Primary classification and phylogeny of the Polemoniaceae, with comments on molecular cladistics

The system of classification of the Polemoniaceae currently in use was published by Grant in 1959. Much new evidence concerning relationships in the family has been obtained by numerous workers since 1959, and the old system is in need of revision. A revised system down to the genus level, based on conventional and unconventional characters, including molecular evidence, is presented here. Nineteen genera are grouped into eight tribes and two subfamilies. Three new tribes are described: Acanthogilieae, Loeselieae, and Leptodactyloneae. Several genera are transferred to new groups. The phylogeny of the family is discussed in the light of both the older and new evidence. The approach used in constructing both the 1959 and new systems is that of evolutionary systematics. Two recent (1996, 1997) family-wide surveys of cpDNA and rDNA use cladistic methods of analysis to arrive at sets of major groups. Some of this molecular evidence has been adopted for the present revised system. However, much incongruence still exists between the new sets of clades, on the one hand, and the present revised system or the still-viable parts of the 1959 system on the other hand. The incongruences call for an examination and comparison of the contrasting methods of evolutionary systematics and molecular cladistics. A fundamental flaw in the 1996 and 1997 treatments is the attempt to classify plants on the basis of single-gene gene trees.     

On cladistics and human–ape relationships

The rebuttal of our correspondence (Lehtonen et al., Journal of Biogeography, 2011, 38, 805–808) by J. R. Grehan and J. H. Schwartz (Journal of Biogeography, 2011, 38, 2397–2404) reveals logical inconsistencies in their methodology. Here, we provide a clarification of these issues.     

The cladistics and biology of the Callajoppa genus-group (Hymenoptera: Ichneumonidae, Ichneumoninae)

A cladistic analysis is presented for the genera of the former ichneumonine tribe Trogini. The tribe Heresiarchini is paraphyletic with respect to the Trogini, and so maintaining Trogini as a separate tribe is unsatisfactory. Within Heresiarchini, the following changes are made: (a) the subtribes Apatetorina and Heresiarchina are referred to as the Apatetor and Heresiarches genus‐groups, (b) the genera of the paraphyletic subtribe Protichneumonina are treated as incerta sedis within Heresiarchini, and (c) the Trogini are referred to as the Callajoppa genus‐group, with the former subtribe Trogina referred to as the Trogus subgroup. Thirty‐five genera are recognized as valid within the Callajoppa genus‐group. Catadelphops, Catadelphus, Cobunus, and Facydes are transferred to this group; Holojoppa is removed and is incertae sedis within Heresiarchini. Three new synonyms are proposed: Araeoscelis and Cryptopyge are junior synonyms of Macrojoppa, and Neamblyjoppa is a junior synonym of Catadelphops. Trogus latipennis Cresson is transferred to Pedinopelte from Macrojoppa, and Trogus mactator Tosquinet and its related species (T. bicolor Radoszkowski, T. heinrichi Uchida, and T. tricephalus Uchida) are transferred to Holcojoppa. Tricyphus is redefined and a neotype is designated for Tricyphus cuspidiger Kriechbaumer, the type‐species of the genus. Thirteen new genera are described (authorship of all is Wahl & Sime): Charmedia (type‐species: Charmedia chavarriai Wahl & Sime, sp. n.) , Daggoo (type‐species: Daggoo philoctetes Wahl & Sime, sp. n.), Dothenia (type‐species: Dothenia hansoni Wahl & Sime, sp. n.), Humbert (type‐species: Humbert humberti Wahl & Sime, sp. n.), Laderrica (type‐species: Laderrica feenyi Wahl & Sime, sp. n.), Mokajoppa (type‐species: Tricyphus respinozai Ward & Gauld), Metallichneumon (type‐species: Metallichneumon neurospastarchus Wahl & Sime, sp. n.), Myocious (type‐species: Myocious orientalis Wahl & Sime, sp. n.) , Quandrus (type‐species: Trogus pepsoides Smith, transferred from Callajoppa), Queequeg (type‐species: Gathetus flavibasalis Uchida, transferred from Neofacydes), Saranaca (type‐species: Trogus elegans Cresson; includes Trogus apicalis Cresson, Tricyphyus ater Hopper, and Tricyphus floridanus Heinrich), Tashtego (type‐species: Tashtego janzeni Wahl & Sime, sp. n.), and Xanthosomnium (type‐species: Xanthosomnium froesei Wahl & Sime, sp. n.). A key to the genera of the Callajoppa genus‐group is provided. The evolution of biological traits within the Callajoppa genus‐group is discussed with reference to the elucidated phylogeny. The groundplan biology is parasitism of Sphingidae, with oviposition into a host pupa/prepupa. There have been two transitions to butterfly parasitism within the Trogus subgroup: one a transition to Papilionidae (followed by a switch to Nymphalidae at Psilomastax) and the other to Nymphalidae (followed by a switch to Papilionidae within Macrojoppa). ©2002 The Linnean Society of London. Zoological Journal of the Linnean Society, 134 , 1–56.     

