Burning Straw Men Sheds Little Light: a Reply to Whiting and Kelly

Wilkinson (1991a) developed arguments that the distributions of primitive character states may delimit clades, and proposed a method that exploited the evidence of primitive character state distributions for inferring clades. Whiting and Kelly (1995) presented a critique of these ideas, arguing that they are logically incoherent and that the method does not succeed in its aims. This critique severely misrepresents the original arguments and the method, and amounts to no more than an attack on a straw man.     

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.     

A fossil clupeomorph fish from the Albian of the Northwest Territories of Canada, with notes on cladistic relationships of clupeomorphs

A primitive clupeomorph, Erichalcis arcta gen. et sp. nov. is described from the Albian of Northwest Territories, Canada. Erichalcis is uniquely specialized among clupeomorphs in the presence of enlarged lateral line scales and in the structure of the caudal skeleton. Erichalcis is classified as Clupeiformes incertae sedis. The two recognized suborders, Clupeoidei and Denticipitoidei are examined with respect to primitive and derived character states. It is concluded that the clupeoids and denticipitoids are divergently specialized in details of the union between the supraorbital and infraorbital sensory canals and the recessus lateralis. It is further suggested that the reduction in size and the posterior shift of the dermosphenotic in clupeoids is correlated with an upper division of the levator arcus palatini muscle and an antero-dorsal process on the hyomandibular. Cladistic relationships of some Cretaceous clupeomorphs are proposed and it is suggested that Diplomystus brevissimus Cope not be included in the Clupeoidei.     

Parallel tion in the context of character analysis

For the establishment of polarity of character transformation prior to phylogenetic analysis, various logical and biological criteria are discussed; some are rejected on grounds of liability to systematic error, circularity or unwarranted assumptions aboutParallel tion is used as a non-polar term, with forward and reverse to indicate polarity. A computer program for the detection of parallel tion is described which takes taxa in groups of four. The characters, with two derived: two primitive states or three derived: one primitive state, are listed according to the distribution of states over the four taxa. To each of the 15 phylogenies there corresponds a compatible pair of character patterns. Discordant 2: 2 patterns are unconditionally incompatible (Le Quesne test failure), discordant 3: 1 patterns are incompatible conditional upon correct scoring of polarity. For any putative phylogeny the concordant and discordant characters are identified. In cases of competing alternatives these character sets have to be weighed against one another. Character weighting is discussed; it is argued that it is the individual character transformation which should be weighted, in each direction separately.     

New craniodental material of Pronothodectes gaoi Fox (Mammalia, "Plesiadapiformes") and relationships among members of Plesiadapidae

Plesiadapidae are a family of Paleogene mammals thought to have phylogenetic affinities with modern Primates. We describe previously unpublished dentitions and the first skull and isolated petrosals of the plesiadapid Pronothodectes gaoi, collected from middle Tiffanian localities of the Paskapoo Formation in Alberta. Other species of Pronothodectes, traditionally considered the most basal members of the Plesiadapidae, occur at earlier, Torrejonian horizons in Montana, Wyoming, and Alberta. Classification of P. gaoi as a species of Pronothodectes has proved controversial; accordingly, we use the newly available samples and the more extensively preserved specimens to re-evaluate the generic affinities of this species. Included in our study are comparisons with craniodental material known for other plesiadapids and plesiadapiforms. Cladistic analysis of craniodental characters is used to assess the hypothesis that P. gaoi and other species in this genus are basal members of the Plesiadapidae. The new dental evidence confirms that P. gaoi lacks derived character states of other plesiadapids except for a variably present fissuring of the m3 hypoconulid. Moreover, several aspects of the cranium seem to be more primitive in P. gaoi (i.e., more like nonplesiadapid plesiadapiforms) than in later occurring plesiadapids, such as Plesiadapis tricuspidens and Plesiadapis cookei. Cladistic analysis of craniodental morphology supports a basal position of P. gaoi among species of Plesiadapidae, with the exception of other species of Pronothodectes. The basicranium of P. gaoi preserves a laterally placed bony canal for the internal carotid neurovascular system, suggesting that this was the ancestral condition for the family.     

