Clade Level Research Articles

Effectiveness of an Innovative Prototype Subtracted Diversity Array (SDA) for Fingerprinting Plant Species of Medicinal Importance

The accurate identification of medicinal plants is becoming increasingly important due to reported concerns about purity, quality and safety. The previously developed prototype subtracted diversity array (SDA) had been validated for the ability to distinguish clade-level targets in a phylogenetically accurate manner. This study represents the rigorous investigation of the SDA for genotyping capabilities, including the genotyping of plant species not included during the construction of the SDA, as well as to lower classification levels including family and species. The results show that the SDA, in its current form, has the ability to accurately genotype species not included during SDA development to clade level. Additionally, for those species that were included during SDA development, genotyping is successful to the family level, and to the species level with minor exceptions. Twenty polymorphic SDA features were sequenced in a first attempt to characterize the polymorphic DNA between species, which showed that transposon-like sequences may be valuable as polymorphic features to differentiate angiosperm families and species. Future refinements of the SDA to allow more sensitive genotyping are discussed with the overall goal of accurate medicinal plant identification in mind.

Deviations from Ultrametricity in Phage Protein Distances

Distances in biological databases are known not to be ultrametric. Deviations from ultrametricity can however reveal useful features of biodata. In the present study we examine deviations from ultrametricity of the distances between known phage proteins quantified in two senses: (1) the failure of triangles to be isosceles and (2) failure of every point to be the center of any sphere in which it resides. The deviations from these two ultrametric properties undergo qualitative changes as a function of the distance. Below we describe these changes and how they can be observed. We further argue that the distances at which the qualitative changes take place reveal intrinsic scales in the dataset. Such scales are important for choosing threshold values of the distance in various algorithms and reveal natural chunking of the data that can be used to decide clade levels in phage phylogeny.

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co‐evolution

Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian-Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous.

Identification of Francisella tularensis subsp. tularensis A1 and A2 infections by real-time polymerase chain reaction

Francisella tularensis subsp. tularensis (type A) is subdivided into clades A1 and A2. Human tularemia infections caused by A1 and A2 differ with respect to clinical outcome; A1 infections are associated with a higher case fatality rate. In this study, we develop and evaluate TaqMan polymerase chain reaction (PCR) assays for identification of A1 and A2. Both assays were shown to be specific to either A1 or A2, with sensitivities of 10 genomic equivalents. Real-time PCR results for identification of A1 and A2 were in complete agreement with results obtained by pulsed field gel electrophoresis analysis or conventional PCR when specimens from sporadic tularemia cases and a tularemia outbreak involving both A1 and A2 were tested. In addition, outbreak samples not previously typed to the clade level could be classified as A1 or A2. The assays described here provide new diagnostic tools with a level of sensitivity not previously available for identification of A1 and A2 infections.

FoxO gene family evolution in vertebrates

BackgroundForkhead box, class O (FoxO) belongs to the large family of forkhead transcription factors that are characterized by a conserved forkhead box DNA-binding domain. To date, the FoxO group has four mammalian members: FoxO1, FoxO3a, FoxO4 and FoxO6, which are orthologs of DAF16, an insulin-responsive transcription factor involved in regulating longevity of worms and flies. The degree of homology between these four members is high, especially in the forkhead domain, which contains the DNA-binding interface. Yet, mouse FoxO knockouts have revealed that each FoxO gene has its unique role in the physiological process. Whether the functional divergences are primarily due to adaptive selection pressure or relaxed selective constraint remains an open question. As such, this study aims to address the evolutionary mode of FoxO, which may lead to the functional divergence.ResultsSequence similarity searches have performed in genome and scaffold data to identify homologues of FoxO in vertebrates. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution. To determine the mode of evolution in vertebrates, we performed a rigorous statistical analysis with FoxO gene sequences, including relative rate ratio tests, branch-specific dN/dS ratio tests, site-specific dN/dS ratio tests, branch-site dN/dS ratio tests and clade level amino acid conservation/variation patterns analysis. Our results suggest that FoxO is constrained by strong purifying selection except four sites in FoxO6, which have undergone positive Darwinian selection. The functional divergence in this family is best explained by either relaxed purifying selection or positive selection.ConclusionWe present a phylogeny describing the evolutionary history of the FoxO gene family and show that the genes have evolved through duplications followed by purifying selection except for four sites in FoxO6 fixed by positive selection lie mostly within the non-conserved optimal PKB motif in the C-terminal part. Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well.

