Taxonomic Heterogeneity Research Articles

Снежный покров: особенности локального распределения в лесных массивах как возможный источник погрешностей спутниковых данных

The errors in the snow reserves recovered from satellite data in forest territories are mainly associated with the nature of the snow thickness and the characteristics of plant communities. The main objective of our research is to assess the local variability of snow reserves in modern climatic conditions in connection with the forest taxonomic heterogeneity as a possible additional source of errors in snow reserves calculating with using satellite information. Errors of snow сover characteristics recovered from satellite data (product GlobSnow (SWE), European Space Agency) for basic points within the forest zone of the East European Plain were calculated for absolute values, indicators of interannual and long-term variability. The errors obtained are connected with the approaches considering in model algorithms the reflective ability of the snow cover in forest tracts (permeability coefficient). Using experimental observations results in the Central Forest Reserve, noticeable local differences in the actual characteristics of the snow cover in the forest territories with a predominance of coniferous or deciduous species are revealed. The obtained patterns can be used to refine regional estimates of snow reserves calculating using satellite imagery.

Intra- and Interspecies Variability of Single-Cell Innate Fluorescence Signature of Microbial Cell.

Here we analyzed the innate fluorescence signature of the single microbial cell, within both clonal and mixed populations of microorganisms. We found that even very similarly shaped cells differ noticeably in their autofluorescence features and that the innate fluorescence signatures change dynamically with growth phases. We demonstrated that machine learning models can be trained with a data set of single-cell innate fluorescence signatures to annotate cells according to their phenotypes and physiological status, for example, distinguishing a wild-type Aspergillus nidulans cell from its nitrogen metabolism mutant counterpart and log-phase cells from stationary-phase cells of Pseudomonas putida We developed a minimally invasive method (confocal reflection microscopy-assisted single-cell innate fluorescence [CRIF] analysis) to optically extract and catalog the innate cellular fluorescence signatures of each of the individual live microbial cells in a three-dimensional space. This technique represents a step forward from traditional techniques which analyze the innate fluorescence signatures at the population level and necessitate a clonal culture. Since the fluorescence signature is an innate property of a cell, our technique allows the prediction of the types or physiological status of intact and tag-free single cells, within a cell population distributed in a three-dimensional space. Our study presents a blueprint for a streamlined cell analysis where one can directly assess the potential phenotype of each single cell in a heterogenous population by its autofluorescence signature under a microscope, without cell tagging.IMPORTANCE A cell's innate fluorescence signature is an assemblage of fluorescence signals emitted by diverse biomolecules within a cell. It is known that the innate fluoresce signature reflects various cellular properties and physiological statuses; thus, they can serve as a rich source of information in cell characterization as well as cell identification. However, conventional techniques focus on the analysis of the innate fluorescence signatures at the population level but not at the single-cell level and thus necessitate a clonal culture. In the present study, we developed a technique to analyze the innate fluorescence signature of a single microbial cell. Using this novel method, we found that even very similarly shaped cells differ noticeably in their autofluorescence features, and the innate fluorescence signature changes dynamically with growth phases. We also demonstrated that the different cell types can be classified accurately within a mixed population under a microscope at the resolution of a single cell, depending solely on the innate fluorescence signature information. We suggest that single-cell autofluoresce signature analysis is a promising tool to directly assess the taxonomic or physiological heterogeneity within a microbial population, without cell tagging.

Relative genome size variation in the African agroforestry tree Parkia biglobosa (Fabaceae: Caesalpinioideae) and its relation to geography, population genetics, and morphology.

Variation in genome size and in chromosome number can be linked to genetic, morphological, and ecological characteristics, and thus be taxonomically significant. We screened the relative genome size (RGS) and counted the number of mitotic chromosomes in the African agroforestry tree Parkia biglobosa, a widely distributed savannah species that shows conspicuous morphological clinal variation and strong genetic structure, and tested for linkage of RGS variation to geography, leaf morphology, and population genetic variation. An improved protocol for the preparation of chromosomes was developed. The study is based on 58 individuals from 15 populations covering most of the distribution range of the species. We observed differences in RGS among individuals of up to 10.2%, with some of the individuals differing statistically in RGS from the bulk of screened individuals. Most of the RGS variation was within populations, whereas variation was unrelated to any of the tested features of the species. Those chromosome numbers that could be exactly established were invariable 2n = 2x = 26. In conclusion, there was no evidence from the karyological data for structured intraspecific taxonomic heterogeneity.

