Uneven Distribution Of Species Research Articles

Applying feature-similarity-metrics for long-tailed problem of phytoplankton microscopic images classification

The distribution of phytoplankton in natural water bodies holds significant importance for aquatic for maintaining healthy aquatic environments. While deep learning has become a popular research field of automating phytoplankton identification, its performance is diminished by the uneven species distribution in nature world, which biases classification models towards more advantaged species. Addressing this long-tailed problem, the paper proposed a novel deep learning idea termed feature-similarity-metrics species which utilizes the principle of decreasing intra-class differences and increasing the inter-class differences. A method called feature-center-constraint is introduced to implement the idea. Initially, a center is presupposed for each category, and these centers are distributed evenly and sparsely within the feature space using a uniform distribution initialization method. During model training, the Euclidean distance is used to measure the similarity between sample features and corresponding center. This approach enhanced the model's ability to predict disadvantaged phytoplankton species without compromising the classification accuracy of advantaged ones. Using a phytoplankton dataset of 26,564 images from 68 genera, collected from Chaohu Lake, this method demonstrates superior performance compared to existing techniques. Specially, it achieves a 5.69 % increase in micro-average F1 score and an 11.85 % rise in macro-average F1 score over general method, while F1 score is widely recognized as a reliable metric for measuring classification models' performance. These enhancements not only increase the accuracy of automated phytoplankton identification but also facilitate more effective monitoring of biodiversity and ecological health in aquatic systems. This makes the research highly beneficial for practical applications in environmental science, offering rapid and accurate insights into phytoplankton community structures, for ecological assessments.

Response of plants and soils to inundation duration and construction of the plant‒soil association mode in the hydro‒fluctuation belt of the reservoir wetland

Hydro-Fluctuation Belt (HFB), a periodically exposed bank area formed by changes in water level fluctuations, is critical for damaging the reservoir wetland landscape and ecological balance. Thus, it is important to explore the mechanism of hydrological conditions on the plant-soil system of the HFB for protection of the reservoir wetland and landscape restoration. Here, we investigated the response of plant community characteristics and soil environment of the HFB of Tonghui River National Wetland Park (China), is a typical reservoir wetland, to the duration of inundation, as well as the correlation between the distribution of dominant plants and soil pH, nutrient contents, and enzyme activity by linear regression and canonical correlation analyses. The results show that as the duration of inundation decreases, the vegetation within the HFB is successional from annual or biennial herbs to perennial herbs and shrubs, with dominant plant species prominent and uneven distribution of species. Soil nutrient contents and enzyme activities of HFB decreased with increasing inundation duration. Dominant species of HFB plant community are related to soil environment, with water content, pH, urease, and available potassium being principle soil environmental factors affecting their distribution. When HFB was inundated for 0–30 days, soil pH was strongly acidic, with available potassium content above 150 mg kg−1 and higher urease activity, distributed with Arundo donax L., Polygonum perfoliatum L., Alternanthera philoxeroides (Mart.) Griseb., and Daucus carota L. communities. When inundated for 30–80 days, soil pH was acidic, with lower available potassium content (50–150 mg kg−1) and urease activity, distributed with Beckmannia syzigachne (Steud.) Fern.+ Polygonum lapathifolium L., Polygonum lapathifolium L., Medicago lupulina L. + Dysphania ambrosioides L. and Leptochloa panicea (Retz.) Ohwi communities. Using the constructed HFB plant-soil correlation model, changes in the wetland soil environment can be quickly judged by the succession of plant dominant species, which provides a simpler method for the monitoring of the soil environment in the reservoir wetland, and is of great significance for the scientific management and reasonable protection of the reservoir-type wetland ecosystem.

