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@INCOLLECTION{WangSchiffels2020,
title = "{MSMC} and {MSMC2}: The Multiple Sequentially Markovian
Coalescent",
booktitle = "Statistical Population Genomics",
author = "Schiffels, Stephan and Wang, Ke",
editor = "Dutheil, Julien Y",
abstract = "The Multiple Sequentially Markovian Coalescent (MSMC) is a
population genetic method and software for inferring demographic
history and population structure through time from genome
sequences. Here we describe the main program MSMC and its
successor MSMC2. We go through all the necessary steps of
processing genomic data from BAM files all the way to generating
plots of inferred population size and separation histories. Some
background on the methodology itself is provided, as well as
bash scripts and python source code to run the necessary
programs. The reader is also referred to community resources
such as a mailing list and github repositories for further
advice.",
publisher = "Springer US",
volume = 2090,
pages = "147--166",
series = "Methods in Molecular Biology",
month = "24~" # jan,
year = 2020,
url = "http://link.springer.com/10.1007/978-1-0716-0199-0_7",
annote = "pdf=https://link.springer.com/content/pdf/10.1007\%2F978-1-0716-0199-0\_7.pdf",
file = "All Papers/S/Schiffels and Wang 2020 - MSMC and MSMC2 - The Multiple Sequentially Markovian Coalescent.pdf",
address = "New York, NY",
keywords = "Coalescent modelling; Complete genome sequencing; Demographic
inference; Phasing; Population structure; role\_lead",
language = "en",
issn = "1064-3745, 1940-6029",
isbn = "9781071601983, 9781071601990",
pmid = "31975167",
doi = "10.1007/978-1-0716-0199-0\_7"
}
@ARTICLE{SchiffelsDurbin2014,
title = "Inferring human population size and separation history from
multiple genome sequences",
author = "Schiffels, Stephan and Durbin, Richard",
abstract = "The availability of complete human genome sequences from
populations across the world has given rise to new population
genetic inference methods that explicitly model ancestral
relationships under recombination and mutation. So far,
application of these methods to evolutionary history more recent
than 20,000-30,000 years ago and to population separations has
been limited. Here we present a new method that overcomes these
shortcomings. The multiple sequentially Markovian coalescent
(MSMC) analyzes the observed pattern of mutations in multiple
individuals, focusing on the first coalescence between any two
individuals. Results from applying MSMC to genome sequences from
nine populations across the world suggest that the genetic
separation of non-African ancestors from African Yoruban
ancestors started long before 50,000 years ago and give
information about human population history as recent as 2,000
years ago, including the bottleneck in the peopling of the
Americas and separations within Africa, East Asia and Europe.",
journal = "Nature Genetics",
publisher = "Nature Publishing Group",
volume = 46,
number = 8,
pages = "919--925",
month = "1~" # aug,
year = 2014,
url = "http://www.nature.com/doifinder/10.1038/ng.3015",
file = "All Papers/S/Schiffels and Durbin 2014 - Inferring human population size and separation history from multiple genome sequences.pdf;All Papers/S/Schiffels and Durbin 2014 - Schiffels and Durbin 2014 - SI.pdf",
issn = "1061-4036"
}
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address={New York, NY},
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