Athena Review Vol. 5, no. 1


Records of Life: Fossils as Original Sources


Classification

Linnean and cladistic approaches 

           

            Studying  ancient life requires dipping into terminology created  by scientific researchers, whose formal written communications are often not very conducive to casual reading. The need for succinctness and accuracy underlies much of the terminology, along with a tradition to name species using descriptive Latin or Greek terms.

    One set of terms to become familiar with are basic units of biological classification such as class, family, genus, and species, which provides a structure for relating all types of organisms. The second necessary set of terms are the geological periods and their date ranges. These must be learned as a kind of basic literacy in the subjects of geology and paleontology. The reader must also learn to cope with chronology shorthand such as “mya” for “million years ago.”

            The terms of paleontology are more involved, not only because of the multiplicity of species and their various levels of grouping,  but also because of the now permeating influence in  publications of cladistics (from the Greek word “clade” for “branch”)  whose terms and criteria are not likely to be at all familiar to most readers. Fortunately, a growing number of scientists in the field of early vertebrate paleontology are now writing books or articles aimed at the general reader, which translate the material into simple English, such as the book Gaining Ground on tetrapod evolution, by British paleontologist Jennifer Clack (2006, 2012).
            The traditional method of biologic classification is the Linnean system, devised in the 18th century by the Swedish naturalist Carolus Linneus or Karl Linne (1758). This is really a system of organized cataloguing (called taxonomy), with a fixed hierarchy of levels of groupings (e.g., class, order, family, genus, species), each of which can be called a taxon (plural, taxa). The Linnean system is not primarily designed to show ancestry or evolution, but placement in the Systema Naturae or the great scheme of  nature. It is probably easier to grasp as a mode of learning species, as when trying to familiarize oneself with a wide range of animals or plants.

           As already noted, a well-entrenched factor of the Linnean system, and cladistics, and of all natural classification, which can be off-putting to introductory readers, is the use of descriptive Latin or Greek terms for the names of species and their families and more general groupings. These names, however, when translated, are usually quite simple and descriptive (e.g., the genus name of an early amphibian, Proterogyrinus, means “early tadpole”).  Fortunately, these are increasingly  being translated, even in some scientific papers.   

            The cladistic method of classification, called phylogenetic systematics, was originally designed by the entomologist Willy Hennig (1966) for classifying insects. It is intended to be used for deciphering and describing the closest evolutionary relations of  species,  both extant and extinct, though the extensive comparison of anatomical traits called characters.  The goal of cladistics is to create phylogenies, or relationship trees showing presence or absence of common ancestors between species and groups of species called clades ("branches"). This approach (which is more frequently self-identified as "phylogenetic,"  rather than "cladistic"),  has fundamentally different goals than the hierarchical ordering of Linnean classification; or than a third approach, called evolutionary systematics, described below.

              Cladistics has its own terminology which is totally distinct from that of the Linnean system (see Benton 2000 for a detailed analysis). The comparative methods used by cladistics involve, first, the selection of various (sometimes hundreds) of anatomical traits thought to be diagnostic for the species under consideration, and the listing of these in tables, for as many species as can be relevantly compared. These trait tables are then analyzed through computer programs such as PAUP, which perform complex pattern-grouping  and parsimony analysis to create “nearest neighbor” tree diagrams. These are considered to reflect the probable closest relations between taxa, which can then be expressed in cladograms.
           
The relationship trees or “cladograms” aim to show clades or branches called "sister groups," (fig.1) of which every member shares a common ancester, and avoids portraying long term groupings such as classes or orders.  The goal of requiring every member of a clade to share the same common ancestor (called a “monophyletic” group) also, in practical terms, requires a constant mode of revisionism by those writing up these findings. Every time a significant new fossil is discovered, it may prompt reorganization of the entire “clade” along with all neighboring branches (Benton 2000).  While the revisions may be radical and improvisational, however, the digital methodology can be rather rigid. A seemingly problematic aspect, related to the standardization sought via using computer grouping methods, is the dependence on discrete traits which are either present or absent. Perhaps, as Professor Jennifer Clack suggests (2012), evolution doesn't always work that way. 
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Genus, species, family, et al.

