[NEW] Species (Stanford Encyclopedia of Philosophy) | species singular – NATAVIGUIDES

First published Thu Jul 4, 2002; substantive revision Tue Aug 29, 2017

The nature of species is controversial in biology and philosophy. Biologists disagree on the definition of the term ‘species,’ and philosophers disagree over the ontological status of species. Yet a proper understanding of species is important for a number of reasons. Species are the fundamental taxonomic units of biological classification. Environmental laws are framed in terms of species. Even our conception of human nature is affected by our understanding of species. In this entry, three issues concerning species are discussed. The first is the ontological status of species. The second is whether biologists should be species pluralists or species monists. The third is whether the theoretical term ‘species’ refers to a real category in nature.

1. Overview

What are biological species? At first glance, this seems like an easy
question to answer. Homo sapiens is a species, and so is
Canis familiaris. Many species can be easily
distinguished. When we turn to the technical literature on species,
the nature of species becomes much less clear. Biologists offer over
twenty definitions of the term ‘species’ (Hey 2001).
These definitions are not fringe accounts of species but prominent
definitions in the biological literature. Philosophers also disagree
on the nature of species. Here the concern is the ontological status
of species. Some philosophers believe that species are natural
kinds. Others maintain that species are particulars or
individuals.

The concept of species plays an important role both in and outside of
biology. Within biology, species are the fundamental units of
biological classification. Species are also units of
evolution—groups of organisms that evolve in a unified
way. Outside of biology, the concept of species plays a role in
debates over environmental law and ecological preservation. Our
conception of species even affects our understanding of human
nature. From a biological perspective, humans are the species Homo
sapiens.

This entry discusses three issues concerning species.
The first issue is their ontological status. Are species natural
kinds, individuals, or sets? The second issue concerns species
pluralism. Monists argue that biologists should attempt to find the
correct definition of ‘species.’ Pluralists disagree. They
argue that there is no single correct definition of
‘species’ but a plurality of equally correct
definitions. The third issue concerns the reality of species. Does
the term ‘species’ refer to a real category in nature? Or,
as some philosophers and biologists argue, is the term
‘species’ a theoretically empty designation?

2. The Ontological Status of Species

2.1 The Death of Essentialism

Since Aristotle, species have been paradigmatic examples of natural
kinds with essences. An essentialist approach to species makes
sense in a pre Darwinian context. God created species and an eternal
essence for each species. After God’s initial creation, each species is
a static, non evolving group of organisms. Darwinism offers a different
view of species. Species are the result of speciation. No qualitative
feature—morphological, genetic, or behavioral—is
considered essential for membership in a species. Despite this change
in biological thinking, many philosophers still believe that species
are natural kinds with essences. Let us start with a brief introduction
to kind essentialism and then turn to the biological reasons why
species fail to have essences.

Kind essentialism has a number of tenets. One tenet is that all and
only the members of a kind have a common essence. A second tenet is
that the essence of a kind is responsible for the traits typically
associated with the members of that kind. For example, gold’s atomic
structure is responsible for gold’s disposition to melt at certain
temperatures. Third, knowing a kind’s essence helps us explain and
predict those properties typically associated with a kind. The
application of any of these tenets to species is problematic. But to
see the failure of essentialism we need only consider the first
tenet.

Biologists have had a hard time finding biological traits that occur
in all and only the members of a species. Even such pre Darwinian
essentialists as Linnaeus could not locate the essences of species
(Ereshefsky 2001). Evolutionary theory explains why. A number of forces
conspire against the universality and uniqueness of a trait in a
species (Hull 1965). Suppose a genetically based trait were found in
all the members of a species. The forces of mutation, recombination and
random drift can cause the disappearance of that trait in a future
member of the species. All it takes is the disappearance of a trait in
one member of a species to show that it is not essential. The
universality of a biological trait in a species is fragile.

Suppose, nevertheless, that a trait occurs in all the members of a
species. That trait is the essence of a species only if it is unique to
that species. Yet organisms in different species often have common
characteristics. Again, biological forces work against the uniqueness
of a trait within a single species. Organisms in related species
inherit similar genes and developmental programs from their common
ancestors. These common stores of developmental resources cause a
number of similarities in the organisms of different species. Another
source of similar traits in different species is parallel evolution.
Species frequently live in similar habitats with comparable selection
pressures. Those selection pressures cause the prominence of similar
traits in more than one species. The parallel evolution of opposable
thumbs in primates and pandas is an example.

The existence of various evolutionary forces does not rule out the
possibility of a trait occurring in all and only the members of a
species. But consider the conditions such a trait must satisfy. A
species’ essential trait must occur in all the members of a species
for the entire life of that species. Moreover, if that trait is to be
unique to that species, it cannot occur in any other species for the
entire existence of life on this planet. The temporal parameters that
species essentialism must satisfy are quite broad. The occurrence of a
biological trait in all and only the members of a species is an
empirical possibility. But given current biological theory, that
possibility is unlikely.

Other arguments have been mustered against species essentialism.
Hull (1965) contends that species have vague boundaries and that such
vagueness is incompatible with the existence of species specific
essences. According to Hull, essentialist definitions of natural kinds
require strict boundaries between those kinds. But the boundaries
between species are vague. In all but a few cases, speciation is a long
and gradual process such that there is no principled way to draw a
precise boundary between one species and the next. As a result, species
cannot be given essentialist definitions. (Hull’s argument against
species essentialism is very similar to one of Locke’s (1690[1975],
III, vi) arguments against kind essentialism.)

Sober (1980) raises a different objection to species essentialism. He
illustrates how essentialist explanations have been replaced by
evolutionary ones. Essentialists explain variation within a species as
the result of interference in the ontogenetic development of
particular members of that species. Organisms have species specific
essences, but interference often prevents the manifestations of those
essences. Contemporary geneticists offer a different explanation of
variation within a species. They cite the gene frequencies of a
species as well as the evolutionary forces that affect those
frequencies. No species specific essences are posited. Contemporary
biology can explain variation within a species without positing a
species’ essence. So according to Sober, species essentialism has
become theoretically superfluous.

In a pre Darwinian age, species essentialism made sense. Such
essentialism, however, is out of step with contemporary evolutionary
theory. Evolutionary theory provides its own methods for explaining
variation within a species. It tells us that the boundaries between
species are vague. And it tells us that a number of forces conspire
against the existence of a trait in all and only the members of a
species. From a biological perspective, species essentialism is no
longer a plausible position. Nevertheless, as we shall see in Section
2.6, some philosophers have recently tried to revive species
essentialism.

2.2 Species as Individuals

Let us turn to the prevailing view of the ontological status of
species. Ghiselin (1974) and Hull (1978) suggest that instead of
viewing species as natural kinds we should think of them as
individuals. Hull draws the ontological distinction this way. (Instead
of the phrase ‘natural kind,’ Hull uses the term
‘class.’) Classes are groups of entities that can function
in scientific laws. One requirement of such laws is that they are true
at any time and at any place in the universe. If ‘All copper
conducts electricity’ is a law, then that law is true here and
now, as well as 100,000 years ago on some distant planet. Copper is a
class because samples of copper are spatiotemporally unrestricted
—copper can occur anywhere in the universe. Individuals, unlike
classes, consist of parts that are spatiotemporally restricted. Think
of a paradigmatic individual, a single mammalian organism. The parts
of that organism cannot be scattered around the universe at different
times if they are parts of a living, functioning organism. Various
biological processes, such as digestion and respiration, require that
those parts be causally and spatiotemporally connected. The parts of
such an organism can only exist in a particular space-time region. In
brief, individuals consist of parts that are spatiotemporally
restricted. Classes consist of members that are spatiotemporally
unrestricted.

