indicator species
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The popularity of aquatic bioassessments has increased in Europe and worldwide, with a considerable number of methods being based on benthic diatoms. Recent evidence from molecular data and mating experiments has shown that some traditional diatom morphospecies represent species complexes, containing several to many cryptic species. This case study is based on epiphytic diatom and environmental data from shallow fishponds, investigating whether the recognition and use of fine taxonomic resolution (cryptic species) can improve assessment of community response to environmental drivers and increase sharpness of classification, compared to coarse taxonomic resolution (genus level and species level with unresolved species complexes). Secondly, trophy bioindication based on a species matrix divided into two compartments (species complexes and remaining species) was evaluated against the expectation that species complexes would be poor trophy indicators, due to their expected wide ecological amplitude. Finally, the response of species complexes and their members (cryptic species) to a trophic gradient (phosphorus) were compared. Multivariate analyses showed similar efficiency of all three taxonomic resolutions in depicting community patterns and their environmental correlates, suggesting that even genus level resolution is sufficient for routine bioassessment of shallow fishponds with a wide trophic range. However, after controlling for coarse taxonomic matrices, fine taxonomic resolution (with resolved cryptic species) still showed sufficient variance related to the environmental variable (habitat groups), and increased the sharpness of classification, number of indicator species for habitat categories, and gave better separation of habitat categories in the ordination space. Regression analysis of trophic bioindication and phosphorus concentration showed a weak relationship for species complexes but a close relationship for the remaining taxa. GLM models also showed that no species complex responded to phosphorus concentration. It follows that the studied species complexes have wide tolerances to, and no apparent optima for, phosphorus concentrations. In contrast, various responses (linear, unimodal, or no response) of cryptic species within species complexes were found to total phosphorus concentration. In some cases, fine taxonomic resolution to species level including cryptic species has the potential to improve data interpretation and extrapolation, supporting recent views of species surrogacy.
- Klíčová slova
- Cryptic species, Ecological preferences, Epiphyton, Indicator species, Taxonomic resolution,
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND AIMS: Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf-height-seed) traits and by actual performance in the botanical garden. METHODS: Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area - height - seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. KEY RESULTS: After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. CONCLUSIONS: Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden performance parameters provide a practical approach to assessing the roles of clonal growth morphological traits (and LHS traits) for large sets of species.
- Klíčová slova
- Clonal plant growth, Ellenberg indicator values, LHS traits, botanical garden collections, lateral expansion, leaf-specific area, plant height, seed mass, seed reproduction, species abundance,
- MeSH
- biodiverzita * MeSH
- biologické modely MeSH
- buněčné klony MeSH
- druhová specificita MeSH
- nepohlavní rozmnožování * MeSH
- vývoj rostlin * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Concern that European forest biodiversity is depleted and declining has provoked widespread efforts to improve management practices. To gauge the success of these actions, appropriate monitoring of forest ecosystems is paramount. Multi-species indicators are frequently used to assess the state of biodiversity and its response to implemented management, but generally applicable and objective methodologies for species' selection are lacking. Here we use a niche-based approach, underpinned by coarse quantification of species' resource use, to objectively select species for inclusion in a pan-European forest bird indicator. We identify both the minimum number of species required to deliver full resource coverage and the most sensitive species' combination, and explore the trade-off between two key characteristics, sensitivity and redundancy, associated with indicators comprising different numbers of species. We compare our indicator to an existing forest bird indicator selected on the basis of expert opinion and show it is more representative of the wider community. We also present alternative indicators for regional and forest type specific monitoring and show that species' choice can have a significant impact on the indicator and consequent projections about the state of the biodiversity it represents. Furthermore, by comparing indicator sets drawn from currently monitored species and the full forest bird community, we identify gaps in the coverage of the current monitoring scheme. We believe that adopting this niche-based framework for species' selection supports the objective development of multi-species indicators and that it has good potential to be extended to a range of habitats and taxa.
- MeSH
- biodiverzita * MeSH
- lesy * MeSH
- ptáci * MeSH
- statistika jako téma metody MeSH
- zachování přírodních zdrojů MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
The current ecological crisis has risen extinction rates to similar levels of ancient mass extinctions. However, it seems to not be acting uniformly across all species but affecting species differentially. This suggests that species' susceptibility to the extinction process is mediated by specific traits. Since understanding this response mechanism at large scales will benefit conservation effort around the world, we used the IUCN global threat status and population trends of 8281 extant bird species as proxies of the extinction risk to identify the species-specific traits affecting their susceptibility to extinction within the biogeographic regions and at the global scale. Using linear mixed effect models and multinomial models, we related the global threat status and the population trends with the following traits: migratory strategy, habitat and diet specialization, body size, and generation length. According to our results and independently of the proxy used, more vulnerable species are sedentary and have larger body size, longer generation time, and higher degree of habitat specialization. These relationships apply globally and show little variation across biogeographic regions. We suggest that such concordant patterns might be caused either by a widespread occurrence of the same threats such as habitat modification or by a uniform capacity of some traits to reflect the impact of different local threats. Regardless of the cause of this pattern, our study identified the traits that affect species' response capability to the current ecological crisis. Conservation effort should focus on the species with trait values indicating the limited response capacity to overcome this crisis.