Extinction and the spatial dynamics of biodiversity

The fossil record amply shows that the spatial fabric of extinction has profoundly shaped the biosphere; this spatial dimension provides a powerful context for integration of paleontological and neontological approaches. Mass extinctions evidently alter extinction selectivity, with many factors losing effectiveness except for a positive relation between survivorship and geographic range at the clade level (confirmed in reanalyses of end-Cretaceous extinction data). This relation probably also holds during "normal" times, but changes both slope and intercept with increasing extinction. The strong geographical component to clade dynamics can obscure causation in the extinction of a feature or a clade, owing to hitchhiking effects on geographic range, so that multifactorial analyses are needed. Some extinctions are spatially complex, and regional extinctions might either reset a diversity ceiling or create a diversification debt open to further diversification or invasion. Evolutionary recoveries also exhibit spatial dynamics, including regional differences in invasibilty, and expansion of clades from the tropics fuels at least some recoveries, as well as biodiversity dynamics during normal times. Incumbency effects apparently correlate more closely with extinction intensities than with standing diversities, so that regions with higher local and global extinctions are more subject to invasion; the latest Cenozoic temperate zones evidently received more invaders than the tropics or poles, but this dynamic could shift dramatically if tropical diversity is strongly depleted. The fossil record can provide valuable insights, and their application to present-day issues will be enhanced by partitioning past and present-day extinctions by driving mechanism rather than emphasizing intensity.

Taxon characteristics that promote survivorship through the Permian–Triassic interval: transition from the Paleozoic to the Mesozoic brachiopod fauna

Examination of organismal characteristics which promote survivorship through both background and mass extinctions may reveal general ecological principles potentially critical to modern conservation efforts. This study explores survivorship of brachiopods, a highly diverse and abundant Paleozoic clade, through the mid-Permian to mid-Triassic interval, which includes the greatest mass extinction in the history of metazoan life. This interval of time separates two of the major Phanerozoic evolutionary faunas. In this regard, survivorship across any one extinction during the interval would not have been relevant if the survivor went extinct shortly after the extinction event; surviving background extinction is as important as surviving a mass extinction. Similarly, taxa that survived but failed to rediversify also were not major elements of the Mesozoic evolutionary fauna. Thus, the analysis aims to analyze survivorship not just across a single extinction but across the entire mid-Permian to mid-Triassic; only survivors through the entire interval can be the ancestors of the Mesozoic clades.Fewer brachiopod genera survived the interval than did brachiopod clades, suggesting that pseudoextinction or insufficient sampling could be a problem in analyzing these extinctions; thus, survivorship analysis should be conducted at the clade level. Nine characteristics were examined for generic representatives of 20 North American brachiopod clades, five of which survived both Permian extinctions and the subsequent earliest Triassic transitional interval. Characteristics include both those that operate on global scales and those that operate on the higher-resolution scales of individuals and populations.Survivors were significantly smaller and occurred less frequently than victims. Mean diversity of communities in which survivors were present was significantly greater. The finding that rare taxa belonging to high-diversity communities were more likely to survive runs counter to traditional predictions. However, these results are consistent with recent studies suggesting that higher diversity within a trophic level may create a buffer, as surviving taxa quickly occupy the vacant niche space of the victims. As size, abundance, and community diversity are all statistically related, the small size of survivors may be an artifact of reduced biovolume per taxon in a diverse community.No significant relationship exists between global-scale processes and survivorship of brachiopods through the mid-Permian to mid-Triassic. The results suggest that ecological processes can strongly influence global extinction patterns.

Evolution and Phylogenetic Importance of Endocarp and Seed Characters inViburnum(Adoxaceae)

Recent phylogenetic analyses based on molecular markers have resulted in a solid phylogeny of Viburnum with 12 well-defined clades. This has allowed us to focus on character evolution, endocarp and seed characters in particular. Members of Viburnum bear drupes that differ considerably between clades. Characters such as pyrene shape and grooving, number of fibrous layers, seed coat anatomy, and seed rumination are phylogenetically highly valuable. Our results largely agree with the results based on molecular data and provide several additional insights. The position of V. clemensae as sister to the rest of Viburnum is supported by several characters. The early diversification of V. clemensae might explain its highly derived features. Furthermore, our results give an indication of the possible paraphyly of the Megalotinus clade, confirm the paraphyly of Hara’s section Solenotinus, and support the split of Hara’s section Odontotinus into four well-defined clades. Endocarp and seed characters are mainly useful at the level of individual clades. Several characters, however, are useful at higher taxonomic levels. The presence of small, amorphous crystals in the endosperm, for example, is most likely to be apomorphic for Viburnum within the order Dipsacales.

