Project A5

Analysis of hybrid zones and introgression using NGS
Lead Partners: NHM London (Charity), VIENNA (University)

State-of-the-Art Problem and its Solution

NGS reveals that some genomes comprise long sections of distinct origin, sometimes many megabases long. These patterns may be signatures of recent selection, but can also be generated by gene flow between taxa, or recent admixture of long separated populations. The NHM, a world centre for characterising biodiversity, need to distinguish between these two types of process in order to understand the nature of the boundary between to taxa of the genus Hyacinthoides. Hence modelling of these particular histories is required to distinguish the effects of selection and genetic drift.


· Use niche modelling combined with phylogeographic analyses to estimate the distance and time over which selected loci have driven into a population – information which is very rarely possible to obtain from a natural population.

· Derive analytical and numerical approximations for the fixation probability of adaptive alleles that introgress, together with linked deleterious variants from a parent species into the genetic background of a different (incipient) species. Analyze how this probability depends on the genetic architecture and the local linkage map.

· Describe the genetic footprints of adaptive gene introgression and implement statistical tests to estimate the location and selection coefficients of inter-species adaptations.


The NHM and collaborators have mapped over 400 populations at the natural boundary of H. hispanica and H. non-scripta. Niche modelling combined with phylogeographic analyses will be used to determine the current location of the hybrid zone and to model how it changed in the past. The interpretation of the new genome-wide SNP data will use an analytical approach based on multi-type branching processes to derive analytical approximations for the fixation processes. Computer simulations will be used to extend the analytical work and to validate approximations. Previous work by the VIENNA lab on the footprint of adaptation from recurrent migration will serve as a starting point to be extended to a three-locus model, where deleterious alleles are linked to the beneficial migrant.

ESRs training by research

The NHM based ESR will lead on the data acquisition and niche modelling. The VIENNA based ESR will lead on model development and they will jointly analyse the Hyacinthoides data.

Job Description 8 (NHM London)
Job Description 9 (Vienna)