Given the class/individual distinction, Ghiselin and Hull argue that
species are individuals, not classes. Their argument assumes that the
term ‘species’ is a theoretical term in evolutionary
theory, so their argument focuses on the role of ‘species’
in that theory. Here is Hull’s version of the argument, which can be
dubbed the ‘evolutionary unit argument.’ Since Darwin,
species have been considered units of evolution. When Hull asserts
that species are units of evolution, he does not simply mean that the
gene frequencies of a species change from one generation to the
next. He has a more significant form of evolution in mind, namely a
trait going from being rare to being prominent in a species. A number
of processes can cause a trait to become prominent in a species. Hull
highlights selection. Selection causes a trait to become prominent in
a species only if that trait is passed down from one generation to the
next. If a trait is not heritable, the frequency of that trait will
not increase cumulatively. Hereditary relations, genetic or otherwise,
require the generations of a species to be causally and hence
spatiotemporally connected. So, if species are to evolve in non
trivial ways by natural selection, they must be spatiotemporally
continuous entities. Given that species are units of evolution,
species are individuals and not classes. (For recent responses to the
Evolutionary Unit Argument see Dupré 2001, Reydon 2003, Crane 2004, and Crawford 2008.)

The conclusion that species are individuals has a number of
interesting implications. For one, the relationship between an
organism and its species is not a member/class relation but a
part/whole relation. An organism belongs to a particular species only
if it is appropriately causally connected to the other organisms in
that species. The organisms of a species must be parts of a single
evolving lineage. If belonging to a species turns on an organism’s
insertion in a lineage, then qualitative similarity can be
misleading. Two organisms may be very similar morphologically,
genetically, and behaviorally, but unless they belong to the same
spatiotemporally continuous lineage they cannot belong to the same
species. Think of an analogy. Being part of my immediate family turns
on my wife, my children and I having certain biological relations to
one another, not our having similar features. It does not matter that
my son’s best friend looks just like him. That friend is not part of
our family. Similarly, organisms belong to a particular species
because they are appropriately causally connected, not because they
look similar (if they indeed do).

Another implication of the species are individuals thesis concerns our
conception of human nature (Hull 1978). As we have seen, species are
first and foremost genealogical lineages. An organism belongs to a
species because it is part of a lineage not because it has a
particular qualitative feature. Humans may be a number of things. One
of them is being the species Homo sapiens. From an
evolutionary perspective, there is no biological essence to being a
human. There is no essential feature that all and only humans must
have to be part of Homo sapiens. Humans are not essentially
rational beings or social animals or ethical agents. An organism can
be born without any of these features and still be a human. From a
biological perspective, being part of the lineage Homo
sapiens is both necessary and sufficient for being a human. (For
further implications of the individuality thesis, see Hull 1978 and
Buller 2005.)

2.3 Species as Sets

Some philosophers think that Hull and Ghiselin too quickly dismiss
the assumption that species are natural kinds. Kitcher (1984) believes
that species are sets of organisms. Thinking of species as sets is an
ontologically neutral stance. It allows that some species are
spatiotemporally restricted sets of organisms, that is, individuals.
And it allows that other species are spatiotemporally unrestricted
sets of organisms.

Why does Kitcher believe that some species are individuals and other
species are spatiotemporally unrestricted sets? Following the biologist
Ernst Mayr, Kitcher suggests that there are two fundamental types of
explanation in biology: those that cite proximate causes and
those that cite ultimate causes. Proximate explanations cite
the more immediate cause of a trait, for example, the genes or
developmental pathways that cause the occurrence of a trait in an
organism. Ultimate explanations cite the evolutionary cause of a trait
in a species, for example, the selection forces that caused the
evolution of thumbs in pandas and their ancestors.

For each type of explanation, Kitcher believes that there are
corresponding definitions of the term ‘species’ (what
biologists call ‘species concepts’). Proximate
explanations cite species concepts based on structural similarities,
such as genetic, chromosomal and developmental similarities. These
species concepts assume that species are spatiotemporally unrestricted
sets of organisms. Ultimate explanations cite species concepts that
assign species evolutionary roles. These species concepts assume that
species are lineages and thus individuals.

Kitcher is correct that biologists attempt to explain the traits of
organisms in two ways: sometimes they cite the ultimate, or
evolutionary, cause of a trait; other times they cite a structural
feature of an organism with that trait. A problem with Kitcher’s
approach is his characterization of biological practice. Biologists
since Darwin have taken species to be evolutionary units. A glance at
a biology text book will reveal that the evolutionary approach to
species is the going concern in biology. The groups that correspond to
Kitcher’s structural concepts are not considered species by
taxonomists. Groups of organisms that have genetic, developmental,
behavioral and ecological similarities, are natural kinds in biology,
but they are not considered species. Consider such groups of organisms
as males, females, tree nesters and diploid organisms. These groups of
organisms cut across species. For instance, some but not all humans
are males and many organisms in other species are males. Male is a
kind in biology, but it is not a species. Kitcher’s motivation for
asserting that species are sets is to allow spatiotemporally
unrestricted groups of organisms to form species. That motivation,
however, is not substantiated by biological theory or practice.

2.4 Species as Homeostatic Property Cluster Kinds

Another response to the species are individuals thesis is offered by
proponents of an alternative approach to natural kinds. According to
Boyd (1999a, 1999b), Griffiths (1999), Wilson (1999), Millikan (1999),
and Wilson et al. (2007), species are natural kinds on
a proper conception of natural kinds. These authors adopt Boyd’s
Homeostatic Property Cluster (HPC) theory of natural kinds. HPC
theory assumes that natural kinds are groups of entities that share
stable similarities. HPC theory does not require that species are
defined by traditional essential properties. The members of Canis
familiaris, for example, tend to share a number of common
properties (having four legs, two eyes, and so on), but given the
forces of evolution, no biological property is essential for
membership in that species. For HPC theory, the similarities among
the members of a kind must be stable enough to allow better than
chance prediction about various properties of a kind. Given that we
know that Sparky is a dog, we can predict with greater than chance
probability that Sparky will have four legs.

HPC kinds are more than groups of entities that share stable clusters
of similarities. HPC kinds also contain “homeostatic causal
mechanisms” that are responsible for the similarities found among the
members of a kind. The members of a biological species interbreed,
share common developmental programs, and are exposed to common
selection regimes. These “homeostatic mechanisms” cause the members
of a species to have similar features. Dogs, for instance, tend to
have four legs and two eyes because they share genetic material and
are exposed to common environmental pressures. An HPC kind consists
of entities that share similarities induced by that kind’s homeostatic
mechanisms. According to Boyd, species are HPC kinds and thus natural
kinds because “species are defined … by … shared properties
and by the mechanisms (including both ”external“ mechanisms and
genetic transmission) which sustain their homeostasis” (1999b,
81).

HPC theory provides a more promising account of species as natural
kinds than essentialism. HPC kinds need not have a common essential
property, so the criticisms of species essentialism are avoided.
Furthermore, HPC theory allows that external relations play a
significant role in inducing similarity among the members of a kind.
Traditional essentialism assumes that the essence of a kind is an
internal or intrinsic property of a kind’s members, such as the atomic
structure of gold or the DNA of tigers. HPC theory is more
inclusive because it recognizes that both the internal properties of
organisms and the external relations of organisms are important causes
of species-wide similarities. For instance, HPC theory but not
essentialism cites interbreeding as a fundamental cause of similarity
among the organisms of many species.

While HPC theory is better at capturing the features of species than
essentialism, does HPC theory provide an adequate account of species
as natural kinds? Here are two potential problems with HPC theory.
HPC theory’s objective is to explain the existence of stable
similarities within groups of entities. However, species are also
characterized by persistent differences. Polymorphism (stable
variation within a species) is an important feature of nearly every
species. Species polymorphisms are easy to find. Consider sexual
dimorphism: within any mammalian species there are pronounced
differences between males and females. Or consider polymorphism in
the life cycles of organisms. The lives of organisms consist of
dramatically different life stages, such as the difference between the
caterpillar and butterfly stages of a single organism. HPC theorists
recognize the existence of polymorphism, but they do not recognize
polymorphism as a central feature of species in need of explanation.
HPC theorists privilege and attempt to explain similarities. In
addition to Boyd’s ‘homeostatic’ mechanisms we need to
recognize ‘heterostatic’ mechanisms that maintain species
variation. (For further discussion of polymorphism in species see Ereshefsky and Matthen 2005 and Magnus 2008.)