The alpha taxonomy of Australopithecus at Sterkfontein: The postcranial evidence

The possibility that the fossils attributed to Australopithecus africanus represent more than a single species is of significance because of the pivotal role that A. africanus has played in discussions about hominin evolution. The A. africanus hypodigm that is currently widely recognized evinces considerable variation in a number of craniodental characters, and this has led to speculation that more than one australopith taxon may be represented among the specimens from Sterkfontein. Although crania, mandibles and teeth have dominated these taxonomic discussions, the Sterkfontein postcranial remains also have been invoked. While several workers have proposed that some of the craniodental remains from Sterkfontein can be partitioned into two groups, there is a notable lack of agreement among them as to their actual sorting. Most of the craniodental observations that have been put forward in support of arguments for taxonomic heterogeneity of the Sterkfontein australopith assemblage have been subjective and anecdotal in nature. So too, the postcranial evidence that has been cited in support of more than one australopith species at Sterkfontein has been largely subjective, and limited to a small number of elements. The results of quantitative statistical analyses of the craniodental and postcranial fossils that have been undertaken to date are not necessarily consistent with the hypothesis of taxonomic heterogeneity.

Composition, richness and taxonomic diversity of Polychaete assemblages from La Paz Bay and adjacent oceanic areas of the Southern Gulf of California

In the present study, the composition and structure of the assemblages of polychaetes of La Paz Bay and adjacent oceanic areas of the Gulf of California was analyzed. A total of 56 species belonging to 39 genera and 22 families were collected from eight stations sampled during the spring of 2006 at 31 to 208 m depth. Onuphidae (14 species), Paraonidae (7 species) and Spionidae (6 species) were the best represented families. The highest number of species and individuals (mean= 13 species station−1; 76.7 ind. 0.1 m−2) was found in stations located in the Gulf shelf while inside of La Paz Bay, the fauna was less abundant and diverse (mean= 9 species station−1; 47.0 ind. 0.1 m−2). Differences in species composition defined two main faunal groups, which were linked by their spatial distribution: assemblage Aricidea (Acmira) simplex – Aglaophamus verrilli inside the Bay, and assemblage Paraexogone molesta – Cirrophorus furcatus – Prionospio dubia in the Gulf shelf. The composition and structure of the fauna was mainly associated with the sediment type (Rho= 0.48; p=0.06): muddy habitats inside the bay and sandy bottoms in the Gulf. Only 11 out of the 39 identified genera (28.2%) had more than two species, and only seven of the 23 families (30.4%) had two or more species. This taxonomic heterogeneity caused a wide variability in the “average taxonomic distance” of every pair of individuals at each station (64.69 to 89.58). Therefore, the distribution patterns of the taxonomic diversity values between the sites inside La Paz Bay (mean= 79.45) and those found outside, in the Gulf (mean= 79.77), were similar.

Spatially resolved abundances of antibiotic resistance genes and intI1 in wastewater treatment biofilms.

Attached growth bioprocesses that use biofilms to remove organic matter or nutrients from wastewater are known to harbor antibiotic resistance genes (ARGs). Biofilms in these processes are spatially heterogeneous, but little is known about depth stratification of ARGs in complex, mixed culture biofilms. To address this knowledge gap, we used an experimental approach combining cryosectioning and quantitative polymerase chain reaction to quantify the spatial distribution of three ARGs (sul1, ermB, and qnrS) and the class 1 integron-integrase gene intI1 in biofilms from a lab-scale rotating annular reactor fed with synthetic wastewater. We also used high throughput 16S ribosomal RNA (rRNA) gene sequencing to characterize community structure with depth in biofilms. The ARG sul1 and the integron-integrase gene intI1 were found in higher abundances in upper layers of biofilm near the fluid-biofilm interface than in lower layers and exhibited significant correlations between the distance from substratum and gene abundances. The genes ermB and qnrS were present in comparatively low relative abundances. Microbial community structure varied significantly by date of sampling and distance from the substratum. These findings highlight the genetic and taxonomic heterogeneity with distance from substratum in wastewater treatment biofilms and show that sul1 and intI1 are particularly abundant near fluid-biofilm interfaces where cells are most likely to detach and flow into downstream portions of treatment systems and can ultimately be released into the environment through effluent.

Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species

Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid–bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies. The P. pectinatus thioautotrophic endosymbiont expressed metabolic gene variants for thioautotrophy, respiration, and nitrogen assimilation distinct from previously characterized lucinid thioautotrophic symbionts and other marine symbionts. At least two other bacterial species with different metabolisms were also consistently identified in the P. pectinatus gill microbiome, including a Kistimonas-like species and a Spirochaeta-like species. Bacterial transcripts involved in adhesion, growth, and virulence and mixotrophy were highly expressed, as were host-related hemoglobin and lysozyme transcripts indicative of sulfide/oxygen/CO2 transport and bactericidal activity. This study suggests the potential roles of P. pectinatus and its gill microbiome species in mangrove sediment biogeochemistry and offers insights into host and microbe metabolisms in the habitat.

Forest soil yeasts: Decomposition potential and the utilization of carbon sources

Abstract Fungi that inhabit forest topsoil can be distinguished into two morphological guilds: filamentous, multicellular fungi and predominantly unicellular yeasts. The nutritional mode of these two groups is expected to differ due to the dependence of yeasts on locally present nutrients. Here we explored the decomposition potential and carbon utilization profiles of dominant yeasts from the temperate forest topsoil. The results indicated that despite taxonomic heterogeneity, yeasts represent a fungal group with a specific nutritional strategy that is dissimilar from other tested fungi. While the efficient decomposition of hemicellulose, cellulose or chitin appeared to be restricted to only a few yeast taxa, carbon source utilization assays indicated that most yeasts could efficiently act as opportunists, utilizing the decomposition products generated by other microbes. Importantly, a large fraction of enzyme activity was associated with yeast cell surfaces indicating their adaptation to generate decomposition products so that they are readily available for intake.

The Evolutionary Diversity of Mosses – Taxonomic Heterogeneity and its Ecological Drivers

Mosses (division Bryophyta) are characterized by the dominance of haploid, poikilohydric gametophytes, and relatively persistent sporophytes that are dependent on the gametophyte generation. Because they are poikilohydric, tend to be desiccation tolerant, and have primarily ectohydric water uptake mechanisms, the ecological requirements of mosses tend to differ from those of vascular plants. We review recent research on phylogenetic relationships and morphological and ecological diversity among mosses. Ancestral character state reconstructions illustrate the evolution of habitat preferences and the relationships between these and morphological variation. These reconstructions reveal the convergent evolution of both epiphytic and aquatic habitat preferences, as well as several reversals from epiphytic to other terrestrial habitats. Morphological character states connected to ectohydry, such as lack of water-conducting stem central strands, may be more prone to adaption driven by environmental conditions, while connections between endohydry and environmental conditions remain ambiguous and require further study. The distribution of the most elaborate endohydric water-conducting structures may be phylogenetically determined rather than resulting from adaptation to habitats. Among the early diverging lineages in the Bryophyta, shifts to cladocarpy may be connected to epiphytic lifestyles. We discuss ecological drivers of aspects of plant architecture including acrocarpous, pleurocarpous and cladocarpous perichaetial positions, and sporophytic reductions, the latter being common in dry, frequently disturbed terrestrial environments and in epiphytic habitats, but also occasionally found in aquatic habitats.

