CastNet: a systems-level sequence evolution simulator.

BACKGROUND: Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used to infer phylogenies which, in the simplest form, simulates a single sequence at a time. However, biological systems are multi-genic, and gene products can affect each other's evolutionary paths through coevolution. These crucial evolutionary dynamics still remain to be simulated, and we believe that modelling them can lead to profound insights for comparative genomics. RESULTS: Here we present CastNet, a genome evolution simulator that assumes each genome is a collection of genes with constantly evolving regulatory interactions in between them. The regulatory interactions produce a phenotype in the form of gene expression profiles, upon which fitness is calculated. A genetic algorithm is then used to evolve a population of such entities through a user-defined phylogeny. Importantly, the regulatory mutations are a response to sequence mutations, thus making a 1-1 relationship between the rate of evolution of sequences and of regulatory parameters. This is, to our knowledge, the first time the evolution of sequences and regulation have been explicitly linked in a simulation, despite there being a multitude of sequence evolution simulators, and a handful of models to simulate Gene Regulatory Network (GRN) evolution. In our test runs, we see a coevolutionary signal among genes that are active in the GRN, and neutral evolution in genes that are not included in the network, showing that selective pressures imposed on the regulatory output of the genes are reflected in their sequences. CONCLUSION: We believe that CastNet represents a substantial step for developing new tools to study genome evolution, and more broadly, coevolutionary webs and complex evolving systems. This simulator also provides a new framework to study molecular evolution where sequence coevolution has a leading role.

LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference.

BACKGROUND: Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a relatively homogeneous rate. However, this algorithm had two major shortcomings: (i) it was automated and published as a set of bash scripts, and hence was Linux-specific, and not user friendly, and (ii) it could result in very stringent sequence subselection when extremely slow-evolving sequences were present. RESULTS: We address these challenges and produce a new, platform-independent program, LSX, written in R, which includes a reprogrammed version of the original LS3 algorithm and has added features to make better lineage rate calculations. In addition, we developed and included an alternative version of the algorithm, LS4, which reduces lineage rate heterogeneity by detecting sequences that evolve too fast and sequences that evolve too slow, resulting in less stringent data subselection when extremely slow-evolving sequences are present. The efficiency of LSX and of LS4 with datasets with extremely slow-evolving sequences is demonstrated with simulated data, and by the resolution of a contentious node in the catfish phylogeny that was affected by an unusually high lineage rate heterogeneity in the dataset. CONCLUSIONS: LSX is a new bioinformatic tool, with an accessible code, and with which the effect of lineage rate heterogeneity can be explored in gene sequence datasets of virtually any size. In addition, the two modalities of the sequence subsampling algorithm included, LS3 and LS4, allow the user to optimize the amount of non-phylogenetic signal removed while keeping a maximum of phylogenetic signal.

Back to the roots: Reducing evolutionary rate heterogeneity among sequences gives support for the early morphological hypothesis of the root of Siluriformes (Teleostei: Ostariophysi).

Catfishes (Teleostei: Siluriformes) are a highly diverse order within Ostariophysi that is distributed worldwide. At the base of this clade emerge three lineages with well-defined monophylies: Diplomystidae, Loricarioidei, and Siluroidei. Morphological phylogeny studies place the Diplomystidae as the earliest branching of these three lineages, but studies based on molecular phylogenetics consistently find the fast-evolving Loricarioidei instead. The high lineage evolutionary rate heterogeneity in this order and the fact that the lineage placed closest to the root in the molecular phylogenies is fast evolving, including many long branches, raises the possibility that the discrepancy between morphological and molecular phylogenies may be the result of a long branch attraction inference artifact. We test this hypothesis by using a 10-gene dataset to evaluate the arrangement of the three main siluriform lineages, and apply the LS3 and LS4 taxon sequence subsampling methods to reduce evolutionary rate heterogeneity among lineages. The initial and complete dataset supports the basal branching of Loricarioidei as in all previous molecular phylogenies, but once lineage rate heterogeneity is reduced with LS3 or LS4 through the removal of sequences disrupting homogeneity, the phylogeny shows Diplomystidae as the earliest branching group, with high supports, as proposed by morphological phylogeny. The result obtained with LS3, however, introduces the misplacement of one of the species with the highest amount of missing data, Scoloplax sp. Because the sequence sub-selection criterion of LS4 has been optimized to reduce data removal, the phylogeny resulting from the LS4-processed data is in agreement with the known intra-lineage relationships in addition to supporting the morphologically-based rooting hypothesis. Our results are the first instance in which a consensus between molecular and morphological phylogeny is reached concerning the root of this order.

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa.

Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³.

Trunk dental tissue evolved independently from underlying dermal bony plates but is associated with surface bones in living odontode-bearing catfish.

Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes. We examined the location and cover of odontodes and trunk dermal bony plates for all six loricarioid families and 17 non-loricarioid catfish families for comparison. We inferred the phylogeny of Loricarioidei using a new 10-gene dataset, eight time-calibration points, and noise-reduction techniques. Based on this phylogeny, we reconstructed the ancestral states of odontode and bony plate cover, and find that trunk odontodes emerged before dermal bony plates in Loricarioidei. Yet we discovered that when bony plates are absent, other surface bones are always associated with odontodes, suggesting a link between osteogenic and odontogenic developmental pathways, and indicating a remarkable trunk odontogenic potential in Loricarioidei.

Landscape analysis of drone congregation areas of the honey bee, Apis mellifera.

Male honey bees fly and gather at Drone Congregation Areas (DCAs), where drones and queens mate in flight. DCAs occur in places with presumably characteristic features. Using previously described landscape characteristics and observations on flight direction of drones in nearby apiaries, 36 candidate locations were chosen across the main island of Puerto Rico. At these locations, the presence or absence of DCAs was tested by lifting a helium balloon equipped with queen-sex-pheromone-impregnated bait, and visually determining the presence of high numbers of drones. Because of the wide distribution of honey bees in Puerto Rico, it was expected that most of the potential DCAs would be used as such by drones and queens from nearby colonies. Eight DCAs were found in the 36 candidate locations. Locations with and without DCAs were compared in a landscape analysis including characteristics that were described to be associated with DCAs and others. Aspect (direction of slope) and density of trails were found to be significantly associated with the presence of DCAs.

Testing prey DNA fingerprinting on Amblyseius largoensis (Acari: Phytoseiidae) predation of Raoiella indica (Acari: Tenuipalpidae).

Molecular detection of predation by identifying prey markers in the digestive tract of predators has developed into a powerful tool to assess predator-prey systems in which diet identification is too time consuming or impossible. Here we explore its utility for detecting predation of the pest mite Raoiella indica Hirst by the predatory mite Amblyseius largoensis Muma, taking advantage of the color the predator acquires after eating this mite to cross-reference our results. For this, a ~410 bp segment of the cytochrome c oxidase subunit I (COI) mitochondrial gene marker specific for the subfamily Tetranychoidea was used. Amblyseius largoensis that had recently eaten were collected from greenhouse colonies containing both mites, and isolated from any other food source. Predator mites were taken for fingerprinting at 24, 48, 72 and 96 h of starving after collection, and the same process was repeated a second time, offering pollen as an alternative food source to see whether detection changed. Lastly, a sampling trial was conducted in the greenhouse, in which mites were collected regardless of their color and frozen immediately for fingerprinting. Raoiella indica DNA was detected for 48 h on starving predators, and for 96 h on those who had eaten pollen. The segment was detected in 26 % of the samples collected on the trial. This technique needs refinement specific for this system, but the results obtained here confirm that it could turn into a very useful tool for assessing aspects of this predator-prey system.