            Most people are familiar with some basic level of Linnean classification in living beings, such as that for different species of birds or plants, or breeds of dogs. In the latter case, all dog breeds are considered as domesticated varieties of the the same species, Canis familiaris. This binomial naming of genus and species (always italicized) is at the root of the Linnean system, along with a larger hierarchy of ranks. As Table 1 shows, the full Linnean taxonomy of a dog includes a number of ranks:  Kingdom (animals), phylum (chordates), subphylum (vertebrates),  Class (mammals), Order (carnivores), Family (canidae), Genus (Canis), and Species (familiaris).  The same ranks or categories used for extant species are also used for fossils. The Linnean system, as in zoology or botany, is built into all discussions of fossils evidence.

Table 1 lists the basic structure of Linnean classification for several well-known animals.

         Table 1: examples of Linnean classification of living animals.

level

Dog (all breeds)

Gray Wolf

Brown Bear

White-tailed Deer

American Crocodile

Eastern Bluebird

Alpine Newt (Salamander)

Brook Trout

kingdom

Animalia

Animalia

Animalia

Animalia

Animalia

Animalia

Animalia

Animalia

phylum

Chordata

Chordata

Chordata

Chordata

Chordata

Chordata

Chordata

Chordata

subphylum

Vertebrate

Vertebrate

Vertebrate

Vertebrate

Vertebrate

Vertebrate

Vertebrate

Vertebrate

class

Mammalia

Mammalia

Mammalia

Mammalia

Reptilia

Aves

Amphibian

Osteichthes

order

Carnivora

Carnivora

Carnivora

Artiodactyl

Crocodylia

 

Passeriformes

 

Caudata

Salmoniformes

family

Canidae

Canidae

Ursidae

Cervidae

Crocodylidae

Turdidae

Salmandroideaa.

Salmonidae

genus

Canis

Canis

Ursus

Odocoileus

Crocodylus

Sialia

 

Triturus

Salvelinus

species

familiaris

lupus

arctius

virginianus

acutus

sialis

alpestris

fontinalis

          

     

              As can be seen from table 1, the taxonomy for the gray wolf (Canis lupus), considered the direct ancestor of domestic dogs, is almost the same as for dogs, except for the species name lupus (table 1). In this case, the dog has changed enough under domesticaton to be considered a distinct species. For other carnivores, such as the brown bear Ursus arctius, all levels above that of family (Ursidae, Latin for “bears”) remain the same as for dogs and wolves. This simply reflects what is quite well attested in the fossil record, that canids, bears, and all other canivores,  have common mammalian ancestors (see also fig.1 below).

              Grazing animals such as a white-tailed deer (Odocoileus virginianus, named for Virginia deer) belong to a different order, Artiodactylus (Greek for “even-toed”), and a different family (Cervidae, Latin for “deer”). Here the common ancestors of both deer and wolves, bears, and other carnivores represent much earlier mammals, dating from the Late Cretaceous through Eocene periods (about 75-55 mya), before their descendants specialized into the different orders of Carnivores and Artiodactyls.


  
Ingroups, Sister Groups, and Outgroups

        Presenting some of the same information as shown in the Linnean grouping in Table 1 could also be done with a cladogram, using cladistic terms (fig.1).

     In this case (again using the domestic dog as the subject taxon), the cladogram shows an "ingroup" consisting of the canidae family. This group of carnivores, in this example, includes  the dog and its direct ancestor, the Gray Wolf, and another wolf from the Pleistocene, the Dire Wolf, which is now extinct. Needless to say, there are many other canids, such as coyotes and jackels or other types of wolves, that could also be included here.

          A related carnivore group, the bear family (ursidae) is shown as a "sister group" to canidae. The two species of ursidae selected here, the Brown Bear and the American Black Bear (Ursus americanus) appear in the cladogram on the same level of ranking as the canids, in terms of Linnean classification. This contrasts with the "outgroup," as shown in fig.1.

Fig.1: Cladogram showing the relations of several modern mammal groupings, including canids, bears, and artiodactyls.

            Placed in the outgroup status, in the case of this example, are two species of the ungulate order of Artiodactyla, the White-tailed Deer, and the Pronghorn Antelope (Antilocapra americana). The order of Artiodactyls split off from the ancestral mammal branch about 54 mya, about the same time that the carnivores also diverged. (This cladogram  does not show details on the ancestral mammal groups). Given the split between orders, the families of this outgroup also do not appear in parallel with the ingroup and sister group. This illustrates an inherent difference between universal categories of the Linnean system, where classes, orders, and families are always shown on the same level, and the ingroup-oriented focus of a cladogram which only places sister taxa on the same level.

