Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

AH Chan, PA Jenkins, YS Song - PLoS genetics, 2012 - journals.plos.org
Estimating fine-scale recombination maps of Drosophila from population genomic data is a
challenging problem, in particular because of the high background recombination rate. In …

Two-locus likelihoods under variable population size and fine-scale recombination rate estimation

JA Kamm, JP Spence, J Chan, YS Song - Genetics, 2016 - academic.oup.com
Two-locus sampling probabilities have played a central role in devising an efficient
composite-likelihood method for estimating fine-scale recombination rates. Due to …

Inferring demographic history using two-locus statistics

AP Ragsdale, RN Gutenkunst - Genetics, 2017 - academic.oup.com
Population demographic history may be learned from contemporary genetic variation data.
Methods based on aggregating the statistics of many single loci into an allele frequency …

A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination

JS Paul, YS Song - Genetics, 2010 - academic.oup.com
The multilocus conditional sampling distribution (CSD) describes the probability that an
additionally sampled DNA sequence is of a certain type, given that a collection of sequences …

[HTML][HTML] Recoverability of ancestral recombination graph topologies

E Hayman, A Ignatieva, J Hein - Theoretical Population Biology, 2023 - Elsevier
Recombination is a powerful evolutionary process that shapes the genetic diversity
observed in the populations of many species. Reconstructing genealogies in the presence …

Sampling probabilities, diffusions, ancestral graphs, and duality under strong selection

M Favero, PA Jenkins - arXiv preprint arXiv:2312.17406, 2023 - arxiv.org
Wright-Fisher diffusions and their dual ancestral graphs occupy a central role in the study of
allele frequency change and genealogical structure, and they provide expressions, explicit …

Closed-form asymptotic sampling distributions under the coalescent with recombination for an arbitrary number of loci

A Bhaskar, YS Song - Advances in Applied Probability, 2012 - cambridge.org
Obtaining a closed-form sampling distribution for the coalescent with recombination is a
challenging problem. In the case of two loci, a new framework based on an asymptotic …

A coalescent dual process for a Wright–Fisher diffusion with recombination and its application to haplotype partitioning

RC Griffiths, PA Jenkins, S Lessard - Theoretical population biology, 2016 - Elsevier
Duality plays an important role in population genetics. It can relate results from forwards-in-
time models of allele frequency evolution with those of backwards-in-time genealogical …

[HTML][HTML] An asymptotic sampling formula for the coalescent with recombination

PA Jenkins, YS Song - The annals of applied probability: an official …, 2010 - ncbi.nlm.nih.gov
Ewens sampling formula (ESF) is a one-parameter family of probability distributions with a
number of intriguing combinatorial connections. This elegant closed-form formula first arose …

Tractable diffusion and coalescent processes for weakly correlated loci

PA Jenkins, P Fearnhead… - Electronic journal of …, 2016 - pmc.ncbi.nlm.nih.gov
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual,
Kingman's coalescent. Each has a multilocus extension but under neither extension is the …