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Life With or Without Names

Article  in  Evolutionary Biology · December 2016

DOI: 10.1007/s11692-016-9384-5

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Evol Biol (2016) 43:582–595
DOI 10.1007/s11692-016-9384-5
SYNTHESIS PAPER
Life With or Without Names
M. Casiraghi1 • A. Galimberti1 • A. Sandionigi1 • A. Bruno1 • M. Labra1
Received: 5 May 2015 / Accepted: 15 April 2016 / Published online: 21 April 2016
Ó Springer Science+Business Media New York 2016
Abstract The terms ‘life’, ‘species’ and ‘individuals’ are
key concepts in biology. However, theoretical and practical
concerns are directly associated with definitions of these
terms and their use in researchers’ work. Although the
practical implications of employing definition of ‘species’
and ‘individuals’ are often clear, it is surprising how most
biologists work in their field of study without adhering to a
specific definition of life. In everyday scientific practice,
biologists rarely define life. This is somewhat understand-
able: the majority of biologists accept the standard definition
of life without exploring it, but this represents a bad attitude.
In this essay, we update the concepts of life, species, and
individuals in the light of the new techniques for massive
DNA sequencing collectively known as high throughput
DNA sequencing (HTS). A re-evaluation of the newest
approaches and traditional concepts is required, because in
many scientific publications, HTS users apply concepts
ambiguously (in particular that of species). However, the
absence of clarity is understandable. For most of the last
250 years, from Linnaeus to the most recent researches,
identification and classification have been performed
applying the same process. On the contrary, through HTS,
biologists have become simply identifiers, who construct
boundaries around the biological entities and do not examine
the taxa at length, resulting in uncertainty in most readers and
displeasure in traditional taxonomists. We organised our
essay to answer a basic question: can we develop new means
to observe living organisms?
& M. Casiraghi
maurizio.casiraghi@unimib.it
1
ZooPlantLab, Department Biotechnology and Biosciences,
University of Milan-Bicocca, Piazza della Scienza, 2,
20126 Milan, Italy
123
Keywords Life
Species
Individual
Biological
entities
High throughput DNA sequencing
Next
generation sequencing
HTS
NGS
‘‘Nomina si nescis, perit et cognitio rerum
(Linnaeus)’’
In the Eighteenth century, Linnaeus famously wrote that
‘‘Knowledge of things is gone if you do not know their
names’’. Today, despite 250 years of modern taxonomy,
millions of species remain to be described (Mora et al.
2011) and the larger part of the living world, in spite of
250 years of modern taxonomy, is still without a name.
This fact was pointed out by the following imaginary sit-
uation (May 2010): ‘‘imagine some aliens landing on the
Earth in their Starship Enterprise. Among their first ques-
tions, the alien visitors might ask the following: ‘‘How
many life forms (species for us) do you have on this pla-
net?’’ Our answer cannot be a precise number, but three to
100 million species. Why such uncertainty?
In the mind of Linnaeus individuals, species, biological
entities were present in god’s will, and he considered
himself a ‘novel Adam’ in the act of naming them. We
have achieved a great deal since Linnaeus, and no gods are
today necessary to name living beings. However, the
general scheme conceived by Linnaeus is still universally
adopted by the epigones. According to the general scheme,
the living beings (i.e. the individuals) are nowadays hier-
archically grouped into species, genera, families, orders,
classes, phyla, kingdoms, and domains. This framework
represents a transformation from Linnaeus’ original ver-
sion, which included species, genera, orders, classes and
kingdom only (Minelli 1993).
Evol Biol (2016) 43:582–595
For most taxonomists, species is the ‘rank among the
ranks’, the foundation on which the entire system is built. In
general, the existence of taxonomic ranks and the centrality
of the species are not questioned by biologists, however
concerns on the necessity of taxonomic ranks have been
raised (see for instance de Queiroz and Cantino 2001;
Ereshefsky 2001) and attempts to generate a more practical
system have been discussed (e.g. PhyloCode, Cantino and de
Queiroz 2000). However, even for the present day biologists,
this issue is of primary interest and has striking consequences
at both theoretical and practical levels.
Simple protocols to identify new species are not avail-
able, and even the common idea of ‘discovering a new
species’ can be highly questionable, as described by Naciri
and Linder (2015). It is a false premise to imagine the
biological world as a mere collection of species just wait-
ing for taxonomists to be brought to light. We should view
species as ‘suggested’ over ‘discovered’.
In Linnaeus’ time scientists were generalists, because
each of them was working on vast sections of the Tree of
Life, ranging from plants to different animal phyla. In the
following centuries, scientists become highly specialised
on relatively smaller taxonomic groups (orders, families,
and sometimes even smaller groups of organisms). Para-
doxically, and quite interestingly, today via spread use of
techniques such as high throughput DNA sequencing
(HTS, also known as next generation sequencing, NGS),
biologists are transitioning back to generalist approaches.
However, substantial differences can be delimited between
traditional and contemporary generalists. Traditionalists
were descriptors of very different biological entities
defined as species, whereas contemporary generalists serve
only as identifiers, most using variation in molecular
marker/s only to discriminate entities, which are not nec-
essarily belonging to the species rank. We will come back
to this point at the end of this essay.
‘Species’ definitions are furthermore dependent on how
we define concepts such as ‘individuals’ and ‘life’. The
question we examine is how the current molecular study of
genes enables us to change our global vision on key bio-
logical concepts. To answer this question, we addressed
several exceptional examples that support the idea of how
difficult it is to define ‘life’, ‘species’, and ‘individuals’ in
biology, and provided guidelines on how to improve the
current theoretical frameworks.
The Difficult Definition of Life: A Biological
Perspective
Biology is literally the ‘study of life’, but the definition of
what life is and what is really alive is far from trivial. Most
biologists work under a ‘life-is-granted’ assumption: they
583
study entities that are most certainly alive, because the life
forms they are studying share carbon based chemistry,
possess DNA responsible for the transmission of informa-
tion, and actively reproduce. These are ‘evolving matter’ in
Darwin’s original meaning. However, at the transition from
an abiotic to biotic world, exceptional cases do exist, such
as viruses. Viruses are obligate, acellular parasites, which
Rybicki (1990) coined ‘organisms at the edge of life’. Most
biologist use the terms ‘organisms’, ‘living beings’ and
