Why are clades described as natural groups

The term stem is commonly used to mean an axis of the above-ground portion of a plant, in the present context, of the metaphorical tree that represents phylogeny.

If the crown of such a tree consists of those parts that have survived to the present time, then the axis of the relevant part of the tree can be equated with the ancestral lineage leading up to that crown Fig. More specifically, the term stem will be used here to refer to the ancestral lineage of a particular crown clade from the point where that lineage separated from the ancestral lineage of the most closely related crown clade to the point where the primary lineages within the crown of interest separated from one another represented by the crown node.

The stem may also be termed the stem lineage. Meier and Richter used the term ancestral lineage for what is here termed the stem lineage ; however, it seems preferable to use the former term in a more general sense that includes not only stem lineages but also lineages that are ancestral to wholly extinct clades.

The stem lineage is commonly composed of several branches in the sense of internodes, which may be termed stem branches , though the term stem branch may be used more specifically for the basal-most of those branches, which represents the ancestral species of the total clade. The branches representing extinct lineages that share a more recent common ancestor with a particular crown different possible meanings mutually exclusive crown clade may be termed side branches relative to the crown clade of interest; Fig.

In this context, a total clade is composed of a particular crown clade, its stem lineage, and the side branches of that stem lineage.

A stem species Hennig, is the ancestral species of a particular clade—the species in which the clade originated and from which it diversified here stem is used only for the most basal part of the axis.

Both crown clades and total clades have stem species, and except for cases in which all species resulting from successive speciation events have extant descendants, those species are different see Meier and Richter, ; fig. A stem group Hennig, , , is the group of extinct species that belong to a particular total clade but not to its crown Fig. It includes both extinct species that are directly ancestral to the crown those of the stem lineage and those that are not directly ancestral side branches , but it does not include species that are ancestral to, or side branches of, more inclusive crowns Hennig, , , ; Meier and Richter, A stem group is paraphyletic, and for that reason some authors have argued that the concept itself should be rejected e.

The utility of the stem group concept, however, is not as the basis for a formally recognized taxon. Instead, its utility is providing a convenient means of referring to the collection of ancestral species and side branches that are members of a particular total clade but not of its crown. The stem group concept provides a means of referring to such a collection that both avoids using a formal scientific name or a vernacular equivalent for a paraphyletic group e.

Hennig , initially treated the categories that I am here calling crown, total, and apomorphy clades as three different meanings of the age of origin of a group, and later Hennig , as three different ways of delimiting i. He argued against conceptualizing a group in terms of an apomorphy on the grounds that such an approach requires distinguishing essential characters from nonessential ones Hennig, : 26 , and even assuming that the essential characters could be defined objectively, they may not be preserved in fossils one of Hennig's primary concerns was referring fossils to groups containing their living relatives.

Moreover, conceptualizing a group in this manner ultimately requires emphasizing only one of the many apomorphies that may be characteristic of the extant members of the group. Hennig e. Therefore, Hennig preferred to conceptualize and name groups as total clades, which permitted him to refer extinct species to the same clades as their extant relatives Fig. In contrast, conceptualizing and naming groups as crowns would require coining additional names for the total clades to accommodate fossils lying outside of the crowns Fig.

Nonetheless, Hennig recognized the importance of distinguishing between crown and total clades, which he accomplished by appending an asterisk to the name when referring to the crown e.

Hennig's reason for conceptualizing taxa and associating names with total clades rather than crown clades. Note, however, that if the distinction between crown and total clades is considered important under the total clade approach a , then a convention to distinguish the two clades is required. Hennig accomplished this by appending an asterisk when the name refers to the crown clade e. Despite the importance of Hennig's insight in identifying different categories of clades, his conventions for distinguishing between the members of those categories leave much to be desired.

The problem is that biologists need to be able to do more than merely refer a fossil to a total clade containing its extant relatives. At the very least, they also need to be able to determine and communicate whether that fossil lies inside or outside of the crown clade.

