@phdthesis{21918,
  author       = {Khudiakova, Kseniia},
  issn         = {2663-337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{How epistasis and purifying selection shape genetic diversity}},
  doi          = {10.15479/AT-ISTA-21918},
  year         = {2026},
}

@unpublished{21968,
  abstract     = {Balancing selection, a form of selection that maintains genetic diversity, is difficult to detect, and the importance of balancing selection for the maintenance of genetic variation may be larger than often assumed. We model the possibility that the diversity-promoting effects of balancing selection extend to other loci that show sign epistasis with a locus under balancing selection. Rather than focusing on overdominance, as was done in previous efforts, we explore the effects of negative frequency dependence and show that this has important effects on the conditions under which the diversity-promoting effect of epistasis can occur in diploids. Our results show that not only recombination rate but also the dominance of sign epistasis are key parameters that determine the maintenance of polymorphism beyond the locus under direct balancing selection. We suggest that the effect we explore may play a significant role, especially when balancing selection acts on major effect loci.},
  author       = {Khudiakova, Kseniia and Barton, Nicholas H and Arnqvist, Goran},
  booktitle    = {bioRxiv},
  title        = {{Sign epistasis extends the effects of balancing selection on genetic diversity}},
  doi          = {10.1101/2025.04.09.647826},
  year         = {2026},
}

@article{21322,
  abstract     = {Habitat fragmentation poses a significant risk to population survival, causing both demographic stochasticity and genetic drift within local populations to increase, thereby increasing genetic load. Higher load causes population numbers to decline, which reduces the efficiency of selection and further increases load, resulting in a positive feedback that may drive entire populations to extinction. Here, we investigate this eco-evolutionary feedback in a metapopulation consisting of local demes connected via migration, with individuals subject to deleterious mutation at a large number of loci. We first analyze the determinants of load under soft selection, where population sizes are fixed, and then build on this to understand hard selection, where population sizes and load coevolve. We show that under soft selection, very little gene flow (less than one migrant per generation) is enough to prevent fixation of deleterious alleles. By contrast, much higher levels of migration are required to mitigate load and prevent extinction when selection is hard, with critical migration thresholds for metapopulation persistence increasing sharply as the genome-wide deleterious mutation rate becomes comparable to the baseline population growth rate. Moreover, critical migration thresholds are highest if deleterious mutations have intermediate selection coefficients but lower if alleles are predominantly recessive rather than additive (due to more efficient purging of recessive load within local populations). Our analysis is based on a combination of analytical approximations and simulations, allowing for a more comprehensive understanding of the factors influencing load and extinction in fragmented populations.},
  author       = {Olusanya, Oluwafunmilola O and Khudiakova, Kseniia and Sachdeva, Himani},
  issn         = {1537-5323},
  journal      = {The American Naturalist},
  number       = {6},
  pages        = {617--636},
  publisher    = {University of Chicago Press},
  title        = {{Genetic load, eco-evolutionary feedback, and extinction in metapopulations}},
  doi          = {10.1086/735562},
  volume       = {205},
  year         = {2025},
}

@article{20050,
  abstract     = {We prove upper bounds on the L∞-Wasserstein distance from optimal transport between strongly log-concave probability densities and log-Lipschitz perturbations. In the simplest setting, such a bound amounts to a transport-information inequality involving the L∞-Wasserstein metric and the relative L∞-Fisher information. We show that this inequality can be sharpened significantly in situations where the involved densities are anisotropic. Our proof is based on probabilistic techniques using Langevin dynamics. As an application of these results, we obtain sharp exponential rates of convergence in Fisher’s infinitesimal model from quantitative genetics, generalising recent results by Calvez, Poyato, and Santambrogio in dimension 1 to arbitrary dimensions.},
  author       = {Khudiakova, Kseniia and Maas, Jan and Pedrotti, Francesco},
  issn         = {1050-5164},
  journal      = {The Annals of Applied Probability},
  number       = {3},
  pages        = {1913--1940},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal model}},
  doi          = {10.1214/25-aap2162},
  volume       = {35},
  year         = {2025},
}

@unpublished{21967,
  abstract     = {Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.

In the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet.},
  author       = {Khudiakova, Kseniia and Boenkost, Florin and Tourniaire, Julie N},
  booktitle    = {bioRxiv},
  title        = {{Genealogies under purifying selection}},
  doi          = {10.1101/2024.10.15.618444},
  year         = {2024},
}

@unpublished{17352,
  abstract     = {We prove upper bounds on the $L^\infty$-Wasserstein distance from optimal
transport between strongly log-concave probability densities and log-Lipschitz
perturbations. In the simplest setting, such a bound amounts to a
transport-information inequality involving the $L^\infty$-Wasserstein metric
and the relative $L^\infty$-Fisher information. We show that this inequality
can be sharpened significantly in situations where the involved densities are
anisotropic. Our proof is based on probabilistic techniques using Langevin
dynamics. As an application of these results, we obtain sharp exponential rates
of convergence in Fisher's infinitesimal model from quantitative genetics,
generalising recent results by Calvez, Poyato, and Santambrogio in dimension 1
to arbitrary dimensions.},
  author       = {Khudiakova, Kseniia and Maas, Jan and Pedrotti, Francesco},
  booktitle    = {arXiv},
  title        = {{L∞-optimal transport of anisotropic log-concave measures and exponential convergence in Fisher's infinitesimal model}},
  doi          = {10.48550/arXiv.2402.04151},
  year         = {2024},
}

@unpublished{14732,
  abstract     = {Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.},
  author       = {Olusanya, Oluwafunmilola O and Khudiakova, Kseniia and Sachdeva, Himani},
  booktitle    = {bioRxiv},
  title        = {{Genetic load, eco-evolutionary feedback and extinction in a metapopulation}},
  doi          = {10.1101/2023.12.02.569702},
  year         = {2023},
}