HYBRIDS AND PHYLOGENETIC SYSTEMATICS I. PATTERNS OF CHARACTER EXPRESSION IN HYBRIDS AND THEIR IMPLICATIONS FOR CLADISTIC ANALYSIS

Interspecific hybridization is considered common among plants, but the methods of cladistic systematics produce only divergently branching phylogenetic hypotheses and thus cannot give the correct phylogeny if an analysis includes hybrids. Empirical studies of the impact of known hybrids on phylogenetic analysis are lacking, and are necessary to begin to understand the problems that we face if hybrids are often included in cladistic analysis. Examination of the implications of hybrids for cladistics must begin with patterns of character expression in hybrids. This study includes 17 hybrids and their nine parental taxa that are Central American species of Aphelandra (Acanthaceae), analyzed using a set of 50 morphological characters. The hybrids are overwhelmingly intermediate as quantitatively scored for phylogenetic analysis. They express maternal and paternal, and primitive and derived characters in equal frequencies, showing no evidence of predominant inheritance of derived character states as has been assumed by most cladists who have considered hybrids theoretically. Because of their known genetic constitution, hybrids were useful in homology assessment and ordering character states. The parental character set was generally robust, but some changes were made to reflect the special evidence offered by the hybrids. These hybrids suggest that the inclusion of hybrids in phylogenetic analysis will not lead to unresolved cladograms with rampant homoplasy, as has been predicted by other authors. Instead, the patterns of character inheritance in these hybrids lead to the prediction that a hybrid will be placed by phylogenetic analysis as a basal lineage to the clade that includes its most derived parent, with relatively little effect on homoplasy. These predictions will be evaluated by incorporation of the hybrids in phylogenetic analyses, to be reported in a subsequent paper.     

Phylogenetic reconstruction and phenetic taxonomy

Cladistic analysis should not be equated with phylogenetic reconstruc Instead it is a means of describing character-state distributions among organisms and in this it resembles phenetic analysis. However, the claim that cladistic methods meet phenetic ('Gilmour-natural') criteria for classification as well as or better than traditional phenetic ones is shown to be based on an inadequate interpretation of these criteria. Instead, a new measure of naturalness is proposed in which the most natural classification is that which describes the distribution of all character states by the smallest number of statements. The possibility of extending this measure to provide a criterion for an optimally simple classification is noted. It is concluded that phylogenetic reconstruction must not only reflect the branching patterns suggested by cladistic analysis but also take account of the tionary history that is reflected in an optimal phenogram.     

The primitive course of the internal carotid artery in mammals.

In all recent mammals the internal carotid artery at the level of the auditory capsule is derived from the embryonic dorsal aorta. In adults of various groups, the artery lies in positions which are classified as medial or promontory. It is shown that these character states arise by a process of differential growth affecting the relative positions of the dorsal aorta and the cochlear promontory. There is no evidence for separate vessels in the embryo which could give rise to non-homologous internal carotid arteries in the two positions. It follows that the concept of a primitive mammalian morphotype with both a medial and a promontory internal carotid artery in the same individual presents a formidable embryological problem. It is recommended that, in the absence of supporting evidence, the widespread current taxonomic and palaeontological use of this hypothetical morphotype should be regarded with suspicion.     

葱属Amerallium亚属 (石蒜科) 的系统发生与性状进化

运用贝叶斯和简约法对葱属（Allium）Amerallium亚属的核糖体DNA内转录间隔区（ITS）进行了分析,对该亚属的系统发生进行了推测。系统分析证实 Amerallium是单系的,并表明该亚属由三个隔离的地理群组成：北美Ameralliums,地中海区Ameralliums和东亚Ameralliums。性状进化的重建表明鳞茎是原始或祖先状态,根状茎和肉质增粗的根是衍生状态且在Amerallium这个亚属的类群中独立进化发生了几次。重建也表明该亚属的原始染色体基数x=7,其它染色体基数（x=8, 9, 10, 11）是由它转化而来的。在北美类群中,异基数性相当罕见,而多倍性似乎是一个相对频繁的进化事件。在地中海区类群和东亚类群中,异基数性和多倍性是染色体进化的两个主要驱动力。     

Phylogenetic relationships among genera of the Tetrabothriidae (Eucestoda)

Cladistic analysis of the generic-level relationships within the family Tetrabothriidae was conducted. A single cladogram resulted from evaluation of 28 homologous transformation series representing 41 character states. The genus Tetrabothrius was recognized as plesiomorphic followed by Chaetophallus and Trigonocotyle. The latter was considered as the sister group for the remaining tetrabothriid genera of marine mammals. Anophryocephalus, Strobilocephalus, and Priapocephalus are among the most highly derived genera and are postulated as having close evolutionary affinities. Comparisons to previous explicit hypotheses for relationships among the genera indicated the present analysis was the most efficient phylogenetic statement (consistency index = 85.4%) for the 28 attributes evaluated. The recognition of Tetrabothrius as primitive and a natural grouping of Anophryocephalus, Strobilocephalus, and Priapocephalus in part confirmed results of previous studies of the Tetrabothriidae.     