Community structure, ecology, and conservation issues of avifauna of two human-dominated landscapes in Faridpur district, Bangladesh during Covid-19 pandemic

A study was conducted on community structure, ecology, and conservation issues of the avifauna of two human-dominated landscapes in a lower Ganges Madhukhali Upazila, under the Faridpur district during the COVID-19 pandemic period. Direct field observations were made from April 2020 to March 2021. In total, 109 species of birds belong to 18 orders, and 49 families were observed, with a total count of 5,453 individuals. Resident bird species (93 species, 85.32%) dominant in the study area, whereas the migratory species were only 16 (14.68%). The highest number of bird species (93 species, 85.32%) with the highest number of individuals (n=3171, 58.15%) was observed in Beleswar (rural site) area. Shannon diversity index value (H=3.89, Ds= 0.9724) was higher in the rural site than Madhukhali municipal area (urban site). In the winter season, the highest number of bird species (95 species, 87.15%) with the highest number of individuals (n=2303, 42.23%) was observed. Among micro-habitats, trees, particularly the native tree species, were the preferable sites for bird nesting, foraging, and roosting. Among birds, Acridotheres tristis was the most abundant species (n=316, 5.79%) in the study area, and an uneven distribution of species in the community structure was observed. The abundance of birds shows that 59 (54.12%) species were very common, 8 (7.33%) common, 9 (8.25%) uncommon, and 33 (30.27%) rare. Among the bird species, Ichthyophaga ichthyaetus was categorised as Near Threatened (NT), and the rest are Least Concerned (IUCN Bangladesh 2015). Illegal hunting of birds, especially waterbirds, is the major threat in the rural site. Preparing a proper management plan based on the baseline data is essential for protecting of avian diversity in the study area. J. Asiat. Soc. Bangladesh, Sci. 48(1-2): 53-66, June-December 2022

Arrested diversification? The phylogenetic distribution of poorly-diversifying lineages

Rapidly-diversifying lineages have been a major focus of modern evolutionary biology, with many hypotheses seeking to explain how they contribute to the uneven distribution of species in space and among taxa. However, an alternative view that is rarely explored is that some lineages evolve to become depauperate clades and show disproportionately low diversification, in a phenomenon we here call arrested diversification. In this study, we analyse several large-scale datasets including amphibian, squamate, mammal, and seed plant species to assess the extent to which poorly-diversifying lineages show distinct phylogenetic and spatial distributions in relation to other lineages. We found significant evidence that clades with low diversification rates tend to be more phylogenetically overdispersed than expected and show more idiosyncratic spatial distributions. These results suggest that arrested diversification is a real phenomenon that might play an important (yet largely overlooked) role in explaining asymmetries in the distribution of species across lineages.

Checklist of coral reef fishes of Darvel Bay, Sabah, Malaysian Coral Triangle, with a note on the biodiversity and community structure.

The Darvel Bay is a large semi-enclosed bay with spectacular natural land and seascape. The inward side of the Bay has only been recently known to be an important foraging ground for the endangered, threatened and protected (ETP) elasmobranch species, such as the Whale Shark and mobulid rays. Following a recent scientific expedition, we present a checklist of the coral reef fishes of Darvel Bay. A note on the biodiversity and community structure is presented, based on our analysis using diversity indices, univariate and multivariate approaches. Seven natural coral reefs comprising two fringing reefs and five patch reefs, were surveyed at 10 m depth using underwater visual census (UVC) and baited remote underwater video station (BRUVS) methods. A diverse list of 66 species of reef fishes from 17 families is recorded. However, this is overwhelmingly dominated by the small-sized omnivorous damselfish, family Pomacentridae (62%; N = 1485 individuals). Species richness and abundance were observed to increase at sites surveyed furthest from the coast within the Bay. Significantly distinct reef fish assemblages were observed between three priori groups, based on proximity to shore (ANOSIM, R = 0.65, p < 0.05). SIMPER analysis further revealed that 22 species of the total reef fish species recorded drive 76% dissimilarities between the groups. The pattern of the reef fish communities observed, reflected as a logseries distribution model, is that commonly found in disturbed habitats or habitats characterised by restricted resources in a community, where the dominant species takes up a high proportion of available resources. The ecological indices (Shannon-Wiener Diversity Index, 2.05; Simpson Index of Diversity, 0.79; Simpson Dominance Index, 0.20; and Pielou's Evenness Index, 0.43), all reflect the relatively low diversity and uneven species distribution of the reef fish community. We conclude that the present status of the coral reef fish community dominating Darvel Bay as having undergone a rapid shift in structure following intense and rampant fishing pressure, as reported by the media.