Although Hennig made that distinction with an asterisk, this convention seems ineffective in that, first, the same symbol is used to designate several other things e. And in many cases, biologists may want to convey even more precise information about the phylogenetic positions of fossils than simply whether they are inside versus outside of the crown. For groups with good fossil records, nomenclatural distinctions conveying such precise phylogenetic information are already being made by naming clades originating with various intermediate nodes, branches, and apomorphies e.

Another problem with Hennig's approach is that it emphasizes the meanings of names rather than the naming of clades see de Queiroz, By treating the different categories of clades as different possible ways to delimit the group designated by a particular name e.

The problem is that once a decision is made to associate a name with one of several possible clades, the other clades tend to be neglected. Thus, once Hennig decided that names should refer to total clades, the other categories of clades and the distinctions that they embodied were largely ignored. Apomorphy clades were not named at all, and crown clades were given the same names as the corresponding total clades, distinguished only by an appended asterisk.

Evolutionary biology in the 21st century can no longer tolerate the ambiguities of naming systems that seemed adequate in the s.

Contemporary evolutionary biology in general, and systematic biology in particular, needs a system for naming clades that conveys the important distinctions in a precise and unambiguous way. To do this, biologists must question Hennig's position that a single name is adequate, or rather preferable, for a nested series of no fewer than three different clades de Queiroz and Gauthier, We need to adopt a system that highlights the distinction between crown clades and total clades, in particular, as well as their nested relationships.

We need to shift our nomenclatural emphasis from a primary concern about the meanings of particular names to a primary concern about the naming of theoretically and operationally significant categories of clades. The remainder of this paper is an attempt to outline such a system under the view that a more precise, less ambiguous, and therefore more useful nomenclature requires different names for different clades. Although the proposed system differs from the approach adopted by Hennig, it is nevertheless based on the categories of clades that he first identified.

An integrated system of clade names involves some general rules for naming clades in the three categories discussed above. The proposal itself revolves around four primary issues: 1 the one-to-one relationship between crown and total clades, 2 the greater familiarity of certain names, 3 the etymological meanings of names, and 4 the current uses of names.

It is important to recognize that the development of an integrated system requires that these issues be considered simultaneously, and a consequence of doing so is that there will necessarily be compromises. That is, although certain conventions may not be optimal according to any of the four above issues considered individually, when all four issues are considered together, those conventions seem best for achieving the overall goal of an integrated system relative to similarly constrained alternatives.

In attempting to develop an integrated but minimally disruptive system of clade names, the ambiguities of the existing nomenclature turn out to be advantageous. That is, when considering whether to apply an existing name to a crown, an apomorphy, or a total clade, most of the best-known names in particular, those used originally for distinctive groups of extant organisms will have been applied to clades in more than one of these categories, and some will have been applied to clades in all of them, as well as to additional nodes, branches, and apomorphies.

For example, Rowe and Gauthier have documented such a diversity of previous uses for the name Mammalia. More generally, Hennig noted that paleontologists have tended to associate such names with key apomorphies e.

As a consequence of this ambiguity, selecting any one of these alternative references is to some degree consistent with the traditional use s of many widely known names. Allowing etymological meanings to influence the selection of clade names does not violate the general principle of both rank-based and phylogenetic nomenclature that the primary function of a name is to provide a means of referring to a taxon—that is, as opposed to indicating its characters, relationships, or membership e.

According to this principle, once a name has been established, it cannot be rejected solely on the grounds that it is descriptively inaccurate. This principle does not require, however, that the etymological meanings of names be ignored prior to establishment.

On the contrary, when the etymological meanings of names are congruent with the properties of the taxa to which those names refer, the names are easier to remember, thus enhancing their primary function of referring to taxa. In other words, the functions of referring to taxa and indicating characters, relationships, or membership need not be in conflict, and when they are in agreement, names are easier to remember and use.

The core of the proposed integrated approach is a standard way of naming crowns and their corresponding total clades that highlights the one-to-one relationship between those two categories of clades Fig.

Apomorphy clades will also be considered; however, because their relationships to both crown and total clades are often many-to-one, it is more appropriate to develop an integrated system around crown and total clades. In describing this system, I will also consider the types of names that are best suited etymologically for clades in the different categories. An example of the proposed approach to naming crown and total clades. Mammalia crown mammals is used for the crown clade, and Pan-Mammalia pan mammals is used for the corresponding total clade.

