DarkDivNet – A global research collaboration to explore the dark diversity of plant communities

DarkDivNet is a global research collaboration which explores dark diversity — the set of species that are absent from a site despite being suitable under the site conditions and present in the region. Participants of the network survey vascular plant diversity both at local (10  m × 10 m) and regional scales (radius 10 km) using a standardized approach. They also measure simple plant traits and collect soil samples. Observed and dark diversity together form the site‐specific species pool, and the ratio of observed diversity and dark diversity describes community completeness. We shall explore how observed and dark diversity, site‐specific species pool and community completeness vary across natural and anthropogenic gradients. We link plant diversity measures to the information obtained from environmental DNA: soil biota and plant taxa that occurred at the site before. We will refine existing dark diversity methods and use large vegetation databases to infer species habitat suitability. We expand the dark diversity concept from a purely taxonomy‐based approach to include the functional and phylogenetic aspects of diversity. DarkDivNet currently includes 161 planned sampling areas globally, but new participants are welcome. The main vegetation sampling period is scheduled until September 2020, with the first research papers being produced after that.     

Applying the dark diversity concept to plants at the European scale

Large‐scale biodiversity maps are essential to macroecology. However, between‐region comparisons can be more useful if patterns of observed species richness are supplemented by variations in dark diversity – the absent portion of the species pool. We aim to quantify and map plant diversity across Europe by using a measure that accounts for both observed and dark diversity. To do this we need to delimit suitable species pools, and evaluate the potential and limitation of a large‐scale dataset. We used Atlas Florae Europaeae (ca 20% of European plant species mapped within 50 × 50 km grid cells) and defined for each grid cell several species pools by applying various geographical and environmental filters: geographic species pool (number of species within 500 km radius), biogeographic species pool (additionally incorporating species distribution patterns, i.e. dispersion fields), site‐specific species pool (additionally integrating environmental preferences of species based on species co‐occurrence). We integrated dark diversity and observed diversity at a relative scale to calculate the completeness of site diversity: logistic expression of observed and dark diversity. We tested whether our results are robust against regional variation in data availability. We used independent regional databases to test if Atlas Florae Europaeae is a representative subset of total species richness. Environmental filtering was the most influential determinant of species pool size with more species filtered out in southern Europe. Both observed and dark diversity adhered to the well‐known latitudinal gradient, but completeness of site diversity varied throughout Europe with no latitudinal trend. Dark diversity patterns were fairly insensitive to variations in regional sampling intensity. Atlas Florae Europaeae represented well the total variation in plant diversity. In summary, dark diversity and completeness of site diversity add valuable information to broad‐scale diversity patterns since observed diversity is expressed at a relative scale.     

Measuring size and composition of species pools: a comparison of dark diversity estimates

Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat‐specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so‐called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co‐occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co‐occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods need attention, especially when dark diversity is estimated at the plot level.     

Community ecology of absent species: hidden and dark diversity

Community ecologists have so far focused mainly on species identified at a site. I suggest that we can understand better patterns and their underlying processes in ecological communities if we also examine those species absent from the sampled community. However, there are various types of absences, which all harbour different information. Hidden diversity comprises species that are absent from our sight: dormant or locally very rare species overlooked by traditional sampling. Fortunately, modern DNA‐based techniques can help us to find hidden species when analysing environmental samples. Depending on habitat type and sampling scale, a large number of co‐existing species might be hidden. Dark diversity comprises absent species that constitute the habitat‐specific species pool. Dark diversity can be determined based on data on species distribution, dispersal potential and ecological requirements. If we know both observed and dark diversity, we can estimate community completeness and infer those processes that determine which species in the species pool actually co‐exist locally. In addition, most species in the world do not actually belong to the habitat‐specific species pool of the community: their ecological requirements differ or their distribution area is elsewhere. Such other absent species are usually not directly relevant to a particular community. However, knowing ecologically suitable species from other regions can give early warning of possible future invasion of alien species (alien dark diversity). To conclude, species presences have meaning only if there are absences (and vice versa). Methods to detect absent species are rapidly developing and will soon form a standard toolbox for community ecology.     

From species distributions to meta‐communities

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta‐community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine‐resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.     

