Estimating population structure from AFLP amplification intensity

In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific F_IS and F_ST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species.     

Enemy release or invasional meltdown? Deer preference for exotic and native trees on Isla Victoria,Argentina

Abstract How interactions between exotic species affect invasion impact is a fundamental issue on both theoretical and applied grounds. Exotics can facilitate establishment and invasion of other exotics (invasional meltdown) or they can restrict them by re‐establishing natural population control (as predicted by the enemy‐release hypothesis). We studied forest invasion on an Argentinean island where 43 species of Pinaceae, including 60% of the world's recorded invasive Pinaceae, were introduced c. 1920 but where few species are colonizing pristine areas. In this area two species of Palearctic deer, natural enemies of most Pinaceae, were introduced 80 years ago. Expecting deer to help to control the exotics, we conducted a cafeteria experiment to assess deer preferences among the two dominant native species (a conifer, Austrocedrus chilensis, and a broadleaf, Nothofagus dombeyi) and two widely introduced exotic tree species (Pseudotsuga menziesii and Pinus ponderosa). Deer browsed much more intensively on native species than on exotic conifers, in terms of number of individuals attacked and degree of browsing. Deer preference for natives could potentially facilitate invasion by exotic pines. However, we hypothesize that the low rates of invasion currently observed can result at least partly from high densities of exotic deer, which, despite their preference for natives, can prevent establishment of both native and exotic trees. Other factors, not mutually exclusive, could produce the observed pattern. Our results underscore the difficulty of predicting how one introduced species will effect impact of another one.     

The relationship between introduced European Starlings and the reproductive activities of Mountain Bluebirds and Tree Swallows in British Columbia,Canada

The European Starling Sturnus vulgaris is an introduced species in North America and is an aggressive competitor for tree cavity nest‐sites. Starlings are commonly considered to influence nest‐site selection and reproductive success of native cavity‐nesting species negatively. We examined the relationship between Starling nest density and the fecundity of two native secondary cavity‐using passerines, Mountain Bluebird Sialia currucoides and Tree Swallow Tachycineta bicolor. We monitored a total of 622 nests (approximately equal numbers for each of the three species) in woodpecker‐excavated and naturally occurring cavities in 29 small forest groves in central British Columbia, Canada, between 2000 and 2009. The dimensions of cavities used and the timing of nest initiation overlapped for all species, although Starlings initiated clutches earliest. Mixed‐effects models were used to assess whether nest abundance, clutch size or nest success were affected directly by Starling nest abundance, or indirectly via a shift in cavity selection or timing of breeding. Starlings and Mountain Bluebirds showed inverse trends in nest abundance. Mountain Bluebird clutch sizes were smaller if they were initiated later in the breeding season. There was weak evidence that Tree Swallow clutch size decreased with cavity depth when Starling nests were abundant, and increased with cavity depth where there were few Starling nests. We conclude that despite the aggressive nature of this exotic cavity‐nester, the influence of Starlings on native secondary cavity‐nesting passerines is modest where cavities are abundant.     

Polymorphic microsatellite loci for the trematode Diplostomum pseudospathaceum

We present primers for five polymorphic microsatellite loci in the eye fluke Diplostomum pseudospathaceum (Trematoda), a widely distributed parasite with a complex life cycle used as a model for parasitology and fish immunology. The loci were identified using a GA/CT‐enriched genomic library by subtractive hybridization with magnetic particles. All five loci were highly polymorphic, displaying 17 to 61 alleles and heterozygosities ranging from 0.53 to 0.92. We isolated populations of parasites within the first (snail) and second (fish) intermediate host and found small but significant genetic differentiation (F_ST = 0.012) between the two life stages of the parasite.     

Development of a new piosphere in arid chenopod shrubland grazed by sheep. 2. Changes to the vegetation

The initial development of a piosphere created by stocking a new watering trough with ca. 200 sheep at a near-pristine site in arid chenopod shrubland near Whyalla, South Australia, was studied. The following variables were monitored for up to 8 years using fenced plots as controls:shrub mortality; forage biomass and defoliation of the dominant shrubs and short-lived grasses; linear dimensions of Rhagodia ulicina; the density of short-lived species; and the invasion of exotics. Patterns in these variables were looked for which reflected the attenuation of stocking pressure with distance from water; that is, ‘piosphere patterns’. Piosphere patterns were detected for many variables. Those with values increasing towards the trough were mortality of the main forage shrub Atriplex vesicaria. the density of three short-lived taxa, viz. the bassias (Sclerolaena obliquicuspis, S. patenticuspis. Maireana sclerolaenoides), Tetragonia tetragonoides, and annual Zygophyllum spp. (Z. crenatum. Z. ovatum), and growth of short-lived grass species when sheep stocking pressure was low. Variables with values decreasing towards the trough were grass biomass, percentage of A. vesicaria individuals in flower, the percentage foliation of A. vesicaria and of the forage shrub Maireana sedifolia, and shrub forage biomass of A. vesicaria and M. sedifolia. The rate at which these patterns were registered varied. After only 3 months, a piosphere pattern was evident for grass biomass. Marrubium vulgare, an introduced weed, invaded the trough site within the first 6 months. Almost no A. vesicaria shrubs had died after 2 years, but after 8 years there was a marked piosphere pattern in their mortality. The piosphere patterns in forage biomass and defoliation of A. vesicaria and M. sedifolia became more pronounced with time. Some variables did not exhibit a piosphere pattern, such as the dimensions of the shrub R. ulicina and the densities of successive cohorts of the forb Erodium spp., even though there was an overall effect of grazing in reducing their values. There was no mortality of two dominant shrubs, M. sedifolia and R. ulicina, during the first 8 years.     

