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.     

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.     

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     

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.     

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.     

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.     

Flexible social organization and high incidence of drifting in the sweat bee, Halictus scabiosae

The very diverse social systems of sweat bees make them interesting models to study social evolution. Here we focus on the dispersal behaviour and social organization of Halictus scabiosae , a common yet poorly known species of Europe. By combining field observations and genetic data, we show that females have multiple reproductive strategies, which generates a large diversity in the social structure of nests. A detailed microsatellite analysis of 60 nests revealed that 55% of the nests contained the offspring of a single female, whereas the rest had more complex social structures, with three clear cases of multiple females reproducing in the same nest and frequent occurrence of unrelated individuals. Drifting among nests was surprisingly common, as 16% of the 122 nests in the overall sample and 44% of the nests with complex social structure contained females that had genotypes consistent with being full-sisters of females sampled in other nests of the population. Drifters originated from nests with an above-average productivity and were unrelated to their nestmates, suggesting that drifting might be a strategy to avoid competition among related females. The sex-specific comparison of genetic differentiation indicated that dispersal was male-biased, which would reinforce local resource competition among females. The pattern of genetic differentiation among populations was consistent with a dynamic process of patch colonization and extinction, as expected from the unstable, anthropogenic habitat of this species. Overall, our data show that H. scabiosae varies greatly in dispersal behaviour and social organization. The surprisingly high frequency of drifters echoes recent findings in wasps and bees, calling for further investigation of the adaptive basis of drifting in the social insects.     

Dispersal abilities and spatial patterns in fragmented landscapes

Recent theoretical studies suggest that the distribution of species in space has important implications for the conservation of communities in fragmented landscapes. Facilitation and dispersal are the primary mechanisms responsible for the formation of spatial patterns. Furthermore, disruptions in the formation of patterns arise after degradation, which can serve as an early indicator of stress in plant communities. Spatial dispersal ability and pattern formation were evaluated in 53 linear transects of 500 m in length within 14 fragments of natural vegetation within a matrix of abandoned crop fields in Cabo de Gata National Park, Almería, Spain. Fragments were classified into three size classes (< 300, 300–900, and > 900 ha). Fragment connectivity was quantified using the distances between fragments. Spatial dispersal ability was quantified for the 187 species recorded in the study. Species with restricted dispersal had the highest degree of long‐range spatial autocorrelation and, species that disperse by biotic vectors (e.g. vertebrates), the lowest. In addition, species most susceptible to fragmentation are vertebrate‐dispersed shrubs, which declined in abundance and was associated with loss of spatial organization in the smallest fragments. It is postulated that the positive feedback between abundance of recruitment and vertebrate visits influences the colonization and persistence of vertebrate‐dispersed shrubs, explaining its abundance in large fragments. Indeed, fragments lower than a certain threshold reduced spatial organization not only in shrubs with biotic dispersal, but also in species with abiotic dispersal (mainly wind) and with restricted dispersal. Fragments lower than a certain threshold may be vulnerable to a cascade of species loss because of reduced recruitment, establishment and patch biomass as a result of natural senescence, finally breaking up facilitative plant interactions. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 935–947.     

Relationships between phenology,radiation and precipitation in the Amazon region

In tropical areas, Dynamic Global Vegetation Models (DGVMs) still have deficiencies in simulating the timing of vegetation phenology. To start addressing this problem, standard Fourier‐based methods are applied to aerosol screened monthly remotely sensed phenology time series (Enhanced Vegetation Index, EVI) and two major driving factors of phenology: solar radiation and precipitation (for March 2000 through December 2006 over northern South America). At 1 × 1 km scale using, power (or variance) spectra on good quality aerosol screened time series, annual cycles in EVI are detected across 58.24% of the study area, the strongest (largest amplitude) occurring in the savanna. Terra Firme forest have weak but significant annual cycles in comparison with savannas because of the heterogeneity of vegetation and nonsynchronous phenological events within 1 × 1 km scale pixels. Significant annual cycles for radiation and precipitation account for 86% and 90% of the region, respectively, with different spatial patterns to phenology. Cross‐spectral analysis was used to compare separately radiation with phenology/EVI, precipitation with phenology/EVI and radiation with precipitation. Overall the majority of the Terra Firme forest appears to have radiation as the driver of phenology (either radiation is in phase or leading phenology/EVI at the annual scale). These results are in agreement with previous research, although in Acre, central and eastern Peru and northern Bolivia there is a coexistence of ‘in phase’ precipitation over Terra Firme forest. In contrast in most areas of savanna precipitation appears to be a driver and savanna areas experiencing an inverse (antiphase) relationship between radiation and phenology is consistent with inhibited grassland growth due to soil moisture limitation. The resulting maps provide a better spatial understanding of phenology–driver relationships offering a bench mark to parameterize ecological models.