Romance of the three domains: how cladistics transformed the classification of cellular organisms

Cladistics is a biological philosophy that uses genealogical relationship among species and an inferred sequence of divergence as the basis of classification. This review critically surveys the chronological development of biological classification from Aristotle through our postgenomic era with a central focus on cladistics. In 1957, Julian Huxley coined cladogenesis to denote splitting from subspeciation. In 1960, the English translation of Willi Hennig’s 1950 work, Systematic Phylogenetics, was published, which received strong opposition from pheneticists, such as numerical taxonomists Peter Sneath and Robert Sokal, and evolutionary taxonomist, Ernst Mayr, and sparked acrimonious debates in 1960–1980. In 1977–1990, Carl Woese pioneered in using small subunit rRNA gene sequences to delimitate the three domains of cellular life and established major prokaryotic phyla. Cladistics has since dominated taxonomy. Despite being compatible with modern microbiological observations, i.e. organisms with unusual phenotypes, restricted expression of characteristics and occasionally being uncultivable, increasing recognition of pervasiveness and abundance of horizontal gene transfer has challenged relevance and validity of cladistics. The mosaic nature of eukaryotic and prokaryotic genomes was also gradually discovered. In the mid-2000s, high-throughput and whole-genome sequencing became routine and complex geneologies of organisms have led to the proposal of a reticulated web of life. While genomics only indirectly leads to understanding of functional adaptations to ecological niches, computational modeling of entire organisms is underway and the gap between genomics and phenetics may soon be bridged. Controversies are not expected to settle as taxonomic classifications shall remain subjective to serve the human scientist, not the classified.     

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.     

Paleontological Patterns, Macroecological Dynamics and the Evolutionary Process

Here we consider evolutionary patterns writ large in the fossil record. We argue that Darwin recognized but downgraded or de-emphasized several of these important patterns, and we consider what a renewed emphasis on these patterns can tell us about the evolutionary process. In particular, one of the key patterns we focus on is the role geographic isolation plays in fomenting evolutionary divergence; another one of the key patterns is stasis of species; the final pattern is turnovers, which exist at several hierarchical scales, including regional ecosystem replacement and pulses of speciation and extinction. We consider how each one of these patterns are related to the dynamic of changing ecological and environmental conditions over time and also investigate their significance in light of other concepts including punctuated equilibria and hierarchy theory. Ultimately, we tie each of these patterns into a framework involving macroecological dynamics and the important role environmental change plays in shaping evolution from the micro- to macroscale.     

Punctuated equilibrium, morphological stasis and the palaeontological documentation of speciation: a reply to Fryer, Greenwood and Peake's critique of the Turkana Basin mollusc sequence

Fryer, Greenwood & Peake (1983) have recently criticized my analysis of morphological variation in a sequence of Plio-Pleistocene freshwater molluse faunas from the Turkana Basin in E Africa, and question my conclusions that these faunas document speciation and the punctuated equilibrium model of evolutionary change. Unfortunately, these authors misinterpret the nature of the phenotypic variation in African freshwater molluscs and its relevance to my study, and apparently misunderstand punctuated equilibrium theory. Although the majority of their criticisms are therefore erroneous, certain of the points they raise are important: they are addressed here.     

