The monophyly of the Characidiinae, a Neotropical group of characiform fishes (Teleostei: Ostariophysi)

Although virtually no phylogenetic evidence (in the sense advocated by Hennig, 1966) had been previously presented to support the monophyly of the Characidiinae, and most 'diagnostic' characters used by previous authors were found to be unacceptable in a cladistic classification, i t is still possible to diagnose the Characidiinae in a phylogenetic sense. This study revealed the existence of 13 synapomorphies supporting the monophyly of the group. Several of these synapomorphies, such as the modifications associated with the mesethmoid, the jaw bones, and the ribs of the fifth vertebra, are unique to the Characidiinae, thus providing a solid basis for recognizing the group as a monophyletic unit of characiform fishes. Demonstration of characidiin monophyly provides a solid foundation for further phylogenetic analysis of characidiin interrelationships, and higher level relationships among characiform fishes.     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

Are lungfishes the sister group of tetrapods?

It is generally accepted that rhipaidistian crossopterygians are the closest relatives of tetrapods. Rosen, Forey, Gardiner & Patterson (1981) challenge this view and contend that lungfishes are the sister group of tetrapods. They present a detailed cladistic analysis and claim to identify a large number of synapomorphies shared by lungfishes and tetrapods but not by rhipidistians. Their analysis is faulty. Although Rosen et al. (1981) correctly emphasize that cladistic relationships must be based on shared derived characters, they often fail to take intragroup variation into account in postulating synapomorphies. They also use evidence inconsistently by attributing greater significance to similarities between lungfishes and tetrapods than to even more detailed similarities between rhipidistians and tetrapods. They misinterpret the skeletal pattern of the paired appendages. The many synapomorphies that they claim to have identified are either invalid, irrelevant, or are characters involving reduction or loss (which have a high probability of convergence). Consequently, they make an unconvincing case for a sister-group relationship between lungfishes and tetrapods. On the other hand, Rosen et al. (1981) do show that evidence for the orthodox view of rhipidistian-tetrapod relationships is not as strong as generally believed. The uncertain interrelationships among rhipidistians is a major problem. Tetrapod-fish relationships need to be re-examined by means of a properly conducted cladistic analysis.     

Spermatozoal ultrastructures of two marine perciform teleost fishes, the goatfish, Paraupeneus spilurus (Mullidae) and the rabbitfish, Siganus fuscescens (Siganidae) from Taiwan

Mature spermatozoa of two perciform teleost fishes, Paraupeneus spilurus (Mullidae) and Siganus fuscescens (Siganidae) from Taiwan were examined using transmission and scanning electron microscopy. Despite the fact that spermatozoa of both species are of the primitive type, the results of the present study highlight the potential application of spermatozoal morphology in studies of fish phylogenetic relationships. To our knowledge, the flattened nucleus observed in P. spilurus spermatozoa is reported for the first time. Several features common to Sigandae spermatozoa-the unusual almost parallel situation of the centrioles, the arrangement of mitochondria and the near absence of shallow nuclear fossa-are significantly different from other common teleost sperm types. These unique features may be synapomorphies for the Siganidae and Mullidae and evidently contribute to the study of phylogenetic relationships in teleosts.     

PHYLOGENY AND BIOGEOGRAPHY OF CONDEEUM GROUP (PROTURA: PROTENTOMIDAE)

Abstract  Using the Hennig 86 phylogenetic analysis program to analyse the taxa in genera related to Condeellum , the phylogenetic relationships among the species are schemed on the basis of potential synapomorphies of the adults, represented by 16 characters. The character evolution and the route of dispersal are also discussed. The cladistic biogeographic analysis is performed. The basal taxon Condeellum exhibits an Indo-Pacific distribution and the sister group Neocondeellum species exhibit a collective Oriental and Holarctic distribution. The distribution patterns and the vicariance events occurred in those areas are hypothesized.     

康蚖群的系统发生和生物地理学的研究(原尾目:始蚖科)(英文)

应用HENNIG86系统发生分析程序,选择出成虫的有代表性的16个共同衍征,分析了与康蚖属相关各属的各个种类,得出了该类群的相关系统树。同时对特征的演化以及其扩散途径等也进行了讨论。文中还应用Page 1993的COMPONENT程序进行了生物地理学的分析;得到种类—地区支序图。其中康蚖属表现为典型的印度—太平洋分布型,而其姐妹群新康蚖属则兼有东洋区和全北区的分布型。至于分布地区的相互关系和在这些地区的分衍替代事件的发生等问题也作了初步的假想。     

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.     

