Projecte ofert

Títol: Comparative evaluation of SFS-based demographic inference using forward-in-time simulations

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Tutor/a o Cotutor/a: CASALS MISSIO, JOAN

Departament: DEAB

Títol: Comparative evaluation of SFS-based demographic inference using forward-in-time simulations

Data inici oferta: 02-03-2026      Data finalització oferta: 02-11-2026

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Estudis d'assignació del projecte:

GR ENG SIS BIOLÒG 23

Lloc de realització:
EEABB

Paraules clau:

Descripció del contingut i pla d'activitats:
A key factor in the study of the evolution of the populations is determining their demographic history. Demographic trajectories of a population across the time (also called demographic landscape) can be inferred from genome sequence data using different methodologies (e.g., PSMC: Schiffels and Durbin 2014, Schweiger and Durbin 2023, MSMC: Li and Durbin 2011, Malaspinas et al. 2016, Stairway plot: Liu and Fu 2015, 2020). These methodologies assume that most positions in the genome are neutral (i.e., not affected by selection), that is, gene regions represent a tiny section of the genome and should not affect the demographic pattern. Nevertheless, it is known that deleterious mutations are spread across the functional regions of the genome, affecting neutral positions surrounding them in the whole genome (e.g., Fay 2011, Cao et al. 2011, Chao et al. 2013, Comeron 2017, Messer and Petrov 2013, Lye et al. 2017), and perhaps affect the inference of demographic patterns. Furthermore, in the case of plant species, self-pollination and low recombination increase linkage and can amplify the deviation from genome neutrality.

In this study, we consider deleterious (and beneficial) mutations distributed across the genome and vary recombination patterns, to contrast simulated demographic scenarios versus their inference. To achieve this analysis, we will (i) perform shell scripts to automatize the simulation study and (ii) obtain genome sequences from a population with SLiM (Haller and Messer 2023), a forward-in-time simulator where complex demographic and selective patterns can be easily included. (iii) Sequence data will be processed to obtain the frequency of the variants (e.g., using SLiM code) and (iv) the inference of the demographic trajectories will be obtained with Stairway Plot (Liu and Fu 2020). (v) Statistical comparisons will be performed in R. The results of this work will help to understand the contradictions between molecular and paleontological dating results.

Orientació a l'estudiant: Aquest treball es realitza al Centre for Research in Agricultural Genomics, ubicat a la UAB (Bellaterra).

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