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Christoph Bleidorn
Phylo-
genomics
An Introduction
Phylogenomics
Christoph Bleidorn
Phylogenomics
An Introduction
Christoph Bleidorn
Museo Nacional de Ciencias Naturales
Spanish National Research Council (CSIC)
Madrid
Spain
ISBN 978-3-319-54062-7
ISBN 978-3-319-54064-1
DOI 10.1007/978-3-319-54064-1
Library of Congress Control Number: 2017942964
(eBook)
© Springer International Publishing AG 2017
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of
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tion, broadcasting, reproduction on microfilms or in any other physical way, and transmission or infor-
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V
Preface
All life on earth shares a common ancestor, and the aim of phylogenetic systematics is
to reconstruct the tree or network of life. Shortly after the availability of the first pro-
tein sequences, molecular phylogenetic approaches were developed to understand the
evolutionary relationships between proteins (or genes). It became clear that gene trees
will also help to unravel the phylogeny of species. The introduction of Sanger sequenc-
ing and polymerase chain reaction (PCR) paved the way that genetic approaches
became available across the scientific community and contributed to the rise of molec-
ular phylogenetics. At the end of the 1990s, results from single-gene studies challenged
the century-old textbook view of evolutionary relationships of many groups (e.g. ani-
mals, plants). Fierce discussions regarding the validity of these results led to important
methodological advances, and, nowadays, molecular phylogenies are broadly accepted
to represent organismal relationships in textbooks. In the mid-2000s, the way of
sequencing has been revolutionized, leading to a huge drop in its costs, and unprece-
dented amounts of sequence data became affordable for every type of study and also
for non-model organisms. This development transformed the field of molecular phy-
logenetics to phylogenomics, where genome-scale data (genomes, transcriptomes) can
be exploited. The term phylogenomics was already coined in 1998 by Jonathan Eisen
(also known under his twitter handle @phylogenomics), who outlined the importance
of phylogenetic methods for the annotation of genes without relying on direct (time
consuming) functional studies. This underlines how deeply embedded phylogenetic
methods are in the field of genomics. The theoretical background for reconstructing
gene trees (functional annotations) and species trees (reconstruction of the tree of life)
is broadly overlapping. In this book I will introduce the major steps of phylogenomic
analyses in general. The first two chapters briefly introduce the field of genomics
(
7
Chap.
1
, «Genomes») and the evolution and peculiarities of organellar genomes
(
7
Chap.
2
, «Organellar Genomes and Endosymbionts»). In
7
Chap.
3
(«Sequencing
Techniques»), I review the most widely used sequencing platforms, which is difficult
in a print format, as the field advances so fast that many numbers describing the output
of these machines might be already out of date when you read this chapter.
7
Chapter
4
(«Sequencing Strategies») gives an overview of different strategies to sequence com-
plete or partial genomes and transcriptomes. The outputs of every sequencing plat-
form are sequences which are considerably shorter than chromosomes and in the case
of short-read sequencing also shorter than most genes. In
7
Chap.
5
(«Assembly and
Data Quality»), ways to puzzle these small pieces into more complete representations
of genomes and genes (called assembly) are introduced. Fundamental steps for every
phylogenomic study are alignments, read mapping and finding homologous genes,
which are explained in
7
Chaps.
6
(«Alignment and Mapping») and
7
(«Finding
Genes»). Based on a sequence alignment, it is possible to reconstruct phylogenetic
trees, and the methods are briefly reviewed in
7
Chap.
8
(«Phylogenetic Analyses»). I
kept this chapter on purpose rather brief, as many excellent textbooks describing these
methods (and its underlying algorithms) in detail are available (see references in
7
Chap.
8
). Moreover, the basic theory underlying these methods did not change much
in the last decade. Surprisingly, even with this vast amount of data, many phylogenetic

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