Observed and dark diversity of alien plant species in Europe: estimating future invasion risk

Invasion by alien species is a growing concern for nature conservation. We estimated the level of invasion by alien plant species and future invasion risks at the European scale. We used a pan-European atlas and eight regional plant atlases to determine the distribution of alien and native plant richness. In addition, we estimated alien and native dark diversity (species currently absent from a site but present in the surrounding region and able to colonize the site). We used relative diversity metrics to indicate current and future risks by alien species: relative alien richness (compared to native species), alien and native completeness (log-ratio of observed to dark diversity) and completeness difference between alien and native species. Observed and relative richness of alien species were greatest in NW Europe; this suggests that sites in NW Europe could be more disturbed. Observed alien and native species richness show clear regional hotspots; the distribution of completeness values is dispersed, indicating local hotspots. Northern Europe has relatively lower alien completeness, likely because potential invaders inhabit the region but have not yet reached many localities, thereby suggesting a risk of future invasion. A greater number of potential alien species in the region increases the probability that some alien species could have detrimental impacts. Both alien richness and completeness are positively correlated with native richness and completeness, respectively, indicating that both groups share similar distribution patterns. Alien species diversity metrics in Europe are related positively to human population density and agricultural land-use. We suggest that the dark diversity concept can broaden our understanding of alien species diversity and future invasion risks.     

Community Completeness: Linking Local and Dark Diversity within the Species Pool Concept

Biodiversity of ecological communities has been examined widely. However, comparisons of observed species richness are limited because they fail to reveal what part of the differences are caused by natural variation in species pool size and what part is due to dark diversity – the absence of suitable species from a species pool. In other words, conventional biodiversity inventories do not convey information about how complete local plant communities are. We therefore propose the community completeness concept – a new perspective on the species pool framework. In order to ascertain community completeness, we need to estimate the extent of dark diversity, for which several methods are under development. We recommend the Community Completeness Index based on a log-ratio (or logistic) expression: ln(observed richness/dark diversity). This metric offers statistical advantages over other methods (e.g. the proportion of observed richness from the species pool). We discuss how community completeness can be related to long-term and successional community stability, landscape properties and disturbance patterns as well as to a variety of biotic interactions within and among trophic levels. The community completeness concept is related to but distinctive from the alpha-beta-gamma diversity approach and the community saturation phenomenon. The Community Completeness Index is a valuable metric for comparing biodiversity of different ecosystems for nature conservation. It can be used to measure the success of ecological restoration and vulnerability to invasion by alien species. In summary, community completeness is an interface between observed local observed species richness and dark diversity, which can be useful both in theoretical and applied biodiversity research.     

Dark diversity in Amazonian stream fish communities: What factors determine species absence along environmental gradients?

1. Species distribution models often fail to predict observed patterns of species diversity, and this is because some species within a regional pool that are tolerant of conditions at a given location may nevertheless be absent from the local community. These missing species have been termed “dark diversity”. In the present study, we investigated which factors explain dark diversity among fish assemblages in Amazonian streams.
2. We sampled 71 streams in areas with different types of land use within two river basins and estimated dark diversity from patterns of species co-occurrence, using Beals’ index, along environmental gradients. From this procedure, taxa are designated as dark diversity components when they are absent from a given stream, but often co-occur with the local species at other streams, indicating similar ecological requirements. We used generalised linear models both to determine whether environmental or landscape variables, connectivity, instream environmental heterogeneity or some combination of these factors explained dark diversity of fishes, and to evaluate whether ecomorphology is associated with the extent to which a species contributes to dark diversity and which specific traits contribute the most to explaining variation in dark diversity.
3. Mean local diversity exceeded observed dark diversity. The magnitude of dark diversity was directly associated with the proportion of secondary forest in the immediate catchment and with the index of proximity to anthropogenic impact. Species that have high affinity for environments with higher current velocity, low swimming ability and that capture food mainly on the surface contributed more to dark diversity, which suggests that swimming ability, habitat preference and aspects related to diet are key predictors of the probability that a given species will be present at locations with suitable habitat.
4. Our findings reinforce the idea that dark diversity results from interactions between species traits and environmental factors, including anthropogenic impacts. Understanding the interplay among environmental factors and species traits that contribute to dark diversity provides targets for improved ecosystem restoration and sustainability of native species assemblages.

