Review

Losing Complexity:
The Role of Simplification in
Macroevolution
Maureen A. O’Malley,1,* Jeremy G. Wideman,2 and
Iñaki Ruiz-Trillo3,4,5
Macroevolutionary patterns can be produced by combinations of diverse and
Trends
even oppositional dynamics. A growing body of data indicates that secondary
Simplification, the reduction of biologi-
simplifications of molecular and cellular structures are common. Some major cal complexity at different levels, has
diversifications in eukaryotes have occurred because of loss and minimalisa- received less scientific attention than
complexification. Large bodies of data
tion; numerous episodes in prokaryote evolution have likewise been driven by (molecular, ultrastructural, morphologi-
the reduction of structure. After examining a range of examples of secondary cal, and behavioural) now reveal that
simplification and its consequences across the tree of life, we address how simplification occurs across the tree of
life, with far-reaching consequences.
macroevolutionary explanations might incorporate simplification as well as
complexification, and adaptive as well as nonadaptive dynamics. Simplification has driven the diversifica-
tion of many eukaryotic lineages,
through the reduction of parts and
The Evolutionary Importance of Simplification even losses of hierarchical complexity.
Explaining how extant diversity evolved remains a major goal of evolutionary biology. In addition
to detailed representations of major divergences in the history of life, evolutionary analyses have Prokaryote evolution has been shaped
by diverse simplification processes that
also identified key mechanisms involved in the diversification of life forms. However, unlike
give insight into past and present eco-
complexification, the role of simplification (Box 1) has not always had the prominent position it logical circumstances.
warrants.
Simplification, just like complexification,
can be either adaptive or nonadaptive.
Recent molecular and ultrastructural work has indisputably established simplification as not
Selection for ‘streamlining’ cannot be
just occasional or insignificant, but a process that has driven diversification across the tree of universally assumed.
life. Here, we examine three examples from the eukaryote tree: (i) simplification events in the
early history of metazoans; (ii) convergent losses of complexity in fungi; and (iii) simplification Simplification and complexification
interactions, and the macroevolution-
in early eukaryote evolution. We then turn to genome reduction in prokaryotes and conclude
ary patterns they produce, are of major
with an analysis of the diverse explanatory frameworks stimulated by findings of importance to evolutionary modelling.
simplification.
1
UMR5164, University of Bordeaux,
146 Rue Léo Saignat, Bordeaux
33076, France
Box 1. Simplification and Complexification 2
Biosciences, University of Exeter,
Simplification, like complexification, can be described in different ways, some of them very abstractly. We discuss Exeter, EX4 4QD, UK
3
simplification pragmatically, in parallel to what has become a well-recognised way to distinguish conceptually two Institut de Biologia Evolutiva (CSIC-
seemingly different senses of complexity and complexification [85]. One is ‘horizontal complexification’, which involves an Universitat Pompeu Fabra), Passeig
increase in the number of parts (e.g., cell types or gene families); the other is ‘vertical complexification’, which is the Marítim de la Barceloneta 37-49,
increase in levels or degrees of nestedness (e.g., prokaryote to eukaryote cell or unicellular eukaryotes to multicellular 08003 Barcelona, Spain
4
eukaryotes). Using this conceptual framework as an initial guide, ‘horizontal simplification’ would refer to the loss of parts Departament de Genètica, Universitat
(e.g., genes, cell types, ultrastructure, or gross morphology) within a hierarchical level, and ‘vertical simplification’ to the de Barcelona, 08028 Barcelona, Spain
5
loss of hierarchical levels themselves (e.g., multicellularity to unicellularity). We show how both types of simplification Institució Catalana de Recerca i
occur and, importantly, how they are connected empirically. The loss of genes, cell types, and organelles (horizontal Estudis Avançats, Pg Lluis Companys
simplification) is the basis of vertical simplification. For example, the loss of multicellularity in fungi (Case 3) depends on, 23, 08010 Barcelona, Spain
and is explained by, the loss of genes for cell-to-cell adhesion. We suggest that several levels of organisation are usually
*Correspondence:
involved in any simplification or complexification event, and that tracking what appears to be a major loss of vertical
maureen.omalley@u-bordeaux.fr
complexity is often done by tracking lower-level losses of parts.
(M.A. O’Malley).

