Paraphyletic status of Polychaeta suggested by phylogenetic analysis based on the amino acid sequences of elongation factor-1 alpha

In order to judge whether or not Polychaeta is a paraphyletic group, I determined almost the entire amino acid sequence of elongation factor-1 alpha from thirteen polychaetes, two oligochaetes, two hirudineans, two vestimentiferans, and two molluscs. Phylogenetic analysis by the neighbor-joining (NJ) method and the maximum likelihood (ML) method indicated the monophyly of Clitellata (the oligochaetes and hirudineans). In both the NJ and ML trees, vestimentiferans and clitellates were derived from polychaetes independently. The present results strongly suggest that Polychaeta is a paraphyletic group.

The context of human genetic evolution

The debate on modern human origins has often focused on the relationship between genes and fossils. Although more and more genetic evidence has been accumulating in favor of a recent African origin for modern humans, it has been assumed by many that the fossil evidence remains ambiguous. On the contrary, it has been clear for some time that the fossil evidence does not support the multiregional model: Fossils and archeology indicate a pattern of multiple dispersals from and beyond Africa, against which the genetic data can be compared. The continuing value of paleobiology is in complementing genetic information by revealing the context of human evolution: locating the dispersals and extinctions of populations in time and space, correlating these events with the environmental forces that shaped them, and providing an increasingly detailed understanding of the morphology and technology of early humans.

Biogeographic origins of goannas (Varanidae): a molecular perspective

This project aims to clarify the phylogenetic relationships among the extant species of Varanus in order to elucidate the origins of Varanidae, using DNA sequences. Results obtained for a minimum of 662 nucleotides of 12S rRNA sequence data from each of 21 extant species of Varanus indicate that the Australian varanids form a single monophyletic clade and also suggest that within the Australian varanids, members of the subgenus Odatria (pygmy monitors) may from a clade separate from those in the subgenus Varanus (large monitors). The Asian species appear to be sister taxa to the Australian species, while the two African species investigated were most divergent, suggesting that the Varanidae are not Gondwanic in origin. Hypothesis testing analyses were performed and involved constraining the 12S sequence data according to previously described topologies and testing the difference using parametric and nonparametric statistics. The phylogeny generated using 12S sequence data was statistically different from previously described morphological trees, while there was some support for topologies based on chomosomal and immunological datasets. Overall, our results suggest that the Australian species may be derived from an Asian source and are, therefore, in agreement with the hypothesis based on the fossil record suggesting that Varanidae may be Asian in origin.

Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates

The Hawaiian Islands form as the Pacific Plate moves over a 'hot spot' in the earth's mantle where magma extrudes through the crust to build huge shield volcanos. The islands subside and erode as the plate carries them to the north-west, eventually to become coral atolls and seamounts. Thus islands are ordered linearly by age, with the oldest islands in the north-west (e.g. Kauai at 5.1 Ma) and the youngest in the south-east (e.g. Hawaii at 0.43 Ma). K-Ar estimates of the date of an island's formation provide a maximum age for the taxa inhabiting the island. These ages can be used to calibrate rates of molecular change under the following assumptions: (i) K-Ar dates are accurate; (ii) tree topologies show that derivation of taxa parallels the timing of island formation; (iii) populations do not colonize long after island emergence; (iv) the coalescent point for sister taxa does not greatly predate the formation of the colonized younger island; (v) saturation effects and (vi) among-lineage rate variation are minimal or correctable; and (vii) unbiased standard errors of distances and regressions can be estimated from multiple pairwise comparisons. We use the approach to obtain overall corrected rate calibrations for: (i) part of the mitochondrial cytochrome b gene in Hawaiian drepanidines (0.016 sequence divergence/Myr); (ii) the Yp1 gene in Hawaiian Drosophila (0.019/Myr Kambysellis et al. 1995); and (iii) parts of the mitochondrial 12S and 16S rRNA and tRNAval in Laupala crickets (0.024-0.102/Myr, Shaw 1996). We discuss the reliability of the estimates given the assumptions (i-vii) above and contrast the results with previous calibrations of Adh in Hawaiian Drosophila and chloroplast DNA in lobeliods.

A different tempo of mitochondrial DNA evolution in birds and their parasitic lice

A phylogeny for the lice (Insecta: Phthiraptera: genus Dennyus) parasitic on swiftlets (Aves: Collocalliinae) was constructed based on mitochondrial cytochrome b DNA sequences. This phylogeny is congruent with previous phenetic analyses of morphometric data for the lice. Comparison with a previously obtained phylogeny for the hosts indicates some degree of cospeciation. These cospeciation events are used to compare relative rates of evolution in the birds and their lice for the same segment of the cytochrome b gene. Cytochrome b is evolving two to three times more rapidly in lice than in birds, and louse cytochrome b is highly divergent compared to that of most other insects. Although generation time has been suggested as an explanation for the disparity in evolutionary rates between lice and their hosts, we suggest that the small effective population sizes of lice coupled with founder events occurring during transmission to new host individuals may be an important factor.

