A Higher Level Classification of All Living Organisms
A Higher Level Classification of All Living Organisms
Michael A. Ruggiero 0 1 2 3
Dennis P. Gordon 0 1 2 3
Thomas M. Orrell 0 1 2 3
Nicolas Bailly 0 1 2 3
Thierry Bourgoin 0 1 2 3
Richard C. Brusca 0 1 2 3
Thomas Cavalier-Smith 0 1 2 3
Michael D. Guiry 0 1 2 3
Paul M. Kirk 0 1 2 3
0 1 Integrated Taxonomic Information System , National Museum of Natural History , Smithsonian Institution, Washington, District of Columbia, United States of America, 2 National Institute of Water & Atmospheric Research , Wellington , New Zealand, 3 WorldFish-FIN, Los Banos, Philippines, 4 Institut Systematique, Evolution, Biodiversite (ISYEB) , UMR 7205 MNHN-CNRS-UPMC-EPHE, Sorbonne Universites, Museum National d'Histoire Naturelle , 57, rue Cuvier, CP 50, F-75005, Paris , France , 5 Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America, 6 Department of Zoology, University of Oxford , Oxford , United Kingdom , 7 The AlgaeBase Foundation & Irish Seaweed Research Group, Ryan Institute, National University of Ireland , Galway, Ireland, 8 Mycology Section, Royal Botanic Gardens, Kew, London , United Kingdom
1 Received: July 8 , 2014
2 Academic Editor: Erik V. Thuesen, The Evergreen State College, UNITED STATES
3 A Higher Level Classification of All Living Organisms
We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists' expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL's database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory backbone for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information files.
Competing Interests: The authors have declared
that no competing interests exist.
Biological classification (taxonomy) aims to simplify and order the immense diversity of life
into coherent units called taxa that have widely accepted names and whose members share
important properties. It synthesizes information concerning a great variety of characters (e.g.,
morphological; molecular: genes, metagenome, and metabolome; etho-ecological). There is
currently no consensus among the world's taxonomists concerning which classification scheme
to use for the overall hierarchy of life, in part because of the confusion resulting from Hennig's
 redefinition of previous terminology of classification, which has not been universally
accepted; the separate goals of cladification and classification ; and conflicting or unresolved
evidence for phylogenetic relationships. The continuing advances in the use of specialized
analytical tools from many different fields and their resulting conclusions and assumptions require
regular updates as advances in knowledge are made.
Biological classification can integrate diverse, character-based data in a phylogenetic
framework, which allows a broad user community to utilize the disparate knowledge of shared
biological properties of taxa. Phylogeny is, therefore, the basis for these biological classifications
but there is still strong debate over their accounting for evolutionary divergence or information
content other than the branching pattern . Accordingly, classifications have often been
labeled either phylogenetic or evolutionary, depending mainly upon whether or not they reject
paraphyletic groups [3, 4].
While the type of classification to be used to support further exploration and analysis of any
biological scenario may be important, it is not the subject of this paper. The proposed
classification does not address detailed phylogenetic questions and, while hierarchical and reflective
of phylogeny, is not itself a phylogenetic tree. The aim of this classification is to be a pragmatic
means of managing the ever-increasing knowledge of the diversity of life, its relationships,
characteristics, and properties. Indeed, the past two decades have witnessed an explosion in
biodiversity research and informatics, emphasizing the need for a quality list of accepted
scientific names of the more than 1.9 million described living species  and for greater consensus
on how to classify them at higher taxonomic ranks. Since 2001, Species 2000 and the Integrated
Taxonomic Information System (ITIS) have worked with their respective contributors to
complete a comprehensive species list, called the Catalogue of Life (CoL). The CoL Annual
Checklist (http://www.catalogueoflife.org/annual-checklist/2014/) already contains more than 1.6
million valid or accepted species names provided by more than 140 taxonomic databases
involving more than 3,000 taxonomists . More than 82% of the global species databases are
provided at the rank of class or below (includes 1.3 million species), and more than 63% are
provided at the rank of order or below (includes 1.0 million species). Owing to the
heterogeneity in higher level classification among the contributed databases, the CoL managers sought a
practical and coherent hierarchical classification that could serve as a framework for data
integration. Here we explain the rationale behind the consensus higher level classification that we
propose for CoL use.