608 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 http://dx.doi.org/10.1016/j.tree.2016.04.004
© 2016 Elsevier Ltd. All rights reserved.
Emerging Understanding of Evolutionary Simplification Glossary
From Darwin onwards, many evolutionary luminaries have observed that simplification is an Adaptin (AP) complexes: five (AP-1
important process in the emergence of diversity [1–5] (Box 2). However, the idea that evolution to AP-5) related heterotetrameric
often proceeds by organisms becoming more complex tends to lurk in the background of many complexes that recruit particular
proteins to membranes to form
evolutionary hypotheses. One key instance of this is the common requirement for the ‘most coated vesicles.
parsimonious’ explanation of any phylogenetic pattern, in which ‘parsimony’ is often consistent Ascomycetes: a fungal phylum that
with the idea that evolution proceeds via complexification [6].i Another such example is in includes the best-studied fungal
macroevolutionary theory, where accounts of major transitions focus on increasing hierarchical models, including Saccharomyces
cerevisiae, Schizosaccharomyces
complexity (Box 1) [7]. pombe, Neurospora crassa, some
multicellular fungi, such as truffles
However, we argue that gains in complexity can be only one aspect of any account of major and morels, and several pathogenic
filamentous fungi.
evolutionary diversification. We show via a phylogenetically broad range of examples that loss or
Basidiomycetes: a fungal phylum
reduction can be not only as common as gains of complexity, but also as evolutionarily and that includes ‘mushrooms’,
explanatorily important. A diversity of explanatory frameworks is probably required to account for filamentous fungi, and some yeasts,
the variety of simplification events and their relation to complexification. as well as pathogenic rusts and
smuts.
Choanoflagellates: a group of
Case One: The Impact of Simplification on Metazoan Evolution flagellate free-living protists that are
Premetazoan Simplification the sister group to animals.
Efforts to understand the origin of animals have revealed surprising insights into simplification. ‘Chytrids’: a common name for the
aquatic flagellated fungi, which
The choanoflagellates (see Glossary), a group of unicellular and colonial free-living protists, are
comprise three major clades:
the sister group to animals and, therefore, an ideal candidate for understanding animal origins. Chytridiomycota, Blastocladiomycota,
By comparing the choanoflagellate Monosiga brevicollis genome with various animal genomes, and Neocallimastigomycota.
the genetic repertoire of the last common ancestor of animals and choanoflagellates can be Dikarya: a major clade of fungi
comprising Basidiomycota and
inferred [8]. This putative ancestor already had some gene families involved in cell adhesion and Ascomycota.
cell communication (e.g., protein tyrosine kinases). However, several important cell signalling Filastereans: a group of amoeboid
pathways, as well as numerous developmental transcription factors, still seemed to be animal protists, both free living and parasitic,
specific, at least according to the taxon sampling used. Overall, this seminal analysis concluded that represent the sister group to
both animals and choanoflagellates.
that the unicellular ancestor of animals was morphologically similar to choanoflagellates, and had FtsZ/Min system: a set of proteins
a rather basic repertoire of genes involved in functions central to multicellularity [8]. required for bacterial cell division that
have been retained in some
eukaryotic lineages for mitochondrial
Box 2. What Did Darwin Say? And Do Darwinian Theorists Agree? and/or plastid division. Several
lineages have convergently lost these
Charles Darwin recognised that becoming more complex did not necessarily mean progress, and that simplification was,
proteins.
in some instances, a common state of affairs. For example, when discussing plants with excess sepals and other
Integrins: transmembrane proteins
features, Darwin argued that ‘if any new principle has to be invoked, it must be one of retrogression rather than of
that represent the major cell to
progression; and so it must be with many parasitic and degraded animals’ ([1] p. 176).
extracellular matrix adhesion
mechanism in animals.
George Gaylord Simpson agreed: ‘the history of life provides examples not only of progress but also of retrogression or
Nucleariids: the sister group to
degeneration’ ([3] p. 243).
fungi. It consists of a small number of
amoeboid species, including
So did Ernst Mayr: ‘We now know that complexity of a structure is not necessarily an indication of evolutionary progress.
Fonticula alba, for which there is a
Cases of secondary simplification are sufficiently frequent to make quite inadmissible the assumption that morphological
genome sequence available for
series from simple to complex are necessarily evolutionary series’ ([2] p. 297).
comparative analyses.
Protists: unicellular eukaryotes
André Lwoff wrote a whole book examining the evolutionary loss of metabolic function due to increasing specialisation
(loosely). More specifically, all
(1944, self-translated passages in [86]; see also [87]).
unicellular eukaryotes that cannot be
categorised as animals, land plants,
However, some of the next generation of evolutionary thinkers thought the simplification message had not reached all
or fungi.
biologists: ‘the pre-Darwinian concept of the scala naturae in which an animal series progresses from simple to
‘Zygomycota’: a now-defunct fungal
morphologically complex organisms still operates in post-Darwinian systematics’ ([5] p. 395).
phylum. The term is currently used to
refer to all terrestrial fungi excluding
Theodosius Dobzhansky himself gave licence to such thoughts, as he mused on ‘retrogression’ (morphological, sensory,
basidiomycetes and ascomycetes.
and physiological loss) within a general schema of increasing complexity: ‘evolution as a whole doubtless had a general
direction, from simple to complex . . . [up until] finally greater and greater consciousness’ ([4] p. 311).

Although there is no doubt complexification occurs, much recent work suggests that it has to be understood more
exactly in relation to equally important simplification events.

Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 609
Recently, however, additional genome sequences of close relatives of animals have challenged
older views about premetazoan life. Notably, an analysis of the Capsaspora owczarzaki genome
(representing the sister group to animals and choanoflagellates) identified several ‘multicellular
genes’ that had not been found in the genome of choanoflagellates and, therefore, had been
deemed animal specific. Those genes, shared by animals and C. owczarzaki, but lost by
choanoflagellates, include integrins [9] and some transcription factors central to animal devel-
opment. These findings showed that the ancestor of filastereans, choanoflagellates, and
animals (and, hence, the ancestor of animals) already had a relatively complex gene repertoire
[10]. Therefore, today's choanoflagellates must have secondarily simplified their genetic reper-
toire from a more complex ancestor (Figure 1).

Metazoan Simplification
A similar but more disputed instance of simplification is suggested for early metazoan evolution.
Sponges have classically been considered the sister group to the remaining Metazoa, due to

Metazoa

Deuterostomia

Protostomia
Bilateria

Complex animal ancestor

with nervous system
Cnidaria
and muscles?

Secondary simplificaon?
Placozoa

Secondary simplificaon?
Ancestors with complex Porifera
gene repertoires

Ctenophora
Integrin
adhesome Several TFs
Choanoflagellata
(Monosiga brevicollis and Salpingoeca rosea)

Filasterea
(Capsaspora owczarzaki
aki))

Ichthyosporea

Fungi

Figure 1. Simplification in the Metazoan and Premetazoan Tree. This schematic tree of the metazoans and their
closest relatives is based on several phylogenomic analyses ([14,15,99] but see [16]). In their evolution from a complex
unicellular ancestor, the two sampled choanoflagellates secondarily lost several components of the integrin pathway, plus
several developmental transcription factors (TFs). If Ctenophora are the sister group to the rest of Metazoa, then both
Porifera and Placozoa have undergone secondary simplifications.

610 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8
their simple body plan. This view, which is questionable [11], was reinforced by molecular
phylogenies that showed sponges as the sister group to the rest of Metazoa [12,13]. However,
some recent phylogenies challenge this representation. They indicate instead that ctenophores
(comb jellies), which are morphologically more complex than sponges (ctenophores have
neurons and muscles), form the sister group to the rest of the Metazoa [14,15] (although
see [16]). This implies that today's sponges might be the products of secondary simplification
processes (Figure 1). Alternatively, ctenophores and other metazoans could have arrived at the
same structural complexities by convergent evolution.

Importance
However, the fact that choanoflagellates and possibly sponges are secondarily simplified from a
more complex ancestor does not undermine their importance as models for understanding
animal origins. Extant choanoflagellates represent the closest living animal relative, and their
study continues to generate important insights into animal origins. Sponges also represent an
ecologically important animal phylum that was derived from early metazoans (either the first
offshoot or the one that came immediately after ctenophores). Sponges continue to be essential
for insights into early animal evolution [12]. However, because of the length of time since
choanoflagellates and sponges diverged from their common ancestor, the evolutionary history
of those lineages might be more complicated than current phylogenetic methods can capture.
Nevertheless, whatever evolutionary scenario is being considered, secondary simplifications
should always be taken into account.

Case Two: Convergent Simplification in the Kingdom Fungi

Convergent Losses of Multicellularity
One of the most striking cases of complexification is the evolution of multicellularity. The best-
known instances include the evolution of the three ‘crown’ groups of eukaryotes (plants,
animals, and fungi). In addition, green, red, and brown algae, and amoebozoan and other
types of slime mould have also independently evolved versions of multicellularity [17,18]. Even
some prokaryotes, such as cyanobacteria, have evolved multicellular forms. This apparent trend
toward multicellularity is often seen as evidence of directionality toward greater complexity. If
‘vertical’ simplification (Box 1) were also a major process in macroevolution, we might expect
unicellular forms to have evolved from these multicellular lineages. The convergent simplification
of yeasts is a paradigm example of this dynamic in the fungal kingdom.

The fungal kingdom includes organisms with three familiar morphologies: unicellular yeasts,
multicellular filaments, and multicellular fruiting bodies. In addition, some fungi are dimorphic and
can grow both as filaments and yeast-like forms. Until the early 20th century, it was thought that
all yeasts were related ascomycetes. This view changed when basidiomycete-specific
structures found in other groups were identified in several yeasts [19]. Phylogenetic analyses
further demonstrated that the two major lineages of ascomycete yeasts evolved independently,
with the earliest diverging members of both of these clades being filamentous or dimorphic fungi
[20,21]. These findings indicate that various unicellular yeasts evolved independently from
different multicellular ancestors (Figure 2).