Other names may be used for various node-based, apomorphy-based, and branch-based clades between Pan-Mammalia and Mammalia , such as Synapsida apomorphy , Therapsida , Cynodontia , Mammaliamorpha node , Mammaliaformes node , Mammalignatha apomorphy , and Apo-Mammalia apomorphy.

The first component of the proposed integrated system is to give crown clades the best-known names commonly if inconsistently used to refer to those clades Fig. This approach was proposed by Gauthier , and has been advocated by several subsequent authors e. The primary reason behind it is that the best known names will refer to the clades about which the most can be known.

Given that many aspects of organismal biology e. Consequently, applying the best-known names to crown clades is the most effective use of those names. If biologists are to adopt a more precise nomenclature concerning the series of clades from stem to crown, then they should use the name of a crown when discussing features that have been surveyed only in extant organisms. They should not use the name of a more inclusive clade. Given that most biological features are surveyed only in extant organisms, the names of crowns should be the most widely used names, and thus it makes sense to select the names that are already most widely used for the crowns.

In addition, for many crown clades, stem group fossils are currently unknown. As a consequence, the widely known names are, in those cases, effectively used for the crowns. Thus, to achieve an integrated system in which clade names are used similarly across all taxa regardless of the quality of their stem group fossil records, the most widely known names must be applied to crown clades.

Another important reason for applying the best-known names to crowns is the one-to-one relationship that exists between crowns and total clades. One of the basic components of the proposed integrated system of clade names as will be described further below is that the name of a clade belonging to one of the relevant categories is based on the name of a clade belonging to another such category the name upon which another name is based is termed the base name , ICPN Art.

Because of the one-to-one relationship between crown and total clades, the names of these two categories of clades are the logical choices for such a convention. That is, either the name of the crown should serve as the base name for the name of the total clade as proposed , or vice versa. On the other hand, that relationship does not preclude forming the name of an apomorphy clade from the name of a crown or total clade see Apomorphy Clades , below.

An advantage of using the best-known names for crown clades is that it prevents the trivialization of those names that tends to occur as stem lineage histories becomes better known under the alternative convention of applying the best-known names to apomorphy clades. Under that alternative, the best-known names are commonly associated with key apomorphies—character states that differ markedly from antecedent conditions, at least among extant taxa—for example, the limbs of tetrapods.

One of the great successes of paleontology, however, has been the discovery of intermediate fossil organisms that demonstrate the step-by-step evolution of many key apomorphies, thus decomposing those apomorphies into their component parts Gauthier and de Queiroz, In order to achieve a precise nomenclature, the association of the name in this case, Tetrapoda must then be restricted to one of these steps or component apomorphies.

The problem is that the well-known name is thereby trivialized in the sense that it no longer refers to the key apomorphy as a whole but only to one of its less distinctive component parts. Moreover, that name is likely to become just one in a series of names along the stem lineage J. Gauthier, personal communication, , some of which mark the various stages in the assembly of the complex apomorphy, others of which are tied to different apomorphies or to nodes or branches.

It should also be noted that using the best-known names for crown clades represents the element of broadest agreement across prior uses of those names concerning included species and organisms. For example, if a name such as Tetrapoda has been used for a series of nested clades from a total clade to its corresponding crown, then everyone will agree that members of the crown are members of Tetrapoda , but the same will not be true for various members of the stem group that are considered members of Tetrapoda under alternative definitions.

Those alternative definitions represent a range in degrees of disagreement about which species are included in the taxon, with the total clade definition representing the case of maximal disagreement in that some of the extinct forms included under that definition will not be included under any of the alternative definitions on the other hand, the total clade definition represents the case of maximal agreement with regard to excluded species.

Although the proposal to use the best-known names for crown clades differs from Hennig's e. Hennig's reason for associating the best-known name with the total clade was to avoid the need for two names e. In the context of the perspective adopted in this paper, his decision placed too much emphasis on assigning a fossil to a previously named taxon e. Moreover, the approach advocated in this paper rejects the premise that phylogenetic research is best served by minimizing the number of named clades.

