Evoluzione orizzontale e ontologia biologica

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Evoluzione orizzontale e ontologia biologica
Emanuele Serrelli
Padova, 8-9 maggio 2012
emanuele.serrelli@unimib.it
http://www.epistemologia.eu

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Selves
Groups
Earth
Chimeras
Consciousness

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. . .the “selves” of viruses, utterly depend on their
physical contact with bacterial or other living cells. If
not connected to a cell, a virus is as inert as a lump of
salt or a cube of sugar. The basic element of life, the
self, is the sensitive bacterial cell; but a virus, as a
courier and an integrator of genes into bacteria and
nucleated organisms (animals, plants, fungi and
proctotists), can be very important to speciﬁc
evolutionary trajectories.
(William Day, ch. 2, p. 17)
Selves
http://jonlieffmd.com/blog/are-viruses-alive-are-viruses-sentient-virus-intelligence

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Selves
http://microbes.nres.uiuc.edu/NRES512.htm
Rymer et al. (2012)

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Selves

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Groups
Ben Jacob et al. (2004)

Groups
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Murray Bowen photo by Andrea Maloney Schara (1979)
http://ideastoaction.wordpress.com/2012/08/29/murray-bowen/

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Chimeras
Chimera di Arezzo, Museo Archeologico, Firenze

Chimeras
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Vad Drisse (2011)
Margulis et al. (2006)

Chimeras
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Invertebrates...
http://in2uract.wordpress.com/2011/11/24/
strengthening-your-immune-system/

Chimeras
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Alves et al.
Lemur
Family: Galagidae
http://collections.burkemuseum.org/mtm/
images/mtm_slideshows/
3027712362_de1ae16a96_o.jpg

Chimeras
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http://neurosciencefundamentals.unsw.wikispaces.net/The+Neurons+that+Shaped+Our+World
http://www.ted.com/talks/vs_ramachandran_the_neurons_that_shaped_civilization.html

Consciousness
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Lemur
Family: Galagidae
http://collections.burkemuseum.org/mtm/
images/mtm_slideshows/
3027712362_de1ae16a96_o.jpg
George Mobus
http://faculty.washington.edu/gmobus/
Background/evolutionsTrajectory.html

Consciousness
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http://thecampbellgrp.com/glonal-network/

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Selves
Groups
Earth
Chimeras
Consciousness

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http://evolutionschool.fc.ul.pt

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For there is, after all, one true tree of life, the
unique pattern of evolutionary branchings that
actually happened. It exists. It is in principle
knowable. We don’t know it all yet. By 2050 we
should—or if we do not, we shall have been
defeated only at the terminal twigs, by the sheer
number of species. ... [H]undreds of separate
genes ... are found to corroborate each other’s
accounts of the one true tree of life (Dawkins
2003, p. 112; see also Eldredge 2005, p. 227).

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http://edge.org/conversation/lynn-margulis1938-2011

SET - Serial Endosymbiosis Theory for the origin of
eukaryotic cells
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http://img.scoop.co.nz/stories/images/0903/
a8de5c88b14851860daa.jpeg
Image courtesy of Lynn Margulis

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http://img.scoop.co.nz/stories/images/0903/a8de5c88b14851860daa.jpeg

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Virolution at the pro- and eukaryotic level
Villarreal & Ryan

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1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on 2004

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W. Ford Doolittle
1957
In the case of higher plants and animals, species can
be grouped into genera, families, and orders on the
basis of their evolutionary relationships, or phylogeny.
Such classifications are called natural classifications. In
the bacteria, however, only a few broad lines of
evolution are dimly perceivable, and the finer details of
phylogeny remain completely obscure. The existing
semiofficial classification of bacteria, Bergey’s Manual,
is thus an arbitrary one, and is useful only to the limited
extent that it serves as a ‘‘key’’ for identification.
(Steiner et al. 1957)
Phylogeny of bacteria

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W. Ford Doolittle
1957
Molecular phylogen.
phylogenies based on the sequences of ‘‘informational
macromolecules’’ are not only more unambiguously
quantiﬁable but closer to what it is that actually evolves
—genes and the genome.
...extend the universal Tree of Life downward to its
deepest roots among the prokaryotes

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
Lateral, Horizontal gene transfer at the prokaryotic level:
gene donations of bacteria: e.g. resistance of bacteria against
antibiotics

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
Lateral, Horizontal gene transfer at the prokaryotic level:
gene donations of bacteria: e.g. resistance of bacteria against
antibiotics
...microbiologists had uncovered a phenomenon that
might have given them cause to worry that the
evolution of genes might not always be tree-like, and
that gene trees might not always be species trees.