Our goal, therefore, is to provide a hierarchical classification for the CoL and its
contributors that (a) is ranked to encompass ordinal-level taxa to facilitate a seamless import of
contributing databases; (b) serves the needs of the diverse public-domain user community, most of
whom are familiar with the Linnaean conceptual system of ordering taxon relationships; and
(c) is likely to be more or less stable for the next five years. Such a modern comprehensive
hierarchy did not previously exist at this level of specificity. In this sense it summarizes overarching
aspects of the tree of life, including both paraphyletic and monophyletic groups, both being
important in facilitating meaningful communication among scientists and between the scientific
community and society.
The most recent higher level classification to this level was published more than 30 years
ago, before the advent of modern molecular analysis . Beyond the immediate use for CoL,
the hierarchy is valuable as a reference for taxonomic and biodiversity research, as a tool for
societal communication, and as a stable classificatory backbone for biodiversity databases,
museum collections, libraries, and textbooks, to name a few applications.
When Linnaeus introduced his novel system of nature in the mid-18th century, he recognized
three kingdoms of nature: Regnum Vegetabile (plants), Regnum Animale (animals), and
Regnum Lapideum (minerals) that has long since been abandoned. However, as is evident from
the title of his work, he introduced lower level taxonomic categories (named class, order,
genus, and species), each successively nested within higher ranked categories. Linnaeus' system
has proven to be robust for more than 250 years (see the comprehensive discussion and
suggestions for dealing with potential conflicts in Vences et al. ). In modern-day classifications, the
starting point for botanical names is Linnaeus Species Plantarum  and for zoological names
it is the tenth edition of the Systema Naturae . Since Linnaeus, the expansion of knowledge
and the increase in the number of described species has required an expansion of the number
of hierarchical levels (ranks) within the system. The categories of family and phylum (or
division) were introduced in the early 19th century and many intermediate categories have been
added since. There is currently little agreement about the general names for categories above
that of kingdom; here we use superkingdom rather than empire or domain. In addition, there
are three separate codes that govern the assignment and use of scientific names, each with
different requirements and terminology and consequences for their classifications. For algae,
fungi, and plants (ICN: International Code of Nomenclature for algae, fungi, and plants), the
principle of priority does not apply above rank of family; for animals (ICZN: International
Code of Zoological Nomenclature), priority does not apply above the family-group ranks; and
for prokaryotes other than Cyanobacteria (ICNB: International Code of Nomenclature of
Bacteria), only the categories ranked as class and below are covered by the code. A recent paper
by the International Committee on Bionomenclature compares terminology among six
current nomenclatural codes and makes recommendations for their use in improving
In 2005, on behalf of the International Society of Protistologists, Adl et al.  presented a
nested eukaryote-only cladification that used the names of six supergroupsAmoebozoa,
Opisthokonta, Rhizaria, Excavata, Chromalveolata, and Archaeplastida (= Plantae) 
as the highest ranked eukaryote groups. Their schema was updated in 2012 , with Rhizaria
and Chromalveolata replaced by SAR plus four small hacrobian groups. Although these taxa
are nested, and ranked by a bulleted system, Adl et al. avoided the use of Linnaean higher
category names (phylum, class, order, family) that would have more usefully denoted rank.
Insofar as the nested groups comprise a mix of taxon names based on priority (i.e., according to the
year of introduction of the name), many individual genera as well as traditional taxon names
(family through class) end up having the same rank in the Adl et al. hierarchy, while at the
same time having different suffixes or none at all. The ranks assigned therein often seem to
reflect our present partial ignorance of relationships more than careful assessment of relative
phenotypic disparity as in Linnaean taxonomy. This is very confusing when these group
names (genus to kingdom) are used in isolation without regard to phylogenetic relativity.
