On the accumulation of deleterious mutations during range expansions.

We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations cosegregate. We perform individual-based simulations of 1D and 2D range expansions and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front, but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load for thousands of generations after the expansion. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyse functional genetic diversity in humans and find patterns that are consistent with our model.

A sequential coalescent algorithm for chromosomal inversions.

Chromosomal inversions are common in natural populations and are believed to be involved in many important evolutionary phenomena, including speciation, the evolution of sex chromosomes and local adaptation. While recent advances in sequencing and genotyping methods are leading to rapidly increasing amounts of genome-wide sequence data that reveal interesting patterns of genetic variation within inverted regions, efficient simulation methods to study these patterns are largely missing. In this work, we extend the sequential Markovian coalescent, an approximation to the coalescent with recombination, to include the effects of polymorphic inversions on patterns of recombination. Results show that our algorithm is fast, memory-efficient and accurate, making it feasible to simulate large inversions in large populations for the first time. The SMC algorithm enables studies of patterns of genetic variation (for example, linkage disequilibria) and tests of hypotheses (using simulation-based approaches) that were previously intractable.

Turnover of sex chromosomes induced by sexual conflict.

Sex-determination genes are among the most fluid features of the genome in many groups of animals. In some taxa the master sex-determining gene moves frequently between chromosomes, whereas in other taxa different genes have been recruited to determine the sex of the zygotes. There is a well developed theory for the origin of stable and highly dimorphic sex chromosomes seen in groups such as the eutherian mammals. In contrast, the evolutionary lability of genetic sex determination in other groups remains largely unexplained. In this theoretical study, we show that an autosomal gene under sexually antagonistic selection can cause the spread of a new sex-determining gene linked to it. The mechanism can account for the origin of new sex-determining loci, the transposition of an ancestral sex-determining gene to an autosome, and the maintenance of multiple sex-determining factors in species that lack heteromorphic sex chromosomes.

Cryptic recombination in the ever-young sex chromosomes of Hylid frogs.

Sex chromosomes are expected to evolve suppressed recombination, which leads to degeneration of the Y and heteromorphism between the X and Y. Some sex chromosomes remain homomorphic, however, and the factors that prevent degeneration of the Y in these cases are not well understood. The homomorphic sex chromosomes of the European tree frogs (Hyla spp.) present an interesting paradox. Recombination in males has never been observed in crossing experiments, but molecular data are suggestive of occasional recombination between the X and Y. The hypothesis that these sex chromosomes recombine has not been tested statistically, however, nor has the X-Y recombination rate been estimated. Here, we use approximate Bayesian computation coupled with coalescent simulations of sex chromosomes to quantify X-Y recombination rate from existent data. We find that microsatellite data from H. arborea, H. intermedia and H. molleri support a recombination rate between X and Y that is significantly different from zero. We estimate that rate to be approximately 10(5) times smaller than that between X chromosomes. Our findings support the notion that very low recombination rate may be sufficient to maintain homomorphism in sex chromosomes.

Species range expansion by beneficial mutations.

A species' range can be limited when there is no genetic variation for a trait that allows for adaptation to more extreme environments. We study how range expansion occurs by the establishment of a new mutation that affects a quantitative trait in a spatially continuous population. The optimal phenotype for the trait varies linearly in space. The survival probabilities of new mutations affecting the trait are found by simulation. Shallow environmental gradients favour mutations that arise nearer to the range margin and that have smaller phenotypic effects than do steep gradients. Mutations that become established in shallow environmental gradients typically result in proportionally larger range expansions than those that establish in steep gradients. Mutations that become established in populations with high maximum growth rates tend to originate nearer to the range edge and to cause relatively smaller range expansion than mutations that establish in populations with low maximum growth rates. Under plausible parameter values, mutations that allow for range expansion tend to have large phenotypic effects (more than one phenotypic standard deviation) and cause substantial range expansions (15% or more). Sexual reproduction allows for larger range expansions and adaptation to more extreme environments than asexual reproduction.

Directional selection and the evolution of breeding date in birds.

In many bird species, those pairs that breed earlier in the season have higher reproductive success than those that breed later. Since breeding date is known to be heritable, it is unclear why it does not evolve to an earlier time. Under assumptions outlined by Fisher, a model is developed that shows how breeding date may have considerable additive genetic variance, appear to be under directional selection, and yet not evolve. These results provide a general explanation for a persistent correlation of fitness with a variety of traits in natural populations.

A model for the evolution of assortative mating.

