Co-inertia analysis: an alternative method for studying species–environment relationships

• 1 Methods used for the study of species–environment relationships can be grouped into: (i) simple indirect and direct gradient analysis and multivariate direct gradient analysis (e.g. canonical correspondence analysis), all of which search for non-symmetric patterns between environmental data sets and species data sets; and (ii) analysis of juxtaposed tables, canonical correlation analysis, and intertable ordination, which examine species–environment relationships by considering each data set equally. Different analytical techniques are appropriate for fulfilling different objectives.
• 2 We propose a method, co-inertia analysis, that can synthesize various approaches encountered in the ecological literature. Co-inertia analysis is based on the mathematically coherent Euclidean model and can be universally reproduced (i.e. independently of software) because of its numerical stability. The method performs simultaneous analysis of two tables. The optimizing criterion in co-inertia analysis is that the resulting sample scores (environmental scores and faunistic scores) are the most covariant. Such analysis is particularly suitable for the simultaneous detection of faunistic and environmental features in studies of ecosystem structure.
• 3 The method was demonstrated using faunistic and environmental data from Friday (Freshwater Biology 18, 87-104, 1987). In this example, non-symmetric analyses is inappropriate because of the large number of variables (species and environmental variables) compared with the small number of samples.
• 4 Co-inertia analysis is an extension of the analysis of cross tables previously attempted by others. It serves as a general method to relate any kinds of data set, using any kinds of standard analysis (e.g. principal components analysis, correspondence analysis, multiple correspondence analysis) or between-class and within-class analyses.

     

The use of artificial neural networks to predict the presence of small-bodied fish in a river

1. Discriminant factorial analysis (DFA) and artificial neural networks (ANN) were used to develop models of presence/absence for three species of small-bodied fish (minnow, Phoxinus phoxinus , gudgeon, Gobio gobio , and stone loach, Barbatula barbatula ).
2. Fish and ten environmental variables were sampled using point abundance sampling by electrofishing in the Ariège River (France) at 464 sampling points.
3. Using DFA, the percentage of correct assignments, expressed as the percentage of individuals correctly classified over the total number of examined individuals, was 62.5% for stone loach, 66.6% for gudgeon and 78% for minnow. With back-propagation of ANN, the recognition performance obtained after 500 iterations was: 82.1% for stone loach, 87.7% for gudgeon and 90.1% for minnow.
4. The better predictive performance of the artificial neural networks holds promise for other situations with non-linearly related variables.     

Modelling the hydraulic preferences of benthic macroinvertebrates in small European streams

1. Relating processes occurring at a local scale to the natural variability of ecosystems at a larger scale requires the design of predictive models both to orientate stream management and to predict the effects of larger scale disturbances such as climate changes. Our study contributes to this effort by providing detailed models of the hydraulic preferences of 151 invertebrate taxa, mostly identified at the species level. We used an extensive data set comprising 580 invertebrate samples collected using a Surber net from nine sites of second and third order streams during one, two or three surveys at each site. We used nested non‐linear mixed models to relate taxon local densities to bed shear stresses estimated from FliesswasserStammTisch hemisphere numbers. 2. An average model by taxon, i.e. independent from surveys, globally explained 25% of the density variations of taxa within surveys. A quadratic relationship existed between the average preferences and the niche breadth of taxa, indicating that taxa preferring extreme hemisphere numbers had a reduced hydraulic niche breadth. A more complete model, where taxa preferences vary across surveys, globally explained 38% of the variation of taxa densities within surveys. Variations in preferences across surveys were weak for taxa preferring extreme hemisphere numbers. 3. There was a significant taxonomic effect on preferences computed from the complete model. By contrast, season, site, average hemisphere number within a survey and average density of taxa within a survey used as covariates did not consistently explain shifts in taxon hydraulic preferences across surveys. 4. The average hydraulic preferences of taxa obtained from the extensive data set were well correlated to those obtained from two additional independent data sets collected in other regions. The consistency of taxon preferences across regions supports the use of regional preference curves for estimating the impact of river management on invertebrate communities. By contrast, the hydraulic niche breadths of taxa computed from the different data sets were not related.     

Invertebrate hydraulic preferences and predicted impacts of changes in discharge in a large river

• 1 Instream habitat models are attractive tools for assessing the impacts of flow restoration on aquatic organisms, but have been rarely used for invertebrates due to the lack of knowledge of their hydraulic preferences.
• 2 In this study, we provide quantitative models of the hydraulic preferences for 66 invertebrate taxa found in the Upper Rhône River (France), and combine these preferences with a statistical habitat model (FSTress) to predict the effects of minimum flow restoration on invertebrate abundances in two bypassed sections of the river.
• 3 Many taxa show marked preferences for particular hydraulic conditions. Average preferred hydraulic conditions were significantly related to those observed in smaller streams (R² = 0.37).
• 4 Our model predicted that habitat values of 27 taxa should be enhanced by restoration operations, but also predicted a decrease of habitat values in the main channel for 12 limnophilic taxa. However, these taxa are expected to maintain populations by finding refuges in restored cut‐off channels and overall invertebrate diversity is predicted to increase in the two bypassed sections studied here.

