Presence-absence Matrix Research Articles

Species richness of living foraminifera in Sepetiba Bay (SE Brazil): a species checklist

AbstractThere is a gap in knowledge about the biodiversity of living foraminifera (protozoa) in Brazil, particularly in coastal environments. In Sepetiba Bay (SE Brazil), a coastal system highly impacted by anthropogenic activities, several previous studies have been carried out on foraminifera based on total (living + dead) assemblages and sub-fossil records. Thus, this study intends to analyze for the first time the species richness of living foraminifera (stained with Rose Bengal) in Sepetiba Bay. Based on the morphological characteristics, 214 living species were identified in 50 samples collected in Sepetiba Bay in May 2022. The number of living specimens was counted as 6548. Living foraminifera density was < 252 specimens per gram of sediment and the species richness (S) ranged from 15 to 61 (mean 16.9 ± 15.5) in the analyzed stations. The main taxonomic classes found were Globothalamea and Tubothalamea. The main Globothalamea taxa belonged to the genus Ammonia, with Ammonia tepida, Ammonia buzasi, and Ammonia rolshauseni standing out, as well as the Bolivina, Buliminella, and Elphidium, represented mainly by Bolivina striatula, Buliminella elegantissima, and Elphidium excavatum. A non-Metric Multidimensional Scaling (nMDS) and cluster analysis based on a presence-absence matrix and Bray–Curtis similarity index allowed the identification of two main groups of stations: 1. Located in the innermost areas of Sepetiba Bay and surrounding the mainland and Marambaia Barrier Island, at shallower depths, with lower diversity; 2. an outermost group of stations with higher diversity in areas with greater oceanic influence. Compared with previous studies, the results of this work suggest an enlargement of the “innermost” zone with less diversity towards the oceanic region of Sepetiba Bay. This work shows that even using a matrix of presence/absence of living foraminifera and species richness, it is possible to distinguish environments in coastal systems. Data based on the living foraminifera is needed to understand current biodiversity to better characterize coastal environments and carry out biomonitoring studies.

Beta diversity patterns in Andean rodents: current and historical factors as drivers of turnover and nestedness

Abstract The Andes are known to be one of the most species-rich regions on Earth, with their origination promoting formation of new habitats and acting as climatic barriers. This orogenic event was structured latitudinally with 3 major segments having different formation times and with different environmental and historical conditions. The Andean region has been historically important in the evolutionary history of small mammals and is considered the region of Earth with the highest values of rodent species richness and turnover. Therefore, the region provides an excellent opportunity to evaluate mechanisms involved in structuring rodent assemblages and beta diversity patterns. Here, we assessed spatial patterns of rodent beta diversity along the Andes Mountains, with specific goals of examining patterns of turnover and nestedness as 2 recognized processes that drive species composition. We explored the role of spatial, climate, and historical factors on beta diversity patterns using geographic range maps for 432 rodent species to construct a species presence–absence matrix. We used piecewise regressions to identify latitudinal breakpoints in turnover and nestedness, and conducted multiple regressions and variation-partitioning approaches to assess the contribution of each set of postulated drivers in shaping beta diversity patterns. Beta diversity decreases from north to south. The highest turnover was located at the Northern Andes (5°N and 10°S) and western-central Andes (20°S and 35°S). Nestedness was higher below 40°S and in some areas of the western-central Andes between 15° and 20°S. Turnover and nestedness registered breakpoints coincident with the Central and Southern Andes limit. Turnover explained most of the beta diversity for all segments, although within the Southern Andes there was also some contribution of nestedness. In all segments, beta diversity was mainly explained by spatial factors with minor contributions from spatially structured climate (Northern Andes), interaction of all factors (Central Andes), and the interaction between current climate and history (Southern Andes).

StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins.

Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis. StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways. StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA. Supplementary data are available at Bioinformatics Advances online.

