Natural Selection: Methods and Applications

274 Pages·2014·4.812 MB·English

by  Mario A. Fares

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NATURAL SELECTION
Methods and Applications

NATURAL SELECTION
Methods and Applications
Mario A. Fares
School of Genetics and Microbiology
Department of Genetics
University of Dublin
Trinity College, Dublin, Ireland
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A SCIENCE PUBLISHERS BOOK
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Dedication
To my parents Kamel and Teresa,
to my daughter Lucia

Preface
Since the discovery of the main principles of Natural
Selection by Charles Darwin, researchers have been
pursuing the identifi cation of the mechanisms that regulate
organism’s adaptations. It took an extraordinary sense
of observation by Darwin and 150 years of research to
realize about two of the main principles characterizing
natural selection: the slow pace at which new adaptations
emerge and that adaptive evolution, that is the emergence
and fi xation of new traits improving organism’s fi tness, is
subtle and many times impossible to spot. The principles
emerging from the study of natural selection have
fascinated evolutionary biologists for over a century. The
fi ngerprints of this force of adaptation has been sought
by many and the existence of a designing hand behind
it has been dismissed by the evolutionary morphological
“monstrosities” emerging in nature. Another leap in the
understanding of natural selection was made by the use
of molecular data emerging from the sequencing of genes
and the realization that mutations in protein-coding genes
are of stochastic nature and that only those with neutral
effects on protein’s function survive in the genome. Kimura
formalized in a mathematically elegant manner how
important neutral mutations are in the generation of genetic
variability. Today we know that such genetic variability is
a reservoir of possible future adaptations as many variants
can be enriched in the population to a point so that when
combined in a single genome can lead to novel adaptations.
Natural Selection: Methods and Applications
The neutral theory that rests on the importance of neutral
mutations in the generation of genetic variability has led
to a better understanding of the complexities of natural
selection. Such complexities comprise more than two
types of mutations: Neutral mutations, adaptive changes,
and those mutations that are neutral but bear potential
for novel adaptations (also known as exaptations). This
intermingled nature of natural selection has made it diffi cult
to disentangle neutral evolution signatures from those
leading to adaptations.
In recent years, a plethora of genomes have been
sequenced and new genomes are being released at an
unprecedented pace. In addition to this, protein structures
are enriching our databases and a bewildering set of network
analyses are being performed at many different complexity
levels, including protein-protein interactions, metabolic
reactions, transcriptomics, etc. Integrating this information
to infer the signatures of natural selection requires highly
sensitive, fast, and accurate methods and computational
tools to deal with the burst of data, together with an
absolute understanding of how natural selection works.
Unfortunately, finding evidence of adaptive evolution
remains a diffi cult task as methods to deal with data and
the models to reproduce the most important parameters
governing the action of natural selection are in their infancy.
Despite limitations, currently it is imperative to have a
complete understanding of the models and methods to read
the history of genes and organisms.
Chapters that guide us into the methods designed
for the identifi cation of natural selection form this book.
It is divided into 9 chapters. The fi rst chapter is a brief
introduction to the importance of identifying natural
selection and how can signatures of natural selection be
found taking into account that distribution of individual’s
viii
Preface
fi tness effects in a fi tness landscape. Basic concepts on genes’
structure, mutations and nucleotide and codon biases are
given in the second chapter. These concepts are important
for later understanding the ways in which deviations
from such structures can help identifying signatures of
adaptive evolution. In particular, mutation and nucleotide
bias is brought forward as two main parameters in helping
to unearth signatures of selection. The basic models of
molecular evolution are described in the third chapter.
Statistical ways to compare the goodness-of-fit of the
models to the data given certain hypothesis are also
detailed. Brushstrokes on the neutral theory of molecular
evolution are provided in the fourth chapter. In this chapter,
we also distinguish two levels of sequence analysis: inter-
species and intra-population. The link between natural
selection and the origination of novel functions is given in
Chapter 5. Indeed, we show that divergence at the amino
acid sequence level can lead to functional divergence, often
leaving phylogenetic patterned fi ngerprints. Two methods
of functional divergence are discussed in this chapter, one
based on a maximum-likelihood framework and another
based on a non-parametric approach. Chapter six calls to
caution in the application of methods to identify natural
selection as methods should account for recombination,
which could have important biasing effects in the
estimations of the parameters of selection. Once methods
to identify natural selection have been examined, chapter
seven puts forward the factors that infl uence the rate of
evolution of protein-coding genes. Plausible hypotheses are
presented in this chapter to explain the variation of protein’s
evolutionary rate. Selective pressures in the context of
molecular networks are presented in Chapter 8. Finally,
how do mutations interact and the consequences of these
interactions in the emergence of adaptations at the molecular
level are discussed and exemplifi ed in Chapter 9.
ix