     

Global patterns of fern species diversity: An evaluation of fern data in GBIF

Despite that several studies have shown that data derived from species lists generated from distribution occurrence records in the Global Biodiversity Information Facility (GBIF) are not appropriate for those ecological and biogeographic studies that require high sampling completeness, because species lists derived from GBIF are generally very incomplete, Suissa et al. (2021) generated fern species lists based on data with GBIF for 100 km × 100 km grid cells across the world, and used the data to determine fern diversity hotspots and species richness–climate relationships. We conduct an evaluation on the completeness of fern species lists derived from GBIF at the grid–cell scale and at a larger spatial scale, and determine whether fern data derived from GBIF are appropriate for studies on the relations of species composition and richness with climatic variables. We show that species sampling completeness of GBIF is low (<40%) for most of the grid cells examined, and such low sampling completeness can substantially bias the investigation of geographic and ecological patterns of species diversity and the identification of diversity hotspots. We conclude that fern species lists derived from GBIF are generally very incomplete across a wide range of spatial scales, and are not appropriate for studies that require data derived from species lists in high completeness. We present a map showing global patterns of fern species diversity based on complete or nearly complete regional fern species lists.     

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.     

Rarity facets of biodiversity: Integrating Zeta diversity and Dark diversity to understand the nature of commonness and rarity

Measuring commonness and rarity is pivotal to ecology and conservation. Zeta diversity, the average number of species shared by multiple sets of assemblages, and Dark diversity, the number of species that could occur in an assemblage but are missing, have been recently proposed to capture two aspects of the commonness‐rarity spectrum. Despite a shared focus on commonness and rarity, thus far, Zeta and Dark diversities have been assessed separately. Here, we review these two frameworks and suggest their integration into a unified paradigm of the “rarity facets of biodiversity.” This can be achieved by partitioning Alpha and Beta diversities into five components (the Zeta, Eta, Theta, Iota, and Kappa rarity facets) defined based on the commonness and rarity of species. Each facet is assessed in traditional and multiassemblage fashions to bridge conceptual differences between Dark diversity and Zeta diversity. We discuss applications of the rarity facets including comparing the taxonomic, functional, and phylogenetic diversity of rare and common species, or measuring species'' prevalence in different facets as a metric of species rarity. The rarity facets integrate two emergent paradigms in biodiversity science to better understand the ecology of commonness and rarity, an important endeavor in a time of widespread changes in biodiversity across the Earth.     

Tackling intraspecific genetic structure in distribution models better reflects species geographical range

Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms’ distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole‐species and genetic‐unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.     

中国江西龙虎山崖顶植物根中深色有隔内生菌多样性

为探明丹霞地貌区崖顶植物深色有隔内生真菌（dark septate endophyte,DSE）多样性、群落组成以及生态分布规律。本文以江西龙虎山崖顶常见植物刺柏、马尾松、青冈栎、檵木、乌饭树、鸭跖草、苦槠、辣木树和香附子9种植物的根为研究对象,采用经典的组织分离方法分离DSE真菌,结合形态学特征和分子生物学数据研究丹霞地貌区崖顶常见植物DSE真菌多样性。结果表明：从9种植物根部990个组织块中,共分离纯化出404株菌株,经鉴定隶属于45个分类单元。其中,青霉属Penicillium、拟内孢霉属Endomycopsis、曲霉属Aspergillus、头囊霉属Ascocybe为优势属群,属种组成在不同植物中存在差异,且内生真菌属的数目与植物优势度极显著正相关（P<0.01）。9种植物深色有隔内生真菌（DSE）总分离率在0.51%-13.33%之间;各植物DSE Shannon指数在0.0743-1.0400之间,与植物优势度极显著正相关（P<0.01）,差异明显;Simpson指数较高（均值>0.7）且Pielou指数较低（均值<0.4）表明DSE真菌在不同植物分布不均匀;相似性指数普遍不高,在0.071-0.467之间。本研究初步揭示了丹霞地貌区崖顶深色有隔内生真菌的分布及多样性情况,为进一步探讨内生真菌在丹霞地貌等特殊生境的生态功能提供参考。     