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.     

Individualism, Type Specimens, and the Scrutability of Species Membership

The view that species are individuals, as developed by Ghiselinand Hull, has been touted as explaining the role of type specimens intaxonomy. The kinship of this explanation with the Kripke-Putnam theoryof names has long been recognized. In light of this kinship, however,Hull's account of type specimens can be seen to entail two relatedinscrutability problems – unreasonable limits placed on the natureand extent of biological knowledge. An appreciation for these problemsinvites us to consider the proper relation between metaphysical andepistemological inquires in the philosophy of science.     

DNA hybridization,cladistics, and the phylogeny of phalangerid marsupials

Summary Single-copy DNA/DNA hybridization experiments and numerical cladistic analyses of anatomical characters were used to investigate relationships among nine phalangerid (Marsupialia) species from four different genera. Both rate-dependent and rate-independent analyses of molecular data indicate that species ofTrichosurus form one clade and thatStrigocuscus, Phalanger, andSpilocuscus form a second. Within the latter group,Spilocuscus is excluded from aStrigocuscus-Phalanger calde, which, in turn, is not fully resolved on a jackknife strict consensus tree. Minimum-length Dollo, Wagner, and Camin-Sokal parsimony trees based on 35 anatomical characters, in contrast, suggest placement ofStrigocuscus withTrichosurus rather than withSpilocuscus andPhalanger. However, there are two derived characters that support the alternative arrange ofStrigocuscus withSpilocuscus andPhalanger and one character that further unitesStrigocuscus andPhalanger. Thus, DNA hybridization results are not inconsistent with the distribution of derived character states among anatomical characters, only with minimum-length trees based on character data.     

Phylogeny of the Cocculinoidea (Mollusca, Gastropoda)

Abstract. The superfamily Cocculinoidea is a group of marine, deep-water, limpet-like gastropods. Recent speculation surrounding their affinities has concentrated on their placement within the Gastropoda. However, phylogenetic relationships within the Cocculinoidea, especially the monophyly of families and genera within the group, remain poorly understood. Phylogenetic analysis of 31 morphological characters for 15 cocculinoidean taxa and 2 outgroups resulted in a single most parsimonious tree, length=70, CI=0.62, and RI=0.71. Monophyly of the Cocculinoidea, Cocculinidae, and the genera Cocculina and Coccopigya was supported; Paracocculina and Coccocrater were found to be paraphyletic. Character optimization demonstrates that many characters often cited as diagnostic of various taxa, are often homoplastic and/or synapomorphies at different hierarchical levels.     

Genetic governance: The risks,oversight and regulation of genetic databases in the UK

Increasing scientific and commercial interest is being paid to the creation of large population-based genetic databases to study the relationship between genes and disease. This paper will use ideas from the sociology of technology to look at the network of actors involved in the production, use and commercial exploitation of human genetic data, the social and ethical issues posed by genetic databases and the development of new governance arrangements in this domain. It will be argued that we are witnessing the creation of a new type of research system in the field of human genetics, which also forms the centre of an emerging market for personal and population-based genetic information. Some proposals for improving the governance of human genetic data in the UK will be offered in conclusion.     

Punctuated equilibria, morphological stasis and the palaeontological documentation of speciation: a biological appraisal of a case history in an African lake

The present-day faunas of the great African lakes present some of the world's best examples of 'explosive speciation'. Lakes Victoria and Malawi each probably have several hundred endemic species of cichlid fishes. Much can be inferred about the evolution of these fishes from morphology, behaviour and intra-lacustrine distribution and from the fact that they include taxa ranging from local races, through sibling species, to forms that display extensive differentiation. The time taken to acquire specific distinctness can sometimes be accurately defined, but fossil lineages are unknown. A recent study of a fossil sequence of molluscs in the Turkana basin throws new light on the history of African lake faunas. It also claims to have resolved events during speciation. While critical analysis based on our knowledge of living molluscs in this area fails to substantiate this claim, the fossil molluscs complement information provided by the biology of extant fishes and invertebrates and emphasize the importance of these lakes in the study of evolution in living and extinct populations.     

