Table Of ContentInterdisciplinary Evolution Research 3
Nathalie Gontier Editor
Reticulate
Evolution
Symbiogenesis, Lateral Gene Transfer,
Hybridization and Infectious Heredity
Interdisciplinary Evolution Research
Volume 3
Series editors
Nathalie Gontier, Lisbon, Portugal
Olga Pombo, Lisbon, Portugal
About the Series
The time when only biologists studied evolution has long since passed. Accepting
evolution requires us to come to terms with the fact that everything that exists must
be the outcome of evolutionary processes. Today, a wide variety of academic dis-
ciplines are therefore confronted with evolutionary problems, ranging from phys-
ics and medicine, to linguistics, anthropology and sociology. Solving evolutionary
problems also necessitates an inter- and transdisciplinary approach, which is why
the Modern Synthesis is currently extended to include drift theory, symbiogenesis,
lateral gene transfer, hybridization, epigenetics and punctuated equilibria theory.
The series Interdisciplinary Evolution Research aims to provide a scholarly
platform for the growing demand to examine specific evolutionary problems from
the perspectives of multiple disciplines. It does not adhere to one specific academic
field, one specific school of thought, or one specific evolutionary theory. Rather,
books in the series thematically analyze how a variety of evolutionary fields and
evolutionary theories provide insights into specific, well-defined evolutionary
problems of life and the socio-cultural domain.
Editors-in-chief of the series are Nathalie Gontier and Olga Pombo. The Series is
edited from within the Applied Evolutionary Epistemology Lab, more information
on the lab is available at http://appeel.fc.ul.pt.
More information about this series at http://www.springer.com/series/13109
Nathalie Gontier
Editor
Reticulate Evolution
Symbiogenesis, Lateral Gene Transfer,
Hybridization and Infectious Heredity
1 3
Editor
Nathalie Gontier
AppEEL—Applied Evolutionary
Epistemology Lab
University of Lisbon
Lisbon
Portugal
ISSN 2199-3068 ISSN 2199-3076 (electronic)
Interdisciplinary Evolution Research
ISBN 978-3-319-16344-4 ISBN 978-3-319-16345-1 (eBook)
DOI 10.1007/978-3-319-16345-1
Library of Congress Control Number: 2015939804
Springer Cham Heidelberg New York Dordrecht London
© Springer International Publishing Switzerland 2015
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Preface and Acknowledgments
Although originally a systematic term associated with speciation by hybridiza-
tion, this book exemplifies “reticulate evolution” as it occurs by mechanisms and
processes of symbiosis, symbiogenesis, lateral gene transfer, hybridization or diver-
gence with gene flow, and infectious heredity. These phenomena are currently taking
up a prominent role in the evolutionary sciences. Almost on a daily basis, new and
fascinating data are presented that prove that evolution can result not merely from
natural selection which brings forth a vertical pattern of linear descent with modifi-
cation, but also from various types of reticulate evolution whereby evolutionary line-
ages connect, merge, and dissolve into one another.
A vast majority of these data are coming in from molecular biology, molecular
systematics, and molecular phylogenetics. These fields developed after the founda-
tion of the Modern Synthesis, and they currently enable a unification of bacteriol-
ogy, virology, medicine, cell biology, exo-, and astrobiology. Together, these fields
are building the new and fascinating research area of reticulate evolution. Many of
the means whereby reticulate evolution can occur, however, were already identi-
fied before the foundation of the Modern Synthesis. Research on hybridization
first developed in pre-evolutionary times and reaches as far back as the seventeenth
century. Symbiosis and symbiogenesis has mostly been associated with ecologi-
cal disciplines as well as with research on (a) biogenesis, developmental biology,
and cell cytology. These disciplines originated in the late nineteenth century, during
a period that has been characterized by Julian Huxley as the “eclipse of Darwin”
because the then rising fields favored non-selectionist evolutionary explanations.
