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1 The General Problem: Discrete Names in a Continuous World

1 The General Problem: Discrete Names in a Continuous World

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Species Delimitation: Discrete Names in a Continuous World with Fuzzy Boundaries

been separated very long and have not accumulated such an amount of distinctness

that their identity as a distinct entity is obvious. Homo sapiens, for example, has not

even been described officially (Linnaeus’s famous “description” was nosce te ipsum

or “know thyself”), yet our status as a distinct species among extant organisms is

never questioned (it becomes much less clear when including extinct hominids).2 It

has been repeatedly argued in this book that because of the fractal nature of the Tree

of Life—its being composed of lineages within lineages—the identification of a

distinct level of lineages, the species category or rank, is a contentious issue. Names

and language, and therefore also taxonomy, are discrete, while evolution is continuous. This discrepancy is real and cannot be bridged, and this is what ultimately

makes species delimitation so difficult. The importance of this insight can hardly be

overestimated because it makes at least parts of the species debate inherently futile.

There are, however, other problems with respect to continuousness, not just the fact

that evolution is continuous. In fact, many biological concepts, and certainly many

that are important in the species debate, are a matter of degree and in that sense also

continuous. Reproductive isolation, for example, is a case in point: “Simply saying

that species are reproductively isolated fails to capture the point that reproductive

isolation is a matter of degree” (Ghiselin 1997, p. 100; see also Lee 2003). Horses

and donkeys sometimes, although rarely, produce fertile offspring—does that make

them a single species, although the two lineages clearly evolve independently of

one another? The Hennigian Species Concept with its emphasis on absolute reproductive isolation seems to insinuate this. And how about cases where one sex is

always sterile? Is it biologically meaningful to lump everything into the same

species that once in a blue moon produces fertile hybrids and thus introduces single

alleles into each other’s gene pool? There is a continuum from complete isolation

via occasional introgression and regular introgression confined to small fractions of

the genome to isolated “speciation islands” in the genome (see the crow example in

Sect. 5.4), and finally a completely homogeneous panmictic population. It is

becoming increasingly clear that what is considered to be the species boundaries,

those “phenotypes/genes/genome regions that remain differentiated in the face of

potential hybridization and introgression”, are “semipermeable, with permeability

(gene exchange) being a function of genome region” (Harrison and Larson 2014,

p. 795; see also Walsh et al. 2016).

Even more important is that not even allopatry can be unambiguously defined.

Under a lineage-based species ontology, species are separately evolving


Humans are an interesting example. It has independently been pointed out by several authors that

Phylogenetic Species Concepts, and in particular the dPSC, would result in the splitting of Homo

sapiens into several species (Willmann and Meier 2000; Ghiselin 2001; Zachos and Lovari 2013).

On the other hand, there is even evidence that palaeoanthropological data are in line with a single

anagenetic lineage for Homo in its totality (Van Arsdale and Wolpoff 2013; Wolpoff, personal

communication). This stands in clear contrast to the 10+ species of Homo that have so far been

described. The scientific and medial attention that comes with the description of a new fossil

human species may contribute to researchers being more prone to splitting in this case (White


6.1 The General Problem: Discrete Names in a Continuous World


population-level lineages. But when exactly are two lineages separately evolving?

This is a difficult question. The only seemingly objective solution, and one that has

indeed been pointed out, is to assign species status to the only population level that

can be (allegedly) delimited non-arbitrarily, i.e. the lowest. This means equating the

species category with allopatric populations because allopatric populations are by

definition separate lineages, regardless of whether or not they are diagnosable,

monophyletic, ecologically different, reproductively isolated, etc. Objectivity is

only attainable at the cost of accepting as species all spatially separate groups of

organisms: “If species are individuals, i.e. populational systems, it follows that

geographically isolated populations are different species” (Mahner 1993, p. 110).