Convergent Losses of Cellular Machinery

The evolution of the flagellar apparatus is a case of the convergent reduction of parts. Flagellum
presence had been used to distinguish between terrestrial and aquatic fungi long before the
phylogenetic relation between these two groups was known. The ‘simplest’ explanation was
that in the transition to land, terrestrial fungi no longer relied on water for the dissemination of
flagellated zoospores. They underwent cellular simplification as they developed other means for
spore dispersal (see [22]). However, after further discoveries of secondary loss were made, and
phylogenetic relations clarified (e.g., [23,24]), a more complicated pattern was revealed, with at

Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 611
 Malassezia sp. ?
Uslago maydis

Cryptococcus neoformans

Basidiomycota
Agaricomycona

Rhodotorula graminis
Pucciniomycona

Schizosaccharomyces pombe
Taphrina deformans

Saccharomyces cerevisiae

Geotrichum candidum
Pezizomycona
Rhizophagus irregularis
Kickxellomycona
Olpidium brassicae
Mucoromycona
Entomophthoromycona
Neocallimasgomycota
12
‘Chytrids’

43 Hyaloraphidium curvatum
Batrachochytrium dendrobadis
Spizellomyces punctatus
Microsporidia
Cryptomycota
Aphelids ?
12
5 Nucleariid amoebae
43
Holozoa

Dimorphic fungus Presence of flagellum

Independent loss of flagellum
Dimorphic fungus: predominant yeast stage Presence/absence of AP complexes
AP4 complex lost
Independent loss of mulcellularity ? AP complexes not analysed

Figure 2. Convergent Simplification in the Kingdom Fungi. The last fungal and nucleariid common ancestor was a
flagellated unicell with all five adaptin (AP) complexes. During the course of fungal evolution, the flagellar apparatus and a
subset of the AP complexes were convergently lost in distantly related lineages. In addition, after multicellularity was
attained, it was convergently lost in at least two yeast lineages. Recent fungal phylogenies have shown that the flagellated
fungus, Olpidium brassicae, is closely related to a group of terrestrial nonflagellated fungi [23], and that the nonflagellated
fungus, Hyaloraphidium curvatum, is a member of the flagellated chytrids [100]. The nonflagellated microsporidia and
nucleariid amoebae are basal branches of the fungal tree [24]. The common ancestor of the Dikarya (Ascomycota and
Basidiomycota), plus the group formerly known as Zygomycota, was probably filamentous and possibly dimorphic. After
their divergence, multicellularity was convergently lost in two lineages of the Ascomycota. Several basidiomycete species
have adopted a yeast-like morphology, but have retained the capacity for multicellular growth. Grey pie slices indicate that
some, but not all, of the AP complex is retained by the lineage.

612 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8
least five flagellar losses in the group including fungi and nucleariids (Figure 2). Therefore, instead
of a straightforward evolutionary narrative depicting a single flagellar loss accompanying the
transition to land, multiple convergent losses must have occurred in distantly related fungi
(Figure 2).

Other convergent simplifications in fungi involve the membrane trafficking system. Adaptin (AP)
complexes can be thought of as molecular markers for different kinds of cell vesicle. Five AP
complexes are currently known, and phylogenetic analyses indicate that all five are widespread
in eukaryotes and were present in the last eukaryotic common ancestor [25]. Fonticula alba, a
member of the sister group to Fungi, retains all five AP complexes, indicating that all were
present in the first fungal common ancestor. Three of the five AP complexes are widespread
among fungi, but, similar to the flagellum example, a single species, Rhizophagus irregularis,
contains a fourth AP complex [26]. Due again to obscure phylogenetic affiliations, the number of
AP losses remains ambiguous, but it is clear that at least five and possibly as many as seven
independent losses of the same proteins have occurred in fungi (Figure 2). These complex
patterns of retention and loss suggest that explaining macroevolutionary events will produce
neither a simple nor a single story.

Case Three: Reductive Evolution in Early Eukaryotes

Enormous progress has been made in delineating the main eukaryote groups on the basis of
molecular and ultrastructural data, as well as with more coarse-grained traditional characteri-
sation [27]. Despite many difficulties in inferring early eukaryote evolution, a range of studies
suggests at least two important features of eukaryote diversification: (i) it probably happened
rapidly, in a ‘big bang’ of cladogenesis [28,29]; and (ii) this radiation occurred in association with
numerous simplification events.

Molecular data have been key to inferring features of the ancestral eukaryote. In addition to
representative genomes from the major eukaryotic groups, there is increasing genome data from
Archaea (the group within which eukaryotes probably evolved). These sequences have allowed
more detailed comparative analyses, which suggest that the ancestral eukaryote had a great
deal of ‘ready-made’ complexity [30]. As well as having mitochondria and a nucleus (arguably
hallmarks of being a eukaryote), the primordial eukaryote had an intricate cytoskeleton (including
flagella), plus a well-developed endomembrane and transport system [31–33]. It also had
capacities for sex [34], regulatory cellular machinery [35,36], and introns [37].

