Mathematical consequences of the genealogical species concept

A genealogical species is defined as a basal group of organisms whose members are all more closely related to each other than they are to any organisms outside the group ("exclusivity"), and which contains no exclusive group within it. In practice, a pair of species is so defined when phylogenies of alleles from a sample of loci shows them to be reciprocally monophyletic at all or some specified fraction of the loci. We investigate the length of time it takes to attain this status when an ancestral population divides into two descendant populations of equal size with no gene exchange, and when genetic drift and mutation are the only evolutionary forces operating. The number of loci used has a substantial effect on the probability of observing reciprocal monophyly at different times after population separation, with very long times needed to observe complete reciprocal monophyly for a large number of loci. In contrast, the number of alleles sampled per locus has a relatively small effect on the probability of reciprocal monophyly. Because a single mitochondrial or chloroplast locus becomes reciprocally monophyletic much faster than does a single nuclear locus, it is not advisable to use mitochondrial and chloroplast DNA to recognize genealogical species for long periods after population divergence. Using a weaker criterion of assigning genealogical species status when more than 50% of sampled nuclear loci show reciprocal monophyly, genealogical species status depends much less on the number of sampled loci, and is attained at roughly 4-7 N generations after populations are isolated, where N is the historically effective population size of each descendant. If genealogical species status is defined as more than 95% of sampled nuclear loci showing reciprocal monophyly, this status is attained after roughly 9-12 N generations.     

Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase

Both 8oxo-guanine and formamidopyrimidines are major products of oxidative DNA damage that can result in the fixation of transversion mutations following replication if left unrepaired. These lesions are targeted by the N-DNA glycosylase hOgg1, which catalyses excision of the aberrant base followed by cleavage of the phosphate backbone directly 5' to the resultant abasic site in a context, dependent manner. We present the crystal structure of native hOgg1 refined to 2.15 A resolution that reveals a number of highly significant conformational changes on association with DNA that are clearly required for substrate recognition and specificity. Changes of this magnitude appear to be unique to hOgg1 and have not been observed in any of the DNA-glycosylase structures analysed to date where both native and DNA-bound forms are available. It has been possible to identify a mechanism whereby the catalytic residue Lys 249 is "primed" for nucleophilic attack of the N-glycosidic bond.     

Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments

We identified environment-dependent constraints on the evolution of plasticity to density under natural conditions in two natural populations of Impatiens capensis. We also examined the expression of population divergence in genetic variance-covariance matrices in these natural environments. Inbred lines, originally collected from a sunny site with high seedling densities and a woodland site with low seedling densities, were planted in both original sites at natural high densities and at low density. Morphological and life-history characters were measured. More genetic variation for plastic responses to density was expressed in the sun site than in the woodland site, so the evolutionary potential of plasticity was greater in the sun site. Strong genetic correlations between the same character expressed at different densities and correlations among different characters could constrain the evolution of plasticity in both sites. Genetically based trade-offs in meristem allocation to vegetative growth and reproduction were apparent only in the high-resource environment with no overhead canopy and no intraspecific competition. Therefore, genetic constraints on the evolution of plasticity depended on the site and density in which plants were grown, and correlated responses to selection on plastic characters are also expected to differ between sites and densities. Population differentiation in genetic variance-covariance matrices was detected, but matrix structural differences, as opposed to proportional differences, were detected between populations only in the sun site at natural high density. Thus, population divergence in genetic architecture can occur rapidly and on a fine spatial scale, but the expression of such divergence may depend on the environment.     

Simulation and Parameter Estimation Study of a Simple Neuronal Model of Rhythm Generation: Role of NMDA and Non-NMDA Receptors

Simple neural network models of the Xenopus embryo swimming CPG, based on the one originally developed by Roberts and Tunstall (1990), were used to investigate the role of the voltage-dependent N-methyl-D-aspartate (NMDA) receptor channels, in conjunction with faster non-NMDA components of synaptic excitation, in rhythm generation. The voltage-dependent NMDA current "follows" the membrane potential, leading to a postinhibitory rebound that is more efficient than one without voltage dependency and allows neurons to fire more than one action potential per cycle. Furthermore, the model demonstrated limited rhythmic activity in the absence of synaptic inhibition, supporting the hypothesis that the NMDA channels provide a basic mechanism for rhythmicity. However, the rhythmic properties induced by the NMDA current were observed only when there was moderate activation of the non-NMDA synaptic channels, suggesting a modulatory role for this component. The simulations also show that the voltage dependency of the NMDA conductance, as well as the fast non-NMDA current, stabilizes the alternation pattern versus synchrony. To verify that these effects and their implications on the mechanism of swimming and transition to other types of activity take place in the real preparation, constraints on parameter values have to be specified. A method to estimate synaptic parameters was tested with generated data. It is shown that a global analysis, based on multiple iterations of the optimization process (Foster et al., 1993), gives a better understanding of the parameter subspace describing network activity than a standard fit with a sensitivity analysis for an individual solution.     