Two of the great benefits of Linnaean-ranked categories and their standardized suffixes are
that they instantly relativize taxa that are otherwise unknown to the non-specialist and also
indicate the relative degree of phenotypic distinctiveness amongst groups. The overarching
higher level classification used by the CoL, therefore, uses the standard formal categories, as
it is intended to be simultaneously pragmatic and informative of both evolutionary
relatedness and relative phylogenetic subordination. A classification should be biologically
wellgrounded and widely useful. In its simplicity, it provides less detail about relationships than a
complete phylogeny but is still congruent with it . Our classification is not intended to
compete with a cladification such as Adl et al.sboth are valid ways of ordering the living
worldbut we would argue that theirs is less comprehensible to many in the public-domain
These actual complexities of phylogenetic history emphasize that classification is a practical
human enterprise where compromises must be made . We have therefore named only
groups generally considered to have had a monophyletic origin, even though some of them
may be paraphyletic (i.e., do not include all descendants of their last common ancestor) and
others, e.g., Euglenozoa, Rhizaria, Cercozoa, include subgroups (such as Euglenophyceae,
Chlorarachnea, and Paulinella) that evolved by the symbiogenetic merger of two
fundamentally different lineages , while others have had infusions of genes from elsewhere  and
therefore do not conform to any purely formal definition of monophyly. We have not adopted
the view that one should never accept paraphyletic groups in a classification but rather have
evaluated each case of paraphyly on its practicability and usage. In some cases (e.g., classical
bryophytes) we accepted the splitting of paraphyletic taxa into holophyletic groups (groups
with a monophyletic origin that also include all descendants of their last common ancestor, i.e.,
clades). In others we retained ancestral (paraphyletic) taxa when it seemed beneficial to do so
(e.g., Prokaryota, Protozoa, Crustacea, Sarcopterygii, Reptilia). For practical purposes we treat
Proteobacteria and Cyanobacteria as holophyletic phyla even though both exclude their
mitochondrial and chloroplast descendants, neither of which is now a bacterium but an
evolutionarily chimaeric cell organelle. We have conservatively retained several groups where evidence
for paraphyly or holophyly is contradictory, such as Archaea (Archaebacteria).
A panel of experts representing the major taxonomic disciplines was convened to review,
revise, and update the existing incomplete CoL hierarchy. These authors consulted more than
200 sources (see S1 Appendix), most of which were from recent taxonomic publications and
websites. The product is a current and practical classification that meets the panels established
goal. In achieving a consensus, the panel was required to make some compromises that may
require future revision as the related issues are resolved. While all of these individuals made
contributions to the hierarchy, not all necessarily endorse every aspect of it. The CoL classification
will undergo review and revision at five-year intervals to consider changes as necessary.
Results and Discussion
We are proposing a two-superkingdom (Prokaryota and Eukaryota), seven-kingdom
classification that is a practical extension of Cavalier-Smiths six-kingdom schema ; the latter has
been used, for example, in the compendious checklist of marine biota of Chinese seas  and
in the first comprehensive national inventory of biodiversity for New Zealand . For
each of these kingdoms we had to exercise our taxonomic judgment and reach a practical
compromise among diverse opinions and usages and conflicting evidence about certain
phylogenetic questions important for defining the boundaries between and ranks of major taxa,
including kingdoms. Our schema includes: the prokaryotic kingdoms Archaea
(Archaebacteria) and Bacteria (Eubacteria), and the eukaryotic kingdoms Protozoa, Chromista, Fungi,
Plantae, and Animalia. We have retained 14 ranks from superkingdom to order (Table 1).
Several key taxonomic issues, some not fully resolved, are discussed below.
