Sébastien Ollier

Phylo-MCOA: A Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics Using Multiple Co-inertia Analysis

Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary history. On the other hand, it is also essential to identify which genes and species produce discordant topologies and therefore evolve in a different way or represent noise in the data. The latter are outlier genes or species and they can provide a wealth of information on potentially interesting biological processes, such as incomplete lineage sorting, hybridization, and horizontal gene transfers. Here, we propose a new method to explore the genomic tree space and detect outlier genes and species based on multiple co-inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced by individual genes. Our method allows the rapid identification of outlier genes and species by extracting the similarities and discrepancies, in terms of the pairwise distances, between all the species in all the trees, simultaneously. This is achieved by using MCOA, which finds successive decomposition axes from individual ordinations (i.e., derived from distance matrices) that maximize a covariance function. The method is freely available as a set of R functions. The source code and tutorial can be found online at http://phylomcoa.cgenomics.org.

Seed Spillage from Grain Trailers on Road Verges during Oilseed Rape Harvest: An Experimental Survey

Context Anthropogenic vectors enhance the natural dispersal capacity of plant seeds significantly in terms of quantity and distance. Human-mediated seed dispersal (i.e. anthropochory) greatly increases the dispersal of crop species across agroecosystems. In the case of oilseed rape (OSR), spillage of seeds from grain trailers during harvest has never been quantified. Methods Our experimental approach involved establishing 85 seed trap-sites on the road verges of an agricultural area around the grain silo of Selommes (Loir-et-Cher, France). We recorded OSR spillage during harvest and applied a linear model to the data. Results The amount of seed spilled was related positively to the area of the OSR fields served by the road, whereas the amount of seed spilled decreased with other variables, such as distance from the trap-site to the verge of the road and to the nearest field. The distance to the grain silo, through local and regional effects, affected seed loss. Local effects from fields adjacent to the road resulted in a cumulative spillage on one-lane roads. On two-lane roads, spillage was nearly constant whatever the distance to the silo due to a mixture of these local effects and of grain trailers that joined the road from more distant fields. From the data, we predicted the number of seeds lost from grain trailers on one road verge in the study area. We predicted a total spillage of 2.05×106 seeds (±4.76×105) along the road length, which represented a mean of 404±94 seeds per m2. Conclusion Containment of OSR seeds will always be challenging. However, seed spillage could be reduced if grain trailers were covered and filled with less seed. Reducing distances travelled between fields and silos could also limit seed loss.

Euclidean Nature of Phylogenetic Distance Matrices

Phylogenies are fundamental to comparative biology as they help to identify independent events on which statistical tests rely. Two groups of phylogenetic comparative methods (PCMs) can be distinguished: those that take phylogenies into account by introducing explicit models of evolution and those that only consider phylogenies as a statistical constraint and aim at partitioning trait values into a phylogenetic component (phylogenetic inertia) and one or multiple specific components related to adaptive evolution. The way phylogenetic information is incorporated into the PCMs depends on the method used. For the first group of methods, phylogenies are converted into variance-covariance matrices of traits following a given model of evolution such as Brownian motion (BM). For the second group of methods, phylogenies are converted into distance matrices that are subsequently transformed into Euclidean distances to perform principal coordinate analyses. Here, we show that simply taking the elementwise square root of a distance matrix extracted from a phylogenetic tree ensures having a Euclidean distance matrix. This is true for any type of distances between species (patristic or nodal) and also for trees harboring multifurcating nodes. Moreover, we illustrate that this simple transformation using the square root imposes less geometric distortion than more complex transformations classically used in the literature such as the Cailliez method. Given the Euclidean nature of the elementwise square root of phylogenetic distance matrices, the positive semidefinitiveness of the phylogenetic variance-covariance matrix of a trait following a BM model, or related models of trait evolution, can be established. In that way, we build a bridge between the two groups of statistical methods widely used in comparative analysis. These results should be of great interest for ecologists and evolutionary biologists performing statistical analyses incorporating phylogenies.

