Molecular Evolution and Population Genetics for Marine Biologists

363 Pages·2015·15.52 MB·English

by  Kartavtsev, Yuri

Molecular Evolution and
Population Genetics for
Marine Biologists
© 2016 by Taylor & Francis Group, LLC
© 2016 by Taylor & Francis Group, LLC
Molecular Evolution and
Population Genetics for
Marine Biologists
Yuri Ph. Kartavtsev
A.V. Zhirmunsky Institute of Marine Biology
Far Eastern Branch of Russian Academy of Sciences; Far Eastern Federal
University
Vladivostok
Russia
Edited by
M.S. Johnson
The University of Western Australia
Crawley
Perth

p,
A SCIENCE PUBLISHERS BOOK
© 2016 by Taylor & Francis Group, LLC
GL--Prelims with new title page.indd ii 4/25/2012 9:52:40 AM
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© 2016 by Taylor & Francis Group, LLC
PREFACE
This course originated from more than 40 years of personal research experience in the
Population, Evolutionary, and Ecological Genetics of marine fi sh and shellfi sh along
with teaching of upper division students at the Far Eastern Federal University in Russia
(Vladivostok) and at two national universities in Republic of Korea: Korea Maritime
University (Busan) and Chungbuk National University (Cheongju), i.e., more than
30 years in Russia and two years in Korea. In recent years the course was adapted
for students’ convenience to modern computer and web-net technologies, including
MS Power-Point mode for lecture presentations, usage of different software, such as
POPULUS, MEGA, BYOSIS, NTSYS, GENEPOP, ARLEQUIN, STATISTICA etc. for
training courses (with numerical simulations and statistical analysis), and the website
support for both. So, the lectures and training courses have a modern shape, and are
easily updated each term. The lectures are normally given in a fl uent verbal mode, and
they are accompanied with questions to the audience, giving the students exact tasks
to solve examples, and fi nd solutions through special classroom sessions, seminars
and preparing the abstracts. Each lecture is accompanied by a training section, where
new terms are summarized and explained. In the book all these sections are combined
in a special appendix. There is also an appendix in which methodical instruction for
learning of the course, literature sources, and exam questions are given.
Originally each lecture presentation together with the training task was
accompanied with the written text. These materials now form the foundation of the
current textbook. The book contains 16 chapters, which are the foundation of the course.

The material is given in accordance to its complexity, giving readers the opportunity to
remember the basic genetic knowledge and later develop these skills within specialized
fi elds and specifi c problems in immunogenetics, biochemical genetics, molecular
genetics, general biology, ecology, evolution and speciation.
It is assumed that a student has basic comprehension of general genetics. That
is why only two themes are devoted to basics of genetics: Material basis of genetics
(Chapter 2) and Translation of genetic information (Chapter 3). Basic knowledge in
genetics is partly covered in the other chapters. In particular, details of the genetic
code and mutations, which have direct connection to the course, are given. Also,
such questions as gene transcription, splicing, gene origin and several other notions
are considered to a certain extent. The book is oriented not only towards students but
may be of interest to a wider audience of specialists who are interested in genetics,
population ecology, taxonomy and speciation.
© 2016 by Taylor & Francis Group, LLC
vi Molecular Evolution and Population Genetics for Marine Biologists
The author is cordially thankful to those who inspired the book, Olga Koren and
Alla Kholina, suggested publication as an integrated material after attending the course.
My special warm thanks to the editors of the fi rst, and second editions in Russian,
Drs. Irina Kartavtseva and Olga Koren. I am also pleased to cordially thanks the fi rst
readers of the English version of the book, Dr. Cynthia Riginos, who proofread several
beginning chapters, and Elena Cogan, who helped with editing of some chapters’
summaries, table headings and fi gure captions.

© 2016 by Taylor & Francis Group, LLC
ACKNOWLEDGEMENTS
The preparation of this book has been possible through the funding provided to the
author by the A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of
Russian Academy of Sciences and Far Eastern Federal University (Vladivostok) where
the author works. That is the reason the author shares part of intellectual property with
the listed institutions. The author also gratefully acknowledges the fi nancial support
received from the Russian Science Foundation (grant #14-50-00034 Molecular
Phylogenetics and Biodiversity), and in part from the Russian Foundation for Basic
Research (grant #15-29-02456 Application to DNA Barcoding, Population Genetics
and Gene Introgression between Species). Editorial help provided by Dr. M. Johnson
is gratefully acknowledged.

