pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Contraception, reproduction and demography of free-ranging Etosha lions (Panthera leo)

The use of long-acting contraceptives as an effective population control mechanism for free-ranging lions was investigated during a three-year study in the Etosha National Park on five lion prides. Lions were immobilized with ketamine hydrochloride and xylazine hydrochloride. Following immobilization, lionesses were weighed, measured and aged, while serum steroid hormone levels were analysed and vaginal smears were obtained. Physical condition and sexual state were assessed. Individuals were used as control animals or given melengestrol acetate (contraceptive) implants, branded and released; the animals were observed for possible changes in behaviour, birth rate and mortality. Ten treated lionesses were recaptured at irregular intervals to reassess weight and steroid hormone levels, while three lionesses had their implants removed to determine if their fertility would return. The contraceptives prevented pregnancy, were reversible when removed and did not alter lion behaviour significantly, except that sexual behaviour was not recorded in treated lionesses.     

FLUXNET and modelling the global carbon cycle

Measurements of the net CO₂ flux between terrestrial ecosystems and the atmosphere using the eddy covariance technique have the potential to underpin our interpretation of regional CO₂ source–sink patterns, CO₂ flux responses to forcings, and predictions of the future terrestrial C balance. Information contained in FLUXNET eddy covariance data has multiple uses for the development and application of global carbon models, including evaluation/validation, calibration, process parameterization, and data assimilation. This paper reviews examples of these uses, compares global estimates of the dynamics of the global carbon cycle, and suggests ways of improving the utility of such data for global carbon modelling. Net ecosystem exchange of CO₂ (NEE) predicted by different terrestrial biosphere models compares favourably with FLUXNET observations at diurnal and seasonal timescales. However, complete model validation, particularly over the full annual cycle, requires information on the balance between assimilation and decomposition processes, information not readily available for most FLUXNET sites. Site history, when known, can greatly help constrain the model‐data comparison. Flux measurements made over four vegetation types were used to calibrate the land‐surface scheme of the Goddard Institute for Space Studies global climate model, significantly improving simulated climate and demonstrating the utility of diurnal FLUXNET data for climate modelling. Land‐surface temperatures in many regions cool due to higher canopy conductances and latent heat fluxes, and the spatial distribution of CO₂ uptake provides a significant additional constraint on the realism of simulated surface fluxes. FLUXNET data are used to calibrate a global production efficiency model (PEM). This model is forced by satellite‐measured absorbed radiation and suggests that global net primary production (NPP) increased 6.2% over 1982–1999. Good agreement is found between global trends in NPP estimated by the PEM and a dynamic global vegetation model (DGVM), and between the DGVM and estimates of global NEE derived from a global inversion of atmospheric CO₂ measurements. Combining the PEM, DGVM, and inversion results suggests that CO₂ fertilization is playing a major role in current increases in NPP, with lesser impacts from increasing N deposition and growing season length. Both the PEM and the inversion identify the Amazon basin as a key region for the current net terrestrial CO₂ uptake (i.e. 33% of global NEE), as well as its interannual variability. The inversion's global NEE estimate of −1.2 Pg [C] yr⁻¹ for 1982–1995 is compatible with the PEM‐ and DGVM‐predicted trends in NPP. There is, thus, a convergence in understanding derived from process‐based models, remote‐sensing‐based observations, and inversion of atmospheric data. Future advances in field measurement techniques, including eddy covariance (particularly concerning the problem of night‐time fluxes in dense canopies and of advection or flow distortion over complex terrain), will result in improved constraints on land‐atmosphere CO₂ fluxes and the rigorous attribution of mechanisms to the current terrestrial net CO₂ uptake and its spatial and temporal heterogeneity. Global ecosystem models play a fundamental role in linking information derived from FLUXNET measurements to atmospheric CO₂ variability. A number of recommendations concerning FLUXNET data are made, including a request for more comprehensive site data (particularly historical information), more measurements in undisturbed ecosystems, and the systematic provision of error estimates. The greatest value of current FLUXNET data for global carbon cycle modelling is in evaluating process representations, rather than in providing an unbiased estimate of net CO₂ exchange.     