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
Why few of us thought that LGT would
interfere seriously with universal tree
construction is an interesting question for
the historian and sociologist...

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
In the extreme, interspecies
exchanges of genes could be
so rampant, so broadspread,
that a bacterium would not
actually have a history in its
own right; it would be an
evolutionary chimera, a
collection of genes (or gene
clusters), each with its own
history...

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
Fortunately the matter is
experimentally decidable.
Were an organism an
evolutionary chimera, then its
various chronometers would
yield different, conﬂicting
phylogenies.

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on
Assessing how many of a genomes’ genes
have been laterally transferred at some time in
its history will always be technically difﬁcult and
fraught with deﬁnitional problems, although few
would now claim that the fraction is less than
one half, and many would accept that it is more
than 95%. It turns out to be simpler to ask how
many and which genes might possibly have
avoided LGT in the last four billion years.

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on

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W. Ford Doolittle
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on

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Network diagrams
combines both horizontal and vertical evolutionary events in prokaryotes
Dagan and Martin, 2009: 2190

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Margulis
Symbiogenesis
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on

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Margulis
Symbiogenesis
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on

Symbiogenesis
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http://img.scoop.co.nz/stories/images/0903/
a8de5c88b14851860daa.jpeg

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Margulis
Symbiogenesis
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on
Original formulation
of symbiosis theory
by Constantin
Mereschkowsky
1909

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How many individuals ? How many kinds of
individuals?
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We need better definitions of individuals
Courtesy of Fred Bouchhard, 2013

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Maureen
O’Malley
Centrality of Biological species and their tree
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on
Ernst Mayr, the tree of life, and philosophy of biology
Maureen A. O’Malley
Published online: 8 May 2010
Ó Springer Science+Business Media B.V. 2010
Abstract Ernst Mayr’s inﬂuence on philosophy of biology has given the ﬁeld a
particular perspective on evolution, phylogeny and life in general. Using debates
about the tree of life as a guide, I show how Mayrian evolutionary biology excludes
numerous forms of life and many important evolutionary processes. Hybridization
and lateral gene transfer are two of these processes, and they occur frequently, with
important outcomes in all domains of life. Eukaryotes appear to have a more tree-
like history because successful lateral events tend to occur among more closely
related species, or at a lower frequency, than in prokaryotes, but this is a difference
of degree rather than kind. Although the tree of life is especially problematic as a
representation of the evolutionary history of prokaryotes, it can function more
generally as an illustration of the limitations of a standard evolutionary perspective.
Moreover, for philosophers, questions about the tree of life can be applied to the
Mayrian inheritance in philosophy of biology. These questions make clear that the
dichotomy of life Mayr suggested is based on too narrow a perspective. An alter-
native to this dichotomy is a multidimensional continuum in which different
strategies of genetic exchange bestow greater adaptiveness and evolvability on pro-
karyotes and eukaryotes.
Keywords Ernst Mayr Á Philosophy of biology Á Evolution Á Tree of life Á
Species Á Lateral gene transfer Á Hybridization
Introduction
Most philosophers of biology have in the back of their mind at least a vague image of
a tree of life that depicts bifurcating species lineages and represents the evolutionary
M. A. O’Malley (&)
Egenis, University of Exeter, St Germans Road, EX4 4PJ Exeter, UK
e-mail: M.A.O’Malley@ex.ac.uk
123
Biol Philos (2010) 25:529–552
DOI 10.1007/s10539-010-9214-6

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Maureen
O’Malley
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on 2004
All so-called asexually reproducing
organisms do not have species.
The prokaryotes are difﬁcult
enough [to deal with], but even
when you get into the low
eukaryotes, there is this group that
is a sort of a garbage can called
the protists. And there are authors
I’m told that recognize 80 phyla of
protists. God knows what there is
in these 80 phyla. And most of
them do not have species in the
normal sense. They don’t have a
proper process of speciation or
anything like that.

