Level Of Natural Selection Research Articles

Quantifying direct and indirect effects of early‐season herbivory on reproduction across four brassicaceous plant species

Abstract Insect herbivores can directly affect plant reproduction by feeding on reproductive tissues, or indirectly by feeding on vegetative tissues for which plants are unable to compensate. Additionally, early arriving herbivores may have cascading effects on plant reproduction by altering the later arriving community. However, the dynamic interplay between plant development and the assembly of herbivore communities remains underexplored. Hence, it is unclear whether non‐outbreak levels of ambient herbivory early in the development of plants can impact plant fitness and to what extent these effects are mediated through changes in plant development and subsequent herbivory. By excluding the herbivore community in an exclosure experiment and by manipulating early‐season herbivory in a common garden field experiment replicated across four Brassicaceae species and 2 years, we tested whether early‐season herbivory by caterpillars (Pieris rapae) or aphids (Myzus persicae) affected development, reproduction, and the herbivore communities associated with individual plants. In addition, we tested a causal hypothesis to assess the relative importance and temporal interplay between variation in herbivore communities and variation in plant development in determining plant reproduction. Early‐season herbivory affected plant reproduction in the exclosure experiment, with effects being highly dependent on the plant species, the herbivore species and the year. However, we found no such effects in the field experiment. The exploratory path analysis indicated that variation in plant reproduction is best predicted by variation in plant development, explaining 80% of the total effect on seed production. This suggests early‐season herbivory had limited effects on later plant development, and plants were able to attenuate the impact of early‐season herbivory. However, no clear compensatory mechanism could be identified. While early‐season herbivory has the potential to affect plant reproduction through changes in plant development or the subsequent development of the associated community, these effects were small and varied across closely related species. This suggests that plant species may be exposed to different levels of natural selection by early‐season herbivores through plant‐ or community‐mediated effects on reproduction. Read the free Plain Language Summary for this article on the Journal blog.

Структура разнообразия по вегетативной и генеративной структуре кроны кедра сибирского на плантации с разреженной посадкой

Studies of the diversity of economically valuable traits in forest tree species are of great interest not only for forest selection and practical silviculture, but also important as a general biological problem. Among the objects of attention of breeders, a special place is occupied by cone-bearing species such as Siberian stone pine. Its cultivation through the forest tree plantations for wood and for cone-bearing will allow in the future to reduce the damage for natural ecosystems significantly. The purpose of this work was to analyze the structure of diversity in growth and generative development of the Siberian stone pine crown on a specially created plantation, where a low level of natural selection makes it possible to more efficiently select for early reproduction, growth and seed productivity. This plantation is located in the south of the area (Western Siberia, south of Tomsk region). It was created from stone pine seeds of the local population, that were sown in 1977 as forest crops with standard density (0,75 х 3 м). At the age of 10, they were planted out at a distance of 8 x 8 m. The vegetative and generative development of 89 trees aged 40 years was analyzed. We used a retrospective method that allows reconstructing of the tree organogenesis and growth on the scars on the bark of the shoots. The start of sexual reproduction has been reconstructed; a comparative characteristic of the vegetative and generative development of the tree crown has been carried out. The results show that, in general, the initial idea of the dependence of the efficiency of selection on the conditions in which the trees were formed is confirmed. In the natural dense stands, many of the leader trees in cone-bearing, which we found in our study, could fall behind due to slow growth and did not live to reproductive age. On the plantation where sparse tree planting was applied, they survived and became the leaders in cone-bearing. Early start of reproduction, even under conditions of sparse tree planting, is positively correlated with the growth rate in the pre-generative period of ontogenesis (r = + 0.65). The level of variations in the generative development of trees was much higher than in the vegetative one. The abundance of male shoots in the crown and the relative length of the male generative zone of crown were determined primarily by the height of the trees. On the contrary, the active growth of the tree in height did not have a noticeable influence on the development of the female shoots and the female generative zone of crown. Contrasting differences in the traits of male and female crown development with growth traits are very interesting result, in our opinion. Tall trees with a narrow crown are most promising for pollen productivity breeding, since they have a longer male generative zone and because of this they have more male shoots in the crown. Trees with a broad crown are promising for seed production breeding. Although seed productivity is not in all cases a direct function of the size of the crown, but depends on the specific genotype of the tree. This is confirmed by the fact that in each group (high, medium and low trees) there are individuals of high-cone-bearing and low-cone-bearing, which is promising for seed production breeding in groups of different growth levels. Using the calculated relative traits «1 m2 of the area of the horizontal projection of the crown onto the ground surface» made it possible to select the best trees for seed production (combining the minimum size of the crown with the number of cones per unit area of the crown) and growth (combining greater height and narrow crown).For citation: Velisevich S.N., Popov A.V. Pattern of diversity in the vegetative and generative crown structure of the siberian stone pine on a seed orchard with sparse tree planting. Lesnoy Zhurnal [Forestry Journal], 2019, no. 5, pp. 35–47. DOI: 10.17238/issn0536-1036.2019.5.35Funding: This work is supported by the Russian Science Foundation under grant no. 18-16-00058. The article is published within the framework of implementation of the scientific journals development program in 2019, based on proceedings of XIX International conference of the young scholars “Forests of Euro-Asia – The Southern Ural” (August 25-30, 2019. Chelyabinsk).