Fouling communities of microscopic fungi on various substrates of the Black Sea

Fungi are the most active biodeteriorators of natural and man-made materials. The article presents generalizations of the studies (2001–2019) of communities of microscopic fungi within biofilms on various substrates: shells of live Mytilus (Mytilus galloprovincialis, 670 specimens) and Ostreidae (Crassostrea gigas, 90 specimens), fragments of driftwood (over 7,000), stones (40), concrete of hydrotechnical constructions along the shoreline (80) and wood between concrete blocks in constructions on the shores (80). The studies were carried out in Odessa Oblast, the coastal zone of Sevastopol and open area of the Black Sea. There were identified 123 species of micromycetes, belonging to 65 genera, 33 families, 21 orders, 10 classes, 4 divisions, 2 kingdoms: Fungi and Chromista (fungi-like organisms). The Chromista kingdom was represented by 1 species – Ostracoblabe implexa, on shells of C. gigas. The number of species of micromycetes on various substrates varied 23 (wood between concrete blocks of hydrotechnical constructions) to 74 (shells of M. galloprovincialis at the depths of 3 and 6 m). On all the substrates, the following species were found; Alternaria alternata, Botryotrichum murorum. The communities were found to contain pathogenic fungi Aspergillus fumigatus (shells of mollusks, stones, concrete), A. terreus (concrete), Fusarium oxysporum, Pseudallescheria boydii (shells of mollusks). The best representation was seen for the Pleosporales order – from 12.9% (shells of M. galloprovincialis, 0.3 m depth) to 33.3% (shells of C. gigas) of the species composition. Toxin-producing species of Microascales in mycological communities accounted for 1.6% (driftwood) to 40.0% (concrete), and were also observed on shells of Bivalvia – 11.1–32.3%. Similarity of species composition of mycological communities according to Bray-Curtis coefficient varied 21.1% (driftwood and concrete, 10 shared species) to 72.7% (shells of M. galloprovincialis, the depths of 3 and 7 m and shells of C. gigas, 45 shared species). Using graphs of indices of mean taxonomic distinctness (AvTD, Δ+) and variation (Variation in Taxonomic Distinctness index, VarTD, Λ+), we determined deviations of taxonomic structure of the studied mycological communities from the level of mean expected values, calculated based on the list of species, taking into account their systematic positions. The lowest values of index Δ+ were determined for communities on shells of M. galloprovincialis, 0.3 m depth, driftwood, stones and concrete. These communities had uneven distribution of species according to higher taxonomic ranks and minimum number of the highest taxa: 4–6 classes, 1–2 divisions, Fungi kingdom. Disproportion in species composition with decrease in the number of the highest taxa occurred in extreme environmental conditions. Using index Λ+, we found that the most complex taxonomic structure of fungi communities has developed on concrete and shells of C. gigas. In mycological communities on those substrates, the number of species was low (25 and 46), but they belonged to 4–7 classes, 2–3 divisions, 1–2 kingdoms. To compare the structures of mycological communities that have developed in such substrates in biotopes sea, sea-land-air, land-air, we compiled a list of fungi based on the literature data, which, taking into account our data, comprised 445 species of 240 genera, 103 families, 51 orders, 15 classes, 5 divisions, 2 kingdoms. The analysis revealed that on substrates with similar chemical composition, in all the biotopes, the species of the same divisions dominated (genus and family may vary). Therefore, in the biotope land-air – Hypocreales, Pleosporales, Eurotiales (genera Acremonium, Fusarium, Alternaria, Aspergillus, Penicillium); sea – Pleosporales, Eurotiales, Microascales (Alternaria, Aspergillus, Penicillium, Corollospora); sea-land-air – Pleosporales, Microascales (Alternaria, Leptosphaeria, Aspergillus, Penicillium, Corollospora, Halosarpheia). Monitoring of species composition of myxomycetes is needed in farms that cultivate industrial objects, recreation sites, various buildings for prevention of mycotoxin intoxication and infestation by mycodermatoses and other diseases caused by opportunistic and pathogenic fungi.