Integration, phylogeny, and the hominid cranial base

Basicranial features were examined in catarrhine primates and early hominids in order to demonstrate how information about morphological integration can be incorporated into phylogenetic analysis. Hypotheses purporting to explain the functional and structural relationships of basicranial characters were tested using factor analysis. Characters found to be functionally or structurally related to each other were then further examined in order to determine whether there was evidence that they were phylogenetically independent. If phylogenetic independence could not be demonstrated, then the characters were presumed to be integrated and were grouped into a complex. That complex was then treated as if it were a single character for the purposes of cladistic analysis. Factor analysis revealed that five basicranial features may be structurally related to relative brain size in hominoids. Depending on how one defines phylogenetic independence, as few as two, or as many as all of those characters might be morphologically integrated. A cladistic analysis of early hominids based on basicranial features revealed that the use of integrated complexes had a substantial effect on the phylogenetic position of Australopithecus africanus, a species whose relationships are poorly resolved. Moreover, the use of complexes also had an effect on reanalyses of certain published cladistic data sets, implying that those studies might have been biased by patterns of basicranial integration. These results demonstrate that patterns of morphological integration need to be considered carefully in all morphology-based cladistic analyses, regardless of taxon or anatomical focus. However, an important caveat is that the functional and structural hypotheses tested here predicted much higher degrees of integration than were observed. This result warns strongly that hypotheses of integration must be tested before they can be adequately employed in phylogenetic analysis. The uncritical acceptance of an untested hypothesis of integration is likely to be as disruptive to a cladistic analysis as when integration is ignored.     

Phylogeny,natural groups and nemertean classification

Contemporary practice in the classification of nemerteans (phylum Nemertea) is critically discussed. It is argued that basing higher taxa on the existence of a unique combination of characters in a species (or genus) is unlikely to lead to monophyletic taxa, and that this approach should be abandoned in favour of a classification based on explicit hypotheses of phylogeny. These hypotheses should be based on all available characters and characters should not be excluded before the analysis. The classification should be based on a reconstruction of the phylogeny and reflect this phylogeny in an unambiquous way.     

Systematic and phylogenetic significance of the seed coat in the shrubby African Iridaceae, Nivenia, Klattia and Witsenia

MANNINGJ. C. & GOLDBLATT, P., 1991. Systematic and phylogenetic significance of the seed coat in the shrubby African Iridaceae, Nivenia, Klattia and Witsenia. The seeds of Nivenia, Klattia and Witsenia, a natural alliance within Nivenioideae, are among their most distinctive features, and seed number and shape constitute at least two synapomorphies for this monophyletic lineage. In this paper we survey the structure of the seed surface of five species of Nivenia and one each of Klattia and Witsenia by scanning electron microsopy (SEM), and study the development of the seed coat in a representative species of each of the three genera. Outgroups for comparison were selected from genera inside and outside the subfamily. The six genera of Nivenioideae are united in having a 3 (– 2) seriate outer integument but the shrubby genera are unique in the family in their tangentially flattened ovules which mature into depressed, flat, scutiform seeds. They display a range of variation in seed coat characters but are specialized in the subfamily and family in having a transparent outer integument. Other genera have pigmented deposits in the outer epidermis of the outer integument. Nivenia and Witsenia are further specialized in having a partially exfoliating outer integument. Klattia is unique among the shrubby genera in having deposits in the second layer of the tegmen, in retaining an intact outer epidermis of the tegmen, and in the fusiform shape of the epidermal cells and striate surface of the seed. Our results are incorporated in a cladogram that expresses our current understanding of the phylogenetic relationships of Nivenioideae.     

New Rotifera from Kenya, with a revision of the Ituridae

Brachionus africanus sp. nov . and Itura symmetrica sp. nov. are described from Kenya. The Ituridae are revised, a key to the species is provided and a cladistic analysis performed. Some remarks on rotifer endemism in Africa are given.