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But again, on the pragmatic grounds of removing the messier, more web-like
Fig. 1 Six eukaryote supergroups. Reprinted from Lane and Archibald (2008), with permission from
Elsevier
538 M. A. O’Malley
From Lane and Archibald (2008), in O’Malley 2010
Maureen
O’Malley
there is growing evidence of gene exchange in protists (Keeling and
Palmer 2008; Andersson 2009). Sequence analyses of several protist
genomes have detected bacterial genes in varying amounts, with as
much as 4% of rumen ciliate genomes being of foreign origin (Ricard et al.
2006). In the genome of the miniscule green alga, Ostreococcus tauri, the
smallest free-living eukaryote, a whole chromosome appears to have
been acquired, although its source is not obvious (Derelle et al. 2006). The
pathogens Giardia lamblia, Trichomonas vaginalis, and Entamoeba
histolytica have ‘borrowed’ large numbers of virulence and metabolism
genes from bacteria (Andersson et al. 2006; Loftus et al. 2005). Transfers
between protists, and from other eukaryotes to protists, have also been
found in increasing numbers, and the data for such acquisitions increase
with every genome sequence deposited in GenBank or other databases
(Andersson 2009). The more lateral gene transfer in protists is studied, in
fact, the more that is learned about interdomain exchange as an ongoing
evolutionary mechanism of genetic diversity (Andersson et al. 2006).

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Elsevier
Maureen
O’Malley

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Elsevier
Maureen
O’Malley
In fungi, there is a growing list of what seem to be fungal hybrids (Schardl
and Craven 2003; Novo et al. 2009). Moreover, there appears to be a
great deal of LGT occurring between prokaryotes and fungi, between
fungal lineages, and between fungi and other multicellular eukaryotes (e.g.
Schardl and Craven 2003; Friesen et al. 2006; Richards et al. 2006,
2009). Numerous phylogenetically discordant plasmids, transposons and
gene clusters have been detected in a range of fungal lineages, and even
some whole chromosome transfers between ﬁlamentous fungi (Walton
2000). In addition, there is good experimental evidence of
transformation (uptake of environmental DNA) in a few fungi (Rosewich
and Kistler 2000). Whether novel DNA is acquired by hybridization or by
LGT, it has either to be excluded from phylogenetic analysis or depicted
as a reticulate event.

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Elsevier
Maureen
O’Malley
They can combine sexual and asexual reproduction (with sexual
reproduction being the ancient state, since lost in many lineages), and it is
still sometimes unclear how particular fungi reproduce (Petersen and
Hughes 1999; Schardl and Craven 2003; Zeyl 2009). One reproductive
peculiarity of fungi involves hyphal fusion, in which fungal ﬁlaments
anastomose parasexually, through somatic recombination rather than
germ cell recombination. Large numbers of nuclei (sometimes thousands)
from the different hyphae share the same enlarged cell compartment. In
many lineages, interspeciﬁc matings are vegetatively incompatible, which
means that the non-self recognition of introduced genetic systems results
in the destruction of the newly merged hyphal cells (Glass and Dementhon
2006; Glass and Kaneko 2003; Giraud et al. 2008). Even when this does
not happen, the heterokaryon products of hyphal fusion (cells with
different genotypes) may be unstable and produce only homokaryotic
offspring. But this is not always the case, and nor does incompatibility
recognition happen for all hyphal fungi.

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Elsevier
Maureen
O’Malley
study after study has documented the adaptiveness and proliferation
of plant hybrids (Heiser 1973; Arnold 2006; Arnold et al. 1999; Soltis and
Soltis 2009). Much known hybridization involves genome doubling
(allopolyploidy), which has played a major role in plant evolution (Adams
and Wendel 2005). Other hybridization events involve genome
recombination (homoploidy). An example of the latter, which is more
difficult to detect, is provided by the sunflowers Helianthus annuus and H.
petiolaris. These parental species have three hybrid offspring (H.
anomalus, H. deserticola, and H. paradoxus) that evolved between
60,000 and 200,000 years ago. While the parent plants favour temperate
climates, the hybrid offspring inhabit and flourish in extreme environments,
such as harsh desert conditions and salt marshes (Rieseberg 1997;
Rieseberg et al. 2003). It is frequently the case that hybrid offspring have
hardier characteristics than their parents, due to new gene combinations
that allow the hybrids to colonize new ecological niches (Rieseberg and
Willis 2007).

