AN INTERPRETATION OF PHENOTYPIC PLASTICITY IN AGROPYRON REPENS (GRAMINAE)

Phenotypic plasticity and genotypic variation were studied in Agropyron repens L. (Beauv.) collected from populations in two grassland communities which differed in the length of time since the last major disturbance. Twenty genotypes were collected from each population. Each genotype was vegetatively propagated, and subjected to six different treatments in a greenhouse. Phenotypic plasticity and genotypic variability were measured as across- and within-treatment standardized variances respectively. Patterns of plasticity were measured by genotype correlations across treatments. The results were presented graphically by the regression method of Garbutt and Zangerl (1983). Analysis of variance revealed significant population, genotype and treatment effects. Significant positive correlations between magnitude and variability of performance were found for all characters. Phenotypic plasticity and magnitude of performance were generally greater in plants collected from the older established field. Evidence for greater specialization in the older population was suggested by negative correlations between performance in the most favorable and least favorable treatments and by greater dissimilarity of genotype response across treatments. A more variable phenotypic response across treatments (i.e., higher plasticity) for plants from the older population may therefore be a consequence of specialization and not an adaptive trait per se.     

Genetic drift and polygenic inheritance

The interaction of random gene drift and selection was studied by computer simulation for two quantitative traits, which were considered to approximate stature and skin color differences in human populations. The expected effects of gene drift, fixation of alleles and reduction of genotypic and phenotypic variances, were found in the simulation. Stabilizing selection, which seems to be the type of selection operating on these traits, was found to increase the effects of gene drift. Since there seems to be no evidence of reduction in phenotypic and presumably genotypic variability in small human populations, the applicability of these simple genetic models to human traits raises problems for which several possible solutions exist.     

Differential selection of baculovirus genotypes mediated by different species of host food plant

Recent studies have demonstrated high levels of genotypic and phenotypic variation in populations of parasites, even within individual hosts. Several genetic, immunological and epidemiological mechanisms have been postulated as promoters of such variation, but little empirical work has addressed the role of host ecology. A nucleopolyhedrovirus that attacks larvae of the pine beauty moth, Panolis flammea , exists as a complex mixture of genotypes within individual host larvae. We demonstrate that the food plant species eaten by the host (Scots pine vs. lodgepole pine) differentially affects the pathogenicity and productivity of two virus genotypes originally purified from a single host individual. We hypothesize that such food plant-mediated differential selection will promote genotypic variation between baculovirus populations, and that subsequent remixing of virus genotypes could maintain genotypic variation within individual hosts. Our results provide a tritrophic explanation for the genotypic and phenotypic complexity of host–parasite interactions with complex ecologies.     

Correlation between male and female reproduction in the subdioecious herb Astilbe biternata (Saxifragaceae)

Genotypic trade-offs between male and female reproduction are commonly assumed in theoretical studies of the evolution of gender specialization. Although these trade-offs are supported by higher seed production of females than hermaphrodites in natural populations of gynodioecious species, comparisons between male and female reproductive allocation among hermaphrodite individuals under controlled conditions are rare. We assessed phenotypic and genotypic correlations between stamen and fruit production in fruiting males of the near-dioecious herb Astilbe biternata. In the field, we found a significant negative phenotypic correlation between stamen production and fruit production within individuals that produced both stamens and fruit as well as higher fruit set in females than fruiting males. The negative correlation between fruit and stamen production that was observed in the field was also apparent across clonally propagated genotypes. These results suggest that negative genetic correlations between male and female reproduction may limit the independent evolution of fruit and stamen production in A. biternata.     

Testing specialization hypothesis on a stress gradient

Specialization can allow plants to perform well in their home environments at the expense of poor performance in other habitats. A great difference in performance across habitats is observed as high phenotypic plasticity in performance traits and a by‐product of selection. However, phenotypic plasticity (particularly adaptive plasticity) can be an active response to the selection by allowing the maintenance of performance. Therefore, specialization and adaptive plasticity delineate two opposing strategies. The specialization hypothesis presents a non‐adaptive interpretation of plasticity and predicts that phenotypic plasticity of performance traits is greater in specialization to good habitats, whereas bad habitat specialists express low plasticity in performance traits. We tested the specialization hypothesis using plants adapted to extremely stressful mine‐site habitats (sites with highly acidic soil and heavy metal contamination). Seeds of five herbaceous species were collected from high stress (mine site) and low stress habitats. We established a glasshouse experiment where seedlings from high and low stress habitats were grown under near neutral pH and acid soil treatments. We compared performance trait plasticity (e.g. biomass) from high stress and low stress populations and found that there was no significant difference in performance traits between high and low stress populations across treatments. The overall result did not support the specialization hypothesis. Moreover, our results suggest that the species invaded the mine sites are either extreme generalists or the surrounding populations retain some stress tolerant genotypes that are capable of invading the mine sites.     

Genetic and phenotypic influences on clone-level success and host specialization in a generalist parasite

Studying resource specialization at the individual level can identify factors constraining the evolution of generalism. We quantified genotypic and phenotypic variability among infective stages of 20 clones of the parasitic trematode Maritrema novaezealandensis and measured their infection success and post-infection fitness (growth, egg output) in several crabs and amphipods. First, different clones varied in their infection success of different crustaceans. Second, neither genetic nor phenotypic traits had consistent effects on infection success across all host species. Although the results suggest a relationship between infection success and phenotypic variability, phenotypically variable clones were not better at infecting more host species than less variable ones. Third, genetic and phenotypic traits also showed no consistent correlations with post-infection fitness measures. Overall, we found no consistent clone-level specialization, with some clones acting as specialists and others, generalists. The trematode population therefore maintains an overall generalist strategy by comprising a mixture of clone-level specialists and generalists.     