The higher classification of prokaryotes is still somewhat unsettled. Woese and Fox  treated
Archaebacteria (Archaea) and Eubacteria (Bacteria) as separate kingdoms. Margulis and
Schwartz  recognized the superkingdom Prokarya, containing one kingdom Bacteria that
Number of Taxa
Main ranks are in bold type; unnamed taxa are not counted.
included a subkingdom Archaea; Cavalier-Smith also treated Archaebacteria and Eubacteria as
prokaryote subkingdoms [19, 29]. Commonly used sources of prokaryote names, such as the
List of Prokaryotic Names with Standing in Nomenclature (LPSN)  and the Taxonomic
Outline of Bacteria and Archaea (TOBA)  treat Bacteria and Archaea as separate domains
but are silent about the category of kingdom. While these sources list the names of phyla in
common use as a service to the user, they are not validly published under the ICNB. We have
not placed phylum names in quotation marks as they have but we have so designated a few
prokaryote names at lower ranks that are in common use but not (or not yet) valid. As no
prokaryote names above the ranks of class are covered by ICNB rules, there is no official higher
classification of prokaryotes  and any attempt at such is necessarily difficult. We have
chosen to adopt the classification in current use by the Catalogue of Life. It is derived from the
TOBA and recognizes Bacteria and Archaea as equivalent in rank to the eukaryote kingdoms.
We treat them as de facto kingdoms until there is a better resolution of their status. The
number of negibacterial phyla currently recognized  is probably excessive compared with
eukaryotes and mainly reflects uncertainty about the true relationships of many small phyla,
probably exaggerating the significance of their biological disparity. Greater use of multigene
trees rather than over reliance on rRNA gene trees alone may eventually allow further
simplification by grouping them into fewer phyla, possibly only about half the present
Protozoa and Chromista
Unicellular eukaryotes, usually called protists, comprise a polyphyletic group of eukaryotes
that do not undergo tissue formation through the process of embryological layering. They
include ancestrally unicellular eukaryotes directly descended from bacteria by the origin of the
nucleus, endomembrane, cytoskeleton, and mitochondria. Assigning them to separate
kingdoms was historically difficult when only light microscopy was available but is now
considerably facilitated because of advances in electron microscopy and gene sequencing.
Formerly, the unicellular amoeboid group Myxozoa with multicellular spores was included in
Protozoa but these protists are now firmly within the animal kingdom, having been proven to be
greatly simplified parasitic animals. Yeasts are unicellular fungi that evolved polyphyletically
from multicellular filamentous ancestors and are assigned to one of three higher fungal phyla.
Microsporidia are highly reduced intracellular parasites traditionally considered to be
Protozoa, but they have been known for two decades to be related to Fungi. At one time it was
thought microsporidia had evolved from Fungi and therefore were placed in that kingdom [19,
33]. For several years multigene trees were contradictory about whether microsporidia
branched within or diverged from Fungi. The latest evidence is that they are most closely
related to rozellids , which also have been treated either as Fungi or Protozoa. If this recent
phylogeny  is correct, both should be in the same kingdom. Here we take the view that the best
demarcation between Protozoa and Fungi lies immediately before the origin of the chitinous
wall around vegetative fungal cells and associated loss of phagotrophy . We therefore
include microsporidia and rozellids in Protozoa (vegetatively wall-less, typically phagotrophs)
not Fungi (vegetatively walled osmotrophs).
For decades, taxonomists have debated the boundary between Protozoa and Plantae. We
accept the view that it should be placed just prior to the evolutionary origin of chloroplasts and
that Plantae should comprise all eukaryotes with plastids directly descending from the initially
enslaved cyanobacterium, i.e., Viridiplantae (green plants), Rhodophyta (red algae), and
Glaucophyta (glaucophyte algae), but exclude those like chromists that got their chloroplasts from
plants secondarily by subsequent eukaryote-to-eukaryote lateral transfers. Therefore, all green
algae are included in Viridiplantae and Plantae and are excluded from Protozoa. The only
photosynthetic Protozoa are Euglenophyceae, which obtained their chloroplasts subsequently from
an enslaved green alga .