Recent human history governs global ant invasion dynamics

Human trade and travel are breaking down biogeographic barriers, resulting in shifts in the geographical distribution of organisms, yet it remains largely unknown whether different alien species generally follow similar spatiotemporal colonization patterns and how such patterns are driven by trends in global trade. Here, we analyse the global distribution of 241 alien ant species and show that these species comprise four distinct groups that inherently differ in their worldwide distribution from that of native species. The global spread of these four distinct species groups has been greatly, but differentially, influenced by major events in recent human history, in particular historical waves of globalization (approximately 1850–1914 and 1960 to present), world wars and global recessions. Species in these four groups also differ in six important morphological and life-history traits and their degree of invasiveness. Combining spatiotemporal distribution data with life-history trait information provides valuable insight into the processes driving biological invasions and facilitates identification of species most likely to become invasive in the future.

Recurrent bridgehead effects accelerate global alien ant spread

Significance Because of the globalization of trade and travel, worldwide invasion rates are high. A potential driver of the global acceleration of new invasions is the so-called bridgehead effect, in which initial invasive populations serve as the source of additional invasions via secondary introductions. However, the frequency and overall importance of secondary introductions remain largely unknown. Using a remarkable dataset, spanning nearly 100 years (1914–2013), of ant interceptions at air and maritime ports in the United States and New Zealand, we found that most ant introductions arise via secondary transport via intermediate regions. Our analyses also reveal positive feedback between the introduction and establishment stages of the invasion process via secondary introductions acting as a critical driver of increasing global invasion rates. Biological invasions are a major threat to biological diversity, agriculture, and human health. To predict and prevent new invasions, it is crucial to develop a better understanding of the drivers of the invasion process. The analysis of 4,533 border interception events revealed that at least 51 different alien ant species were intercepted at US ports over a period of 70 years (1914–1984), and 45 alien species were intercepted entering New Zealand over a period of 68 years (1955–2013). Most of the interceptions did not originate from species’ native ranges but instead came from invaded areas. In the United States, 75.7% of the interceptions came from a country where the intercepted ant species had been previously introduced. In New Zealand, this value was even higher, at 87.8%. There was an overrepresentation of interceptions from nearby locations (Latin America for species intercepted in the United States and Oceania for species intercepted in New Zealand). The probability of a species’ successful establishment in both the United States and New Zealand was positively related to the number of interceptions of the species in these countries. Moreover, species that have spread to more continents are also more likely to be intercepted and to make secondary introductions. This creates a positive feedback loop between the introduction and establishment stages of the invasion process, in which initial establishments promote secondary introductions. Overall, these results reveal that secondary introductions act as a critical driver of increasing global rates of invasions.

Genetic Diversity of Oilseed Rape Fields and Feral Populations in the Context of Coexistence with GM Crops

Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and feral populations over 4 years in an agricultural landscape of 41 km2. We used exact compatibility and maximum likelihood assignment methods to assign these plants to cultivars. Even pure lines and hybrid cultivar seed lots contained several genotypes. The cultivar diversity in fields reflected the conventional view of agroecosystems quite well: that is, there was a succession of cultivars, some grown for longer than others because of their good performance, some used for one year and then abandoned, and others gradually adopted. Three types of field emerged: fields sown with a single cultivar, fields sown with two cultivars, and unassigned fields (too many cultivars or unassigned plants to reliably assign the field). Field plant diversity was higher than expected, indicating the persistence of cultivars that were grown for only one year. The cultivar composition of feral populations was similar to that of field plants, with an increasing number of cultivars each year. By using genetic tools, we found a link between the cultivars of field plants in a particular year and the cultivars of feral population plants in the following year. Feral populations on road verges were more diverse than those on path verges. All of these findings are discussed in terms of their consequences in the context of coexistence with genetically modified crops.

Questioning Holocene community shifts

Demonstrating changes in the structure of plant and animal communities over geological time scales and linking these changes to human impacts in the Holocene epoch would be an important contribution to the fields of ecology and conservation biology1. Lyons et al.2 claim to provide such evidence based on a decrease in the proportion of spatially aggregated species pairs, using co-occurrence data from assemblages spanning the past 300 million years. However, we suggest that apparent flaws in their predictions, assumptions, methods and interpretations undermine this claim, and we question the conclusion that the structure of communities has fundamentally changed during the Holocene.