A second concern with HPC theory involves the identity conditions of
species. The members of a species vary in their traits. Moreover,
they vary in their homeostatic mechanisms. Over time and across
geographic regions, the members of a single species are often exposed
to different homeostatic mechanisms. Given such variation, what
causes organisms with different traits and exposed to different
homeostatic mechanisms to be members of the same species? The common
answer is genealogy: the members of a species form a continuous
genealogical entity on the tree of life. A species’ homeostatic
mechanisms are mechanisms of one species because they affect organisms
that form a unique lineage. Boyd and promoters of HPC theory
recognize the importance of genealogy and see historical relations as
one type of homeostatic mechanism. However, Boyd does not see
genealogy as the defining aspect of species, and this goes against a
fundamental assumption of biological systematics: species are first
and foremost continuous genealogical entities. Boyd is quite clear
that similarity and not genealogical connectedness is the final
arbitrator of species sameness (1999b, 80). This assumption makes sense given
that Boyd believes that species are kinds and kinds are ultimately
similarity-based classes that play a role in induction. But this view
of the identity conditions of species conflicts with the standard view
in biological systematics that species are continuous genealogical
lineages (Ereshefsky 2007).

2.5 Species and Population Structure Theory

Another approach to species, which is in line with the view that
species are individuals, is offered by Ereshefsky and Matthen’s (2005)
“Population Structure Theory” (PST). PST treats similarity
as just one type of trait distribution in species. PST does not
privilege similarity over polymorphism, so PST offers a more inclusive
account of trait distributions in species than HPC theory. In
addition, PST highlights a common type of explanation in biology,
namely one that cites the population and inter-population structures
of species. Such population structure explanations explain trait
distributions in species, whether those distributions involve
similarity or dissimilarity.

Population structure explanations are pervasive in biology. Consider
a population structure explanation of sexual dimorphism within a
species. Male elk have a number of similarities, including having
large, fuzzy antlers. What explains this similarity? One cause, the
proximal cause, is the individual development of each male elk.
Another explanation, the distal cause, turns on relationships between
male and female elks. Male antlers are the result of sexual
selection. Such selection requires the participation of both male and
female elk. Looked at in this way, we see that the existence of
similarities within lower level groups (here within the genders)
depends on higher level groups (here species) and the diversity within
them. That is, polymorphism at the higher level, and the population
structure that binds polymorphism, is essential in explaining lower
level similarities within the genders and other sub-groups of a
species.

Population structure explanations are common, and arguably essential,
for understanding diversity and similarity within species. Such
explanations are also essential for understanding the identity
conditions of species. As we have seen, species are first and
foremost genealogical entities. Genealogy is an inter-population
structure: species are lineages of populations. So according to
biological systematics, species identity is defined in terms of
population and inter-populational structures, not organismic
similarity. PST theory properly captures the identity conditions of
species.

2.6 The New Biological Essentialism

Griffiths (1999), Okasha (2002), and LaPorte (2004) have
suggested a form of species essentialism which can be called
‘relational essentialism’. According to relational essentialism,
certain relations among organisms, or between organisms and the
environment, are necessary and sufficient for membership in a species.
Such relations, argue Griffiths, Okasha, and LaPorte, are species
essences. For example, they suggest that being descendent from a
particular ancestor is necessary and sufficient for being a member of
a species.

Devitt (2008) rejects relational essentialism. He argues that
relational essentialism fails to answer two crucial questions. The
taxon question: Why is organism a member of species ?
The trait question: Why do members of species typically have trait
? Devitt suggests that to answer these questions species need
intrinsic essences; and because relational essentialism only posits
relational essences, relational essentialism fails to answer these
questions. Devitt’s target is not merely to discredit
relational essentialism, but also to argue for a new form of intrinsic
biological essentialism. According to Devitt (2008), a species’
essence is the cluster of intrinsic properties and perhaps the
relations that cause the typical traits of a taxon’s members.
Let us consider Devitt’s critique of relational essentialism.
In doing so, we will learn about both relational essentialism and
Devitt’s intrinsic biological essentialism.

Recall the trait question: Why do zebras have stripes? Devitt (2008,
352ff.) argues that explanations that merely cite relations are
insufficient to explain the traits typically found among zebras. We
must cite intrinsic properties as well, and such properties are
essential intrinsic properties of zebras. Devitt is right that we
need to cite more than relations to explain why zebras have stripes.
Generally, to explain the occurrence of a homologue, such as stripes
in zebras, we need to cite both relations among organisms and
intrinsic factors within organisms. More precisely, embryonic zebras
have developmental mechanisms that cause zebras to have stripes.
These mechanisms are intrinsic features of embryonic zebras. But
those developmental mechanisms must be passed down from parent to
offspring, via genealogical relations. So a robust explanation of why
zebras have stripes cites both the relations and intrinsic properties
that cause stripes.

Given the observation that we should cite both genealogy and
developmental mechanisms to understand why zebras have stripes, should
we infer, as Devitt does, that the taxon Zebra has an intrinsic
essence? Some argue ‘no’ (Ereshefsky 2010a).
Biologists explain the characters of organisms by citing other
characters, without the added metaphysical claim that a character
cited in an explanans is essential for membership in a taxon.
Consider how a biologist explains the occurrence of stripes in a
zebra. In its embryonic state, a zebra has an ontogenetic mechanism
that causes it to develop stripes. That developmental mechanism is
neither necessary nor sufficient for membership in Zebra. Some zebras
lack that mechanism. Moreover, the developmental mechanism that
causes stripes in zebras causes stripes in a variety of mammals,
including cats. Generally, the intrinsic properties that cause
organismic traits do not coincide with taxonomic boundaries: they
cross-cut such boundaries. The belief that such intrinsic properties
are essential for taxon membership is not part of biological
theory.

Let’s turn to the taxon question: Why are certain organisms members of
species ? Relational essentialists argue that modern species
concepts posit relational properties, such as interbreeding,
genealogy, and occupying a specific niche, as the defining features of
species. Relational essentialists tell us that biologists do not
posit intrinsic properties as the defining features of species.
Devitt responds (2008) that citing the relations among the organisms
of a species does not explain why particular organisms are members of
a certain species. According to Devitt, saying that organism can
interbreed with other Homo sapiens leaves unanswered why
those other organisms are Homo sapiens. There’s an
unanswered regress: why are any of them Homo sapiens?
According to Devitt, to answer that question we must cite essential
intrinsic properties in organisms.

Has Devitt made the case for intrinsic essentialism? Perhaps not.
Once again, Why are certain organisms members of species ? According
to our best biological theory, if is an interbreeding species, then
those organisms have intrinsic reproductive mechanisms that allow them
to interbreed with one another. However, we do not know which
intrinsic mechanisms are mechanisms that cause an organism to be a
member of a particular species. We need some way of determining which
mechanisms cause an organism to be a member of one species versus a
member of another species. Here we must turn to relations: particular
population and genealogical relations among organisms. The answer to
why particular reproductive mechanisms are mechanisms of species is
that those mechanisms occur in organisms whose populations are
genealogically connected in a single lineage. Relations are
explanatorily prior in explaining taxon identity, not intrinsic
properties.

To reinforce this point, consider which aspects of an organism can be
changed while it remains a member of the same species, and which
aspects cannot be changed. The intrinsic reproductive mechanisms
within the organisms of a species can be changed, but being part of
the same lineage or gene pool cannot be changed. To make this more
concrete consider the case of ring species. A ring species consists
of a geographic ring of populations such that organisms in contiguous
populations can successfully mate, but organisms in populations at
distant links in the ring cannot successfully mate. Interestingly,
the organisms in distant populations of a ring species have different
reproductive mechanisms (Mayr 1963, 512ff.). Suppose Joe is a member
of a ring species. Joe could have had a different intrinsic
reproductive mechanism than the one he has. Imagine counterfactually
that he is a member of a different population of his ring species,
namely one with different reproductive mechanisms than those found in
his actual population. In this counterfactual situation Joe is still
a member of his species so long as we do not remove him from the
lineage and gene pool of that ring species. Generally, an organism in
a species can have a different reproductive mechanism and still be a
part of that species. But an organism cannot be removed from its
original lineage and put in another lineage and remain part of the
original species. When it comes to species membership, intrinsic
mechanisms within the organisms of a species can vary, but certain
relations among its organisms cannot vary (Ereshefsky 2010a). (For other critiques of Devitt’s intrinsic essentialism see Barker 2010 and Lewens 2012.)

