Jean-Michel Olivier

ADE-4: a multivariate analysis and graphical display software

We present ADE-4, a multivariate analysis and graphical display software. Multivariate analysis methods available in ADE-4 include usual one-table methods like principal component analysis and correspondence analysis, spatial data analysis methods (using a total variance decomposition into local and global components, analogous to Moran and Geary indices), discriminant analysis and within/between groups analyses, many linear regression methods including lowess and polynomial regression, multiple and PLS (partial least squares) regression and orthogonal regression (principal component regression), projection methods like principal component analysis on instrumental variables, canonical correspondence analysis and many other variants, coinertia analysis and the RLQ method, and several three-way table (k-table) analysis methods. Graphical display techniques include an automatic collection of elementary graphics corresponding to groups of rows or to columns in the data table, thus providing a very efficient way for automatic k-table graphics and geographical mapping options. A dynamic graphic module allows interactive operations like searching, zooming, selection of points, and display of data values on factor maps. The user interface is simple and homogeneous among all the programs; this contributes to making the use of ADE-4 very easy for non- specialists in statistics, data analysis or computer science.

A Review of Upstream Migration and Movements in Inland Waters by Anguillid Eels: Toward a General Theory

Anguillid eels are well known as catadromous highly migratory species, with marine spawning grounds well separated from inshore and inland growth areas. However, invasion mechanisms of river systems are poorly documented. This theory is based upon the identification of four distinct movement behaviors: „founders“ that colonize rivers until they settle in the first available suitable habitat they encounter; „pioneers“ that migrate upstream to the upper boundaries of the system; „home range dwellers“ that establish in a given area for several months to several years; and „nomads;“ which are erratic eels that perform a general upstream shift as they search for suitable areas to forage or to settle. These behaviors are not mutually exclusive, any eel shifting from one behavior to another, depending upon ontogenetic attributes (age, experience, morphology, physiological stage, etc.), population parameters that determine density-dependent movements; and environmental parameters such as food availability, temperature, flow, and the carrying capacity of the ecosystem.

Chapter 7 – The Rhône River Basin

Publisher Summary The Rhone links several valleys and rivers from the upper Alps with the Mediterranean Sea. The Alps provided a strong economic and cultural unity to the Rhone throughout the last 1,000 years. Today, the Rhone River is a highly regulated river, viewed as a large waterway for commerce. It is a major source of nutrients and particulate matter to the Mediterranean Sea and a major factor in sole fishery yields from the Gulf of Lyons. The public and politicians are increasingly aware of environmental problems and sociologists indicate a new interest toward integrating river environments in everyday life, so called “river re-appropriation by riverine people”. Recent floods also show that the Rhone, although regulated, can still overflow its banks and pose a risk hazard. Energy production, navigation, irrigation, tourism, habitat and biodiversity protection and cultural activities all must be taken into account by river managers and local decision-makers. The complex uses of the river have also caused new initiatives between Switzerland and France. This chapter presents the general physical, chemical, and biological characteristics of the Rhone River. All tributaries on the Swiss side are alpine rivers and have been used for water storage and hydroelectricity. Several tributaries from the French side play an important role in the Rhone discharge and are included in the chapter, the rivers Ain, Saone and Durance in particular. The Isere River also is an important tributary but it was historically affected by regulation, channelization, and industrialization. Lake Leman is an important feature of the river and its effects on the river downstream also are discussed in the chapter.

Field evidence of reproduction impairment through sperm DNA damage in the fish nase (Chondrostoma nasus) in anthropized hydrosystems

