A framework for estimating the sensitivity of eDNA surveys

Imperfect sensitivity, or imperfect detection, is a feature of all survey methods that needs to be accounted for when interpreting survey results. Detection of environmental DNA (eDNA) is increasingly being used to infer species distributions, yet the sensitivity of the technique has not been fully evaluated. Sensitivity, or the probability of detecting target DNA given it is present at a site, will depend on both the survey method and the concentration and dispersion of target DNA molecules at a site. We present a model to estimate target DNA concentration and dispersion at survey sites and to estimate the sensitivity of an eDNA survey method. We fitted this model to data from a species‐specific eDNA survey for Oriental weatherloach, Misgurnus anguillicaudatus, at three sites sampled in both autumn and spring. The concentration of target DNA molecules was similar at all three sites in autumn but much higher at two sites in spring. Our analysis showed the survey method had ≥95% sensitivity at sites where target DNA concentrations were ≥11 molecules per litre. We show how these data can be used to compare sampling schemes that differ in the number of field samples collected per site and number of PCR replicates per sample to achieve ≥95% sensitivity at a given target DNA concentration. These models allow researchers to quantify the sensitivity of eDNA survey methods to optimize the probability of detecting target species, and to compare DNA concentrations spatially and temporarily.     

West Africa - A Safe Haven for Frogs? A Sub-Continental Assessment of the Chytrid Fungus (Batrachochytrium dendrobatidis)

A putative driver of global amphibian decline is the panzootic chytrid fungus Batrachochytrium dendrobatidis (Bd). While Bd has been documented across continental Africa, its distribution in West Africa remains ambiguous. We tested 793 West African amphibians (one caecilian and 61 anuran species) for the presence of Bd. The samples originated from seven West African countries - Bénin, Burkina Faso, Côte d''Ivoire, Ghana, Guinea, Liberia, Sierra Leone - and were collected from a variety of habitats, ranging from lowland rainforests to montane forests, montane grasslands to humid and dry lowland savannahs. The species investigated comprised various life-history strategies, but we focused particularly on aquatic and riparian species. We used diagnostic PCR to screen 656 specimen swabs and histology to analyse 137 specimen toe tips. All samples tested negative for Bd, including a widespread habitat generalist Hoplobatrachus occipitalis which is intensively traded on the West African food market and thus could be a potential dispersal agent for Bd. Continental fine-grained (30 arc seconds) environmental niche models suggest that Bd should have a broad distribution across West Africa that includes most of the regions and habitats that we surveyed. The surprising apparent absence of Bd in West Africa indicates that the Dahomey Gap may have acted as a natural barrier. Herein we highlight the importance of this Bd-free region of the African continent - especially for the long-term conservation of several threatened species depending on fast flowing forest streams (Conraua alleni (“Vulnerable”) and Petropedetes natator (“Near Threatened”)) as well as the “Critically Endangered” viviparous toad endemic to the montane grasslands of Mount Nimba (Nimbaphrynoides occidentalis).     

Genome sizes of Eucomis L’Hér. (Hyacinthaceae) and a description of the new species Eucomis grimshawii G.D.Duncan & Zonneveld

Nuclear genome size, as measured by flow cytometry with propidium iodide, was used to investigate the relationships within the genus Eucomis L’Hér. (Hyacinthaceae). Most species of Eucomis have the same basic chromosome number, x = 15. However, the somatic DNA 2C-value (2C) is shown to range from 21 to 31 pg for the diploids. The largest genome contains roughly 10¹⁰ more base pairs than the smallest. Genome sizes are evaluated here in combination with available morphological and geographical data. Therefore, the taxonomy proposed here is not based on genome size alone. The genus Eucomis, as here determined, has 12 species. These can be divided into two groups: mainly dwarf diploid species and large-sized, tetraploid species. A small diploid plant, Eucomis (autumnalis subsp.) amaryllidifolia, is restored to species status, as a diploid subspecies seems incongruent with an allotetraploid Eucomis autumnalis. Moreover, as a diploid it is separated reproductively from the allotetraploid E. autumnalis. A new diploid species that has the lowest C value, E. grimshawii, is described here. On the basis of DNA content and other morphological characters, possible parents are suggested for all tetraploid species. Nuclear DNA content as measured by using flow cytometry may conveniently be used to produce systematic data. It is applicable even in dormant bulbs or sterile plants for the monitoring of the trade in bulbous species.     