‘individual’ as synonyms, even if there are differences
among them. Based on Rybicki’s (1990) definition, the use
of the term ‘organism’ places viruses within the Tree of
Life (where the living beings or organisms are), but the
problem with viral classification is not merely word choice.
Conventionally, viruses are not included into existing
biodiversity frameworks due to the following: (1) viruses
do not exist independent of an host and (2) viruses are not
cells (Moreira and López-Garcı́a 2009). The Tree of Life is
typically represented by relationships among cellular
organisms. The Tree of Life Web Project (ToL, http://tol
web.org/) includes viruses, but without relationships to
other living organisms and with a question mark at the root.
We know that viruses have their own genomes, but this
property is not considered sufficient to classify them as
living, because viruses lack an independent lifestyle
(Moreira and López-Garcı́a 2009). On the contrary, many
symbionts (e.g. parasites; intracellular bacteria, among
others) are considered ‘alive’ under the same conditions.
Until recently the genomes of studied viruses were very
small and viruses therefore appeared to be little more than
short DNA or RNA molecules coupled with a few proteins.
The vicious human immunodeficiency virus (HIV), for
example, is a lentivirus (i.e. a retrovirus), with a RNA
genome less than 10,000 bp long, encoding 19 proteins (Li
et al. 1992). It is not difficult to conclude HIV is non-
living; it is acellular, it has very few genes, and it is
completely metabolically and physiologically dependent
upon on its host. At the onset of the twenty-first century, La
Scola et al. (2003) described Acanthamoeba polyphaga
(mimivirus) (APMV), a virus of gigantic size and genome,
with a 400 lm capsid, 1.2 Mb genome and more than 900
coded proteins (La Scola et al. 2003). APMV was not an
isolated case, Arslan et al. (2011) described Megavirus and
Philippe et al. (2013) Pandoravirus, with these latter viru-
ses possessing larger genomes than those present in the
smallest eukaryotes. Therefore, recent wide screening
based on HTS resulted in unexpected observations of giant
viruses (also called ‘giruses’) and the genes and genomes
of these giruses generated theoretical problems (Claverie
and Abergel 2010). If it is relatively simple to refer to HIV
as ‘non-living’, what are the boundaries between non-liv-
ing giruses and living intracellular symbiotic bacteria?
Candidatus Hodgkinia cicadicola is amongst the smallest
123
584
known intracellular bacteria (less than 144 kb genome), a
symbiont within the cells of its insect host the cicada
Diceroprocta semicincta (McCutcheon et al. 2009). What
is Candidatus Hodgkinia cicadicola from a theoretical
point of view? Researchers are not unanimous and tend to
use the terms ‘bacteria’ (alive) or ‘incipient organelles’
(not fully alive) or ‘organelles’ (not alive). Mitochondria
were independent organisms about 2.5 billions years ago
(alive), but in the strict sense, they are now fully integrated
into the living eukaryotic cell (not alive). It is a foggy
landscape; philosophers would argue that a mitochondrion
is an individual, although not a living being. However, if
we consider the definition of ‘individual’ (see below), from
a strict biological sense, mitochondria cannot be considered
as biological individuals.
Intracellular symbionts with highly shrank genomes and
organelles with few genes are on life’s border. Sometimes,
these entities are composed of only few thousands DNA
bases. Currently, we use DNA as a proxy to detect past or
present life, even though DNA is a chemical compound and
technically is not alive, but it is a relevant component of a
living organism. It should be emphasised that at the
beginning of life on Earth, around 4 billions years ago,
conditions were different. Woese (1967), Crick (1968),
Orgel (1968) and Gilbert (1986) argued that an ‘RNA
world’ predated the ‘DNA world’. The first replicators
originated through abiogenetic processes (sensu Huxley
1870) and were far from being cells with nucleic acids (the
‘life-is-granted’ idea of life). Parsons et al. (1998) proposed
the first advances towards life occurred on mineral sur-
faces, such as silica-rich feldspars, with ‘proteins-like’
molecules. These structures were presumably not alive in
the strict sense we use today, but were the essential steps
towards the present-day conditions where nucleic acids
formed cellular components. Prusiner (1982) hypothesized
that life/not life condition on feldspars was similar to the
one currently observed in molecules such as prions, self-
replicated and transmissible proteins.
Even if the presence of RNA or DNA were not enough
to establish life, genomes and the cells in which the genetic
material were contained were considered stable pheno-
types, and supported the status of life and individuality.
Our modern views of life can be extended by case studies,
for example the canine transmissible venereal tumour
(CTVT), an iconic example of how difficult it is to place
borders around the definition of life. CTVT is a dog tumour
affecting the external genitalia, transmitted during mating
and other animal-to-animal interactions. The big surprise to
researchers was CTVT was transmissible as an allograft,
and even though the genome is aneuploid, CTVT showed
an internal coherence; recent common origin/ancestry
(between 250 and 2500 years ago), a clear ancestry from
the wolf/dog genome, and a reproductive system different
123
Evol Biol (2016) 43:582–595
from that of its ancestors (Murgia et al. 2006). In other
words, genome-based analyses showed that CTVT was a
highly modified and ‘‘parasitic dog’’, alive and with all the
peculiarities of a ‘new species’, which Frank (2007) called
‘malignant dog’.
In conclusion, although researches based on HTS cannot
provide definitive answers, it can shed new light on the
nature of ‘borderline’ entities such as viruses and cellular
entities, and when life first evolved. The most recent DNA
sequencing innovations brought life-scientists to previously
unexplored fields. It is now possible to examine biodiver-
sity at levels unimaginable just a few years ago. We are
certain HTS techniques cannot directly solve the problem
of defining life, but an enhanced knowledge of biodiversity
is pivotal to derive any global (and theoretic) view of life.
Presently, it is only through HTS that we will understand
the distribution, for instance, of giruses or even the pres-
ence of further life domains in the so-called ‘biological
dark matter’ (Wu et al. 2011; Rinke et al. 2013).
The Multifaceted Species Concept: Is It the Core
Unit for Biologists?
The word ‘species’ is Latin for what it is evident, what you
can see, a sight, look, view, appearance. Therefore, in its
original meaning a species is a visible organism, but many
problems are associated with the species definition. A
representative case is the evolutionary relationships of
African elephants, where a molecular approach to taxon-
omy clarified a complex question, which had eluded tax-
onomists for over a century. At the end of the 18th century,
it was assumed that there were two monotypic extant ele-
phant species: one in Africa (Loxodonta africana) and one