Predominance of clade D Symbiodinium in shallow-water reef-building corals off Kish and Larak Islands (Persian Gulf, Iran)

Scleractinian coral species harbour communities of photosynthetic taxa of the genus Symbiodinium. As many as eight genetic clades (A, B, C, D, E, F, G and H) of Symbiodinium have been discovered using molecular biology. These clades may differ from each other in their physiology, and thus influence the ecological distribution and resilience of their host corals to environmental stresses. Corals of the Persian Gulf are normally subject to extreme environmental conditions including high salinity and seasonal variation in temperature. This study is the first to use molecular techniques to identify the Symbiodinium of the Iranian coral reefs to the level of phylogenetic clades. Samples of eight coral species were collected at two different depths from the eastern part of Kish Island in the northern Persian Gulf, and Larak Island in the Strait of Hormuz. Partial 28S nuclear ribosomal (nr) DNA of Symbiodinium (D1/D2 domains) were amplified by polymerase chain reaction (PCR). PCR products were analyzed using single stranded conformational polymorphism and phylogenetic analyses of the LSU DNA sequences from a subset of the samples. The results showed that Symbiodinium populations were generally uniform among and within the populations of eight coral species studied, and there are at least two clades of Symbiodinium from Kish and Larak islands. Clade D was detected from eight of the coral species while clade C was found in two of species only (one species hosted two clades simultaneously). The dominance of clade D might be explained by high temperatures or the extreme temperature variation, typical of the Persian Gulf.

Phylogeography of a ground beetle species in La Gomera (Canary Islands): the effects of landscape topology and population history

Paraeutrichopus pecoudi (Coleoptera, Carabidae) is a species endemic to the mountain laurel forests of La Gomera in the Canary archipelago. La Gomera is an island of volcanic origin (9.4 mya), where a well-preserved laurel forest is partly fragmented by valleys and ridges. Historically restricted gene flow with isolation by distance are deduced at different clade levels for P. pecoudi populations, an expected scenario arising from landscape discontinuity, which has caused local isolation of these flightless insects. Methodological considerations were investigated for nested clade phylogeographic analysis (NCPA), comparing the results obtained using either (a) pairwise distances between collecting sites measured as surface (route) distances or (b) standard geographical distances calculated from latitude-longitude coordinates. Some differences were found in the NCPA statistics and associated inferences at the higher clade levels in relation to the assumed distance criteria. Coalescent simulations and posterior automated NCPAs assuming different geographical distances were performed to test the robustness of the method when considering the distances used. These analyses showed no significant differences in NCPA conclusions, and the scenario of restricted gene flow was recovered using both distance calculators at the same rate, although the parameter statistics were slightly different. We suggest that in landscapes with extreme topography, geographical distances separating populations are certainly underestimated by standard techniques. More complex and explicit descriptions of the potential dispersal of terrestrial organisms should be explored for implementation in statistical phylogeography in such cases.

Multiple symbiotic partnerships are common in scleractinian corals, but not in octocorals: Comment on Goulet (2006)