Detection and validation of EST‐derived SNPs for poplar leaf rust Melampsora medusae f. sp. deltoidae

We report the discovery, characterization and validation of 118 single nucleotide polymorphisms (SNPs) for poplar leaf rust Melampsora medusae f. sp. deltoidae identified using a gene‐targeted approach in an expressed sequence tag (EST) library. We developed a genotyping assay using the iPLEX? primer extension method for two multiplex assays of 28 and 22 SNPs.     

Socio-genetic structure of mound-building mice, Mus spicilegus, in autumn and early spring

Mus spicilegus has become a popular biological model species in the last decade because of the evolutionary interest of its behavioural particularities (the building of mounds, bi-parental care and monogamous mating system). The genetic structure of M. spicilegus populations should reflect those life-history traits. Although many studies have reported on mound-building mouse populations in the field or in a semi-natural enclosure, only one used hyper variable genetic markers to assess parentage and social structure. In the present study conducted in Hungary, we analysed individuals from seven highly populous mounds in autumn with the set of loci used in a previous study. Our results confirmed that mounds are inhabited by juveniles from several parental units, but revealed population differences. In a capture–recapture field session in spring, we assessed genetic relationships between individuals after dispersal from the mounds, the other key moment of the life cycle of this species. The results indicate that the social structure at this moment reflects a transition phase between the large over-wintering groups and the monogamous pairs described later in the year. Social bounds forged during the long winter cohabitation may have lasting effects on social and genetic structure of this species. This scenario is discussed in respect of the available literature on this species as well as other species.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 689–699.     

Organization,development, and effects of infraorbital nerve transection on galanin binding sites in the trigeminal brainstem complex

Previous experiments from this laboratory have indicated that transection of the infraorbital nerve (ION, the trigeminal \[V] branch that supplies the mystacial vibrissae follicles) at birth and in adulthood has markedly different effects on galanin immunoreactivity in the V brainstem complex. Adult nerve transection increases galanin immunoreactivity in the superficial layers of V subnucleus caudalis (SpC) only, while neonatal nerve transection results in increased galanin expression in vibrissae-related primary afferents throughout the V brainstem complex. The present study describes the distribution of binding sites for this peptide in the mature and developing V ganglion and brainstem complex and determines the effects of neonatal and adult ION damage and the associated changes in galanin levels upon their distribution and density. Galanin binding sites are densely distributed in all V brainstem subnuclei and are particularly dense in V subnucleus interpolaris and the superficial layers of SpC. They are present at birth (P-0) and their distribution is similar to that in adult animals. Transection of the ION in adulthood and examination of brainstem 7 days later indicated marked reductions in the density of galanin binding sites in the V brainstem complex. With the exception of the superficial laminae of SpC, the same reduction in density remained apparent in rats that survived 45 days after nerve cuts. Transection of the ION on P-0 resulted in no change in the density of galanin binding sites in the brainstem after either 7 or 60 days survival. These results indicate that densely distributed galanin binding sites are present in the V brainstem complex of both neonatal and adult rats, that they are located in regions not innervated by galanin-positive axons, and that their density is not significantly influenced by large lesion-induced changes in the primary afferent content of their natural ligand.     

Fish community changes after minimum flow increase: testing quantitative predictions in the Rhône River at Pierre-Bénite, France

1. Many aspects of the flow regime influence the structure of stream communities, among which the minimum discharge left in rivers has received particular attention. However, instream habitat models predicting the ecological impacts of discharge management often lack biological validation and spatial generality, particularly for large rivers with many fish species. 2. The minimum flow at Pierre‐Bénite, a reach of the Rhône river bypassed by artificial channels, was increased from 10 to 100 m³ s^?1 in August 2000 (natural mean discharge 1030 m³ s^?1), resulting in a fivefold increase in average velocity at minimum flow. Fish were electrofished in several habitat units on 12 surveys between 1995 and 2004. 3. Principal components analysis revealed a significant change in the relative abundance of fish species. The relative abundance of species preferring fast‐flowing and/or deep microhabitats increased from two‐ to fourfold after minimum flow increase. A change in community structure confirmed independent quantitative predictions of an instream habitat model. This change was significantly linked to minimum flow increase, but not to any other environmental variables describing high flows or temperature at key periods of fish life cycle. The rapidity of the fish response compared with the lifespan of individual species can be explained by a differential response of specific size classes. 4. The fish community at Pierre‐Bénite is in a transitional stage and only continued monitoring will indicate if the observed shift in community structure is perennial. We expect that our case study will be compared with other predictive tests of the impacts of flow restoration in large rivers, in the Rhône catchment and elsewhere.     

