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Deciphering a rapid and old species radiation

Phylogeny of banded newts from the Near East

Supervisors
Isolde van Riemsdijk, Pim Arntzen, Ben Wielstra

Contact
isolde.vanriemsdijk@naturalis.nl

Period & duration
6-9 months

Study & level
Biology, MSc

Background & context
The three species of banded newt (genus Ommatotriton) are distributed in Anatolia, the Caucasus and the Levant. They radiated in a short time span, c. 25 million years ago. As a consequence, the relationships among the species is difficult to determine. Our previous study, using traditional phylogenetic methods and a small number of markers, could not distinguish between the three possible phylogenetic hypotheses.

Objectives & goals
We have generated next-generation sequence data for c. 220 nuclear markers, from samples across the entire range of the genus. The aim of this project is to employ modern techniques, developed to specifically handle this type of data, to resolve the phylogeny of the three Ommatotriton species.

Methods, tasks and approach
Specific softwares (e.g. SNAPP) have recently been developed to conduct phylogenetic analyses based on short DNA markers with relatively low variation. The task will be for the student to identify an appropriate pipeline and reconstruct a phylogeny for Ommatotriton.

Requirements
The applicant needs to have passed a course on phylogenetics and/or bioinformatics.