The effect of excluding taxa with low abundances or taxa with small distribution ranges on ecological assessment

The present study aims to investigate whether taxa with a small distribution range or taxa with low abundances indicate specific habitats or a high ecological quality and what the effect is if these taxa are excluded from ecological assessment. We compared autecological features between stream dwelling taxa with a mean abundance >5 individuals per sample and a mean abundance ≤5 individuals per sample as well as between taxa with a small distribution range and taxa with a large distribution range. The number of rare taxa (either with a small distribution range or with low abundances) in a sample was related to the ecological quality classes. To test the effect of exclusion of rare taxa we constructed 8 data sets all including 142 samples of Dutch lowland streams. From each data set we stepwise excluded taxa that had low abundances or taxa that were known to be restricted in their distribution range. With help of the AQEM assessment software we calculated the final ecological quality classes and the metrics that were included in the multimetric for the original data and the 8 selected data sets. Autecological features of the taxa within the different selections showed that taxa with small distribution ranges were often running water taxa, living on stones and gravel and indicating oligosaprobic water conditions in contrast to taxa that had a large distribution range. There were only small differences between taxa with low and high abundances. However, current velocity preference was lower for taxa with abundance ≤5 individuals per sample, saprobic values were higher and scores for typical stream habitats, such as lithal, psammal and akal were lower compared to high abundant taxa. If taxa with low abundances were excluded a higher ecological quality class was achieved in most cases, while excluding taxa with a small distribution range resulted in lower ecological quality classes. In conclusion, excluding taxa with a small distribution range led to worse ecological quality classes because these taxa have special autecological features that often indicate natural streams. On the other hand, excluding taxa with low abundances resulted in higher ecological quality classes because these taxa indicate more disturbed situations and because the number of taxa per sample was strongly reduced. Although the documentation of rare taxa (either with low abundances or with small distribution ranges) is often time and cost-intensive regarding field work, laboratory work, data processing, and analyses, the indicative power of these taxa for natural circumstances is essential and therefore rare taxa should be included in ecological assessment studies.     

Chemosystematic aspects of flavonoid distribution in twenty-two taxa of Helenium

Distributional data for 12 flavonoids in twenty-two taxa of Helenium are presented. Flavonoids identified to date are all flavones based on luteolin and apigenin. Chemosystematic interpretations are made concerning several species and species groups.     

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9°S) to the UK (46.4°N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 ± 9%) and Prochlorococcus (12 ± 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both ～15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi‐related clade SAR202 occurred preferentially below the DCM (4–6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre (～25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient‐rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.     

Elevational distribution of restricted range forest tree taxa in eastern Tanzania

The forests of eastern Tanzania are a globally important biodiversity hotspot. In this study 361 eastern Tanzanian restricted range forest tree taxa were assessed. Of these taxa, 223 occurred in the Eastern Arc, 150 in Coastal forests, 17 in Northern forests and 21 in the Lake Nyasa forests. The majority of the taxa had restricted elevational ranges with 76.3% occurring in no more than two 200 m elevational bands out of a total potential elevation range of 3000 m. The majority of the taxa occupied a small area in the eastern Tanzanian forests, with 201 taxa being only found at a few sites. In determining priority areas for conservation, selection of taxon definitions can have important effects. For example, tree size varies with elevation, so if only large trees are used then site selection will be biased towards particular areas.     

Charge clusters signatures in prokaryotic proteomes: Temperature-dependence and distribution

The identification and the screening of Charged Clusters (CCs) residues in proteins is a key analysis to assess any quantitative structure-function correlation in proteins. Here, we present a proteome wide scan for the occurrence of (CCs) in 99292 proteins using a new tool. Finding Clusters Charge in Protein Sequences Program (FCCP). The FCCP has been employed to search CCs in 35 prokaryotic proteomes (7 Psychrophiles, 10 Mesophiles, 9 thermophiles and for 9 hyperthermophiles). A new repository of 855 CC has been created. Results showed that the mapped proteins containing positive and negative charge clusters are mostly transmembrane proteins while the conserved CCs within the same proteome are transposases or involved in DNA binding and integration. Interestingly, the negative charged cluster was associated to bacteria growth's temperature (p=0.002) acting as proteins' core signature. Taken together the various results provide a consistent picture of these screened CCs in terms of its potentials functional roles.     