Effects of Drought on Partitioning of Nitrogen in Two Wheat Varieties Differing in Drought-tolerance

A model was constructed to describe the translocation and partitioningof nitrogen on the seventh day after anthesis for well-wateredand droughted plants of two wheat varieties (Triticum aestivumL. cv. Warigal and Condor). The glasshouse-grown plants weredetillered so that a simplified model could be derived for themain stem. A 9-d drought treatment was imposed just after anthesisand this coincided with the period of endosperm cell divisionin the grains. Warigal, which had a higher grain yield thanCondor under drought, absorbed up to 15-times more nitrogenand translocated 1.5-fold more nitrogen to the shoot via thexylem. In both varieties, nitrogen redistributed from vegetativeorgans accounted for more than 60 per cent in control and 70per cent in droughted plants of the nitrogen needed for eargrowth. The net loss of nitrogen increased by 4-3 per cent inthe leaves, but decreased by 60 per cent in the stem under drought.Stem and roots appeared to play an important role in the nitrogeneconomy of droughted plants: less nitrogen was translocateddirectly to the grains from the senescing leaves and 40–60per cent more nitrogen was translocated to the roots. Nearlyall the nitrogen reaching the roots in the phloem was reloadedinto the xylem stream and translocated back to the shoot. Thetransfer of nitrogen through the stem was reduced under droughtand this resulted in a constant C:N ratio of the grains whichmay be important in the regulation of endosperm cell division. Triticum aestivum L., wheat, drought, nitrogen, senescence, translocation     

Modelling intraspecific resting egg shape variation in a freshwater fairy shrimp Tanymastix stagnalis (L., 1758) (Crustacea, Branchiopoda)

The shape of the resting eggs of a large branchiopod crustacean, the Anostraca Tanymastix stagnalis , is represented very accurately by analytical expressions. The occurrence of atypical shape of some T. stagnalis eggs may be viewed as a simple change of the analytical expression describing the usual egg shape. Their unusual shape may be explained by a higher embryo volume within an envelope of a given size. Biological implications are briefly discussed and hypothesized in an evolutionary point of view.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 55–60.     

Role of terpenes from aphid-infested potato on searching and oviposition behavior of Episyrphus balteatus

To cope with pathogen and insect attacks, plants develop different mechanisms of defence, in both direct （physical and chemical） and indirect ways （attractive volatiles to entomophagous beneficials）. Plants are then able to express traits that facilitate ＂top-down＂ control of pests by attracting herbivore predators. Here we investigate the indirect defence mechanism of potato plants by analyzing the volatile patterns of both healthy and aphid- infested plants. Important changes in the emitted terpene pattern by the Myzus persicae infested host plant were observed. Using Solid Phase MicroExtraction （SPME） and GC-MS, the （E）-fl-farnesene （EBF） appeared to be emitted by aphid-infested potato and not by healthy plants. To assess the infochemical role of these volatile releases after aphid damage on the aphidophagous predators Episyrphus balteams, the hoverfly foraging behavior was assessed using the Observer 5.0 software （Noldus, Wageningen, The Netherlands）. Aphidfree potato plants were also used as a control volatile source in the predator behavioral study. While aphid-infested plants induced efficient searching and acceptation behaviors leading to egg-laying, no kairomonal effect of healthy potato plants was observed, leading to longer immobility durations and shorter searching periods in the net cage. High oviposition rate of E. balteatus was observed when aphid-infested potato was used （mean of 48.9 eggs per laying and per female）. On the other hand, no egg was produced by the hoverfly on healthy aphid-free plants. The E. balteatus foraging and reproductive behaviors according to the volatile emission from aphid-infested plants are discussed in relation to the potential use of active infochemical molecules in integrated aphid pest management.