Cladistics and the hominid fossil record

Cladistic methodology has become common in phylogenetic analyses of the hominid fossil record. Even though it has correctly placed emphasis on morphology for the primary determination of affinities between groups and on explicit statements regarding traits and methods employed in making phylogenetic assessments, cladistics nonetheless has limitations when applied to the hominid fossil record. These include 1) the uncritical assumption of parsimony, 2) uncertainties in the identification of homoplasies, 3) difficulties in the appropriate delimitation of samples for analysis, 4) failure to account for normal patterns of variation, 5) methodological problems with the appropriate identification of morphological traits involving issues of biological relevance, intercorrelation, primary versus secondary characters, and the use of continuous variables, 6) issues of polarity identification, and 7) problems in hypothesis testing. While cladistics has focused attention on alternative phylogenetic reconstructions in hominid paleontology and on explicit statements regarding their morphological and methodological underpinnings, its biological limitations are too abundant for it to be more than a heuristic device for the preliminary ordering of complex human paleontological and neonatological data.     

Geographic Differentiation, Cladistics, and Vicariance Biogeography: Reconstructing the Tempo and Mode of Evolution

SYNOPSIS. Although the literature on speciation is large, surprisinglylittle attention has been paid to methodological considerations.If there is a general methodology within this literature, itconsists of delimiting taxa and their distributions, describingpatterns of phenotypic (and occasionally genotypic) variation,noting contact zones and hybridization, reviewing informationon past climates and vegetations, and from these constructinga narrative scenario of the pathway of speciation. However,two kinds of knowledge, essential for reconstructing speciation,are typically lacking: a genealogical hypothesis of the relevanttaxa based on cladistic analysis, and a hypothesis of the interrelationshipsof areas of endemism based on vicariance biogeography. Bothare necessary to develop and test alternative hypotheses aboutthe mode of taxonomic differentiation. A model of speciationanalysis is constructed using taxa of Australian birds as theempirical data base. Cladistic relationships among taxa andvicariance patterns among areas of endemism reveal a specific,nonrandom historical relationship among the areas of differentiationfor Australian birds and suggest that type la allopatric speciation(of Bush, 1975) is more common than type lb, that peripheralisolates are less important than previously maintained, andthat parapatric speciation is rare. The model can also be usedto examine the patterns of concordance between phenotypic andgenotypic characteristics during geographic differentiationand to investigate their relative and absolute rates of change.     

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.     

Arthropod Cladistics: Combined Analysis of Histone H3 and U2 snRNA Sequences and Morphology

Morphological, developmental, ultrastructural, and gene order characters are catalogued for the same set of arthropod terminals as we have scored in a recent study of histone H3 and U2 snRNA sequences (D. J. Colgan et al. , 1998, Aust. J. Zool. 46, 419–437). We examine the implications of separate and simultaneous analyses of sequence and non-sequence data for arthropod relationships. The most parsimonious trees based on 211 non-sequence characters (273 apomorphic states) support traditional higher taxa as clades, including Mandibulata, Crustacea, Atelocerata, Myriapoda, and Hexapoda. Combined analysis of morphology with histone H3 and U2 sequences with equal character weights differs from the morphological results alone in supporting Progoneata + Hexapoda (= Labiophora) in favor of a monophyletic Myriapoda, resolves the entognathous hexapods as a grade, and supports pycnogonids as sister group to Euchelicerata (rather than as basal euarthropods). Monophyly of Chelicerata (including pycnogonids), Mandibulata, Crustacea, Progoneata, Chilopoda, and Hexapoda is maintained under a range of transition/transversion and third codon weights, whereas Atelocerata and Myriapoda/Labiophora do not withstand all sensitivity analyses.     

Anthropology, Demography, and the Search for a Critical Analysis of Fertility: Insights from Russia

The socialist and postsocialist contexts offer important challenges for anthropologists developing a critical analysis of fertility. The need for fertility studies to address class and gender inequities is often overlooked by postsocialist scholars, whose work is mired in responses to the socialist past and ongoing pronatalist campaigns. I examine the ways that fertility analysis has been used in national political struggles in Russia, and explain why supporters of democratic reforms and women's rights have neglected to address gender and class issues in their fertility studies. While Russian nationalists cite fertility decline as proof that market reforms threaten Russia's existence, defenders of neoliberalism draw on demographic transition theory to redefine fertility decline as a universal sign of socioeconomic development. Working with conventional demographic paradigms and a postsocialist cultural logic, Russian transition theorists simultaneously oppose pronatalist politics, support women's reproductive choice, and reproduce the limitations of liberal paradigms regarding the family, society, and public policy. This article shows how anthropological critiques of demographic transition theory can be expanded and nuanced by considering the ways this theory gets adapted to particular cultural logics and political contests. [Keywords: anthropology and demography, postsocialism, Russia, fertility decline]     

The Veil of Objectivity: Prophecy, Divination, and Social Inquiry

It is possible for folk inquiry to become a source for the modification of anthropological thought. This paper discusses two alternative knowledge systems: traditional divination and syncretic prophecy in Central Africa. The processes of scientific discovery, causal reasoning, and the evaluation of evidence are compared with oracular reasoning and prophetic prediction. The oracular aspects of scientific reasoning are delineated along with the problems of reformulating and presenting basic data. Part of this presentational process is the "translation" of events from the context of their occurrence into a theoretical framework. The modifications generated by data analysis affect the explanatory adequacy of the method of inquiry. A rapprochement between folk inquiry and Western scientific assumptions diminishes the forms of theoretical reductionism that inhibit the possibility for describing and analyzing contrasting belief systems within an anthropological framework . [folk inquiry, prophecy, divination, scientific reasoning, Africa]     