Species distribution modelling as a macroecological tool: a case study using New World amphibians

Although species distribution modelling (SDM) is widely accepted among the scientific community and is increasingly used in ecology, conservation biology and biogeography, methodological limitations generate potential problems for its application in macroecology. Using amphibian species richness in North and South America, we compare species richness patterns derived from SDM maps and ‘expert’ maps to evaluate if: 1) richness patterns derived from SDM are biased toward climate‐based explanations for diversity when compared to expert maps, since SDM methods are typically based on climatic variables; and 2) SDM is a reliable tool for generating richness maps in hyperrich regions where point occurrence data are limited for many species. We found that although three widely used SDM methods overestimated amphibian species richness in grid cells when compared to expert richness maps in both North and South America due to systematic overestimation of range sizes, diversity gradients were reasonably robust at broad scales. Further, climatic variables statistically explained patterns of richness at similar levels among the different richness sources, although climatic relationships were stronger in the much better known North America than in South America. We conclude that in the face of the high deforestation rates coupled with incomplete data on species distributions, especially in the tropics, SDM represents a useful macroecological tool for investigating broad‐scale richness patterns and the dynamics between species richness and climate.     

The Erwin equation of biodiversity: From little steps to quantum leaps in the discovery of tropical insect diversity

Almost 40 years ago, Terry L. Erwin published a seemingly audacious proposition: There may be as many as 30 million species of insects in the world. Here, we translate Erwin's verbal argument into a diversity-ratio model—the Erwin Equation of Biodiversity—and discuss how it has inspired other biodiversity estimates. We categorize, describe the assumptions for, and summarize the most commonly used methods for calculating estimates of global biodiversity. Subsequent diversity-ratio extrapolations have incorporated parameters representing empirical insect specialization ratios, and how insect specialization changes at different spatial scales. Other approaches include macroecological diversity models and diversity curves. For many insect groups with poorly known taxonomies, diversity estimates are based on the opinions of taxonomic experts. We illustrate our current understanding of insect diversity by focusing on the six most speciose insect orders worldwide. For each order, we compiled estimates of the (a) maximum estimated number of species, (b) minimum estimated number of species, and (c) number of currently described species. By integrating these approaches and considering new information, we believe an estimate of 5.5 million species of insects in the world is much too low. New molecular methodologies (e.g., metabarcoding and NGS studies) are revealing daunting numbers of cryptic and previously undescribed species, at the same time increasing our precision but also uncertainty about present estimates. Not until technologies advance and sampling become more comprehensive, especially of tropical biotas, will we be able to make robust estimates of the total number of insect species on Earth.     

Tree species diversity driven by environmental and anthropogenic factors in tropical dry forest fragments of central Veracruz, Mexico

We examined vegetation structure and woody species diversity in relation to 14 environmental and anthropogenic factors in ten tropical dry forest (TDF) fragments in central Veracruz, Mexico. The basal area of the canopy (30.2 ± 2.11 m²/ha) and understory (1.96 ± 0.12 m²/ha) trees was similar, but density (1,014 ± 104 and 2,532 ± 227 individuals/ha, respectively) differed among sites. We recorded 98 canopy, 77 understory, and 60 seedling species. Richness was 24–45 species per site, Fisher’s alpha and Shannon’s indices increased with site altitude. Chao Jaccard indices revealed high species turnover, and a consistently higher similarity within the sites at the lowest and within the highest elevation sites. Ordination identified altitude, aspect, slope, water proximity, cattle and trails as significant explanatory variables of species patterns, and showed that sites at lower elevations were clearly separated from the other sites. Environmental heterogeneity alone did not control species diversity distribution, but species were affected by environmental filters at different stages in their life cycle, e.g., water proximity was significant for saplings and seedlings but not for adults. Anthropogenic disturbances act synergistically, e.g., trails played a key role in determining structure and tree diversity patterns. An important finding is that human disturbance diminishes species diversity in this TDF, but sites at lower elevations were more disturbed and less diverse, therefore we need to study how environmental factors would act if there were no anthropogenic disturbance.     