Fouling communities of microscopic fungi on various substrates of the Black Sea

Fungi are the most active biodeteriorators of natural and man-made materials. The article presents generalizations of the studies (2001–2019) of communities of microscopic fungi within biofilms on various substrates: shells of live Mytilus (Mytilus galloprovincialis, 670 specimens) and Ostreidae (Crassostrea gigas, 90 specimens), fragments of driftwood (over 7,000), stones (40), concrete of hydrotechnical constructions along the shoreline (80) and wood between concrete blocks in constructions on the shores (80). The studies were carried out in Odessa Oblast, the coastal zone of Sevastopol and open area of the Black Sea. There were identified 123 species of micromycetes, belonging to 65 genera, 33 families, 21 orders, 10 classes, 4 divisions, 2 kingdoms: Fungi and Chromista (fungi-like organisms). The Chromista kingdom was represented by 1 species – Ostracoblabe implexa, on shells of C. gigas. The number of species of micromycetes on various substrates varied 23 (wood between concrete blocks of hydrotechnical constructions) to 74 (shells of M. galloprovincialis at the depths of 3 and 6 m). On all the substrates, the following species were found; Alternaria alternata, Botryotrichum murorum. The communities were found to contain pathogenic fungi Aspergillus fumigatus (shells of mollusks, stones, concrete), A. terreus (concrete), Fusarium oxysporum, Pseudallescheria boydii (shells of mollusks). The best representation was seen for the Pleosporales order – from 12.9% (shells of M. galloprovincialis, 0.3 m depth) to 33.3% (shells of C. gigas) of the species composition. Toxin-producing species of Microascales in mycological communities accounted for 1.6% (driftwood) to 40.0% (concrete), and were also observed on shells of Bivalvia – 11.1–32.3%. Similarity of species composition of mycological communities according to Bray-Curtis coefficient varied 21.1% (driftwood and concrete, 10 shared species) to 72.7% (shells of M. galloprovincialis, the depths of 3 and 7 m and shells of C. gigas, 45 shared species). Using graphs of indices of mean taxonomic distinctness (AvTD, Δ+) and variation (Variation in Taxonomic Distinctness index, VarTD, Λ+), we determined deviations of taxonomic structure of the studied mycological communities from the level of mean expected values, calculated based on the list of species, taking into account their systematic positions. The lowest values of index Δ+ were determined for communities on shells of M. galloprovincialis, 0.3 m depth, driftwood, stones and concrete. These communities had uneven distribution of species according to higher taxonomic ranks and minimum number of the highest taxa: 4–6 classes, 1–2 divisions, Fungi kingdom. Disproportion in species composition with decrease in the number of the highest taxa occurred in extreme environmental conditions. Using index Λ+, we found that the most complex taxonomic structure of fungi communities has developed on concrete and shells of C. gigas. In mycological communities on those substrates, the number of species was low (25 and 46), but they belonged to 4–7 classes, 2–3 divisions, 1–2 kingdoms. To compare the structures of mycological communities that have developed in such substrates in biotopes sea, sea-land-air, land-air, we compiled a list of fungi based on the literature data, which, taking into account our data, comprised 445 species of 240 genera, 103 families, 51 orders, 15 classes, 5 divisions, 2 kingdoms. The analysis revealed that on substrates with similar chemical composition, in all the biotopes, the species of the same divisions dominated (genus and family may vary). Therefore, in the biotope land-air – Hypocreales, Pleosporales, Eurotiales (genera Acremonium, Fusarium, Alternaria, Aspergillus, Penicillium); sea – Pleosporales, Eurotiales, Microascales (Alternaria, Aspergillus, Penicillium, Corollospora); sea-land-air – Pleosporales, Microascales (Alternaria, Leptosphaeria, Aspergillus, Penicillium, Corollospora, Halosarpheia). Monitoring of species composition of myxomycetes is needed in farms that cultivate industrial objects, recreation sites, various buildings for prevention of mycotoxin intoxication and infestation by mycodermatoses and other diseases caused by opportunistic and pathogenic fungi.