Do the results of this section thus far imply that relational
essentialism is correct? Consider two traditional requirements of
essentialism highlighted by Okasha (2002). The membership
requirement: the essence of a kind provides the necessary and
sufficient conditions for membership in that kind. The explanatory
requirement: citing a kind’s essence is central in explaining the
properties typically associated with the members of that kind. Given
these two requirements Okasha offers the following argument. Because
certain relations are necessary and sufficient for membership in a
species, such relations satisfy the membership requirement of
essentialism. However, those relations do not satisfy the explanatory
requirement. According to Okasha, relations such as genealogy and
interbreeding fail to explain the traits typically found among the
members of a species. Instead, we must cite the “genotype and
its developmental environment” (2002, 204) to explain such
traits. Despite failing to meet the explanatory requirement, Okasha
thinks that certain relations are taxon essences. Okasha writes that
there is no a priori reason to retain the explanatory
requirement of essentialism and suggests that it should be dropped.
With the explanatory requirement out of the way and the membership
requirement satisfied, Okasha concludes that species have relational
essences.

The problem with Okasha’s relational essentialism is that if the
relations that serve as the identity conditions for a species are not
central in explaining the typical traits among a species’ members,
then such relations are not essences. Okasha too quickly jettisons a
core feature of essentialism: that the essence of a kind plays a
central role in explaining the typical features of a kind’s members.
Essentialists, from Aristotle to Locke, from Kripke to Devitt, believe
that essences figure centrally in explaining the traits typically
found among the members of a kind. If we give up that explanatory
component of essentialism we give up a core feature of essentialism, a
feature that distinguishes real essences from nominal essences.
Nominal essences demarcate membership in a kind, but they do not
explain the typical traits of a kind. Arguably, any approach to
natural kinds that aims to capture the kinds of science should
preserve this explanatory feature of kinds. So in the end, relational
essentialism is not essentialism because it fails to satisfy a core
aim of essentialism. (For a detailed response to Okasha’s relational essentialism see Pedroso 2014.)

3. Species Pluralism

Biologists offer various definitions of the term
‘species’ (Claridge, Dawah, and Wilson 1997). Biologists
call these different definitions ‘species concepts.’ The
Biological Species Concept defines a species as a group of organisms
that can successfully interbreed and produce fertile offspring. The
Phylogenetic Species Concept (which itself has multiple versions)
defines a species as a group of organisms bound by a unique
ancestry. The Ecological Species Concept defines a species as a group
of organisms that share a distinct ecological niche. These species
concepts are just three among over a dozen prominent species concepts in the
biological literature.

What are we to make of this variety of species concepts? Monists
believe that an aim of biological taxonomy is to identify the single
correct species concept. Perhaps that concept is among the species
concepts currently proposed and we need to determine which concept is
the right one. Or perhaps we have not yet found the correct species
concept and we need to wait for further progress in
biology. Pluralists take a different stand. They do not believe that
there is a single correct species concept. Biology, they argue,
contains a number of legitimate species concepts. Pluralists believe
that the monist’s goal of a single correct species concept should be
abandoned.

3.1 Varieties of Pluralism

Species pluralism comes in various forms (for example, Kitcher 1984,
Mishler and Brandon 1987, Dupré 1993, and Ereshefsky 2001).
Kitcher and Dupré offer forms of species pluralism that
recognize the species concepts mentioned above—biological
species, phylogenetic species, and ecological species—as well
as other species concepts. As we saw in Section 1.2, Kitcher accepts
species concepts that require species to be individuals, and he
accepts species concepts based on the structural similarities of
organisms. The latter type of species are not spatiotemporally
continuous entities. Such species merely need to contain organisms
that share theoretically significant properties. Dupré’s
version of species pluralism is more robust. He recognizes all of the
species concepts found in Kitcher’s version of
pluralism. Dupré’s pluralism also allows species concepts based
on similarities highlighted by non biologists. For example,
Dupré accepts species concepts based on gastronomically
significant properties.

If one thinks that the term ‘species’ is a theoretical
term found within evolutionary biology, then one might find
Dupré’s version of pluralism too promiscuous. If the question
is how the term ‘species’ is defined in biology, then how
it is defined outside of biology does not count. Think of a parallel
situation in physics. When we are interested in the scientific meaning
of the term ‘work’ we do not attend to its meaning in the
sentence ‘How was work today?’ Similarly, the use of the
word ‘species’ by culinary experts does not reveal the
theoretical meaning of ‘species.’

Kitcher’s pluralism is more circumspect: it limits species concepts to
those that are legitimized by theoretical biology. Still, one might
worry that Kitcher’s form of pluralism is too liberal. Kitcher’s
pluralism allows that some species are spatiotemporally continuous
entities (individuals), while other species may be spatiotemporally
unrestricted entities (natural kinds). As we saw in Section 2.1,
Hull’s evolutionary unit argument states that within the purview of
evolutionary biology, species must be individuals. Kitcher’s pluralism
does not satisfy this requirement. If one assumes that
‘species’ is a theoretical term in evolutionary theory and
that species are individuals, then Kitcher’s pluralism is too
inclusive.

Another version of species pluralism is found in Ereshefsky (2001).
This version of pluralism adopts Hull’s conclusion that species must
be spatiotemporally continuous lineages. Nevertheless, this version of
pluralism asserts that there are different types of lineages called
‘species.’ The Biological Species Concept and related
concepts highlight those lineages bound by the process of
interbreeding. The Phylogenetic Species Concepts highlight those
lineages of organisms that share a common and unique
ancestry. Ecological approaches to species highlight lineages of
organisms that are exposed to common sets of stabilizing selection. On
this form of species pluralism, the tree of life is segmented by
different processes into different types of species lineages.

It is worth noting that the motivation behind Dupré’s,
Kitcher’s and Ereshefsky’s versions of pluralism is ontological not
epistemological. Some authors (for example, Rosenberg 1994) suggest
that we adopt pluralism because of our epistemological
limitations. The world is exceedingly complex and we have limited
cognitive abilities, so we should accept a plurality of simplified and
inaccurate classifications of the world. The species pluralism offered
by Dupré, Kitcher, and Ereshefsky is not epistemologically
driven. Evolutionary theory, a well substantiated theory, tells us
that the organic world is multifaceted. According to Dupré,
Kitcher, and Ereshefsky, species pluralism is a result of a fecundity
of biological forces rather than a paucity of scientific
information.

3.2 Responses to Pluralism

Not everyone is willing to accept species pluralism. Monists (for
example, Sober 1984, Ghiselin 1987, Hull 1987, de Queiroz 1999, Mayden
2002, Brigandt 2003, Pigliucci 2003, Wilkins 2003, and Richards 2010) have launched a
number of objections to species pluralism. One objection centers on
the type of lineage that should be accepted as species. Some monists
allow the existence of different types of base lineages but contend
that only one type of lineage should be called ‘species’
(Ghiselin 1987). For instance, supporters of the Biological Species
Concept believe that lineages of interbreeding sexual organisms are
much more important in the evolution of life on this planet (Eldredge
1985, Lee 2003, Coyne and Orr 2004). They argue that only the
Biological Species Concept, or some interbreeding concept, should be
accepted.