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 335:237-242 (2007) - doi:10.3354/meps335237 Multiple symbiotic partnerships are common in scleractinian corals, but not in octocorals: Comment on Goulet (2006) Andrew C. Baker1,2,*, Adrienne M. Romanski2 1Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, Florida 33149, USA 2Department of Ecology, Evolution and Environmental Biology, Columbia University, MC 5557, 1200 Amsterdam Avenue, New York, New York 10027, USA *Email: abaker@rsmas.miami.edu ABSTRACT: The ability of reef corals to adapt or acclimatize to projected climate change is a critical, but controversial, question in contemporary coral reef science and conservation. Much research has focused on whether or not corals are able to flexibly associate with diverse symbionts (‘zooxanthellae’) whose different physiologies may impart greater resistance to environmental extremes. Goulet (2006; Mar Ecol Prog Ser 321:1–7) concluded that most coral species only host zooxanthellae from a single Symbiodinium clade, and that these symbionts do not change in response to environmental disturbance, disease, or temperature stress. We re-evaluate her data and show that: (1) almost two-thirds of the coral species investigated have been severely undersampled (N ≤ 5); (2) more than three-quarters of the scleractinian (stony) coral species sampled more adequately (N > 10) host multiple Symbiodinium clades, or multiple types within a clade; (3) scleractinian corals are more flexible than octocorals; (4) almost all scleractinian coral families can host more than one symbiont clade. Moreover, the molecular approaches used by many studies are likely to have underestimated Symbiodinium diversity, because they are unable to detect symbionts at low abundance and because they cannot distinguish between closely related types. In addition, various other studies show that: (1) scleractinian corals commonly host multiple symbiont types within a Symbiodinium clade; (2) symbiont communities in scleractinian corals are dynamic; (3) ‘cryptic’ symbiont taxa found at low abundance within colonies are unlikely to be molecular artifacts. We suggest that the majority of scleractinian coral species, including virtually all of the dominant reef-building taxa, can be found hosting multiple symbiont types, even at the clade level. This flexibility is important in under-standing the past evolutionary success of these species and their future survival trajectories in the face of projected climate change. KEY WORDS: Coral · Symbiodinium · Symbiosis · Climate change · Bleaching · Zooxanthellae · Diversity Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 335. Online publication date: April 16, 2007 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2007 Inter-Research.

The allometry of echolocation call frequencies of insectivorous bats: why do some species deviate from the pattern?

The peak echolocation frequency of insectivorous bats generally declines as body size increases. However, there are notable exceptions to this rule, with some species, such as Rhinolophus clivosus, having a higher than expected peak frequency for their body size. Such deviations from allometry may be associated with partitioning of foraging habitat (the foraging habitat hypothesis) or insect prey (the prey detection hypothesis). Alternatively, the deviations may be associated with the partitioning of sonar frequency bands to allow effective communication in a social context (the acoustic communication hypothesis). We tested the predictions of these hypotheses through comparisons at the family, clade and species level, using species of rhinolophids in general and R. clivosus, a species with a wide distribution, as a specific test case. We compared the wing parameters, echolocation frequency and ecology of R. clivosus to those of the sympatric R. capensis. Rhinolophus clivosus has a much higher echolocation frequency than predicted from its wing loading or body mass. Furthermore, contrary to the predictions of the foraging habitat hypothesis, we found no difference in foraging habitat between R. clivosus and R. capensis. The size range of insect prey taken by the two species also overlapped almost completely, contrary to the prey detection hypothesis. On the other hand, the variation of echolocation frequencies around the allometric relationship for rhinolophids was smaller than that for Myotis spp., supporting the prediction of the acoustic communication hypothesis. We thus propose that the relatively high peak frequency of R. clivosus is the result of partitioning of sonar frequency bands to minimize the ambiguity of echolocation calls during social interactions.

No contribution of angiotensin-converting enzyme (ACE) gene variants to severe obesity: a model for comprehensive case/control and quantitative cladistic analysis of ACE in human diseases

Candidate gene analyses are often inconclusive owing to genetic or phenotypic heterogeneity, low statistical power, selection of nonfunctional SNPs, and inadequate statistical analysis of the genetic architecture. Angiotensin-converting enzyme (ACE) is involved in adipocyte growth and function and the ACE-processed angiotensin II inhibits adipocyte differentiation. Associations between body mass index (BMI) and ACE polymorphisms have been reported in general populations, but the contribution to severe obesity of this gene, which is located under an obesity genome-scan linkage peak on 17q23, is unknown. ACE is one of the most studied genes and markers responsible for variation in circulating ACE enzyme levels have been extensively characterised. Eight of these variants were genotyped in 1054 severely obese cases and 918 nonobese controls, as well as 116 nuclear families from the genome scan (n=447), enabling the known clades to be inferred. Qualitative analysis of individual single-nucleotide polymorphisms (SNPs), haplotypes, clades, and diploclades demonstrated no significant associations (P<0.05) after minimal correction for multiple testing. Quantitative analysis of clades and diploclades for BMI, waist-to-hip ratio, or ZBMI in children were also not significant. This rigorous, large-scale study of common, well-defined, severe polygenic obesity provides strong evidence that functionally relevant sequence variation in ACE, whether it is defined at the level of SNPs, haplotypes, or clades, is not associated with severe obesity in French Caucasians. Such a study design exemplifies the strategy needed to clearly define the contribution of the ACE gene to the plethora of complex genetic diseases where weak associations have been previously reported.