in Asia (Elephas maximus). At the very beginning of
twentieth century, Matschie (1900) described the minor
African elephant species (Loxodonta cyclotis) on a mor-
phological basis. Subsequently, questions regarding the
recognition of the two new African elephant species fol-
lowed and many researchers suggested the species repre-
sented two subspecies (i.e. Loxodonta africana africana
and Loxodonta africana cyclotis). Roca et al. (2001) later
provided molecular evidence that the two African ele-
phants represented two diverging lineages, which should be
considered two separated species, associated to forest and
savannah environments, respectively. The conclusion is
that in taxonomy genotypes are as important as phenotypes,
if not more important. In our African elephant example,
two phylogenetic lineages observed at the molecular level
(that you cannot easily see), are at the end considered
stronger than the similar/dissimilar phenotypes (that you
can see, but were not conclusive). Therefore, African ele-
phants demonstrated how species can be intrinsically
Evol Biol (2016) 43:582–595
difficult to delimit, even in apparently clear cases. Wilkins
(2011) reported ‘‘there are n ? 1 definitions of species in a
room of n biologists’’. Table 1 provides a non-exhaustive,
list of 29 species concepts. Questions such as: ‘‘How many
species are on the Earth?’’ or ‘‘How many species have
appeared in all the Earth’s history of life?’’ cannot be easily
answered without also delineating the species concept used
to answer the question (Claridge et al. 1997). Indeed,
adopting different species concepts can notably change the
numbers of species recognized. How is this possible? A cat
is clearly different from a dog, and ‘two are counted’ no
matter the species concept adopted! Unfortunately, even in
such a ‘clear’ case, there are exceptions. For example, dog
races show differences leading to doubts about their real
reproductive potential, but dogs, wolves and coyotes freely
interbreed. In many parts of the Tree of Life, boundaries
are fuzzy and the choice of different species concepts
results in different species counts. Species are evolving
biological entities, and considering species as static
objects, i.e. as in the typological species concept, is far
from theoretically correct. Species are more like clouds;
everyone can see them, and even count them when they are
few and scattered in a blue sky; but when the sky is cloudy
and when the clouds merge into one another, it is impos-
sible to place boundaries around them. However, clouds
are present in both blue and cloudy skies.
In the absence of clear boundaries lies the essence of the
species problem; we need to find the balance between
theory and practice. A practical procedure to define species
must be identified and implemented. When we are dealing
with something, the first step is to give it a name, as in
Linnaeus’ quote at the beginning of this essay. It might be a
type of horror vacui, where we are ‘scared’ of the
unnamed, and the entity becomes more unknown if it does
not have a name applied to it. However, this practice has
theoretical limitations. Walls cannot be raised around
entities that continually change. All biologists are aware
that even if not theoretically correct, the Linnaeus’ typo-
logical species concept is basically the only operational
concept we can rapidly apply. During Linnaeus’s time,
morphology was the only feature used to discriminate
organisms. Today, we use a vast set of discriminators (e.g.
morphology, anatomy, biogeography, embryology, molec-
ular data, among others) to support relationships and
classifications. In particular, DNA data seems highly
innovative, but theoretically, there are no differences from
the classical Linnaean approach. In both cases, species are
an ‘average’ model, the type, which is the reference used
for the specific species as the basis of comparison. What
differs here is not related to theory, but rests in the dis-
crimination process, using morphology or molecular data.
Carstens et al. (2013) reviewed the modern view of species
delimitation and emphasized the difficulties inherent in this
585
process. As Ernst Mayr (1998) stated: ‘‘Evolution is an
affair of phenotypes. It is phenotypes, not genes, that are
the objects (targets) of selection’’. Generally speaking this
can be considered true, but phenotypes are nowadays
identified on molecular basis too and this helps in delim-
iting biological entities.
This strategy is necessary because in certain sections of
the Tree of Life, relationships are more obscure or unre-
solved than in others. Bacteria and Archaea demonstrate
this most clearly. Simonsiella (Betaproteobacteria), for
example, is a genus of commensal bacteria, which reside in
the oral cavities of many animals, including mammals.
Recent findings reported more than 5000 Simonsiella lin-
eages or clades, which nearly correspond to the number of
known mammalian species. Hedlund and Staley (2002)
proposed Simonsiella experienced co-speciational pro-
cesses with their mammalian hosts. Staley (2006) indicated
delimiting bacterial species is often challenging. Consider
the well known bacterium Escherichia coli. Here the right
question is: what is this bacterium? Does E. coli represent a
single species or a mosaic of organisms? Originally, the
E. coli genome was mapped to about 4.700 genes, but after
sequencing hundreds of strains, it was clear that only a
small fraction of genes is shared among all the strains (less
than 2000), while up to 18.000 genes formed the diffuse
E. coli ‘‘pan genome’’ (Kaas et al., 2012). In such a fluid
scenario, the species concept has been often left to zoolo-
gists, who readily distinguish among well-defined sexual
populations. But species concepts are not limited to sexual
organisms. For example, the freshwater bdelloid rotifers
have species in which males are absent and traditional
sexual reproduction is impossible. Even in absence of sex
for millions of years, bdelloid rotifers have diversified to
more than 450 well-recognised species (Fontaneto et al.
2007). These organisms have evolved the capacity to
undergo desiccation-induced dormancy (anhydrobiosis)
based on their environment. Under desiccation, rotifers
experience frequent DNA double-strand breaks, resulting,
when rehydrated, in large horizontal gene transfer events
from other genomes (conspecific or not and even from
fungi and bacteria), evidence generated primarily by HTS
(see Flot et al. 2013; Umen 2015). Consequently, it is not
clear if bdelloid rotifers are really sex-free; we might
consider them hyper-sexual organisms, with elevated levels
of horizontal gene transfer!
In conclusion, the solution to the ‘species problem’ is far
from solved. We remain between the two ends of a con-
tinuum; on one end, researchers consider a species every-
thing an expert taxonomist of a particular branch of the
Tree of Life calls it ‘species’. On the other end, researchers
are thinking that the acceptance of a universal species
concept is only ‘‘a matter of time, (little) money investment
and researchers goodwill’’ (Staley 2009). Prior to choosing
123
 Table 1 Main species concepts, with definitions, synonyms and principal references
586

