Cladistics and the land plants: A response to Robinson

The reconstruction of phylogenetic relationships should be based not on belief but on an explicit and logical analysis of all available characters. Hennigian phylogenetic systematics (cladistics) provides a framework for evaluating putative homologies characterizing particular hierarchical levels, determining relationships of taxa sharing congruent patterns of homologies, and constructing a classification based on this information. Fossils can and should be included in the analysis if enough of the relevant characters are preserved; this is not currently possible for early land plants because of the fragmentary fossil record. To avoid circularity, adaptive and functional considerations should be addressed only after a phylogenetic hypothesis based on patterns on patterns of shared homologies is available.     

Problematica old and new

Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.     

Species,genera, and phylogenetic structure in the human fossil record: a modest proposal

Because of the greater morphological distances among them, genera should be more robustly recognizable in the fossil record than species are. But there are clearly upper as well as lower bounds to their species inclusivity. Currently, the vast majority of fossils composing the large and rapidly expanding paleoanthropological record are crammed into one of two genera (Australopithecus vs Homo), expanding the latter, especially, far beyond any reasonable morphological or phylogenetic limits. This excessive inclusivity obscures both diversity and the complexities of phylogenetic structure within the hominid family.     

Two issues in archaeological phylogenetics: taxon construction and outgroup selection

Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup.     

How much can cladistics tell us about early hominid relationships?

Although cladistic analysis has been used to compare hypotheses of relationships among early hominids, the outcomes of different studies have depended entirely on the assumptions made by different investigators. Problems include the close genetic relationship of early hominid taxa, small fossil sample sizes, possible correlations among characters, and a lack of understanding about the evolutionary factors affecting characters. This study investigates the interaction of some of these problems affecting early hominid phylogenetics. Monte Carlo simulations of character state evolution in closely related taxa demonstrate that the sample sizes and close genetic relationships of early hominids do not permit cladistic analyses to obtain unequivocal results. Even with unrealistically good assumptions about the evolutionary dynamics affecting characters, the probability of the most parsimonious hypothesis being true is unacceptably small. In the face of these problems, even phylogenetic statements that are supported by a strong consensus of cladistic studies may nevertheless be in error, and such errors are likely to confound the placement of new specimens and taxa. Advancement in our knowledge of hominid phylogeny can depend only on a fuller understanding of the natural history and evolutionary dynamics of traits.     

The current state of korean paleoanthropology

The hominid fossil and Paleolithic archaeology records from the Korean Peninsula are extensive, but relatively little is known about the Korean human evolutionary record outside this region. The Korean paleoanthropological record is reviewed here in light of major research issues, including the hominid fossil record, relative and chronometric dating, lithic analysis, hominid subsistence, and the presence of bone tools, art and symbolism. Some of the major conclusions drawn from this review include: (1) hominid fossils have been found in nine separate sites on the Korean Peninsula; (2) possible Homo erectus fossils are present in North Korea; (3) Ryonggok Cave, in North Korea, has exposed the remains of at least five archaic Homo sapiens individuals; (4) a possible burial of an anatomically modern Homo sapiens child, discovered in Hungsu Cave in South Korea, has been tentatively dated to roughly 40,000 years ago; (5) handaxes and cleavers have been found at a number of sites near Chongokni and they appear to date to at least 100,000 years ago; and (6) taphonomic studies are necessary for addressing issues related to determining the nature of hominid-carnivore interaction over similar resources (e.g. carcasses and shelter); and the presence/absence of Early Paleolithic bone tools, art, and symbolism in Korea.     

Temporal information,fossil record and phylogeny

Fossils, i.e. remains of living organisms, provide critical data to reconstruct the history of life on Earth because they are the source of unique information concerning the past. Fossils allow statements to be made about morphological features that would otherwise remain unknown, that also help clarifying the phylogenetic relationships of organisms, which results in a better knowledge of the fossil record and, partly, of the stratigraphic record. The latter constitutes the basic source for palaeontologists in order to reconstruct the History of Life. Some palaeontologists consider that the stratigraphical record provides us with essential information necessary to propose phylogenetic hypotheses and to build evolutionary scenarios. However, this point of view is not generally accepted, some authors putting forward that the fossil record is too fragmentary to be accurate (see, e.g.: G.J. Nelson, N.I. Platnick, Systematics and Biogeography: Cladistics and Vicariance, Columbia University Press, New York, 1981; K.J. Peterson, A phylogenetic test of the calcichordate scenario, Lethaia 28 (1995) 25–38). We critically analyze the indices used to estimate the quality of the fossil record and the fit of phylogenetic hypotheses to stratigraphy. We use the concept of temporal paralogy to explain why all these measurements are biased.     