Phylogenetic relationships of the western North American phoxinins (Actinopterygii: Cyprinidae) as inferred from mitochondrial 12S and 16S ribosomal RNA sequences

Parsimony analysis of the mitochondrial 12S and 16S rRNA sequences of North American phoxinin taxa indicated the existence of three major clades, the Western Clade, the Creek Chub Clade, and the Open Posterior Myodome Clade. The monophyletic Western Clade identified in this paper contained fewer taxa than that identified by previous authors. This clade contained species restricted to drainages west of the Continental Divide, such as Gila, Acrocheilus, Relictus, Eremichthys, Siphateles, Ptychocheilus, Lavinia, and Orthodon, and the wide-ranging genus Phoxinus found in eastern North America and Eurasia. Within this Western Clade Phoxinus was the basal sister group. Gila was recognized as a monophyletic group exclusive of Siphateles and Snyderichthys, clades traditionally recognized as subgenera of Gila. The genus Gila was most closely related to the genus Acrocheilus and together these formed the sister group to the genus Relictus. These relationships were supported independent of weighting schemes used in analyses. Identification of Phoxinus as the basal sister taxon of the Western clade implies that other major clades of North American Phoxinins likely have Asian or European relatives.

Francolin phylogenetics: molecular, morphobehavioral, and combined evidence

The phylogenetics of francolins (Francolinus species) were reassessed by obtaining 660 bp of sequence of the mitochondrial DNA (mtDNA) cytochrome b gene from 20 species, the Common Quail Coturnix coturnix africana, and the Madagascar Partridge Margaroperdix madagarensis. Published sequences of the Japanese Quail C. c. japonica, Alectoris partridges, and the Junglefowl Gallus gallus were also included. Separate analysis of the 200 phylogenetically informative cytochrome b characters and the 25 informative morphobehavioral characters, as well as a combined analysis of molecular and morphobehavioral data, do not support francolin monophyly but provide strong evidence for two previously suggested clades--the quail-francolins (or partridges) and the partridge-francolins (pheasants/francolins). The quail-francolin clade comprises three groups of African francolins and three Asian species that were previously considered more closely related to the partridge-francolins. The partridge-francolin clade, which includes four groups of African francolins, forms a sister group to the Coturnix quails, the Madagascar Partridge, and the Alectoris partridges. The molecular data suggest that the two francolin clades diverged approximately 3-6 MYA. Climatic fluctuations of the past 2.5 MYA may have led to the diversification of the ecologically different francolin species groups and speciation within them.

Base-compositional biases and the bat problem. II. DNA-hybridization trees based on AT- and GC-enriched tracers

We conducted a series of parallel DNA-hybridization experiments on a small group of bats (species of Pteropus, Rhinolophus, Noctilio and Pteronotus) and outgroups (Lemur, Cynocephalus, Didelphis), using whole-genome labels and tracers made from extracts enriched with AT and two levels of GC content. FITCH (additive phylogenetic trees) topologies were constructed from the four sets of comparisons, indexed as both delta Tmode and delta NPHs (normalized percentage of hybridization). Based on our previous work showing that the shared AT bias of pteropodids and some microchiropterans may affect the rank-ordering of taxa based on either AT- or GC-rich labels, our expectation was that the resulting trees would show differing topologies when generated from tracers made with the variously enriched DNA extracts. Whereas there was some variation among the trees, most of them grouped the bats together, and almost all paired the representative megachiropteran and rhinolophoid microchiropteran as sister-taxa in contrast to the other microchiropterans. As the pteropodid-rhinolophoid relationship is an unexpected and unlikely one, we attribute this association to an AT bias that was not obviated even by our most GC-rich labels, and suggest that such a bias may compromise the truth of some molecular trees. Accordingly, we believe the broader issue of bat monophyly remains unresolved by DNA-hybridization and probably also by gene-sequencing studies.

Base-compositional biases and the bat problem. I. DNA-hybridization melting curves based on AT- and GC-enriched tracers

We explored the interordinal relationships of mammals using DNA-DNA hybridization, with particular reference to the much-debated problem of whether the megabats and microbats are more closely related to each other than the megabats are to primates. To try to improve resolution when taxa are distantly related and the melting points of hybrids are low and difficult to distinguish, we increased the GC content of DNA by a fractionation method that used the same melting-point apparatus used in the hybridization studies. When we used GC-rich DNA as the tracer to make hybrids, the melting point of the self-hybrid shifted to a higher temperature as expected, but the behaviour of heterologous hybrids varied with the taxa being compared. When the melting point of the heterologous hybrid also shifted to a higher temperature so that the two compared taxa maintained the same or proportional distance, we called this 'following behaviour', because the heterologous hybrid made with GC-rich tracer 'followed' the GC-rich self-hybrid to higher temperatures. We also commonly saw anomalous behaviour, where the melting point of the heterologous hybrid shifted to a lower temperature when compared with an AT-rich hybrid. In these anomalous cases, the distance measured between the taxa increased markedly as a result of GC-enrichment, indicating that an underestimate of distance may have resulted from AT bias in DNA. This inference was supported by the finding that it was rare to observe a decrease in measured distance between taxa using GC-rich DNA, but very common to find an increase as would be expected from the generally higher AT contents of eutherian DNAs. Moreover, the most extreme cases, where distances changed most using GC-rich DNA, were usually those involving comparisons between taxa known to have the most extreme AT-biases among mammals, such as the megabats and rhinolophoid (including megadermatid) microbats. Our results show consistent underestimates of measured differences between eutherian taxa with extreme AT-biases.