Biotic regionalization of freshwater fishes in Northern Middle America highlights high beta diversity created by prominent biogeographic barriers

Northern Middle America (NoMA) is considered a transition zone between the Nearctic and Neotropical biogeographic realms. In this region, Nearctic and Neotropical freshwater fishes create regional faunas of mixed origin, but their general biogeographic patterns have not been quantified. To identify such patterns, we delineate biogeographic regions (BRs) and major biogeographic barriers of NoMA and summarize patterns of faunal similarity among BRs. We used clustering analysis on a presence-absence matrix of primary and secondary freshwater fishes to group 97 level-6 HydroBASINs units spanning NoMA into BRs. We assessed statistical support of clusters using one-way analysis of similarity and implemented a species-indicator analysis. We delineated biogeographic barriers with the software Barrier 2.2 and determined faunal similarity among BRs using beta diversity-Jaccard dissimilarity and producing a minimum-spanning tree. Seven statistically distinctive and geographically coherent BRs were delineated and described. Barrier analysis identified three major barriers within NoMA. The first barrier combines the Sea of Cortés (Gulf of California) and Sierra de Juárez-Cerro Gordo highlands. The second combines the Trans-Mexican Volcanic Belt, Sierra Madre del Sur, and Sierra Madre de Chiapas highlands. The third combines the Río Grande Rift, Sierra Madre Occidental, and Mesa Central highlands. Faunal dissimilarity was very high among BRs, with lowest dissimilarity (92%) between the Balsas-Nacaome and Grijalva-Usumacinta BRs. Boundaries of NoMA BRs do not correspond with political boundaries. We concluded that bioregions of NoMA are faunally distinct, with limited overlap due to presence of strong, long-standing geographical barriers enhanced by aridity in the North.

Resource use divergence facilitates the evolution of secondary syntopy in a continental radiation of songbirds (Meliphagoidea): insights from unbiased co‐occurrence analyses

Allopatric speciation followed by the evolution of range overlap (sympatry) allows the build‐up of regional diversity. However, local species richness requires that species co‐occur locally (syntopy). Importantly, correct estimates of syntopy must be available to identify ecological traits facilitating it. We thus provide a method to correctly estimate local co‐occurrence and demonstrate it on the evolution of secondary syntopy. First, we performed probabilistic co‐occurrence analyses on simulated data across a sympatry gradient from 0 to 100%. Second, we extracted 116 species pairs younger than 10 My from a dated phylogeny of Meliphagoidea songbirds. We constructed a presence–absence matrix of 58 species across 470 sites based on 37 250 censuses in Australia and Tasmania from 1989 to 1995. We also constructed a spatial mask based on species ranges, identifying sites within versus outside the area of sympatry. We ran both unconstrained and range mask‐constrained co‐occurrence analyses. We compared the resulting syntopy and predicted it by species ecology. Simulations and exact analyses showed that co‐occurrence analyses must be limited to sites in the area of sympatry between species. Without this spatial limit, syntopy was negatively biased, especially in common species. Accordingly, syntopy was negatively biased in Meliphagoidea when data from all sites were used, but this bias decreased with increasing sympatry, in agreement with numerical and exact analyses. When using correct estimates, syntopy increased with increasing divergence in the use of foraging stratum (ground, shrub, subcanopy and canopy) and with decreasing divergence in diet. In conclusion, we introduced a general method for calculating local species co‐occurrence and confirmed its validity by simulations. We illustrated its use by analyzing the evolution of secondary syntopy in a phylogenetic framework. We found support for both niche divergence (foraging stratum) and niche conservatism (diet) in facilitating evolutionary transitions to secondary syntopy, allowing the build‐up of local species richness.

