Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life

393 Pages·2014·8.917 MB·English

by  Pierre Pontarotti (eds.)

Pierre Pontarotti Editor
Evolutionary Biology:
Genome Evolution,
Speciation, Coevolution
and Origin of Life
Evolutionary Biology: Genome Evolution,
Speciation, Coevolution and Origin of Life
Pierre Pontarotti
Editor
Evolutionary Biology:
Genome Evolution,
Speciation, Coevolution
and Origin of Life
123
Editor
Pierre Pontarotti
CNRS, Laboratoire Évolution Biologique
etModélisation
Université d’Aix-Marseille
Marseille
France
ISBN 978-3-319-07622-5 ISBN 978-3-319-07623-2 (eBook)
DOI 10.1007/978-3-319-07623-2
Springer ChamHeidelberg New YorkDordrecht London
LibraryofCongressControlNumber:2014943947
(cid:2)SpringerInternationalPublishingSwitzerland2014
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Preface
Forthe17thtime,theEvolutionaryBiologyMeetingatMarseillestookplace.The
goalofthisannualmeetingistoallowscientistsofdifferentdisciplines,whoshare
a deep interest in evolutionary biology concepts, knowledge and applications, to
meet and exchange and enhance interdisciplinary collaborations.
The Evolutionary Biology Meeting in Marseilles is now recognised interna-
tionally as an important exchange platform and a booster for the use of evolu-
tionary-based approaches in biology and also in other scientific areas.
This year more than 100 presentations were selected by the evolutionary
biology meeting scientific committee. We have further selected 18 of the most
representative ones for the book.
The book will give the reader an overview of the state of the art in the evo-
lutionary biology field. The book is the seventh that we have published further to
themeeting.Iwouldliketounderlinethatthesevenbooksarecomplementaryone
to another and should be considered as tomes.
Thereaderoftheevolutionarybiologybooksaswellasthemeetingparticipants
would maybe like me witness years after years during the different meetings and
book editions a shift in the evolutionary biology concepts as for example the
possibilityofHGTinmetazoan.Thefactthatthechaptersofthebookareselected
from a meeting enables the quick diffusion of the novelties.
Concerning the book, the chapters are organised in the following parts:
Molecular and Genome Evolution (Chaps. 1–10)
Phylogeography, Speciation and Coevolution (Chaps. 11–17)
Exobiology and Origin of Life (Chap. 18)
Iwouldliketothankalltheauthors,themeetingparticipants,thesponsors:Aix
MarseilleUniversité,CNRS,ITMO,ECCOREVFEDERATION,ConseilGénéral
13, Ville de Marseille.
I also wish to thank Springer’s edition staff and in particular Andrea Schlitz-
berger for her competence and help.
I wish also to thank members of the Association pour l’Etude de l’Evolution
Biologique(AEEB)andthemembersoftheAixMarseilleUniversityfortheirhelp
in the meeting organisation.
v
vi Preface
Finally,IthanktheAEEBmanager:MarieHélèneRomefortheorganisationof
the 17th Evolutionary Biology Meeting and her help with the book.
Marseille, France, April 2014 Pierre Pontarotti
Contents
Part I Molecular and Genome Evolution
1 Comparative Biochemistry and Evolution
of Milk Oligosaccharides of Monotremes, Marsupials,
and Eutherians. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Tadasu Urashima, Michael Messer and Olav T. Oftedal
2 Genomics-Based Insights into the Evolution of Secondary
Metabolite Biosynthesis in Actinomycete Bacteria . . . . . . . . . . . . 35
Sergey B. Zotchev
3 A Preliminary Transcriptomic Study of Galaxiid Fishes
Reveals a Larval Glycoprotein Gene Under Strong Positive
Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Graham P. Wallis and Lise J. Wallis
4 Land Bridge Calibration of Rates of Molecular Evolution
in a Widespread Rodent. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
J. S. Herman, J. Paupério, P. C. Alves and J. B. Searle
5 Polyploid Speciation and Genome Evolution: Lessons
from Recent Allopolyploids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Malika L. Ainouche and Jonathan F. Wendel
6 Evolutionary Divergence in Human Versus Mouse Innate
Immune Gene Regulation and Function . . . . . . . . . . . . . . . . . . . 115
Ronan Kapetanovic, Juliana K. Ariffin and Matthew J. Sweet
7 Evolutionary Genomics of Miniature Inverted-Repeat
Transposable Elements (MITEs) in Plants. . . . . . . . . . . . . . . . . . 157
Jiongjiong Chen, Qun Hu, Chen Lu and Hanhui Kuang
vii
viii Contents
8 Horizontal Gene Transfer and the Role
of Restriction-Modification Systems in Bacterial
Population Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
George Vernikos and Duccio Medini
9 Quartet Partitioning Reveals Hybrid Origins
of the Vertebrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Michael Syvanen, Bryan Ericksen, Simone Linz
and Jonathan Ducore
10 Evidence for Ancient Horizontal Gene Acquisitions
in Bdelloid Rotifers of the Genus Adineta . . . . . . . . . . . . . . . . . . 207
Boris Hespeels, Jean-François Flot, Alessandro Derzelle
and Karine Van Doninck
Part II Phylogeography, Speciation and Coevolution
11 Evolutionary History of Maternal Plant-Manipulation
and Larval Feeding Behaviours in Attelabidae
(Coleoptera; Curculionoidea) and Evolution of Plant-Basal
Weevil Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Chisato Kobayashi, Yudai Okuyama, Kazuhide Kawazoe,
Masakado Kawata and Makoto Kato
12 Microevolution of Insect–Bacterial Mutualists:
A Population Genomics Perspective . . . . . . . . . . . . . . . . . . . . . . 247
Amanda M. V. Brown
13 Why Did Terrestrial Insect Diversity Not Increase
During the Angiosperm Radiation? Mid-Mesozoic,
Plant-Associated Insect Lineages Harbor Clues. . . . . . . . . . . . . . 261
Conrad Labandeira
14 The Evolution and Pollination of Oceanic Bellflowers
(Campanulaceae) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
Marisa Alarcón, Juan José Aldasoro, Cristina Roquet
and Jens M. Olesen
15 In Search of Phylogeographic Patterns in the Northeastern
Atlantic and Adjacent Seas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Sara M. Francisco, Joana I. Robalo, André Levy
and Vítor C. Almada
Contents ix
16 The Evolutionary Space Model to be Used
for the Metagenomic Analysis of Molecular
and Adaptive Evolution in the Bacterial Communities. . . . . . . . . 339
E. V. Pershina, A. S. Dolnik, G. S. Tamazyan, K. V. Vyatkina,
Y. B. Porozov, A. G. Pinaev, S. O. Karimov, N. A. Provorov
and E. E. Andronov
17 Topopatric Speciation: From Simulations to Theory . . . . . . . . . . 357
David M. Schneider
Part III Exobiology and Origin of Life
18 A Trip Through Chemical Space: Why Life Has Evolved
the Chemistry That It Has . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
William Bains
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395
Part I
Molecular and Genome Evolution