Mitochondrial Simplification
From this initially complex eukaryotic state, a combination of secondary simplification and
divergence of lineages occurred. Simplification occurred not only to genomes, but also to
organelles, other cellular structures, and behaviours, such as sex and motility [38]. Mitochondria
are an illuminating example. It makes intuitive sense that the genome of the endosymbiont was
whittled down as it was maintained within the host cell, and the host nucleus exerted increasing
control over what became the mitochondrion [39]. However, simplification continued to occur in
some lineages after a functional mitochondrion had stabilised (Figure 3). A diversity of mito-
chondrion-derived organelles are known today, and some not only have highly reduced
functions, but also no remnant genome or ATP generation at all [40–42].

The evolution of reduced mitochondria can be tied to the loss of particular genes. For example,
simplified mitochondria without mitochondrial cristae have lost the genes required for the
formation and maintenance of these structures [43]. Although these losses led to similar
mitochondrial ultrastructure, they occurred independently in lineages separated by over a billion
years of evolution. A similarly suggestive finding involves the bacterial FtsZ and Min systems
that are retained in diverse eukaryotes for mitochondrial division. Many eukaryotes lost their

Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 613
 Holozoa
Neocallimasgomycota H
Other fungi
Microsporidia M
Thecamonas trahens Min/Ftz
? Pygsuia biforma H Min/Ftz

Amorphea
? Masgamoeba balamuthi H
Entamoeba histolyca M
Dictyostelium sp. Min/Ftz
Malawimonas californiana Min/Ftz
Trichomonas vaginalis H
Giardia lamblia M
? Sawyeria marylandensis H
Naegleria gruberi
Pharyngomonas kirbyi Min/Ftz

Excavata
Euglenozoa
? Andalucia incarcerata H Min/Ftz
Andalucia godoyi Min/Ftz
? Anaerobic ciliates H
Other alveolates
Labyrithulomycota
Blastocyss hominis H
Diaphoreckes

Other stramenopiles Min/Ftz

? Mikrocytos mackini M
Other rhizarians
Archaeplasda
Min/Ftz Presence of Min/Ftz mitochondrial division system
Loss of Min/Ftz mitochondrial division system
Loss of MICOS
? Hypothesised loss of MICOS
H Presence of reduced mitochondrion (hydrogenosome)
M Presence of reduced mitochondrion (mitosome)

Figure 3. Mitochondrial Simplification across Major Eukaryote Groups. Mitochondria have undergone convergent
simplification of bacterial-derived division systems. Based on accepted eukaryote phylogenies, at least ten independent
losses of the Min/Ftz system have occurred (represented by red bars) [44]. Additionally, simplified anaerobic mitochondria-
related organelles (MROs), such as mitosomes and hydrogenosomes, have convergently evolved in at least ten different
lineages across the tree of eukaryotes. Losses of cristae correlate with the loss of the mitochondrial contact site and cristae-
organising system (MICOS) (blue bars). Lineages with MROs that do not yet have sequenced genomes are hypothesised to
have lost MICOS (light-blue bars with question marks).

prokaryotic mechanisms for mitochondrial division, and then gained their new eukaryotic
versions independently [44] (Figure 3).

Losses plus Gains

These losses of early complexity overturn background assumptions that simpler eukaryotic
states are ancestral. In other words, current appearances of complexity can be derived from a
more elaborate ancestral state [45]. Not everything simplified, of course. For example, the
ubiquitin signalling system expanded and diversified in some lineages after an early eukaryotic

614 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8
origination [35], as did G-protein-coupled receptor signalling [46], transcription factors [47],
cytoskeletal motor proteins [48,49], and membrane trafficking [50]. However, some of these
systems could also have been secondarily simplified in certain taxa after expansion occurred.
Frequently, therefore, gains and expansions have occurred against a backdrop of extensive loss
at different levels [6,51,52]. Importantly, contemporary eukaryotes rarely regained any particular
loss in complexity, but instead diversified in other respects.

From our three eukaryotic cases (see Box 3 for additional eukaryotic examples), it might appear
that these instances of simplification were adaptively driven and produced positive consequen-
ces for the simplifying lineages. However, by looking more broadly and deeply across the tree of
life, we see that the story has additional explanatory dimensions.

Prokaryote Simplification: Common, Diverse, Important

Although many simplification events have been recognised only recently in eukaryotes, it has
long been known that prokaryotes undergo reductive evolution. The classic account of genome
reduction in prokaryotes is usually thought of in the context of the evolution of endosymbionts
and intracellular parasites, as an outcome of the interdependence of host and symbiont [53,54].

Box 3. Examples of the Diversity of Evolutionary Simplification in Eukaryotes

Algae

Red algal parasites parasitise free-living algae that are often sister species (i.e., the parasites are derived from their hosts).
In the process, the former have reduced their genomes, mitochondria, and plastids [88]. Free-living red algae might have
launched their evolutionary career with genome reduction, after which they acquired numerous bacterial genes [89].
Green algae-derived parasites, which parasitise insects and do not photosynthesise, have not lost a great deal of
functional capacity despite some nuclear genome reduction [90].