However, adopting only an interbreeding approach to species has its
costs: it would exclude all asexual organisms from forming
species. Interbreeding requires the genetic contributions of two
sexual organisms. Asexual organisms reproduce by themselves, either
through cloning, vegetative means or self fertilization. Some reptiles
and amphibians reproduce asexually. Many insects reproduce
asexually. And asexuality is rampant in plants, fungi and bacteria. In
fact, asexual reproduction is the prominent form of reproduction on
Earth (Hull 1988, Templeton 1989). If one adopts an interbreeding
approach to species, then most organisms do not form species. This
seems a high price to pay for species monism.

Another objection to species pluralism is that pluralism is an overly
liberal position (Sober 1984, Ghiselin 1987, and Hull 1987). Pluralists
allow a number of legitimate species concepts, but how do pluralists
determine which concepts should be accepted as legitimate? Should any
species concept proposed by a biologist be accepted? What about those
concepts proposed by non biologists? Without criteria for determining
the legitimacy of a proposed species concept, species pluralism boils
down to a position of anything goes.

Species pluralists respond to this objection by suggesting criteria
for judging the legitimacy of a proposed species concept.
(Dupré 1993, Ereshefsky 2001). Such criteria can be used to
determine which species concepts should be accepted into the plurality
of legitimate species concepts. Candidate criteria are the epistemic
virtues that scientists typically use for determining the scientific
worthiness of a theory. For example, in judging a species concept, one
might ask if the theoretical assumptions of a concept are empirically
testable. The Biological Species Concept relies on the assumption that
interbreeding causes the existence of stable lineages. It also
assumes that organisms that cannot interbreed do not form stable
lineages. Whether interbreeding and only interbreeding causes the
existence of stable lineages is empirically testable. So the
Biological Species Concept has the virtue of empirical sensitivity.
Other criteria for judging species concepts include intertheoretic
coherence and internal consistency. Pluralists can provide criteria
for discerning which concepts should be accepted as legitimate. Thus
the ‘anything goes’ objection can be answered.

A recent response to species pluralism is de Queiroz’s (1999, 2005,
2007) General Lineage Concept. De Queiroz suggests that despite
differences among various species concepts, all such concepts agree on
one thing: species are “separately evolving metapopulation
lineages” (2005, 1263). De Queiroz writes that his conception
of species is the “single, more general, concept of
species” that reconciles all other species concepts (2007, 880).
What is the relationship between the General Lineage Concept and those
concepts? De Queiroz suggests that the General Lineage Concept
provides the necessary criterion for being a species. The properties
that other species concepts disagree over, for example, a lineage’s
occupying a unique niche, being monophyletic, or being reproductively
isolated, are contingent properties of species. They are
“secondary” properties of species (de Queiroz 2005, 1264).
All species taxa must be metapopulation lineages, but they can vary in
their secondary properties. De Queiroz contrasts the necessary
property of species from their secondary properties in another way.
Whereas the necessary property cited by the General Species Concept
captures the fundamental nature of species, the secondary properties
of species are merely “operational criteria” (2007, 882)
for “inferring the boundaries and numbers of species”
(2005, 264). According to de Queiroz, disagreements among other
species concepts merely concern operational and evidential issues.
Proponents of other species concepts are confusing
“methodological” disagreements with
“conceptual” ones (de Queiroz 2005, 1267).

One potential problem with de Queiroz’s attempt to unify the species
category is that proponents of other species concepts would disagree
with de Queiroz’s assertion that their disagreements are merely over
evidence for the numbers and boundaries of species. Proponents of the
interbreeding, ecological and phylogenetic approaches believe that
they are identifying different types of lineages (interbreeding
lineages, ecological lineages, phylogenetic lineages), not merely
disagreeing over evidence for the same type of lineage. For example,
when supporters of the interbreeding approach say that asexual
organisms do not form species they are making a conceptual or
ontological claim, not an operational claim. De Queiroz’s unified
approach seems to mischaracterize disagreements among proponents of
other species concepts.

Another problem is how the General Lineage Concept distinguishes
species from higher taxa. According to de Queiroz, species are single
lineages whereas higher taxa are clades of multiple lineages. What,
then, distinguishes a single lineage from a branch with multiple
lineages according to the General Lineage Concept? De Queiroz (2005,
1265) writes that the General Lineage Concept does not need to cite
the secondary properties mentioned in other species concepts to answer
this. However, de Queiroz offers no alternative criteria for
determining when a single lineage becomes a branch of multiple
lineages. Moreover, the secondary properties of other species
concepts are commonly used to make that determination. Therein lies a
problem with the General Lineage Concept’s attempt to unify the
species category. According to the General Lineage Concept, species
are lineages. But to determine what is a lineage we must turn to
other species concepts, and in doing so the heterogeneity of the
species category rears its head again. De Queiroz attempts to unify
the species category by asserting that all and only lineages are
species. But that just masks the heterogeneity of the species
category because what constitutes a lineage has multiple answers, and
those answers vary according to which species concept one adopts.

3.3 Microbiology and Pluralism

Much of the debate over species pluralism focuses on multicellular
organisms. In other words, the debate focuses on how to sort mammals,
birds, fish, plants, and other multicellular organisms into species.
However, most of life is not multicellular. Most organisms in the
world are single cell microbial organisms (Rossello-Mora and Amann
2001). Just as biologists sort multicellular organisms into species,
microbiologists sort microbial organisms into species. Advancements
in genetic technology in the last twenty yeas have caused an increase
in taxonomic work in microbiology, including ways to think about
microbial species. Microbial biologists have their own species
concepts—definitions of ‘species’ that apply to only microbial
organisms. Microbial species concepts vary, and as we shall see,
cross-classify microbial organisms into different species. Once again
we come to the question of species pluralism.

Consider some of the species concepts developed by microbiologists.
One microbial species concept, the Recombination Species Concept,
asserts that species are groups of microbes whose genomes can
recombine (Dykuizen and Green 1991). The motivation behind this
species concept is that though microbes generally do not reproduce
sexually, they form gene pools of organisms connected by
recombination. Another microbial species concept is Cohan’s
(2001, 467) ecological concept in which a “species in the
bacterial world may be understood as an evolutionary lineage bound by
ecotype-periodic selection.” According to Nesbo et al. (2006)
and others, these two microbial species concepts sometimes sort the
same organisms into different species. A third microbial species
concept, the Phylo-Phenetic Species Concept (Rossello-Mora and Amann
2001), is different than the first two. While the Recombination and
Ecological Concepts are based on biological theory about the nature of
microbial species, the Phylo-Phenetic Species Concept is designed to
obtain stable classifications of species that can be used in medical
and microbial research.

Yet another approach to microbial species uses genetic data to
determine phylogenetic relations and assigns organisms to species
according to those relations. Microbiologists use various types of
genetic data for recognizing microbial species, such as 16S rRNA
genes, DNA:DNA hybridization, ANI or average nucleotide identity, and
core or house-keeping genes. Using such genetic data to classify
microbes into species is complicated by the existence of lateral gene
transfer. Lateral gene transfer occurs when microbes share genetic
material with microbes near them. Lateral gene transfer is not the
transfer of genetic material due to reproduction, but a different way
microbes share genes. Lateral gene transfer is frequent in microbes.
(See O’Malley 2014 for an explanation of lateral gene transfer.)
Given the frequent occurrence of lateral gene transfer among microbes,
different parts of a microbe’s genome will have different
evolutionary histories. Microbiologists use different genes when
classifying microbes into species. As a result, they obtain different
classifications of species.

Stepping back from these details, we see that depending on the
microbial species concept or the type of genetic data used,
microbiologists will obtain different species classifications for a
particular set of organisms. One might wonder if this situation gives
us reason to be species pluralists when it comes to microbiology. Is
one microbial species concept, or one type of genetic data, better
than all the rest and we should adopt monism? Or is there no best way
to sort microbes into species but a variety of equally adequate ways?
If the latter is correct then we should be pluralists concerning
microbial species. For further discussion of microbiology and species
pluralism, see O’Malley and Dupré 2007, Franklin 2007,
Morgan and Pitts 2008, Doolittle and Bapteste 2007, Doolittle and
Zhaxybayeva 2009, Ereshefsky 2010b, and O’Malley 2014.