The agony of choice: Species richness and range size in the determination of hotspots for the conservation of phyllostomid bats

Area-based strategies for conservation include defining species richness and rarity hotspots. However, excluding vulnerable species (e.g., with restricted distribution and categorized as threatened), in establishing such hotspots may limit their representativeness, so the convenience of asserting them has been widely debated. To inform conservation assessments for the New World leaf-nosed bats (Chiroptera: Phyllostomidae), we identified hotspots based simultaneously on species richness and rarity of 214 species. We projected species range maps on a 0.5° × 0.5° longitude-latitude grid, from which we built a presence-absence matrix with 6951 sites. Using range-diversity plots, we described richness-rarity hotspots (sites with high species richness and presence of rare species) and poorness-rarity hotspots (with low species richness and presence of rare species). We assess the representativeness of the hotspots within established protected areas using the World Database on Protected Areas. The richness-rarity hotspot was located in the Andean zone from Peru to Panama within which 46 species of phyllostomid bats are distributed and 37% of its surface is protected. While the poorness-rarity hotspot was located in the northern region of Mexico and the Caribbean with 50 phyllostomid bats species and 19% of its surface protected. We hope that our analysis represents a relevant tool for the conservation of phyllostomid bats, which provide several ecosystem services and are currently facing different threats derived from anthropogenic activities.

The katydid country: bioacoustics and ecology of tettigoniid communities from the Indian subcontinent

ABSTRACT The study provides the first description of acoustic communities from a subtropical rainforest in Northeast India and a previously unexplored site from the Western Ghats. We describe call structures of 15 katydid species from the Indian subcontinent. The habitat and seasonal variations of the communities were investigated at both sites. Most species observed produced ultrasonic broadband calls (bandwidth: 11.07–42.5 kHz); only two Pseudophyllinae members produced pure tone calls. The study includes calls of two previously undescribed species of the genus Ducetia (subfamily: Phaneropterinae) from the subcontinent. We observed diverse acoustic communities at both sites represented by five major subfamilies: Conocephalinae, Hexacentriane, Mecopodinae, Phaneropterinae and Pseudophyllinae. The acoustic communities at each site exhibited seasonal variations and habitat preferences. The post-monsoon season had a richer community composition than the dry season. We compared differences in the community compositions between habitats using a presence–absence matrix based on 526 individuals from the two sites. Species composition was found to be different among habitats (stress = .06, dimension: 2), with ANOSIM indicating separation of species among understorey, shrubland and grassland habitats.

Diversity and Seasonal Occurrence of Native and Nonnative Ants (Hymenoptera: Formicidae) in Long-Term Experimental Chinese Privet (Lamiales: Oleaceae) Plots in Georgia, USA

Diversity and Seasonal Occurrence of Native and Nonnative Ants (Hymenoptera: Formicidae) in Long-Term Experimental Chinese Privet (Lamiales: Oleaceae) Plots in Georgia, USA

Using intraspecific variation of functional traits and environmental factors to understand the formation of nestedness patterns of a local forest community

Abstract The concept of nestedness originated from the field of biogeography decades ago and has been widely used in metacommunities and biological interaction networks, but there is still a lack of research within local communities. Moreover, studies on nestedness usually rarely incorporate the functional traits of the species and the environmental characteristics of the sites. In this study, we constructed a species presence–absence matrix of a 50-ha forest plot, used the simulated annealing algorithm to reveal the maximum nested structure and further tested the significance of nestedness patterns by constructing null ensembles. The nested ranks were used to represent the orders of species and quadrats in the maximum nestedness matrix. The regression tree analysis was used to reveal the relationships of nested ranks with environmental factors and functional traits. We found that the co-occurrence pattern of local plant communities was significantly nested. The regression tree results showed that the nested ranks of quadrats were determined by soil available phosphorus, soil water content, soil organic carbon and soil pH. Intraspecific variation of functional traits, including leaf C, leaf pH, leaf dry matter content and maximum photosynthetic rate rather than means of functional traits, provided a better explanation for the formation of species’ nested ranks. Understanding the causes of species and quadrats nested ranks provides novel lens and useful insights into ecological processes underlying nestedness, and further improves our knowledge of how local plant communities are assembled.

Hierarchical analyses of avian community biogeography in the Afromontane highlands.