Cladogenesis and anagenesis: a confusion of synapomorphies

Much cladistic theory is flawed because it confuses two temporal sequences: 1. cladogenetic (branching) chronology; 2. anagenetic (primitive-advanced) polarity. The first is largely inherent and exposed by a straigram; the second requires an independent polarisation of the changes subsequent to cladogenetic branchings. Failure to consistently distinguish between these always causes confusion, but destroys cladistic theory, because plesiomorphy and apomorphy refer to anagenesis, and autapomorphy and synapomorphy refer to cladogenetis. They cannot, however, be identified wholly independently, because cladogenetic chronology establishes anagenetic polarity by out-grouping, under limited conditions; and anagenetic polarity establishes cladogenetic chronology in multiple cladistic events. The principle ‘common characters are primitive’ is more accurately expressed as ‘characters of greater s read are cladogenetically earlier', and establishes cladogenetic relationships, never anagenetic polarity as usually thought. The full temporal analysis of biological patterns, therefore, involves eight stages: 1. Homologue identification; 2. Homolostrata delimitation and definition; 3. Stratigram formation; 4. Cladogenetic sequencing; 5. Anagenetic polarity determination (chronogramy); 6. Cladogenetic and anagenetic co-analysis; 7. Cladogram construction; 8. Phylogenetic interpretation.     

Sophisticated falsification and research cycles: Consequences for differential character weighting in phylogenetic systematics

Practicing phylogenetic systematics as a sophisticated falsification research program provides a basis for claiming increased knowledge of sister species relationships and synapomorphies as evidence for those cladistic propositions. Research in phylogenetic systematics is necessarily cyclic, and the place where the positive shift in understanding occurs is subsequent to discovering the most parsimonious cladogram(s). A priori differential character weighting is inconsistent with seeking the maximally corroborated cladogram (sensu Popper), because weighting adds to background knowledge, the evidence being then less improbable than it would be otherwise. Also, estimating weights from character state frequencies on a cladogram is inconsistent with the view that history is unique. Sophisticated falsification provides the place in the cycle of phylogenetic systematic research where weight of evidence can be evaluated and these inconsistencies do not apply. On balance, phylogenetic systematics appears to achieve greater coherence and generality as a result of focusing on the foundations for claiming increased knowledge and avoiding efforts to differentially weight characters.     

睡莲科的属间关系研究

本文用谱系分支法分析睡莲科的属间关系,３５个衍征中,分析了３１个特征的进化趋势,根据分析将睡莲科提升为睡莲目,分为３个科,莲科、水盾草科、睡莲科。     

Recent developments in the analysis of comparative data

Comparative methods can be used to test ideas about adaptation by identifying cases of either parallel or convergent evolutionary change across taxa. Phylogenetic relationships must be known or inferred if comparative methods are to separate the cross-taxonomic covariation among traits associated with evolutionary change from that attributable to common ancestry. Only the former can be used to test ideas linking convergent or parallel evolutionary change to some aspect of the environment. The comparative methods that are currently available differ in how they manage the effects brought about by phylogenetic relationships. One method is applicable only to discrete data, and uses cladistic techniques to identify evolutionary events that depart from phylogenetic trends. Techniques for continuous variables attempt to control for phylogenetic effects in a variety of ways. One method examines the taxonomic distribution of variance to identify the taxa within which character variation is small. The method assumes that taxa with small amounts of variation are those in which little evolutionary change has occurred, and thus variation is unlikely to be independent of ancestral trends. Analyses are then concentrated among taxa that show more variation, on the assumption that greater evolutionary change in the character has taken place. Several methods estimate directly the extent to which ancestry can predict the observed variation of a character, and subtract the ancestral effect to reveal variation of phylogeny. Yet another can remove phylogenetic effects if the true phylogeny is known. One class of comparative methods controls for phylogenetic effects by searching for comparative trends within rather than across taxa. With current knowledge of phylogenies, there is a trade-off in the choice of a comparative method: those that control phylogenetic effects with greater certainty are either less applicable to real data, or they make restrictive or untestable assumptions. Those that rely on statistical patterns to infer phylogenetic effects may not control phylogeny as efficiently but are more readily applied to existing data sets.     

Phylogenetic systematics of the nymphaeales

A cladistic analysis was applied to reveal the phylogenetic relationships among the Nymphaeales. Seventeen out of twenty three characters in gross morphology, anatomy and palynology were analyzed, for their evolutionary polarities. From the results of the present analysis, the phylogenetic status of each genus and their relationships were clarified: 1)Nelumbo is a distinct taxon and is presumed to have originated from an ancestral stock of the Nymphaeales; 2)Ceratophyllum has a close phylogenetic relationship withCabomba; and 3) in the Nymphaeaceaesensu stricto, Nuphar and the remaining genral constitute a monophyletic group. A conclusion obtained from the present analysis was that the following three families should be recognized in the Nymphaeales; Nelumbonaceae Nymphaeaceae, and Ceratophyllaceae. The generaBrasenia andCabomba are traditionally classified in the Nymphaeaceae or in the independent family Cabombaceae. However, they should be included in the family Ceratophyllaceae.     

Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.     