Seed Predators, not Herbivores, Exert Natural Selection on Solidago spp. in an Urban Archipelago.

The effects of urbanization on biodiversity are well established, as a growing city will reduce the size and diversity of patches of native plants. Recolonization of old patches and discovery of new ones by arthropod herbivores should occur as predicted by island biogeography theory. Although colonization represents an increase in biodiversity, such arrivals may exert new forms of natural selection on plants through herbivory and seed predation. Using a single species of old-field aster (Solidago altissima L.), we found that the level of natural selection by seed predators and herbivores follows patterns of island biogeography, with lower amounts of damage on smaller islands, where there are fewer species, and hypothetically smaller populations of arthropods. We also found that in an urban system, levels of herbivory are far below the tolerance levels of Solidago, and that seed predators are likely to be the only arthropod to cause reduced fitness. The pattern seen also implies that as a patch of Solidago grows through clonal expansion, it will come under higher selective pressure.

Changes in blister rust infection and mortality in whitebark pine over time

Whitebark pine (Pinus albicaulis Engelm.), a keystone species in subalpine ecosystems of western North America, is under threat across its range from white pine blister rust, mountain pine beetle, fire exclusion, and climate change. Loss of whitebark pine is predicted to have cascading effects on many ecosystem services. We remeasured 115 whitebark pine plots in the Canadian Rocky Mountains to determine whether infection and mortality rates from blister rust were changing over time and (or) latitude. Average rust infection of trees among plots increased from 42% in 2003–2004 to 52% in 2009, while mortality increased from 18% to 28%. In eight plots that have been measured three times, infection increased from 43% of live trees in 1996 to 70% in 2003 and 78% in 2009. Mortality increased from 26% to 65% in the same time period. Overall, infection and mortality have increased 3%/year over the 13 years of the study. Incidence of infection and mortality was highest among plots in the southern part of the study area, particularly on the western side of the Continental Divide. The slowing rates of infection and mortality that we found suggest that some level of natural selection may already be occurring in areas with high levels of both.

Confounding between recombination and selection, and the Ped/Pop method for detecting selection

In recent years, there have been major developments of population genetics methods to estimate both rates of recombination and levels of natural selection. However, genomic variants subject to positive selection are likely to have arisen recently and, consequently, had less opportunity to be affected by recombination. Thus, the two processes have an intimately related impact on genetic variation, and inference of either may be vulnerable to confounding by the other. We illustrate here that even modest levels of positive selection can substantially reduce population-based recombination rate estimates. We also show that genome-wide scans to detect loci under recent selection in humans have tended to highlight loci in regions of low recombination, suggesting that confounding by recombination rate may have reduced the power of these studies. Motivated by these findings, we introduce a new genome-wide approach for detecting selection, based on the ratio of pedigree-based to population-based estimates of recombination rate. Simulations suggest that our "Ped/Pop" method, which is designed to capture completed sweeps, has good power to discriminate between neutral and adaptive evolution. Unusually for a multimarker method, our approach performs well in regions of high recombination and also has good power for many generations after the fixation of an advantageous variant. We apply the method to human HapMap and Perlegen data sets, finding confirmation of reported candidates as well as identifying new loci that may have undergone recent intense selection.