Infectious heredity and the mechanisms of lateral gene transfer in prokaryotic
organisms were first identified in the beginning of the twentieth century, within the
bacterial and biomedical sciences, and today associated with virology, bacteriology,
and genetic engineering and with attempts to personalize medicine. None of these
fields belong to the classic Modern Synthesis that combined theoretical population
genetics with Mendelian hereditary laws and aspects of diverse mutation theories.
Today, scholars are therefore more and more pleading for an Extended Synthesis
that integrates these research fields and their important data into a larger and richer
theoretical framework whereby we can understand the evolution of life.
v
vi Preface and Acknowledgments
There is a general recognition that reticulate evolutionary mechanisms are stir-
ring up and overthrowing many tenets of the standard neo-Darwinian framework,
but how the new findings can become integrated with the standard paradigm, and
how a new evolutionary biology might look like, is nonetheless still very much
in the open. Natural selection, for example, is traditionally defined as a slow and
gradual process, while symbiogenesis and lateral gene transfer are argued to occur
rapidly in time. Research today is adding to the complexity, by demonstrating
that the various evolutionary mechanisms are often simultaneously active within
the various domains of life. Symbiotically acquired organelles, for example, or
ontogenetically acquired viruses, can exchange genes laterally with the nuclear
genes. Horizontally transferred genes in turn become integrated into the germ line
where they evolve via natural and sexual selection mechanisms. When both verti-
cal and reticulate mechanisms are active within the same individual or population,
then how do we define the pace(s) and mode(s) of overall evolution? At present,
we do not have the epistemic frameworks that synthesize vertical with reticulate
evolutionary theories. The mechanisms of reticulate evolution are currently (1)
awaiting synthesis into a standard reticulate evolutionary paradigm, and (2) that
paradigm in turn is awaiting integration with the classic, neo-Darwinian one.
Though knowledge on the various means by which reticulate evolution occurs
has never been so vast, a wider recognition and dissemination of these ideas
toward the public sphere as well as within and across the general evolutionary
sciences continues to lag behind. Almost all founders of the Modern Synthesis,
and many leading neo-Darwinian scholars, brought natural selection to a wider
academic and non-academic audience by publishing accessible books on their
findings. It brought forth a general recognition that, regardless of our private or
public institutional affiliations, the study of evolution by means of natural selec-
tion concerns us all and therefore needs integration in all scientific and public
domains. Whether we are biologists or not, and academics or not, reticulate evolu-
tion equally impacts how we are to understand life’s natural history, and it has a
vast array of applications in the study of human health and disease, genetic engi-
neering, or agriculture. Today, few experts unfortunately feel chosen to bring their
work outside their field-specific disciplines, and instead, they report their results
in technical journals. Field-specific handbooks that have as goal to train future
expert-scientists are equally inaccessible to non-experts because of the necessary
technical language.
The goal of this book is to provide an introduction on reticulate evolution to
scholars and students working outside the fields, but it is not an encyclopedia of
the numerous advocates. Such encyclopedias will eventually be edited by the biol-
ogists themselves. For this book, I chose to focus on the mechanisms that under-
lie reticulate evolution. Here too, choices had to be made, because there are many
ways in which reticulate evolutionary mechanisms can be explained and exempli-
fied. One can choose to provide a dictionary or glossary of new scientific jargon;
one can give a state of the art on a selection of current data; one can dive into
history and examine the original context of discovery wherein the mechanisms
were first identified and perform an epistemic, philosophical analysis on how these
Preface and Acknowledgments vii
ideas were and are received as well as what their consequences are for scientific
theory in general; one can exemplify one reticulate evolutionary mechanism by
providing examples of how it occurs within diverse lineages; or one can exemplify
the relation between the various reticulate evolutionary mechanisms by exempli-
fying how they together bring forth the evolution of one or a couple of species.
In agreement with the theme, the authors in this work have merged these various
approaches, and their works focus either on theory formation or on particular case
studies, or they either provide historical and philosophical contextualization or
introductions to the state of the art.
This book also draws the line under a one-year long project funded by the
Templeton Foundation that set out to investigate how reticulate evolutionary the-
ories, and also macroevolutionary theories, are currently expanding evolution-
ary thought and how they can be implemented into the sociocultural domain.