Other Reduced Parasitic Eukaryotic Microbes

Many protists have lost photosynthesis genes and organelles, particularly the Apicomplexa (e.g., Plasmodium and
Toxoplasma), which live parasitic intracellular lifestyles. Giardia, Entamoeba, and Trichomonas are other parasitic protist
exemplars of organelle and genome reduction. Microsporidia are a classic example of simplification in unicellular fungi.
They exhibit not only extremely reduced genomes, metabolic losses, and secondarily simplified mitochondria, but also
gene acquisition and gene family expansion [91,92].

Plant Simplifications

Flagella loss is a defining feature of most land plants, especially angiosperms (plus, it occurred independently in fungi,
green and red algae, amoebae, and some other protists). It happened at least twice during the evolution of land plants
[93]. Some plants have convergently lost their ancient symbiosis genes and have evolved ways to gain nutrients
autonomously, without symbionts [94]. Multiple plant lineages have taken the dependent route to simplification and
become parasites, which involves the loss of plastid genes and the capacity to photosynthesise [95].

Reduced Metazoans

Myxozoa are ‘degenerate’ cnidarians (the group that includes jellyfish and sea anemones). They have dramatically
reduced genomes and body plans as a consequence of a parasitic lifestyle [96]. Other metazoans have also lost
significant amounts of genomic and bodily complexity, but not because of parasitism. Tardigrades [97] and (probably)
Placozoa are two important exemplars.

Transmissible Cancers: ‘Unicellular Metazoans’

Clonally transmissible cancers have a life and evolutionary trajectory beyond that of their hosts. Because of host-to-host
transmission, they form ‘species’ lineages and are not merely part of the hosts. Although they emerge from metazoan
lineages, they are simplified diversifications of their hosts. Thus, they represent another loss of ‘vertical’ complexity (i.e.,
multicellularity). There are two known examples: canine transmissible venereal tumour (around 11 000 years old, and
sustainable) and Tasmanian devil facial tumour disease, which emerged only a few decades ago and appears to be
heading toward extinction by wiping out its host [98].

Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 615
Transmission bottlenecks reduce the population size of endosymbionts and, thus, the efficacy of
selection, leading to increased fixation of mutations and gene deletion [55,56].

However, some genome reduction in bacteria is clearly not of this type. Free-living marine
bacteria, notably Prochlorococcus and Pelagibacter, have miniature genomes and cell sizes
[57,58]. They live in low-nutrient but stable environments that appear to select for jettisoning the
genes of many metabolic pathways. Genome reduction probably played a major role in the early
diversification of Prochlorococcus, an extremely abundant photosynthesiser [59]. Notably,
however, these minimised organisms often operate in dependence on public goods that other
lineages inadvertently provide.

It is not just bacteria that undergo simplification, of course. Large-scale analyses of archaeal
genomes suggest that extensive losses of complexity underpin major cladogenesis events
[60,61]. Whether the focus is explaining the ancient past or current diversity of prokaryotes,
simplification will be central. The question now is how simplification itself is explained.

Evolutionary Explanations of Simplification

Darwin's early recognition of ‘retrogression’ and ‘degradation’ (Box 2) was more of an obser-
vation than a theoretical statement. Now, with large bodies of evidence from across the tree of
life, frameworks are emerging that attempt to explain a range of simplification processes and
outcomes.

Adaptive Streamlining
Lwoff discussed a version of streamlining during the 1940s, as he examined how ‘poor
synthesizers’ derived from ‘high synthesizers’. He thought these ‘losses might actually bring
a selective advantage, provided the medium contains enough ready-made metabolites,’ and
that this phenomenon would be found outside microorganisms ([62], p. 152]. The Black Queen
Hypothesis, which is a considerable elaboration of this idea, might apply in some specific
instances of genome reduction. It builds on the notion of adaptive genome streamlining by
emphasising ‘leaky’ functions (the uncontrollable sharing of resources). Selection favours the
less common nonproducers, which could then lose genes for producing the public good [63,64].
This form of negative frequency-dependent selection might not apply to all instances of free-
living organisms engaged in genome reduction (e.g., [65]), but is proving a plausible explanation
for some evolutionary and ecological situations.

However, genome reduction does not apply only to prokaryotes, as Lwoff suggested. Some
important phases of eukaryote evolution can probably be explained by adaptive genome
reduction, such as animal metabolic simplification [52]. Other eukaryotic simplification also
tends to be explained as ‘a result of adaptation to specific environments, where reductive
pressure includes energetic reasons’ ([51] p. 390). For example, the reduction of mitochondria
and plastid organelles is often argued to be the outcome of selection for economy (e.g., [45,66]).
Selection for smallness is an explanation for some of the smallest free-living eukaryotes, the
microalgae or picophytoplankton (e.g., [67]).