Certain types of names are particularly appropriate for crown clades. Among existing scientific names, the most appropriate ones are those derived from the vernacular names for particular kinds of organisms e.

Part of the reason that these kinds of names are particularly appropriate for crowns is that they do not describe characters apomorphies. Other names that are well suited for crown clades are those that describe apomorphies present in members of the relevant crowns but are unlikely to be preserved in fossils e.

The reason is that it will be rare to have direct evidence that these characters occur in fossil taxa outside of the crown. Names that describe characters that are commonly preserved in fossils e.

To acknowledge the fact that names in these last two categories describe apomorphies, it may be appropriate to define them using apomorphy-modified node-based definitions rather than standard node-based definitions see ICPN , Art. For example, Mammalia could be defined not as the least inclusive clade containing Ornithorhynchus anatinus and Homo sapiens but as the least inclusive crown clade containing all extant organisms that possess mammary glands homologous with those of Homo sapiens. The second part of the proposal is to form the names of total clades by combining the names of their crowns with a standard affix prefix or suffix Fig.

The prefix Pan- was proposed by Lauterbach and adopted by several subsequent authors e. Thus, the names of the total clades of the crown clades Aves , Deuterostomia , and Spermatophyta would be Pan-Aves , Pan-Deuterostomia , Pan-Spermatophyta , respectively. Most authors who have formed the names of total clades in this manner have capitalized the first letter of the prefix, included a hyphen between the prefix and the name of the crown, and capitalized the first letter of the name of the crown.

An advantage of the second and third conventions is that they distinguish the names of total clades from other names that begin with Pan- e. They have been adopted in the current version of the ICPN , where the names of total clades formed according to these conventions are termed panclade names.

However, because some members of the Committee on Phylogenetic Nomenclature CPN objected to using panclade names in cases where alternative names had previously been explicitly defined as referring to total clades, the ICPN does not require that the names of all total clades be formed in this manner.

That is, the ICPN has not fully adopted an integrated approach to the names of crown and total clades. With the exception of a few panclade names that have already been proposed e. Nevertheless, adoption of the panclade name convention would not necessarily result in a great number of name changes.

The reason is that the references of most names that could be argued as having traditionally been associated with total clades are sufficiently ambiguous that they could just as easily be interpreted as having been associated with nearby nodes or apomorphies. On the other hand, some existing names have been used unambiguously for total clades.

Moreover, the proposal of methods for formulating explicit phylogenetic definitions led to a number of names being explicitly defined as referring to total clades including Synapsida , see de Queiroz and Gauthier, These trees are often called phylograms, and they generally depict either the amount of evolution occurring in a particular gene sequence or the estimated duration of branches.

Usually, the context of such trees makes it clear that the branch lengths have meaning. However, when this is not the case, it is important to avoid reading in any temporal information that is not shown. For example, Figure 8 may appear to suggest that the node marking the last split leading to tips A and B marked x occurred after the node separating tip C from tips D and E marked y. However, this should not be read into the tree; in reality, node x could have occurred either before or after node y.

Given the increasing use of phylogenies across the biological sciences, it is now essential that biology students learn what tree diagrams do and do not communicate. Developing "tree thinking" skills also has other benefits. Most importantly, trees provide an efficient structure for organizing knowledge of biodiversity and allow one to develop an accurate, nonprogressive conception of the totality of evolutionary history.

It is therefore important for all aspiring biologists to develop the skills and knowledge needed to understand phylogenetic trees and their place in modern evolutionary theory. Figure 8: Trees contain information on the relative timing of nodes only when the nodes are on the same path from the root i.

In this tree, nodes x and y are not on the same path, so we cannot tell whether the ancestral organisms in node x lived before or after those in node y.

Avise, J. Baum, D. The tree thinking challenge. Science , — Phylogenies and tree thinking. American Biology Teacher 70 , — Dawkins, R. O'Hara, R. Homage to Clio: Toward an historical philosophy for evolutionary biology. Systematic Zoology 37 , — Population thinking and tree thinking in systematics. Zoologica Scripta 26 , — Maddison, W. Origins of New Genes and Pseudogenes. Evolutionary Adaptation in the Human Lineage.