First steps towards a floral structural characterization of the major rosid subclades

A survey of our own comparative studies on several larger clades of rosids and over 1400 original publications on rosid flowers shows that floral structural features support to various degrees the supraordinal relationships in rosids proposed by molecular phylogenetic studies. However, as many apparent relationships are not yet well resolved, the structural support also remains tentative. Some of the features that turned out to be of interest in the present study had not previously been considered in earlier supraordinal studies. The strongest floral structural support is for malvids (Brassicales, Malvales, Sapindales), which reflects the strong support of phylogenetic analyses. Somewhat less structurally supported are the COM (Celastrales, Oxalidales, Malpighiales) and the nitrogen-fixing (Cucurbitales, Fagales, Fabales, Rosales) clades of fabids, which are both also only weakly supported in phylogenetic analyses. The sister pairs, Cucurbitales plus Fagales, and Malvales plus Sapindales, are structurally only weakly supported, and for the entire fabids there is no clear support by the present floral structural data. However, an additional grouping, the COM clade plus malvids, shares some interesting features but does not appear as a clade in phylogenetic analyses. Thus it appears that the deepest split within eurosids–that between fabids and malvids - in molecular phylogenetic analyses (however weakly supported) is not matched by the present structural data. Features of ovules including thickness of integuments, thickness of nucellus, and degree of ovular curvature, appear to be especially interesting for higher level relationships and should be further explored. Although features of interest are not necessarily stable at the level of a large clade, they do show a considerable concentration in particular clades and are rare or lacking in others. This may be viewed as a special trend for this feature to evolve in this group or to be conserved as a synapomorphy (or a combination of both).

Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae:Potamonautes) reveals the signature of historical climatic oscillations

AbstractAim The phylogeographic relationships among populations of the common Cape River crab,Potamonautes perlatus, are examined to investigate whether the contemporary population genetic structure is congruent with the hypothesized hydrographic evolution of drainage systems established during the Pliocene, or whether it reflects an older Miocene climatic amelioration.Location 139 samples ofP. perlatuswere collected from 31 populations distributed among the five major perennial drainage systems and a number of smaller catchments in the Western and Eastern Cape, South Africa.Methods Phylogeographic analysis using parsimony, maximum likelihood, minimum evolution and Bayesian inferences was employed for the 16S rRNA mtDNA gene region, while bootstrapping and posterior probabilities were used to assess the robustness of clades. In addition, nested clade analysis was performed in an attempt to disentangle the contemporary and historical factors that have sculpted genealogical relationships among conspecific populations ofP. perlatus.Results Phylogenetic topologies were congruent irrespective of the evolutionary method employed. Two highly distinct reciprocally monophyletic clades characterized by marked levels of corrected sequence divergence were present, with no shared haplotypes between the two major phylogroups. Phylogroup one comprises the populations of the westward‐flowing drainages (mainly the Berg and Olifants drainages), and phylogroup two comprises all of the southward‐flowing drainages and can further be divided into two subclades – one containing the Breede River populations, and the other containing the Gamtoos and Gourits drainage systems. The nested clade analysis demonstrated restricted gene flow and long‐distance dispersal for a number of higher clade levels. The higher‐level groups and results for the total cladogram suggest either fragmentation or isolation by distance.Main conclusions Freshwater crabs are generally highly philopatric, and dispersal, although not common, has occurred historically. The westward‐flowing drainages (Berg, Olifants, Eerste, Liesbeeck and Tokai) are isolated from the southward‐flowing drainages by the Cape Fold Mountains, while the southward‐flowing drainages have a number of tributaries that extend into the low‐lying regions, allowing for gene flow between these three major drainages systems (Breede, Gamtoos and Gourits). Among the westward‐flowing drainages, a more intensive sampling regime is required to understand evolutionary relationships. Our molecular results suggest that the observed patterns pre‐date the formation of contemporary hydrographic patterns in the Cape. This suggests that an older Late Miocene event has severely impacted the contemporary population structure in this species, as recent Pliocene hydrographic boundaries do not correspond to the phylogeographic pattern observed. Conservation efforts for aquatic taxa should clearly be directed at the catchments, in an attempt to conserve biological diversity.