The Afromontane mountains are a complex series of highlands that have intermittently been connected by habitat corridors during climatic cycles, resulting in a mosaic of range disjunctions and allospecies complexes in the present day. Patterns of community relatedness between geographic regions are often determined through single-species analyses or spatial analyses of diversity and nestedness at the species level. To understand patterns of Afromontane community evolution and to assess the effects of taxonomy on our understanding of biogeographic patterns, I concatenated three lists of Afromontane bird taxa divided into five taxonomic hierarchies. These lists were converted into a presence-absence matrix across 42 montane regions and analyzed using a variety of clustering techniques based on a replicable coding pipeline. I used these lists and methods to determine patterns of relatedness between montane blocks, to assess the consistency with which biogeographic regions were recovered, and to shed light on the patterns of connectivity within the Afromontane region. My results reaffirm the distinctiveness of many biogeographic regions (e.g., the Cameroon Highlands) while also clarifying regional relationships and the presence of 'transition zones' between regions. Differences between lists illustrated how our understanding of taxonomy and distribution in the Afromontane highlands can also change our understanding of Afromontane biogeography. Most notably, I found evidence for an Expanded Eastern Arc that included the Eastern Arc Mountains and highlands in Malawi, Mozambique, and Zimbabwe. This study presents a rigorous yet easily adjustable pipeline for studying regional biogeography from multiple taxonomic perspectives using both traditional and novel approaches.

Rich but random: parasite communities of snouted treefrog, Scinax fuscovarius (Anura: Hylidae), in Bodoquena Mountains, western Brazil.

Hosts represent discrete habitats that contain finite parasite communities, and individual hosts can be used as replicates in parasitism studies, such as investigations of the processes that mediate the formation of parasite communities. However, within a single host population, there may be singularities among individuals that affect parasite contact rates. Accordingly, the goals of the present study were to document the parasites associated with the small treefrog Scinax fuscovarius, to verify possible variation and co-occurrences in parasite infracommunities, and to assess the effects of host characteristics (size and sex) on infracommunity structure. Treefrog specimens (n = 75) were collected from the Bodoquena Mountains in Mato Grosso do Sul, Brazil. After collection, the specimens were transported to the laboratory, and examined for parasitic. The parasites found were removed, fixed, and identified. Patterns in parasite infracommunity organization were analyzed using the checkerboard score index, which was calculated using a presence-absence matrix. The matrix was randomized under the null hypothesis that the infracommunities independently represent the component community. Forty-two (56%) of the individuals harbored at least one parasite, and a total of 500 metazoan parasites were recovered, with a particularly rich composite community of 18 taxa, including 13 nematodes, two trematodes, one cestode, one oligochaete, and one mite larvae. The parasite species were randomly distributed among the infracommunities, with no evidence of co-occurrence, segregation, or aggregation. However, both body size and sex influenced infection, with larger hosts harboring more parasites and parasites were more abundant in male specimens and more species rich in female specimens. These results suggest that the parasite infracommunities of S. fuscovarius are shaped by both random factors and individual host characteristics.

Determinants of species assemblages of insect pests in alpine forest ecosystems of western China

BackgroundInsect pests are a significant threat to natural resources and social development. Modeling species assemblages of insect pests can predict spatiotemporal pest dynamics. However, research gaps remain regarding the mechanism for determining species assemblages of insect pests in alpine forest ecosystems. Here, we explored these determinants using a field investigation conducted for insect pests in a region of the Qinghai-Tibet Plateau. We assessed the species assemblages of insect pests in alpine forest ecosystems based on species co-occurrence patterns and species diversity (i.e., observed diversity, dark diversity, community completeness, and species pool). A probabilistic model was used to test for statistically significant pairwise patterns of species co-occurrence using the presence-absence matrix of pest species based on species interactions. We used ordinary least squares regression modeling to explore relationships between abiotic factors (i.e., climate factors and human influence) and species diversity.ResultsPositive pest species interactions and many association links can occur widely across different investigation sites and parts of plant hosts in alpine forest ecosystems. We detected high dark diversity and low community completeness of insect pests in alpine forest ecosystems. High temperature and precipitation could promote pest species diversity, particularly dark diversity and species pools. Human influence could drive high levels of pest species diversity and lead to dark diversity and species pools. Community completeness could be an effective indicator for insect pest risk assessment.ConclusionsOur study provides new evidence for the determinants of insect pest species assemblages in alpine forest ecosystems from the perspectives of pest species interactions and abiotic factors. The findings of our study could reveal the mechanism for shaping species assemblages and support the prevention and control of insect pests in alpine forest ecosystems.

