Jaccard Dissimilarity Index Research Articles

Dramatic Enhancement of Macrozoobenthic Species β-Diversity in Response to Artificial Breakwater Construction Along a Tropical Coastline

The beneficial or detrimental effects of human-built marine structures (piers, breakwaters, and seawalls) on macrozoobenthic assemblages and diversities are currently underexplored. The present study investigated the enhancement of β-diversity of oysterbed-associated species on breakwaters constructed along sandy beaches. We compared habitat complexities and species assemblages among artificial breakwater shores (ABS), a natural rocky shore (NS), and an embayment shore (ES). Oysterbed habitat complexity was found to be greatest on the ABS due to the successional colonization of the reef-forming estuarine oyster, Saccostrea echinata, followed by the colonization of boring bivalves and burrowing annelids. High-resolution taxonomic data revealed that the ABS supports the greatest species richness, including 48.1% unique species and 33.3% species shared with the embayment shore. The other shores uniquely or in combination with ABS support up to 11.1% of the total species richness associated with the oysterbeds (n = 81). Taxonomic dominance in terms of species number was Mollusca > Annelida > Arthropoda. This study reveals that ABS enhances β-diversity by ~91% (Jaccard dissimilarity index), which is driven by the sequential cascading events of (1) sheltering of shores, (2) colonization of novel habitat-forming oysters, (3) novel macrozoobenthic species recruitment from adjacent shores and sheltered embayments, including habitat-forming bivalves and annelids, and (4) the recruitment of macrozoobenthic species to boreholes. ABS habitat complexity derives from a spatially distinct, three-tiered ecological engineering system, involving (1) breakwater construction (100 m), (2) reef-forming oysters (10 m), and (3) boring bivalves and burrowing annelids (<10 cm). Irrespective of the purpose of their construction, breakwaters along extended sandy shores can potentially increase the resilience (β-diversity) and regional interconnectivity of hard surface macrozoobenthic species.

Diversity of Improved Diploids and Commercial Triploids from Musa spp. via Molecular Markers.

Banana breeding consists of obtaining diploid, triploid, and tetraploid intra- and interspecific hybrids by conventional breeding methods with the objective of aggregating characteristics of agronomic and commercial interest. Given the narrow genetic base of bananas, Embrapa's Banana Genetic Breeding Program (BGBP) aims at crosses between improved diploids (ID) (ID × ID) and between improved diploids (ID) and commercial triploids (ID × CTP) and tetraploids (ID × CTT), in order to increase the genetic base and variability in bananas regarding agronomic traits of interest and resistance to main biotic and abiotic factors. These improved diploids are resistant to main fungal diseases such as yellow (YSD) and black Sigatoka (BSD) disease and Fusarium wilt (race 1 and subtropical race 4), the latter being one of the most devastating diseases in bananas. The genetic diversity between 22 improved diploids and seven commercial banana triploids was analyzed using DNA molecular markers. Five IRAP (Inter-Retrotransposon Amplified Polymorphism, 7 ISSR (Inter-Simple Sequence Repeats) and 12 SSR (Simple Sequence Repeat) markers were used. The genetic dissimilarity matrix was based on the Jaccard dissimilarity index; clusters were separated using the UPGMA (Unweighted Pair Group Method With Arithmetic Mean) method and cophenetic correlation of 0.8755. This study of the genetic diversity between improved diploids and commercial triploids, based on the genetic dissimilarity matrix, revealed that the most dissimilar diploids were DM23 and DM15 (74%) and DM16 and DM15 (74%). The smallest genetic distances between the improved diploids and commercial triploids were between TCGN25 and DM17 (50%) and TCN26 and DM17 (50%). The genetic distance matrix also revealed important genotypes to be used in crosses in order to maintain good characteristics in commercial triploids when crossed with improved diploids. The results of our study provide better breeding strategies for one of the largest banana-breeding programs worldwide focused on the development of banana varieties resistant to main biotic and abiotic factors.

Historic checklist, core species and temporal composition turnover of birds in an urban protected natural area in central México over 50 years.