History of American paleoanthropological research on early Hominidae, 1925–1980

Understanding of the early stages of hominid evolution prior to 1925 was based primarily on comparative morphological evidence derived from extant primates. With the publication of Australopithecus by Dart in 1925 and subsequent research in South Africa, new possibilities for empirical assessment of early hominid evolutionary history were opened. It was Gregory's work, with Hellman, reported at the first meeting of the AAPA in 1930, that convinced many workers of the hominid status of Australopithecus. The debunking of Eoanthropus as a Pliocene hominid, far from having a totally negative effect, showed that cranial expansion had occurred after bipedalism in hominid evolution, demonstrated that chemical dating had come of age, and in a broader sense, had underlined that phylogenetic hypotheses are falsifiable by recourse to the evidence. The input of biological sciences into early hominid studies, as exemplified by Washburn's “new physical anthropology,” reduced taxonomic diversity and focused attention on paleoecology and behavior. The development of the multidisciplinary approach to field research, pioneered by L. Leakey and brought to fruition by Howell, was of fundamental importance in accurately dating and understanding the context of early hominids. Archaeology, primatology, comparative and functional morphology, and morphometrics have contributed substantially in recent years to a fuller understanding of early hominid evolution. American granting agencies have heavily supported early hominid research but patterns of funding have not kept pace with the change from research based largely on individualistic enterprise to multidisciplinary research projects. Future early hominid research, if funding is available, will likely be directed toward investigating temporal and geographic gaps now known in the fossil record and in more rigorous and multidisciplinary investigations of early hominid behavior.     