4. Does the Species Category Exist?

There is one other item concerning species pluralism worth
discussing. Suppose one accepts species pluralism. The term
‘species’ then refers to different types of lineages. Some
species are groups of interbreeding organisms, other species are
groups of organisms that share a common ecological niche, and still
other species are phylogenetic units. Given that there are different
types of species, one might wonder what feature causes these different
types of species to be species?

Perhaps they share a common property that renders them species. If one
adopts the thesis that all species are genealogical lineages, then a
common feature of species is their being lineages. However, this
feature is also shared by other types of taxa in the Linnaean
Hierarchy. From an evolutionary perspective, all taxa, whether they be
species, genera, or tribes, are genealogical lineages. We need to
locate a feature that is not only common in species but also
distinguishes species from other types of taxa.

Biological taxonomists often talk in terms of the patterns and
processes of evolution. Perhaps there is a process or a pattern that
occurs in species but not in other types of taxa. Such a process or
pattern would unify the types of lineages we call
‘species.’ Let us start with process. The Biological
Species Concept highlights those species bound by the process of
interbreeding. The Ecological Species Concept identifies those species
unified by stabilizing selection. The species highlighted by
Phylogenetic Species Concepts are unified by such historical processes
as genetic and developmental homeostasis. A survey of these different
species concepts reveals that species are bound by different types of
processes. So no single type of process is common to all
species. Arguably, none of these processes are unique to species
either (Mishler and Donoghue 1982).

What about pattern? Do species display a pattern that distinguishes
them from other types of taxa? If by pattern we mean ontological
structure, then species have different patterns. Species are
individuals, but they are different types of individuals. Species of
asexual organisms and species of sexual organisms have different
structures. Both types of species contain organisms that are
genealogically connected to a common ancestor. But the organisms in a
sexual species are also connected by interbreeding. Thus species of
sexual organisms form causally integrated entities: within a given
generation, their members exchange genetic material through sexual
reproduction. Species of asexual organisms do not form causally
integrated entities: their organisms are merely connected to a common
ancestor.

There are other suggestions for the common and unique pattern of
species. Many observe that the organisms of a species often look the
same or that the organisms of a species share a cluster of reoccurring
properties. To the extent that this is true, it is also true of genera
and some other higher taxa. The members of some genera tend to look the
same and have a cluster of stable properties. Another suggestion for
the pattern that distinguishes species is their ability to evolve as a
unit—species are the units of evolution, other types of taxa
are not. But again, many higher taxa have such unity as well (Mishler
and Donoghue 1982).

The above survey of candidate unifying features is far from
exhaustive. But the result is clear enough. Species vary in their
unifying processes and ontological structure. Furthermore, many
features that biologists and philosophers highlight as unique to
species occur in many higher taxa as well. Given this survey, what
position should we adopt concerning the nature of species? There are
several options. According to one option we should keep looking for
the unifying feature of species. This is the option favored by some
monists (Sober 1984). Contemporary
biology may not have discovered the unifying feature of species, but
that does not mean that biology will not find such a feature in the
future. To give up the search for the unifying nature of species would
be too hasty.

Another option starts with the assumption that the search for the
unifying feature of species has gone on long enough. Biologists have
looked long and hard for the correct definition of
‘species.’ The result of that search is not that we do not
know what species are. The result is that the organic world contains
different types of species. The conclusion drawn by some pluralists
(Kitcher 1984, Dupré 1993) is that the term
‘species’ should be given a disjunctive
definition. Species are either interbreeding lineages, or ecological
lineages, or phylogenetic units, or ….

A third option, like the previous one, assumes that biologists have
looked long enough for the unifying feature of species. In that
search, biology has learned that there are different types of lineages
called ‘species.’ But proponents (Ereshefsky 1998) of this
option do not opt for a disjunctive definition of
‘species.’ According to this option, we should doubt the
very existence of the category species. Those lineages we call
‘species’ vary in their patterns and
processes. Furthermore, the distinction between species and other
types of taxa is riddled with vagueness. Consequently, we should doubt
whether the term ‘species’ refers to a real category in
nature.

To better understand this third option it is useful to see more
precisely what is being doubted. Biologists make a distinction between
the species category and species taxa. Species taxa
are the individual lineages we call ‘species.’ Homo
sapiens and Canis familiaris are species taxa. The
species category is a more inclusive entity. The species category is
the class of all species taxa. The third option does not call into
question the existence of Homo sapiens or Canis
familiaris or any other lineage that we call
‘species.’ The third option just calls into question the
existence of the categorical rank of species. (For a recent defence of the reality of the species category see Currie 2016.)

5. Darwin and Species

What did Darwin mean by the word ‘species’? Answers to
that question vary (see Ghiselin 1969, Mayr 1982, Beatty 1992, Stamos
2007, Mallet 2008, Kohn 2008, Wilkins 2009, and Ereshefsky 2010c). Nevertheless, it seems that Darwin was an anti-realist when it
comes to the species category, though a realist concerning those taxa
called ‘species’ by competent naturalists. Consider what
he wrote to his friend, the botanist Joseph Hooker.

It is really laughable to see what different ideas are
prominent in various naturalists’ minds, when they speak of
‘species’; in some, resemblance is everything and descent
of little weight—in some, resemblance seems to go for nothing,
and Creation the reigning idea—in some, sterility an unfailing
test, with others it is not worth a farthing. It all comes, I believe,
from trying to define the indefinable. (December 24, 1856; in F. Darwin
1887, vol. 2, 88)

For Darwin, the word ‘species’ is indefinable. And he
thought it was indefinable because he was skeptical of the distinction
between species and varieties. For example, in the Origin of
Species, he writes, “I look at the term species as one
arbitrarily given for the sake of convenience to a set of individuals
closely resembling each other, and that it does not essentially differ
from the term variety” (1859 [1964], 52). In other words,
‘species’ is indefinable because there is no difference
between species and varieties. But why would Darwin think there is no
distinction between species and varieties? Darwin offers three
reasons (Ereshefsky 2010c). First, Darwin argues that no
process distinguishes varieties from species. Second, he contends
that any differences drawn between them lie on a seamless continuum
and are drawn for pragmatic reasons. Third, Darwin rejects the
distinction between varieties and species because it is built on ideas
concerning creation rather than natural selection. In what follows we
will just look at why Darwin thought there was no process difference
between species and varieties.

Chapter 8 of the Origin of Species titled
“Hybridism” is devoted to discussing whether hybrid
sterility serves as an adequate criterion for distinguishing species
from varieties. Such naturalists as John Ray and Buffon held that
hybrid sterility marked the species/variety boundary. They believed
that offspring from parents of different species are sterile, whereas
offspring from parents of different varieties of the same species are
fertile. Much of Darwin’s chapter on hybridism is dedicated to
providing counterexamples to the claim that hybrid sterility marks a
distinction between species and varieties. In the end, Darwin rejects
hybrid sterility as a criterion for distinguishing species and
varieties. He writes, “It can thus be shown that neither
sterility nor fertility affords a clear distinction between species
and varieties” (1859 [1964], 248).

Further evidence that Darwin doubted a process distinction between
species and varieties is found in Chapter 4 of the Origin,
titled “Natural Selection.” Darwin proposes two
principles, which he calls The Principle of Character Divergence and
The Principle of Extinction. Together these principles explain the
origin of new taxa and morphological gaps among taxa. The Principle
of Character Divergence has a familiar Darwinian starting point.
Suppose that a geographic region contains several closely related
groups of organisms. Within one of those groups, some organisms are
selected because they have a trait that gives them an adaptive
advantage. Divergent selection occurs in future generations when
organisms with even better adapted forms of that trait are selected,
eventually causing pronounced morphological gaps between that group of
organisms and its parent and sister groups (Darwin 1859 [1964],
112ff.). Darwin illustrates this process with a number of examples.
Consider his example of a pigeon fancier (1859 [1964],112). A pigeon
fancier is struck by the slightly longer beak of some birds. He then
selects birds with slightly longer beaks in that generation, and
continues to do so in subsequent generations until there is a
pronounced morphological gap between the selected group and the
original stock. Darwin argues that the process of divergent selection
causes the origin of new taxa and is the source of branching on the
tree of life.