     

Multiple refugia and barriers explain the phylogeography of the Valais shrew,Sorex antinorii (Mammalia: Soricomorpha)

The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the analysis. The phylogeographical pattern was assessed by Bayesian molecular phylogenetic reconstruction, population genetic analyses, and a species distribution modelling (SDM)‐based hindcasting approach. We also used landscape genetics (including isolation‐by‐resistance) to infer the determinants of current intra‐specific genetic structure. The phylogeographical analysis revealed shallow divergence among haplotypes and no clear substructure within S. antinorii. The starlike structure of the median‐joining network is consistent with population expansion from a single refugium, probably located in the Apennines. Long branches observed on the same network also suggest that another refugium may have existed in the north‐eastern part of Italy. This result is consistent with SDM, which also suggests several habitable areas for S. antinorii in the Italian peninsula during the LGM. Therefore S. antinorii appears to have occupied disconnected glacial refugia in the Italian peninsula, supporting previous data for other species showing multiple refugia within southern refugial areas. By coupling genetic analyses and SDM, we were able to infer how past climatic suitability contributed to genetic divergence of populations. The genetic differentiation shown in the present study does not support the specific status of S. arunchi. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 864–880.     

Invertebrate community responses to land use at a broad spatial scale: trait and taxonomic measures compared in New Zealand rivers

1. Large‐scale comparative studies of ecological responses to anthropological stressors in rivers require measures that are consistent across a range of spatial scales. The biological trait profile of communities offers an alternative approach to traditional measures of macroinvertebrate taxonomic identity and is less constrained by biogeographic influences. 2. We compared the capacities of taxonomic composition and biological trait composition to discriminate the effects of land use (measured as percentage of the catchment in pasture) across a large geographic zone (the whole of New Zealand) in 30 sub‐catchments grouped into five ecoregions throughout the North and South Islands of New Zealand. In addition, we investigated trait consistency (i.e. whether similar traits had similar trait responses to land use at local (catchment) and broad scales). 3. The analysis of taxonomic composition showed that community structure was indeed influenced by land‐use intensity, but that relationships differed among ecoregions. In contrast, traditional assessment metrics (Macroinvertebrate Community Index, richness in Ephemeroptera, Plecoptera and Trichoptera taxa) and trait composition were uninfluenced by region. Trait responses were consistent at the broad and catchment scales, with similar traits responding to pastoral land use at both scales. 4. We used general linear modelling to investigate individual trait responses to land‐use intensity, catchment area and region, focussing on 15 trait categories known to be influenced by land‐use intensity at the catchment scale. Several trait categories varied with land‐use intensity and demonstrated consistency at both catchment and broad scales. Of these, the representation of shorter generation time, asexual reproduction and hermaphroditism, ability to lay eggs beneath the water surface, egg protection and respiration types tolerant of oxygen depletion generally increased in assemblages exposed to more intense pastoral land use. At the same time, the representation of short life duration of adults, prevalence of laying eggs at the water surface, sexual reproduction and low body flexibility decreased in assemblages exposed to land‐use intensification. 5. Our results highlight the value of developing predictive response measures that are relevant at multiple scales and provide the basis for new measures of river condition that are as effective as taxonomic identity in terms of response reliability.     

Metabolic origin of δ15N values in nitrogenous compounds from Brassica napus L. leaves

Nitrogen isotope composition (δ¹⁵N) in plant organic matter is currently used as a natural tracer of nitrogen acquisition efficiency. However, the δ¹⁵N value of whole leaf material does not properly reflect the way in which N is assimilated because isotope fractionations along metabolic reactions may cause substantial differences among leaf compounds. In other words, any change in metabolic composition or allocation pattern may cause undesirable variability in leaf δ¹⁵N. Here, we investigated the δ¹⁵N in different leaf fractions and individual metabolites from rapeseed (Brassica napus) leaves. We show that there were substantial differences in δ¹⁵N between nitrogenous compounds (up to 30‰) and the content in (¹⁵N enriched) nitrate had a clear influence on leaf δ¹⁵N. Using a simple steady‐state model of day metabolism, we suggest that the δ¹⁵N value in major amino acids was mostly explained by isotope fractionation associated with isotope effects on enzyme‐catalysed reactions in primary nitrogen metabolism. δ¹⁵N values were further influenced by light versus dark conditions and the probable occurrence of alternative biosynthetic pathways. We conclude that both biochemical pathways (that fractionate between isotopes) and nitrogen sources (used for amino acid production) should be considered when interpreting the δ¹⁵N value of leaf nitrogenous compounds.