Association between geographic range and initial survival of Mesozoic marine animal genera: circumventing the confounding effects of temporal and taxonomic heterogeneity

AbstractWe investigate the association between geographic range and survival in Mesozoic marine animal genera. Previous work using data from the Paleobiology Database (paleobiodb.org) demonstrated greater survivorship overall among Phanerozoic genera that were widespread during their stage of first appearance, but this relationship did not hold during the Mesozoic. To explore this unexpected result, we consider geographic range in conjunction with temporal variation in survival and variation in survival among higher taxa. Because average range and average survival are negatively correlated among stages, for reasons that are still unclear, and because the data are heavily influenced by cephalopods, which include many wide-ranging and short-lived genera, the effect of geographic range on survival is obscured in the aggregate data. Thus, range is not a significant predictor of survival when data are analyzed in aggregate, but it does have a significant effect when variation in average range and average survival among stages and classes is taken into account. The best-fitting models combine range with both temporal and taxonomic heterogeneity as predictive factors. Moreover, when we take stage-to-stage variation into account, geographic range is an important predictor of survival within most classes. Cephalopod genera must be more widespread than genera in other classes for geographic range to significantly increase odds of survival, and factoring in survival heterogeneity of superfamilies further increases model fit, demonstrating a nested nature in the sensitivity of range and taxonomic aggregation.

Dissecting out the taxonomic heterogeneity within Propionibacterium acnes and proposal for two novel subspecies of the species

Dissecting out the taxonomic heterogeneity within Propionibacterium acnes and proposal for two novel subspecies of the species

Preliminary study on 2 colour patterns in Ochlerotatus caspius (Pallas, 1771) (Diptera, Culicidae).

Ochlerotatus caspius is a mosquito of medical and veterinary relevance both for its synanthropy and for its potential role in transmission of viruses and nematodes in the areas that it inhabits. Due to its wide range and the marked variability in the adult colour pattern, some authors have recognized Ochlerotatus caspius as a complex of species. In this study, we purposed to evaluate the possible taxonomic heterogeneity between 2 chromatic forms by using both morphological and molecular approaches. The preliminary results based on the identity of the rRNA internal transcribed spacer 2 (ITS-2) lead us to believe the 2 forms as a single species with a chromatic polymorphism.

Extreme climate events counteract the effects of climate and land-use changes in Alpine treelines.

1. Climate change and extreme events, such as drought, threaten ecosystems worldwide and in particular mountain ecosystems, where species often live at their environmental tolerance limits. In the European Alps, plant communities are also influenced by land-use abandonment leading to woody encroachment of subalpine and alpine grasslands. 2. In this study, we explored how the forest-grassland ecotone of Alpine treelines will respond to gradual climate warming, drought events and land-use change in terms of forest expansion rates, taxonomic diversity and functional composition. We used a previously validated dynamic vegetation model, FATE-HD, parameterised for plant communities in the Ecrins National Park in the French Alps. 3. Our results showed that intense drought counteracted the forest expansion at higher elevations driven by land-use abandonment and climate change, especially when combined with high drought frequency (occurring every 2 or less than 2 years). 4. Furthermore, intense and frequent drought accelerated the rates of taxonomic change and resulted in overall higher taxonomic spatial heterogeneity of the ecotone than would be expected under gradual climate and land-use changes only. 5. Synthesis and applications. The results from our model show that intense and frequent drought counteracts forest expansion driven by climate and land-use changes in the forest-grassland ecotone of Alpine treelines. We argue that land-use planning must consider the effects of extreme events, such as drought, as well as climate and land-use changes, since extreme events might interfere with trends predicted under gradual climate warming and agricultural abandonment.

Subsistence strategies in Argentina during the late Pleistocene and early Holocene

This paper highlights regional and temporal variation in the presence and exploitation of faunal resources from different regions of Argentina during the late Pleistocene and early Holocene. Specifically, the faunal analysis considered here includes the zooarchaeological remains from all sites older than 7500 14C years BP. We include quantitative information for each reported species (genus, family, or order) and we use the number of identified specimens (NISP per taxon and the NISPtotal by sites) as the quantitative measure of taxonomic abundance. The taxonomic richness (Ntaxatotal and Ntaxaexploited) and the taxonomic heterogeneity or Shannon-Wiener index are estimated in order to consider dietary generalization or specialization, and ternary diagrams are used to categorize subsistence patterns of particular sites and regions. The archaeological database is composed of 78 sites which are represented by 110 stratigraphic contexts. Our results demonstrate that although some quantitative differences between regions are observed, artiodactyls (camelids and deer) were the most frequently consumed animal resource in Argentina. Early hunter-gatherers did not follow a specialized predation strategy in megamammals. A variety in subsistence systems, operating in parallel with a strong regional emphasis is shown, according to specific environmental conditions and cultural trajectories.