A Review on Cladistics

The theoretical bases and approaches of cladistics and some specific problems that, directly or indirectly, rely on cladistic analysis for their revolution, are outlined and discussed. Seven sections comprise this paper: a ) the philosophical foundation of cladistics; b) the theoretical tenets of cladistics; c) the operational procedure of cladisties; d) three schools of classification; e) cladistics and biogeography; f) cladistics and hybrid recognition; and g) is cladistic systematics a scientific theory ? Considerations of scientific methodology involve philosophical questions. From this point, Popper'falsificationism serves a good foundation. Popper emphasizes that all scientific knowledge is hypothetical-deductive, consisting of general statements (theories) that can never be confirmed or verified but only falsified. The theories, that can be tested most effectively, are preferable. Cladistics, aiming at generating accurately expressed and strictly testable systematic hypotheses, is well compatible with this requirement. The principles central to the cladistic theory and methodology are: the Principle of Synapomorphy; the Principle of Strict Monophyly; and the Principle of Strict Parsimony. The first requires forming nested groups by nesting statements about shared evolutionary novelties (synapomorphy) postulated from observed similarities and is the primary one. The second is mainly methodological, subject to modification and compromise. The principle of strict parsimony specifies the most preferable hypothesis (namely the one exhibiting the most congruence in the synapomorphy pattern). The operational procedure that might be followed in formulating and testing hypotheses of the synapomorphy pattern (the cladogram itself) consists of five steps. The erections of monophyletic groups, to a greater or lesser extent, rely on the hypothesis of the previous systematic studies and is the starting point for cladistic analysis. Character analysis, which focuses on character distribution and determination of the polarities, decides the reconstructed phylogeny. A detailed discussion on the methodological principles for identifying transformation sequence is presented. Many algorithms have been designated to infer the cladogram, and are basically of parsimony techniques and Compatibility techiques. The thus yielded cladograms, with their expected pattern of congruent synapomorphies, are tests of a particular hypothesis of synapomorphy and reciprocally synapomorphies are tests of cladistic hypothesis (cladogram). Such reciprocity is a strong stimulus to profound understanding on phylogenetic process and phyletic relationships. The cladogram and the Linnaean classification have the identical logic structure and the set-membership of the two can be made isomorphic. There are three principal approaches to biological classification : cladistics, phenetics and evolutionary classification. Cladistics is the determination of the branching pattern of evolution, and in the context of classification, the development of nested sets based on cladograms. Phenetics is the classification by overall similarities, without regard to evolutionary considerations. Evolutionary classification attempts to consider all meaningful aspects of phylogeny and to use these for making a classification. The last approach has been done intuitively, without explicit methods. An enumeration of their differences and a discussion on their relative merits are presented. Three theoretical approaches have been proposed for interpreting biogeographical history: the phylogenetic theory of biogeography, classical evolutionary biogeography and vicariance biogeography. The former two show some similarities in that they usually look upon biogeography in terms of centers of origin and dispersal from the centers. But the first puts a strong emphasis on the construction of hypotheses about the phylogenetic relationships of the organisms in question and the subsequent inference of their geographic relationships; the second advocates a theory which does not have a precise deductive link with phylogenetic construction and often results in wildly narratative-type hypotheses. The vicariance approach de-emphasizes the concepts of centers of origin and dispersal and attempts to analyse distribution patterns in terms of subdivision (vicariance) of ancestral biotas. The development of the theory of plate tectonics and its universal acceptance enormously stimulate biogeographers to look at the world's continents and oceans from a mobilist point, which, along with the establishment of the rigorous tool of the phylogenetic analysis (cladistics), profoundly reshapes the above three theories. Hybridization and polyploidy are outstanding features of many plant groups. But hybridization, or reticulate evolution, is inconsistent with the basic concepts of cladistics which is an ever-branching pattern. Cladists have suggested several approaches. One of them analyses all the taxa by a standard cladistic procedure and closely examines the cladograms for polytomies and character conflicts that may indicate possible hybrids. Such generated hypothesis of hybridization can be corroborated or falsified by other forms of data, such as distribution, polyploidy, karyotype and pollen fertility. There are three criteria to justify a theory to be scientific: a) whether it is a theory composed of hypotheses strictly falsifiable; b) whether it has predictive effect; and c) whether it has a explanatory value. Cladistic systematics aims at generating cladograms, which are hypotheses of the nested pattern of synapomorphy, phylogenetic process and phyletic relationships, susceptible to testing by postulated synapomorphies. The predictive effect of systematics relies on the acceptance of hypotheses of congruence about the correlation of characters, which has been well founded. For non-systematic biologists, phylogenetic classification can be used as axiom to form a preliminary and fundamental explanation.     

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata)

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.     

Ecogeochemistry potential in deep time biodiversity illustrated using a modern deep-water case study

The fossil record provides the only direct evidence of temporal trends in biodiversity over evolutionary timescales. Studies of biodiversity using the fossil record are, however, largely limited to discussions of taxonomic and/or morphological diversity. Behavioural and physiological traits that are likely to be under strong selection are largely obscured from the body fossil record. Similar problems exist in modern ecosystems where animals are difficult to access. In this review, we illustrate some of the common conceptual and methodological ground shared between those studying behavioural ecology in deep time and in inaccessible modern ecosystems. We discuss emerging ecogeochemical methods used to explore population connectivity and genetic drift, life-history traits and field metabolic rate and discuss some of the additional problems associated with applying these methods in deep time.     

Evolution of life history and behavior in Hominidae: Towards phylogenetic reconstruction of the chimpanzee–human last common ancestor