The ‘less-is-more principle’ suggests that adaptive gene loss (particularly loss-of-function
mutations) makes lineages from microbes to mammals more evolvable [68]. The ‘subtraction
of complexity’ account posits that early complexity is pared away by selection to produce
‘effective and efficient function’ ([69] p. 514). However, in cases of eukaryotes with reduced and
compacted genomes, such as Microsporidia and microalgae, considerable complications in
translation might be the outcome of such compaction [70]. Thus, even in simplification cases
where a general adaptationist explanation can be applied, there are likely to be numerous
maladaptive or suboptimal outcomes.

616 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8
Nonadaptive Simplification
When ‘streamlining’ is invoked, it usually implies positive selection for gene or other losses (not
just relaxation of the selection maintaining the structure, which also occurs). However, as noted
above, standard microevolutionary population genetic accounts of endosymbiont and other
prokaryotic genome reductions are usually nonadaptive [55]. Slightly deleterious mutations due
to drift can accumulate in small host-bounded populations, with the subsequent loss of affected
genes due to a bias toward deletion in prokaryotes [56,71]. Losses of metabolic and biosyn-
thesis pathways in fungi have also been explained as a consequence of small population size
and genetic drift (e.g., [72]).

The exact roles of nonadaptive processes, such as mutation and drift, need careful analysis
when invoked to explain simplification [56]. In addition, there can also be adaptive aspects to
consider. For instance, the more dependent the endosymbiont and, particularly, the more it is
sequestered to host cells and inherited vertically, the more reduced the genome and function of
the symbiont is likely to be. In these cases, the evolutionary trajectory of endosymbiont reduction
will also include many coevolved adaptive features [73,74]. However, ‘streamlining’ in any
explanation could be a misnomer, because organisms undergoing ratchets of simplification
can be teetering on the verge of extinction [74]. Extinction itself is an important evolutionary
outcome that will often involve simplification processes.

Synthesising Explanations
Synthetic evolutionary theory already combines distinct processes (mutation, selection, recom-
bination, and drift), and accepting that evolutionary simplification is driven by adaptive and
nonadaptive interactions would be a necessary corollary. From this perspective, there is nothing
further required to unify microevolutionary accounts of simplification. For example, the genome
reduction that is central to the deep and major diversifications of archaeal lineages can tentatively
be explained both by small population size and adaptive metabolic efficiencies [61]. However,
explaining particular macroevolutionary events, such as archaeal diversification, might need
additional explanatory machinery to capture how genomes and other structures have increased
and decreased in complexity, and how those processes work together.

In all the examples of simplification we discuss, prokaryotic and eukaryotic, there were certainly
preceding and succeeding increases in complexity. To represent how simplification and com-
plexification work together, Wolf and Koonin [38] suggest a ‘biphasic’ model of evolution, in
which gains of structure and function are purged by processes of loss, producing a pattern they
argue to be similar to that of punctuated equilibrium. McShea [75] also postulates increases in
complexity that are frequently followed by selectionist streamlining. Even though much com-
plexity in eukaryotes appears not to have attracted selectionist streamlining or even nonadaptive
loss, some eukaryotic and prokaryotic evolution does appear to exhibit a ‘punctuated’ pattern of
extensive gains and losses (e.g., [38,76]). However, at the current stage of research, we suggest
that interactions between simplification and complexification are not predictable, and each
‘trend’ is best treated as an accumulation of many individual and separate processes (Figure 4).

How effectively do current methods detect simplification of any sort? Although considerable
advances have been made in identifying losses, others could still be obscured by what appears
to be a ‘trend’ toward complexity [77]. Moreover, simplification, like much complexification,
might be detectable but evolutionarily unimportant. For example, a significant amount of genome
reduction could be short lived, due to the horizontal reacquisition of discarded genes, or the
extinction of simplified lineages [78] (Figure 4). Even when reduced complexity persists in a
lineage, it might not produce any notable macroevolutionary difference. Just as expectations of
complexity can sometimes have biased theorising about major evolutionary transitions, so too
could overblown expectations of simplification.

Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8 617
 H Outstanding Questions
Key: F How do simplification and complexifi-
Gene repertoire/structure
Adhesion cation work together in short and long
Morphogenesis timescales? Do they produce ‘punctu-
Development I ated’ evolutionary patterns, or some-
Signalling C
Metabolism thing more diverse?

Can adaptive and nonadaptive explan-

J ations of simplification be integrated
G
simply by subsuming them under stan-
dard microevolutionary theory? These
B are very different processes, and their
K
D interaction does not seem to be predict-
able even in similar circumstances (e.g.,
different aspects of endosymbiont evo-
lution can be adaptive or nonadaptive).
By recognising more instances of sim-
plification, will we be able to forecast
L more exactly these evolutionary dynam-
E
ics in similar ecological situations?