The Pedregal de San Ángel Ecological Reserve (REPSA) is located within the central campus of the National Autonomous University of Mexico (UNAM), in southwestern Mexico City. This area is known for its bird richness, which has been documented over time. However, this historical information has not been compiled, nor has it been assessed whether species composition has changed over time. In this study, we generated the historical checklist of avifauna in the REPSA by integrating data from systematic monitoring, bibliographic review and citizen science. Additionally, we calculated Jaccard's dissimilarity Index (nestedness and species turnover) among bird checklists from each year and evaluated whether this index and its components changed over time. In addition, we estimate whether the proportion of species arriving and becoming extinct in the REPSA is influenced by time (census interval) and by the migratory status of the species. Finally, we identified the core species of the REPSA. Our results indicate that from 1967 to 2023, 258 bird species have been recorded in the REPSA. The Jaccard's dissimilarity and turnover increased and reached an asymptotic trend over time while nestedness showed similar values throughout time. The time and species residency status did not have significant effect on the proportion of species that arrival and become extinct in the reserve. We identified 58 core species based on their persistence; 35 of these are residents, 22 have some migratory movement and one exotic species. Our results highlight the importance of the REPSA as a fundamental habitat for the avifauna of Mexico City, including a wide variety of migratory bird species.

Assessment of the role of the protected land in the preservation of the steppe in Southwest Algeria (Case of the Rogassa Region)

In the Algerian steppe (Rogassa) overgrazing led to the reduction of the surface of the pasture land and its biodiversity. The objective of this work was to highlight the importance of the protected land in maintaining biodiversity and preserving the degraded areas. A mixed sampling for the two different sites was adopted, where fifty floristic surveys were conducted using the Braun-Blanquet method. The analysis of the real biological spectrum of the unprotected land was marked by the strong dominance of the therophytes. However, in the protected land the chamaephytes dominated all of the biological types. The analysis of the biogeographic spectra revealed the reappearance of the endemic species (+3%). The Shannon Index was very important in this matter (2.43). The Student’s t-test of the biodiversity’s index showed a highly significant difference between the two sites. The ascending hierarchical classification revealed that the protected land is subdivided into four groups dominated respectively by: Macrochloa tenacissima, Lygeum spartum, Artemisia erba-alba and Hordeum murinum. The results of the Jaccard dissimilarity index indicated a strong difference of the order of 80% between the two areas.

Taxonomic Documentation and Statistical Analysis of Soil Mycoflora of Sanjay Gandhi National Park, Maharashtra, India

Aims: The present paper deals with documentation of diversity and analysis of ecological aspects of soil microfungal flora of Sanjay Gandhi National Park (SGNP).
 Study Design: The study area was divided into five zones, defined over span of three ranges and 10% peripheral area.
 Place and Duration of Study: SGNP, Maharashtra, India between September 2016 and September 2020.
 Methodology: A total of 43 soil samples were collected from 5 zones. Microscopic and molecular methods were used for identification of species. We examine dissimilarity in species composition by pairwise Jaccard Dissimilarity Index. We examine diversity of microfungi using diversity indices of Gini-Simpson’s and Shannon’s, true diversity (Shannon’s effective number of species) and equitability of species with Pielou’s evenness index.
 Results: The study resulted in a total of 77 isolates of 77 soil fungi obtained from 43 soil samples. A total of 36 species were documented under 15 genera. Aspergillus was dominant genus with 16 species, whereas Aspergillus niger was dominant species representing maximum 12 isolates. Pairwise Jaccard Dissimilarity Index was found to be above 66% in all cases, with only one species common in all the zones. In diversity indices, Gini-Simpson’s was 0.9347, and Shannon’s, was 3.1450. Pielou’s evenness index was 0.8776, causing true diversity, calculated as effective number of species (23), to be less than observed species richness (36).
 Conclusion: Thus, based on systematics and statistical analysis, it can be concluded that SGNP exhibits rich diversity of soil microfungi.

