2007) of funding (n = 134 projects) and plant species records (n = 75,631) from a newly compiled database. Perceived plant diversity, over three decades, is regressed against funding and environmental factors, and variances decomposed in partial regressions. Cross‐correlations are used to assess whether perceived biodiversity drives funding or vice versa. Results Funding explained 65% of variation in perceived biodiversity patterns – six times more variation than accounted for by 34 candidate environmental factors. Cross‐correlation analysis showed that funding is likely to be driving conservation priorities and not vice versa. It was also apparent that investment itself may trigger further investments as a result of reduced start‐up costs for new projects in areas where infrastructure already exists. It is therefore difficult to establish whether funding, perceived biodiversity, or both drive further funding. However, in all cases, the results suggest that regional assessments of biodiversity conservation importance may be biased by investment. Funding effects might also confound studies on mechanisms of species richness patterns. Main conclusions Continued biodiversity loss commands urgent conservation action even if our knowledge of its whereabouts is incomplete; however, by concentrating inventory funds in areas already perceived as important in terms of biodiversity and/or where start‐up costs are lower, we risk losing other areas of underestimated or unknown value.     

Biodiversity Clearing-House Mechanism in China: present status and future needs

China is one of the 'megadiversity' countries of the world, and is therefore rich in biodiversity information. The decision making on biodiversity conservation and sustainable utilization demands sufficient, accurate, data and information which covers living things as well as natural background and human activities. It is estimated that 152 biodiversity databases have been developed in China, mainly distributed in the thematic information categories of forestry, nature reserve, forest ecosystem, animal, plant, crop germplasm resource, traditional Chinese medicine, water resource, geology/geography, and climate/meteorology, etc. The status quo of biodiversity information system was also reviewed and main information networks related to biodiversity were presented. There are problems in the CHM construction in China, such as insufficient funding, unreasonable organizational mechanism, and low-level information sharing. Future needs for the CHM construction were discussed.     

Identifying practical indicators of biodiversity for stand-level management of plantation forests

Identification of valid indicators of biodiversity is a critical need for sustainable forest management. We developed compositional, structural and functional indicators of biodiversity for five taxonomic groups—bryophytes, vascular plants, spiders, hoverflies and birds—using data from 44 Sitka spruce (Picea sitchensis) and ash (Fraxinus excelsior) plantation forests in Ireland. The best structural biodiversity indicator was stand stage, defined using a multivariate classification of forest structure variables. However, biodiversity trends over the forest cycle and between tree species differ among the taxonomic groups studied. Canopy cover was the main structural indicator and affected other structural variables such as cover of lower vegetation layers. Other structural indicators included deadwood and distances to forest edge and to broadleaved woodland. Functional indicators included stand age, site environmental characteristics and management practices. Compositional indicators were limited to more easily identifiable plant and bird species. Our results suggest that the biodiversity of any one of the species groups we surveyed cannot act as a surrogate for all of the other species groups. However, certain subgroups, such as forest bryophytes and saproxylic hoverflies, may be able to act as surrogates for each other. The indicators we have identified should be used together to identify stands of potentially high biodiversity or to evaluate the biodiversity effects of silvicultural management practices. They are readily assessed by non-specialists, ecologically meaningful and applicable over a broad area with similar climate conditions and silvicultural systems. The approach we have used to develop biodiversity indicators, including stand structural types, is widely relevant and can enhance sustainable forest management of plantations.     

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence‐only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi‐source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter‐ or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi‐source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA‐based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.     

Improving biodiversity monitoring

Effective biodiversity monitoring is critical to evaluate, learn from, and ultimately improve conservation practice. Well conceived, designed and implemented monitoring of biodiversity should: (i) deliver information on trends in key aspects of biodiversity (e.g. population changes); (ii) provide early warning of problems that might otherwise be difficult or expensive to reverse; (iii) generate quantifiable evidence of conservation successes (e.g. species recovery following management) and conservation failures; (iv) highlight ways to make management more effective; and (v) provide information on return on conservation investment. The importance of effective biodiversity monitoring is widely recognized (e.g. Australian Biodiversity Strategy). Yet, while everyone thinks biodiversity monitoring is a good idea, this has not translated into a culture of sound biodiversity monitoring, or widespread use of monitoring data. We identify four barriers to more effective biodiversity monitoring in Australia. These are: (i) many conservation programmes have poorly articulated or vague objectives against which it is difficult to measure progress contributing to design and implementation problems; (ii) the case for long‐term and sustained biodiversity monitoring is often poorly developed and/or articulated; (iii) there is often a lack of appropriate institutional support, co‐ordination, and targeted funding for biodiversity monitoring; and (iv) there is often a lack of appropriate standards to guide monitoring activities and make data available from these programmes. To deal with these issues, we suggest that policy makers, resource managers and scientists better and more explicitly articulate the objectives of biodiversity monitoring and better demonstrate the case for greater investments in biodiversitymonitoring. There is an urgent need for improved institutional support for biodiversity monitoring in Australia, for improved monitoring standards, and for improved archiving of, and access to, monitoring data. We suggest that more strategic financial, institutional and intellectual investments in monitoring will lead to more efficient use of the resources available for biodiversity conservation and ultimately better conservation outcomes.     