The origin of the fundamental behavioral differences between humans and our closest living relatives is one of the central issues of evolutionary anthropology. The prominent, chimpanzee-based referential model of early hominin behavior has recently been challenged on the basis of broad multispecies comparisons and newly discovered fossil evidence. Here, we argue that while behavioral data on extant great apes are extremely relevant for reconstruction of ancestral behaviors, these behaviors should be reconstructed trait by trait using formal phylogenetic methods. Using the widely accepted hominoid phylogenetic tree, we perform a series of character optimization analyses using 65 selected life-history and behavioral characters for all extant hominid species. This analysis allows us to reconstruct the character states of the last common ancestors of Hominoidea, Hominidae, and the chimpanzee–human last common ancestor. Our analyses demonstrate that many fundamental behavioral and life-history attributes of hominids (including humans) are evidently ancient and likely inherited from the common ancestor of all hominids. However, numerous behaviors present in extant great apes represent their own terminal autapomorphies (both uniquely derived and homoplastic). Any evolutionary model that uses a single extant species to explain behavioral evolution of early hominins is therefore of limited use. In contrast, phylogenetic reconstruction of ancestral states is able to provide a detailed suite of behavioral, ecological and life-history characters for each hypothetical ancestor. The living great apes therefore play an important role for the confident identification of the traits found in the chimpanzee–human last common ancestor, some of which are likely to represent behaviors of the fossil hominins.     

When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss

Molecular and morphological data sets have yielded conflicting phylogenies for the Metazoa. So far, no general explanation for the existence of this conflict has been suggested. However, I believe that a neglected aspect of metazoan cladistics has introduced a systematic and substantial bias into morphological phylogenetic analyses. Most characters used for metazoan cladistics are coded as binary absence/presence characters. For most of these characters, the absence states are assumed to be uninformative default plesiomorphies, if they are defined at all. This character coding strategy could seriously underestimate the number of informative apomorphic absences or secondary character losses. Because nodes in morphological metazoan phylogenies are typically supported by relatively small numbers of characters each with a potentially strong impact on tree topology, failure to distinguish between primary absence and secondary loss of characters before a cladistic analysis may mislead morphological cladistics. This may falsely suggest conflict with molecular phylogenies, which are not sensitive to this bias. To test the existence of this bias, I compare the phylogenetic placement of a variety of metazoan taxa in molecular and morphological trees. In all instances investigated here, phylogenetic conflict can be resolved by allowing for secondary loss of morphological characters, which were assumed to be primitively absent in cladistic analyses. These findings suggest that we should be cautious in interpreting the results of morphological metazoan cladistic analyses and additionally illustrate the value of a more functional approach to comparative morphology in certain circumstances.     

化石人类脑演化研究概况

脑演化是人类演化的一个重要组成部分,其研究可以为人类起源、演化、人群关系及语言、智力等方面提供重要的信息。脑演化的主要证据是通过研究颅内模（endocast）及颅骨的形态得到的。颅内模是从颅骨内表面得到的脑的外部形态。有时颅骨的内腔充满泥沙,并且为钙质所结固,可以自然形成颅内模。也可以人工制作颅内模。颅内模和颅骨的内表面能够提供人类脑髓及神经进化方面的直接证据。对化石人类脑演化的研究主要包括以下几个方面的内容：测量或估计脑量的大小及其和身体大小之间的关系;研究脑量随时间的变化过程;通过对早期人类颅内模表面沟回形态特征的研究,探索脑功能区在早期人类和猿类的区别及在演化上的变化;左右大脑不对称性与一侧优势关系,探讨语言的起源和惯用手的脑功能基础等;脑膜中动脉系统、静脉窦系统及与血液循环相关的排泄孔的变化,探讨大脑各部分比例的变化和功能的日益复杂对供血需求的影响;通过对人类脑演化的研究,探讨人类进化的原因。本文通过对以上几个方面及其中国化石脑演化研究的介绍,对化石人类脑演化的研究概况作综合论述和简单回顾。     

Issues related to mineralized tissue biology in human evolutionary research

This comunication has two primary aims concerned with mineralized tissue biology (e.g. hard tissue biology of bone and tooth) research in human evolutionary studies: First, to introduce the literature and the methods (at the time of this symposium) so that one has an idea of the nature of this research and where one can go for details of the methodologies, etc; Second — and of primary concern here — to discuss issues that have come to light as a result of these studies mainly because of its recent beginnings as a subfield within paleoanthropology. Issues related to skeletal studies include; 1) whether different cortical surface pattens and bone tissue types influence the appearance and interpretation of bone growth activity states; 2) if SEM analyses of cortical surfaces in fossil hominids allow one to construct meaningful representations of remodeling patterns; 3) whether these representations can be used in phylogenetic arguments; and 4) how intraspecific variability would affect these issues. Issues related to dental studies include: 1) the relationship between the rate and pattern of eraly hominid dental development; 2) experimental support for the calibration of eraly hominid dental developmental rates; and 3) whether replica techniques are suitable for microanatomical studies of these sorts.     

