---
res:
bibo_abstract:
- The inference of demographic history from genome data is hindered by a lack of
efficient computational approaches. In particular, it has proved difficult to
exploit the information contained in the distribution of genealogies across the
genome. We have previously shown that the generating function (GF) of genealogies
can be used to analytically compute likelihoods of demographic models from configurations
of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
a simple, recursive form, the size of such likelihood calculations explodes quickly
with the number of individuals and applications of this framework have so far
been mainly limited to small samples (pairs and triplets) for which the GF can
be written by hand. Here we investigate several strategies for exploiting the
inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
can be decomposed into a set of equivalence classes that allows likelihood calculations
from nontrivial samples. Using this strategy, we automated blockwise likelihood
calculations for a general set of demographic scenarios in Mathematica. These
histories may involve population size changes, continuous migration, discrete
divergence, and admixture between multiple populations. To give a concrete example,
we calculate the likelihood for a model of isolation with migration (IM), assuming
two diploid samples without phase and outgroup information. We demonstrate the
new inference scheme with an analysis of two individual butterfly genomes from
the sister species Heliconius melpomene rosina and H. cydno.@eng
bibo_authorlist:
- foaf_Person:
foaf_givenName: Konrad
foaf_name: Lohse, Konrad
foaf_surname: Lohse
- foaf_Person:
foaf_givenName: Martin
foaf_name: Chmelik, Martin
foaf_surname: Chmelik
foaf_workInfoHomepage: http://www.librecat.org/personId=3624234E-F248-11E8-B48F-1D18A9856A87
- foaf_Person:
foaf_givenName: Simon
foaf_name: Martin, Simon
foaf_surname: Martin
- 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.115.183814
bibo_issue: '2'
bibo_volume: 202
dct_date: 2016^xs_gYear
dct_language: eng
dct_publisher: Genetics Society of America@
dct_title: Efficient strategies for calculating blockwise likelihoods under the
coalescent@
...