Emerging patterns in the comparative analysis of phylogenetic community structure.

The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty-three of 39 studies (59%) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over-represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one-dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.

Spatial and genetic structure of host-associated differentiation in the parasitoid Copidosoma gelechiae.

Host-associated differentiation (HAD) appears to be an important driver of diversification in the hyperdiverse phytophagous and parasitoid insects. The gallmaking moth Gnorimoschema gallaesolidaginis has undergone HAD on two sympatric goldenrods (Solidago), and HAD has also been documented in its parasitoid Copidosoma gelechiae, with the intriguing suggestion that differentiation has proceeded independently in multiple populations. We tested this suggestion with analysis of Amplified Fragment Length Polymorphism (AFLP) markers for C. gelechiae collections from the midwestern and northeastern United States and eastern Canada. AFLP data were consistent with the existence of HAD, with between-host F(ST) significant before Bonferroni correction in two of seven sympatric populations. amova analysis strongly rejected a model of HAD with a single historical origin, and thus supported the repeated-HAD hypothesis. Copidosoma gelechiae shows significant host-associated divergence at a number of allozyme loci (Stireman et al., 2006), but only weak evidence via AFLPs for genome-wide differentiation, suggesting that this species is at a very early stage of HAD.

Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions.

If we are to plan conservation strategies that minimize the loss of evolutionary history through human-caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee & May (1997, Science 278, 692-694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction-management pay-off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human-caused extinctions may therefore be more severe, yet more manageable, than first suggested.

Collagenase studies in bones of guinea pigs.

A specific collagenase has been demonstrated in culture fluids of guinea pig bones. Based on the acrylamide gel electrophoretic pattern, the mechanism of action of guinea pig bone collagenase appears similar to other known vertebrate collagenases. 2 peaks of enzymatic activity were found upon assay of fractions from gel chromatography, corresponding to molecular weights in the range of 137,000 daltons and 29,000 daltons. The enzyme is inhibited by cysteine and EDTA. Alpha1-macroglobulin is a much stronger inhibitor of the collagenase than alpha-antitrypsin. Activation studies suggested the presence of a proenzyme to guinea pig bone collagenase that was converted to an active enzyme by proteases present in the culture fluid.

Clutch-size behavior and coexistence in ephemeral-patch competition models.

Systems of patchy, ephemeral resources often support surprisingly diverse assemblages of consumer insects. Aggregation of consumer individuals over the landscape of patches has been suggested as one mechanism that can stabilize competition among consumer species. One mechanism for larval aggregation is the laying of eggs in clutches by females traveling among patches to distribute their total fecundity. We use simulation models to explore the consequences, for coexistence of competitors, of larval aggregation that arises from clutch laying. Contrary to some previous treatments, we find that clutch laying can be strongly stabilizing and under certain conditions can be sufficient to allow competitors to coexist stably. We extend these models by considering clutch size as a variable that responds to the abundance of resource patches. Such a relationship might be expected because females should lay their eggs in fewer but larger clutches when the cost of travel among patches is high (because patches are rare). When females adjust clutch size in response to resource abundance, coexistence can be easiest when resource patches are scarce and most difficult when resources are abundant.

Local movement and edge effects on competition and coexistence in ephemeral-patch models.

For insects exploiting spatially structured arrays of resource patches (host plants, fungi, carrion, etc.), the distribution of individuals among patches can have important consequences for the coexistence of competitors. In general, intraspecific aggregation of consumer individuals over the landscape of patches stabilizes competition. Oviposition behavior of individual females can generate aggregation of larvae across patches and, therefore, strongly influences the outcome of competition between co-occurring species. We used simulation models to evaluate the consequences (for the coexistence of competitors) of different movement behaviors by females before and between oviposition events. Coexistence times increase when females are more likely to travel among neighboring patches than among distant ones. Coexistence times are also longer when females begin egg laying near the site of their emergence. Preoviposition dispersal is, therefore, destabilizing. We also considered responses by females to edges of resource arrays. Edge effects are generally stabilizing, delaying competitive exclusion by increasing larval aggregation, but different responses to edges have dramatically different effects on coexistence. The longest coexistence times occur when edges are "sticky", such that females encountering an edge tend to remain there.

Peptidyl (acyloxy)methyl ketones and the quiescent affinity label concept: the departing group as a variable structural element in the design of inactivators of cysteine proteinases.

(Acyloxy)methyl ketones, of general structure Z-[AA2]-[AA1]-CH2OCOAr, are potent inactivators of the cysteine proteinase cathepsin B. These reagents have been designed as affinity labels in which the dipeptidyl moiety serves as an affinity group (complementary to the S1 and S2 sites of the enzyme), while the (acyloxy)methyl ketone unit (-COCH2OCOR), containing a weak leaving group in the form of a carboxylate nucleofuge, functions as the potentially reactive entity that labels the enzyme. The inhibition is time dependent, active site directed, and irreversible. The apparent second-order rate constant kinact/Kinact, which characterizes the inhibition of cathepsin B by this series, spans several orders of magnitude and in certain cases exceeds 10(6) M-1 s-1. The activity of this series of inhibitors was found to be exquisitely sensitive to the nature of the carboxylate leaving group as well as the affinity group. A strong dependence of second-order inactivation rate on leaving group pKa was uncovered for Z-Phe-Ala (acyloxy)methyl ketones [log(k/K) = 1.1 (+/- 0.1) X pKa + 7.2 (+/- 0.4); r2 = 0.82, n = 26]. Heretofore in constructing affinity labels the choice of leaving group was quite restricted. The aryl carboxylate group thus offers considerable variation as a design element in that both its binding affinity and reactivity can be controlled by substituent effects. Specific peptidyl (acyloxy)methyl ketones thus represent prime examples of highly potent, chemically stable enzyme inhibitors with variable structural elements in both the affinity and departing groups.

Selection of CTL escape mutants in mice infected with a neurotropic coronavirus: quantitative estimate of TCR diversity in the infected central nervous system.

Variant viruses mutated in the immunodominant cytotoxic T cell epitope surface (S) glycoprotein S-510-518 are selected in mice chronically infected with mouse hepatitis virus, strain JHM. We determined whether this selection occurred in the presence of an oligoclonal or polyclonal T cell response using soluble MHC/peptide tetramers in direct ex vivo analyses of CNS-derived lymphocytes. A total of 42% (range, 29-60%) of CD8 T cells in the CNS of mice with acute encephalitis recognized epitope S-510-518. A total of 34% (range, 18-62%) of cells from mice with hind limb paralysis (and chronic demyelination) were also epitope specific, even though only virus expressing mutated epitope is detected in these animals. Sequence analysis of the beta-chain CDR3 of 487 tetramer S-510-518-positive cDNA clones from nine mice showed that a majority of clonotypes were identified in more than one mouse. From these analyses, we estimated that 300-500 different CD8 T cell clonotypes responsive to epitope S-510-518 were present in each acutely infected brain, while 100-900 were present in the CNS of each mouse with chronic disease. In conclusion, a polyclonal CD8 T cell response to an epitope does not preclude the selection of T cell escape mutants, and epitope-specific T cells are still present at high levels even after RNA-encoding wild-type sequence is no longer detectable.