Abstract: Many animals and plants show a correlation between the traits of the individuals in the mating pair, implying assortative mating. Given the ubiquity of assortative mating in nature, why and how it has evolved remain open questions. Here we attempt to answer these questions in those cases where the trait under assortment is the same in males and females. We consider the most favorable scenario for assortment to evolve, where the same trait is under assortment and viability selection. We find conditions for assortment to evolve using a multilocus formalism in a haploid population. Our results show how epistasis in fitness between the loci that control the focal trait is crucial for assortment to evolve. We then assume specific forms of assortment in haploids and diploids and study the limiting cases of selective and nonselective mating. We find that selection for increased assortment is weak and that where increased assortment is costly, it does not invade.

Effects of the [PSI+] prion on rates of adaptation in yeast.

The [PSI(+)] prion in yeast has been shown to improve short-term growth in some environments, but its effects on rates of adaptation have not been assessed before now. We adapted three yeast genotypes to three novel environments in the presence and the absence of the prion. There were significant differences in adaptation rates between lines with different combinations of genotype, environment, and prion status. We saw no consistent effect, however, of the prion on the rate of adaptation to new environments. A major factor affecting the rate of adaptation was initial fitness in the new environment: lines with low initial fitness evolved faster than lines with high initial fitness.

On the forward modeling of radar Doppler spectrum width from LES: Implications for model evaluation.

Large-eddy simulations of an observed single-layer Arctic mixed-phase cloud are analyzed to study the value of forward modeling of profiling millimeter-wave cloud radar Doppler spectral width for model evaluation. Individual broadening terms and their uncertainties are quantified for the observed spectral width and compared to modeled broadening terms. Modeled turbulent broadening is narrower than the observed values when the turbulent kinetic energy dissipation rate from the subgrid-scale model is used in the forward model. The total dissipation rates, estimated with the subgrid-scale dissipation rates and the numerical dissipation rates, agree much better with both the retrieved dissipation rates and those inferred from the power spectra of the simulated vertical air velocity. The comparison of the microphysical broadening provides another evaluative measure of the ice properties in the simulation. To accurately retrieve dissipation rates as well as each broadening term from the observations, we suggest a few modifications to previously presented techniques. First, we show that the inertial subrange spectra filtered with the radar sampling volume is a better underlying model than the unfiltered -5/3 law for the retrieval of the dissipation rate from the power spectra of the mean Doppler velocity. Second, we demonstrate that it is important to filter out turbulence and remove the layer-mean reflectivity-weighted mean fall speed from the observed mean Doppler velocity to avoid overestimation of shear broadening. Finally, we provide a method to quantify the uncertainty in the retrieved dissipation rates, which eventually propagates to the uncertainty in the microphysical broadening.

Migration and the genetic covariance between habitat preference and performance.

Studies of the genetic covariance between habitat preference and performance have reported conflicting outcomes ranging from no covariance to strong covariance. The causes of this variability remain unclear. Here we show that variation in the magnitude of genetic covariance can result from variability in migration regimes. Using data from walking stick insects and a mathematical model, we find that genetic covariance within populations between host plant preference and a trait affecting performance on different hosts (cryptic color pattern) varies in magnitude predictably among populations according to migration regimes. Specifically, genetic covariance within populations is high in heterogeneous habitats where migration between populations locally adapted to different host plants generates nonrandom associations (i.e., linkage disequilibrium) between alleles at color pattern and host preference loci. Conversely, genetic covariance is low in homogeneous habitats where a single host exists and migration between hosts does not occur. Our results show that habitat structure and patterns of migration can strongly affect the evolution and variability of genetic covariance within populations.

Soybean Response to Flooded Soil Conditions and the Association with Soilborne Plant Pathogenic Genera.

The role of soilborne pathogens in flood damage on soybeans, Glycine max, was examined using six genotypes representing a reputed range of flood tolerances. Genotypes were planted in single-row plots from 1996 to 1998 with flood treatments of no flood, flood at emergence (3-day duration), or flood at the fourth leaf node growth stage (7-day duration). Three or four days after removing each flood treatment, plant stands were estimated and 15 plants were collected from each plot, weighed, and rated for root discoloration. Roots were assayed for the presence of fungi and other filamentous eukaryotic organisms. Plant stands were reduced by flooding at emergence compared with the nonflooded control. Flooding at both growth stages caused significant increases in root discoloration compared with nonflooded soybeans. Plant weights were reduced in 2 of 3 years for flooding at emergence. Pythium was the only genus of filamentous organisms whose isolation frequency increased with flooding. Of the 60 Pythium isolates evaluated representing the different cultural groups based on appearance and growth rate on potato dextrose agar, cornmeal agar, and V8 agar, 47% were moderately to highly virulent on soybean. Pythium spp. isolated from soybean included the pathogenic species P. ultimum, P. aphanidermatum, P. irregulare, and P. vexans and Group HS. Nonpathogenic P. oligandrum also was isolated from soybean.

