Temporal Phylogenetic Networks and Logic Programming

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages. To appear in Theory and Practice of Logic Programming (TPLP)

Networking Phylogeny for Indo-European and Austronesian Languages

Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the ‘express train’ model of Austronesian expansion from South-East Asia, with an essential role for the Batanes islands located between the Philippines and Taiwan

The Crop-Group and the inconsistent use of Linnean names in the taxonomy of domesticated plants

There have been several proposals for classification categories for systematic groups of domesticated plants. In the 6th edition of the International Code for Nomenclature of Cultivated Plants (ICNCP) only two main categories were included, the cultivar and the cultivar-group. The 7th edition of ICNCP saw the introduction of the Group to encompass the cultivar-group together with other kinds of groupings, also of unnamed material. Despite the existence of the ICNCP, many names for systematic groups of domesticated plants are still in purely Linnean form, following the rules of the International Code of Botanical Nomenclature (ICBN). This practice illustrates a lack of insight in the workings and logic of systematic thinking with respect to domesticated plants and muddles the borderline between the contexts of domestication and evolution. The inclusion of the Crop category in the ICNCP would accommodate the nomenclature and classification of all systematic groups of domesticated plants in one logically consistent system, setting it apart from the realm of the classical botanical classification in use for wild plants

Evolutionary biology for the 21st century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.Molecular and Cellular BiologyOrganismic and Evolutionary Biolog

Lateral transfer in Stochastic Dollo models

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages and obtain an improved fit over the corresponding model without lateral transfer.Comment: Improvements suggested by reviewer