The boundary between Protozoa and Chromista has been more controversial. Chromista
was established to include all chromophyte algae (those with chlorophyll c, not b) considered
to have evolved by symbiogenetic enslavement of another eukaryote (a red alga) as well as all
heterotrophic protists descended from them by loss of photosynthesis or entire plastids .
With phylogenetic advances it has become clearer that alveolates (once considered Protozoa)
are related to chromistan heterokont algae (and related heterotrophic heterokonts) and more
distantly to Rhizaria, the three together forming the major group Harosa (equivalent to SAR).
Consequently, Chromista has been greatly expanded to include all Harosa as well as other
former protozoa that turned out to be related to haptophytes or cryptophytes. Chromista now
includes many groups once treated as Protozoa , an expansion followed here. In multigene
trees, this expansion is the most difficult part of the entire eukaryote tree to resolve. They
sometimes show one or both of Plantae and Chromista as a clade but often their major subgroups
are intermingled in contradictory ways [36, 37]. This may be a consequence of the
eukaryoteeukaryote chimaeric history of chromists that acquired some genes from red algae or of the
very rapid basal radiation of the robust corticate clade (i.e. Plantae plus Chromista). Because of
this, some question whether Chromista represents a clade, yet trees are still too poorly resolved
to eliminate the likelihood from cell evolutionary considerations that Chromista and Plantae
are genuinely distinct sister clades. Evidence that Harosa is a clade is very strong. Evidence
that Haptista plus Cryptista are a clade Hacrobia is strong on some trees but questioned by
Protozoa, like Prokaryota, is certainly a paraphyletic taxon ; Animalia, Fungi, Plantae,
and Chromista all evolved from it. In our hierarchy Protozoa comprises seven phyla, of which
four are probably clades and three paraphyletic. We do not consider it useful in a general
classification to subdivide the paraphyletic phyla into numerous smaller ones, often with only a
handful of species that most have never heard of, even though a few specialists might favor that
despite their constituent subgroups not differing radically in cell structure. For both Protozoa
and Chromista we have favored large groups with shared body plans, analogous to extremely
diverse animal phyla like Chordata and Arthropoda. The higher proportion of ancestral
(paraphyletic) phyla in Protozoa compared with terminal groups like animals and plants is
unsurprising because they were the first eukaryotes and they diverged early on but with many fewer
associated major changes in body plan than occurred during the much later radiation of
bilateral animals. Distinct early diverging protozoan clades can be remarkably similar
morphologically and biologically .
As stated earlier, we take the view that the best demarcation between Protozoa and Fungi lies
immediately before the origin of the chitinous wall around vegetative fungal cells and
associated loss of phagotrophy. We use an updated version of the higher classification presented in the
10th Edition of the Dictionary of Fungi . The evolutionarily convergent Oomycetes such as
the serious pest Phytophthora, formerly treated as Fungi, belong instead in phylum
Pseudofungi of the heterokont Chromista.
As with the other kingdoms, Plantae is classified in a variety of ways. Margulis and Schwartz
 restricted Plantae to land plants (embryophytes or higher plants) and popularized the use
of kingdom Protoctista to include lower plants (green, red, and glaucophyte algae) and lower
Fungi as well as chromists with classical protozoa. Many now consider such a kingdom too
broad and heterogeneous and the associated separation of lower and higher plants in different
kingdoms to be undesirable. Now taxonomists almost universally classify lower and higher
plants together in the single kingdom Plantae and lower and higher fungi within the single
kingdom Fungi. We have adopted this delimitation of Plantae here [19, 35] (for which
Archaeplastida [12, 18] is a less familiar recent synonym). The structure of plastid genomes and the
derived chloroplast protein-import machinery support a single origin of glaucophytes, red
algae, green algae, and embryophytes (land plants). The ancestral embryophyte is thought to
have originated from relatives of the Charales (stoneworts) or Coleochaetales (Charophyta).
