Low Genotyping Error Rates and Noninvasive Sampling in Bighorn Sheep

Abstract Noninvasive DNA sampling allows studies of natural populations without disturbing the target animals. Unfortunately, high genotyping error rates often make noninvasive studies difficult. We report low error rates (0.0–7.5%/locus) when genotyping 18 microsatellite loci in only 4 multiplex polymerase chain reaction amplifications using fecal DNA from bighorn sheep (Ovis canadensis). The average locus-specific error rates varied significantly between the 2 populations (0.13% vs. 1.6%; P < 0.001), as did multi-locus genotype error rates (2.3% vs. 14.1%; P < 0.007). This illustrates the importance of quantifying error rates in each study population (and for each season and sample preservation method) before initiating a noninvasive study. Our error rates are among the lowest reported for fecal samples collected noninvasively in the field. This and other recent studies suggest that noninvasive fecal samples can be used in species with pellet-form feces for nearly any study (e.g., of population structure, gene flow, dispersal, parentage, and even genome-wide studies to detect local adaptation) that previously required high-quality blood or tissue samples.     

Intra-ovarian trichomes in Jackiopsis ornata (Wallich) Ridsdale (Rubiaceae-Jackieae)

The ovary and young fruit of Jackiopsis ornata has internal, unbranched, septate hairs which are more or less evenly dispersed over the entire interior surface of the locules and present in quite large numbers. This is the first record of intra-ovarian trichomes in the Rubiaceae. The trichomes do not seem to have an obvious function in that they do not appear to serve as a specialized pollen transmitting tissue or play a role in directing pollen tube growth.     

An optimized protocol for the identification of diatoms,flagellated algae and pathogenic protozoa with phylochips

In the past decade, molecular probe‐based methods have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that are devoid of distinct morphological features. However until recently, these methods had the major drawback of being limited to the identification of only one or just a few species at a time. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single‐glass slide, the so‐called phylochip. There are numerous microarray protocols in the literature. These protocols share the same principles, but vary in details, e.g. labelling approach or detergent concentration in the washing buffer. In this study, we show that even small variations in hybridization protocols can have a strong impact on the outcome of the microarray hybridization. An optimized protocol for species identification on phylochips is presented. The optimized protocol is the result of a joined effort of three laboratories to develop phylochips for microbial species identification.     

Thermal adaptation of heterotrophic soil respiration in laboratory microcosms

Respiration of heterotrophic microorganisms decomposing soil organic carbon releases carbon dioxide from soils to the atmosphere. In the short term, soil microbial respiration is strongly dependent on temperature. In the long term, the response of heterotrophic soil respiration to temperature is uncertain. However, following established evolutionary trade‐offs, mass‐specific respiration (R_mass) rates of heterotrophic soil microbes should decrease in response to sustained increases in temperature (and vice‐versa). Using a laboratory microcosm approach, we tested the potential for the R_mass of the microbial biomass in six different soils to adapt to three, experimentally imposed, thermal regimes (constant 10, 20 or 30 °C). To determine R_mass rates of the heterotrophic soil microbial biomass across the temperature range of the imposed thermal regimes, we periodically assayed soil subsamples using similar approaches to those used in plant, animal and microbial thermal adaptation studies. As would be expected given trade‐offs between maximum catalytic rates and the stability of the binding structure of enzymes, after 77 days of incubation R_mass rates across the range of assay temperatures were greatest for the 10 °C experimentally incubated soils and lowest for the 30 °C soils, with the 20 °C incubated soils intermediate. The relative magnitude of the difference in R_mass rates between the different incubation temperature treatments was unaffected by assay temperature, suggesting that maximum activities and not Q₁₀ were the characteristics involved in thermal adaptation. The time taken for changes in R_mass to manifest (77 days) suggests they likely resulted from population or species shifts during the experimental incubations; we discuss alternate mechanistic explanations for those results we observed. A future research priority is to evaluate the role that thermal adaptation plays in regulating heterotrophic respiration rates from field soils in response to changing temperature, whether seasonally or through climate change.     

