How to capture fish in a school? Effect of successive predator attacks on seabird feeding success.

Prey aggregations, such as fish schools, attract numerous predators. This typically leads to the formation of multispecific groups of predators. These aggregations can be seen both as a place of increased competition and as a place of possible facilitation between predators. Consequently, the functional role of such predator-prey aggregation is uncertain, and its effect on individual feeding success is virtually unknown. Using underwater film footage of different predators feeding on fish schools during the sardine run in South Africa, we directly measured the in situ feeding success of individual Cape gannets Morus capensis in different foraging situations. We determined the types of Cape gannet attacks (direct plunge dive or plunge dive followed by underwater pursuit) and we measured the occurrences and timing of attacks from the different species (mostly Cape gannets and long-beaked common dolphins Delphinus capensis). We also estimated the size of the targeted fish schools. These observations were complemented with a simulation model to evaluate the cumulative effect of successive predator attacks on the prey aggregation structure. The probability to capture a fish in one feeding attempt by Cape gannets averaged 0·28. It was lower when gannets engaged in underwater prey pursuit after the plunge compared to direct plunge (0·13 vs. 0·36). We found no effect of the number of prey on gannets' feeding success. However, the timing and frequency of attacks influenced strongly and positively the feeding success of individuals. The probability to capture a fish was the lowest (0·16) when no attack occurred in the few seconds (1-15 s) prior to a dive and the highest (˜0·4, i.e. more than twice) when one or two attacks occurred during this time window. The simulation model showed that a prey aggregation disorganized just after an attack and that the maximum of disturbance was obtained a few seconds after the initiation of the successive attacks. Our study suggests that, in multispecies predator assemblages, the cumulative effect (through disorganization of school cohesiveness) of the multiple species attacking a prey aggregation may increase the feeding success of each individual. Therefore, facilitation between predators is likely to overcome competition in these multispecific assemblages.

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.

BACKGROUND: Most models of genome evolution concern either genetic sequences, gene content or gene order. They sometimes integrate two of the three levels, but rarely the three of them. Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content. RESULTS: We propose a probabilistic evolutionary model for gene neighborhoods, allowing genes to be inserted, duplicated or lost. It uses reconciled phylogenies, which integrate sequence and gene content evolution. We are then able to optimize parameters such as phylogeny branch lengths, or probabilistic laws depicting the diversity of susceptibility of syntenic regions to rearrangements. We reconstruct a structure for ancestral genomes by optimizing a likelihood, keeping track of all evolutionary events at the level of gene content and gene synteny. Ancestral syntenies are associated with a probability of presence.

Gene tree correction guided by orthology.

BACKGROUND: Reconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, such as conserved synteny. RESULTS: We explore a way to include external information on orthology in the process of gene tree construction. Given an initial gene tree and a set of orthology constraints on pairs of genes or on clades, we give polynomial-time algorithms for producing a modified gene tree satisfying the set of constraints, that is as close as possible to the original one according to the Robinson-Foulds distance. We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two trees are statistically equivalent. AVAILABILITY: Software and data available upon request to the corresponding author.

Efficient Gene Tree Correction Guided by Genome Evolution.

MOTIVATIONS: Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, often rely on a computationally intensive tree space search which forecloses an application to large genomic databases. RESULTS: We propose a new method, called ProfileNJ, that takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of information from a species tree and a distance matrix. Its low running time enabled us to use it on the whole Ensembl Compara database, for which we propose an alternative, arguably more plausible set of gene trees. This allowed us to perform a genome-wide analysis of duplication and loss patterns on the history of 63 eukaryote species, and predict ancestral gene content and order for all ancestors along the phylogeny. AVAILABILITY: A web interface called RefineTree, including ProfileNJ as well as a other gene tree correction methods, which we also test on the Ensembl gene families, is available at: http://www-ens.iro.umontreal.ca/~adbit/polytomysolver.html. The code of ProfileNJ as well as the set of gene trees corrected by ProfileNJ from Ensembl Compara version 73 families are also made available.