Coherence, Consistency, and Cohesion: Clade Selection in Okasha and Beyond

Samir Okasha argues that clade selection is an incoherent concept, because the relation that constitutes clades is such that it renders parent-offspring (reproduction) relations between clades impossible. He reasons that since clades cannot reproduce, it is not coherent to speak of natural selection operating at the clade level. We argue, however, that when species-level lineages and clade-level lineages are treated consistently according to standard cladist commitments, clade reproduction is indeed possible and clade selection is coherent if certain conditions obtain. Despite clade selection's logical coherence, however, we share some of Okasha's pessimism. Whether or not clades are a unit of selection is ultimately a question of empirical support and theoretical import.

Prevalence and Clustering Patterns of Human Papillomavirus Genotypes in Multiple Infections

Prevalence of multiple human papillomavirus (HPV) infections, involvement of specific HPV phylogenetic clades in multiple infections, and clustering patterns of multiple infections at the clade level were assessed in 854 HIV (-) and 275 HIV (+) women cross-sectionally. Reverse line blot assay was used to detect 27 HPV genotypes. Involvement of specific clades in coinfections and clustering patterns were assessed using HPV clade/genotype as the unit of analyses. Expected frequencies assuming independence for all possible clade combinations in two-genotype infections were derived using a multinomial expansion and comparisons of observed and expected frequencies were done using a composite goodness-of-fit test. In all, 100 two-genotype infections were detected; 61 in HIV (-) and 39 in HIV (+) women. Clade A9 (HPV types 16, 31, 33, 35, 52, and 58) was significantly less likely to be involved in multiple infections compared with all other clades (55.2% versus 64.6%; adjusted odds ratios, 0.68; 95% confidence interval, 0.48-0.95). Observed patterns for all possible clade combinations (among HPV clades A3, A5, A6, A7, A9, and A10) in two-genotype infections did not significantly differ from those expected in the entire sample, across HIV, Pap smear, and age strata (all goodness-of-fit exact P > 0.20). These results indicate that clade A9 is less likely to be involved in multiple infections and that HPV genotypes predominantly establish multiple infections at random, with little positive/negative clustering for either phylogenetically related or unrelated types. The current method of analysis affords the opportunity to test clustering of a large number of HPV genotype/clade combinations at nominal alpha levels.

Mass extinctions and macroevolution

Mass extinctions are important to macroevolution not only because they involve a sharp increase in extinction intensity over “background” levels, but also because they bring a change in extinction selectivity, and these quantitative and qualitative shifts set the stage for evolutionary recoveries. The set of extinction intensities for all stratigraphic stages appears to fall into a single right-skewed distribution, but this apparent continuity may derive from failure to factor out the well-known secular trend in background extinction: high early Paleozoic rates fill in the gap between later background extinction and the major mass extinctions. In any case, the failure of many organism-, species-, and clade-level traits to predict survivorship during mass extinctions is a more important challenge to the extrapolationist premise that all macroevolutionary processes are simply smooth extensions of microevolution. Although a variety of factors have been found to correlate with taxon survivorship for particular extinction events, the most pervasive effect involves geographic range at the clade level, an emergent property independent of the range sizes of constituent species. Such differential extinction would impose “nonconstructive selectivity,” in which survivorship is unrelated to many organismic traits but is not strictly random. It also implies that correlations among taxon attributes may obscure causation, and even the focal level of selection, in the survival of a trait or clade, for example when widespread taxa within a major group tend to have particular body sizes, trophic habits, or metabolic rates. Survivorship patterns will also be sensitive to the inexact correlations of taxonomic, morphological, and functional diversity, to phylogenetically nonrandom extinction, and to the topology of evolutionary trees. Evolutionary recoveries may be as important as the extinction events themselves in shaping the long-term trajectories of individual clades and permitting once-marginal groups to diversify, but we know little about sorting processes during recovery intervals. However, both empirical extrapolationism (where outcomes can be predicted from observation of pre- or post-extinction patterns) and theoretical extrapolationism (where mechanisms reside exclusively at the level of organisms within populations) evidently fail during mass extinctions and their evolutionary aftermath. This does not mean that conventional natural selection was inoperative during mass extinctions, but that many features that promoted survivorship during background times were superseded as predictive factors by higher-level attributes. Many intriguing issues remain, including the generality of survivorship rules across extinction events; the potential for gradational changes in selectivity patterns with extinction intensity or the volatility of target clades; the heritability of clade-level traits; the macroevolutionary consequences of the inexact correlations between taxonomic, morphological, and functional diversity; the factors governing the dynamics and outcome of recoveries; and the spatial fabric of extinctions and recoveries. The detection of general survivorship rules—including the disappearance of many patterns evident during background times—demonstrates that studies of mass extinctions and recovery can contribute substantially to evolutionary theory.