Vertical distribution of the prokaryotic cell size in the Mediterranean Sea

Distributions of prokaryotic cell size and morphology were studied in different areas of the Mediterranean Sea by using image analysis on samples collected from surface down to bathypelagic layers (max depth 4,900?m) in the Southern Tyrrhenian, Southern Adriatic and Eastern Mediterranean Seas. Distribution of cell size of prokaryotes in marine ecosystem is very often not considered, which makes our study first in the context of prokaryotic ecology. In the deep Mediterranean layers, an usually-not-considered form of carbon sequestration through prokaryotic cells has been highlighted, which is consistent with an increase in cell size with the depth of the water column. A wide range in prokaryotic cell volumes was observed (between 0.045 and 0.566?μm³). Increase in cell size with depth was opposed to cell abundance distribution. Our results from microscopic observations were confirmed by the increasing HNA/LNA ratio (HNA, cells with high nucleic acid content; LNA, cells with low nucleic acid content) along the water column. Implications of our results on the increasing cell size with depth are in the fact that the quantitative estimation of prokaryotic biomass changes along the water column and the amount of carbon sequestered in the deep biota is enhanced.     

影响生物土壤结皮分布的环境因子

生物土壤结皮广泛分布于干旱荒漠地区,在干旱和荒漠生态系统中,有重要的生态功能。然而,并不是所有的干旱荒漠区都有生物土壤结皮的分布。在全球和区域尺度上,生物土壤结皮的分布与年降水、凝结水量和土壤含水量呈正相关趋势;温度对生物土壤结皮分布的影响因组成生物土壤结皮的物种而异。小尺度范围内,生物土壤结皮的分布受土壤类型、质地和养分的限制;维管植物对生物土壤结皮分布的影响,暂没有一致的结论。适度干扰对生物土壤结皮分布和生态功能无明显影响,但高强度干扰导致生物土壤结皮结构、功能和分布的退化与减少。全球变化背景下生物土壤结皮的分布变化、不同区域生物土壤结皮分布和演替的差异机理以及受损后恢复过程中的生态功能,将成为以后工作的重点。     

Environmental predictions and distributional limits of chromosomal taxa in the Australian grasshopperCaledia captiva (F.)

Summary Correlations between environmental parameters and the distribution of four chromosomal taxa in the acridine grasshopperCaledia captiva (F.) have been analyzed. A bioclimate prediction system (BIOCLIM) was used as a model to determine their bioclimatic envelopes and to predict their probable geographic distributions, based on climatic similarities with actual distributions. New, and formerly unsuspected, distribution areas are predicted. Parapatric boundaries are defined that actually coincide with known limits. The general distribution of the four taxa is correlated with rainfall seasonality and a temperature gradient. Their distributional boundaries are mostly in accordance with extreme values in rainfall in an east-west direction and temperature in a north-south direction. A nonmetric multidimensional scaling analysis of one selected narrow parapatric boundary confirms the nature of the geographic correlation with several climatic extreme values. The climatic and vegetation analyses suggest that sharp parapatric distributions can be maintained by gradual environmental influences and that coincidence with abrupt ecotones is not necessary. At least one of the parapatric boundaries seems to be relatively recent in origin (2000–6000 years) and on the basis of the location of extreme climatic values as well as chromosomal and genetic markers it is expected to slowly move further south and east of its present location apparently following a climatically established boundary.     