Species concept Definition Synonyms Citations

123
Agamospecies Asexual lineages, uniparental organisms (parthenogens and apomicts), Microspecies; paraspecies; pseudospecies; semispecies; Cain (1954), Stuessy (1990),
that cluster together in terms of their genome. May be secondarily quasispecies; genomospecies Eigen (1993)
uniparental from biparental ancestors
Autapomorphic The smallest aggregation of (sexual) populations or (asexual) lineages Phylospecies; Phylogenetic taxon species Rosen (1979), Nelson and
species diagnosable by a unique combination of character traits Platnick (1981); Wheeler
et al. (2000)
Biological species Groups of actually or potentially interbreeding natural populations which Biospecies; syngen; speciationist species Poulton (1904), Dobzhansky
are reproductively isolated from other such groups by reproductive (1935, 1937, 1950), Mayr
isolating mechanisms (1940, 1957)
Cladistic species Set of organisms between two speciation events, or between one Internodal species (in part); cohesion species (in part) Ridley (1989)
speciation event and one extinction event, or that are descended from a
speciation event
Cohesion species The most inclusive population of individuals having the potential for Cohesive individual (in part) Templeton (1989)
phenotypic cohesion through intrinsic cohesion mechanisms
Compilospecies A species pair where one species ‘plunders’ the genetic resources of – Harlan and De Wet (1963)
another via introgressive interbreeding
Composite species All organisms belonging to an internodon and its descendents until any Phylospecies (in part); Internodal species (in part); Kornet (1993)
subsequent internodon. An internodon is defined as a set of organisms cladospecies (in part)
whose parent–child relations are not split (i.e. have the internal relation)
Ecological species A lineage (or closely related set of lineages) which occupies an adaptive Ecospecies; ecotypes Turesson (1922), Van Valen
zone minimally different from that of any other lineage in its range and (1976), Sterelny (1999)
which evolves separately from all lineages outside its range
Evolutionary A population (or group of populations) that (1) is substantially Biospecies (in part); evolutionary species (in part); unit of Ryder (1986), Waples
significant unit reproductively isolated from other conspecific population units, and (2) conservation (in part); Integrative Operational (1991), Dodson et al.
represents an important component in the evolutionary legacy of the Taxonomic Units—IOTU (in part) (1998), Galimberti et al.
species (2012)
Evolutionary species A lineage (an ancestral-descendant sequence of populations) evolving Unit of evolution; evolutionary group Simpson (1961), Wiley
separately from others and with its own unitary evolutionary role and (1978, 1981)
tendencies
Genealogic Population subdivisions concordantly identified by multiple independent Biospecies (in part); cladospecies (in part); phylospecies Avise and Ball (1990)
concordance genetic traits constitute the population units worthy of recognition as (in part)
phylogenetic taxa
Genetic species Group of organisms that may inherit characters from each other, common Gentes (sing. gens) Dobzhansky (1950), Mayr
gene pool, reproductive community that forms a genetic unit (1969)
Genotypic cluster Clusters of monotypic or polytypic biological entities, identified using Polythetic species Mallet (1995)
morphology or genetics, forming groups that have few or no
intermediates when in contact
Hennigian species Species are reproductively isolated natural populations or groups of Biospecies (in part); cladospecies (in part); phylospecies Hennig (1950), Willmann
natural populations. They originate via the dissolution of the stem (in part); internodal species and Meier (2000)
species in a speciation event and cease to exist either through extinction
or speciation; stem species cannot survive speciation; a species must
comprise the entire branch segment between two speciation events
Evol Biol (2016) 43:582–595
 Table 1 continued
Species concept Definition Synonyms Citations

Internodal species Organisms are conspecific in virtue of their common membership of a Cladospecies and Hennigian species (in part); phylospecies Kornet (1993)
part of a genealogical network between two permanent splitting events
or a splitting event and extinction
Least inclusive A taxonomic group that is diagnosable in terms of its autapomorphies, Autapomorphic species (in part); evolutionary significant Pleijel (1999), Pleijel and
taxonomic unit but has no fixed rank or binomial unit (in part); phylogenetic species; Molecular Rouse (2000), Floyd et al.
Operational Taxonomic Units, MOTU (in part) (2002)
Evol Biol (2016) 43:582–595