A brief history of the foundation of an emblematic university in the rain forest of Ecuador and an innovative approach to the design and planning of academic program curricula for Latin America

The marginal role of higher education in Latin America led to technological dependency, poor economic growth, and social inequity. In the article, we discuss the challenging context in which higher education in Latin America developed and explain the motives behind the creation of a public university in the tropical rain forest of Ecuador. New and reformed higher education institutions in Latin America require innovative approaches to design academic programs and implement novel educational paradigms. We propose a quantitative and unorthodox method for analyzing the structure of program curricula in this historical and social context. This approach highlights the need for strategic academic planning and informed public policies. The inherent variation in program curricula across universities can be systematized in a presence-absence matrix, with courses and academic programs as columns and rows. By representing the patterns of variation in curricular structure across universities in the space provided by canonical axes, new perspectives arise which can lead to the development of further discussions towards optimal and innovative academic programs. The methods presented could be extended into the study of how academic disciplines, fields of study, and conceptual approaches to the design of program curricula vary and are structured across sociocultural contexts.

Lichen community structure and richness in three mid-elevation secondary forests in Costa Rica

Introduction: Lichen diversity, community structure, composition and species abundance have been used as indicators of the integrity and ecological continuity of tropical forest ecosystems. Objectives: To assess corticolous lichen species composition, diversity, and ecological importance of three forested stands differing in time of abandonment as indicators of how passive restoration influences the lichen community assemblage. Methods: We surveyed individual lichens on tree stems of a reference old secondary forest and a young secondary forest (50 and 14-year-old natural regeneration after pasture abandonment, respectively), and in a 35-year-old exotic cypress tree plantation, in the oriental Central Valley, in Orosí, Costa Rica. Standard diversity, similarity indexes, and the importance value index were calculated. An NMDS analysis was performed on the community structure parameters and in a presence-absence matrix. Results: We found 64 lichen species in 25 families with 42, 21, and 23 species, and 20, 10, and 15 families, in the young and old secondary forests, and the cypress plantation, respectively. Cryptothecia sp. possessed the highest importance across sites. More than 87 % of the species are rare. The combined IVI of the top three families were: 36, 48.5, and 74.8 % in the young and old forests and the Cypress plantation sites, respectively. Overall, Arthoniaceae is in the top three families. The young forest had the highest species richness, but the old forest presented the best evenness. Similarity and diversity indexes suggest a particularly low resemblance in the lichen communities but a smooth gradient differentiation between the three forests, which was confirmed by the NMDS test. The homogeneity test identified great differences in ecological importance and composition. Conclusions: This region contains a distinctive assemblage of species resulting in a strong community differentiation by site, reflecting the influence of ecophysiological and microclimatic factors that define lichen establishment and survival and suggesting a great regional beta diversity, within a fragmented landscape. Greater connectivity and passive restoration strategies resulted in greater diversity and a more heterogeneous community structure on both forests than the corticolous community of the abandoned plantation. Protection of forest fragments will maximize the integrity of future forests.

Vicariance and regionalization patterns in snakes of the South American Atlantic Forest megadiverse hotspot