中国紫金牛属的分支分类学研究

基于60个形态学性状,对中国广义报春花科（Primulaceae s.l.）紫金牛属（Ardisia）90个分类群的系统发育关系运用分支分析方法进行了分析。采用最简约性分析得到了100个同等简约树。50%多数规则一致树的分支结构与以前建立的紫金牛亚属划分系统基本一致。外类群酸藤子属、铁仔属、密花树属聚在分支树的最基部,紫金牛属为一单系类群。形态分支树的一致性指数和保持性指数和各分支内部支持率均较低,只在种与变种或亚种之间获得较高的支持率。高木亚属、腋序亚属、短序亚属、顶序亚属处于分支树较为基部的位置,推测这四个亚属的类群在紫金牛属中较为原始;圆齿亚属和锯齿亚属共同组成一大支,二者亲缘关系紧密,推测这两个亚属为该属中最为进化的类群。结合形态学对属内系统发育关系进行了讨论和推测了一些性状的演化趋势,以期为分类修订提供依据。     

Cladistics of the genera of Mesochorinae (Hymenoptera: Ichneumonidae)

Abstract. A cladistic analysis is presented for the genera of the ichneumonid subfamily Mesochorinae. Nine genera are recognized as valid. Previous work on larval morphology is reviewed and a number of larvae are newly illustrated and discussed. Four new synonyms are proposed: Oncocotta, Piestetron, Plectochorus and Rhaibaspis are all synonymized with Mesochorus , and Stictopisthus is placed back as a synonym of Mesochorus. Four new genera are described: Artherola from South Africa, Chineater from Chile, Thamester from Japan, and Varnado from Morocco. A new key is provided to the mesochorine genera of the world.     

Cladistics and the comparative morphology of linyphiid spiders and their relatives (Araneae, Araneoidea, Linyphiidae)

This paper provides the first quantitative cladistic analysis of linyphiid morphology. Classical and novel homology hypotheses for a variety of character systems (male and female genitalia, somatic morphology, spinneret silk spigot morphology, etc.) are critically examined and studied within a phylogenetic context. Critical characters have been illustrated. A sample of linyphiid taxa (nine genera in four subfamilies), five species of Pimoa (Pimoidae), and two other araneoid families (Tetragnathidae and Araneidae, represented by Tetragnatha and Zygiella , respectively) were used to study the implications of the phylogeny of Pimoidae for the systematics of linyphiids. The phylogenetic relationships of these 16 exemplar taxa, as coded for the 47 characters studied, were analysed using numerical cladistic methods. In the preferred cladogram Pimoidae and Linyphiidae are sister groups, Stemonyphantinae are sister group to the remaining linyphiids, and Mynogleninae are sister group to the clade composed of Erigoninae plus Linyphiinae. These results agree with the relationships recently proposed by Wunderlich, except by finding erigonines as the sister group to linyphiines rather than to mynoglenines.     

Conodonts Meet Cladistics: Recovering Relationships and Assessing the Completeness of the Conodont Fossil Record

A numerical cladistic analysis of the conodont family Palmatolepidae has been undertaken to determine the applicability of the technique to group-wide systematic revision. Results suggest a new hypothesis of relationships that is considerably more parsimonious than trees compatible with existing hypotheses of relationships, or trees that are even loosely constrained stratigraphically. This may occur either because the fossil record is incomplete, because taxon sampling for the cladistic analysis is low, or because the most parsimonious trees approximate the true tree less well than do stratigraphically-constrained trees (or because of a combination of these factors). Although more taxa and more characters would be preferable in choosing between these possibilities, the tree derived solely from morphological data is adopted. Thus, stratigraphic data can be used to test hypotheses of relationships and construct phylogenies; hypotheses of relationships can be used to test the completeness of the conodont fossil record. Existing schemes of classification within the Palmatolepidae are rejected because most groups within them are either polyphyletic or paraphyletic. A new scheme is presented. Character changes suggest correlated, progressive and mosaic evolution within the Palmatolepidae. Parsimony analysis of partitioned datasets indicates that more phylogenetic information can be recovered from S rather than P or M element positions, although data from all three positional groups are preferable to data from just one. Thus, multielement taxonomy is essential to the resolution of conodont interrelationships.     

All-Orientation Search and All-Placement Search in Comparative Molecular Field Analysis

Three sets of molecules have been used to study the conventional CoMFA procedure. For all the three test sets, the resulting q² values were observed to vary simply because of the change in the orientation or placement of the aligned molecules. The reason is believed to root in the imperfect sampling of the molecular field. We have introduced two new strategies, all-orientation search (AOS) and all-placement search (APS), to optimize the sampling process. By rotating and translating the molecular aggregate within the grid systematically, all the possible samplings of the molecular field are tested and subsequently the one with the highest q² value can be picked out. We have also demonstrated that the combined application of AOS/APS with GOLPE procedure can yield results better than the ones by using them respectively.Electronic Supplementary Material available.     

Holistic Pattern Analysis as an Alternative to Pattern Cladistics in Hypothesizing Crustacean Phylogenetic Sequences

There has been a growing realization that ‘true’ phylogenetic relationships cannot be determined using pattern cladistical methods alone. The applications of such techniques to the problem of crustacean evolution is first examined using the results presented by Wilson (in this issue). It is found that the degree of correlation of characters in the head vs trunk regions explains very well the grouping of taxa in the cladograms, suggesting that the groups are nothing more than mathematical constructs. The argument is presented that functions of different parts of the crustacean body need to be determined, along with an understanding of how the body morphology is designed in accordance with the dominant functions. A method for producing hypothesized phylogenetic sequences from an analysis of body morphology is proposed and examined using the amphipod family Iphimediidae. It is suggested that cladograms are merely hypotheses and can be tested using functional morphological information of the type outlined.