Homology and synapomorphy‐symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. correspondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primitive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig's terms synapomorphy and symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however, is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).     

The first instar larva of Eripus oaxacanus Straneo & Ball (Coleoptera: Carabidae: Peleciini): indicator of affinity or convergence?

Abstract. The first instar larva of Eripus oaxacanus Straneo & Ball is diagnosed and described, representing the first laboratory-described larval stage for a species of the tribe Peleciini. The larva possesses the derived character states of: (1) stemmata lacking, (2) mandible lacking penicillus, (3) maxilla with setose lacinia, (4) labium lacking a ligula, (5) claws single, (6) urogomphi short, rounded. These derived character states, if considered synapomorphic, would place Peleciini as a close relative to Brachi-nini. Classifications based on adult characters are not concordant with this interpretaton, and the weight of evidence suggests that convergence due to a similar parasitic lifestyle is the basis for the derived similarity of Eripus and Brachinus larvae.     

葱属Amerallium亚属（石蒜科）的系统发生与性状进化

运用贝叶斯和简约法对葱属（Allium）Amerallium亚属的核糖体DNA内转录间隔区（ITS）进行了分析,对该亚属的系统发生进行了推测。系统分析证实 Amerallium是单系的,并表明该亚属由三个隔离的地理群组成：北美Ameralliums,地中海区Ameralliums和东亚Ameralliums。性状进化的重建表明鳞茎是原始或祖先状态,根状茎和肉质增粗的根是衍生状态且在Amerallium这个亚属的类群中独立进化发生了几次。重建也表明该亚属的原始染色体基数x=7,其它染色体基数（x=8, 9, 10, 11）是由它转化而来的。在北美类群中,异基数性相当罕见,而多倍性似乎是一个相对频繁的进化事件。在地中海区类群和东亚类群中,异基数性和多倍性是染色体进化的两个主要驱动力。     

Cladistic analysis of cercopithecid relationships

The phyletic relationships of cercopithecid higher taxa are fairly well understood. By reference to the outgroup Hominoidea, character state distributions for a variety of dental, cranial and posteranial features are reviewed and morphotypes are presented for supra-generic taxa. Cercopithecids show 13 derived conditions relative to the eucatarrhine morphotype. Cercopithecines are further derived by eight features while the colobine morphotype shows an additional nine synapomorphies, including three newly identified pedal features. Within Cercopithecinae, the tribes Papionini and Cercopithecini are each characterized by several derived states. In turn, each tribe includes a relatively conservative and a more derived clade, recognized at the subtribal level: Macacina and Papionina (including the previously recognized Theropithecina) for Papionini: and the newly defined Allenopithecina and Cercopithecina among Cercopithecini. The distinctions within Colobinae appear comparable to those defining cercopithecine subtribes, and two taxa are accepted at that rank: the African Colobina, defined by three derived states: and the possibly paraphyletic Asian Presbytina. Piliocolobus shares four synapomorphies with Procolobus and therefore is ranked as a subgenus of that taxon. The hypothesis that Dolichopithecus is the direct descendant of Mesopithecus is weakened on the basis of contrary pedal evidence.     

Nystroemiaceae,a new family of Permian gymnosperms from China with an unusual combination of features

Nystroemiaceae is proposed as a new family of gymnosperms from the Permian of Cathaysia that adds to the diversity of gymnosperms known from this critical time in seed plant evolution. This family is characterized by bifurcating and highly branched pinnate ovuliferous organs bearing bicornute ovules (seeds) and entire leaves with anastomozing veins that are born on complex and modern-looking branching systems with clear axillary branching. The reconstruction is based on numerous large specimens from two localities in North China, in which the different plant parts are attached to each other. The ovulate structures show some apparently plesiomorphic (primitive) character states more typical of early seed plants, whereas the leaves and branches show the clearly apomorphic (derived) character states of broad-leaved gymnosperms.     

A human mandible (BH-1) from the Pleistocene deposits of Mala Balanica cave (Sićevo Gorge, Niš, Serbia)

Neandertals and their immediate predecessors are commonly considered to be the only humans inhabiting Europe in the Middle and early Late Pleistocene. Most Middle Pleistocene western European specimens show evidence of a developing Neandertal morphology, supporting the notion that these traits evolved at the extreme West of the continent due, at least partially, to the isolation produced by glacial events. The recent discovery of a mandible, BH-1, from Mala Balanica (Serbia), with primitive character states comparable with Early Pleistocene mandibular specimens, is associated with a minimum radiometric date of 113 + 72 − 43 ka. Given the fragmented nature of the hemi-mandible and the fact that primitive character states preclude assignment to a species, the taxonomic status of the specimen is best described as an archaic Homo sp. The combination of primitive traits and a possible Late Pleistocene date suggests that a more primitive morphology, one that does not show Neandertal traits, could have persisted in the region. Different hominin morphologies could have survived and coexisted in the Balkans, the “hotspot of biodiversity.” This first hominin specimen to come from a secure stratigraphic context in the Central Balkans indicates a potentially important role for the region in understanding human evolution in Europe that will only be resolved with more concentrated research efforts in the area.     

