Taxonomic rank | EPFL Graph Search

In biology, taxonomic rank is the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system of biological classification (taxonomy) consists of species, genus, family, order, class, phylum, kingdom, and domain. While older approaches to taxonomic classification were phenomenological, forming groups on the basis of similarities in appearance, organic structure and behaviour, methods based on genetic analysis have opened the road to cladistics. A given rank subsumes under it less general categories, that is, more specific descriptions of life forms. Above it, each rank is classified within more general categories of organisms and groups of organisms related to each other through inheritance of traits or features from common ancestors. The rank of any species and the description of its genus is basic; which means that to identify a particular organism, it is usually not necessary to specify ranks other than these first two. Consider a

Ecological response of a multi-purpose river development project using macro-invertebrates richness and fish habitat value

Marc Pellaud

It has been acknowledged that river morphology and hydrology have been intensively altered due to the anthropic demands in floodplain land use and management, flood protection, promotion of navigability or energy production. Rivers were transformed in water highways, having lost contact with their surrounding floodplain as well as the plethora of ecological processes and occupants once thriving in these ecotonal zones. The identification of this emerging threat of morphological and hydrological alteration on ecological integrity adds further complexity in the exploitation of hydrosystem resources. These resources are heavily coveted and guarded by different lobbies each having strategic views on future project development. Stakeholders may want to promote hydro-electricity, ecologists a natural reserve, communes may wish to have an increased flood protection and leisure promoters a nautical center. As a result, the proposition of a river development project is certain to face opposition of one party or the other. The motivations of this dissertation are anchored in this context, where various and sometimes conflicting potentials for hydrosystem exploitation remain. This works aims at contributing scientifically to an innovative approach at the conception phase of a multi-purpose river development project by developing the ecological module to be implemented in the general project's optimizer. The SYNERGIE project hypothesis is that it should be possible to identify a synergetic pattern joining the interests of ecological integrity, flood safety, energy production and leisure development. Such a multi-objective river development project would stand more chance of acceptance. This dissertation focuses on the ecological aspects of such a river development project and an application on the regulated Swiss Upper Rhone River. Is expected an ecological answer to a river development project design / management which has to be compatible with Heller's Heller (2007) general SYNERGIE project optimizer taking into account all the project poles. The system of interest is composed of a buffering reservoir of ca. 1 km2, a run-of-the-river dam, a hydro power-plant, and an artificial river ensuring longitudinal continuum. The primary part of the work consisted in an extensive literature review on system understanding, anthropic alterations and quality assessment / prediction tool available. The approach consisted of two levels (1) the general ecological considerations to be followed at the project reservoir scale and (2) the measure of the downstream ecological response through modeling. General ecological considerations at the reservoir scale were the implementation of an artificial river ensuring longitudinal connectivity, implementation of artificial ecotonal boosters and the allocation of a sanctuary zone with limited public access. The downstream measure of ecological integrity was based on the choice of three taxonomic groups of macro-invertebrates and four ecological guilds (groups) of fish. Mayflies (Ephemeroptera), stoneflies (Plecoptera) and caddisflies (Trichoptera) richness were predicted using simple hydrological and morphological covariates (i.e. substrate, current speed,...) coupled to system specific faunistic surveys. Bank, riffle, pool and midstream fish guilds habitat values were determined using existing methods. By using the simulation results of river development project scenarios as inputs, the ecological response (i.e. the measure of ecological integrity) was computed following the assumptions that high predicted macro-invertebrate richness and high guilds habitat values were linked to a high ecological integrity. An emphasis on the hydropeaking effect in relation with river morphology was performed on macro-invertebrates. They were found to respond well to hydrological and morphological changes induced by river development projects while the approach by fish habitat value encountered limitations in its applicability. Four multi-objective project scenarios were analyzed, (1) the actual state of the Swiss Upper Rhone River at the Riddes site (VS), (2) a hypothetical hydropeaking mitigation project, (3) a hypothetical bed widening project and (4) a hypothetical bed widening coupled to hydropeakaing mitigation project. The actual state resulted in the worst measure of ecological integrity, with comparable results for hydropeaking mitigation project or the bed widening project. The highest measure of ecological integrity was observed for the coupling of hydropeaking mitigation and bed widening. These results showed that a multi-purpose project can increase the ecological integrity of the Swiss Upper Rhone River, produce electricity, provide protection from floods and develop local leisure activities. The synergetic effect of the project could be measured by project acceptance. Nevertheless, our knowledge on the hydropeaking effect on hydrosystem should still be completed by more research in order to give more weight to the ecological implication of hydropeaking.