Jeffrey  first grouped charophytes and embryophytes as a clade Streptophyta, which was
later validated as a superphylum  and reduced to phylum by Bremer .
Chase and Reveal  published a phylogenetic classification of land plants, reasoning that
If the major clades of green algae are recognized as classes, then all land plants, the
embryophytes, should be included in a single class, here recognized as Equisetopsida. This argument,
however, overemphasizes cladistic level compared with phenotypic disparity, and is contrary to
traditional assignment of phylum (or division) status to the main bryophyte, pteridophyte
and seed-plant subgroups. This latter treatment was exemplified in the 2008 Annual Checklist
of the CoL, which listed three bryophyte phyla, four pteridophyte phyla, and five seed-plant
phyla, reflecting the arrangement found in many university textbooks of the late 20th century
and in Margulis and Schwartzs Five Kingdoms . Here we recognize four embryophyte
phylathree of bryophytes (liverworts, hornworts, and mosses) and a single phylum
Tracheophyta for vascular plantswith all species characterized by a diploid phase having xylem
and phloem. Bryophyte specialists tend to treat each of the three major bryophyte groups
as phylaMarchantiophyta, Anthocerotophyta, Bryophyta [45, 46]. We have chosen a
conservative approach to the higher classification of plants, largely consistent with Mabberley
 for the embryophyte ranks above class, while using Chase and Reveal  and Stevens
 for the lower ranks.
The numbers of phyla and classes with extant species in kingdom Animalia differ according to
molecular and morphological partitioning in phylogenies  as well as the preferred
treatments of specialists of particular traditional phyla and where to draw the line between related
taxa and how to rank themthe ranking of phylum versus subphylum is sometimes rather
subjective. Based on the contributions of taxonomic experts to an outline of higher level
classification and survey of taxonomic richness [60, 61], as many as 39 animal phyla might be
recognized (more, if Porifera were abandoned as a phylum and constituent major clades given
higher rank ). Below we discuss some issues encountered in arriving at decisions for our
proposed classification, which accepts 34 animal phyla.
(1) Poriferaone phylum or three? Nielsen  argued that The three apparently
monophyletic sponge groups Silicea, Calcarea, and Homoscleromorpha do not constitute a
monophyletic group, and the phylum Porifera thus has to be abandoned. More recent
studies alternatively support paraphyly  or holophyly [58, 64] of sponges. Until the issue is
resolved, we will follow the Porifera community  in retaining one phylum Porifera with
(2) Status of Myxozoa. Recent work on the vermiform myxozoan Buddenbrockia has
demonstrated conclusively that myxozoans are extremely simplified Cnidaria, possibly
Medusozoa [68, 69]. We classify Myxozoa as a subphylum of Phylum Cnidaria.
(3) Flatwormsmonophyletic or not? In 1995, Nielsen  wrote The delimitation of
the phylum [Platyhelminthes] is not much in question, but recent molecular analyses,
combined with a careful reconsideration of morphology and anatomy, have confused the
classification of Platyhelminthes, affecting particularly Acoela, Xenoturbella, and Nemertodermatida.
Egger et al.  reviewed the evidence, noting the contrast between morphological and
phylogenomic data. Whereas the stem-cell system and the mode of replacing epidermal cells unite
both Acoela and Rhabditophora and are not found in any other bilaterian lineage,
phylogenomic data support a separation of these two groups, a conclusion reached by Philippe et al.
 based on mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions,
and miRNA complements. We follow Philippe et al.  and Tyler and Schilling  in
uniting Acoela, Xenoturbella, and Nemertodermatida as the deuterostome phylum
Xenacoelomorpha. The remaining internal classification of Platyhelminthes is also somewhat problematic.
We propose a classification that is based in part on Riutort et al.  and Tyler .
