Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonpar...

Knowledge of phylogeny is of fundamental importance for understanding evolution. It has become an indispensable tool in modern genomics as a framework for interpreting genomes and metagenomes, for understanding the evolution of genes, proteins, and noncoding RNAs, as well as gene regulation by secondary RNA and protein structures, or for reconstructing ancestral genomes [1]. The era of next-gen...

Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured by demanding that the set of rate-matrices belonging to the model class form a Lie algebra. It is the case that some well-known Markov models do form Lie algebras and we re...

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison...

Symbiotic associations between invertebrates and dinoflagellates of the genus Symbiodinium are a common occurrence in marine environments. However, despite our extensive knowledge concerning the physiological contributions of these algae to their symbiotic partners, our understanding of zooxanthella phylogenetics is still in its early stages. In the past 10 years, studies of Symbiodinium phylog...

The success of model-based methods in phylogenetics has motivated much research aimed at generating new, biologically informative models. This new computer-intensive approach to phylogenetics demands validation studies and sound measures of performance. To date there has been little practical guidance available as to when and why the parameters in a particular model can be identified reliably. ...

Phylogenetics is the area of research concerned with finding the genetic relationships between species. The basic idea is to compare specific characters (features) of the species, under the natural assumption that similar species (i.e., species with similar characters) are genetically close. The term phylogeny refers to these relationships, usually presented as a phylogenetic tree (see Figures ...

Cultural transmission typically results in a network of connections between cultural units (such as individuals or social groups), not the branching patterns of descent seen in genetic inheritance. As a consequence, the application of phylogenetic (or evolutionary clustering) methods to cultural history faces methodological problems. Most importantly, the history of relationships inferred throu...

Advocates of maximum likelihood (ML) approaches to phylogenetics commonly cite as one of their primary advantages the use of objective statistical criteria for model selection. Currently, a particular implementation of the likelihood ratio test (LRT) is the most commonly used model-selection criterion in phylogenetics. This approach requires the choice of a starting point and a parameter additi...

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as rele...