Interannual summer biodiversity changes in ichthyoplankton assemblages of the Strait of Sicily (Central Mediterranean) over the period 2001–2016

Interannual fluctuations in the structure and the composition of ichthyoplankton assemblages in the pelagic waters of the Strait of Sicily (SoS, Central Mediterranean) were investigated, trying to relate them to the observed variability in oceanographic conditions. Plankton data used in this study were from 16 summer surveys carried out in the SoS every year from 2001 to 2016, using oblique bongo plankton net (0–100 m) tows. Out of more than 12,000 fish larvae collected in the sampling stations included in the analysis, 9,519 of them were identified and regularly classified in 15 orders and 49 families. Ichthyoplankton assemblages, defined at the family level due to the uniform availability of this information along the time series, showed a decreasing trend over time in total larval abundance, along with taxonomic (family) richness and Shannon index (α diversity), more pronounced in the shelf area and in the slope area, respectively. Conversely, the relatively high levels of yearly compositional changes observed in the larval assemblage from both shelf and slope areas, as estimated by the Jaccard dissimilarity index (β diversity), did not show any significant linear trend. In addition, a biodiversity hotspot (both in terms of family richness and Shannon index) was evidenced in the frontal structure characterizing the southeastern part of the study area. Generalized additive models were used to evaluate the effect of oceanographic conditions on the temporal and spatial patterns of ichthyoplankton biodiversity. Results evidenced the role of salinity, surface temperature, and surface currents in modulating biodiversity indices, especially in the shelf area. Finally, the relevance of local frontal oceanographic structures in sustaining high biodiversity levels is postulated.

Assessing protected area network effectiveness through the temporal change in avian communities’ composition

Current rates of land use are driving temporal changes in avian communities. Thus, it is essential to properly designate and manage protected areas since they mitigate the adverse effects of temporal changes on species populations. By using common bird monitoring data in Czechia from two periods (2005/2006 and 2014/2015), we calculated two indices of temporal change per each site, the Jaccard dissimilarity index (temporal dissimilarity between the community composition) and the difference in bird species richness between both periods (delta bird species richness). We tested three main predictions on temporal change in bird communities between protected and unprotected areas: (i) bird species richness will be higher inside protected areas, (ii) temporal changes in avian communities will be lower inside protected areas, (iii) the effect of protected areas will interact with land-use types, land-use richness, and altitudinal zones. Bird species richness was higher inside protected areas in 2014/2015, ten years after the implementation of Natura 2000 in Czechia. Both indices of temporal change were lower inside protected areas. The interactions of protected areas and land-use types on the indices of temporal change were not significant. However, interactions with altitudinal zones had a significant positive effect on the indices, i.e., in higher altitudes, delta bird species richness and higher dissimilarity levels. Our study underlines the importance of protected areas for conservation by buffering the consequences of factors driving temporal community changes. Together, our results indicate a positive ‘umbrella’ effect of protected areas on avian communities that was likely facilitated by the implementation of Natura 2000.

A maiden application of Jaccard similarity for identification of tripped branch utilizing current synchronized measurement considering false data injection attack

The accurate identification of tripped branch (ITB) is an essential requirement to maintain the reliability and security of modern smart grid. Most of the existing phasor angle based approaches fail to identify the tripping of parallel branches. To this end, a novel method is presented in this study using current measurements of phasor measurement unit (PMU). A new term namely Jaccard dissimilarity index (JDI) is proposed and the ITB problem is solved through JDI based novel objective function. Furthermore, a generalized mathematical model of false data injection (FDI) attack is formulated considering two types of attack such as in phase attack and angular attack. Considering the FDI attack, the proposed method is implemented on different IEEE systems in MATLAB software. The identification rate of the proposed method is found to be competitive compared to some well-established methods. Test results considering various aspects such attack factor variation and attack location variation prove the applicability and effectiveness of the proposed method.

Intraspecific Diversity in Aquatic Ecosystems: Comparison between Spirodela polyrhiza and Lemna minor in Natural Populations of Duckweed.

Samples of two duckweed species, Spirodela polyrhiza and Lemna minor, were collected around small ponds and investigated concerning the question of whether natural populations of duckweeds constitute a single clone, or whether clonal diversity exists. Amplified fragment length polymorphism was used as a molecular method to distinguish clones of the same species. Possible intraspecific diversity was evaluated by average-linkage clustering. The main criterion to distinguish one clone from another was the 95% significance level of the Jaccard dissimilarity index for replicated samples. Within natural populations of L. minor, significant intraspecific genetic differences were detected. In each of the three small ponds harbouring populations of L. minor, based on twelve samples, between four and nine distinct clones were detected. Natural populations of L. minor consist of a mixture of several clones representing intraspecific biodiversity in an aquatic ecosystem. Moreover, identical distinct clones were discovered in more than one pond, located at a distance of 1 km and 2.4 km from each other. Evidently, fronds of L. minor were transported between these different ponds. The genetic differences for S. polyrhiza, however, were below the error-threshold of the method within a pond to detect distinct clones, but were pronounced between samples of two different ponds.

