Population genetics

Recent publications

1. L Ferretti and P Ribeca, “Allelic Entropy and Times until Loss or Fixation of Neutral Polymorphisms”, Genes, 14, 1751 (2023).

2. SE Ramos-Onsins*, G Marmorini*, G Achaz and L Ferretti, “A General Framework for Neutrality Tests Based on the Site Frequency Spectrum”, Genes, 14, 1714 (2023).

3. F Freund*, E Kerdoncuff* et al, “Interpreting the pervasive observation of U-shaped Site Frequency Spectra”, PLoS Genetics 19(3): e1010677 (2023).

4. J Carson, A Ledda, L Ferretti, M Keeling and X Didelot, “The bounded coalescent model: conditioning a genealogy on a minimum root date”, Journal of Theoretical Biology, 548 111186 (2022).

5. Vara C, Capilla L, Ferretti L, Ledda A, Sanchez-Guillen RA, Gabriel SI, Albert-Lizandra G, Florit-Sabater B, Bello-Rodriguez J, Ventura J, Searle JB, Mathias ML and Ruiz-Herrera A, “PRDM9 diversity at fine geographical scale reveals contrasting evolutionary patterns and functional constraints in natural populations of house mice”, Molecular Biology and Evolution, 36 (8):1686-1700 (2019).

Population genetics of selected variants

• We developed a null framework to test selection on specific variants based on the patterns of linked mutations [1,2]. These methods are being applied to an evolutionary classification of chromosomal inversions detected as polymorphic in human populations [3].

  1. Ferretti L, Klassmann A, Raineri E, Ramos-Onsins SE, Wiehe T and Achaz G, “The neutral frequency spectrum of linked sites”, accepted in Theoretical Population Biology (2018). 

  2. Klassmann A and Ferretti L, “The third moments of the site frequency spectrum”, Theoretical Population Biology, 120:16-28 (2018). 

  3. Giner-Delgado C, Villatoro S, Lerga-Jaso J, Gayà-Vidal M, Oliva M, Castellano D, Izquierdo D, Noguera I, Bitarello B, Olalde I, Delprat A, Blancher A, Lalueza C, Esko T, O’Reilly P, Andrés A, Ferretti L, Pantano L, Puig M and Cáceres M, “Functional and evolutionary impact of polymorphic inversions in the human genome”, Nature Communication (2019). 

Population genetics estimators and neutrality tests

• We proposed a class of ''optimal'' neutrality tests similar to Tajima's D but optimized for a given alternative model of evolution [1] and we described a method to build them from the expected frequency spectrum of the alternative model. These tests belong to the general class of tests proposed by Achaz (Genetics, 2009). Moreover, we studied some of their properties and extensions [2]. We also discuss the relation between neutrality tests and their interpretation in terms of genealogical trees [3].

  1. Ferretti L, Perez-Enciso M, Ramos-Onsins SE, Optimal neutrality tests based on the frequency spectrum, Genetics 186(1):353-65 (2010).

  2. Ferretti L, Marmorini G, Ramos-Onsins SE, Properties of neutrality tests based on allele frequency spectrum, arXiv.

  3. Ferretti L, Ledda A, Achaz G, Wiehe T and Ramos-Onsins SE, “Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests”, Genetics, 207(1):229-240 (2017). 

Tree balance in the coalescent 

• We derived the probabilities of recombination events that change tree height in the neutral model and we derived first-order transition probabilities for the root inbalance (which is a simple measure of tree balance) after a single recombination event [1]. These results are a first step towards a theoretical basis for haplotype tests of selection.

  1. Ferretti L, Disanto F, Wiehe T, The effect of single recombination events on coalescent tree height and shape, PLoS One. 2013 Apr 8;8(4):e60123. PLoS One.

Methods for population genetics from Next Generation Sequencing data

• We developed several methods for NGS data. We extended neutrality tests like Tajima's D and Fay and Wu's H to NGS data, both using called sequences with missing data and correcting for missing information [3]. We presented a general framework for Watterson estimators of variability from all kinds of NGS data, including haploid and diploid individuals, trios, pools and polyploids [2] as well as a general analysis of the frequency spectrum in autopolyploids [7]. For pooled data, we developed a Bayesian SNP caller using the neutral frequency spectrum as a prior [4] and proposed a Maximum Composite Likelihood estimator of variability and a complete set of tests: Tajima's D, Fay and Wu's H, HKA etc, specific for pooled NGS samples [1]. We also wrote a recent review on population genomics methods for neglected genomes, focused on arthropods [5] and a (slightly outdated) review on the methods and applications of NGS for animal genetics, containing some material on pool sequencing [6].

  1. Ferretti L, Ramos-Onsins SE and Perez-Enciso M, Population genomics from pool sequencing, Molecular Ecology (2013), 22: 5561-5576.

  2. Ferretti L and Ramos-Onsins SE, Watterson estimators for Next Generation Sequencing: from trios to autopolyploids, Theor Popul Biol. 100C:79-87 (2015). arXiv.

  3. Ferretti L*, Raineri E* and Ramos-Onsins SE, Neutrality tests for sequences with missing data, Genetics 191(4):1397-401 (2012).

  4. Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S and Perez-Enciso M, SNP calling by sequencing pooled samples, BMC Bioinformatics 13:239 (2012).

  5. Hasselmann M, Ferretti L and Zayed A, “Beyond fruit-flies: Population genomic advances in non-dipteran arthropods”, Briefings in Functional Genomics, 14 (6): 424-431 (2015). 

  6. Perez-Enciso M and Ferretti L, Massive parallel sequencing in animal genetics: wherefroms and wheretos, Anim Genet. 41(6):561-9 (2010).

  7. Ferretti L, Ribeca P and Ramos-Onsins SE, "The Site Frequency/Dosage Spectrum of autopolyploid populations", Frontiers in Genetics (2018).