Taxic homology and three-taxon statement analysis

Three-taxon statement analysis (3TA) and standard cladistic analysis (SCA) were evaluated relative to propositions of taxic homology. There are definite distinctions between complement relation homologs and paired homologs. The complement relation is discussed, relative to rooting, parsimony, and taxic propositions of homology. The complement relation, as implemented in SCA, makes sense only because SCA is a simple evolutionary model of character-state transformation. 3TA is a method for implementing complement relation data from a taxic perspective. The standard approach to cladistic analysis distinguishes taxa by rooting a tree, which means that that approach is incompatible with taxic propositions of homology, because a taxic homology is a hypothesis of relationship between taxa that possess a homolog relative to taxa that lack a homolog. It is not necessary to treat paired homologs from a transformational perspective to distinguish informative from uninformative data. 3TA yields results markedly different from those of SCA. SCA, which seeks to minimize tree length, may not maximize the relation of homology (congruence) relative to a tree.     

Evaluating phylogenetic hypotheses of carpoids using stratigraphic congruence indices

Fossil carpoids possess a unique anatomy that is difficult to interpret; as a result, there are a number of competing phylogenetic hypotheses for carpoid taxa. Stratigraphic congruence indices provide a quantitative means of evaluating alternative cladograms where character coding is contentious; trees that show a statistically significant fit between stratigraphy and phylogeny are better supported by the fossil record. We here test the agreement between stratigraphic and cladistic data for 27 carpoid cladograms (24 have previously been published, three are novel). The results demonstrate that in analyses of subsets of carpoid taxa, the stratigraphic congruence of trees is not strongly affected by the interpretative model followed. However, when studying the relationships of carpoids with other deuterostomes, assuming that carpoids should be interpreted by reference to chordates/hemichordates (rather than echinoderms) leads to a poorer fit with the known stratigraphic ranges of taxa. Thus, the disputed calcichordate hypothesis (carpoids interpreted as stem and crown-group chordates and stem-group hemichordates) is much less congruent with stratigraphy than alternative models interpreting carpoids as stem or crown-group echinoderms.     

Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty

Data on fossil taxa can, and should, be incorporated into cladistic analyses. Potential problems with such analyses include large amounts of missing data, and uncertainty about homology of parts that are present. Ambiguity of character data may also occur with extant taxa, but rarely to the extent that it occurs in fossil data. Such ambiguity reduces the strength of the test of character congruence among taxa, in effect relaxing the criterion of parsimony. In order to minimize such effects, composite fossil taxa should be avoided when possible, and polymorphisms reduced by breaking terminals into monomorphic subunits. When results including fossils differ radically from those that exclude fossils, such differences should be approached with caution, keeping in mind the reduced strength of the parsimony analysis when large numbers of cells in a matrix are scored as ambiguous. At this point, there is no simple way to compare the “strength” of parsimony between two data sets that have different numbers of characters and/or taxa in relation to missing data. However, methods under development may provide ways to incorporate the effect of missing values into relative measures of group support such as Bremer support, character removal, and the bootstrap.     

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.     

Exhaustion of morphologic character states among fossil taxa

Frequencies of new character state derivations are analyzed for 56 fossil taxa. The hypothesis that new character states are added continuously throughout clade history can be rejected for 48 of these clades. Two alternative explanations are considered: finite states and ordered states. The former hypothesizes a limited number of states available to each character and is tested using rarefaction equations. The latter hypothesizes that there are limited possible descendant morphologies for any state, even if the character has infinite potential states. This is tested using power functions. The finite states hypothesis explains states: steps relationships significantly better than does the ordered states hypothesis in 14 cases; the converse is true for 14 other cases. Under either hypothesis, trilobite clades show appreciably more homoplasty after the same numbers of steps than do molluscs, echinoderms, or vertebrates. The prevalence of the exhaustion pattern among different taxonomic groups implies that worker biases are not to blame and instead implicates biological explanations such as intrinsic constraints or persistent selective trends. Regardless of the source of increased homoplasy, clades appear to exhaust their available character spaces. Nearly all examined taxa show significant increases in proportions of incompatible character pairs (i.e., those necessarily implying homoplasy) as progressively younger taxa are added to character matrices. Thus, a deterioration of hierarchical structure accompanies character state exhaustion. Exhaustion has several implications: (1) the basic premise of cladistic analyses (i.e., that maximum congruence reflects homology rather than homoplasy) becomes increasingly less sound as clades age; (2) sampling high proportions of taxa probably is needed for congruence to discern homoplasy from homology; (3) stratigraphic data might be necessary to discern congruent homoplasy from congruent homology; and (4) in many cases, character states appear to have evolved in ordered patterns.     