This work aims to explore in the field the relationship between the integrity of sperm DNA and the quality of offspring as a possible cause of the decline of a feral fish population through reproduction impairment. Mature nase (Chondrostoma nasus) were caught during the breeding season in three locations (A-C) of the Rhône River basin and gametes collected by stripping. Sampling locations were chosen according to the following gradient of contamination due to human activities on the watershed: A≤B<C. Samples of a pool of collected oocytes were fertilized with the sperm of individual males and then incubated individually back in the lab to study embryo-larval development as well as using sperm samples to assess DNA integrity. Genetic analysis clearly showed the absence of a difference in genetic structure between the three studied C. nasus populations from the Rhône basin. Sperm DNA integrity was significantly lower in males from station C compared to other ones while sperm biochemical characteristics and fertilization rate remained almost unchanged whatever the station. Mortality and abnormality rates measured at both hatching and at the end of yolk sac resorption stages followed the same trend as the sperm DNA damage, demonstrating an impact of river water quality on nase fitness through a loss of sperm DNA integrity. Since the level of both abnormalities and mortality measured in offspring of fish caught in the most contaminated area reached high values up to 15% and 80%, respectively, the hypothesis that the observed nase decline in Rhône River stemming through selection forces can be put forward.

Elver invasion, population structure and growth of marbled eels Anguilla marmorata in a tropical river on Réunion Island in the Indian Ocean

Invasion mechanisms of Anguillid eels in tropical freshwater systems have seldom been described but are supposed to be similar to those of temperate eels. We used electrofishing and continuous trapping to define recruitment dynamics in spatial and temporal organization of marbled eels, Anguillamarmorata, in the Mat River, Réunion Island, Indian Ocean. Upstream migration of A. marmorata elvers lasted all year long, with a marked enhancement from January to April. We observed six successive length-classes during the 8 months period from December 2000 to July 2001, corresponding to the successive estuarine recruitments of elvers, of which three happened during the study. Mean growth estimation (15.3±3.5 mm month−1), calculated by linking modal-classes in length–frequency polynomial compositions of electrofishing data was corroborated by otolithometry performed on eels collected in the trap (17.4 ± 3.4 mm month−1). Migrant elvers (mean length 117.3 ± 24.6 mm) invaded the middle stream course 2, 3 or 4 months after they entered the river system. This is a marked difference from temperate Anguilla species that grow more slowly and usually reside 1 year downstream before they migrate or settle. Moreover, upstream invasion patterns of A. marmorata elvers in this tropical river appear to be synchronized with regular cyclonic floods occurring in the Indian Ocean.

Non-homogeneous combination of two porous genomes induces complex body shape trajectories in cyprinid hybrids

IntroductionHybridization is a common phenomenon in fish and is considered to be a major source of diversification. Deciphering the remoulding of genomic regions and phenotypes in zones where hybrid specimens occur is of particular interest to elucidate the emergence of evolutionary novelties. This approach is particularly challenging because the first step of hybridization seems to be the most important stage in the emergence of hybrid lineages. However, the signal can be significantly altered after only a few generations.ResultsWe studied 41 microsatellites and partial cytochrome b gene sequences in 970 specimens belonging to two fish species (Chondrostoma nasus and Parachondrostoma toxostoma) in allopatric/parapatric zones, hybrids between them in a natural sympatric zone: the Ardèche basin. We showed that the genomic architecture in hybrids presented pattern heterogeneity of selection for the different loci. Indeed, the upstream part of the river (Rosières and Labeaume) presented an overdominant fitness of heterozygotes (12.20%) corresponding to a genomic compatibility, and underselection was observed for 4.88%-7.32% of the loci tested indicating a genomic incompatibility. Moreover the upstream station (Rosières) presented a positive selection of invasive C. nasus homozygotes (17.07% to 21.95%) indicating that hybridization may increase the fitness of admixed individuals.We showed that hybrid morphology (body shape based on 21 landmarks) correlated with genomic dilution indicating a species fingerprint. However, we demonstrated that the hybrid morphology was not a linear modification between the two parental species but a trade-off between several correlated traits.ConclusionsHybrid specimens present a mosaic of genomic combination, showing regions with genomic compatibility and others with genomic incompatibility between the two species. Positive selection (invasive advantage ranging from 9.76% to 21.95% of the loci) was evidenced in the upstream part of the Ardèche indicating that environmental selection makes a substantial contribution. Although the presence of a dam is known to impose heterogeneous hybrid zones between these two species, we demonstrated in this study that a natural environment can also generate a hybrid zone with a large number (and diversity) of hybrids. The combination of the two genomes in the hybrids results in complex ontogenetic trajectories (with different morphological traits evolving at different rates) that correspond to novel developmental pathways.