Phylogeny and co-speciation in feather mites of the subfamily Avenzoariinae (Analgoidea: Avenzoariidae)

A cladistic analysis of phylogenetic relationships is carried out for the feather mite subfamily Avenzoariinae. The analysis is made at two different taxonomic levels, for 19 genera of the all family Avenzoariidae and for taxa of species rank for the Avenzoaria and Bychovskiata generic groups. A subsequent comparative analysis of phylogenetic hypotheseis for the subfamily Avenzoariinae and recently accepted phylogenetic hypotheses of the shorebirds Charadriiformes indicates co-speciation of feather mites with their hosts. As a result of the comparative analysis it is suggested, that the subfamily Avenzoariinae originated from an ancestor of the order Charadriiformes and co-speciated with this host order. The expected pattern of parallel evolution is disturbed by different evolutionary events, such as host shifts, extinction of mites and differential evolutionary rates of mite lineages in different phyletic branches of feather parasites.     

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.     

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.     

果蝇Drosophila saltans种亚组（双翅目：果蝇科）系统发育关系：形态学能否解决分子冲突？

正确的系统发生重建对于理解进化事件至关重要.尽管分子系统学对于解决此类问题取得了极大的成功,由于一些诸如密码子使用偏性等的内在约束,来源于DNA的信息可能仍然存在着局限.因为发生在祖先的替代性转换,果蝇Drosophila saltans 5个种亚组由不同基因构建的分子系统树之间存在着冲突(在以往发表的分子系统学研究中,这些种组的每一个种亚组全少有一个代表).本文用40个形态学特征重新分析了这些种组.不同于以前发表的大多数假说,本研究支序分类学的结果表明,果蝇sturtevanti种亚组是一个较早的分支,而剩下的4个亚组形成一个支持度较高的类群;后者又可以再分为两个姐妹群:一个包含cordata和elliptica亚组,另一个包含parasaltans和saltans亚来组.本研究结果修正了果蝇saltans种组的分子进化(密码子使用偏性),并强调形态学对于系统发生重建和理解分子进化现象的重要作用.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

An investigation into the cladistic relationships and monophyly of therocephalian therapsids (Amniota: Synapsida)

A comprehensive phylogenetic investigation was performed to elucidate the cladistic relationships and possible monophyly of therocephalian therapsids (Amniota: Synapsida). The phylogenetic positions of 30 therapsid taxa were examined under maximum parsimony, including 23 therocephalian genera. The analysis incorporated 110 cranial and postcranial characters in order to assess the interrelationships of basal therocephalians and eutherocephalians and their relationships to Cynodontia, representing the most complete review of therocephalian phylogeny to date. The analysis supports the hypothesis that Therocephalia represents the monophyletic sister taxon to Cynodontia, with as many as 15 morphological synapomorphies, in contrast with other recent analyses of lesser taxon sampling. The results also support the hypothesis that Scylacosauridae is more closely related to Eutherocephalia than to the basal therocephalian family Lycosuchidae, supporting a ‘Scylacosauria’ clade. The taxa suggested here to be neotenic forms (e.g. Ictidosuchoides and Ictidosuchops) are positioned near the base of a monophyletic Baurioidea. Neotenic development of the therocephalian feeding apparatus and evolutionary parallelism with cynodonts are suggested to have been important trends in the early evolution of baurioid therocephalians into the Late Permian and Early Triassic.     

Angiosperm wood evolution and the potential contribution of paleontological data

Wood anatomy is often viewed as a source of independent data that may be used to assess evolutionary relationships among angiosperms. Comparative anatomical studies document suites of correlated characters that have been interpreted as general evolutionary trends, of which several have been asserted to be irreversible. Paleobotanical data summarized by Wheeler and Baas provide broad chronological corroboration of some wood anatomical trends, such as evolution from scalariform to simple perforation plates and long to short vessel elements. However, the focus on general evolutionary trends rather than on analyzing character distribution patterns in a cladistic phylogenetic context obscures a more detailed understanding of the evolution of wood anatomical features. Patterns of character evolution, including the assertions of irreversibility, need to be tested through cladistic analyses. In this paper selected wood anatomical features from families of Magnoliidae and “lower” Hamamelididae are summarized and mapped onto previously published cladograms as a preliminary means of testing previous hypotheses of wood evolution. The results show that many of the characters are homoplasious and have evolved both in accord with, and counter to, the hypothesized general trends in different groups of flowering plants. In general, changes that confirm generalized trends are more common than changes that are counter to those trends. Future studies should combine wood anatomical characters with other features as part of a cladistic analysis. Fossil woods have not yet contributed significantly to phylogenetic studies, but in the very few cases where they have been linked to fossil reproductive structures, the woods have provided a better understanding of wood anatomy in early members of some families. Data from fossil wood expand the diversity of anatomical structure known in some angiosperm taxa and thus provide additional evidence that might be used in phylogenetic analyses. Fossil woods have the greatest potential to affect phylogenetic analyses where they can be linked to other fossil organs. The best chance for establishing such a linkage is through the study of fossil charcoalified woods that co-occur with other dispersed mesofossils.