Morphological Varieties between which there are no concept or few morphological Classical species; Linnaean species; monothetic species; Linnaeus (1758), Darwin
species intermediates monotypes; morphospecies; phenospecies; types (1859), Cronquist (1978)
Non-dimensional Species delimitation in a non-dimensional system (a system without the Folk taxonomical kinds Mayr (1963); Atran (1990)
species dimensions of space and time)
Nothospecies Species formed from the hybridization of two distinct parental species, Hybrid species; reticulate species Wagner (1983)
often by polyploidy
Phenetic species Clusters of individuals circumscribed using multivariate statistical Phenospecies; phena (sing. phenon); phenospecies; Sokal and Sneath (1963),
analysis. A class of organisms that share most of a set of characters operational taxonomic unit (OTU) Sokal and Crovello (1970)
Phylogenetic species The smallest diagnosable cluster of individual organisms within which Cladistic species; composite species (in part); genetic Eldredge and Cracraft (1980),
1—Diagnosable there is a parental pattern of ancestry and descent, beyond which there species; internodal species (in part); phenetic species; Cracraft (1983)
version is not polythetic species; taxonomic species
Phylogenetic species The least inclusive taxon recognized in a formal phylogenetic Autapomorphic species; cladistic species (in part); Mishler and Theriot (2000)
2—Monophyly classification. Taxa are ranked as species rather than at some higher internodal species (in part)
version level because they are the smallest monophyletic groups deemed
worthy of formal recognition
Phylogenetic species The smallest aggregation of (sexual) populations or (asexual) lineages Cladistic species (in part); composite species (in part); Wheeler and Platnick (2000)
3—Diagnosable/ diagnosable by a unique combination of character states internodal species (in part)
Monophyly version
Polythetic species Taxa having many ‘types’, i.e., geographic subspecies. Geographic Polytypic Species Mayr (1970), Mallet (1995,
populations are part of the same species if they intergrade in areas of 2004)
overlap
Recognition species The most inclusive population of individual biparental organisms that Specific mate recognition system Paterson (1978, 1981, 1985)
share a common fertilization system
Reproductive The most extensive units in the natural economy such that reproductive Hypermodern species concept; Biospecies (in part) Ghiselin (1974)
competition competition occurs among their parts
Successional species Arbitrary anagenetic stages in morphological forms, mainly in the Paleospecies; evolutionary species (in part); chronospecies Simpson (1943, 1961)
paleontological record
Taxonomic species Specimens considered by a taxonomist to be members of a kind on the Cynical species concept Blackwelder (1967), Kitcher
evidence or on the assumption they are as alike as their offspring of (1984)
hereditary relatives within a few generations. Whatever a competent
taxonomist chooses to call a species
587

123
588 Evol Biol (2016) 43:582–595

Mishler (1999), Hendry et al.

Integrated and modified from: Mayden (1997), Mallet (1995, 2006), Hey (2001); ‘‘Evolving thoughts’’ (http://scienceblogs.com/evolvingthoughts/2006/10/01/a-list-of-26-species-concepts/);
a position, it is fundamental to understand why we are
searching for a universal species concept. It is undoubtedly
for practical purposes, because comparisons among dif-
ferent organisms are easier if we adopt a unifying species
concept (see below for a possible proposal). Is there a
theoretical reason to adopt such a unifying concept, too?
Citations

(2000)

Making a decision is much less clear on this side of the

continuum. In the last 4 billion years of evolution, billions
of biological entities (for the sake of simplicity we will call
them ‘species’) have appeared on Earth. By definition,
evolution is changing, but not only phenotypes or geno-
types are changing as many could think. Evolutionary
processes, i.e. ‘the rules’, too are under modification,
because they do not exist without life. It is quite naive to
expect that species concepts are immutable over 4 billion
years. Throughout the history of biology, it was a great step
forward when biologists ceased to consider species as
fixed. In 2016, we readily accept our species concepts as
flexible and HTS is revolutionizing our way of thinking.
HTS is making it possible to delimit clouds of molecular
variation (i.e. MOTUs, see Table 1). However, a MOTU is
not a species, at least based on most (but not all) the species
concepts shown in Table 1. We disapprove of any attempts
Synonyms

to define a molecular species concept; it is simply not

necessary. On the contrary, HTS might facilitate new
–

approaches, in which taxonomy, nomenclature, phylogeny,

Species are no more real than any other hierarchical level in the tree of

‘rank-free taxonomy’ or by genotypic clusters described according to

theory, and practice are independent matters (see also

life. Species and other taxonomic ranks should be replaced either by

below).

Biological Individuals: How Our View Have

Changed

‘Individual’ is Latin for something ‘not divisible’; specific

their genetic divergence from other clusters

parts of an individual are not independent from the whole,

because these parts are not self-sustaining. But what does
‘not divisible’ actually mean?
Huxley (1851) provided a clear definition of individual
among metazoans: ‘‘The individual animal is the sum of
the phenomena presented by a single life; in other words, it
is all those animal forms which proceed from a single egg
taken together’’. In practice Huxley indicated a caterpillar
and a butterfly or a tadpole and a frog are the same indi-
Definition

viduals, even if they are morphologically quite different. In

his definitions, Huxley unwittingly advocated one of the
primary characteristics of individuality we can measure
Minelli and Fusco (2012)

today, but the attribute was not known at Huxley (also

known as the ‘Darwin’s bulldog’), genetic uniqueness.
Taxonomy without
Table 1 continued