AbstractAimVicariance has often been invoked to explain bioregionalization patterns in the Neotropics. Using a revised point locality data for endemic species, we aimed to test for the first time the predictions of the vicariance model in shaping biogeographical regions for endemic snakes in the Atlantic Forest (AF) megadiverse hotspot.LocationSouth American Atlantic Forest.TaxonSnakes (Reptilia, Serpentes).MethodsTo identify the non‐random groups of co‐distributed species, we mapped 21,101 point locality records in a grid cell of 0.5° × 0.5° across the AF, and constructed a presence–absence matrix of endemic species. The two major predictions of vicariance model were tested by Biotic Elements (BE) analysis, searching for groups of significantly co‐distributed species (Biotic Elements) by comparing distances between observed and artificial random ranges, produced under null models from Monte Carlo simulations. We also tested for the occurrence of sister species in different Biotic Elements, and compared our results with previous bioregionalization schemes revealed by other organisms in the AF.ResultsWe recorded 252 species of snakes in the Atlantic Forest, of which 79 (31%) are endemic to this domain. Biotic Elements analysis with endemic species revealed seven clusters of co‐distributed species (BEs) corresponding to biogeographical regions. The significant non‐random clusters of geographical ranges revealed in BE analysis, and the distribution of sister species in different BEs, validated both central predictions of the vicariance model.Main conclusionsSnakes defined non‐random biogeographical regions in the Atlantic Forest, and these were congruent with previously identified areas based on other groups of organisms, indicating that general processes influenced geographical ranges across the region. Both central predictions of the vicariance model were valid, indicating that vicariant events must have been important in shaping non‐random clusters of co‐distributed snakes in this biodiversity hotspot, harbouring some of the richest snake faunas on the planet.

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

BackgroundHorizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions.ResultsWe have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated.ConclusionGeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.

Early−Middle Devonian brachiopod provincialism and bioregionalization at high latitudes: A case study from southwestern Gondwana

The paleobiogeography of Early−Middle Devonian (Pragian−Eifelian) brachiopods from West Gondwana was assessed to determine any potential controls (regional climatic differences or global eustasy) that may have driven bioregionalization. The Pragian−Eifelian interval of West Gondwana was examined because work by previous authors suggested that this was a period when regionally extensive areas of provincialism among marine invertebrates were present and most pronounced. Factors of particular interest in this study were the controls over brachiopod bioregionalization at high (60°−90°) southern latitudes, which the Malvinokaffric Realm is thought to have entirely occupied. A large presence-absence data matrix was compiled consisting of the occurrences of 206 genera from 17 localities across West Gondwana, and an array of multivariate methods (cluster analysis, nonmetric multidimensional scaling, and network analysis) was employed to assess regional bioregionalization trends. The results of our study suggest that regional climatic differences brought on by latitudinal effects were the determining driver for bioregionalism of brachiopods during the Pragian−Eifelian, and these trends were coincident with a global cooling period during the Early−Middle Devonian. Our study further suggests that of the three regional paleobiogeographic realms thought to be present in West Gondwana during the Early−Middle Devonian (Eastern Americas, Old World, and Malvinokaffric), only the Malvinokaffric Realm is valid as a single biogeographic area. Its area, however, is reduced; it is interpreted to have been a second-order biogeographic area and not a first-order area as suggested by previous authors. Given these factors, we suggest a new demonym for this area, the “Malvinoxhosan,” given the racially charged connotations of “Malvinokaffric.” We present a new biogeographic framework for West Gondwana that is free of preconceived biogeographic area and rank biases, with the understanding that a more globally expansive study should be undertaken to elucidate these areas and their rank within the correct hierarchy. Two first-order paleobiogeographic areas are recognized in West Gondwana and are named according to their latitudinal extent, namely, the high-latitude (60°S−90°S) and temperate-latitude (30°S−60°S) bioregions. The temperate-latitude bioregion consists of a single second-order paleobiogeographic area, the “Colombian−West African” bioregion. Two second-order bioregions are present in the high-latitude bioregion, namely, the Amazonian and Malvinoxhosan bioregions. Here, the Amazonian (∼50°S−70°S), compositionally, was an intermediate region between the Colombian−West African (∼30°S−50°S) and Malvinoxhosan (70°S−90°S) end members. Latitudinal effects may also have been responsible for dividing the Malvinoxhosan bioregion into two tentative third-order paleobiogeographic areas, namely, the Andeo−South African (∼70°S−80°S) and the Paraná (∼80°S−90°S) bioregions.