The Effect of Pythium ultimum and Soil Flooding on Two Soybean Cultivars.

The effect of flooding and Pythium ultimum on soybean, Glycine max, was determined in a series of greenhouse experiments using the cultivars Hutcheson and Archer. Seeds were planted into pasteurized soil either not infested or infested with sand-cornmeal inoculum of P. ultimum and either flooded at emergence for 2 days or at the four leaf node stage (V4) for 5 days. A nonflooded control was included in each experiment. Seeds placed directly into infested soil resulted in little or no stand for Hutcheson regardless of flood treatment, whereas stand was reduced for Archer only in the flooded infested soil treatment. Additional experiments were conducted by placing seed onto a 2- to 5-mm layer of pathogen-free soil on top of the infested soil. Flooding at emergence reduced plant height, growth stage, and top dry weight for Hutcheson and root fresh weight for both cultivars. Greater reductions for Hutcheson in root weight, and top dry weight in P. ultimum-infested soil in the soil layer experiments, also indicated that Hutcheson was more susceptible than Archer. Flooding alone decreased root weights, and infestation with P. ultimum reduced weights further resulting in an additive effect. This also was the case for plant height, growth stage, and top dry weight for Hutcheson for flooding at emergence. Root discoloration was greatly increased for both cultivars in infested soil flooded at emergence. Similar results were found when plants were flooded at V4; however, the effect was not as great as with flooding at emergence. These studies indicate that Pythium damping-off and root rot may account for a portion of the negative response of soybean to flooding. The results also indicate that Archer has some resistance to P. ultimum.

Analysis of the inheritance, selection and evolution of growth trajectories.

We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full" model that fully fits the data and a "reduced" model that generates a smoothed estimate consistent with the sampling errors in the data. By decomposing the covariance function into its eigenvalues and eigenfunctions, it is possible to identify potential evolutionary changes in the population's mean growth trajectory for which there is (and those for which there is not) genetic variation. Algorithms for estimating these quantities, their confidence intervals, and for testing hypotheses about them are developed. These techniques are illustrated by an analysis of early growth in mice. Compatible methods for estimating the selection gradient function acting on growth trajectories in natural or domesticated populations are presented. We show how the estimates for the additive genetic covariance function and the selection gradient function can be used to predict the evolutionary change in a population's mean growth trajectory.

The reinforcement of mating preferences on an island.

We develop a haploid model for the reinforcement of female mating preferences on an island that receives migrants from a continent. We find that preferences will evolve to favor island males under a broad range of conditions: when the average male display trait on the island and continent differ, when the preference acts on that difference, and when there is standing genetic variance for the preference. A difference between the mean display trait on the continent and on the island is sufficient to drive reinforcement of preferences. Additional postzygotic isolation, caused, for example, by either epistatic incompatibility or ecological selection against hybrids, will amplify reinforcement but is not necessary. Under some conditions, the degree of preference reinforcement is a simple function of quantities that can be estimated entirely from phenotypic data. We go on to study how postzygotic isolation caused by epistatic incompatibilities affects reinforcement of the preference. With only one pair of epistatic loci, reinforcement is enhanced by tighter linkage between the preference genes and the genes causing hybrid incompatibility. Reinforcement of the preference is also affected by the number of epistatically interacting genes involved in incompatibility, independent of the overall intensity of selection against hybrids.

Treatment of requests for sex-change surgery with psychotherapy.

The authors describe two patients whose requests for sex-change surgery represented crises in sexual identity and anxiety-masking symptoms. Brief psychotherapy enabled these patients to relinquish their belief in a surgical "cure". In evaluating such request, the psychiatrist should consider the patient's total personality rather than focusing on the genuineness of the perceived gender disorder. Whatever the final decision, the opportunity for continued psychotherapy should be provided.

When sources become sinks: migrational meltdown in heterogeneous habitats.

We consider the evolution of ecological specialization in a landscape with two discrete habitat types connected by migration, for example, a plant-insect system with two plant hosts. Using a quantitative genetic approach. we study the joint evolution of a quantitative character determining performance in each habitat together with the changes in the population density. We find that specialization on a single habitat evolves with intermediate migration rates, whereas a generalist species evolves with both very low and very large rates of movement between habitats. There is a threshold at which a small increase in the connectivity of the two habitats will result in dramatic decrease in the total population size and the nearly complete loss of use of one of the two habitats through a process of "migrational meltdown." In some situations, equilibria corresponding to a specialist and a generalist species are simultaneously stable. Analysis of our model also shows cases of hysteresis in which small transient changes in the landscape structure or accidental demographic disturbances have irreversible effects on the evolution of specialization.