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Elsevier
Maureen
O’Malley
One classic study that did not quite fit Mayr’s expectations was carried out by
Lewontin and L. C. Birch (1966). They argued that hybridization was a source of
variation for adaptation to new environments in particular groups of Queensland fruit
flies (then Dacus, now Bactrocera tryoni and B. neohumeralis)...
...because hybridization is usually investigated in relation to visibly distinguishable
taxa, it has probably been systematically underestimated in duller, more uniform types
of organisms such as little brown birds or butterflies (Mallet 2005; Dowling and Secor
1997). Some classic examples include ducks (much collected during hunting
seasons, and therefore well observed), birds of paradise, cichlids and butterflies
(see Mallet et al. 2007). Cichlids and other freshwater fish are well known for their
hybridization capacities, partly because of the very divergent morphologies and colour
patterns produced by introgression (Koblmüller et al. 2007). In representing these
introgressions phylogenetically, many branches have to be reticulated to make sense
of incongruent gene phylogenies.
Although there may be low levels of fertility in the first generation of hybrids, later
generations frequently stabilize, often with fitness advantages in new or expanded
environments (Anderson 1948; Arnold 2006). And although rates of hybridization may
be low, they can have major evolutionary consequences (Seehausen 2004; Dowling
and Secor 1997).

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Villarreal & Ryan

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Villarreal & Ryan
Much of the known LGT in animals involves acquisitions from prokaryotes, such as
genes for cellulose biosynthesis in marine invertebrates, and glyoxylate-cycle
enzymes in a number of animals (Nakashima et al. 2004; Kondrashov et al. 2006).
The genomes of Wolbachia-infected insects can carry large fragments of
Wolbachia DNA— nearly a whole Wolbachia genome in one case (Hotopp et al.
2007).
An even more intriguing example of animal LGT is that of bdelloid rotifers (a
microscopic multicellular aquatic animal), the genomes of which show evidence of
recent and ancient acquisitions of bacterial, fungal, and plant genes (Gladyshev et al.
2008). Rotifers have a life cycle that can include dessication, and as the dessicated
body revives in the presence of water, environmental DNA seems to be integrated into
the rotifer’s genome through a combination of membrane damage and DNA repair
mechanisms, and then inherited in the absence of sexual recombination. Most of the
intact foreign genes code for simple enzymatic functions such as carbohydrate
decomposition (rather than multi- component biochemical pathways)...
Some plant-parasitic nematodes have acquired bacterial genes that enable the
nematodes to modify plant cell walls, thereby damaging the plant but nourishing the
nematode (Scholl et al. 2003).

54
Maureen
O’Malley
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on 2004

55
Hybridization
Schwenk et al. (2008)

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Hybridization
1957
Molecular phylogen.
SSU rRNA (Woese)
1987
1990s on 2004

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Animal (and plant)
evolution
Representative
Well represented
by tree
Impact on TOL
Mayr Yes Yes -
Doolittle No Yes Circumscribe
Margulis No No Replace
O’Malley No No
Multidimensional
space
Hybrid. studies N/A (yes) Yes
Speciation and
adaptation mech.

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Animal (and plant)
evolution
Representative
Well represented
by tree
Impact on TOL
Mayr Yes Yes -
O’Malley No No
Multidimensional
space
Speciation and
adaptation mech.
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evolution of multicellular
animals and plants can still be
well understood as a branching
process (albeit with some
fuzziness)
prokaryotic evolution may be better
modeled as a reticulated web. This is
because prokaryotes (bacteria and
archaea) much more readily exchange
genes ‘‘across species lines’’, by several
genetic mechanisms collectively known
as lateral gene transfer (LGT). Since
prokaryotes comprise the majority of
living things, and since the ﬁrst two-
thirds of Life’s history is exclusively
prokaryotic, the TOL is of limited
explanatory scope.

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Animal (and plant)
evolution
Representative
Well represented
by tree
Impact on TOL
Mayr Yes Yes -
O’Malley No No
Multidimensional
space
Speciation and
adaptation mech.
A key residual question from the
discussion above is whether evolutionary
biology and its philosophy should follow
Mayr and split evolution into two types: the
processes and outcomes that occur with
‘good’ speciators, and those that occur
with ‘bad’ speciators...
a continuum perspective is the only
remaining option
multiple intersecting continua: asexual-
sexual, much-less-exchange, uni-
multicellular...
an approach along these lines would be more informative than a
focus on which organisms have evolved in tree-like patterns. A
multidimensional approach by no means rejects the importance of
such patterns, nor of the processes that gave rise to them, but it
sees them as just one possible focus and not always the most
valuable one.

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