Biogeographical characterisation of Egypt based on environmental features and endemic vascular plants distribution

Biogeographical studies are considered effective for investigations on macroecology and evolution, as well as for delineating patterns of endemism and identifying the key drivers influencing the historical distribution of species. Clustering techniques, based on environmental datasets and distribution of endemic species, have been largely used in biogeography and for the definition of endemic-rich regions where conservation actions should be implemented. Despite several earlier studies have dealt with the biogeographical territories in Egypt, none of them have provided a replicable method to support such regionalisation. We proposed a two-step procedure for the biogeographical regionalisation of Egypt consisting in (1) the definition of environmental clusters (based on 24 climatic, three topographic, two soil organic carbon content and pH, and four habitat heterogeneity variables) by using the k-nearest neighbours algorithm and (2) the spatial clustering of such clusters according to the distribution of 140 endemic vascular plants. The hierarchical clustering and indicator values analyses, based on the presence-absence matrix of endemic taxa in each cluster were performed to define two cut-off levels of biogeographical sectors and subsectors. A total of six sectors and nine subsectors were identified. Climatic-related variables, elevation and soil organic carbon were the most important determinants for environmental clustering of Egypt. The highest endemic richness was recorded in the Marioutico-Arishian (71 species), Sinaico-Arabian (62 species) and Nilotic (16 species) sectors, and in Sinaic (54 species), Arishian (45 species) and Marioutic (40 species) subsectors. Nonetheless, the most protected sectors were Elbanian and Suezian (62.73 and 29.05%, respectively) while the lowest sectors were Nilotic and Marioutico-Arishian (9.86 and 13.26%, respectively). The already established protected areas in Egypt are not sufficient for conserving the representation of the identified endemic rich plant sectors. This two-step procedure confirms the usefulness of environmental attributes together with the spatial distribution of endemic vascular plants to define the biogeographical units in Egypt. Our regionalisation method could be replicated for other species’ groups, with the ultimate goal of integration all species of interest in a single biogeographical system. Furthermore, the presented regionalisation will help to identify weaknesses in current protection actions and to understand biogeographical processes.

Nestedness-patterns of Odonata assemblages in artificial and natural aquatic habitats reveal the potential role of drinking troughs for aquatic insect conservation

Nestedness patterns including both artificial and natural habitat may represent evidence of such habitats’ importance in community assembly and conservation of animals inhabiting those sites. Odonata often colonize drinking troughs (artificial water reservoirs) and thus they are good study models as umbrella species. We investigated if a network of artificial (troughs) and natural (pools) aquatic habitats could create a nested subset pattern for Odonata assemblages. We surveyed all the troughs present in the Castelporziano Estate (Italy, Lazio). Odonata larvae have been collected and identified. Data of a previous paper on 18 natural pools and ponds, and our samplings of 16 troughs were organized into a presence-absence matrix. The Odonata assemblage within natural and artificial habitats is significantly nested with both NODF and T metrics. Odonata species found in the troughs represented 40% of the total species pool. Some troughs interspersed with the natural pools in the nested order: eight troughs were richer in species than some natural pools, despite the big difference in surface area. Pristine water bodies and their area may not represent major constraints for species to oviposit and for larvae to grow. Drinking troughs can be highly relevant for representing refuges in the absence or decline of natural ponds and pools: lacking in top-predators (fishes), they are small “island” habitats that support the generations of Odonata (or other aquatic macroinvertebrates) during dry periods of natural water bodies. The use and focused management of such habitats can be an effective practice for freshwater ecosystems management and Odonata conservation.

Analysis of Arbuscular Mycorrhizal Fungal Communities by Terminal Restriction Fragment Length Polymorphism (TRFLP).

Terminal restriction fragment length polymorphism (TRFLP) approaches enable the detection and identification of microbial taxa into samples coming from root or soil material DNA extraction. The low taxonomic diversity of arbuscular mycorrhizal (AM) fungi makes this technique a cheap and adequate method for fingerprinting their communities. Here, I describe the TRFLP database approach, a version of the technique in which the AM fungal taxa present in the sample pool is identified for, later, match their presence in the different samples contained in the experiment. A final AM fungal operational taxonomic unit x sample presence-absence matrix is obtained, which allows the subsequent multivariate statistical analysis of the experimental results.