Windward vs. leeward: Inter-site variation in marine resource exploitation on Ebon Atoll, Republic of the Marshall Islands

The variation in windward and leeward marine environments has been linked to distinctions in marine subsistence on large, high volcanic Pacific Islands, but these patterns have not been explored on low coral atolls. We document windward vs. leeward islet site variation in the taxonomic composition of fish bone and mollusc shell assemblages from three archaeological sites at Ebon Atoll, Republic of the Marshall Islands, to elucidate the relationship between local environment, archaeological site type and the taxonomic composition of marine archaeofaunal assemblages. While the representation of taxa at each site was broadly similar in terms of measures of taxonomic heterogeneity (richness, evenness and dominance), chord distance and correspondence analysis reported variation in taxonomic composition at each site. For mollusc shell assemblages, variation in taxonomic abundance indicates the influence of the marine environments adjacent to each site and the relative exposure of these coastlines to heavy surf, wind, waves and extreme weather events. Fish bone assemblages recovered from 6.4mm screens had less inter-site variation in richness, evenness and rank order, but differences were noted in the rank order of fish taxa recovered from selective 3.2mm screening of archaeological deposits when compared between sites. In contrast to patterns for molluscs, variation in the taxonomic composition of fish bone assemblages likely relates to site function, rather than the marine environments adjacent to each site. These trends highlight for the first time the complex range of factors that influenced the prehistoric acquisition of marine resources between leeward and windward islets, and document variation in prehistoric marine subsistence within one atoll.

What is driving the community structure of insects in arid ecosystems of Southern Africa? An example with blister beetles (Coleoptera: Meloidae)

A considerable part of community ecology literature questioned what are the main drivers of ecological relationships in an organismal community. We analysed this focal question by studying blister beetle (Meloidae) assemblages in Southern Africa. We explored the ecological distribution of 48 species across underlying bioclimatic (e.g. temperatures and precipitation regimes), environmental factors (biomes, vegetation structure) and the taxonomic heterogeneity of each groups inhabiting major biomes of Namibia across their main biological and ecological traits, by Canonical Correspondence in order to get an ordination plot. Monte Carlo methods were used to test for randomness of the data ordination. Ordination plot identified three main assemblages, one being constituted by strictly semiarid savannah species (camelthorn, mountain, karstweld, thornbush, mixed tree and shrub, dwarf shrub, mopane and forest savannahs), one much larger and less homogenous second assemblage, inclusive of more generalist species f...

The body weight of capercaillie, Tetrao urogallus: spatial variability in Northern Eurasia

Published data on the body weight of capercaillie, Tetrao urogallus , from the region mostly situated north of 60° latitude were analyzed. With the addition of new estimates from some points in the species range one can see that the study area is almost exclusively populated by large individuals (cocks ≥ 4.0 kg, hens ≥ 2.0 kg). Taking all the populations included in the analysis as a whole, the body weight of birds changed independently of the geographic latitude and longitude. Apparently, the intra-species taxonomic heterogeneity in the study area was the main source of the spatial variability of body weight. If we remove the influence of the ≪taxonomy≫ factor by excluding the populations chiefly represented by small-size birds, the weight of males demonstrates a significant direct dependence on longitude and latitude, the one of females shows a slight direct correlation with geographical latitude only. These correlations allow interpreting the spatial variability of body weight in accordance with Bergmann's rule (for both sexes) and/or the rule of optimum (for males only). The nature of inter-population changes in the asymmetry of the frequency distributions of male body weight indicates the direction of the resultant effect of all (multidirectional) vectors of natural selection in accordance with these rules.

