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The Evolution of Phylogenetic Systematics aims to make sense of the rise of phylogenetic systematics—its methods, its objects of study, and its theoretical foundations—with contributions from historians, philosophers, and biologists.
Table of contents
Need a review of phylogenetic classification? Advantages of phylogenetic classification Phylogenetic classification has two main advantages over the Linnaean system. First, phylogenetic classification tells you something important about the organism: its evolutionary history.
Phylogenetics
Second, phylogenetic classification does not attempt to "rank" organisms. Linnaean classification "ranks" groups of organisms artificially into kingdoms, phyla, orders, etc. This can be misleading as it seems to suggest that different groupings with the same rank are equivalent. For example, the cats Felidae and the orchids Orchidaceae are both family level groups in Linnaean classification.
However, the two groups are not comparable: One has a longer history than the other. The first representatives of the cat family Felidae probably lived about 30 million years ago, while the first orchids may have lived more than million years ago. Reading trees: Phylogenetic pitchforks.
Reconstructing trees: Cladistics. While in molecular biology, the number of identical nucleotides of a DNA fragment is a reliable indicator for the probability that genes are homologous e.
Oliver Rieppel's focus Chapter 5 is the history of pattern cladistics and the transformation of Hennig's logic into a mechanistic tool that does not require concepts about evolution. It seems that Gareth Nelson's discovery of Lars Brundin's exegesis of Hennig's work started this process.
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Rieppel discusses Brundin's views in comparison with Hennig's. Brundin emphasized the search for sister-group relationships, with speciation processes as the cause for the divergence of lineages.
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The graphical representation of these processes in the form of trees or Venn diagrams with characters mapped on them led to the development of the logical consequence, namely basing hierarchical classifications on phylogenetic relationships, as promoted by Gareth Nelson. Rieppel discusses many philosophical questions related to this history and emphasizes in his contribution that ahistorical methods of analysis still prevail in modern systematics. What Rieppel does not discuss is that this development of ahistorical methods is probably also a result of Hennig's neglect of the role and the evaluation of hypotheses of homology.
It is possible to reconcile numerical cladistics with a realistic analysis of evolutionary processes by studying the evolution and polarization of characters before they are coded in a data matrix, and using estimates of the probability of homology to weight characters. Patterson's congruence test leads to a circular argumentation, because the value of characters as evidence for a phylogeny is determined after the construction of a tree.
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Gareth Nelson himself Chapter 6 provides interesting autobiographic notes which nicely complement Rieppel's text. David Williams and Malte Ebach Chapter 7 add biographical notes on Colin Patterson and continue to explain the differences between Hennigian phylogenetic systematics, evolutionary systematics sensu Ernst Mayr, and numerical taxonomy. The avoidance of tree-independent homology statements in this school of cladistics causes trees to be ahistorical phenograms instead of phylograms, which is a direct continuation of numerical taxonomy sensu Sneath and Sokal, only with other algorithms using Wagner parsimony.
It is interesting to learn that Patterson in his later years emphasized that tree-building programs just make trees without evolutionary theory, and that in numerical cladistics the matrix is just a black box, a problem also insinuated in other chapters of this book.
Brent Mishler Chapter 8 describes the somewhat different history of phylogenetics in botany, where the emphasis on regional floras, phenetic classification, and a phenetic species concept prevailed over Hennigian logic, until authors like Koponen, Parenti, Donoghue, Bremer, Mishler, and others started to use the Hennigian argumentation. It is remarkable that the early results of these simple manual phylogenetic analyses are still accepted by contemporaneous botanists—morphology is informative after all.
We learn how and why Peter Sneath and Robert R.
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Sokal and also A. Cain, G. Harrison, and C. Michener started to introduce statistics and mathematics into systematics to solve local problems e. Although later it became clear that Sokal's method did not uncover evolution but only phenetic similarity, numerical taxonomy was probably a necessary step for the subsequent development of tools that use the power of computers, and also to separate the search for adequate methods from the empirical study of organisms.
The article by Norman Macleod Chapter 10 is different to the others: MacLeod presents automated methods that can be used to discern species based on images. His example is planktonic Foraminifera.
Systematics
The author assumes that in future these methods will be more reliable and faster than the currently practiced hasty identification by specialists. Phylogenetic systematics Cladistics. Cladistics classifies organisms according to the order in time that branches arise along a phylogenetic tree, without considering the degree of divergence how much difference.
Groups subordinate to other groups in the taxonomic hierarchy should represent finer and finer branching of phylogenetic trees. Molecular clocks - In the past used morphological characters still do , but now can also use molecular techniques :. A phylogenetic tree should have an outgroup that is a closely related taxon recently ancestral to the organisms for which the phylogeny is being constructed.