Cladistics and the fossil record: the uses of history (original) (raw)

Cladistic and phylogenetic biogeography: the art and the science of discovery

Journal of Biogeography, 2003

All methods used in historical biogeographic analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by Ebach & Humphries (2002) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programs, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon-area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographic context of speciation events. The recent contribution by Ebach & Humphries (2002) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research program, whereas phylogenetic biogeography is hypothetico-deductivist/falsificationist. Cladistic biogeography can become hypothetic-deductive by using a posteriori methods of analysis.

The compleat cladist: A primer of phylogenetic procedures

1991

The core concept of phylogenetic systematics is the use of derived or apomorphic characters to reconstruct common ancestry relationships and the grouping of taxa based on common ancestry. This concept, first formalized by Hennig (1950, 1966), has been slowly, and not so quietly, changing the nature of systematics. Why should we be interested in this approach? What about phylogenetic systematics is different from traditional systematics? The answer is simple: classifications that are not known to be phylogenetic are possibly artificial and are, therefore, useful only for identification and not for asking questions about evolution. There are two other means of making statements of relationship: traditional systematics and phenetics. Traditional systematic methods employ intuition. In practical terms, intuition is character weighting. The scientist studies a group of organisms, selects the character(s) believed to be important (i.e., conservative), and delimits species and groups of species based on these characters. Disagreements usually arise when different scientists think different characters are important. It is difficult to evaluate the evolutionary significance of groups classified by intuition because we do not know why they were created or whether they represent anything real in nature. Because these groups may not be defined at all or may be defined by characters that have no evolutionary significance, such groups may be artificial. Phenetics is an attempt to devise an empirical method for determining taxonomic

A Framework for Post-Phylogenetic Systematics (Online Version, Complete)

The Framework for Post-Phylogenetic Systematics reframes biological systematics to reconcile classical and cladistic schools. It combines scientific intuition and statistical inference in a new form of total evidence analysis developing a joint macroevolutionary process-based causal theory. Discrepancies between classical results and morphological and molecular cladograms are explained through heterophyletic inference of deep ancestral taxa, coarse priors leading to Bayesian Solution of total evidence, self-nesting ladders that can reverse branching order, and a superoptimization protocol that aids in distinguishing pseudoextinction from budding evolution. It determines direction of transformative evolution through Dollo evaluation at the taxon level. The genus as a basic, practical unit of evolution is postulated for taxa with dissilient evolution. Scientific intuition is defended as highly developed heuristics based on physical principles. The geometric mean and Fibonacci series in powers of the golden ratio explain distributions of measurements of the form (a–)b–c(–d) when close to zero. This series is basic both to S. J. Gould’s speciational reformulation of macroevolution and to psychologically salient numbers. The effect of molecular systematics on conservation and bio¬diversity research is shown to be of immediate concern. The value of cladistic study for serial macroevolutionary reconstruction is reduced to—in morphological studies, evaluation of relatively primitive or advanced taxa, and distinction of taxa by autapomorphies, and—in molecular studies, identification of deep ancestors via heterophyly or unreasonable patristic distance not explainable by extinct or unsampled extended paraphyly. Evolutionary paraphyly is common in cladistics and is to be avoided; phylogenetic paraphyly, however, can be informative.

Classification: More than Just Branching Patterns of Evolution

Aliso

The past 35 years in biological systematics have been a time of remarkable philosophical and methodological developments. For nearly a century after Darwin's Origin of Species, systematists worked to understand the diversity of nature based on evolutionary relationships. Numerous concepts were presented and elaborated upon, such as homology, parallelism, divergence, primitiveness and advancedness, cladogenesis and anagenesis. Classifications were based solidly on phylogenetic concepts; they were avowedly monophyletic. Phenetics emphasized the immense challenges represented by phylogeny reconstruction and advised against basing classifications upon it. Pheneticists forced reevaluation of all previous classificatory efforts, and objectivity and repeatability in both grouping and ranking were stressed. The concept of character state was developed, and numerous debates focused on other concepts, such as unit character, homology, similarity, and distance. The simultaneous availability of computers allowed phenetics to explore new limits. Despite numerous positive aspects of phenetics, the near absence of evolutionary insights led eventually to cladistics. Drawing directly from phenetics and from the Hennigian philosophical school, cladistics evolved as an explicit means of deriving branching patterns of phylogeny and upon which classifications might be based. Two decades of cladistics have given us: refined arguments on homology and the evolutionary content of characters and states, views of classifications as testable hypotheses, and computer algorithms for constructing branching patterns of evolution. In contrast to the phenetic movement, which was noteworthy for seeking newer concepts and methods, even including determining evolutionary relationships (which led eventually to numerical cladistics), many cladists have solidified their approaches based on parsimony, outgroups, and holophyly. Instead of looking for newer ways to represent phylogeny, some cladists have attempted to use branching patterns: (1) as a strict basis for biological classification and nomenclature and (2) to explain the origin of biological diversity even down to the populational level. This paper argues that cladistics is inappropriate to both these goals due to: (1) inability of branching patterns to reveal all significant dimensions of phylogeny; (2) acknowledged patterns of reticulate evolution, especially in flowering plants; (3) documented nonparsimonious pathways of evolution: and (4) nondichotomous distribution of genetic variation within populations. New concepts and methods of reconstructing phylogeny and developing classifications must be sought. Most important is incorporation of genetic-based evolutionary divergence within lineages for purposes of grouping and ranking.

On the other "phylogenetic systematics"

Cladistics, 2000

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor “widely held belief” systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new “Phylogenetic Systematics” - instead we have been presented with a vague and sketchy manifesto based upon the assertion that “clades are individuals” and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for “node pointing,” yet even their own examples show that the opposite is true, and their “node pointing” system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the “node pointing” system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.