Drivers and dynamics of a massive adaptive radiation in cichlid fishes.

Adaptive radiation is the likely source of much of the ecological and morphological diversity of life1-4. How adaptive radiations proceed and what determines their extent remains unclear in most cases1,4. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika. On the basis of whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology and lower pharyngeal jaw shape), scoring of pigmentation patterns and approximations of the ecology of nearly all of theapproximately 240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of rapid morphospace expansion. We provide empirical support for two theoretical predictions of how adaptive radiations proceed, the 'early-burst' scenario1,5 (for body shape) and the stages model1,6,7 (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per-individual heterozygosity, but is not correlated with transposable element content, number of gene duplications or genome-wide levels of selection in coding sequences.

Protected Area Biodiversity Conservation: Population Dynamics

One of the methods for protecting the environment and conserving species biodiversity is the creation of protected areas, the task of which is to conserve rare species of animals and plants. The dynamics of populations can be studied quite effectively with the mathematical models. Modeling allows to study all possible scenarios of interaction and development of populations, to evaluate the influence of the environment on the spatial-temporal dynamics of biological communities. The paper considers a non-linear model of a protected population, the feature of which is the presence of a bilocal range and the exchange of species between its parts. It is a system of nonlinear parabolic partial differential equations that describes the dependence of migration flows on the uneven distribution of species in an area with a generalized resource. A complex of programs was coded in Python programming language for numerical study of diffusion models and visualization of the results obtained. Numerical simulation results of cross-diffusion effects and influence of generalized resource are analyzed in detail. The obtained results of research can be used for studying the processes in the protected population, for assessing the size of the protected areas being created, determining the conditions of population degeneration and recommendations for their stable existence.

Relationship Between The Diversity of Mycorrhizal Arbuscule Fungi with The Physic-Chemical of Dystropept Soil

The one of poor soil in West Kalimantan is the dystropept soil which includes sub ordo of inceptisol. This soil spread sporadic and relatively much in the production forest areal. Increasing the dystropept soil quality through the microbial approach is very rare or even may not have been done. As a first step, the purpose of the research was to determine the abundance and diversity of AMF (arbuscular mycorrhizal fungi) and the relationship of dystropepts soil characteristic with AMF diversity. The method consisted of taking soil samples at the location in depth of 0-20 cm, 20-40 cm and 40-60 cm, and location II in depth of 0-20 cm; identifying spore-based on morphology. Analyzing data used the pattern of relative abundance, diversity index, evenness index, and biplot RDA. The results were Glomus was dominant genera with high abundance and low species diversity in all location and uneven distribution of species. This diversity of species positively with excellent sand content, Mg, CEC, N, BS, K, and C.