The phylogeny and classification of Scaphopoda (Mollusca): an assessment of current resolution and cladistic reanalysis

The first cladistic analysis of phylogeny in the class Scaphopoda (Steiner 1992a,1996) examined relationships among family and selected sub-family taxa using morphological data. A preferred/ consensus tree of relationships illustrated monophyly of the orders Dentaliida and Gadilida, partial resolution among dentaliid families, and complete resolution among gadilid taxa. However, several alternative replications of the analysis, including use of a revised data matrix, did not produce the reported tree number or level of resolution; in all cases, monophyly of the Dentaliida was not supported by strict consensus of resultant parsimonious trees. Reanalysis, using unordered characters and outgroup rooting, only clearly resolves monophyly of the Gadilida and the sister relationship of the Entalinidae with the remaining gadilid families. These analyses emphasize the need for more comparative data and thorough parsimony analysis in scaphopod cladistic phylogenetics, as relationships in this class are still some way from resolution.     

Nachtrag zu ‘Hepaticae Bomeenses (Oxford University Expedition to Sarawak, 1932)’

Abstract

Recent empirical advances in bryophyte systematics have been made in the discovery and detailed study of new characters. However, theoretical considerations have not kept pace. Proper attention has not been paid to how these new characters can be used to discover relationships among groups and produce classifications. Recent cladistic studies of the relationships of the major groups of bryophytes have demonstrated the feasibility and usefulness of an approach to phylogenetic systematics derived from the works of Hennig. A Hennigian approach attempts to find the particular hierarchical level at which a given character is a homology (i.e. a synapomorphy or shared, derived character), relationships are established by searching for congruent patterns of homologies, and the resulting hierarchical scheme is used as the basis for a classification. Such an approach provides a rigorous and explicit logic for investigating phylogeny and recognizing natural, historically discrete taxa. The theoretical advantages of a Hennigian approach are discussed and illustrated by examining the congruence of new characters data with preliminary cladograms of the major bryophyte groups.     

An investigation into the application of the Wagner parsimony method in synecology

Synecological analyses are usually based on typological, phenetic and cladistic methods. The disadvantages of these techniques are shown. The application of the Wagner parsimony method to synecology is considered. All the methods need some prerequisites, viz. definitions of localities and characters (the most simple one being the presence/absence of taxa); the choice of taxonomic level of taxa; their autochthony. The application of Wagner parsimony needs a new terminology. The congruence of any environmental condition, including freshwater monitoring indices, can be tested on parsimonious trees. The Wagner parsimony method not only provides various indices (tree length, CI, HI, RC, RI) which allow the comparison of trees but also minimal trees which are direct tools in synecology.     

Congruence,non‐homology,and the phylogeny of basal turtles

Joyce, W.G. and Sterli J. 2010. Congruence, non‐homology, and the phylogeny of basal turtles.–Acta Zoologica (Stockholm) Modern cladistic analysis is characterized by the assembly of increasingly larger data sets coupled with the use of congruence as the final test of homology. Some critics of this development have recently called for a return to more detailed primary homology analysis while questioning the utility of congruence. This discussion appears to be central to the debate regarding the phylogenetic relationships of basal turtles, as the large data sets developed by us have been criticized recently for utilizing poorly constructed characters and including too many homoplasy‐prone characters. Our analysis of this critique reveals that (1) new information regarding poorly understood taxa has a greater impact on the outcome of turtle phylogenies than the characters under dispute; (2) most current turtle phylogenies differ in taxon sampling, not character sampling, and so it appears illogical to condemn a particular analysis for its character sampling; (3) even evolutionary taxonomists should agree that key characters utilized to resolve basal turtle relationships cannot be thought to be ‘infallible’; (4) whereas various criteria provide positive evidence for homology, only congruence provides positive evidence for non‐homology; and (5) a stalemate between conflicting camps within a congruence frame work is preferable to the ad hoc dismissal of data sets, because authoritative statements are untestable.     