Evidence for symplastic phloem unloading in sink leaves of barley

The pathway of phloem unloading in sink barley (Hordeum vulgare) leaves was studied using a combination of electron microscopy, carboxyfluorescein transport, and systemic movement of barley stripe mosaic virus expressing the green fluorescent protein. Studies of plasmodesmatal frequencies between the phloem and mesophyll indicated a symplastic sieve element- (SE) unloading pathway involving thick-walled and thin-walled SEs. Phloem-translocated carboxyfluorescein was unloaded rapidly from major longitudinal veins and entered the mesophyll cells of sink leaves. Unloading was "patchy" along the length of a vein, indicating that sieve element unloading may be discontinuous along a single vascular bundle. This pattern was mirrored precisely by the unloading of barley stripe mosaic virus expressing the green fluorescent protein. Transverse veins were not utilized in the unloading process. The data collectively indicate a symplastic mechanism of SE unloading in the sink barley leaf.     

Mate Guarding in the Cricket Gryllodes sigillatus: Influence of Multiple Potential Partners

There are several hypotheses as to the function of postcopulatory mate guarding. Control over the mate-guarding period by either sex could potentially influence relative reproductive success. Mate-guarding behaviour in Gryllodes sigillatus was studied under several conditions: 1. undisturbed pairs; 2. pairs with a single male intruder; 3. pairs exposed acoustically, visually and olfactorily to several other males; 4. pairs exposed freely to several other males; and 5. pairs exposed freely to several other females. The results provide support for the spermatophore retention and rival defence hypotheses. The efficacy of mate guarding was not compromised by the pair being in acoustic, visual and olfactory contact with several other males. Once pairs were exposed to free contact with several other males, the spermatophore retention time by the female declined significantly, indicating that the mate guarder's efficiency declines under competition from several rivals. In pairs exposed to contact with several females after mating, the mate-guarding period and spermatophore retention time declined as the mate guarder abandoned the mated female and pursued the other females. Termination of the effective mate-guarding period by either sex seems to be influenced by the number of other potential partners present.     

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

Background

Most protein mass spectrometry (MS) experiments rely on searches against a database of known or predicted proteins, limiting their ability as a gene discovery tool.

Results

Using a search against an in silico translation of the entire human genome, combined with a series of annotation filters, we identified 346 putative novel peptides [False Discovery Rate (FDR)<5%] in a MS dataset derived from two human breast epithelial cell lines. A subset of these were then successfully validated by a different MS technique. Two of these correspond to novel isoforms of Heterogeneous Ribonuclear Proteins, while the rest correspond to novel loci.

Conclusions

MS technology can be used for ab initio gene discovery in human data, which, since it is based on different underlying assumptions, identifies protein-coding genes not found by other techniques. As MS technology continues to evolve, such approaches will become increasingly powerful.     

Responses of the saucer scallop Amusium balloti to potential predators

A high natural mortality rate has been documented for the saucer scallop Amusium balloti, an Australian scallop found on sediment bottoms at 30–60 m deep, but little is known about the causes of mortality. We studied escape responses of A. balloti to five consumers common in the bycatch of the scallop fishery as a means of identifying potential predators. The scallop showed a negligible to weak response when touched with the sea star Pentaceraster regulus and the red portunid crab Portunus rubromarginatus. The response was similar to that observed when the scallop was touched with a plastic object. In contrast, A. balloti showed a consistent and vigorous swimming response to contact with the slipper lobster Thenus orientalis, the blue swimmer crab Portunus pelagicus and the coral crab Charybdis cruciata. This was not a generalized response to crustaceans, given the scallop's weak response to the red portunid crab. This is the first report of a scallop that has a strong swimming escape response to contact with decapod crustacean predators.