Quaternary mollusc assemblages from the lower basin of Salado River, Buenos Aires Province: Their use as paleoenvironmental indicators

Quaternary mollusc assemblages preserved in the Salado basin are described and analyzed in order to reconstruct past environments and evaluate spatial and temporal variations. Five localities were analyzed, in which 48,998 individuals of eight continental gastropod species were recovered: Heleobia parchappii, Antillorbis nordestensis, Biomphalaria peregrina, Drepanotrema heloicum, Uncancylus concentricus, Pomacea canaliculata, Succinea meridionalis and Miradiscops brasiliensis. As well, other species typical of marine-estuarine environments have been found, among which Heleobia australis is highlighted. Based on changes in the composition and abundance of the assemblages, different environments could be recognized. Quaternary mollusc assemblages have low taxonomic heterogeneity and spatial and temporal variations. Assemblages recovered from Late Pleistocene–Early Holocene sediments are characterized by low species richness and abundance, with a single species in numerous examples. In the Middle Holocene, the shells became more constant and more diverse. Late Holocene assemblages have high species richness, freshwater, terrestrial and amphibious habits, and show some differences among different localities. Several episodes of flooding have been identified through the record of fossiliferous horizons with high density of shells, mainly Heleobia parchappii. These events that affected the area of influence of the Salado River occurred at least during the Late Holocene.

The middle lower Cambrian (Ovetian)Lunagraulosn. gen. from Spain and the oldest trilobite records

AbstractThe type material ofAgraulos antiquusSdzuy, 1961 from the La Herrería Formation, northern Spain, is revised together with additional material and included in the new genusLunagraulos. The stratigraphical range ofLunagraulos antiquus(Sdzuy, 1961) – occurring below that of the trilobite species of the generaLunolenus,MetadoxidesandDolerolenusin the type locality of Los Barrios de Luna in the province of León, northern Spain – and the accompanying ichnofossil assemblage demonstrate an Ovetian age (lower part of Cambrian Stage 3, currently being discussed by the International Subcommission on Cambrian Stratigraphy) for this species. Moreover, the trilobiteLunagraulos tamamensisn. gen. n. sp. is found in the Tamames Sandstone near the village of La Rinconada in the province of Salamanca, central Spain. The biostratigraphical position of this new taxon and its accompanying ichnoassemblage is also analysed and assigned to the lowermost Ovetian Stage. The genusLunagraulosis therefore the oldest agraulid found in the fossil record. The exceptional presence ofLunagraulosin a marine coarse siliciclastic succession – a facies rather typical for the ichnofossilsCruzianaandRusophycus, some of the oldest signs of trilobite activity – suggests that first trilobite representatives may have inhabited high- to middle-energy, marine environments. This hypothesis may also explain both the taxonomic and biostratigraphic heterogeneity of the first trilobite genera appearing across the world, due to preservation problems in this type of facies. Comparison of theLunagraulos biostratigraphy with other coeval Spanish fossil assemblages allows us to propose its intercontinental correlation with the oldest records of currently known trilobites.

Congruence between species phylogenetic and trophic distinctiveness

Preserving biodiversity has become vital in a time of rapid environmental changes since biodiversity loss compromises ecosystem functioning and subsequently services on which human welfare depends. Biodiversity encompasses taxonomic, process and structure heterogeneity and its evaluation requires an integrative approach. Additionally, different taxa have been shown to unequally contribute to biodiversity. Conservation efforts would benefit from focusing on taxa bearing a highly distinct contribution to multiple biodiversity components, for a more efficient retention of a sustainable level of biodiversity. Both phylogenetic diversity and interaction diversity are essential components of biodiversity. An association between phylogenetic affiliations and ecological interactions has been found for a wide range of organisms, with closely related species engaging in similar interactions. Further, nested (specialists using a subset of the resources used by generalists) and modular (subguilds of consumer–resource relationships) interaction structures have been identified to enhance the resilience of ecosystem dynamics. We combine phylogenetic and network analyses to evaluate the relationship between species contributions to phylogenetic diversity and their contributions to the diversity and structure of trophic interactions in an African assemblage of mammalian herbivores. We identified positive relationships between species contributions to phylogenetic diversity, interaction diversity and nested interaction structure. This means that conservation actions aiming at protecting evolutionary distinct species have the potential to simultaneously maximise interaction diversity and nested architecture. Species contributions to modular interaction patterns were nonetheless uncorrelated to contributions to phylogenetic diversity, and indicated the importance of some phylogenetic redundancy between species for retaining a modular structure in the system.