The Principle of Extinction further explains the gaps we find in
biodiversity. As groups become more distinctive and better adapted to
their environment, their parental and sister groups are pushed to
extinction. This extinction of “intermediates,” as Darwin calls them,
causes the observed gaps among taxa (1859 [1964],121ff.). Extinction,
in other words, prunes branches on tree of life so that it has the
shape we observe. Together, the Principles of Character Divergence
and Extinction explain the origin of varieties and species, and the
observed patterns of biodiversity in the world. The relevant point
for our discussion of Darwin is that there is no special speciation
mechanism that marks the difference between species and varieties. As
Kohn (2008) notes, Darwin did not use the word ‘speciation’ in
the Origin. For Darwin, the origin of varieties and species
is due to divergent selection. As Darwin writes: “The origin of
the existence of groups subordinate to groups, is the same with
varieties as with species, namely, closeness of descent with various
degrees of modification” (1859 [1964], 423).

Thus far it has been suggested that Darwin doubted the existence of
the species category because he doubted the distinction between
species and varieties. What about those taxa called
‘species’ by competent naturalists, are they real taxa for
Darwin? It seems that Darwin was a realist when it comes to taxa. A
passage at the start of the Origin’s chapter on
classification, Chapter 13, confirms this. Darwin writes that
“[f]rom the first dawn of life, all organic beings are found to
resemble each other in descending degrees, so that they can be classed
in groups under groups. This classification is evidently not
arbitrary like the grouping of the stars in constellations”
(1859 [1964], 411). Those taxa (“groups”) identified by
competent naturalists can be real. And classifications of groups
within groups, if properly constructed, reflect the hierarchical
arrangement of taxa in the world. Thus, Darwin’s skepticism of the
species category did not extend to taxa and those taxa called
‘species.’

6. Summary

This encyclopedia entry started with the observation that at an
intuitive level the nature of species seems fairly obvious. But a
review of the technical literature reveals that our theoretical
understanding of species is far from settled. The debate over the
nature of species involves a number of issues. One issue is their
ontological status: are species natural kinds or individuals? A second
issue concerns pluralism: should we adopt species monism or species
pluralism? A third issue, and perhaps the most fundamental issue, is
whether the term ‘species’ refers to a real category in
nature. Even Darwin, it seems, doubted that ‘species’
refers to a real category in nature.

Italics are used for bacterial and viral taxa at the level of family and below. All bacterial and many viral genes are italicized. Serovars of Salmonella enterica are not italicized.

For organisms other than bacteria, fungi, and viruses, scientific names of taxa above the genus level (families, orders, etc.) should be in roman type.

Because abbreviations for restriction endonucleases are derived from the name of the organism (usually bacteria) from which they are isolated, they should be italicized.

SmaI was isolated from Serratia marcescens.

Taq polymerase, which is used in PCRs, was isolated from Thermus aquaticus.

Use italics for genus and species in virus names.

A/Cygnus cygnus/Germany/R65/2006

Italicize species, variety or subspecies, and genus when used in the singular. Do not italicize or capitalize genus name when used in the plural.

Listeria monocytogenes is

…listeria are; salmonellae; mycobacteria

The genus Salmonella consists of only 2 species: S. enterica (divided into 6 subspecies) and S. bongori. Most salmonellae encountered in EID will be serotypes (serovars) belonging to S. enterica. Put the genus and species in italics, followed by initially capped serotype in Roman (e.g., Salmonella enterica serotype Paratyphi). The genus shorthand “S.” should never be used without a species name

Correct: S. enterica

Correct: S. enterica serovar Typhimurium

Correct: S. enterica ser. Typhimurium

Incorrect: Salmonella Typhimurium

Incorrect: S. Typhimurium

Serotypes belonging to other subspecies are designated by their antigenic formulae following the subspecies name (e.g., S. enterica subspecies diarizonae 60:k:z or S. IIIb 60:k:z).

For an article about 1 genus, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, P. putida, P. fluorescens, and P. denitrificans.

For an article about multiple genera that each have a different abbreviation, the author can use abbreviation to introduce new species.

We studied Pseudomonas aeruginosa, Streptococcus pyogenes, P. putida, and S. felis.

For an article about multiple genera, some of which have the same abbreviation, write out first mention of new species.  Abbreviate later.

We studied the relationship between Trypanosoma cruzi and Triatoma infestans.

We found the relationship between T. infestans and T. cruzi to be…

For an article about several species of the same genus, the genus must be spelled out only in the title and at first use in the abstract, text, tables, and figures. It may subsequently be abbreviated for other species.

We studied Pseudomonas aeruginosa, P. putida, and P. fluorescens.

However, if >1 genus begins with the same letter in an article, the full genus name must be spelled out the first time it is used with a new species. On subsequent mentions of a species, the genus may be abbreviated.

Ticks were discovered on Canis lupus, Canis latrans, Cerdocyon thous, and Chrysocyon brachyurus, but C. lupus hosted the greatest number of ticks.

Bacteria

Italicize family, genus, species, and variety or subspecies. Begin family and genus with a capital letter. Kingdom, phylum, class, order, and suborder begin with a capital letter but are not italicized. If a generic plural for an organism exists (see Dorland’s), it is neither capitalized nor italicized.

Mycobacterium tuberculosis

family Mycobacteriaceae, order Actinomycetales

mycobacteria

Binary genus-species combinations are always used in the singular. Genus used alone (capitalized and italicized) is usually used in the singular, but it may be used in the plural (not italicized) if it refers to all species within that genus.

Salmonella enterica is…

Salmonellae are ubiquitous…

Do not use spaces for MRSA isolates.

Preferrred: USA300

Avoid: USA 300

Fungi

Use Valley fever, not Valley Fever, when referring coccidioidomycosis. The use of a lowercase “f” in “fever” is consistent with use in the Communicable Diseases Manual and with AMA style for Rift Valley fever.

Genes

Gene designations are generally italicized, which helps clarify whether the writer is referring to a gene or to another entity that might be confused with a gene. Style for genes varies according to organism.

There is no real consensus on style of depicting acronyms for Plasmodium genes, except that when referred to as genes, they are italicized; when referred to as proteins, they are not. The style is more dependent on the particular journal. In molecular microbiology the gene and species abbreviation, i.e., pf, is italicized and all of the term is in lowercase; pfmdr1, pfatp6, pvdhfr. This particular gene was presented in The Lancet as PfATPase6. The main idea is to be consistent throughout the manuscript.

Acronyms for Plasmodium genes are italicized when referring to a gene. When referring to a protein they are not italicized.

Many virus gene names are written in italics and are traditionally 3 letters, lowercase, although some will be written in all caps, roman. No definitive rules exist for naming such genes, and you will see them described in a variety of different ways.

src gene, myc gene, HA, NA

Bacteria gene names are always written in italics.

lacZ gene

Fungus gene names are generally treated the same as virus gene names (i.e., 3 italicized letters, lowercase). With a multigene family, a numeric notation is included. When different alleles of the same gene are noted, the terminology allows for a superscript.

Mitochondrial genes add an “mt” prefix to the 3- or 4-letter gene, which may or may not be in lowercase. Drug target genes are all capped, no italics.

msg1, msg2, msg3 (multigene)

xyz1 (different alleles of same gene)

mtLSU (mitochondrial genes)

DHPS and DHFR (drug target genes)

Cholera toxin gene is written as ctx, and cholera toxin gene subunit A is written as ctxA.

Insertion sequences are written as “IS” plus an italicized number (IS6110).

Human gene names are all caps and italicized. May be all uppercase Latin letters or a combination of uppercase letters and Arabic numbers, ideally no longer than 6 characters. Initial character is always a letter. No subscript, superscript, roman numerals, or Greek letters are used.

