Replication levels,false presences and the estimation of the presence/absence from eDNA metabarcoding data

Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false‐positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.     

Pattern of distribution of the American bullfrog <Emphasis Type="Italic">Rana catesbeiana</Emphasis> in Europe

Despite early reports of its presence, no recent data exist on the distribution of the American bullfrog in Europe, the causes of introduction, or the trends of populations. We monitored the European situation at two spatial scales. In SW France, we performed call surveys over 2,500 wetlands. We found bullfrogs over about 2,000 km², apparently the European area in which the strongest expansion of bullfrogs is taking place. In addition, we used questionnaires to investigate the situation at the continental scale. At least 25 independent introductions occurred in Europe; eradication attempts were successful three times, and bullfrog populations are present in five countries. Education programs and monitoring are necessary to reduce the rate of introduction and to start management action as soon as possible. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Evolution of biological interaction networks: from models to real data

We are beginning to uncover common mechanisms leading to the evolution of biological networks. The driving force behind these advances is the increasing availability of comparative data in several species.     

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip,a rapid cycling and a Chinese cabbage

Background

Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops.

Results

To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA).

Conclusions

By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.     

Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica

Background

Powdery mildew (PM) is a major fungal disease of thousands of plant species, including many cultivated Rosaceae. PM pathogenesis is associated with up-regulation of MLO genes during early stages of infection, causing down-regulation of plant defense pathways. Specific members of the MLO gene family act as PM-susceptibility genes, as their loss-of-function mutations grant durable and broad-spectrum resistance.

Results

We carried out a genome-wide characterization of the MLO gene family in apple, peach and strawberry, and we isolated apricot MLO homologs through a PCR-approach. Evolutionary relationships between MLO homologs were studied and syntenic blocks constructed. Homologs that are candidates for being PM susceptibility genes were inferred by phylogenetic relationships with functionally characterized MLO genes and, in apple, by monitoring their expression following inoculation with the PM causal pathogen Podosphaera leucotricha.

Conclusions

Genomic tools available for Rosaceae were exploited in order to characterize the MLO gene family. Candidate MLO susceptibility genes were identified. In follow-up studies it can be investigated whether silencing or a loss-of-function mutations in one or more of these candidate genes leads to PM resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-618) contains supplementary material, which is available to authorized users.     

Evolution of Sexual Dimorphism in the Number of Tail Vertebrae in Salamanders: Comparing Multiple Hypotheses

The evolution of sexual dimorphism is an important topic of evolutionary biology, but few studies have investigated the determinants of sexual dimorphism over broad phylogenetic scales. The number of vertebrae is a discrete character influencing multiple traits of individuals, and is particularly suitable to analyze processes determining morphological variation. We evaluated the support of multiple hypotheses concerning evolutionary processes that may cause sexual dimorphism in the number of caudal vertebrae in Urodela (tailed amphibians). We obtained counts of caudal vertebrae from >2,000 individuals representing 27 species of salamanders and newts from Europe and the Near East, and integrated these data with a molecular phylogeny and multiple information on species natural history. Per each species, we estimated sexual dimorphism in caudal vertebrae number. We then used phylogenetic least squares to relate this sexual dimorphism to natural history features (courtship complexity, body size dimorphism, sexual ornamentation, aquatic phenology) representing alternative hypotheses on processes that may explain sexual dimorphism. In 18 % of species, males had significantly more caudal vertebrae than females, while in no species did females have significantly more caudal vertebrae. Dimorphism was highest in species where males have more complex courtship behaviours, while the support of other candidate mechanisms was weak. In many species, males use the tail during courtship displays, and sexual selection probably favours tails with more vertebrae. Dimorphism for the number of tail vertebrae was unrelated to other forms of dimorphism, such as sexual ornamentation or body size differences. Multiple sexually dimorphic features may evolve independently because of the interplay between sexual selection, fecundity and natural selection.