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the degree of fragmentation of each genome in the sample, which is dependent on the sequencing effort and the genome length. Depending on ecological, biological, or procedural biases, some fragments have a higher prevalence, or coverage, in the assembly. However, assemblers must face challenges, such as the formation of chimerical structures and intra-species variability. Diversity calculation relies on the classification of the sequences that comprise a metagenomic dataset. Whenever the corresponding genomic and taxonomic information is available, contigs matching the same species can be classified accordingly and the coverage of its genome can be calculated for that species. This may be used to compare populations by estimating abundance and assessing species distribution from this data. Nevertheless, the coverage does not take into account the degree of fragmentation, or else genome completeness, and is not necessarily representative of actual species distribution in the samples. Furthermore, undetermined sequences are abundant in viral metagenomic datasets, resulting in several independent contigs that cannot be assigned by homology or genomic information. These may only be classified as different operational taxonomic units (OTUs), sometimes remaining inadvisably unrelated. Thus, calculations using contigs as different OTUs ultimately overestimate diversity when compared to diversity calculated from species coverage. In order to compare the effect of coverage and fragmentation, we generated three sets of simulated Illumina paired-end reads with different sequencing depths. We compared different assemblies performed with RayMeta, CLC Assembly Cell, MEGAHIT, SPAdes, Meta-IDBA, SOAPdenovo, Velvet, Metavelvet, and MIRA with the best attainable assemblies for each dataset (formed by arranging data using known genome coordinates) by calculating different assembly statistics. A new fragmentation score was included to estimate the degree of genome fragmentation of each taxon and adjust the coverage accordingly. The abundance in the metagenome was compared by bootstrapping the assembly data and hierarchically clustering them with the best possible assembly. Additionally, richness and diversity indexes were calculated for all the resulting assemblies and were assessed under two distributions: contigs as independent OTUs and sequences classified by species. Finally, we search for the strongest correlations between the diversity indexes and the different assembly statistics. Although fragmentation was dependent of genome coverage, it was not as heavily influenced by the assembler. The sequencing depth was the predominant attractor that influenced the success of the assemblies. The coverage increased notoriously in larger datasets, whereas fragmentation values remained lower and unsaturated. While still far from obtaining the ideal assemblies, the RayMeta, SPAdes, and the CLC assemblers managed to build the most accurate contigs with larger datasets while Meta-IDBA showed a good performance with the medium-sized dataset, even after the adjusted coverage was calculated. Their resulting assemblies showed the highest coverage scores and the lowest fragmentation values. Alpha diversity calculated from contigs as OTUs resulted in significantly higher values for all assemblies when compared with actual species distribution, showing an overestimation due to the increased predicted abundance. Conversely, using PHACCS resulted in lower values for all assemblers. Different association methods (random-forest, generalized linear models, and the Spearman correlation index) support the number of contigs, the coverage, and fragmentation as the assembly parameters that most affect the estimation of the alpha diversity. Coverage calculations may provide an insight into relative completeness of a genome but they overlook missing fragments or overly separated sequences in a genome. The assembly of a highly fragmented genomes with high coverage may still lead to the clustering of different OTUs that are actually different fragments of a genome. Thus, it proves useful to penalize coverage with a fragmentation score. Using contigs for calculating alpha diversity result in overestimation but it is usually the only approach available. Still, it is enough for sample comparison. The best approach may be determined by choosing the assembler that better fits the sequencing depth and adjusting the parameters for longer accurate contigs whenever possible whereas diversity may be calculated considering taxonomical and genomic information if available.

Macro-ecological patterns of the endemic Afrosoricida and Rodentia of Madagascar

We examined the macro-ecological and species richness correlates of the endemic mammal fauna (Afrosoricida and Rodentia) of Madagascar. We divided the whole of Madagascar into 307, 50◊50 km cells, and showed that there was a significantly uneven distribution of species across cells in both Afrosoricida and Rodentia, with a higher number of species per cell in the former taxon (peaks at around 19‐21 species per cell in Afrosoricida versus 11‐12 species in Rodentia). In each cell, the number of Afrosoricida species was positively correlated with the number of Rodentia species. Cell vegetation category aected species richness per cell in both Afrosoricida and Rodentia (evergreen forest cells had higher species richness than cells of any other type of vegetation). There was a significant eect of altitude category on species richness per cell in both Afrosoricida and Rodentia, with a confirmed Mid Domain Eect in both groups. Heterogeneity of habitat also influenced significantly and positively the species richness per cell in either Afrosoricida or Rodentia. About 15% of Afrosoricida and 28% of Rodentia are threatened according to IUCN. The distribution of threatened species of the two groups per cell showed (i) a low density of threatened species (just one species per cell in most cases) and (ii) distinct patterns for the two studied groups. Afrosoricida had two main regions where threatened species are concentrated (the evergreen forest belt in Eastern Madagascar and the deciduous broad-leaf forest in Central-Western Madagascar). Threatened Rodentia occur only in the portion of cells covered by evergreen forest, thus overlapping with part of the region where also threatened Afrosoricida occur.

Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae.

The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in diversification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus-level phylogenetic trees of the Proteaceae. Character-dependent analyses were used to test for differences in diversification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5-10 major diversification rate shifts in the Proteaceae tree. The character-dependent analyses showed that speciation rates, extinction rates and net diversification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net diversification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae diversification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success.

Diversity and community composition of methanogenic archaea in the rumen of Scottish upland sheep assessed by different methods.

Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae (≥91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6–V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to16S rRNA gene references produced taxonomic identification to Order level including 2–3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19–35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10–18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6–V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed eight independent loci for 1–7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate.

Classification of habitats highlights priorities for conservation policies: The case of Spanish Mediterranean tall humid herb grasslands

The Mediterranean grasslands of Molinio-Holoschoenion are one of the lesser known natural habitat types of interest for conservation in the European Community. A study on their content with regard to their plant-communities and interest for plant conservation is conducted on a regional scale for the first time. A new comprehensive classification is proposed for this habitat type in Spain (Iberian Peninsula and Balearic and Canary Islands) where they have their highest European diversity. Twenty-five plant-community types are floristically identified by k-means clustering. Cluster analysis reveals a major hierarchical aggregation in two vegetation groups: (i) rush meadows of Scirpoides holoschoenus (L.) Soják; and (ii) communities of herbs and forbs dominated by Molinia caerulea (L.) Moench subsp. arundinacea (Schrank) H. Paul and/or Schoenus nigricans L. These groups are associated with different positions along a soil moisture gradient where rush formations occupy the positions farthest from the water table. Cluster Analysis also shows an uneven distribution of species with conservation interest. The highest content in endangered species is found in halophilous rushes. Grasslands on mineralised soils host the highest number of vulnerable species. Spanish Molinio-Holoschoenion plant communities were ranked using three criteria (regional responsibility, local rarity and habitat vulnerability) in order to set conservation priorities. The highest conservation values were achieved by coastal rush communities developing on dune slacks, and by forbs and rushes in the Baetic System growing on banks of streams with oligotrophic waters.

Community analysis of sublittoral Harpacticoida (Copepoda, Crustacea) in the western Baltic Sea

This study compares two stations each sampled at the Oresund (Denmark) and the German coast (western Baltic Sea), with respect to sublittoral Harpacticoida. The associations were found to differ considerably in diversity, species numbers, evenness and also in the species composition. At the two northern stations, mainly polyhaline species were found and they showed the highest species and individual numbers as well as the most even species distribution. At the two southern stations, mainly pleiomesohaline species were found and they were dominated by one species that was very resistant to eutrophication, so that they showed an uneven species distribution, but also had lower individual numbers and thus lower diversity. Some samples at the German coast were found to have an extremely low harpacticoid number, which was attributed to the severe oxygen deficiency that occurred in autumn 2002 in the western Baltic Sea. This can also be considered to be the main reason for the low species diversity of the southern stations.

Prediction of street tree morphological parameters using artificial neural networks