TESTING A VICARIANCE MODEL TO EXPLAIN HAPLOTYPE DISTRIBUTION IN THE PSAMMOPHILIC SCORPION PARUROCTONUS UTAHENSIS

A model of vicariance speciation has been proposed to explain the proliferation of psammophilic (sand loving) species in several endemic genera of scorpions. The current distribution of Paruroctonus utahensis (Williams, 1968) populations on isolated sand dunes seems to fit this model; therefore, this species was examined to test the model for psammophilic population distribution and haplotype variation. A portion of the mitochondrial rDNA gene was sequenced from 44 individuals representing 7 populations of P. utahensis. Three individuals of Paruroctonus gracilior (Hoffmann, 1931) and 1 individual of Paruroctonus boquillas Sissom and Henson, 1998, were used for outgroup comparison. A maximum parsimony heuristic search indicated that the basal populations were in the south and derived populations occurred in the northeastern portion of the range. A nested clade analysis found a statistically significant correlation between haplotypes and their geographical distribution at several clade levels. The biological cause of this association was best explained by allopatric fragmentation. Our data supported the vicariance model of isolation by fragmentation of a larger habitat to explain the variation seen among populations of P. utahensis.

Diversity of algal endosymbionts (zooxanthellae) in octocorals: the roles of geography and host relationships

The presence, genetic identity and diversity of algal endosymbionts (Symbiodinium) in 114 species from 69 genera (20 families) of octocorals from the Great Barrier Reef (GBR), the far eastern Pacific (EP) and the Caribbean was examined, and patterns of the octocoral-algal symbiosis were compared with patterns in the host phylogeny. Genetic analyses of the zooxanthellae were based on ribosomal DNA internal transcribed spacer 1 (ITS1) region. In the GBR samples, Symbiodinium clades A and G were encountered with A and G being rare. Clade B zooxanthellae have been previously reported from a GBR octocoral, but are also rare in octocorals from this region. Symbiodinium G has so far only been found in Foraminifera, but is rare in these organisms. In the Caribbean samples, only Symbiodinium clades B and C are present. Hence, Symbiodinium diversity at the level of phylogenetic clades is lower in octocorals from the Caribbean compared to those from the GBR. However, an unprecedented level of ITS1 diversity was observed within individual colonies of some Caribbean gorgonians, implying either that these simultaneously harbour multiple strains of clade B zooxanthellae, or that ITS1 heterogeneity exists within the genomes of some zooxanthellae. Intracladal diversity based on ITS should therefore be interpreted with caution, especially in cases where no independent evidence exists to support distinctiveness, such as ecological distribution or physiological characteristics. All samples from EP are azooxanthellate. Three unrelated GBR taxa that are described in the literature as azooxanthellate (Junceella fragilis, Euplexaura nuttingi and Stereonephthya sp. 1) contain clade G zooxanthellae, and their symbiotic association with zooxanthellae was confirmed by histology. These corals are pale in colour, whereas related azooxanthellate species are brightly coloured. The evolutionary loss or gain of zooxanthellae may have altered the light sensitivity of the host tissues, requiring the animals to adopt or reduce pigmentation. Finally, we superimposed patterns of the octocoral-algal symbiosis onto a molecular phylogeny of the host. The data show that many losses/gains of endosymbiosis have occurred during the evolution of octocorals. The ancestral state (azooxanthellate or zooxanthellate) in octocorals remains unclear, but the data suggest that on an evolutionary timescale octocorals can switch more easily between mixotrophy and heterotrophy compared to scleractinian corals, which coincides with a low reliance on photosynthetic carbon gain in the former group of organisms.