生物多样性与生态系统服务评估指标与方法

评估、模拟和预测全球生物多样性和生态系统服务的状态、趋势及其对人类福祉的影响,是当前生物多样性和生态系统服务研究领域的重要任务。指标和数据、模型和情景是推动生物多样性与生态系统服务评估研究理论建设和方法集成的重要工具。但是,目前对生物多样性和生态系统服务评估的指标体系和技术方法的综合对比研究相对缺乏。因而,系统评述了生物多样性和生态系统服务评估的概念框架、评估指标以及各类评估模型和方法的最新进展。生物多样性—生态系统功能—生态系统服务—人类福祉的级联框架是极具逻辑性的生物多样性和生态系统服务评估框架。现有的评估指标体系和模型方法还存在很多的问题和挑战,难以充分揭示生态系统服务的形成和影响机制、服务之间的联系和作用机理,有效地指导生态系统服务管理和决策制定。然而,这些评估指标和方法可为构建生物多样性与生态系统服务综合集成模型研究的框架提供重要的切入点。基于此,提出了生物多样性与生态系统服务综合集成模型研究的核心内容:i)目的:基于自然—社会综合特征的情景分析确定所解决的科学问题,输出生态系统服务管理和决策制定方案;ii)内容:尺度、生态系统服务类型、生物多样性的层次结构、组分间相互关系、驱动要素、多源数据的综合分析;iii)方法:对现有的各类模型和模型组合进行比较和不确定性分析,建立符合区域实际需求的生物多样性与生态系统服务综合制图模型库。在此基础上,建议我国应尽快发展适合中国区域特点的标准化指标体系和综合评估模型系统,定期对生物多样性和生态系统服务进行综合评估,掌握生物多样性和生态系统服务的变化趋势,提升我国在生物多样性和生态系统服务研究领域的国际地位和话语权。     

Avian biodiversity in the coastal wetlands of the Okahukura Peninsula

The Tapora Landcare Group, operating on the Okahukura Peninsula, has the long-term goal of making this region predator fenced. The aim of this study was to obtain information on the current status of avian biodiversity and the bird community across the band of coastal wetlands on the Okahukura Peninsula. Bird counts were conducted and playback lures used to detect three cryptic wetland species: fernbirds (Bowdleria punctata); spotless crakes (Porzana tabuensis); and banded rails (Gallirallus philippensis). Fernbirds and banded rails were detected at seven of the eight wetland sites sampled whereas spotless crakes were detected at two sites. The native species with the highest relative abundance across the eight sites were silvereyes (Zosterops lateralis) and South Island pied oystercatchers (Haematopus finschi). Changes in avian biodiversity over time in the region can now be monitored, and comprehensive long-term data on the status of avian biodiversity over time obtained.     

Tectonics,climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.     

Assessing the performance of DNA barcoding using posterior predictive simulations

Accurate estimates of biodiversity are required for research in a broad array of biological subdisciplines including ecology, evolution, systematics, conservation and biodiversity science. The use of statistical models and genetic data, particularly DNA barcoding, has been suggested as an important tool for remedying the large gaps in our current understanding of biodiversity. However, the reliability of biodiversity estimates obtained using these approaches depends on how well the statistical models that are used describe the evolutionary process underlying the genetic data. In this study, we utilize data from the Barcode of Life Database and posterior predictive simulations to assess the performance of DNA barcoding under commonly used substitution models. We demonstrate that the success of DNA barcoding varies widely across DNA substitution models and that model choice has a substantial impact on the number of operational taxonomic units identified (changing results by ~4–31%). Additionally, we demonstrate that the widely followed practice of a priori assuming the Kimura 2‐parameter model for DNA barcoding is statistically unjustified and should be avoided. Using both data‐based and inference‐based test statistics, we detect variation in model performance across taxonomic groups, clustering algorithms, genetic divergence thresholds and substitution models. Taken together, these results illustrate the importance of considering both model selection and model adequacy in studies quantifying biodiversity.     

Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province

The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal‐limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate‐induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low‐dispersing species to shed light on small‐scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots.     

Managed livestock grazing for conservation outcomes in a Queensland fragmented landscape

Protecting native biodiversity is a difficult prospect in extremely modified landscapes, especially where high‐impact exotic species are widespread. Using new data and a review of the literature, this paper comments on the use of livestock grazing to manage the invasive and highly combustible pasture grass species, Buffel Grass (Cenchrus ciliaris) and thereby help conserve fire‐sensitive Brigalow (Acacia harpophylla) vegetation in reserves in Queensland, Australia. We cite evidence that shows that grazing is a potentially useful management tool in such cases and its use can be compatible with the protection of both fire‐sensitive vegetation and other native plant species within the understorey. However, there are limitations in implementing grazing within conservation reserves including the lack of a clear understanding of the influence of grazing on biodiversity and resource condition. Importantly, we highlight secondary invasion by the exotic grass Indian Couch (Bothriochloa pertusa) as a key emerging threat that may undermine the biodiversity benefits gained by grazing in reserves. Grazing can be a useful tool for conservation management in particular scenarios, but the associated risks demand accompanying monitoring and reporting of positive and negative impacts to ensure the fundamental aim of biodiversity protection is being achieved.