Impact of early Polynesian occupation on the land snail fauna of Henderson Island, Pitcairn group (South Pacific)

Henderson Island, an uninhabited raised coral atoll in the Pitcairn group, has recently been designated a World Heritage Site because of its unique and relatively undisturbed ecosystem. The island is believed to have been uplifted and subaerially exposed during the last 275 kyr. This therefore provides the maximum age for the terrestrial biota that includes several endemic taxa. Henderson today supports 16 strictly terrestrial species of snails, about half of which are endemic. Analyses of sediments beneath Polynesian occupation horizons dated between the 11th and 17th centuries AD, have yielded 11 species of land snail present in the modern fauna, together with at least six (and possibly as many as eight) further species that no longer occur on the island. These extinct taxa are illustrated and formal descriptions provided for five ( Pleuropoma hendersoni , Orobophana carinacosta , Minidonta macromphalus , Philonesia pyramidalis , P. weisleri ); a sixth, known only from broken shells, appears to belong to the genus Hiona . The two remaining taxa are ‘tornatellinids’ that have not been recognized among the modern fauna. Radiocarbon dates from bones of associated extinct land birds confirm their occurrence on Henderson before the first signs of Polynesian settlement. The extinction of these taxa seems to coincide with the Polynesian occupation and evidence for large-scale burning, at least around parts of the plateau margin, suggests that their demise can be linked with habitat destruction. At least three species, Gastrocopta pediculus , Lamellidea oblonga and Pupisoma orcula , first appear in Polynesian occupation horizons. Their status as prehistoric introductions is therefore confirmed but G. pediculus no longer lives on Henderson. Pacificella variabilis , Tornatellides oblongus parvulus and Elasmias sp., all previously thought to have been other prehistoric introductions to Henderson, were recovered from pre-Polynesian levels and are therefore native.

Non-respiratory blood vessels in Latimeria gill filaments

A study of the blood pathways within the gills ofLatimeriahas been carried out using light and transmission electron microscopy. Clear evidence has been found for the presence of a secondary non–respiratory circulation in addition to the well–established respiratory pathway through the gill lamellae. All essential components of this system have been observed and have the same relationships and basic structure as comparable secondary systems in actinopterygian and elasmobranch fishes. These include a central venous sinus (CVS), arterio–venous anastomoses (AVAs) and central filament arteries (CFAs). AVAs connect both arterial vessels of the primary circulation and CFAs of the secondary circulation to the CVS. The latter contained many red blood cells. The presence of this secondary circulation inLatimeriagills contrasts with the situation in the gills of the three living genera of lungfishes where a system possessing the essential features of the tetrapod lymphatic vessel system has been recognized. No suggestions of a true lymphatic vessel system were observed inLatimeria. Other features of gill and vascular anatomy inLatimeriashow its closer relationship to dipnoans than other groups of living fishes but evidence derived from this study of the secondary circulation clearly supports the view that the Dipnoi rather thanLatimeriarepresent the living fishes most closely related to the tetrapods.

Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa)

Nuclear and mtDNA sequences from selected short-looped terebratuloid (terebratulacean) articulate brachiopods yield congruent and genetically independent phylogenetic reconstructions by parsimony, neighbour-joining and maximum likelihood methods, suggesting that both sources of data are reliable guides to brachiopod species phylogeny. The present-day genealogical relationships and geographical distributions of the tested terebratuloid brachiopods are consistent with a tethyan dispersal and subsequent radiation. Concordance of nuclear and mitochondrial gene phylogenies reinforces previous indications that articulate brachiopods, inarticulate brachiopods, phoronids and ectoprocts cluster with other organisms generally regarded as protostomes. Since ontogeny and morphology in brachiopods, ectoprocts and phoronids depart in important respects from those features supposedly diagnostic of protostomes, this demonstrates that the operational definition of protostomy by the usual ontological characters must be misleading or unreliable. New, molecular, operational definitions are proposed to replace the traditional criteria for the recognition of protostomes and deuterostomes, and the clade-based terms 'Protostomoza' and 'Deuterostomozoa' are proposed to replace the existing term 'Protostomia' and 'Deuterostomia'.

Male courtship song frequency as an indicator of male genetic quality in an insect species, Drosophila montana

Most theoretical models on evolution of male secondary sexual characters and female preferences for these characters suggest that the male characters evolve in response to female preferences that may themselves evolve in response to direct or indirect benefits of choice. In Drosophila montana (a species of the D. virilis group), females use male song in their mate choice, preferring males that produce songs with short sound pulses and a high carrier frequency. We demonstrate here that the females get indirect benefits from their choice: in our data the frequency of the male song correlated with the survival rate of the male's progeny from egg to adulthood (indirect benefit for the female), but not with the fecundity of his mating partner (no direct benefit for the female). Male wing centroid asymmetry did not correlate with male wing song characters, nor with female egg production nor the fitness of her progeny, suggesting that fluctuating asymmetry in male wings does not play a major role in sexual signalling. The fact that the male song gives the female information on the male's condition/genetic quality in D. montana suggests that in this species the evolution of female preferences for male song characters could have evolved through condition-dependent viability selection presented in some 'good genes' models.

Multiple evolutionary origins of the fungus causing Panama disease of banana: concordant evidence from nuclear and mitochondrial gene genealogies

Panama disease of banana, caused by the fungus Fusarium oxysporum f. sp. cubense, is a serious constraint both to the commercial production of banana and cultivation for subsistence agriculture. Previous work has indicated that F. oxysporum f. sp. cubense consists of several clonal lineages that may be genetically distant. In this study we tested whether lineages of the Panama disease pathogen have a monophyletic origin by comparing DNA sequences of nuclear and mitochondrial genes. DNA sequences were obtained for translation elongation factor 1alpha and the mitochondrial small subunit ribosomal RNA genes for F. oxysporum strains from banana, pathogenic strains from other hosts and putatively nonpathogenic isolates of F. oxysporum. Cladograms for the two genes were highly concordant and a partition-homogeneity test indicated the two datasets could be combined. The tree inferred from the combined dataset resolved five lineages corresponding to "F. oxysporum f. sp. cubense" with a large dichotomy between two taxa represented by strains most commonly isolated from bananas with Panama disease. The results also demonstrate that the latter two taxa have significantly different chromosome numbers. F. oxysporum isolates collected as nonpathogenic or pathogenic to other hosts that have very similar or identical elongation factor 1alpha and mitochondrial small subunit genotypes as banana pathogens were shown to cause little or no disease on banana. Taken together, these results indicate Panama disease of banana is caused by fungi with independent evolutionary origins.