As a consequence, it has been suggested to have not only one but two classification

systems—one that serves as a convenient information storage system but disregards

truly objective ranking criteria and one that is based on strict scientific and logical

consistency (e.g., Kunz 2012, p. 44). In other words: one would deliberately have a

classification of T species and one of (hypothesized) E species. Kunz (2012)

advocates the notion of species as gene flow communities, and therefore accepting

any kind of gene flow disruption as the ultimate arbiter (whether intrinsic or

extrinsic, temporary or permanent) is the only non-arbitrary way of delimiting

species. After all, gene pools in allopatry become abstract entities (Stamos 2003,

p. 196). Such a logically consistent system, however, is impossible to realize. It

would have to accept every little allopatric offshoot of a larger population as a

distinct species because the connection between the two is interrupted, even if this

is only temporarily the case. For example, every little propagule of every fly or

mosquito species that is dispersed in aircraft across the world and survives (and

reproduces?) would have to be considered a distinct species. The same holds for

every population of goats or tortoises on Mediterranean islands and every closed

breeding group in captivity. If you add to this the demand of the Hennigian

Convention that upon species splitting the ancestral species goes extinct, you will

have to rename the original fly or mosquito species every single time a propagule

gets dispersed—probably hundreds of times every day! It is very obvious that any

such attempt could at best mitigate the inconsistencies of our present system - a

truly objective system based on allopatric populations is unattainable in practice,

and if it were, it would serve no purpose. This is what I meant earlier when I said

that the (biological) baby is thrown out with the bathwater or that biological

relevance is sacrificed on the altar of logical consistency. But there is a deeper

lesson behind this example: allopatry is a matter of degree, too. How far away from

the mother population must organisms venture to count as “allo”-patric? One

kilometre or two? Twice the usual dispersal distance or only 1.5 times? And how

many individuals constitute an allopatric population? Is a single pair enough or

even a pregnant female? A single individual in asexual organisms? And how often

must the allopatric group reproduce, for one generation or two or 31? What is

seemingly an inconvenient but at least objective cut-off criterion turns out to be



Species Delimitation: Discrete Names in a Continuous World with Fuzzy Boundaries

very inconvenient indeed, but unfortunately not so objective after all.3 This is by no

means a new insight. Remember, for example, Poulton’s judgment quoted in Sect.

2.4: “transitions are infinite in their variety; while the subjective element is obviously dominant in the selection of gaps just wide enough to constitute interspecific

breaks, just narrow enough to fuse the species separated by some other writer,

dominant also in the choice of the specific characters themselves” (Poulton 1904,

quoted from Wilkins 2009b, p. 114). The conclusion that some draw from this is

species category nominalism (see Sect. 3.6): “Species are equivalent by designation, only not in terms of their state of evolutionary, genetic or ecological differentiation or divergence” (Heywood 1998, p. 211). But because a truly non-arbitrary

classification is impossible one might as well go on with a flawed but practical one

(but be aware of it!): “the species must continue to be defined pragmatically by

practising taxonomists in the way that most effectively divides the group of

organisms in question into units which it is useful to recognize and name, bearing

in mind the needs of the various user groups. Comparisons across classes of

organisms in terms of species must be treated as no more than general indications

of amounts of biodiversity, not as precise statistics” (ibidem). The last part of this

quotation encapsulates what is so important about having an objectively real

species rank: comparative analyses based on species taxa. The ramifications of

this will be discussed in Chap. 7.

It is worth noting that while messy situations are expected under an evolutionary

paradigm—in fact, the lack of messy situations would be a serious blow to the

theory of evolution, as has often been stated (e.g. Stamos 2003, p. 3324)—most

pairwise comparisons between any two populations of organisms on earth are

unequivocal as the introductory example of the elephant, mosquito and tulip has

shown. Similarly, nobody doubts the distinct species status of newly discovered

organisms that have no close living relatives,5 such as the coelacanth, the okapi or

Symbion pandora. It is only among taxa going back to a common ancestor in the

recent past that things become fuzzy (the grey area in the speciation process in

Fig. 5.2). However, this “excuse” only holds with respect to whether there are one

or two lineages. The problem of ranking these lineages remains.


Kunz (2012, p. 133) correctly argues that a descent community only has connection, but not

delimitation, and therefore boundaries must be added through convention. He views species as

gene flow communities as the solution, because gene flow communities show both connection and

delimitation. Again he is right. However, he is wrong when he believes that this is a clear-cut

solution because, as shown, even if all allopatric groups were considered distinct species, boundaries would still be vague due to the continuous nature of allopatry itself.