Species distribution models backing taxa delimitation: the case of the lichen Squamarina cartilaginea in Italy

Species distribution models (SDMs) have been extensively used for a variety of purposes, including investigation of taxonomic problems, together with molecular, chemical and morphological analysis. The two varieties of the lichen Squamarina cartilaginea known to occur in Italy (var. cartilaginea and var. pseudocrassa), which are morphologically indistinguishable, can be identified only by a medullar chemical spot test. In this paper, SDMs are used to support the separation of these two varieties, to determine whether they are also characterized by a differential spatial distribution. Occurrence data were obtained by geo-referencing a posteriori 114 herbarium specimens identified to variety level by a medullar spot test. The spatial distribution was modeled by using Random Forest (RF) and Generalized Linear Models. Suitability areas were obtained by applying the 0% omission error criterion in the probability map produced by RF, which proved to be the more statistically reliable of the two methods. Kendall's tau statistic test applied to RF suitability maps indicates that the two varieties tend to segregate ecologically in the Italian peninsula. Var. pseudocrassa appears to be more widespread in the Mediterranean region, as well as in coastal and hilly areas, while var. cartilaginea is more abundant in the temperate region and mountainous areas. For both varieties the spatial distribution is determined by similar climatic variables (mean yearly temperature, mean temperature of the coldest month and summer precipitation). These findings lead to a new hypothesis on the role of these environmental factors on the evolutionary history and geographical distribution of the two varieties. This study also corroborates the usefulness of SDMs in delimiting taxonomical entities.     

Benthic meiofauna assemblage structure of headwater streams: density and distribution of taxa relative to substrate size

Permanent meiofauna taxa and portions of the population of other invertebrates that are temporarily in the meiofauna size class are often precluded from stream studies and assessments. This study was designed to determine the identity, density, and distribution of major meiofauna taxa relative to substrate size in a set of similar headwater streams. Using a coring technique, meiofauna (80 μm–1 mm) and substrate samples were collected from 11 Ozark headwater streams in the Boston Mountain ecoregion of Arkansas, USA. Mean meiofauna density among streams was 1739 ± 436 organisms per l. Permanent meiofauna taxa (Copepoda, Cladocera, Ostracoda, Rotifera, Nematoda, Hydrachnida, and Tardigrada) comprised 22.5% of the organisms collected with a mean density of 394 ± 233 organisms per l; temporary meiofauna taxa (Oligochaeta, Turbellaria, Hydroidea, Chironomidae, Ephemeroptera, and other insects) comprised the remainder with a density of 1346 ± 308 organisms per l. Chironomidae was the most numerous temporary meiofauna taxon, and Hydrachnida was the most numerous permanent taxon. Streams were found to differ significantly in substrate composition and densities of major taxonomic categories. Substrate size was found to predict densities for most of these taxonomic categories. Meiofauna patchiness was reflected in high variability within streams. Canonical correspondence analysis revealed positive associations between Copepoda and Nematoda and silt, and between Copepoda, Nematoda, and Rotifera and fine sand. Hydrachnida and Rotifera were negatively associated with silt and coarse sand, respectively. The potential value of inclusion of meiofauna in stream environmental assessments is discussed.     

Evolutionary trends in the prokaryotic community and prokaryotic community-phage systems

The Evolutionary Constructor software has been used for computer simulation of the life and evolution of communities of unicellular haploid organisms (prokaryotic cells). Opposite trends of the community evolution (simplification and complication of the genome) have been studied. It has been demonstrated that species with reduced genomes tend to replace genetically and metabolically rich species under highly favorable environmental conditions. Under unfavorable conditions, the opposite tendency is observed. It has also been shown that introduction of phages capable of killing the cells into the system may radically change the current evolutionary trend.     

Multiple origins of circumboreal taxa in Pyrola (Ericaceae), a group with a Tertiary relict distribution

MethodsEstimates of divergence times and ancestral geographical distributions based on neutrally evolving DNA sequence variation were used to develop a spatio-temporal model of colonization patterns for Pyrola.ConclusionsThree circumboreal Pyrola lineages have arisen independently and at least two of these appear to have originated in Asia. The cool, high-altitude habitats of many Pyrola species and the fact that diversification in the genus coincided with global cooling from the late Miocene onwards fits a hypothesis of pre-adaptation to become circumboreal within this group.     

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.