The ubiquity of phenotypic plasticity in plants: a synthesis

Adaptation to heterogeneous environments can occur via phenotypic plasticity, but how often this occurs is unknown. Reciprocal transplant studies provide a rich dataset to address this issue in plant populations because they allow for a determination of the prevalence of plastic versus canalized responses. From 31 reciprocal transplant studies, we quantified the frequency of five possible evolutionary patterns: (1) canalized response–no differentiation: no plasticity, the mean phenotypes of the populations are not different; (2) canalized response–population differentiation: no plasticity, the mean phenotypes of the populations are different; (3) perfect adaptive plasticity: plastic responses with similar reaction norms between populations; (4) adaptive plasticity: plastic responses with parallel, but not congruent reaction norms between populations; and (5) nonadaptive plasticity: plastic responses with differences in the slope of the reaction norms. The analysis included 362 records: 50.8% life‐history traits, 43.6% morphological traits, and 5.5% physiological traits. Across all traits, 52% of the trait records were not plastic, and either showed no difference in means across sites (17%) or differed among sites (83%). Among the 48% of trait records that showed some sort of plasticity, 49.4% showed perfect adaptive plasticity, 19.5% adaptive plasticity, and 31% nonadaptive plasticity. These results suggest that canalized responses are more common than adaptive plasticity as an evolutionary response to environmental heterogeneity.     

Heme-heme and heme-ligand interactions in the di-heme oxygen-reducing site of cytochrome bd from Escherichia coli revealed by nanosecond absorption spectroscopy

Cytochrome bd is a terminal quinol:O₂ oxidoreductase of respiratory chains of many bacteria. It contains three hemes, b₅₅₈, b₅₉₅, and d. The role of heme b₅₉₅ remains obscure. A CO photolysis/recombination study of the membranes of Escherichia coli containing either wild type cytochrome bd or inactive E445A mutant was performed using nanosecond absorption spectroscopy. We compared photoinduced changes of heme d-CO complex in one-electron-reduced, two-electron-reduced, and fully reduced states of cytochromes bd. The line shape of spectra of photodissociation of one-electron-reduced and two-electron-reduced enzymes is strikingly different from that of the fully reduced enzyme. The difference demonstrates that in the fully reduced enzyme photolysis of CO from heme d perturbs ferrous heme b₅₉₅ causing loss of an absorption band centered at 435 nm, thus supporting interactions between heme b₅₉₅ and heme d in the di-heme oxygen-reducing site, in agreement with previous works. Photolyzed CO recombines with the fully reduced enzyme monoexponentially with τ ∼ 12 μs, whereas recombination of CO with one-electron-reduced cytochrome bd shows three kinetic phases, with τ ∼ 14 ns, 14 μs, and 280 μs. The spectra of the absorption changes associated with these components are different in line shape. The 14 ns phase, absent in the fully reduced enzyme, reflects geminate recombination of CO with part of heme d. The 14-μs component reflects bimolecular recombination of CO with heme d and electron backflow from heme d to hemes b in ∼ 4% of the enzyme population. The final, 280-μs component, reflects return of the electron from hemes b to heme d and bimolecular recombination of CO in that population. The fact that even in the two-electron-reduced enzyme, a nanosecond geminate recombination is observed, suggests that namely the redox state of heme b₅₉₅, and not that of heme b₅₅₈, controls the pathway(s) by which CO migrates between heme d and the medium.     

