---
res:
bibo_abstract:
- 'Analysis of genomic data requires an efficient way to calculate likelihoods across
very large numbers of loci. We describe a general method for finding the distribution
of genealogies: we allow migration between demes, splitting of demes [as in the
isolation-with-migration (IM) model], and recombination between linked loci. These
processes are described by a set of linear recursions for the generating function
of branch lengths. Under the infinite-sites model, the probability of any configuration
of mutations can be found by differentiating this generating function. Such calculations
are feasible for small numbers of sampled genomes: as an example, we show how
the generating function can be derived explicitly for three genes under the two-deme
IM model. This derivation is done automatically, using Mathematica. Given data
from a large number of unlinked and nonrecombining blocks of sequence, these results
can be used to find maximum-likelihood estimates of model parameters by tabulating
the probabilities of all relevant mutational configurations and then multiplying
across loci. The feasibility of the method is demonstrated by applying it to simulated
data and to a data set previously analyzed by Wang and Hey (2010) consisting of
26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results
suggest that such likelihood calculations are scalable to genomic data as long
as the numbers of sampled individuals and mutations per sequence block are small.@eng'
bibo_authorlist:
- foaf_Person:
foaf_givenName: Konrad
foaf_name: Lohse, Konrad
foaf_surname: Lohse
- foaf_Person:
foaf_givenName: Richard
foaf_name: Harrison, Richard
foaf_surname: Harrison
- foaf_Person:
foaf_givenName: Nicholas H
foaf_name: Barton, Nicholas H
foaf_surname: Barton
foaf_workInfoHomepage: http://www.librecat.org/personId=4880FE40-F248-11E8-B48F-1D18A9856A87
orcid: 0000-0002-8548-5240
bibo_doi: 10.1534/genetics.111.129569
bibo_issue: '3'
bibo_volume: 189
dct_date: 2011^xs_gYear
dct_language: eng
dct_publisher: Genetics Society of America@
dct_title: A general method for calculating likelihoods under the coalescent process@
...