The use of parsimony in testing phylogenetic hypotheses

With the advance of cladistic theory differences in principle between it and other systematic techniques are few but of fundamental importance. In the mechanics of classification they are confined to ranking and the rejection of paraphyletic taxa. In cladistic analysis, leading to cladograms, trees and phylogeny reconstruction, inconsistencies in apparent synapomorphies are said to be resolved using Popper's hypothetico-deductive method together with the principle of parsi However, not only do cladists not use Popper's methodology, which is inconsistent with parsimony, but their use of parsimony is invalid as a test of phylo The only accepted extrinsic test of a classification is that enunciated by John Stuart Mill. It has been claimed that cladistic classifications yield the best results when judged by Mill's criteria, but this is only possibly the case with analytic classifications produced by numerical techniques. No satisfactory test exists in normal (synthetic) cladism for distinguishing synapomorphy from homoplasy. The effects of this are particularly dire in cladograms and classifications involving fossils in which a Stufenreihe arrangement is adopted.     

The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization

A recent total evidence analysis of the position of cetaceans(whales, dolphins and porpoises and extinct relatives) amongmammals indicated that the phylogeny of these taxa remains poorlyresolved. Molecular data show that 1) the order Artiodactyla(even-toed ungulates) is paraphyletic unless whales are includedwithin it and 2) that the traditional relationships of cladeswithin Artiodactyla are not supported. This controversy alsoaffects the position of a wholly extinct clade, Mesonychia,which has been argued to be the group of terrestrial mammalsmost closely related to whales. Here I update a previous totalevidence analysis by adding several hundred new informativemolecular characters from the literature. Even with the additionof these characters the phylogeny remains unresolved. All mostparsimonious trees, however, indicate a paraphyletic Artiodactylawith conflict existing over the exact sister taxon of Cetacea.Congruence between different equally parsimonious cladogramsand the stratigraphic record as measured using the modifiedManhattan Stratigraphic Measure shows that all of the competingtopologies, including those with a paraphyletic Artiodactyla,are significantly congruent with the stratigraphic record. Infossil taxa cladistic optimization can be used as an alternativeto "argument from design" (Lauder, 1996) to reconstruct behaviorand soft tissues that do not fossilize or osteological charactersthat have not preserved. In certain scenarios of cetacean phylogeny,optimization indicates that taxa such as the archaic whalesAmbulocetus and Pakicetus, and possibly mesonychians, are morecorrectly reconstructed without hair.     

Outline of an Explanatory Account of Cladistic Practice

A naturalistic account of the strengths and limitations of cladistic practice is offered. The success of cladistics is claimed to be largely rooted in the parsimony-implementing congruence test. Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics. In a related theme, the concept of homeostatic property cluster natural kinds is used to explain why cladistics is well suited to provide a traditional, verbal reference system for the evolutionary properties of species and clades. The advantages of more explicitly probabilistic approaches to phylogenetic inference appear to manifest themselves in situations where evolutionary homeostasis has for the most part broken down, and predictive classifications are no longer possible.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Parsimony Analysis as a Specific Kind of Homology Estimation and the Implications for Character Weighting

“Remane-Hennigian systematists” still reject parsimony analysis for phylogenetics, because homology or apomorphy analyses are not included. In contrast, “pattern cladists” regard homology as a deductive concept after applying a parsimony test of character congruence. However, as in molecular phylogeny, selection of “good” characters is always done on the basis of ana priorihomology analysis. The distribution criterion of homology—“homologous characters have identical or hierarchical distribution”—is the basis of parsimony analysis. Because this criterion also might fail in cases of genealogical reticulation or concerted homoplasy, character congruence is not a strict test but another probabilistic criterion of homology. A synthetic approach is proposed for phenotypic analysis with application ofa prioricriteria of homology. The resultinga prioriprobabilities of homology serve as criteria for selection and weighting of characters (very low = not selected/poor/mediocre/good/Dollo characters). After application of a parsimony algorithm the final cladogram decides homology estimations.     