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.     

Rates of evolution: Is there a conflict between neo-darwinian evolutionary theory and the fossil record?

Neo-darwinian and population genetics theory assumes that the necessary and sufficient set of conditions for all genetic, therefore evolutionary, change has been identified. Punctuationalists have assumed the opposite and cite the fossil record as evidence for change too rapid to be explained in neo-darwinian theory. Data is given here to provide estimates of the rate of evolution in hominid fossils, in living populations, and of that rate which would qualify as punctuational in the hominid fossil record. Evolution in living populations is orders of magnitude greater than that found in the fossil record and far greater than necessary to create apparently instantaneous saltations in the fossil record. It is suggested that such saltations may not represent more rapid rates of evolution but, rather, the persistence of evolutionary change in a given direction for a longer than normal period.     

Molecular phylogeny and evolution of phenotype in silica‐scaled chrysophyte genus Mallomonas

The evolution of phenotypes is highly understudied in protists, due to the dearth of morphological characters, missing fossil record, and/or unresolved phylogeny in the majority of taxa. The chrysophyte genus Mallomonas (Stramenopiles) forms species‐specific silica scales with extraordinary diversity of their ornamentation. In this paper, we molecularly characterized three additional species to provide an updated phylogeny of 43 species, and combined this with evaluations of 24 morphological traits. Using phylogenetic comparative methods, we evaluated phylogenetic signal in traits, reconstructed the trait evolution, and compared the overall phylogenetic and morphological diversity. The majority of traits showed strong phylogenetic signal and mostly dynamic evolution. Phylogenetic relatedness was often reflected by the phenotypic similarity. Both V‐rib and dome are very conservative structures that are presumably involved in precise scale overlap and bristle attachment, respectively. Based on modern species, it seems the dome firstly appeared on apical and/or caudal scales, and only later emerged on body scales. Bristle was presumably present in the common ancestor and gradually elongated ever since. However, most other morphological traits readily changed during the evolution of Mallomonas.     

Problems with the use of cladistic analysis in palaeoanthropology

Cladistic analysis is a popular method for reconstructing evolutionary relationships on the human lineage. However, it has limitations and hidden assumptions that are often not considered by palaeoanthropologists. Some researchers who are opposed to its use regard cladistics as the preferred method for taxonomic «splitters» and claim it has lead to a revitalisation of typology. Typology remains a part of human evolutionary studies, regardless of the acceptance or use of cladistics. The assumption/preference for «splitting» over «lumping» in cladistics (alpha) taxonomy and the general failure to evaluate (post-hoc) such taxonomies have served to reinforce this assertion.

Researchers have also adopted a number of practices that are logically untenable or introduce considerable error. The evolutionary trend of human encephalisation, apparently isometric with body size, and concurrent reduction in the gut and masticatory apparatus, suggests continuous cladistic characters are biased by problems of body size.

The method suffers a logical weakness, or circularity, leading to bias when characters with multiple states are used. Coding of such characters can only be done using prior criteria, and this is usually done using an existing phylogenetic scheme. Another problem with coding character states is the handling of variation within species. While this form of variation is usually ignored by palaeoanthropologists, when characters are recognised as varying, their treatment as a separate state adds considerable error to cladograms.

The genetic proximity of humans, chimpanzees and gorillas has important implications for cladistic analyses. It is argued that chimpanzees and gorillas should be treated as ingroup taxa and an alternative outgroup such as orangutans should be used, or an (hypothetical) ancestral body plan developed. Making chimpanzees and gorillas ingroup taxa would considerably enhance the biological utility of anthropological cladograms.

All published human cladograms fail to meet standard quality criteria indicating that none of them may be considered reliable. The continuing uncertainty over the number and composition of fossil human species is the largest single source of error for cladistics and human phylogenetic reconstruction.     

Deep homology: A view from systematics

Over the past decade, it has been discovered that disparate aspects of morphology – often of distantly related groups of organisms – are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed ‘deep homology’. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples – three from plants and one from animals – demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.