A
Is simplification produced by the same
M processes and does it follow the same
patterns in prokaryotes and eukar-
yotes, or in unicellular and multicellular
life forms? From an explanatory per-
spective, are simplification phenomena
Q at one organisational level (e.g., organ-
isms) always fully explained by analysis
at ‘lower’ levels of organisation (e.g.,
N
P molecular)?
R
What methods need development to
gain deeper and more extensive insight
O S into evolutionary simplification? Much
work currently involves inferences on
the basis of molecular data and ultra-
structural comparisons. Is there a big-
ger role for experimental evolution, and
how might such experimental work be
T designed to address the issue of
simplification?

Are new macroevolutionary models

Figure 4. Simplification and Complexification Interactions across the Tree of Life. Taxon A has a relatively complex
needed to capture simplification?
ancestral genome, with different genes involved in different functions. Each colour bar depicts a different function, such as
Major transitions in evolution are often
cell adhesion, cell morphogenesis, development, cell communication, and metabolism. From that ancestor, simplification
portrayed as increases in complexity,
and complexification events can occur. In the upper part of the tree, there is initially a simplification step (shorter red bars in
but this is clearly only one side of the
B), followed by either more simplification (E) or a complexification step for other structures and functions (yellow and blue, in
evolutionary story. Do separate models
C). From a simplified ancestor (such as E) there can be even more simplification events, such as those which occur in
have to deal with major simplification
parasites (M), or expansion of other structure functions (green in L). Already reduced functions can expand too, but with
episodes, or can a more unified
different gene innovations (red in L). Independent convergent reversions to ancestral states might happen, such as the
descriptive and explanatory account
reversion to unicellularity in fungi (H and J revert to the ancestral B state). In some cases, because only extant taxa can be
be constructed?
analysed molecularly, several consecutive simplification and complexification steps, followed by further simplification, might
remain obscure.

Concluding Remarks
Evolutionary biology has come some way from the 1990s, when it was still possible to argue that:
‘Even with the advent of molecular sequence data, we have failed to break some of our bad
habits in interpreting phylogenetic trees. The common false assumption, in all its guises, can
be boiled down to one phrase—simple equals primitive. The fundamental flaw that has been
ignored time and time again is that simple can also mean derived’ ([79] p. 385).

618 Trends in Ecology & Evolution, August 2016, Vol. 31, No. 8
We have shown how, during the decade and a half since this statement, considerable recognition
of secondary simplification has been achieved. Not only has it been recognised empirically, but also
theoretically. Several lessons can be drawn from these many accounts of simplification: (i) Positive
message: simplification is important for detecting and explaining major evolutionary events and
diversifications; (ii) Negative message: simplification processes further complicate the extraction of
evolutionary signal from data, because ‘parsimonious’ assumptions (that it takes fewer steps for
simple states to precede more complex ones) cannot be used to guide analysis; and (iii) Neutral
message: there are more questions than answers right now about simplification. Many of these
questions would benefit from further scrutiny (see Outstanding Questions).

Ongoing Issues
One such question would be whether it is easier for biological systems to complexify than
simplify. Is there any inevitability to either? Early eukaryotes or Archaea appear to have had
sophisticated structures and capabilities that, while launching new lifestyles and constructing
new environments, were for many lineages just too much structural and functional baggage to
carry around. However, if complexity often ratchets up uncontrollably without need for any
adaptive explanation [69,80,81], so might loss ratchet down. By contrast, just as complexity has
thresholds that are difficult to cross, some forms of loss, such as the total loss of endosymbiotic
organelles, are so difficult as to be rare [82]. In addition, losses can conceivably lead to extra
costs for the organism, as well as economies. More experimental work could offer valuable
insight into rates and mechanisms of gene and other structural losses (e.g., [83,84]).

Given the importance of many individual events of simplification, do we need an expanded model
of major transitions in evolution? The currently dominant version focusses on hierarchical
increases in complexity: genes to gene networks, prokaryotes to eukaryotes, unicells to multi-
cells, single organisms to societies [7]. Simplification can undo this hierarchical complexity (e.g.,
reversions from multicellularity to unicellularity; endosymbiont and organelle losses; the aban-
donment of cellularity altogether) by purging horizontal or structural complexity (Box 1). Simplifi-
cation might in addition create conditions for vertical transitions in complexity (e.g.,
eukaryogenesis, multicellularity). Explicitly including simplification dynamics will produce more
complete macro- and microevolutionary explanations, and enable closer scrutiny of the inter-
actions between simplification and complexification throughout the history of life.

Acknowledgments
M.A.O.’s research and the ISHPSSB symposium on which this paper is based were funded by a University of Sydney Bridging
Support Grant and a University of Bordeaux IdEx Chair of Excellence. J.G.W. is supported by European Molecular Biology
Organization ALTF 761-2014, and EMBOCOFUND2012, GA-2012-600394. I.R.T.’s research is supported by ERC-2012-Co-
616960, BFU2014-57779-P, and Project 2014 SGR 619. We thank audience members at ISHPSSB for comments on verbal
presentations of this work, our referees for constructive comments, and Dan McShea for further valuable feedback.

Resources
i
http://evolution.berkeley.edu/evolibrary/article/phylogenetics_08

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