Https://asianjournalofmycology.org/pdf/AJOM_5_1_10-1.pdf

The present paper aims at studying the diversity of phyllospheric, rhizospheric soil and aquatic microfungal flora of Sanjay Gandhi National Park (SGNP) and its 10% peripheral area with statistical analysis of the diversity data to draw inferences about microfungal diversity. For analysis, the study area was divided into five zones, defined over a span of three ranges and a 10% peripheral area. Standard methods and keys were followed for the isolation and identification of fungi from different substrates, with routine microscopic work supplemented by scanning electron microscopy and molecular methods for some novel fungi. A total of 334 isolates obtained included 186 litter fungi (55.69%), 77 soil fungi (23.05%), 43 foliicolous fungi (12.87%), and 28 water fungi (8.38%). A total of 231 species in 121 genera were documented, of which 120 genera belong to Ascomycota and one to Basidiomycota. The study resulted in the publication of three new species, 13 new records for India, and two new records for Maharashtra. Aspergillus was dominant with 23 species, followed by Diatrype and Meliola (eight species each). In statistical analysis, we first examine differences in observed species richness across the zones using dummy variable regression and Kruskal-Wallis Test, with species count as the dependent variable. Both yielded similar statistically significant (p-value<0.01) differences in mean and median species counts, respectively. Dissimilarity in species composition, analysed by pairwise Jaccard Dissimilarity Index, was above 82% in all cases, with only one species common in all the zones. In diversity indices, Gini-Simpson’s was above 0.9 for all the zones, and Shannon’s was maximum (=4.4118) for Yeoor [South] and minimum (=2.7185) for Peripheral areas. Pielou’s evenness index was maximum (=0.9954) for Krishnagiri range and minimum (=0.9539) for Yeoor [South]. True diversity (based on Shannon’s Index) was highest (=82) for Yeoor [South] and lowest (=15) for Peripheral. Thus, based on systematics and statistical analysis, it can be concluded that SGNP exhibits a very rich diversity of microfungi.

Exploring Temporal Trends of Plant Invasion in Mediterranean Coastal Dunes

Alien plants represent a significant threat to species diversity and composition in natural habitats. Nevertheless, little is known about the dynamic of the invasion process and how its effects on native species change over time. In this study, we explored vegetation changes that occurred in invaded coastal dune habitats over the last 10–15 years (2005–2020), particularly addressing impacts on alien and diagnostic species. To monitor temporal trends, we used data resulting from a revisitation study. After detecting overall changes in alien species occurrence and cover over time, 127 total plots were grouped into plots experiencing colonization, loss, or persistence of alien species. For these three categories, we compared historical and resurveyed plots to quantify changes in native species composition (using the Jaccard dissimilarity index) and to measure variations in diagnostic species cover. The number of alien species doubled over time (from 6 to 12) and two species, Yucca gloriosa and Agave americana, strongly increased their cover (+5.3% and +11.4%, respectively). Furthermore, plots newly invaded appeared to record the greatest changes in both native and diagnostic species. Our results suggest the need for regular monitoring actions to better understand invasion processes over time and to implement effective management strategies in invaded coastal dune habitats.

Local-scale impact of wind energy farms on rare, endemic, and threatened plant species