Patterns of Y and X chromosome DNA sequence divergence during the Felidae radiation

The 37 species of modern cats have evolved from approximately eight phylogenetic lineages within the past 10 to 15 million years. The Felidae family has been described with multiple measures of morphologic and molecular evolutionary methods that serve as a framework for tracking gene divergence during brief evolutionary periods. In this report, we compare the mode and tempo of evolution of noncoding sequences of a large intron within Zfy (783 bp) and Zfx (854 bp), homologous genes located on the felid Y and X chromosomes, respectively. Zfy sequence variation evolves at about twice the rate of Zfx, and both gene intron sequences track feline hierarchical topologies accurately. As homoplasies are infrequent in patterns of nucleotide substitution, the Y chromosome sequence displays a remarkable degree of phylogenetic consistency among cat species and provides a highly informative glimpse of divergence of sex chromosome sequences in Felidae.

PTP is Meaningless, T-PTP is Contradictory: A Reply to Trueman

- The T-PTP test for monophyly can attribute significance to entirely unsupported groups and even to both of two contradictory alternatives. The method of evaluating "support" after replacing selected groups of terminals with reconstructed ancestors has similar drawbacks. The proposed placement of Onychophora among Arthropoda is unsupported by 12S data, and strongly refuted by other evidence. Attempts to justify T-PTP on Popperian grounds rest entirely on misunderstanding Popper's ideas. The PTP test assesses neither Popperian corroboration nor statistical confidence of phylogenetic conclusions. It can attribute high significance to data that support no resolved grouping. Efforts to salvage PTP by proposing new interpretations share the weakness that none of the proposed interpretations generally holds. None of these methods seems useful in phylogenetic.

Diversity of the human immunodeficiency virus type 1 envelope glycoprotein in San Francisco Men's Health Study participants

Multiple genetic subtypes of HIV-1, differing by up to 30% of nucleotides in their envelope coding sequences, have been identified in the global epidemic. In the United States, where HIV-1 infection with subtype B predominates, the interisolate diversity in envelope is 15% or more. It is recognized that geographic, temporal, and demographic variables can affect the genetic diversity of HIV-1 strains, but there have been few opportunities to evaluate these factors by population-based sampling. We have evaluated HIV-1 envelope diversity among participants in the San Francisco Men's Health Study (SFMHS), which represents a geographically, temporally, and demographically defined subset of HIV-1 infections in the United States. DNA was extracted from primary PBMCs obtained within 6 months of seroconversion and from individuals whose HIV-1 infection occurred between 1985 and 1989. The full-length envelope gene was PCR amplified, cloned, and sequenced from 17 different individuals. The sequences were compared within the cohort and with reference sequences from the United States and overseas, and their relationship to vaccine prototype strains LAI, MN, and SF2 was evaluated. SFMHS participants harbored HIV-1 subtype B infections with limited interpatient variation and a higher proportion of atypical V3 loop crown sequences than reference sequences of this subtype. Throughout gp160, the MN strain was less representative than LAI or SF2 among the patients examined. The geographic component of variation was apparently more substantial than the temporal, emphasizing the need for widely distributed geographic sampling in estimations of HIV diversity.

Punctuated Equilibrium or Gradualism in the Lizard Genus Sceloporus? Lost in Plesiograms and a Forest of Trees

- Conclusions about the rates of evolution among a group of organisms are only are only as sound as the phylogeny upon which the conclusions are based. We re-evaluated the rates of allozyme evolution amoung lizards of the speciose genus Sceloporus. The initial evaluation was suspect because a modification of the invalid, presence or absence method of data coding was employed in genealogical estimation. We recoded the allozyme data using the locus as the character and observed that the previous best explanation of the data fell within a forest of an estimated 107 trees. Further explorations into the invalidity of the independent alleles model of data coding attributed much, but not all, of the shape of the extremely unlikely, independent alleles tree to the parallel loss of plesiotypic alleles, and not the acquistion of novel alleles resulting from mutations. When the data were more appropriately evaluated using mutation coding, there was no unequivocal evidence for a punctuated equilibrium tempo of evolutionary change.

Levels of genetic polymorphism: marker loci versus quantitative traits

Species are the units used to measure ecological diversity and alleles are the units of genetic diversity. Genetic variation within and among species has been documented most extensively using allozyme electrophoresis. This reveals wide differences in genetic variability within, and genetic distances among, species, demonstrating that species are not equivalent units of diversity. The extent to which the pattern observed for allozymes can be used to infer patterns of genetic variation in quantitative traits depends on the forces generating and maintaining variability. Allozyme variation is probably not strictly neutral but, nevertheless, heterozygosity is expected to be influenced by population size and genetic distance will be affected by time since divergence. The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. It is a better predictor of general phenotypic divergence and of postzygotic isolation between populations or species, but is only weakly correlated with prezygotic isolation. Studies of grasshopper and planthopper mating signal variation and assortative mating illustrate how these characters evolve independently of general genetic and morphological variation. The role of such traits in prezygotic isolation, and hence speciation, means that they will contribute significantly to the diversity of levels of genetic variation within and among species.