Stamos suggests the term “messyspecies” for the grey area along the sundering process of



Of course, every population or species has a closest relative, its sister taxon. This follows from the

unique origin of life on earth. What is meant here is that the closest living relative, i.e. the extant

sister taxon, and the newly discovered organism go back to a common ancestor that lived long

enough ago for the two daughter taxa to have diverged beyond doubt as to their distinct species


6.1 The General Problem: Discrete Names in a Continuous World


One almost universal consensus with respect to ranking, suggestions regarding

two separate classifications (see above) notwithstanding, is to assign species status

only to non-ephemeral entities to avoid the problem of having to name every shortlived allopatric population: “all concepts avoid naming formal species taxa where

they might be ephemeral or temporary (e.g., small geographically isolated

populations), even when they otherwise fit the criteria of the concept. Some

judgment of significance is involved” (Mishler and Theriot 2000b, p. 121). Mishler

and Theriot (ibidem, p. 132) compare this judgment of significance with respect to

species taxa with higher monophyla: not all of these must be named, just the ones

we deem worthy of it because we need this for our communication. “It is alright

[. . .] to be subjective if by that we mean naming only those lineages (at whatever

level) we have reason to talk about”. It should be remembered here that Mishler and

Theriot do not think that a distinct species level exists, but that the species rank is as

arbitrary as that of higher taxa and that only nested monophyletic groups exist. This

makes it easier for them to allow for subjective judgment, but in principle, the

question whether or not this is necessary is independent of their views of the species

rank. The avoidance of naming ephemeral entities is the reason why many authors

agree that species delimitation can only be meaningfully achieved in hindsight,

i.e. after lineages have been separated for enough time to evaluate whether the split

is or is going to be permanent. This is why Kornet, in her internodal species

concept, insists on permanent splits (strictly speaking, only extinction is conclusive

evidence of a split being permanent), and this is also the rationale behind the second

half of the Evolutionary Species Concept (“own evolutionary tendencies and

historical fate”). Stamos’s claim that this is teleological “backwards causation”

has already been rejected in Chap. 4 (see footnote 11).

Sober (1984) and O’Hara (1993) explicitly defend the retrospective approach in

species delimitation. O’Hara (1993) specifically analyzes the Evolutionary, Biological and Phylogenetic (diagnosability) Species Concepts, but in principle what

he says applies to any species concept: that they “depend upon prospective narration: upon notions of fate, temporariness, and permanence”, and he considers

“Wiley’s explicit recognition of future dependence, under the name of ‘historical

fate’, to be particularly insightful” (p. 242). Sober (1984, p. 339) argues in a very

similar fashion: “species individuation is retrospective [. . .] The founders were

founders of a new species precisely because of what happened later, and not in

virtue of anything special about them. In the same way, an offspring may be as

different as you wish from its parents. Whether it falls into a new species depends

on what happens later”. In a footnote to this paragraph, Sober cites an old TV

programme where someone read a newspaper whose headline reads “World War I

breaks out!” Of course, upon its outbreak World War I was not yet World War I

(that it only became when there was also a World War II), and Sober writes that

species delimitation is settled in the same way. That lineage divergence is, for quite

some time, reversible has been shown by incidents of so-called reverse speciation

where mate-choice-induced reproductive isolation broke down again (Seehausen

et al. 1997; Seehausen 2006; Maan et al. 2010, Vonlanthen et al. 2012, Grant and

Grant 2014, Kleindorfer et al. 2014; see Sect. 1.4). Upon the strict view of species

being irreversibly diverged lineages, speciation would not have been complete in



Species Delimitation: Discrete Names in a Continuous World with Fuzzy Boundaries

these cases and the term “reverse speciation” would be flawed, but this is only a

terminological issue. Also, accepting every permanent split as a speciation event

and thus the daughter lineages as species has the bizarre and unintended (although

logically consistent) consequence that an allopatric propagule that dies out after a

single generation would have to be assigned species status, and this “is not what is

meant by a species in most theories of speciation” (Ghiselin 1997, p. 115). The

decision, ultimately at least partly arbitrary, which level of distinctness one ranks as

specific will therefore have to be based not only on genealogy but on something else

as well. The obvious candidate—and the one that is being used by most—is some

measure of similarity (see Sect. 6.4).


The Tokogeny/Phylogeny Divide: Saviour

of the Species Rank?