Street trees positively affect the everyday life of city inhabitants and therefore successful management of this resource is important. A tree inventory is an essential first step towards this end, but this activity can be complex, costly and must be optimized. In order to reduce time and effort required for data acquisition either when using traditional field work or airborne laser systems, a method is proposed to predict the value of essential tree morphological parameters with surrogate variables and artificial intelligence multilayer perceptron networks (MLPs). To evaluate MLPs, seven different models were tested on Acer platanoides L., Acer saccharinum L., Celtis occidentalis L., Fraxinus pennsylvanica Marsh., Gleditsia triacanthos L., Tilia cordata Mill., and Ulmus pumila L. data sets. Three models were intended to predict diameter at breast height (DBH), annual DBH increment and crown volume with a minimal number of input measurements to be extracted from aerial LIDAR (Light Detection and Ranging) data. The last four were associated with traditional ground inventory methods and aimed to predict height, crown volume and their respective annual increments using less labour-intensive variables. The prediction performance was assessed with the Pearson r correlation coefficient, computed between the measured and estimated output values for each of the cross-validation test files per tree species and model. By using carefully selected biotic and abiotic input parameters, the prediction performance of multilayer perceptron showed robustness and precision despite different age–class distribution per species, dissimilar species morphological characteristics, uneven distribution of species within defined urban ecological zones, and varied abiotic growth conditions. More precisely, prediction coefficients were greater than 70% for all models with very small probability levels except for two predictions were input data exhibited strongly non-Gaussian distributions. Overall, the average prediction for all scenarios was 91%. Considering these results, it was found that prediction of DBH, annual DBH increment and crown volume is possible with limited aerial LIDAR laser information. Moreover, it was established that traditional field work effort can be further reduced by predicting the value of unmeasured morphological parameters within acceptable levels of precision. These findings can have an impact on future urban tree inventories. Depending on the number of trees to be measured, municipal administrations have the choice to use either airborne or traditional data acquisition methods. In both cases, this research proposes optimized procedures that may reduce the overall inventory costs.

Atlantic reef fish biogeography and evolution

AbstractAim To understand why and when areas of endemism (provinces) of the tropical Atlantic Ocean were formed, how they relate to each other, and what processes have contributed to faunal enrichment.Location Atlantic Ocean.Methods The distributions of 2605 species of reef fishes were compiled for 25 areas of the Atlantic and southern Africa. Maximum‐parsimony and distance analyses were employed to investigate biogeographical relationships among those areas. A collection of 26 phylogenies of various Atlantic reef fish taxa was used to assess patterns of origin and diversification relative to evolutionary scenarios based on spatio‐temporal sequences of species splitting produced by geological and palaeoceanographic events. We present data on faunal (species and genera) richness, endemism patterns, diversity buildup (i.e. speciation processes), and evaluate the operation of the main biogeographical barriers and/or filters.Results Phylogenetic (proportion of sister species) and distributional (number of shared species) patterns are generally concordant with recognized biogeographical provinces in the Atlantic. The highly uneven distribution of species in certain genera appears to be related to their origin, with highest species richness in areas with the greatest phylogenetic depth. Diversity buildup in Atlantic reef fishes involved (1) diversification within each province, (2) isolation as a result of biogeographical barriers, and (3) stochastic accretion by means of dispersal between provinces. The timing of divergence events is not concordant among taxonomic groups. The three soft (non‐terrestrial) inter‐regional barriers (mid‐Atlantic, Amazon, and Benguela) clearly act as ‘filters’ by restricting dispersal but at the same time allowing occasional crossings that apparently lead to the establishment of new populations and species. Fluctuations in the effectiveness of the filters, combined with ecological differences among provinces, apparently provide a mechanism for much of the recent diversification of reef fishes in the Atlantic.Main conclusions Our data set indicates that both historical events (e.g. Tethys closure) and relatively recent dispersal (with or without further speciation) have had a strong influence on Atlantic tropical marine biodiversity and have contributed to the biogeographical patterns we observe today; however, examples of the latter process outnumber those of the former.

Magnitude and variability of process rates in fungal diversity‐litter decomposition relationships

There is compelling evidence that losses in plant diversity can alter ecosystem functioning, particularly by reducing primary production. However, impacts of biodiversity loss on decomposition, the complementary process in the carbon cycle, are highly uncertain. By manipulating fungal decomposer diversity in stream microcosm experiments we found that rates of litter decomposition and associated fungal spore production are unaffected by changes in decomposer diversity under benign and harsher environmental conditions. This result calls for caution when generalizing outcomes of biodiversity experiments across systems. In contrast to their magnitude, the variability of process rates among communities increased when species numbers were reduced. This was most likely caused by a portfolio effect (i.e. statistical averaging), with the uneven species distribution typical of natural communities tending to weaken that effect. Curbing species extinctions to maintain ecosystem functioning thus can be important even in situations where process rates are unaffected.