Sexual selection and natural selection in bird speciation

The role of sexual selection in speciation is investigated, addressing two main issues. First, how do sexually selected traits become species recognition traits? Theory and empirical evidence suggest that female preferences often do not evolve as a correlated response to evolution of male traits. This implies that, contrary to runaway (Fisherian) models of sexual selection, premating isolation will not arise as an automatic side effect of divergence between populations in sexually selected traits. I evaluate premating isolating mechanisms in one group, the birds. In this group premating isolation is often a consequence of sexual imprinting, whereby young birds learn features of their parents and use these features in mate choice. Song, morphology and plumage are known recognition cues. I conclude that perhaps the main role for sexual selection in speciation is in generating differences between populations in traits. Sexual imprinting then leads to these traits being used as species recognition mechanisms. The second issue addressed in this paper is the role of sexual selection in adaptive radiation, again concentrating on birds. Ecological differences between species include large differences in size, which may in themselves be sufficient for species recognition, and differences in habitat, which seem to evolve frequently and at all stages of an adaptive radiation. Differences in habitat often cause song and plumage patterns to evolve as a result of sexual selection for efficient communication. Therefore sexual selection is likely to have an important role in generating premating isolating mechanisms throughout an adaptive radiation. It is also possible that sexual selection, by creating more allopatric species, creates more opportunity for ecological divergence to occur. The limited available evidence does not support this idea. A role for sexual selection in accelerating ecological diversification has yet to be demonstrated.

The evolution of diversity in ancient ecosystems: a review

On a perfect planet, such as might be acceptable to a physicist, one might predict that from its origin the diversity of life would grow exponentially until the carrying capacity, however defined, was reached. The fossil record of the Earth, however, tells a very different story. One of the most striking aspects of this record is the apparent evolutionary longueur, marked by the Precambrian record of prokaryotes and primitive eukaryotes, although our estimates of microbial diversity may be seriously incomplete. Subsequently there were various dramatic increases in diversity, including the Cambrian ‘explosion’ and the radiation of Palaeozoic–style faunas in the Ordovician. The causes of these events are far from resolved. It has also long been appreciated that the history of diversity has been punctuated by important extinctions. The subtleties and nuances of extinction as well as the survival of particular clades have to date, however, received rather too little attention, and there is still a tendency towards blanket assertions rather than a dissection of these extraordinary events. In addition, some but perhaps not all mass extinctions are characterized by long lag–times of recovery, which may reflect the slowing waning of extrinsic forcing factors or alternatively the incoherence associated with biological reassembly of stable ecosystems. The intervening periods between the identified mass extinctions may be less stable and benign than popularly thought, and in particular the frequency of extraterrestrial impacts leads to predictions of recurrent disturbance on timescales significantly shorter than the intervals separating the largest extinction events. Even at times of quietude it is far from clear whether biological communities enjoy stability and interlocked stasis or are dynamically reconstituted at regular intervals. Finally, can we yet rely on the present depictions of the rise and falls in the levels of ancient diversity? Existing data is almost entirely based on Linnean taxa, and the application of phylogenetic systematics to this problem is still in its infancy. Not only that, but even more intriguingly the pronounced divergence in estimates of origination times of groups as diverse as angiosperms, diatoms and mammals in terms of the fossil record as against molecular data point to the possibilities of protracted intervals of geological time with a cryptic diversity. If this is correct, and there are alternative explanations, then some of the mystery of adaptive radiations may be dispelled, in as much as the assembly of key features in the stem groups could be placed in a gradualistic framework of local adaptive response punctuated by intervals of opportunity.

Species-range size distributions: products of speciation, extinction and transformation

One basic summary of the spatial pattern of biodiversity across the surface of the Earth is provided by a species–range size distribution, the frequency distribution of the numbers of species exhibiting geographic ranges of different sizes. Although widely considered to be approximately lognormal, increasingly it appears that across a variety of groups of organisms this distribution systematically departs from such a form. Whatever its detailed shape, however, the distribution must arise as a product of three processes, speciation, extinction and transformation (the temporal dynamics of the range sizes of species during their life times). Considering the role potentially played by each of these processes necessitates drawing on information from a diverse array of research fields, and highlights the possible role of geographic range size as a common currency uniting them.

From genes to individuals: developmental genes and the generation of the phenotype

The success of the genetic approach to developmental biology has provided us with a suite of genes that are involved in the regulation of ontogenetic pathways. It is therefore time to ask whether and how such genes might be involved in the generation of adaptive phenotypes. Unfortunately, the current results do not provide a clear answer. Most of the genes that have been studied by developmental biologists affect early embryonic traits with significant effects on the whole organism. These genes are often highly conserved which allows us to do comparative studies even across phyla. However, whether the same genes are also involved in short-term ecological adaptations remains unclear. The suggestion that early acting ontogenetic genes may also affect late phenotypes comes from the genetic analysis of quantitative traits like bristle numbers in Drosophila. A rough mapping of the major loci affecting these traits shows that these loci might correspond to well known early acting genes. On the other hand, there are also many minor effect loci that are as yet uncharacterized. We suggest that these minor loci might correspond to a different class of genes. In comparative studies of randomly drawn cDNAs from Drosophila we find that there is a large group of genes that evolve fast and that are significantly under-represented in normal genetic screens. We speculate that these genes might provide a large, as yet poorly understood, reservoir of genes that might be involved in the evolution of quantitative traits and short-term adaptations.

Rates of speciation in the fossil record

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.