- Klíčová slova
- Bird species, Ecological crisis, Ecological traits, Extinction risk, Extinction susceptibility, Global scale,
- MeSH
- biodiverzita MeSH
- druhová specificita MeSH
- ekosystém MeSH
- extinkce biologická * MeSH
- klimatické změny * MeSH
- ptáci MeSH
- zachování přírodních zdrojů MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Common cuckoo Cuculus canorus is a charismatic bird species with a dominant presence in human culture: from folklore legends to nowadays there is evidence of cuckoos being a prime candidate as a surrogate of bird diversity. Recent studies demonstrated that the cuckoo can predict hotspots of taxonomic diversity and functional diversity of bird communities in European countries. In this study, we demonstrated that the cuckoo is an excellent bioindicator at multi-spatial scale, extending cuckoo surrogacy from Europe to Asia. Even using three different survey methods (transect, square, point counts), comparing the new findings with results of our research in Europe, sites where the cuckoo is present were characterized by greater species richness, while the cuckoo was absent from sites with low species richness. The goodness of fit of models based on point counts ranged between 71 and 92%. Furthermore, the cuckoo population trend mirrors the average population trend and climate suitability of overall bird communities in Europe. The common cuckoo is therefore a suitable intercontinental bioindicator of hotspots of bird richness, even under climate change scenarios or in areas where the species co-occurs with other cuckoo species, opening a new avenue for standardized citizen science on bird biodiversity surveys worldwide.
BACKGROUND AND AIMS: While we know a lot about variation of root traits across large set of species, knowledge on differences in root traits among species with different ecological optima, simultaneously considering species life span and phylogeny, is limited. We also do not know if inter-specific differences in root traits measured in one environment apply in another environment. Such knowledge is crucial to predict species responses to future environments. METHODS: Using 65 species cultivated under uniform conditions, we studied effects of species habitat preference, describing under which conditions the species naturally occur, on root morphological and chemical traits and allocation to roots while also considering species life span, phenology at harvest and phylogeny. In a subset of species, we explored if species rankings in values of different traits depend on specific substrate of growth. KEY RESULTS: Inter-specific trait differences were strongly linked to species habitat preferences. The best predictor was indicator value for soil disturbance with roots of species preferring disturbed habitats having higher specific root length and lower diameter, suggesting low collaboration with mutualists. While life span and phylogeny also determined trait values, their inclusion into models did not change effects of habitat preferences. The patterns are thus not a result of species niche conservatism, but contemporary species adaptations. Species ranking in different substrates was more consistent for root morphology than for root chemistry and root/shoot ratio. CONCLUSIONS: Root trait variation is driven by species habitat preferences indicating that inter-specific root trait variation is a result of species adaptations to different environments. Interestingly, disturbance indicator value was a better predictor of root trait variation than other, more commonly, considered habitat characteristics. Inter-specific differentiation in root morphology is consistent among substrates and can thus be compared across studies, but root chemistry and allocation data have to be used with caution.
- MeSH
- bakteriologické techniky * MeSH
- indikátory a reagencie * MeSH
- kultivační média MeSH
- oxidace-redukce MeSH
- Rhizobium klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- indikátory a reagencie * MeSH
- kultivační média MeSH
The colorimetric DNA-DNA hybridization method for the identification of 18 strains of Aeromonas spp. isolated from human stools was used. Bacterial isolates were also examined by phenotypic characteristics. On the basis of biochemical tests 13 strains were included in phenogroup A. caviae and 5 strains in A. sobria. Identification to the species level was obtained by colorimetric hybridization method. DNA-DNA similarity values showed that isolates of A. caviae group belong to hybridization group (HG) 4 whereas isolates of A. sobria belong to HG 8/10. DNA relatedness results obtained by the colorimetric method showed good agreement with values detected by the spectrophotometric method. The background in the colorimetric method is lower than in the spectrophotometric one. Results of this study indicate the usefulness of the colorimetric DNA-DNA hybridization in microplates method for the identification of Aeromonas genomic species, isolated from human diarrheal stools.
- MeSH
- Aeromonas klasifikace genetika izolace a purifikace MeSH
- difenylamin MeSH
- dítě MeSH
- DNA bakterií analýza genetika MeSH
- dospělí MeSH
- druhová specificita MeSH
- feces mikrobiologie MeSH
- gramnegativní bakteriální infekce mikrobiologie MeSH
- hybridizace nukleových kyselin metody MeSH
- indikátory a reagencie MeSH
- kojenec MeSH
- kolorimetrie metody MeSH
- lidé MeSH
- předškolní dítě MeSH
- průjem mikrobiologie MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé MeSH
- předškolní dítě MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- difenylamin MeSH
- DNA bakterií MeSH
- indikátory a reagencie MeSH
3-nitrotyrosine (3NTYR) produced by the reaction of nitrogen and oxygen species is used as a suitable marker of radical mediated tissue damage. Free or protein-bound tyrosin residues are in vivo nitrated most likely by peroxynitrite or myeloperoxidase. Processes involved in formation and degradation of 3NTYR are not completely clear. It seems that degradation depends on the way in which 3NTYR is formed, characteristics of the tissue or organ where 3NTYR was formed and even general condition of the organism. Nitration of tyrosine does not only modify the biochemical structure of the protein but usually affects its function. Nitrated proteins are probably specific for each organ and may influence the pathogenesis of the disease. The review also describes the methods of 3NTYR detection and summarizes published data on 3NTYR concentration in various human diseases.
- MeSH
- biologické markery analýza MeSH
- lidé MeSH
- reaktivní formy dusíku biosyntéza MeSH
- reaktivní formy kyslíku metabolismus MeSH
- tyrosin analogy a deriváty analýza MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- 3-nitrotyrosine MeSH Prohlížeč
- biologické markery MeSH
- reaktivní formy dusíku MeSH
- reaktivní formy kyslíku MeSH
- tyrosin MeSH
Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat-specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so-called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co-occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co-occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods need attention, especially when dark diversity is estimated at the plot level.
- Klíčová slova
- Beals smoothing, Biomod, Ellenberg indicator values, biodiversity monitoring, dark diversity, method comparison, species distribution modeling,
- Publikační typ
- časopisecké články MeSH