The question if we can delimit species completely non-arbitrarily has been

answered in the negative in the preceding chapter. But that does not mean that

species delimitation must be completely arbitrary either. However, for the species

rank to be biologically meaningful, it has to be different from all other ranks that

lineages can have in the Tree of Life. That there is such a unique level is denied by

some whose position is called species category nominalism (see Sect. 3.6). Remember, for example, Mishler (1999, p. 309): “we have no and are unlikely to have any

criterion for distinguishing species from other ranks in the Linnean hierarchy,

which is not to say that particular species taxa are unreal. They are real, but only

in the sense that taxa at all levels are real. Species are not special”. Similarly,

Mishler and Theriot (2000a, p. 48) write that “there is no species problem per se in

systematics. Rather, there is a taxon problem. Once one has decided what taxon

names are to represent in general, then species taxa should be the same kind of

things, just the least inclusive”. And indeed, it is not easy to find a criterion by

which the species level could be uniquely described, although “[b]iodiversity does

appear to be clustered around species, even if un-sharply so, and species themselves

recognize these organized clusters” (Rieppel 2007, p. 378). Probably the only

qualitative break within the fractal pattern of the Tree of Life is the level where

reticulate relationships among organisms within lineages dissolve into the hierarchical relationships between lineages. This is the famous tokogeny/phylogeny

divide (Hennig 1966, especially his Fig. 6). It is the sundering of two populations

within which there is horizontal reticulation through reproduction but between

which there is not. There is only one such level in the Tree of Life, and it is at

the level of populations, which makes it the ideal candidate for an objective

demarcation criterion for the species category. Above this level, which is itself

phylogenetically indivisible, there is the realm of interspecific relationships as

analysed by phylogenetic analyses aiming at finding monophyletic groups; below

6.2 The Tokogeny/Phylogeny Divide: Saviour of the Species Rank?


this level is the realm of intraspecific population biology.6 Accordingly, this

distinction is viewed by many as the solution to the question about the species

rank. However, there are some serious problems with this view.

First of all, asexual organisms do not have tokogenetic relationships if by this

reticulation through sexual reproduction is meant.7 In asexuals, hierarchical relationships go down to the level of the individual organisms. In other words: there is

no tokogeny/phylogeny divide in asexuals. This leads us back to the question if

“species” can refer to the same thing in sexuals and asexuals or whether asexuals

form something else altogether (“agamotaxa” or “agamospecies”, see Sect. 5.1).

Perhaps we have to accept that a unique species level only exists in sexually

reproducing organisms. But then, reproduction is a continuum with exclusively

sexual and asexual reproduction as its extremes but many organisms in between. It

may thus not even be clear in all cases whether the tokogeny/phylogeny divide is

applicable or not. A second problem is that what the tokogeny/phylogeny divide

really denotes is the point where one reproductive community splits into two and

that is first and foremost the case when a formerly connected population splits into

two allopatric populations. That is, the real level of the tokogeny/phylogeny divide

sensu stricto is below what is usually recognized as the species level. To raise it to

the level where only non-ephemeral and (what we consider) biologically meaningful entities would be assigned species status, we have to refrain from classifying

recently sundered lineages but confine ourselves to those which, in hindsight (!),

have proved to be not only temporarily separate entities but lineages with a unique

“historical fate”. That is, the tokogeny/phylogeny divide alone is not enough—it

must be complemented by some kind of threshold to avoid assigning species status

to every allopatric population. Another problem is that gene flow occurs at higher

levels, too. Reticulation, according to Mishler and Theriot (2000a) occurs throughout the Tree of Life, and Vrana and Wheeler (1992, p. 68) argue that Hennig’s

figure showing the divide “presumes that some inexplicable process at the ‘Species’

level renders an entirely clean break between reticulation and divergence, that this

break is obvious, and the process is constant across all organisms. In other words,

this figure rather than an empirical fact, is an unfounded process statement”. That

this break is anything but “entirely clean” has, I think, become sufficiently clear so

far. In fact, rather than a break or line, it is an area with, once again, fuzzy

boundaries, and reticulation through hybridization can occur long after the splitting

of the lineages that we usually call species. The more species groups are analysed

genetically and the more sophisticated our genetic methodologies become, the more

it becomes obvious that interspecific introgression is rampant, that reproductive


These two levels, being represented by phylogenetics and population genetics, respectively, for a

long time developed independently and in parallel but were ultimately united by phylogeography

and the insight that stochastic processes within populations had deeper implications for phylogenetics (gene tree/species tree discordances) (see Sect. 5.6.1).


Mishler and Theriot (2000b) argue that tokogeny is not the same as reticulation but that it is

parent–offspring relationships in both sexuals and asexuals. This is, as far as I know, an unusual

interpretation, and in any case, they are of course aware of the lack of reticulation in asexuals.

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