However, it is not always so straightforward and there are

Species concept

notable exceptions to this rule. Monovular twins represent

a well known example: if we consider our species, there is
species

no doubt twins are separate individuals that are not

genetically unique (with the exception of epigenetic

123
Evol Biol (2016) 43:582–595
variation). In humans, this is a relatively rare event, but in
other animals, polyembryony is a standard condition. In
armadillos (Dasypus novemcinctus), every birth results in
four identical twins (Bagatto et al. 2000) and in the para-
sitoid wasps of the family Encyrtidae (Hymenoptera), such
as Copidosoma floridanum, up to 1.200–1.500 clonal
individuals are generated from a single egg (Strand and
Grbic 1997). Genetic uniqueness is not a mandatory
requirement to delimit an individual and the human Sia-
mese twins case (i.e. two bodies more ore less fused with
shared parts) poses even more doubt on the hypothesis. If a
general rule was assigned to consider two heads the means
to discriminate two Siamese individuals, Gould (1985)
emphasised it is not always that simple.
Barnes (1982) discusses a second case where the borders
of individuality among animals are far more difficult to
delimit. In Scyphozoa and Hydrozoa (phylum Cnidaria),
the medusae are generated clonally from a polyp. In these
cnidarians, what we might call ‘one individual’, even if it
might be better to call it an ‘organism’, originates several
forms, which were traditionally considered other individ-
uals, organisms, or generations. However, if we return to
Huxley (1851), why are a tadpole and a frog considered the
same individual, while a polyp and a medusa considered
two? The differences lie in the processes of modification;
metamorphosis versus metagenesis. A tadpole undergoes a
metamorphosis into a frog, while not only the genome is
the same, but some functional parts remain the same,
including the brain, heart, mouth and liver. In metagenesis
(Steenstrup 1842) polyps and medusae are considered
different organisms (i.e. different generations), because the
latter are generated from few cells in an asexual cycle,
while the medusae undergo a sexual reproductive stage
(Minelli 2009). Metagenesis is not limited to Cnidaria, but
found in at least in several invertebrates and in certain
chordates, such as salpae (belonging to the Tunicata sub-
phylum). The definition of an individual becomes more
difficult with plants, fungi, and bacteria. Sexuality and
asexuality are often mixed in these groups, therefore the
‘genet’ concept was introduced to identify the group of
organisms derived asexually from the same ancestor (i.e.
organisms sharing the same genotype), to differentiate
them from the ‘ramet’ concept (i.e. single individual within
the populations) (Harper 1977).
The above examples are only few cases that demonstrate
how genetic uniqueness is not sufficient to delimit an
individual (Santelices 1999). Indeed, another parallel
attribute of individuality is genetic homogeneity. Accord-
ing to Weismann (1904) not all the cells in an individual
contain heritable material, and consequently an individual
is not genetically homogeneous in all its cells; the only
exception are the germinal ones. On the other side, clonal
organisms show that somatic mutations, variations in
589
ploidy and other changes in somatic lineage, can be
directly heritable. Therefore, in different ways, sexual
organisms are genetically homogeneous in the germ line
(with all the variation introduced by the crossing over),
while asexual organisms are in somatic line, and both are
considerable ‘good’ individuals. It seems clear that there is
more than one way to think at individuals in biology.
Huxley (1932), nephew of Thomas Henry, followed in the
footsteps of his grandfather and suggested that, at least for
animals, autonomy and physiological unity are the essential
characteristics of individuality. In other words, two indi-
viduals are separated if they are autonomous independent
systems. However, this is not a sufficient attribute: the
typical exception is represented by social insects, in which
it has been claimed that individuality is shifted to the
colony level (Wilson 1971).
Santelices (1999) reported genetic uniqueness, genetic
homogeneity, and physiological integration were the three
attributes that defined individuality, and the absence of
congruency among these attributes resulted in different
types of individuals.
Eukaryotic cells exhibit a striking peculiarity. These
cells are intrinsically a community of Archaea and Bacteria
and Williams et al. (2013) recently questioned the exis-
tence of the entire domain. Indeed, eukaryotes are char-
acterised by the presence of two (animals), three (plants),
and even more genomes (animals such as aphids, tsetse
flies, and many others) in the same cell. Also, protists
without mitochondria (the so-called ‘amitochondrial
organisms’) have mitochondrial remnants in their cyto-
plasms, and/or mitochondrial genes in their nuclear gen-
omes derived from cells with mitochondria (Van der
Giezen 2009). Based on this evidence, we could say that all
the eukaryotes are formed by more than one individual
(now called mitochondria, chloroplasts, and other incipient
organelles), deeply integrated insofar as a clade separation
among them is not possible. Many biologists very often
forget this. Symbioses generated what Dupré (2010)
defined as ‘polygenomic organisms’. One of the most
famous (and unquestioned) examples of polygenomic
organisms are lichens; composites formed by an alga and a
fungus living in a symbiotic relationship. No one has
doubts that in lichens two different species, or two indi-
viduals, constitute a unitary species/individual. The
polygenomic organism resulted in a paradigm shift in how
we define an organism, including individuals and species.
Moya et al. (2008) and Casiraghi (2012) reported that
there are thousands of intracellular symbiosis cases, par-
ticularly where the fusion of individuals of different spe-
cies occurred. Buchnera and aphids; Wigglesworthia and
tse–tse flies; Wolbachia and some species of filaria nema-
todes are only few well-known cases. Other cases are ‘on
the edge’: almost all the animal guts host a rich bacterial
123
590
biodiversity, traditionally known as ‘gut or intestinal flora’,
and now defined as a ‘microbiota or microbiome’ (Leder-
berg and McCray 2001). The two new terms are largely
used as synonyms, but there is indeed a difference due to
the adoption of the suffixes ‘biota’ and ‘biome’, two dis-
tinct ecological concepts. A ‘microbiota’ is the sum of all
the living organisms present in a certain environment,
while a ‘microbiome’ is the entire environment, including
the organisms and all their attributes (genes, genomes), and
abiotic conditions, among others. The human microbiome
is of substantial scientific interest, therefore the USA
National Institutes of Health (NIH) promoted the largest
project ever launched on the characterisation of a sym-