EPFL2007

Vegetation-environment relationships in alpine mires of the West Carpathians and the Alps

Lucia Sekulova

QuestionsHow do two distant mountain ranges differ in their vegetation-environment relationships, overall species composition and its variability and species richness of vascular plants and bryophytes in alpine fens and bogs? Is the floristic difference consistent along the acidity-alkalinity gradient? LocationWest Carpathians (Poland, Slovakia) and Swiss Alps. MethodsVascular plant and bryophyte species compositions and environmental characteristics were sampled along the large acidity-alkalinity gradient within the alpine belts. PERMANOVA was used for testing floristic differences between the regions, DCA for the patterns description, CCA for testing the vegetation-environment relationships and linear models for testing the local species richness determinants. Compositional -diversity (rate of compositional turnover) and regional species pool were compared using PERMDISP and sample-based rarefaction curves. ResultsMost floristic variation was explained by water pH in both regions. Macroclimate was the second most important gradient in the Alps, correlating with the second DCA axis delimiting the moderately poor brown-moss fens from the Sphagnum bogs. The species composition differed significantly between the regions in all three pH classes, expect for bryophytes in the middle pH class. Bryophytes exhibited higher similarities between the regions, except in acidic mires. Vascular plant composition differed most in the middle pH class. The local species richness was predominantly determined by pH, except for bryophytes in the Alps. As compared to bryophytes, vascular plant local species richness was affected by more factors and showed a clear linear response to pH. Within the particular pH classes, there were few differences in local species richness, compositional -diversity and regional species pool between the two mountain ranges. ConclusionsThe pattern in inter-regional floristic dissimilarities differs between bryophytes and vascular plants, probably because of better dispersal ability of bryophytes, and different causes of these dissimilarities: lower mass effect at extreme ends of the acidity-alkalinity gradient in the case of vascular plants and higher compositional -diversity of acidic mires in the case of bryophytes. Contrary to previously explored alpine springs of the same regions, local species richness and composition were determined rather by pH than mineral richness, and all patterns were more consistent between the regions and the taxonomic groups.

Wiley-Blackwell2013

Functional data analysis by matrix completion

Marie-Hélène Descary

Traditional approaches to analysing functional data typically follow a two-step procedure, consisting in first smoothing and then carrying out a functional principal component analysis. The idea underlying this procedure is that functional data are well approximated by smooth functions, and that rough variations are due to noise. However, it may very well happen that localised features are rough at a global scale but still smooth at some finer scale. In this thesis we put forward a new statistical approach for functional data arising as the sum of two uncorrelated components: one smooth plus one rough. We give non-parametric conditions under which the covariance operators of the smooth and of the rough components are jointly identifiable on the basis of discretely observed data: the covariance operator corresponding to the smooth component must be of finite rank and have real analytic eigenfunctions, while the one corresponding to the rough component must have a banded covariance function. We construct consistent estimators of both covariance operators without assuming knowledge of the true rank or bandwidth. We then use them to estimate the best linear predictors of the the smooth and the rough components of each functional datum. In both the identifiability and the inference part, we do not follow the usual strategy used in functional data analysis which is to first employ smoothing and work with continuous estimate of the covariance operator. Instead, we work directly with the covariance matrix of the discretely observed data, which allows us to use results and tools from linear algebra. In fact, we show that the whole problem of uniquely recovering the covariance operator of the smooth component given the one of the raw data can be seen as a low-rank matrix completion problem, and we make great use of a classical relation between the rank and the minors of a matrix to solve this matrix completion problem. The finite-sample performance of our approach is studied by means of simulation study.

EPFL2017