(4) Phylum Gnathifera or phyla Acanthocephala, Gnathostomulida, Micrognathozoa,
and Rotifera? Until recently, all four of these groups were commonly treated as separate
phyla [28, 61, 7680]. However, numerous recent molecular and morphological analyses nest
Acanthocephala within Rotifera . A syncytial epidermis links rotifers, Seison and
Acanthocephala; Ahlrichs [87, 88] proposed Syndermata for this clade. As revealed by
transmission electron microscopy  and scanning electron microscopy , the jaw apparatus of
gnathostomulids and rotifers is remarkably similar. That of Seison is less obviously
homologous  and the Seisonidea may have diverged from rotifers at an early stage of their
evolution. On the other hand, Seison has similar sperm to acanthocephalans and the epidermis of
both groups contains bundles of filaments. Limnognathia maerski, representing a new category
of organism (Micrognathozoa) from cold fresh waters in Greenland and the Crozet Islands [92,
93], has a remarkable jaw apparatus (the most complicated known among invertebrates) with
clear homologies, in both the jaw elements and musculature, with the trophi in Rotifera and
the jaws in Gnathostomulida. The jaw apparatus and musculature, as well as molecular
analyses, unite these taxa as a clade known as Gnathifera (see [86, 92]). In the analysis by Giribet
et al. , the issue remained unresolved, as Micrognathozoa appeared independent of
Gnathostomulida and Rotifera, with unclear affiliation. Edgecombe et al.  and Nielsen 
retain phylum status for Gnathostomulida, Micrognathozoa, and Rotifera but not
Acanthocephala. We treat each of the major gnathiferan groups as a phylum, including Acanthocephala,
following Monks and Richardson , though some of us think that the number of gnathiferan
phyla ought to be substantially reduced when their phylogeny, including ingroup relationships
of Rotifera sensu lato, is more firmly established.
(5) The scalidophoran phyla Adrianov and Malakhov  erected phylum
Cephalorhyncha for Kinorhyncha, Loricifera, Priapula, and Nematomorpha. The first three of these
phyla have in common an eversible snout (introvert) with scalid spines and inner and outer
retractor muscles, a similar excretory filter (protonephridium), and similar sense organs,
providing strong justification for uniting them in a single clade, the Scalidophora . There is also
molecular support, though not unanimity, for a clade of Kinorhyncha, Loricifera, and Priapula,
known as Scalidophora. On the other hand, Kinorhyncha has internal and external body
segmentation lacking in the other groups. Neuhaus and Higgins  noted that conflicting
evidence exists for every one of the possible sister-group relationships among these phyla and
prefer to keep them separate in a superphylum Scalidophora (which is preferred over
Cephalorhyncha, the latter name originally including the Nematomorpha). We recommend separate
scalidophoran phyla, though the number might be greatly reduced when the phylogeny
(6) The chordate subphyla Cephalochordata and Urochordata Some sequence analyses
have questioned the monophyly of Chordata [99, 100]. Nielsen  maintains Urochordata
(or Tunicata) and Cephalochordata as separate phyla, whereas the group Urochordata is closer
to Vertebrata (craniates), in a clade Olfactores, than Cephalochordata. We retain all three
groups as traditional chordate subphyla.
Many users of classifications would prefer a stable, unchanging system. Yet classifications
are syntheses of biological knowledge, particularly contemporary phylogenetic understanding
of taxa, that must be regularly updated in accord with new scientific discoveries. Taxonomy
must therefore navigate between the dual perils of ignoring important advances and making
premature or unnecessary changes. We seek stability in nomenclature at the species level but at
higher levels the concepts and compositions of major taxa, and therefore the scope of
wellknown names, must inevitably shift as new organisms are discovered and evolutionary
affinities are better understood. The fact that we have been able to agree on a practical unified
classification shows that taxonomists can broadly agree, despite the diverse experiences, viewpoints,
and to some extent, differing philosophies of classification represented on our panel. The
present classification (as, indeed, all classifications) should be regarded as interim, and it will
inevitably change in certain respects, some hinted at above. However, we suspect that the recent
torrent of radical re-evaluations (resulting especially from the application of DNA sequencing
and other new techniques) may lessen as time passes. We hope that this unusually
comprehensive classification will be widely useful and provide a sound basis for further improvement.