Recipient Environment More Important than Community Composition in Determining the Success of an Experimental Sponge Transplant

Human activities have inflicted profound damage upon many ecosystems, and ecologists are now seeking effective means of restoring ecosystems to their natural state. Industrial ports and harbors are highly modified and often depauperate in native fauna. They are typically characterized by poor water quality and modified community composition, both of which may hinder attempts to reintroduce native species. Here, we conducted a field experiment to separate the effects of the recipient environment and community composition on the success of endemic sponge explants in Port Kembla Harbor, NSW, Australia. A reciprocal transplant was conducted between communities originating from six sites that varied in water quality and community composition, enabling us to assess the relative factors simultaneously. A colony of the endemic sponge Tedania anhelans was then inserted into the center of each community, and we quantified the survival, growth, and metal bioaccumulation of sponges over three months. Endemic sponges consistently performed better against resident assemblages when water quality was good. Sponges transplanted to cleaner sites had over double the survivorship and approximately three times the surface area of sponges transplanted to disturbed sites. These patterns were independent of community composition. Bioaccumulation of metals in sponges was correlated with survival; however, other factors such as turbidity may be required to explain sponge mortality at some sites. This study adds to evidence that remediation of the physical and chemical environments may be a prerequisite for biological remediation and demonstrates the value of experimental transplants in assessing restoration potential.     

High-testosterone men reject low ultimatum game offers

The ultimatum game is a simple negotiation with the interesting property that people frequently reject offers of 'free' money. These rejections contradict the standard view of economic rationality. This divergence between economic theory and human behaviour is important and has no broadly accepted cause. This study examines the relationship between ultimatum game rejections and testosterone. In a variety of species, testosterone is associated with male seeking dominance. If low ultimatum game offers are interpreted as challenges, then high-testosterone men may be more likely to reject such offers. In this experiment, men who reject low offers ($5 out of $40) have significantly higher testosterone levels than those who accept. In addition, high testosterone levels are associated with higher ultimatum game offers, but this second finding is not statistically significant.     

Local Adaptation and the Effects of Isolation and Population Size – the Semelparous Perennial <Emphasis Type="Italic">Carlina vulgaris</Emphasis> as a Study Case

We made a reciprocal transplantation experiment with Carlina vulgaris, among 12 semi-natural grassland sites situated in southwest Sweden. The fate of seeds and seedlings were followed during 2 years. Local adaptation was investigated both by native superiority over non-natives, and by comparing the observed performance of a population to the fitted value of a reduced statistical model that showed the populations’ performance at all sites and the performance of all other populations at its home site. The latter method indicates presence of local adaptation even when natives are inferior to introduced populations as long as the negative difference in fitness between the populations is smaller at the native population’s home site. The strength of local adaptation was measured as the ratio of the observed to the expected performance in reduced statistical models and regressed on the degree of isolation and population size. We found no evidence of local adaptation in terms of native superiority compared to non-natives, but with the relative method we found one of six fitness components, juvenile survival, to be 6% higher for natives at their home sites compared to how they performed at other sites and how others performed at their site. Further, our results indicate that both isolation and population size have a positive effect on the process of local adaptation. Co-ordinating editor: J. Tuomi     

Ecological factors influencing tetraploid speciation in snow buttercups (Ranunculus Adoneus): niche differentiation and tetraploid establishment

Chromosome doubling plays an important role in generating new species of flowering plants. However, reproductive incompatibilities between newly formed tetraploid plants and their diploid progenitors are expected to create a significant barrier to the persistence and establishment of neopolyploid populations. Ecological differentiation can reduce this barrier via prezygotic isolation arising from spatial separation. Alternatively, superior viability or fecundity of neotetraploid plants might compensate for the reproductive cost of incompatible pollen from diploid neighbors. The performance of plants of both cytotypes can be assessed in their respective habitats through reciprocal transplants, although such experiments have not been used previously in the study of tetraploid speciation. We used a series of seed and seedling transplant experiments to assess ecological differentiation and competitive ability during early establishment phases for tetraploid and diploid forms of the snow buttercup (Ranunculus adoneus). At two sites, seeds from diploids and tetraploids had similar germination probabilities. Tetraploid snow buttercup seedlings had a significant growth advantage in a controlled environment chamber experiment. However, in the field diploid and tetraploid buttercup seedlings did not differ consistently in survival or growth, nor did the two cytotypes show reciprocal advantages in performance, as expected if ecological differentiation has occurred. At the seed and seedling stages, neither niche differentiation nor tetraploid competitive superiority appears sufficient to explain neotetraploid success in the presence of their diploid progenitors.