A phylogeny is an evolutionary history of an organism or group of organisms; it may be interpreted as a genealogical tree, an ancestor and descendant lineage, or as systematic relationships of form within a classification scheme. Phylogenies are studied principally in the fields of phylogenetics and systematics.
History of Phylogenetics
Phylogeny was discussed in detail by the 19th-century German morphologist Ernst Haeckel, who proposed a biogenetic law (or the law of recapitulation). The biogenetic law states that phylogeny, or the evolutionary history of an organism, is recapitulated through its ontogeny, or the development of an individual organism in embryo.
The subsequent rejection of Haeckel’s law was a significant move away from using mechanical explanations or causes, such as embryonic development, to explain the relationship between organisms. Haeckel’s most significant contribution was that of the phylogenetic tree (Phylogenetisches Stambaum), the now universally accepted way to depict genealogical relationships.
History of Phylogenetics
A phylogenetic tree may depict hypothetical ancestordescendant relationships, sometimes called a transformation series, between groups of organisms (species, genera, and families) or their characteristics, through time. Such phylogenetic trees have been popular tools of paleontologists who use them to establish socalled ghost lineages between similarlooking fossils throughout the stratigraphic record.
Phylogenetic trees were challenged in the early 20th century by the Germanspeaking systematic morphologists, led by Adolf Naef. The evolutionary relationships that phylogenetic trees were claimed to depict were based on linking similarlooking organisms that overlapped through time, rather than considering relationships of form.
The systematic morphologists considered homologues (different manifestations of the same morphological structure) to be a sounder basis for the discovery of relationship than the assembly of ghost lineages. If organisms are related, their characters are homologous, that is, the same; as opposed to analogous, that is, similar but not the same.
Naef’s trees related organisms only at the terminal branches, rather than depicting hypothetical lineages, with organisms (hypothetical or real) at both the nodes and tips. Homologous organisms belonged to “natural groups or classifications” that share a greater relationship among themselves than they do to any other group.
The rejection of phylogenetic trees and the concomitant support for natural groups was criticized by Anglo American phylogeneticists such as George Gaylord Simpson and Ernst Mayr, who defended the depiction of lineages in phylogenetic trees rather than the discovery of natural groups, which challenged some traditional taxonomic groups.
Anglo American phylogenetics, however, changed considerably in the latter half of the 20th century when the work of Willi Hennig, a German entomologist, was translated into English.
Hennig’s Phylogenetic Systematics attempted to resurrect Haeckel’s systematic phylogenetics by reintroducing the causal mechanisms that had been rejected by Adolf Naef.
Hennig’s phylogenetic systematics combined Haeckel’s transformational viewpoint—but at the level of character rather than taxon—with Naef’s trees of relationships to form ancestordescendant schemes of relationship with organisms only at the tips, and character transformations leading from the nodes to the tips.
The resulting trees attempted to group homologous organisms into “natural” or monophyletic classifications based on a causal mechanism, thus combining Haeckel’s phylogenetic tree with Naef’s systematic morphology.
Phylogenetic systematics developed into a numerical method by incorporating the principal notion of phenetics, that is, similarity concepts, with a causal mechanism to find optimal trees.
Phylogenetic systematics, later referred to as cladistics, underwent a revolution in the work of Gareth Nelson by returning to systematic morphology. Pattern cladistics rejected causal homologies and ancestordescendant relationships as uninformative and misleading, because they introduced bias into phylogenetics.
The pattern cladists, led by Ronald Brady and Gareth Nelson, considered monophyly to indicate “natural groups,” which can be used to test existing taxonomies rather than to identify causal relationships (a common ancestor). The resulting diagrams, called cladograms, could represent numerous lineages but only a single classification.
Hennig’s elimination of paraphyly and its connection made with ancestry by cladists such as Colin Patterson helped to define phylogenetics as a science of classification based on the relationships of form.
Molecular phylogenetics is the study of amino acid or DNA sequences and how they may be related among different organisms. The field has grown exponentially and amassed a significant volume of data.
Unlike phylogenetic systematics, molecular phylogenies tend to consist of individual character trees (relationships between organisms based on a single character) and are used to hypothesize recent genealogies in populations as well as ancestordescendant relationships in species.
Despite its popularity, very little theoretical work has been done on the relevance of homology of DNA sequences. Molecular phylogenetics, however, has progressed methodologically and technologically in such issues as alignment of sequences and in mapping the similarity distances in phenetic methods.
Phylogenies may be interpreted as explicit evolutionary pathways, natural groups (classifications), or a combination of both. The latter has caused the most controversy in its claim for phylogenetic classifications.
Recent debate has focused on defend ing lineages rather than classifications in taxonomy. A nonmonophyletic group (also known as a paraphyletic or polyphyletic group) is an artificial or incongruous set that shares greater relationship to other groups than to its own.
A proposed lineage may be paraphyletic and therefore contradict any given natural classification. Reptiles are an example of a paraphyletic group that exists in name only, not within a natural classification.
The defense of paraphyletic groups in classification reflects the battle between the Anglo American paleontologists and systematic morphologists in the early 20th century, during which classification and hypothetical lineages were confused.
Phylogenies have been used in biogeography (the study of biotic distributions) during three periods: in the late 19th century, with the advent of natural selection as a viable mechanism for species evolution (e.g., Haeckel); in the 1960s, with the onset of Hennig’s phylogenetic systematics; and in the late 20th century, with the use of molecular phylogenies.
The same method has been used in each of these periods, namely that of proposing a center of origin and drawing the direction of dispersal and/or vicariance events (allopatry) on a phylogenetic tree.
Since the late 19th century, fossils were used to date such events within any given phylogenetic tree. The method is still widely practiced today (i.e., using a molecular clock). The only difference between these periods is the data used.
Nineteenth-century phylogeneticists relied on fossils, mid-20th-century phylogeneticists on the morphology of extant taxa, and 21st-century molecular systematists on molecular data.