© 2016 by Taylor & Francis Group, LLC
© 2016 by Taylor & Francis Group, LLC
INTRODUCTION
Population genetics and molecular evolutions may seem too dissimilar themes to be
united in a single book. However, that is not so. Modern experimental and theoretical
population genetics got great impulse from the development of molecular methods
for the analysis of genetic variability. On the other hand, investigation of divergence
of organisms over time or evolution at the molecular level is unimaginable without
understanding the fundamental genetic properties of organisms themselves and their
groups, which comprise in nature such reproductive units as local populations and
biological species.
Population dynamics in time cannot be separated from spatial dynamics, from
understanding the basics of intraspecifi c genetic variability and differentiation.
Carried away by the vast abilities of molecular phylogenetic analysis of sequences
of deoxy ribonucleic acid (DNA), some authors even completely refuse the necessity
of spatial diversity analysis, contra-positioning the phylogenetic species concept to
the biological species concept. However, many geneticists do not hold such extreme
views, understanding the unity of mechanisms of intra- and interspecifi c divergence
(Altukhov 1983; 1989; Ayala 1984; Nei 1987; Avise and Wollenberg 1997). These
questions as well as many others are considered in the current book in quite a popular
form, presenting information to the student audience and a wide range of non-expert
readers. At the same time, the majority of the book chapters are short assignments
that may be interesting to the experts in certain fi elds. The author of this textbook is a
marine biologist. This peculiarity places its own perspective on the content, relating
many examples to the marine realm, particularly by using fi sh and shellfi sh data; the

latter led to the title of the book.
Chapter 1 is devoted to the history of the Earth, organic evolution and the origin
of life, while ending the book, Chapter 16 is about the evolution of the genome. The
basics of genetic knowledge are repeated in Chapters 2 and 3. Intense research on
the molecular basis of evolution is introduced by developing a broad introduction to
the relevant biological methods, fi rstly immunogenetic, then biochemical genetics,
and fi nally molecular genetic methods of analysis of different macromolecules.
Immunogenetic methods developed in the mid 20th century, and entered evolutionary
genetics by quantifying genetic divergence by microcomplement fi xation of purifi ed
protein. The protein used for this reaction is serum albumin. In connection with this,
the main concepts of immunity and immunogenetics are given; also, some materials
on population genetic and molecular phylogenetic analysis of certain groups of
organisms are presented (Chapter 4). Biochemical genetics (Chapter 5) in the mid
© 2016 by Taylor & Francis Group, LLC
x Molecular Evolution and Population Genetics for Marine Biologists
1960s became an experimental base for modern population genetics of natural stocks.
Proteins as a rule are enzymes, and are used as gene markers even today. They are
competitive to more modern DNA markers by their ability to be used in vast population
analysis and low cost. Databases that gathered in this fi eld, which fi rst of all included
heterozygosity and distance/similarity records, have reasonable signifi cance even now
for comparative analysis of genetic variability and divergence that is very important
for evolutionary, ecological and population genetics. In particular, in their relationship
to protein variability many issues are considered regarding mutations (Chapter 6),
genetic aspects of speciation (Chapter 7), population genetic structure of the species
(Chapter 8), analysis of genetic diversity within the species (Chapter 9), hybridization
and genetic introgression in nature (Chapter 10), heterosis and its connection with
heterozygosity, as well as interrelationships of heterozygosity vs. quantitative traits
in general (Chapter 12). Quantitative traits and their inheritance are also considered
in a separate chapter (Chapter 11).
With deciphering of the molecular essence of genes, it appeared self-evident
that evolutionary relationships of organisms could be investigated by means of
comparison of nucleotide sequences of DNA or amino acids in protein chains,
which are encoded by DNA. DNA polymorphism within and between populations is
considered in two consecutive chapters (Chapters 13–14). The boom that was created
by vast opportunities of analysis of divergence in different phyletic lines and taxa of
organisms on the base of nucleotide sequences in genes gave rise to a new frontier in
evolutionary biology, molecular phylogenetics. Its birth and development gave not
only solutions for many hot questions of evolution of the organic world, but have
demanded as well the development of new methods of mathematical analysis and
software production. This book is not specially addressed to molecular phylogenetics;
nevertheless a signifi cant portion of the text is devoted to this fi eld. To address it,
the rate of mutation, DNA diversity and tree building methodology are considered.
There is special chapter devoted to practical analysis of sequences of nucleotides (also
applicable to proteins) and software needed for their editing, submission to gene banks,
estimation of models of substitutions and fi nally gene tree building (Chapter 15). The
textbook is equipped with several supplements, which allow the student to get themes
and questions for seminars, fi nd a list of questions for the exam, learn terms and solve

tasks during special training courses developed for each chapter.
© 2016 by Taylor & Francis Group, LLC