Assessment of fish communities using environmental DNA: Effect of spatial sampling design in lentic systems of different sizes

Freshwater fish biodiversity is quickly decreasing and requires effective monitoring and conservation. Environmental DNA (eDNA)‐based methods have been shown to be highly sensitive and cost‐efficient for aquatic biodiversity surveys, but few studies have systematically investigated how spatial sampling design affects eDNA‐detected fish communities across lentic systems of different sizes. We compared the spatial patterns of fish diversity determined using eDNA in three lakes of small (SL; 3 ha), medium (ML; 122 ha) and large (LL; 4,343 ha) size using a spatially explicit grid sampling method. A total of 100 water samples (including nine, 17 and 18 shoreline samples and six, 14 and 36 interior samples from SL, ML and LL, respectively) were collected, and fish communities were analysed using eDNA metabarcoding of the mitochondrial 12S region. Together, 30, 35 and 41 fish taxa were detected in samples from SL, ML, and LL, respectively. We observed that eDNA from shoreline samples effectively captured the majority of the fish diversity of entire waterbodies, and pooled samples recovered fewer species than individually processed samples. Significant spatial autocorrelations between fish communities within 250 m and 2 km of each other were detected in ML and LL, respectively. Additionally, the relative sequence abundances of many fish species exhibited spatial distribution patterns that correlated with their typical habitat occupation. Overall, our results support the validity of a shoreline sampling strategy for eDNA‐based fish community surveys in lentic systems but also suggest that a spatially comprehensive sampling design can reveal finer distribution patterns of individual species.     

Monitoring large herbivore diversity at different scales: comparing direct and indirect methods

Monitoring of large herbivores is central to research and management activities in many protected areas. Monitoring programs were originally developed to estimate (trends in) population sizes of individual species. However, emphasis is shifting increasingly towards conservation of diversity and communities instead of individual species, as a growing literature shows the importance of herbivore diversity for ecosystem functioning. We argue that the design of monitoring programs has not yet been adapted well to this new conservation paradigm. Using large herbivore census data from Hluhluwe-iMfolozi Park, South Africa, we studied how monitoring methodology (observational counts vs. dung counts) and spatial scale interact in influencing estimates of large herbivore species richness and diversity. Dung counts resulted in higher herbivore species richness and diversity estimates than direct observational counts, especially at finer monitoring resolutions (grid cells smaller than 25 km²). At monitoring resolutions coarser than 25 km² both methods gave comparable diversity estimates. The methods also yielded different spatial diversity estimates, especially at finer resolutions. Grid cells with high diversity according to the dung count data did not necessarily have high diversity according to the observational counts, as shown by low correlation of grid cell values of both methods. We discuss these results in the light of estimates of the sampling effort of each method and, hence, suggest new monitoring designs that are more suitable for tracking temporal and spatial trends in large herbivore diversity and community composition.     

人为干扰对溪流鱼类功能多样性及其纵向梯度格局的影响

溪流鱼类多样性沿着河流纵向梯度的空间分布规律已得到大量报道, 但这些研究大多聚焦基于物种组成的分类α多样性, 而有关分类β多样性和功能多样性的纵向梯度分布规律及其对人类干扰的响应研究较少。本文以青弋江上游3条人为干扰程度不同的河源溪流为研究区域, 比较研究了人为干扰对溪流鱼类功能α和β多样性及其纵向梯度分布格局的影响。结果显示, 人类干扰改变了河源溪流鱼类功能多样性的纵向梯度格局——由线性变化变为二项式分布。此外, 我们发现, 人为干扰导致土著种被本地入侵种取代, 且较强的土地利用和水污染排放可能增大环境的不连续性, 而群落周转和嵌套变化往往取决于环境的变化。尽管功能β多样性由嵌套成分主导, 但周转成分占比相对于人为干扰较小的溪流而言明显增加。人为干扰显著改变了受干扰溪流鱼类的物种组成和功能多样性, 且功能多样性的纵向梯度格局在不同的多样性指标上存在差异。本研究强调, 在评估人为干扰下多样性的变化时, 需要从多方面考虑, 包括空间尺度和多样性指标等。     

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification,evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark‐spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark‐spored myxomycetes.