Gnathostomulida--an enigmatic metazoan phylum from both morphological and molecular perspectives

On the basis of few and contentious morphological characters Gnathostomulids have been thought to be the sister-group of either the Platyhelminthes or the Syndermata (Rotifera + Acanthocephala). We provide a full 18S rDNA sequence for a species of Gnathostomula and attempt to resolve its position among the Metazoa, on the basis of molecular evidence. Sixty sequences, representing 30 nominal phyla and including new entoproct and gastrotrich sequences, were used to reconstruct phylogenies using maximum-parsimony, neighbor-joining, and minimum evolution models. We were unable to support either of the morphological hypotheses outright and, moreover, our data supported more strongly a third possible relationship with the gnathostomulids as a member of the Nematoda + Chaetognatha clade. Superficially, as active benthic, vermiform creatures with sclerotized cuticular jaws, they fit a predicted ancestral form of the Nematoda + Chaetognatha clade and, as such, would arguably be members of the Ecdysozoa. The molecular data at least call for a reevaluation of the morphological data and a denser sampling of the lesser phyla. Data from morphology and molecules act synergistically in estimating phylogeny; morphology alone provided limited phylogenetic signal and alternative phylogenetic hypotheses, whereas the molecular solution suggested an alternative topology which, when interpreted in the light of comparative anatomy, may suggest previously unconsidered possibilities.

Phylogenetics of social behavior in Australian gall-forming thrips: evidence from mitochondrial DNA sequence, adult morphology and behavior, and gall morphology

Six species of Australian gall-forming thrips (Insecta: Thysanoptera) on Acacia exhibit soldier castes, individuals with reduced wings and enlarged forelegs that defend their gall against interspecific invaders. We used data from two mitochondrial genes (cytochrome oxidase I and 16S rDNA), adult morphology and behavior, and gall morphology to infer a phylogeny for Acacia gall-forming thrips with and without soldiers, and we used this phylogeny to evaluate hypotheses concerning soldier evolution. Phylogenies inferred from each data set analyzed separately yielded large numbers of most-parsimonious trees and weak support for most nodes. However, when analyzed together the data sets complemented and reinforced one another in such a way as to yield a well-resolved phylogeny. Our phylogeny implies that soldiers originated once or twice early in the history of this clade, that soldiers were lost once or twice, and that soldiers evolved from winged dispersers rather than from nonsoldier within-gall reproductive offspring of foundresses. The phylogeny also provides evidence for long-term morphological stasis, an ancient split between eastern and western gall thrips species, and a high degree of conservatism in host-plant affiliations.

Molecular phylogeny of Acipenserinae

The family Acipenseridae consists of 25 extant sturgeon species (19 species of Acipenserinae and 6 species of Scaphirhynchinae). Together with two extant paddlefish species, Polyodon spathula and Psephurus gladius (Polyodontidae), it composes the order Acipenseriformes, the most numerous of all living "fossil" fishes. This paper presents results of sequencing of three regions of the cytochrome b gene (650 bp), and fragments of 12S (150 bp) and 16S (350 bp) rRNA genes, from all extant species of Acipenserinae (species of Acipenser and Huso) and Scaphirhynchus albus (Scaphirhynchinae). The phylogenetic tree obtained for combined data is the first comprehensive treatment of phylogeny within the Acipenserinae. Three general conclusions are inferred from the tree: (1) The pallid sturgeon, S. albus, is the sister-species of all species of Acipenser and Huso. (2) The two species of Huso are embedded within the genus Acipenser. It also appears that Huso is not a separate taxonomic unit. (3) There are at least three main clades within Acipenser: A. sturio-A. oxyrinchus, A. schrenckii-A. transmontanus, and all Ponto-Caspian species plus A. dabryanus and A. brevirostrum. There is congruence between ploidy and the branching patterns of the sturgeon species. A hypothetical evolutionary history of the Acipenseriformes based on the paleontological, geological, and molecular data is discussed.

Immunological and virological analyses of persons infected by human immunodeficiency virus type 1 while participating in trials of recombinant gp120 subunit vaccines

We have studied 18 participants in phase I/II clinical trials of recombinant gp120 (rgp120) subunit vaccines (MN and SF-2) who became infected with human immunodeficiency virus type 1 (HIV-1) during the course of the trials. Of the 18 individuals, 2 had received a placebo vaccine, 9 had been immunized with MN rgp120, and seven had been immunized with SF-2 rgp120. Thirteen of the 18 infected vaccinees had received three or four immunizations prior to becoming infected. Of these, two were placebo recipients, six had received MN rgp120, and five had received SF-2 rgp120. Only 1 of the 11 rgp120 recipients who had multiple immunizations failed to develop a strong immunoglobulin G antibody response to the immunogen. However, the antibody response to rgp120 was transient, typically having a half-life of 40 to 60 days. No significant neutralizing activity against the infecting strain was detected in any of the infected individuals at any time prior to infection. Antibody titers in subjects infected despite vaccination and in noninfected subjects were not significantly different. Envelope-specific cytotoxic T-lymphocyte responses measured after infection were infrequent and weak in the nine vaccinees who were tested. HIV-1 was isolated successfully from all 18 individuals. Sixteen of these strains had a non-syncytium-inducing (NSI) phenotype, while two had a syncytium-inducing (SI) phenotype. NSI strains used the CCR5 coreceptor to enter CD4+ cells, while an SI strain from one of the vaccinees also used CXCR4. Viruses isolated from the blood of rgp120 vaccinees were indistinguishable from viruses isolated from control individuals in terms of their inherent sensitivity to neutralization by specific monoclonal antibodies and their replication rates in vitro. Furthermore, genetic sequencing of the env genes of strains infecting the vaccinees did not reveal any features that clearly distinguished these viruses from contemporary clade B viruses circulating in the United States. Thus, despite rigorous genetic analyses, using various breakdowns of the data sets, we could find no evidence that rgp120 vaccination exerted selection pressure on the infecting HIV-1 strains. The viral burdens in the infected rgp120 vaccine recipients were also determined, and they were found to be not significantly different from those in cohorts of placebo-vaccinated and nonvaccinated individuals. In summary, we conclude that vaccination with rgp120 has had,to date, no obvious beneficial or adverse effects on the individuals we have studied.