Genetic Mutation. Negative Selection. Sexual Reproduction and the Evolution of Sex. Haldane's Rule: the Heterogametic Sex. Hybrid Incompatibility and Speciation. Hybridization and Gene Flow. Why Should We Care about Species? Citation: Baum, D. Nature Education 1 1 Phylogenies are a fundamental tool for organizing our knowledge of the biological diversity we observe on our planet. But how exactly do we understand and use these devices? Aa Aa Aa. What an Evolutionary Tree Represents.

Figure 1. Figure Detail. The Lexicon of Phylogenetic Inference. A node represents a branching point from the ancestral population. Terminals occur at the topmost part of each branch, and they are labeled by the taxa of the population represented by that branch.

Figure 4: A monophyletic group, sometimes called a clade, includes an ancestral taxon and all of its descendants. A monophyletic group can be separated from the root with a single cut, whereas a non-monophyletic group needs two or more cuts. How to Read an Evolutionary Tree. Homeostasis Higher Level 7: Nucleic Acids 1.

DNA Structure 2. Transcription 3. Translation 8: Metabolism 1. Metabolism 2. Cell Respiration 3. Photosynthesis 9: Plant Biology 1. Xylem Transport 2. Phloem Transport 3. Plant Growth 4. Plant Reproduction Genetics 1. Meiosis 2. Inheritance 3. Speciation Animal Physiology 1. Moreover, what is an autapomorphy for one group say, monkeys can be a synapomorphy for a wider group say, primates. Cladism lacks absolute ranks and states, unlike the older Linnaean classification which forces taxa into a set number of taxonomic levels.

It helps, I find, to think of clades as being Venn diagrams, and to think of those as being cross-sections, as it were, through the evolutionary tree. A clade can be a set of organisms, but that set can also be a proper subset of another set, and can contain sets inside it.

Only a proper set - one which does not intersect with any other but wholly contains or does not contain at all other sets of taxa - is thought to be a "natural" group. Two kinds of un natural groups in cladism are polyphyletic many origins, that is to say, many cuts of the branches groups, or paraphyletic not containing all the descendants of the original cut, like taking humans out of the ape clade groups. They look like this:. Here it is as a Venn diagram:.

So too are "Pisces" green are; fishes , and "Reptilia" orange area; reptiles. The same is for the "Crossopterygians" dark green; extinct fishes , which have living ancestors not included in their group, and which cover the root of more than one group.

A cladogram can be made on extinct and extant species, and in a simple cladogram, no distinction is made - they are all at the top of the cladogram. But you often get "mixed" cladograms like this one. A simple rule in cladistics is that once a member of a group, always a member of that group.

So we are, as the cladist will tell you, bony fishes. Likewise, if some group is formed that has, say, four limbs Tetrapoda , the fact that some member, like snakes or whales, has secondarily lost some or all limbs doesn't mean they are no longer part of that group. They simply have a "derived form of being four-legged" i.

It sounds unintuitive, but if you think it through, it makes sense as an evolutionary perspective. If you look at the Venn diagram and ignore the colours, then each group except "Crossopterygians" and "Homothermians" is a proper subset of its enclosing group, and so we are "invertebrates" and "fishes" because one of our ancestors or more was an invertebrate and a fish. This is why these excluding classifications are not "natural" in systematics.

Invertebrates is just what is left over from Animalia once the vertebrates have been taken out. So now, when someone talks about cladistics, you will know what they are talking about or get a feeling whether they know what they're talking about Biological classifications tickle me pink, first because of the childish urge to be able to name everything I point at, second because I can easily visit Linnaeus gardens in Uppsala where he had a chair of medicine and later botany.

Btw, good idea proposing SB blogging basic concepts. If it is not done overly often it is a great addition to the menu. If you revise, you may consider making the effort of correcting "that were invented, [ Since the rest was so nicely done.

In that case I will nitpick, since the factorial increases faster than exponential. Checking: "As n grows, the factorial n! Very nice post- every time I thought you had missed a point- there it was in the next paragraph or section. I agree with Matt that this might lose laymen. Assuming I understand clades right, you could probably throw in the following example:.