BackgroundWind energy farms have become a popular solution to produce green energy worldwide. Their development within protected areas has increased dramatically in the past decade, and the effects on the rare, endemic and threatened plant species (i.e., protected plant species), essential for habitat conservation and management, are little known. Only a few studies directly quantify the impacts of wind energy farms on them. Our study analyzes the impact of wind energy farms on rare, endemic, and threatened plant species in steppic habitats and their recovery potential over a ten-year period on a wind energy farm within the Dealurile Agighiolului Natura 2000 site (Dobrogea Region, SE Romania).MethodsWe surveyed the rare, endemic, and threatened plant species within a radius of approximately 50 m around each of the 17 wind towers during the wind farm operational phase. We selected 34 plots to allow the investigation of two types of areas: (1) a disturbed area overlapping the technological platform, where the vegetation was removed before construction, and (2) an adjacent undisturbed area. To understand the effects of the wind energy farm on the rare, endemic, and threatened plant species diversity and the differences between the disturbed and undisturbed areas, we calculated under both conditions: (1) plant species richness; (2) sample-size-based rarefaction and extrapolation with Hill numbers parameterized by species richness; (3) non-metric multidimensional scaling of Jaccard dissimilarity index; (4) functional diversity; (5) beta-diversity (including replacement and nestedness of species).ResultsAs a result of the disturbances caused by the wind energy farm’s development, we identified a sharp contrast between the diversity of rare, endemic, and threatened plants inhabiting disturbed and undisturbed areas near the wind towers. Our research showed that less than 40% of the total inventoried rare, endemic, and threatened species colonized the disturbed sites. Species turnover within undisturbed plots was higher than disturbed plots, implying that the plant community’s heterogeneity was high. However, a higher richness in rare, endemic, and threatened plant species was found in the plots around the wind towers in grasslands of primary type. Sample-size-based rarefaction and extrapolation with Hill numbers by observed species richness indicated an accurate estimation of species richness in disturbed habitats, demonstrating that recovery after wind energy farm construction was incomplete after ten years of low-intensity plant restoration and conservation activities. Thus, we consider that operating activities must be reconfigured to allow the complete recovery of the communities with rare, endemic, and threatened plant species.

Zooplankton β diversity dynamics and metacommunity structure depend on spatial and temporal scales in a Neotropical floodplain

Abstract Both β diversity and metacommunity structure vary in time and space. It is necessary to examine different scales, especially in the face of extreme hydrological conditions. We investigated seasonal variation in β diversity and Elements of Metacommunity Structure [EMS] of zooplankton during four years (two years of prolonged drought and two years with extreme flood events) and at two spatial scales (sub‐basins and floodplain; smaller and larger spatial scale, respectively). We sampled 29 lakes quarterly during four years in the Upper Paraná River floodplain, Brazil. We estimated the replacement component of β diversity using the Jaccard dissimilarity index. We also used EMS to determine the metacommunity pattern of zooplankton distribution in each period and spatial scale. The flood peak observed in the snapshot sampling drove the homogenization of zooplanktonic assemblages. However, β diversity was not reduced in the two years with extreme flood events compared to the period of prolonged drought at either of the spatial scales (floodplain and sub‐basins), except for a single sub‐basin. This finding shows the importance of longer‐term ecological studies to better capture the dynamics of the zooplanktonic metacommunity. Regardless of the hydrological period and spatial scale zooplanktonic metacommunity structure remained practically constant throughout the four years, with a predominance of species range turnover (Clementsian). At the smallest spatial scale (sub‐basins), we found quasi‐structural patterns (quasi‐Clementsian and quasi‐Gleasonian). The predominance of the Clementsian pattern suggests that the associations of zooplankton species in the floodplain responded similarly to the environmental gradient and that the responses differed among species groups. Over time, the smaller spatial scale (sub‐basin) better represents the dynamics of β diversity than the larger spatial scale (floodplain), and better represents the structure of the zooplankton metacommunity. However, we emphasize the need for further studies to consider different biological groups and larger spatial scale over time to maximize the understanding of aquatic metacommunities dynamics. ​

Comparisons of the Spatial Extent of Eastern U.S. Tree Species between Expert-Drawn Little’s Range Map and Forest Inventory and Analysis

Elbert Little’s tree species range maps and Forest Inventory and Analysis (FIA) are two important data sources used to create historic and current tree species distributions. Yet, explicit comparisons do not exist between the two data sets. We developed a statistical procedure to compare forty-seven tree species of expert-drawn Little’s range maps to point-to-grid maps of FIA in terms of their northern and southern range extent and range porosity. First, we computed varying percentiles of species occurrence for northern and southern ranges using empirical cumulative distribution functions. Then, we evaluated distributional differences between the maps using the nonparametric two-sample Kolmogorov–Smirnov and Anderson–Darling statistics and compared these results to the conventional Jaccard dissimilarity index. Our methods found map dissimilarities near northern and southern range extents and range porosity that conventional methods failed to detect. We also found that map disparity is related to an untraceable source of errors related to abundance of species for Little’s range map and, to a lesser extent, forest area changes over the forty years. We conclude that Little’s range map has an overall tendency to draw generous range extents with little emphasis on range porosity for abundant species compared to FIA.