Cladistic Analysis of Human Evolution: Some Points on Character Selection

Cladistic analysis strongly depends on accurate character choice. Usually, characters include morphology or molecules, but other sources of evidence are also employed. These include stratigraphic ages of taxa and behavioural data. The inclusion of time is a controversial issue, which has no Darwinian basis. However, the cladistic treatment of stratigraphic age has the potential to resolve problematic phylogenies. Here, it is proposed that the use of stratigraphic data in phylogenetic inference should be seen as a temporary shortcut, to resolve complex phylogenies in the wait for new character and taxonomic samplings, because phylogenetic hypotheses should be based on biological evidence only. Archaeologists working on toolmaking can provide behavioural data in human prehistory. In fact, while a tool itself is not biological evidence, the movements of hands and arms needed to prepare it are biological evidence and can be compared and scored for cladistic analysis. Such an approach has been formalized in studies on functional morphology of some vertebrates. The taxonomic data set to be used in cladistic analysis should include as many taxa as possible, and also very incomplete specimens should be used. In many cases, incomplete specimens had the potential to resolve complex phylogenies by adding new character combinations that cannot be scored in molecule-based phylogenetic studies.     

Has the importance of the amniote egg been overstated?

The evolution of the amniote egg is commonly regarded as an important milestone in the history of the vertebrates, an innovation that completed the transition from aquatic to fully terrestrial existence by permitting eggs to be laid away from standing water. This view derives ultimately from the recapitulationist theories of Haeckel, and rests on the assumption that extant frogs and salamanders are good models for the reproductive habits of early tetrapods and the ancestors of the amniotes. It also assumes that it is more difficult to lay eggs on land than in water, and that the amniote egg is an adaptation to the physical rigours that eggs encounter in terrestrial environments. Taken together, these assumptions comprise what may be termed the 'Haeckelian framework' for the origin of vertebrate terrestriality. Several independent lines of evidence suggest that the assumptions of the Haeckelian framework are false. There appear to be no theoretical reasons to assume that the evolution of terrestrial egg-laying was difficult, or required a structure as elaborate as the amniote egg. The physical conditions eggs encounter in the terrestrial environments where they are actually laid are quite mild. Land may in fact be an easier place to lay eggs than water. In addition, analysis of the distribution of key reproductive character states among vertebrates provides no evidence that the 'typical amphibian' reproductive mode is primitive for tetrapods. Amniotes are as likely as frogs or salamanders to retain primitive reproductive character states.     

Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis

BAUM, B. R. & SAVILE, D. B. O., 1985. Rusts (Uredinales) of Triticeae: evolution and extent of coevolution, a cladistic analysis. Established evolutionary trends in Uredinales as a whole are reviewed, and primitive and advanced characters are presented. The rusts of all Poaceae arc presented in a table that strongly indicates Bambusoideae to be the oldest and Pooideae the youngest subfamily. The rusts of Triticeae and their ecogeography are outlined; the rusts of Cyperaceae, selected as an out-group, are beiefly summarized; and the available characters and character states for rusts of Triticeae are given. Host alternation complicates the analysis. The aerial host (never a grass) is ecologically associated with the unrelated telial (grass) host. There are no appropriate methods to permit analysis of the combined components: aecial host evolution, telial host evolution, rust evolution, and their coevolution. Also, several aecial hosts are unknown. Consequently it was necessary to omit aecial hosts from the analysis. Cladistic analysis of the rusts of Triticeae was performed using five methods and consisted of cycles of tree analysis and modification of character state trees. A cladogram put together from a Dollo and a Wagner cladogram was used as a basis for the classification of rusts given. Subsequently a cladistic analysis of genera of Triticeae, using presence/absence of rusts as characters (Brooks' approach) was performed. The Triticeae cladogram of Baum (1983) was also analysed. Distances between the cladogram generated by various methods and that of Baum were computed for each possible pair, using the method of Robinson & Foulds, and then the resulting distance matrix was reduced in dimensionality by principal components and non-metric multidimensional scaling. The results are discussed in light of the limitation of the analyses and the data. It is concluded that coevolution is limited and that frequent jumps to ecologically associated hosts explain the parallelism in evolution of rusts on Triticeae.