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.

LS: 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 LS, 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.

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.

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.

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).