Long‐term monitoring of seed dispersal by Asian elephants in a Sundaland rainforest

AbstractAsian elephants (Elephas maximus) have inhabited almost all forests in tropical Asia until recently, yet little is known about their role in ecological processes, particularly in the Sundaic forests of South‐East Asia. These forests are peculiar in their phenology, with supra‐annual and highly irregular episodes of mast fruiting. Here, we present a long‐term (6‐year) monitoring of the seeds dispersed by elephants in dipterocarp forests of northern Peninsular Malaysia. We conducted monthly dung surveys at two mineral licks (11.3 km apart) frequently visited by elephants. Additionally, we recorded haphazard observations of seeds and seedlings in elephant dung at other locations. We recorded a minimum of 48 morphospecies from at least 25 plant families dispersed by elephants. Elephant seed dispersal was very heterogenous in space, with only 30.3% of the morphospecies dispersed at both sites (Jaccard dissimilarity index = 0.48). Temporally, elephants dispersed seeds in sporadic pulses of abundance and diversity, without any apparent seasonality (seeds appeared in 19.1% of 1,284 dung piles and 57.1% of the 63 months in which we found dung) and with long periods without any seed being dispersed. Nearly half (48%) of the plants dispersed by elephants belong to a megafaunal dispersal syndrome. Our long‐term approach allowed us to unravel an important aspect of Asian elephants’ role and effectiveness in the seed dispersal cycle. Sundaland's forests are undergoing a rapid loss of their previously common megaherbivores (rhinos and elephants), with profound and long‐term consequences for ecosystem functioning.Abstract in Malay is available with online material.

Genetic diversity of Soybean Cyst Nematode (Heterodera glycines) populations in Southeastern Goiás state, Brasil

Heterodera glycines, also known as Soybean Cyst Nematode (SCN), is one of the phytosanitary issues that prevents high soybean yields (Glycine max) due to its dissemination capacity and high physiological race variability. The first step towards the proper and safe use of resistant cultivars lies on correctly identifying the physiological race of this nematode in the crop in order to avoid new breed-selection pressure. Thus, the aim of the present study was to genetically characterize the races of Heterodera glycines populations from soybean-producer counties belonging to the Railroad (Estrada de Ferro) Region (Goiás State, Brazil), as well as to investigate their molecular characterization based on RAPD markers. RAPD data were evaluated in a binary way, in which values (1) and (0) were attributed to the presence and absence of amplified bands for each primer, respectively. The binary matrix was used to estimate the genetic distance between populations, based on the Jaccard dissimilarity index. The clustering analysis was carried out based on the calculated genetic dissimilarity matrix, according to Ward’s method. Eight (8) different physiological Heterodera glycines races were found in the investigated counties. Only 10 out of 28 RAPD primers were polymorphic among SCN populations, whereas the remaining primers either did not amplify, or presented low amplification of the DNA fragment. Five genetically-different groups were recorded among H. glycines population accessions, which presented high genetic variability rate.

A Generalized Framework for Analyzing Taxonomic, Phylogenetic, and Functional Community Structure Based on Presence–Absence Data

Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated.

Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods

Abstract We present a performance evaluation of environmental DNA (eDNA) metabarcoding with MiFish‐U/E primers to investigate local and regional diversities of stream fish species to examine potential effectiveness, limits and future remedies of this technique in large‐scale monitoring. We hypothesised that eDNA inferences are more consistent with fish assemblages observed upstream than downstream due to a directional flow of river water. River water was sampled at 102 sites in 51 rivers around Lake Biwa in the central part of Honshu Island, Japan, within 10 person‐days, and fish species compositions inferred from eDNA and existing observational data were compared. Observation sites were chosen from the observational data that were within a certain distance (buffer range) of a water‐sampling site along a river trajectory. The hypothesis of the detection bias of eDNA towards upstream assemblage was tested by comparing results with all of the observational data, data from a higher elevation and data from a lower elevation. The Jaccard dissimilarity index was plotted between the observational data and the eDNA estimates against the buffer range; the buffer range with minimum dissimilarity was chosen. When using existing observational data from within 6 km upstream of the eDNA sampling sites, the eDNA results were the most consistent with the observational data and inferred 86.4% of the species reported (38/44), as well as two additional species. eDNA results also showed patterns consistent with known upstream–downstream turnover of related species and biogeographical assemblage patterns of certain species. Our 10‐person‐days survey using the metabarcoding technique enabled us to obtain as much regional fish diversity data including the hypothesised pattern of eDNA detection with an upstream bias as the accumulated observational data obtained through greater amounts of time, money and labour. The problems regarding false‐positive/negative detection were suggested in our survey; however, these should be decreased or removed by modifying the sampling methods and experimental procedures in future works. Therefore, we concluded this new tool to enable monitoring that has never been implemented, such as cross‐nation, and even whole‐Earth monitoring with the data at yearly, seasonal or finer temporal scales.