biosis, the Human Microbiome Project (HMP, http://
hmpdacc.org/). Data on the human microbiome are
impressive. For example, human body is formed by around
1013 cells, while 10 times more (1014) cells form the gut
microbiota alone. Studies acknowledge the challenges to
formerly recognise bacterial species (see above), however
the count indicates about 1000 bacterial species reside in
our gut (Rajilić-Stojanović et al. 2007) and up to 2.000
species occur throughout the human body (Henderson
2005). This is not merely a matter of numbers. The
microbiome is most interesting due to the following: (1) it
is involved in metabolism (vitamins and hormones pro-
duction); (2) it is a part of the innate immune system; (3) it
produces an antibiotics; (4) it is the first barrier against
foreign harmful and pathogenic bacteria; (5) it consumes
unused energy substrates and many other functions are still
to be uncovered (Guarner and Malagelada 2003; Zilber-
Rosenberg and Rosenberg 2008). Based on these findings,
O’Hara and Shanahan (2006) defined the gut microbiome
as the ‘forgotten organ’ and McFall-Ngai (2008) as the
‘organ yet to be described’. This microbiome in its entirely
comprises a physical structure quite present, because it
represents up to 3 kg of our body weight. Hypothetically, if
cells of a thousand of species or 1014 cells (=individuals in
an approximate sense without considering the genet and
ramet problem, see above) can be re-evaluated and viewed
as ‘one organ’ in an individual of a single species, we can
now confirm that a human individual actually represents
plurality, rather than a single isolated organism. This view
might be quite a shock for many biologists, who are used to
thinking in terms of ‘one nuclear genome = one-organism’
(Sapp 2010). Lynn Margulis (1993) called ‘holobiont’ the
organism (=individual) deriving from the contribution of
more than one species/individuals. Wilson and Sober
(1989) proposed a narrower concept of the ‘superorganism’
to identify colonies or societies of individuals of the same
species living and functioning as one single organisms.
Years later, Zilber-Rosenberg and Rosenberg (2008) ter-
med the sum of all the genomic contributions to the same
phenotype the ‘hologenome’. Another term used to define
123
Evol Biol (2016) 43:582–595
holobionts and hologenomes is ‘symbiome’, which means
all the contributions to the resulting organism (Sapp 2004).
In terms of our microbiome, as we stated above, we host up
to 2.000 bacterial species in our holobiont. An average
bacterial genome contains 2.500 genes, and then each
human supports around five million bacterial genes. Most
of these genes are shared among different bacterial species,
which indicates these genes have the same function, even if
the gene sequence exhibits polymorphisms and a rough and
conservative estimate is that at least the 5 % of these genes
are unique, i.e. the genes have no equivalent in other
bacteria (Casiraghi 2012). Furthermore, the numbers are
impressive; She et al. (2004) reported we have *20.000
human genes in our hologenome and *250.000 exclusive
bacterial genes. We have to thank our bigger cells if we are
not just a slimy pile of bacteria!
One of the consequences of being a holobiont is that
alteration to the bacterial composition, called ‘dysbiosis’
(also known as ‘dysbacteriosis’) can result in pathological
conditions. This is not a surprise. A holobiont is a unit of
selection (see Table 1) and has all the features required to
be regarded as a ‘true’ individual (Brucker and Bordenstein
2013). Moreover, symbioses serve a preeminent role in
speciation (Brucker and Bordenstein 2012). One of the
main critics to the holobiont seen as a unit of selection is
that the symbionts transmission does not reach the fidelity
of host genome transmission. However, Funkhouser and
Bordenstein (2013) showed that the routes of bacterial
transmission through generations are broader than previ-
ously thought, therefore it seems redundant to underline the
transmission levels obtained are sufficient to influence
evolutionary processes.
Even if this is a very modern thought, quite ahead of his
time, von Goethe (1807, but written earlier, in 1795)
observed: ‘‘Every living being is not a unity but a plurality.
Even when it appears as an individual, it is the reunion of
beings living and existing in themselves, identical in origin,
but which may appear identical or similar, different or
dissimilar’’.
Eventually, we are left with two primary choices to
define individuality. First, we do not have one type of
individual among all the living forms, but at least eight
(Santelices 1999). This results from all possible combina-
tions of the three attributes of individuality: genetic
uniqueness, genetic homogeneity, and autonomy and
physiological independence. In other words, the unitary
individual (the ‘common vision’ in our view) is not the
rule, but just one case among several. The second choice is
more practical. A possible operational definition of indi-
viduality derives from a bridge between evolutionary lin-
eage and metabolism (Dupré and O’Malley 2009);
individuals are organisms that share common ancestry and
represent an ‘independent’ metabolic unit. However, we
Evol Biol (2016) 43:582–595
assume the concept of an independent metabolic unit is
highly questionable, because all organisms depend on other
living organisms to fulfil their metabolic requirements.
A final remark: even the individual level can be con-
sidered a transient phase. Consider the case of the slime
mould Dictyostelium discoideum, an amoeba belonging to
the phylum Mycetozoa. Like most of the protists, D. dis-
coideum is a unicellular organism (i.e. a unicellular indi-
vidual) living on the soil and feeding on bacteria. When
bacteria are not available, D. discoideum coalesce to form a
multicellular entity (i.e. a multicellular individual) and
moves on the soil in a manner reminiscent of slugs.
Movement continues until formation of a stalk structure,
which carries few cells with a thick wall on the top, the
fruiting body. Spores disperse a distance of several mil-
limetres from the fruiting body. Spores give rise to new
unicellular organisms, which will eventually form new
multicellular entity (Raper 1935). Organisms such as D.
discoideum challenge our scheme. Individuals are unicel-
lular or multicellular at different phases of the life cycle
and multicellular ones are simply an organised colony of
unicellular individuals. The life of multicellular eukaryotes
is generally not much different, because divisions of a
single cell (egg or zygote) originate multicellular individ-
uals; are we all not successions of unicellular and multi-
cellular forms, too?
The holobiont represents the modern view of the indi-
vidual. It is now clear, the general rule is ‘in the light of
evolution’, the individual is more a community than a
single entity. The holobiont theory was proposed previous
to the availability of HTS (Margulis 1993), but the exis-