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 Amniotes and Synapsids  

            Another, earlier split in vertebrate evolution, that between reptiles and mammals, has been subject to some thorough redefinition. As indicated on fig.1, fossil evidence shows the first appearance of mammals by the Late Triassic and Early Jurassic periods (about 220-180 mya).

       The German anatomist Ernst Haeckel added to Linnean classification the evolutionary distinction between amniotic and non-amniotic eggs used in reproduction. This basic trait showed that mammals and reptiles share a more recent common ancestor than do mammals and amphibians.
   
Amniotic eggs were first formally defined by Haeckel  in 1866 on the basis of the amnion, a protective sheath around the embryo (ig.2). Vertebrates which give birth through amniotic eggs which contain the embryo in a protective, amniotic sac. Examples are a chicken egg, a turtle or crocodile egg, or a mammalian foetus.Thus the group of amniotes  includes the classes of birds, reptiles, and mammals,  but excludes all members of the classes of  fish and amphibians. The latter (called anamniotes), have eggs which are hatched in open water and whose hatchlings, larvae, or tadpoles develop largely unprotected.

Fig.2: Diagram of the amniotic egg of a reptile.


            Haeckel (1866) was very involved in the study of developmental or embryonic similarities and differences between vertebrates, which frequently yields important  information, such as on the long-term evolution of the mammalian ear. Such analysis of key developments in fossil groups are an important part of what is now called evolutionary systematics (see  below).
            For those beginning to learn about the evolution of mammals, probably the single most notable advance in interpretation  is the recognition of the Synapsid group or clade as the early ancestors of mammals. Based on the current fossil record, the origins of Synapsids, who descended from basal amniotes called Sauropsids, occurred by the Late Mississippian or early Pennsylvanian periods (335-320 mya).  Both the sauropsids and the descendant early synapsid groups would previously have been called reptiles. The term Synapsid, however,  has now largely replaced that of mammal-like reptile.
   
         Mammals (who are both amniotes and the descendants of synapsids) are also divided from birds and reptiles by the number of holes or fenestrae in the back part of their skulls, behind the eyes, used as attachment slots for jaw muscles. As further discussed in another section of this report, mammals have one such hole on each side of their skull, and are thus called synapsids (“single arch”). Birds, crocodiles, and some other reptiles each have two skull openings, and are called diapsids (“two arches”). Still other reptiles, including turtles, have no such holes, and are called anapsids ("no arches").  The basal amniote ancestor of all these groups is called a Sauropsid ("lizard face"), a term devised in the 1860s by the English anatomist Thomas Henry Huxley (1862, 1878).           
          Equally much in the forefront of current debate is the still earlier scenario of the first evidence of  land animals, called tetrapods (“four limbs”). The trait of having four legs (tetrapody) separates fish and all other early chordates from amphibians, reptiles, mammals, and birds (who descended from diapsid reptiles, as T.H. Huxley [1878] recognized).  This process occurred in the Late Devonian period (about 385-360 mya)when lobe-finned fish (Sarcopterygians) developed limbs and adapted to land, giving rise to amphibians. An example of a transitional fish who was almost a tetrapod (called a tetrapodomorph)  is Acanthostega gunnari, a species named for the "spiny roof"  of its skull, and for its 1930’s discoverer in Greenland, Gunnar Save-Sodebergh (1932; Clack 1992).

Fig.3.  Cladogram of vertebrate groups.

                The traits of both tetrapodyand the number of skull fenestrae, are of key practical imporance in separating groups of vertebrates, because they are observable in the fossil record. The trait of being an amniote or anamniote, on the other hand, is not identifiable in the fossil record, and can only be inferred when the fossil has otherwise been identified through observable traits to be an a) an amphibian, or b) a sauropsid or other reptile. These and other key trait are shown in cladogram format in fig.3.

 

Evolutionary systematics

             A third approach to the  classification of fossil species is known as evolutionary systematics (Palaios 2014e). This viewpoint, attempting to synthesize Darwinian theories and new fossil findings with the Linnean system, began with late 19th century anatomists such as T.H. Huxley and Ernst Haeckel. A similar approach continued in the "new synthesis" of Darwinian theory with genetics in the 1920s-60s, as shown by the zoologist Ernst Mayr (1944), and paleontologist George Gaylord Simpson (1961). Evolutionary systematics also developed over the same period in the writings of the anatomist Alfred S. Romer (1966); and has more recently been practiced by various paleontologists, including R.L. Carroll (1988) and Michael Benton (2000, 2004). 