Genetic divergence in elite castor bean lineages based on TRAP markers.

Castor bean (Ricinus communis L.) is a tropical plant of great commercial interest and a potential source of biodiesel. The development of genetically improved cultivars with high amounts of oil in the seeds and low ricin toxicity is crucial to increase the productivity of this crop. The use of TRAP (target region amplification polymorphism) markers to develop elite lineages and study genetic divergence is fundamental to advance the genetic improvement of this species. The goal of this study was to evaluate the genetic divergence among 40 elite lineages of R. communis, which belong to the NBIO-UFRB Genetic Improvement Program, using TRAP markers involved in the biosynthesis of oil and ricin. Total DNA was extracted and quantified from the leaf tissue of the castor bean plants, and 70 TRAP combinations (fixed and arbitrary primers) were used to genotype the 40 lineages. Of the 580 fragments amplified, 335 were polymorphic (58%). The genetic dissimilarity among the lineages was calculated by the Jaccard dissimilarity index using the UPGMA grouping method. A dendrogram was generated, and four groups formed, showing divergence among the elite lineages that favors selection. The TRAP molecular markers were efficient at characterizing the genetic variability among the lineages and, because TRAP markers are functional markers involved in the biosynthesis of oil and ricin, they are important when studying the association between a marker and a candidate gene.

Substratum simplification reduces beta diversity of stream algal communities

Summary Reduced species richness with increased habitat simplification is a well‐known relationship in community ecology. However, habitat simplification can also lead to a reduction in beta diversity if the loss of species is not random. We tested the hypothesis that beta diversity of periphytic algae is lower among simple than among complex substrata. We conducted a field experiment using simple (smooth) and complex (rough) artificial substrata colonised by periphytic algae to calculate beta diversity among each substratum type. We initially estimated beta diversity using the Jaccard dissimilarity index and its turnover component. As species richness differed between substratum types, we also employed the Raup–Crick dissimilarity index that estimates beta diversity by resampling from the species pool. We also deconstructed the total dataset into three functional groups based on the position occupied by each species within the periphytic matrix (low‐profile, high‐profile and motile functional groups). Beta diversity estimated using both Jaccard dissimilarity and its turnover component was higher among simplified substrata for the all‐species dataset and for high‐profile and motile groups. However, after taking into account the differences in species richness between substratum types using the Raup–Crick index, beta diversity was higher among complex substrata than among simple ones for the total dataset and for the low‐profile group. We emphasise that differences in species richness must be considered for the quantification of beta diversity, because this might confound the dissimilarity identified and, consequently, lead to erroneous conclusions. The higher beta diversity among complex substrata might be the result of priority effects, in which early colonists constrain the establishment of later arriving species, causing each patch to harbour a distinct species composition. Furthermore, algae life strategies may be an important driver of beta diversity among simple and among complex substrata, as periphytic algae position in the biofilm may affect their susceptibility to shear stress. On the one hand, stochasticity in colonisation history on complex substrata may have driven high beta diversity for the low‐profile group among this type of substratum. On the other hand, the reduced set of high‐profile and motile species on simple habitats may have driven these species to more occasional and rare occurrence, increasing beta diversity among this type of substratum and resulting in similar beta diversity among both types of substrata. Priority effects should be most frequent on complex substrata. However, only a reduced set of species might survive on simple substrata, occupying most of the available patches and causing beta diversity reduction.