Comparing Patterns of Natural Selection across Species Using Selective Signatures

Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell.

European Mathematical Genetics Meeting, Heidelberg, Germany, 12th–13th April 2007

European Mathematical Genetics Meeting, Heidelberg, Germany, 12^th–13^th April 2007

Natural selection of asymmetric traits operates at multiple levels

natural selection of asymmetric traits operates at multiple levels. some asymmetric traits (like having a dominant eye) are tied to more universal aspects of the environment and are coded genetically, while others (like pedestrian turning biases) are tied to more ephemeral patterns and are largely learned. species-wide trends of asymmetry can be better modeled when different levels of natural selection are specified.

Natural Selection During Functional Divergence to LMP7 and Proteasome Subunit X (PSMB5) Following Gene Duplication

The LMP7 and PSMB5 genes were created through an ancient gene duplication event of their ancestral locus. These proteins contain an active site of proteolysis, and LMP7 replaces PSMB5 as a component of the 20S proteasome after stimulation of cells by interferon-gamma. Replacement of PSMB5 by LMP7 changes the profile of the products of 20S proteasome processing, predisposing digested peptides for transport to and display by the immune system. The purpose of this study is to investigate evolutionary forces influencing functional divergence between LMP7 and PSMB5 following duplication. Levels of synonymous and nonsynonymous substitution rates are estimated to infer differences in levels of natural selection. Estimates of substitution rates indicate that natural selection elevated rates of nonsynonymous substitution in LMP7 following gene duplication, whereas PSMB5 experienced an increase in substitution rate that was not likely due to diversifying natural selection following duplication. Following initial divergence, nearly neutral mutations have dominated gene evolution in both lineages. The LMP7 gene locus provides a rare example of a protein with specialized function arising from duplication and divergence of a housekeeping protein by way of natural selection.

Maladaptation and phenotypic mismatch in cultured Atlantic salmon used for stocking

Compared to wild populations, cultured Atlantic salmon often sustain higher mortality rates and lower adult return rates when stocked as juveniles into natural streams. The ultimate causes for such differences in fitness, however, are not clear. Here we tested if relaxed levels of natural selection and improved survival in the hatchery environment could account for the observed degree of maladaptation among stocked fish. To do this, we assessed the degree of phenotypic mismatch between wild and cultured fish in three populations over five consecutive years. Significant differences were found in several phenotypic traits that are likely to have fitness implications. Thus, if the objective is to mimic wild individuals for restoration purposes, current hatchery practices aimed at maximising juvenile survival and enhancing growth may need to be revised.

A Novel Genetic Algorithm for the Design of a Signed Power-of-Two Coefficient Quadrature Mirror Filter Lattice Filter Bank

A novel genetic algorithm (GA) for the design of a canonical signed power-of-two (SPT) coefficient lattice structure quadrature mirror filter bank is presented in this paper. Genetic operations may render the SPT representation of a value noncanonical. In this paper, a new encoding scheme is introduced to encode the SPT values. In this new scheme, the canonical property of the SPT values is preserved under genetic operations. Additionally, two new features that drastically improve the performance of our GA are introduced. (1) An additional level of natural selection is introduced to simulate the effect of natural selection when sperm cells compete to fertilize an ovule; this dramatically improves the offspring survival rate. A conventional GA is analogous to intracytoplasmic sperm injection and has an extremely low offspring survival rate, resulting in very slow convergence. (2) The probability of mutation for each codon of a chromosome is weighted by the reciprocal of its effect. Because of these new features, the performance of our new GA outperforms conventional GAs.