            In recent paleontology, this approach has combined Linnaean classification with ancestral or evolutionary relationships, by emphasising the stratigraphic sequence in the fossil record, with paleontology playing an important role in providing criteria for organizing the interpretations of fossil taxa. The emphasis on stratigraphy links evolutionary systematics with the original "bedrock" concept of sequential  interpretation used in geology and paleontology. Emphasis is placed on understanding more general levels of classification such as orders or classes (i.e., Placoderms [early armored fishes] and lobe-finned fishes; fig.4) , which are considered to be basal or stem groups from which later groups radiated. The methodology involves correlating horizontal or contemporary groupings of taxa with changes in their anatomy and environments over time, as seen in stratigraphic contexts.

             A type of graphic represention often used by Romer and other evolutionary systematists are so-called spindle diagrams showing relative frequencies over time for selected taxa. An example is shown in fig.4 for the long-term occurrences of fish and tetrapod families (Benton 2004). Such graphs use lengthy time-spans of a succession of geological periods, to evaluate trends of ancestral groups with primitive anatomical traits. 

Fig.4: Chart of relative frequences over time of fish groups and tetrapods (after Benton 2004).

            Cladistic methodology seems little interested in charts of this kind, since the classes or orders thus portayed extended a long way through time (Palaios 2014e). Consequently, in cladistic terms, these are paraphyletic groups (i.e., with mixed phylogenies or ancestry), and do not illuminate the sister relationships of individual species  Nor is the cladistics approach very interested in stratigraphy in the interpretation of fossil taxa. Instead, a "molecular clock" is relied on, based on genetic differences between species to calculate the past time of their divergence. There are sometimes, however, marked discrepancies between dates obtained by stratigraphic means, as opposed to a molecular clock  (Benton 2000).

             Such matters seem remote in terms of the day-to-day, practical realities of reporting new fossil taxa. Optimal standard practice, at present, is that each time a new, well-preserved fossil is found and described (for example a new Silurian fish fossil from China, such as Entelognathus primordialis  (Zhu et al. 2013), the anatomy of the fossil is presented in as much detail as the preservation permits, and its identification is done via cladistic methods, using the most detailed possible comparisons of the anatomical traits found in the new fossil. It may well be (as in the case of Entelegnathus) that the fossil also provides significant help in answering basic questions of interest to evolutionary systematics, such as when the first bony fish-type jaws appear in the fossil record (the answer, based on Entelegnathus: 319 mya). Nothing further could be asked from a classification .

 

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Glossary  

References:

Benton, M.J. 2000 , "Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead?"  Biol. Rev. (2000), 75: pp. 633-648

Benton, M.J. 2004. Vertebrate Paleontology. Blackwell Publishers. xii–452

Carroll, R. L. 1988. Vertebrate Paleontology and Evolution, WH Freeman & Co.

Clack, J.  1992

Clack, J. 2012. Gaining Ground

Haeckel, E. 1866  Generelle Morphologie der Organismen : allgemeine Grundzüge der organischen Formen-Wissenschaft, mechanisch begründet durch die von C. Darwin reformirte Decendenz-Theorie. ) Berlin 

Hennig, W. (1966). Phylogenetic systematics. University of Illinois Press, Urbana

Huxley, J. S.  1940. "Towards the new systematics." In The new systematics (ed. J. S. Huxley), pp. 1±46. Clarendon Press, Oxford.

Huxley, T.H.  1863.  "The Structure and Classification of the Mammalia." Hunterian lectures, presented in Medical Times and Gazette.

 Huxley, T.H.  1876. "Lectures on Evolution. New York Tribune." Extra. no 36. In Collected Essays IV: pp 46-138

Laurin, M. and R.R. Reisz, 1995. "A reevaluation of early amniote phylogeny." Zoological Journal of the Linnean Society, 113: 165–223


Linnaeus, C.  1758. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Editio decima, reformata, Tomus 1, Laurentii Salvii, Holmiae.

Mayr, E.  1942. Systematics and the origin of species from the viewpoint of a zoologist. Harvard University Press, Cambridge,

Palaios 2014e, "Evolutionary systematics."

Palaios 2014f, "Cladistics."

Save-Sodebergh, G.  1932

Simpson, G. G. 1961. Principles of animal taxonomy. Columbia University Press, New York

Zhu, M. et al. 2013, "A Silurian placoderm with osteichthyan-like marginal jaw bones." Nature 50:  pp.188–193.



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