A complete proposed classification from superkingdom to order is provided in Table 2 and
is available for download at <http://www.catalogueoflife.org/col/>. Below the rank of
infrakingdom, we have followed the convention used in the Catalogue of Life and listed taxon
names alphabetically. This allows easier searching by those not familiar with the phylogenies of
KINGDOM ARCHAEA [= ARCHAEBACTERIA]
KINGDOM BACTERIA [= EUBACTERIA]
Order N.N. ("Ca. Caldiarchaeum")
Order N.N. ("Ca. Korarchaeum")
Class N.N. (Bryobacter)
Order N.N. (e.g., "Ca. Nanosalinarum")
Order N.N. (e.g., Deferrisoma)
Phylum Chloroflexi [= Chlorobacteria]
INFRAKINGDOM EUGLENOZOA Phylum Euglenozoa Subphylum N.N. Subphylum Euglenoida
INFRAKINGDOM EXCAVATA Phylum Loukozoa Subphylum Eolouka Subphylum Neolouka
SUBKINGDOM SARCOMASTIGOTA Phylum Amoebozoa Subphylum Conosa Class Trichonymphea
Class Myxogastrea [= Myxomycetes]
Class Tubulinea [= Lobosea]
Subphylum Choanofila Class Choanoflagellatea
Order N.N. (e.g., Nosema)
SUBKINGDOM HACROBIA Phylum N.N. Phylum Cryptista Subphylum Palpitia
Class Placozoa (Trichoplax)
INFRAKINGDOM PROTOSTOMIA Superphylum N.N. Phylum Chaetognatha Phylum Orthonectida
Subclass Tantulocarida (e.g., Basipodellidae)
Order N.N. (e.g., Japygidae)
Class Symphyla (e.g., Scolopendrellidae)
Phylum Priapula [= Priapulida]
Superphylum Spiralia [= Lophotrochozoa]
Class N.N. (e.g., Priapulidae)
Order N.N. (e.g., Nerillidae)
Subclass Cocculiniformia (e.g., Cocculinidae)
Order N.N. (e.g., Neomphalidae)
Order N.N. (e.g., Patellidae)
Order N.N. (e.g., Ataphridae)
Class Paleonemertea (e.g., Carinomidae)
Order N.N. (e.g., Gorgonorhynchidae)
Class N.N. (e.g., Phoronis)
INFRAKINGDOM DEUTEROSTOMIA Phylum Chordata Subphylum Cephalochordata Subphylum Urochordata
Subphylum Vertebrata [= Craniata]
Class Enteropneusta (e.g., Harrimaniidae)
Subclass Cephalodiscida (Cephalodiscus)
Class Acoela (e.g., Diopisthoporidae)
Class Nemertodermatida (e.g., Nemertodermatidae)
Class N.N. (Xenoturbellidae)
Names below rank of infrakingdom are arranged alphabetically within each parent rank, except for taxa that are not named (N.N.). Brackets indicate
synonyms. Quoted names are not validly published but in common use.
the many taxa therein and provides for easier import and manipulation of data by
S1 Appendix. List of sources consulted for proposed higher level classification of all living
S1 Table. Proposed hierarchical classification from superkingdom to order.
We thank those on the expert panel who are not authors of this paper for their valuable
contributions earlier in this process. In addition, we are very grateful to David Nicolson for his help
in reviewing and improving the many drafts of the classification, Brian Tindall and Peter
Stevens for their helpful review of the draft manuscript, and the three PLoS reviewers for their
useful comments. We also thank Gloria Ruggiero for her excellent editorial work on
Conceived and designed the experiments: MR DG NB TB RB TC-S MG PK TO. Analyzed the
data: MR DG NB TB RB TC-S MG PK TO. Wrote the paper: MR DG NB TB RB TC-S MG PK
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