The Bonobo–Dialium Positive Interactions: Seed Dispersal Mutualism

A positive interaction is any interaction between individuals of the same or different species (mutualism) that provides a benefit to both partners such as increased fitness. Here we focus on seed dispersal mutualism between an animal (bonobo, Pan paniscus) and a plant (velvet tamarind trees, Dialium spp.). In the LuiKotale rainforest southwest of Salonga National Park, Democratic Republic of Congo, seven species of the genus Dialium account for 29.3% of all trees. Dialium is thus the dominant genus in this forest. Dialium fruits make up a large proportion of the diet of a habituated bonobo community in this forest. During the 6 months of the fruiting season, more than half of the bonobos’ feeding time is devoted to Dialium fruits. Furthermore, Dialium fruits contribute a considerable proportion of sugar and protein to bonobos’ dietary intake, being among the richest fruits for these nutrients. Bonobos in turn ingest fruits with seeds that are disseminated in their feces (endozoochory) at considerable distances (average: 1.25 km after 24 hr of average transit time). Endozoochory through the gut causes loss of the cuticle protection and tegumentary dormancy, as well as an increase in size by water uptake. Thus, after gut passage, seeds are better able to germinate. We consider other primate species as a potential seed disperser and conclude that Dialium germination is dependent on passage through bonobo guts. This plant–animal interaction highlights positive effects between two major organisms of the Congo basin rainforest, and establishes the role of the bonobo as an efficient disperser of Dialium seeds. Am. J. Primatol. 75:394‐403, 2013. © 2013 Wiley Periodicals, Inc.     

Genetic homogeneity among breeding grounds and nursery areas of an exploited Lake Malawi cichlid fish

1. Nursery areas are commonly recognized as important habitats for the management and conservation of fish stocks. Here we report the use of nursery areas by an exploited offshore cichlid in Lake Malawi, Rhamphochromis longiceps .
2. Like all haplochromine cichlids that have been studied, the species is a maternal mouthbrooder that broods eggs for several weeks following spawning. We found evidence that during this brooding period females migrate from open water to release juveniles in three shallow peripheral waterbodies (Chia Lagoon, Unaka Lagoon, Lake Malombe). However, it was unclear whether there is geographical population structuring within the species, which could indicate stock differences in their use of these nursery habitats, or if the lake contains a genetically panmictic population that employs nursery habitats opportunistically.
3. To investigate spatial and temporal population structuring within the lake we genotyped populations at seven microsatellite DNA loci. Overall, we found no significant spatial structuring among juveniles from the peripheral lagoons or among breeding males within the main lake body. Moreover, we found no evidence of temporal structuring among males on the breeding grounds within Lake Malawi or females entering Chia lagoon. Together, these results suggest that Lake Malawi contains a genetically homogeneous population of R. longiceps .
4. At present we know little of the distribution of juvenile R. longiceps elsewhere in the Lake Malawi basin, but their absence from surveyed rocky and sandy littoral habitats makes it possible that the species is dependent upon a small number of nearshore nursery areas, including these lagoons. As such, conservation of lagoon habitats and monitoring of exploited fish stocks within them may be important for effective preservation of biodiversity within the catchment.     

No overall stimulation of soil respiration under mature deciduous forest trees after 7 years of CO2 enrichment

The anthropogenic rise in atmospheric CO₂ is expected to impact carbon (C) fluxes not only at ecosystem level but also at the global scale by altering C cycle processes in soils. At the Swiss Canopy Crane (SCC), we examined how 7 years of free air CO₂ enrichment (FACE) affected soil CO₂ dynamics in a ca. 100‐year‐old mixed deciduous forest. The use of ¹³C‐depleted CO₂ for canopy enrichment allowed us to trace the flow of recently fixed C. In the 7th year of growth at ～550 ppm CO₂, soil respiratory CO₂ consisted of 39% labelled C. During the growing season, soil air CO₂ concentration was significantly enhanced under CO₂‐exposed trees. However, elevated CO₂ failed to stimulate cumulative soil respiration (R_s) over the growing season. We found periodic reductions as well as increases in instantaneous rates of R_s in response to elevated CO₂, depending on soil temperature and soil volumetric water content (VWC; significant three‐way interaction). During wet periods, soil water savings under CO₂‐enriched trees led to excessive VWC (>45%) that suppressed R_s. Elevated CO₂ stimulated R_s only when VWC was ≤40% and concurrent soil temperature was high (>15 °C). Seasonal Q₁₀ estimates of R_s were significantly lower under elevated (Q₁₀=3.30) compared with ambient CO₂ (Q₁₀=3.97). However, this effect disappeared when three consecutive sampling dates of extremely high VWC were disregarded. This suggests that elevated CO₂ affected Q₁₀ mainly indirectly through changes in VWC. Fine root respiration did not differ significantly between treatments but soil microbial biomass (C_mic) increased by 14% under elevated CO₂ (marginally significant). Our findings do not indicate enhanced soil C emissions in such stands under future atmospheric CO₂. It remains to be shown whether C losses via leaching of dissolved organic or inorganic C (DOC, DIC) help to balance the C budget in this forest.     

Involvement of auxin pathways in modulating root architecture during beneficial plant–microorganism interactions

A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover, other signals produced by microorganisms affect auxin pathways in host plants. However, the precise role of auxin and auxin‐signalling pathways in modulating plant–microbe interactions is unknown. Dissecting out the auxin synthesis, transport and signalling pathways resulting in the characteristic molecular, physiological and developmental response in plants will further illuminate upon how these intriguing inter‐species interactions of environmental, ecological and economic significance occur. The present review seeks to survey and summarize the scattered evidence in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants. Finally, through a synthesis of the current body of work, we present outstanding challenges and potential future research directions on studies related to auxin signalling in plant–microbe interactions.