A falsificationist perspective on the usage of process frequencies in phylogenetics

By referring to Popperian falsificationism, proponents of cladistic parsimony claim the superiority of parsimony over likelihood. They conclude that likelihood as a statistical approach is inconsistent with falsificationism, and base their argumentation on four claims: (1) congruence tests cladograms against observational evidence and represents the most important test in phylogenetics, in which minimum‐step trees represent most corroborated trees; (2) frequency probabilities cannot be used for evaluating degree of corroboration; (3) phylogeny represents a unique process and thus frequencies cannot be applied as they require statistical reference classes that are necessarily general; (4) likelihood is a verificationist approach. After discussing the deficiencies of the cladistic phylogeneticists’ conceptualisation of the congruence test and the presentation of an alternative conceptualisation, it is shown that these four claims cannot be sustained within a falsificationist framework, and that the weighting of characters is a necessity. A differentiation between the theoretical concept of apomorphy and the epistemological concept of character weight is proposed. While apomorphies have to be independent from each other, the weighting of characters is interdependent due to human inability to distinguish organismic traits that are structurally identical though they do not share a common evolutionary origin. The possibility of this epistemological interdependence can best be dealt with by the application of process frequencies. The importance of process frequencies of specific transformation classes is exemplified in reference to Popper's formula for the measure of degree of corroboration and its consistency is shown. Therefore, the application of statistical methods is reasonable. As a consequence, the question whether likelihood or parsimony methods represent the best approaches in phylogenetics remains a genuinely empirical question that cannot be decided only in reference to Popper's falsificationism.     

Taxic and Transformational Homology: Different Ways of Seeing

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.     

Basal ischnoceran louse phylogeny (Phthiraptera: Ischnocera: Goniodidae and Heptapsogasteridae)

A phylogenetic analysis of generic relationships for avian chewing lice of families Goniodidae and Heptapsogasteridae (Phthiraptera: Ischnocera) is presented. These lice, hosted by galliform, columbiform and tinamiform birds are reputedly basal in the phylogeny of Ischnocera. A cladistic analysis of sixty‐two adult morphological characters from thirty‐one taxa revealed thirty equally parsimonious cladograms. The phylogeny is well resolved within Heptap‐sogasteridae and supports the monophyly of subfamily Strongylocotinae (sensu Eichler 1963 ). Resolution within Goniodidae is lower but suggests that the genera hosted by Columbiformes are largely monophyletic. Mapping host taxonomy on to the phylogeny of the lice reveals a consistent pattern which is largely congruent down to the rank of host family, although at lower taxonomic levels the association appears to be more complex. The inclusion of more louse taxa may help considerably to unravel the coevolutionary history of both the hosts and their parasites.     

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.     

Phylogenetic relationships of spatangoid sea urchins (Echinoidea): taxon sampling density and congruence between morphological and molecular estimates

A phylogeny for 21 species of spatangoid sea urchins is constructed using data from three genes and results compared with morphology-based phylogenies derived for the same taxa and for a much larger sample of 88 Recent and fossil taxa. Different data sets and methods of analysis generate different phylogenetic hypotheses, although congruence tests show that all molecular approaches produce trees that are congruent with each other. By contrast, the trees generated from morphological data differ significantly according to taxon sampling density and only those with dense sampling (after a posteriori weighting) are congruent with molecular estimates. With limited taxon sampling, secondary reversals in deep-water taxa are interpreted as plesiomorphies, pulling them to a basal position. The addition of fossil taxa with their unique character combinations reveals hidden homoplasy and generates a phylogeny that is compatible with molecular estimates. As homoplasy levels were found to be broadly similar across different anatomical structures in the echinoid test, no one suite of morphological characters can be considered to provide more reliable phylogenetic information. Some traditional groupings are supported, including the grouping of Loveniidae, Brissidae and Spatangidae within the Micrasterina, but the Asterostomatidae is shown to be polyphyletic with members scattered amongst at least five different clades. As these are mostly deep-sea taxa, this finding implies multiple independent invasions into the deep sea.