Runaway sexual selection when female preferences are directly selected.

We introduce models for the runaway coevolution of female mating preferences and male display traits. The models generalize earlier results by allowing for direct natural selection on the preference, arbitrary forms of mate choice, and fairly general assumptions about the underlying genetics. Results show that a runaway is less likely when there is direct selection on the preference, but that it is still possible if there is a sufficiently large phenotypic correlation between the female's preference and the male's trait among mated pairs. Comparison of three preference functions introduced by Lande (1981) shows that open-ended preferences are particularly prone to a runaway, and that absolute preferences require very large differences between females in their preferences. We analyze the causes of the runaway seen in a model developed by Iwasa and Pomiankowski (1995).

Results of bronchoscopically obtained lower airway cultures from adult sickle cell disease patients with the acute chest syndrome.

PURPOSE: The purpose of this study was to determine the frequency of bacterial pneumonia as a cause of the acute chest syndrome in adult patients with sickle cell disease based on bronchoscopically obtained lower airway cultures and to describe the clinical, laboratory, and roentgenographic features of the acute chest syndrome in a series composed entirely of adult patients with sickle cell disease. PATIENTS AND METHODS: We reviewed the hospital records from 19 episodes (18 patients) of acute chest syndrome in adult patients with sickle cell disease (greater than or equal to 19 years of age) who had undergone flexible bronchoscopy to obtain lower airway cultures between January 1979 and July 1987. We also recorded patients' clinical, laboratory, and roentgenographic characteristics. RESULTS: Pneumonia was diagnosed in four of 19 episodes (21%) of acute chest syndrome based on quantitative cultures obtained at bronchoscopy. The pneumonia was caused by Streptococcus pneumoniae in two patients and mixed aerobic and anaerobic organisms in the other two patients. Forty-four of 45 blood cultures were negative, and one grew Staphylococcus epidermidis, which was considered a contaminant. Chest roentgenograms revealed lower lobe involvement in 17 episodes (90%) and bilateral infiltrates in six (32%). Pleural effusions occurred in seven episodes (37%), and pleural fluid samples obtained from five of these revealed sterile exudates. CONCLUSION: The results of this retrospective study suggest that bacterial pneumonia is an uncommon cause of acute chest syndrome in adult patients with sickle cell disease. These results are consistent with previous retrospective studies using noninvasive techniques to diagnose pneumonia. Nevertheless, there appeared to be no reliable noninvasive variables that could accurately differentiate between patients with and without pneumonia and, consequently, we recommend empiric antibiotic therapy in addition to usual supportive care of these patients.

Reinforcement and divergence under assortative mating.

Traits that cause assortative mating such as the flowering time in plants and body size in animals can produce reproductive isolation between hybridizing populations. Can selection against unfit hybrids cause two populations to diverge in their mean values for these kinds of traits? Here I present a haploid analytical model of one population that receives gene flow from another. The partial pre-zygotic isolation between the two populations is caused by assortative mating for a trait that is influenced by any number of genes with additive effects. The post-zygotic isolation is caused by selection against genetic incompatibilities that can involve any form of selection on individual genes and gene combinations (epistasis). The analysis assumes that the introgression rate and selection coefficients are small. The results show that the assortment trait mean will not diverge from the immigrants unless there is direct selection on the trait favouring it to do so or there are genes of very large effect. The amount of divergence at equilibrium is determined by a balance between direct selection on the assortment trait and introgression from the other population. Additional selection against hybrid genetic incompatibilities reduces the effective migration rate and allows greater divergence. The role of assortment in speciation is discussed in the light of these results.

Reinforcement during ecological speciation.

Reinforcement of pre-zygotic isolation can result when any of several kinds of selection act against hybrids. This paper investigates the situation where hybrids are selected against for ecological reasons, for example when there is no niche for individuals that are phenotypically intermediate between the parental species. The calculations here show how much ecological selection can lead to the reinforcement of a female mating preference or an assortative mating trait that is expressed in both sexes. The model allows for the ecological trait to be affected by any number of loci, but assumes that selection is weak and the introgression rate small. The effect of selection against hybrids increases rapidly as the difference between the mean phenotypes of the two populations increases. When genetic variation in the ecological trait is caused by many loci, stabilizing selection on it further contributes to reinforcement.