tence of holobionts is deeply supported by the HTS tech-
nologies, in particular in all the cases in which
microbiomes/microbiotas are involved (see for instance
Foster et al. 2012). Similar to Pandora’s vase myth, HTS
has contributed to opening many new ways to look and
interpret the world, leading to a change of our opinion on
biological individuals.
A (Possible) Conclusion?
Once life arose from non-life and started to efficiently
propagate itself, it was organised in discrete entities. Life,
species, and individuals are those ‘natural’ entities, but the
problem remains; are these human artefacts in their defi-
nition and ranking?
Stephen Jay Gould (2002) wrote: ‘‘biologists spent more
than a fruitless century trying to decide whether the parts of
siphonophores [organisms resembling a medusa, like the
Portuguese man o’ war (Physalia physalis), but formed by
hundreds of individuals; present article, authors’ brackets]
are persons in a colony or organs of an organism’’.
591
Life and species can be viewed similarly. Practicality in
a theoretical context means we must consider common
origin from the Last Universal Common Ancestor (LUCA)
as a matter of fact. It is clear that biological entities do
exist, but defining what these entities are is far from simple.
Even Darwin was sceptical about species existence,
because he was unsure about the boundaries between the
ranks of varieties, species, and genera. Nevertheless, since
Linnaeus, the species is the core unit of the taxonomic
hierarchy. The time has come to start asking if this remains
true or if there is a need to update our overall vision. The
answer depends on our objective of the classification. All
classification types, not only in biology, are information
storage and retrieval systems. Wilkins and Ebach (2013)
proposed a radically different perspective, arguing classi-
fication of natural objects is often independent of theory.
Application of the simplest classification systems confirms
the primary objective is to speed up and univocally locate
the classified subjects. The subject matter is irrelevant; it
can be books, mechanical car parts, or biological species.
We classify them on the basis of similarity, but in a par-
ticular kind of classification (i.e. biological classification),
the history (i.e. phylogeny) that generated the forms to be
classified should also be included. Congruence between
classification and phylogeny was not always of interest.
Linnaeus did not classify organisms applying a strict
phylogenetic approach. Only later, and especially since the
advent of cladistics in the late 1960s of the last century
(Hennig 1966), it became ‘naturally obvious’. However, if
the practical aspect of classification (e.g. the ease of finding
or naming objects based on utility) is our priority, the
process of evolutionary classification was not strictly nec-
essary. A debate regarding this point that was thoroughly
discussed over the last 50 years of research (see for a
review Hennig 1966; Mayr 1969; Minelli 1993, 2009;
Mishler and Theriot 2000; Wheeler et al. 2000). In this
context, a description of Nimis’ (2001) imaginary world of
Bioutopia is appropriate. Nimis wrote a short, but very
evocative paper where he depicted a place where two tribes
(the Real taxonomists and the Name users) found a way to
live in peace by eliminating binomial nomenclature and
assigning identified entities a universal code without phy-
logenetic implications. In the last decades many things
have been written on this point and we do not address the
reviews here. However, in our opinion, Nimis’ message is
relatively simple; taxonomy, nomenclature, and phylogeny
are interconnected subjects, often applied together. It is
possible and ‘not heretical’, to consider them as indepen-
dent processes.
This is not too absurd; but we must be cognizant of the
risk of generating too many entities on the basis of simple
variations. Consider the species for which more data on
individuality are available: Homo sapiens, our own species.
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592
Each of us has a name given by different rules (father
based, father and mother based and so on). Most of us also
have a vernacular name deriving from a part of our name,
or from something else characterising us (e.g. physical or
behavioural features). And then everybody is also charac-
terised by a code number given to us at birth, called in
different ways (e.g. social security number, tax code, fiscal
code and so on), which unequivocally identifies human
individuals in administrative systems. If it is possible for
humans, why is it not possible for all the living organisms
(Nimis 2001)? Codes, vernacular and binomial names can
operate together.
The final consideration: why do we care? In our opinion,
the answer is directly linked to the dawn of the new
technologies for massive DNA sequencing, collectively
known as HTS. Through their applications, biologists
interested in identifying and conserving biodiversity are
moving back towards generalism, similar to the work
conducted in Linnaeus’ time. However, one notable differ-
ence exists, modern biologists are not truly classifiers, like
Linnaeus, contemporary biologists are simply identifiers,
because in modern taxonomy, identification and classifi-
cation are distinct processes. More than 15 years following
publication, Nimis’ (2001) world of Bioutopia is no longer
imaginary. Codes can replace names, identification is at the
centre and is not strictly dependent upon highly specialised
researchers (obviously within the confines of the scientific
method). Researchers have now the possibility to speculate
on the relationships among codes, and life and biological
entities now exist with or without names.
The adoption of this philosophy has consequences at the
theoretical level. For example, NASA is searching for alien
life in the space; the astrobiologists basic premise is life is
organised matter (defined in variety of ways) undergoing
Darwinian evolution. The focus on the evolutionary pro-
cesses emphasises the unit of selection is the core entity for
biologists, not species or individuals that, we have seen, are
very difficult to be correctly defined. No matter what you
have in your hands: a unit of selection might be a girus, a
cellular line, a species, or a holobiont, among other types.
Paraphrasing Theodosius Dobzhansky we can affirm that
today nothing in biology makes sense except in the light of
‘the unit’ of evolution.
Acknowledgments The authors are indebted to the anonymous
reviewers whose acute comments allowed us to improve consistently
our work. Authors are also indebted with Paul D. Roberts and Joanna
Schultz for the linguistic revision of the manuscript.
Compliance with Ethical Standards
Conflict of Interest The authors declare that they have no conflict
of interest.
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Evol Biol (2016) 43:582–595
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