With the project, my collaborators, Marcia Belchior, Francisco Carrapiço, Luís
Correia, Larissa Mendoza Straffon, Marco Pina, Olga Pombo, and Emanuele
Serrelli, and I organized evolution schools for pre- and postdoctoral research
scholars that featured courses on reticulate evolution taught by Michael Arnold,
Frédéric Bouchard, Francisco Dionisio, Luis Villarreal, and Douglas Zook
(http://evolutionschool.fc.ul.pt/videos); a symposium session on how symbiogen-
esis, lateral gene transfer, and virolution extend the synthesis for the 2013 meet-
ing of the American Association for the Advancement of Science (http://appeel.
fc.ul.pt/sub/eve/dir/aaas/aaas2013.html); a public conference on evolution that fea-
tured talks for a general audience and classes for teenagers on topics of reticulate
evolution (http://evolutionconference.fc.ul.pt); and a conference on Evolutionary
Patterns: Horizontal and Vertical, Micro- and Macroevolutionary Patterns
of Biological and Sociocultural Sciences (http://evolutionarypatterns.fc.ul.pt/
videos). Along the way, we captured several video interviews with the schol-
ars involved, which can be viewed either on the respective video channels men-
tioned above, or directly on Appeel’s YouTube channel (https://www.youtube.com/
user/appeellisboa).
Many of the scholars that partook in the project and its associated events are
also featured in this volume. I am very grateful to the authors who were willing
to disseminate their and other people’s work on reticulate evolution to a larger
academic community, and I am quite confident that this book will provide an
excellent entry point to interested scholars outside the field. Cordial thanks fur-
thermore go out to Andreas Bohn, Frédéric Bouchard, Jorge Carneiro, Maurizio
Casiraghi, Claudine Chaouiya, Eveline Kolijn, Alan Cooper, Cristina Cruz, Tal
Dagan, Lee Dugatkin, Ricardo Guerrero, Frank Kressing, Paulo Madruga, William
Martin, Ana Noronha, Frank Ryan, Jan Sapp, Rosalia Vargas, Davide Vecchi, Luis
Villarreal, Tyler Volk, Richard Watson, and Slava V.I. Yukalov. Finally, my grati-
tude, as always, goes out to the entire Springer team, especially Anette Lindqvist,
Sabine Schwarz, and the team in India.
Nathalie Gontier
Contents
Reticulate Evolution Everywhere ................................. 1
Nathalie Gontier
Symbiosis—Evolution’s Co-Author ................................ 41
Douglas Zook
Can We Understand Evolution Without Symbiogenesis? .............. 81
Francisco Carrapiço
Novel Endosymbioses as a Catalyst of Fast Speciation ................ 107
Vitor G. Faria and Élio Sucena
Historical and Epistemological Perspectives on What Horizontal
Gene Transfer Mechanisms Contribute to Our Understanding
of Evolution ................................................... 121
Nathalie Gontier
Plasmids: Histories of a Concept .................................. 179
William C. Summers
Symbiosis Between Non-Transferable Plasmids and Prokaryotic Cells ... 191
Francisco Dionisio, João Alves Gama and André F.P. Carvalho
Host–Symbiont–Pathogen–Host Interactions: Wolbachia,
Vector-Transmitted Human Pathogens, and the Importance
of Quantitative Models of Multipartite Coevolution .................. 207
Caetano Souto-Maior
Evolution of the Human Microbiome and Impacts on Human Health,
Infectious Disease, and Hominid Evolution ......................... 231
Laura S. Weyrich
ix
x Contents
Divergence-with-Gene-Flow—What Humans
and Other Mammals Got up to ................................... 255
Michael L. Arnold, Amanda N. Brothers, Jennafer A.P. Hamlin,
Sunni J. Taylor and Noland H. Martin
A Multiset Model of Multi-Species Evolution
to Solve Big Deceptive Problems .................................. 297
Luís Correia and António Manso