Similar gene names may exist for humans and mice. For example, AMA Manual of Style lists the following genes:

β2-microglobulin: B2m (mice) and B2M (humans)

CD5 antigen: Cd5 (mice) and CD5 (humans)

A list of human gene names is available at http://www.genenames.org/guidelines.html

Proteins

Proteins, the combinations of amino acids that make up plants and animals, including humans, often have the same name as a gene but are not italicized and always begin with a capital letter. For example, 1 of the outer surface proteins of Borrelia burgdorferi is named outer surface protein A. It is encoded by ospA (the gene), and the protein is OspA.

Proteins often have common names (e.g., β-galactosidase is the gene product of lacZ).

How to tell difference between proteins and genes? If a term is combined with 1 of the following words, it is probably describing a gene:

Promoter (e.g., P2 core promoter [of myc gene]); promoters are parts of genes, not proteins

Terminator, operator, attenuator sites

If term is combined with one of following words, it is probably describing a protein.

Repress—a protein represses, a gene doesn’t.

React—a protein reacts, a gene doesn’t

Heterodimerization

Elevated levels of ____ [A common usage error is for authors to write “elevated myc” when they mean: “elevated levels of myc.”]

Italicizing MMR is another common usage error. This term, which means “mismatch repair,” is never a gene, just an abbreviation for a process. But you may see “Mice with specific alterations in a number of MMR genes have been developed…”

Restriction Enzymes

Restriction enzymes are identified with a 3-letter designation of the bacterium from which they are isolated, plus a single-letter strain designation (as needed) and a roman numeral showing the order in which it was identified. The 3-letter bacterium designation should begin with a capital letter and is italicized; the rest of the enzyme name is set roman.

SmaI, EcoRI, BamHI

Viruses

Italics Use with Virus Names

A virus is not a species; a virus belongs to a species. Italicize species, genus, and family of a virus when used in a taxonomic sense. Note however, that it is fine to not mention taxonomy of a virus, especially one like dengue or polio that is well known.

Do not italicize a virus name when used generically. If you capitalize a virus name (other than one that has a proper name in it so that you must capitalize it), then you need to italicize it.

bovine kobuviruses, a kobuvirus, kobuviruses, but Kobuvirus spp.

The presence of West Nile virus was confirmed in mosquitoes and dead crows. (AMA Style Guide, p. 758).

Epidemic transmission of West Nile virus (WNV)…prompted aerial application.

The species West Nile virus is a member of the genus Flavivirus.

Family Bunyaviridae, genus Phlebovirus, species Rift Valley fever virus

Recent attention has been drawn to Toscana virus (family Bunyaviridae, genus Phlebovirus, species Sandfly fever Naples virus) in countries…

Acronyms Use with Virus names

It is permissible to use an acronym for a virus (e.g., WNV for West Nile virus), after defining it. However, do not abbreviate a species (including the species West Nile virus). In short, if you do italicize, don’t use an acronym.

Correct: West Nile virus (WNV; family Flaviviridae, genus Flavivirus) is transmitted to humans [here the virus is being transmitted, not the species name; so West Nile virus is roman type and may be abbreviated]. 

For viruses that begin with a Greek letter, write it out and close up space between the letter and the rest of the word.

            Betaherpesvirus

For human coronavirus, use the abbreviation hCoV. Be aware that there is a genus/species named Human coronavirus, which should be abbreviated as H. coronavirus, not hCoV.

For numbered echoviruses (e.g., echovirus 13), use the following format: E13 (do not use EV)

For hepatitis E virus, use the acryonym HEV.

Use a capital H for human virus abbreviations (e.g., HMPV, not hMPV), unless otherwise directed by author or precedent (see human coronavirus above).

For human enterovirus, use human EV, not HEV.  For numbered enteroviruses, use the following format: EV75.

For influenza virus, see separate section (i.e., following West Nile virus below).

For polyomaviruses, use the following:

KIPyV for KI polyomaviruses (formerly known as Karolinska Institute polyomavirus)

MCPyV, not MCV, for Merkel cell polyomavirus, and

WUPyV for WU polyomaviruses (formerly known as Washington University polyomavirus).

For West Nile virus, use WNV.

Influenza

On October 18, 2011, WHO published guidelines for the standardization of terminology of the pandemic A(H1N1)2009 virus (see http://www.who.int/influenza/gisrs_laboratory/terminology_ah1n1pdm09/en/index.html). The guidelines are intended to minimize confusion and differentiate the pandemic virus from the old seasonal A (H1N1) viruses circulating in humans before pandemic A(H1N1)2009 virus. In agreement with WHO guidelines, EID will use the following nomenclature for the pandemic A(H1N1)2009 virus:

influenza A(H1N1)pdm09 virus

 After a first mention of the full virus name, including the word “influenza,” it is sufficient to use “A(H1N1)pdm09”;  however, the word “virus,”  “infection,” or “outbreak” should be added to the name, as appropriate. If the term appears frequently, the abbreviation “pH1N1” may be used.

Examples of other influenza virus nomenclature used by EID:

avian influenza A(H7N9) virus

avian influenza A(H5N1) virus

As stated above for influenza A(H1N1)pdm09 virus, other influenza virus names can be shortened after a first mention that includes the word “influenza,” but, as appropriate, the word word “virus,”  “infection,” or “outbreak” should be added to the name. Examples: A(H7N9) virus, A(H7N9) infection, A(H7N9) outbreak.

The H and N subtype should always be in parentheses when it follows “influenza”: 

influenza virus A (H5N1) (for “influenza virus A subtype H5N1”)

A (H3N2)v (for “variant influenza A (H3N2)”)

When used alone, subtypes do not need parentheses but must be accompanied by the word “subtype.”

The H5N1 subtype is…

Different subtypes, such as H5N1…

Note: H5N1 is neither a virus, nor a disease; it is merely a subtype designation of influenza virus type A. If you want to drop anything later in the article, you may leave out the subtype designation. If only 1 virus is being studied, you can say in the Methods that influenza virus means influenza virus A subtype H5N1, and leave the subtype out from then on.

Influenza virus (H5N1) can have high or low pathogenicity. It is not redundant to include “highly pathogenic” in the title.

For information on this virus nomenclature style, adopted by several international organizations, see International Committee on Taxonomy of Viruses.

For influenza virus isolates, include the virus subtype, write out in full the host of origin (omit if human), include the site of isolation and strain number, and use the 4-digit year if the virus was isolated in 2000 or later. For viruses isolated during the 1900s, use the 2-digit year.

Incorrect: dk/Laos/3295/06

Correct: A/duck/Laos/3295/2006

Italicize genus and species of the host in isolate names.

A/Cygnus cygnus/Germany/R65/2006

The formal nomenclature for the designation of influenza viruses was revised and published by the World Health Organization (WHO). (WHO. A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull.World Health Organ. 1980;58;585–9). The full and correct nomenclature includes the type of virus (A, B, or C), the host of origin (except for human), the geographic site of isolation, the strain number, the year of isolation (4-digit year for viruses isolated in 2000 or later; 2-digit year for viruses isolated during the 1900s), and the subtype (16 possible H and 9 possible N subtypes).

Thus a type A virus isolated in 1995 from a Mallard duck in Memphis Tennessee with a strain number of 123 and an H5N1 subtype is designated:

Influenza A/mallard/Memphis/123/95 (H5N1).

Site can be abbreviated in human viruses, as in the following for which PR (Puerto Rico) and FM (Fort Monmouth) are well known and not written out.

Influenza viruses used were A/PR/8/34 (H1N1), A/FM/1/47 (H1N1), and
A/Thailand/SP-83/2004 (H5N1).

When referring to avian influenza viruses that have low pathogenicity, use the term “low pathogenicity avian influenza” not “low pathogenic avian influenza.” If used 3 or more times, the term can be abbreviated as LPAI.

When referring to avian influenza viruses that have high pathogenicity, use the term “highly pathogenic avian influenza” not “high pathogenicity avian influenza.” If used ≥3 times, the term can be abbreviated as HPAI.

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