Infra‐red thermometry of alpine landscapes challenges climatic warming projections

Rough mountain terrain offers climatic conditions (niches) to plants and animals poorly represented by conventional climate station data. However, the extent to which actual temperatures deviate from those of the freely circulating atmosphere had never been assessed at a landscape level. Here, we quantify thermal life conditions across topographically rich mountain terrain by using a combination of thermal (IR) imagery of surface temperature with data from a large number of miniature data loggers buried at 3 cm soil depth. The data obtained from six alpine (Alps) and arctic‐alpine slopes (Norway, Sweden, Svalbard) evidence persistent root zone temperatures of 2–4 K above air temperature during summer. Surface temperatures show strong positive (2–9 K) and negative (3–8 K) deviations from air temperature on bright days and clear nights, respectively. As to be expected, south oriented slopes are warmer than west and north slopes but microclimatic variation on clear sky days was strong within all slopes, with 8.4±2.5 K (mean±SD) surface temperature differences persisting over several hours per day along horizontal (i.e., equal elevation) transects. Life conditions of alpine organisms are thus strongly decoupled from conditions in the free atmosphere and cannot reliably be inferred from climate station data in both, temperate and arctic latitudes. Microtopography can mimic temperature differences of large elevational (or latitudinal) gradients over very short horizontal distances. This is important in the context of climate change because it shows that species do not necessarily need to climb several hundred meters in elevation to escape the warmth. Quite often, few meters of horizontal shift will do. For plants unable to, or too slow to adapt to a warmer climate, thermal microhabitat mosaics offer both refuge habitats as well as stepping stones as atmospheric temperatures rise.     

Vocal culture in New Caledonian crows Corvus moneduloides

While recent research suggests that some animal species may possess ‘cultural’ traditions, much of the current evidence for wild populations remains contentious. This is largely due to the difficulty of demonstrating a fundamental prerequisite for the existence of culture: social learning. As the only case where social learning has been demonstrated conclusively, and subsequently linked to spatial or temporal trait variation, avian vocal dialects are the best studied, and most widely accepted, form of animal culture. Here, we investigate the potential for vocal culture in one of the few animals for which material culture has been suggested: the New Caledonian crow Corvus moneduloides. We show that this species: (1) possesses the capacity for social learning of vocalizations (experimental evidence in the form of a captive subject that reproduces human speech and other anthropogenic noises); and (2) exhibits significant large‐scale, population‐level variation in its vocalizations (cross‐island playback experiments, with analyses controlling for a substantial set of potentially confounding variables). In combination, this provides strong evidence for the existence of ‘culture’ in these birds. More specifically, our findings reveal that the species exhibits sufficient social learning mechanisms, and within‐population structuring, to generate and perpetuate cultural variation in at least one behavioural domain. This is a critical first step towards demonstrating cultural transmission in other behaviours, including tool manufacture and tool use, opening the door for the simultaneous investigation of vocal and material culture in a nonhuman species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 767–776.     

In defence of model‐based inference in phylogeography

Recent papers have promoted the view that model‐based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model‐based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model‐based inference in population genetics.     

Advanced snowmelt causes shift towards positive neighbour interactions in a subarctic tundra community

Positive and negative species interactions are important factors in structuring vegetation communities. Studies in many ecosystems have focussed on competition; however, facilitation has often been found to outweigh competition under harsh environmental conditions. The balance between positive and negative species interactions is known to shift along spatial, temporal and environmental gradients and thus is likely to be affected by climate change. Winter temperature and precipitation patterns in Interior Alaska are rapidly changing and could lead to warmer winters with a shallow, early melting snow cover in the near future. We conducted snow manipulation and neighbour removal experiments to test whether the relative importance of positive and negative species interactions differs between three winter climate scenarios in a subarctic tundra community. In plots with ambient, manually advanced or delayed snowmelt, we assessed the relative importance of neighbours for survival, phenology, growth and reproduction of two dwarf shrub species. Under ambient conditions and after delayed snowmelt, positive and negative neighbour effects were generally balanced, but when snowmelt was advanced we found overall facilitative neighbour effects on survival, phenology, growth and reproduction of Empetrum nigrum, the earlier developing of the two target species. As earlier snowmelt was correlated with colder spring temperatures and a higher number of frosts, we conclude that plants experienced harsher environmental conditions after early snowmelt and that neighbours could have played an important role in ameliorating the physical environment at the beginning of the growing season.     

Microsatellite loci for population and behavioural studies of Horsfield's bronze‐cuckoo (Chalcites basalis: Aves)

Eight polymorphic microsatellite loci were identified for Horsfield's bronze‐cuckoo (Chalcites basalis). These include seven newly isolated loci from cuckoo genomic libraries enriched for GA and GAAA repeat‐containing clones. These loci have a mean expected heterozygosity of 0.71, a mean number of alleles of 13.8 and a combined exclusion probability (one parent known) of 0.9999. Two loci (Cba01 and Cba07) showed a significant deficiency of heterozygotes and may therefore have null alleles, although this effect could be the result of nonrandom population sampling.