Two nuclear genes yield concordant relationships within Attacini (Lepidoptera: Saturniidae)

To extend initial characterizations of their phylogenetic utility, sequences from the nuclear genes for elongation factor-1 alpha (EF-1 alpha) and dopa decarboxylase (DDC) are tested for phylogenetic concordance with each other and with previous morphological evidence within the giant silk moth tribe Attacini (Lepidoptera: Saturniidae). The sampling of DDC is expanded from the 690 basepairs of previous studies to 1051 basepairs in the current study. All nine attacine genera are sampled. EF-1 alpha and DDC agree in the placement of seven of nine genera, with placement of the other two not in strong conflict. Combination of the gene sequences results in a nearly fully resolved tree that is consistent with EF-1 alpha alone and agrees with morphology in five of eight groups. Conflict between molecules and morphology is confined to deeper-level relationships within Attacini, where node support for the molecular hypotheses, but not the morphological hypotheses, is generally very strong. A strong signal is contributed by synonymous substitutions in both genes, and by nonsynonymous change particularly in DDC. The molecular phylogeny supports a revision of attacine biogeography in that neither East Asian nor New World genera form monophyletic groups.

Phylogenetic relationships and geographic structure in pocket gophers in the genus Thomomys

Phylogenetic relationships among pocket gophers were examined based on the complete sequence for the mitochondrial cytochrome b gene (1140 base pairs). The tribe Geomyini (Geomys, Orthogeomys, Cratogeomys, and Pappogeomys) was well differentiated from the tribe Thomomyini (Thomomys), using the heteromyid genera Dipodomys and Perognathus as the out-group. Within the genus Thomomys, the species in the subgenus Thomomys (T. talpoides, T. monticola, and T. mazama) differed from those in the subgenus Megascapheus (T. bottae, T. townsendii, and T. umbrinus) by an average of 19.3% uncorrected sequence divergence. Extensive sampling within one species, T. bottae, revealed strongly differentiated geographic units, with a maximum difference among localities of 15.7%. The geographic units within T. bottae coincided with geographic regions based on allozyme data in some areas, but not at all boundaries. The geographic units within currently recognized species in the bottae group (subgenus Megascapheus) were not grouped together with a high level of confidence. The pattern suggests a rapid radiation of the bottae group, followed by geographic subdivision.

Details of gastropod phylogeny inferred from 18S rRNA sequences

Some generally accepted viewpoints on the phylogenetic relationships within the molluscan class Gastropoda are reassessed by comparing complete 18S rRNA sequences. Phylogenetic analyses were performed using the neighbor-joining and maximum parsimony methods. The previously suggested basal position of Archaeogastropoda, including Neritimorpha and Vetigastropoda, in the gastropod clade is confirmed. The present study also provides new molecular evidence for the monophyly of both Caenogastropoda and Euthyneura (Pulmonata and Opisthobranchia), making Prosobranchia paraphyletic. The relationships within Caenogastropoda and Euthyneura data turn out to be very unstable on the basis of the present 18S rRNA sequences. The present 18S rRNA data question, but are insufficient to decide on, muricacean (Neogastropoda), neotaenioglossan, pulmonate, or stylommatophoran monophyly. The analyses also focus on two systellommatophoran families, namely, Veronicellidae and Onchidiidae. It is suggested that Systellommatophora are not a monophyletic unit but, due to the lack of stability in the euthyneuran clade, their affinity to either Opisthobranchia or Pulmonata could not be determined.

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene (rp49) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the nearctic species (pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O3) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O3 gene arrangement, present in D. guanche (together with inversion g) and in D. madeirensis, is ancestral to gene arrangements O3 + 4 and Ost present in extant populations of D. subobscura.

Population biology of an endangered butterfly, Lycaeides melissa samuelis (Lepidoptera; Lycaenidae): genetic variation, gene flow, and taxonomic status

We present data from 34 allozyme loci to test whether the Karner Blue butterfly is specifically differentiated from the Melissa Blue. Furthermore, as the Karner Blue is an endangered organism of low vagility that occurs predominantly in small, widely separated populations, we investigated (i) whether the Karner Blue is depauperate in genetic variation and (ii) whether gene flow between sampled populations is unusually low. Genetic identities between New York and Wisconsin populations of the Karner Blue and a sample of Melissa Blue from Minnesota are all statistically indistinguishable. Neither genetic identity data nor application of the phylogenetic species concept support formal recognition of the Karner Blue as a species separate from the Melissa Blue. Nonetheless, the data indicate that gene flow among the samples was very low compared with that among populations of other Lepidoptera. Heterozygosity estimates for all three samples were comparable to data for other Lepidoptera and indicate that the Karner Blue populations surveyed are not under immediate threat of extirpation due to loss of genetic diversity. Although the available data are limited, if the Karner Blue is to be managed as an evolutionarily significant unit, then the eastern and western populations should probably be treated independently and each should receive high conservation priority.

The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation

Variation in the nucleotide sequence of the entire mitochondrial cytochrome b gene (1140 bp) was examined for 27 individuals representing 13 species of South American rodents of the genera Ctenomys, Octodontomys, Tympanoctomys, and Spalacopus. Representatives of the family Echimyidae, Euryzygomatomys and Mesomys, were used as outgroups to test the monophyly of the Octodontinae and Ctenomyinae. Relationships among species of tuco-tucos (genus Ctenomys) were also examined including representatives of the three described subgenera and the two sperm morphs. Reciprocal monophyly of the Octodontinae and Ctenomyinae is strongly supported. Several basal relationships among species of the genus Ctenomys are poorly resolved, suggesting the possibility of a hard polytomy due to a rapid and potentially simultaneous radiation early in the history of the genus. In other cases, clades within the Ctenomyinae previously identified on the basis of allozymes, chromosomes, parasites, or skull morphology were supported. Calibrations based on the fossil record suggest that the mitochondrial cytochrome b of these caviomorphs has evolved at a rapid rate, comparable to those proposed for Mus-Rattus, and three to four times higher than ungulate rates.

Phylogeny of leeches (Hirudinea) based on mitochondrial cytochrome c oxidase subunit I

The phylogenetic relationships of leeches were investigated for the first time using molecular data. Twenty-one species were examined representing 7 of the 10 conventionally recognized euhirudinean families. In addition, Acanthobdella peledina, a branchiobdellid, four oligochaetes, and two polychaetes were included. Cladistic analysis of the mitochondrial cytochrome c oxidase subunit I gene yielded one most-parsimonious tree. Contemporary taxonomic groupings of leeches into higher categories were found to be largely consistent with monophyletic groups identified in the analysis. Unusual relationships for which there is some precedent include a sister-group relationship between the piscicolids and Arhynchobdellida, as well as the grouping of the haemopids within Hirudinidae.

Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the Quorn mycoprotein fungus as Fusarium venenatum

Molecular phylogenetic, morphological, and mycotoxin data were obtained in order to investigate the relationships and identity of the Quorn mycoprotein fungus within Fusarium and to examine Quorn strains and commercial Quorn food products for trichothecene mycotoxins. Phylogenetic analyses of aligned DNA sequences obtained via the polymerase chain reaction from the nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer region, and beta-tubulin gene exons and introns indicate that the Quorn fungus is Fusarium venenatum, rather than F. graminearum as previously reported. All of the Quorn strains examined were morphologically degenerate aconidial colonial mutants except for NRRL 25139, which produced chlamydospores in recurved terminal chains together with mostly 5-septate sporodochial conidia on doliform monophialides diagnostic of F. venenatum. Bootstrap and decay analyses provide strong support for a monophyletic lineage containing F. venenatum and several other type A trichothecene-producing species, while reference strains of F. graminearum were nested in a separate clade of species that produce type B trichothecenes and/or zearalenone. Analysis of mycotoxins from rice cultures inoculated with Quorn strain NRRL 25416 revealed that four type A trichothecenes are produced, but at low levels relative to strain NRRL 22198 of F. venenatum. No trichothecene mycotoxins, however, were detected from the analysis of three commercial Quorn products marketed for human consumption in England.

Body size and species-richness in carnivores and primates

We use complete species-level phylogenies of extant Carnivora and Primates to perform the first thorough phylogenetic tests, in mammals, of the hypothesis that small body size is associated with species-richness. Our overall results, based on comparisons between sister clades, indicate a weak tendency for lineages with smaller bodies to contain more species. The tendency is much stronger within caniform carnivores (canids, procyonids, pinnipeds, ursids and mustelids), perhaps relating to the dietary flexibility and hence lower extinction rates in small, meat-eating species. We find significant heterogeneity in the size-diversity relationship within and among carnivore families. There is no significant association between body mass and species-richness in primates or feliform carnivores. Although body size is implicated as a correlate of species-richness in mammals, much of the variation in diversity cannot be attributed to size differences.

Origin of the metazoan phyla: molecular clocks confirm paleontological estimates

The time of origin of the animal phyla is controversial. Abundant fossils from the major animal phyla are found in the Cambrian, starting 544 million years ago. Many paleontologists hold that these phyla originated in the late Neoproterozoic, during the 160 million years preceding the Cambrian fossil explosion. We have analyzed 18 protein-coding gene loci and estimated that protostomes (arthropods, annelids, and mollusks) diverged from deuterostomes (echinoderms and chordates) about 670 million years ago, and chordates from echinoderms about 600 million years ago. Both estimates are consistent with paleontological estimates. A published analysis of seven gene loci that concludes that the corresponding divergence times are 1,200 and 1,000 million years ago is shown to be flawed because it extrapolates from slow-evolving vertebrate rates to faster-evolving invertebrate rates, as well as in other ways.

Phylogeny and evolution of host-parasitoid interactions in hymenoptera

Recent studies of hymenopteran phylogeny using both comparative morphology and DNA sequence data have greatly enhanced our understanding of the evolution of that order. Resulting phylogenetic hypotheses make possible more rigorous investigations of the evolution of various biological life-styles, among them the parasitoid habit. This paper reviews the current findings from higher-taxon phylogenetic analyses of the order. A "consensus" phylogeny derived from these findings is used to trace the most likely evolutionary pathways leading to the current diversity of parasitoid habits. Taxa and biological phenomena for which our current understanding is fragmentary are highlighted. Based on current evidence, it appears that parasitism arose, from mycophagous ancestors, a single time within the order. Many subsequent elaborations of the parasitic mode of life (e.g. endoparasitism, secondary phytophagy, etc) apparently evolved independently more than once.