Evolution of sexual isolation during secondary contact: genotypic versus phenotypic changes in laboratory populations

We monitored the phenotypic and genotypic changes that occur when two behavioral races come into contact in laboratory populations. Drosophila melanogaster from Zimbabwe and nearby regions (Z type) show strong but asymmetric sexual isolation from their cosmopolitan counterparts (M type). Crosses of Z females and M males do not take place readily when other choices are available. At least 15 loci are known to control Z-type mating preferences and performance. By thoroughly mixing the genomes of the two types in laboratory populations, we artificially created maximum secondary contact. Despite the strength of sexual selection favoring Z-type male characters, Z-type behavior is eliminated or greatly diminished in all 12 hybrid populations after only 60 generations. This trend is consistent with the spread of the M-type behavior throughout the world as well as a detailed analysis of fitness components. Surprisingly, in contrast with the phenotypic convergence toward the M-type, genotypic samples broadly covering the genomic regions of mapped behavioral loci show no such trend. The genome appears to be "fine grained," with adjacent loci having different evolutionary dynamics and genealogical histories.     

Spatial distribution of juvenile masu salmon (Oncorhynchus masou) with incongruent genotypic and phenotypic sex in Hokkaido, Japan

To clarify the spatial distribution of masu salmon Oncorhynchus masou with incongruent genotypic and phenotypic sex, we compared the phenotypic sex determined by gonad analysis with the genotypic sex identified by a male-specific genetic marker, Growth hormone pseudogene (GHp), in 584 individuals inhabiting 23 rivers in Hokkaido, Japan. We found that the genotypic sex is different from the phenotypic sex for 39 individuals in 10 rivers. Among them, 35 individuals (89.7?%) were GHp?+?females phenotypically. The opposite feature was noted in the remaining four individuals (10.3?%). This study also revealed that GHp?+?phenotypic females are distributed mainly in the Sea of Japan, whereas GHp- phenotypic male tend to appear in the Sea of Okhotsk. In addition, there was a significant negative correlation between the distance from the Bishabetsu River, where frequency of GHp?+?phenotypic females was the highest, and the frequency of those individuals in each river. These results suggest that the distribution of masu salmon with incongruent genotypic and phenotypic sex would be related to the movement of individuals among the populations and regions.     

Phenotypic plasticity and specialization in clonal versus non-clonal plants: A data synthesis

Reproductive strategies can be associated with ecological specialization and generalization. Clonal plants produce lineages adapted to the maternal habitat that can lead to specialization. However, clonal plants frequently display high phenotypic plasticity (e.g. clonal foraging for resources), factors linked to ecological generalization. Alternately, sexual reproduction can be associated with generalization via increasing genetic variation or specialization through rapid adaptive evolution. Moreover, specializing to high or low quality habitats can determine how phenotypic plasticity is expressed in plants. The specialization hypothesis predicts that specialization to good environments results in high performance trait plasticity and specialization to bad environments results in low performance trait plasticity. The interplay between reproductive strategies, phenotypic plasticity, and ecological specialization is important for understanding how plants adapt to variable environments. However, we currently have a poor understanding of these relationships. In this study, we addressed following questions: 1) Is there a relationship between phenotypic plasticity, specialization, and reproductive strategies in plants? 2) Do good habitat specialists express greater performance trait plasticity than bad habitat specialists? We searched the literature for studies examining plasticity for performance traits and functional traits in clonal and non-clonal plant species from different habitat types. We found that non-clonal (obligate sexual) plants expressed greater performance trait plasticity and functional trait plasticity than clonal plants. That is, non-clonal plants exhibited a specialist strategy where they perform well only in a limited range of habitats. Clonal plants expressed less performance loss across habitats and a more generalist strategy. In addition, specialization to good habitats did not result in greater performance trait plasticity. This result was contrary to the predictions of the specialization hypothesis. Overall, reproductive strategies are associated with ecological specialization or generalization through phenotypic plasticity. While specialization is common in plant populations, the evolution of specialization does not control the nature of phenotypic plasticity as predicted under the specialization hypothesis.     

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.     

Genotypic correlations and QTL correspondence between line per se and testcross performance in sugar beet (Beta vulgaris L.) for the three agronomic traits beet yield,potassium content,and sodium content

The genotypic correlation between line per se and testcross performance is an important quantitative genetic parameter in the design of hybrid breeding programs. The main goal of this survey was to study the association of line per se and testcross performance at the phenotypic and molecular levels by applying multiple-line cross quantitative trait locus (QTL) mapping. We used experimental data from line per se and testcross performance of three segregating sugar beet (Beta vulgaris L.) populations. The segregating progenies were genotyped with 481 single nucleotide polymorphism and 40 simple sequence repeat markers and evaluated in field trials for beet yield as well as potassium and sodium content. We observed a decrease in the genotypic correlations between testcross and line per se performance with increasing complexity of the analyzed trait. This picture was also reflected at a molecular level by the presence of overlapping QTLs. A more detailed analysis of the forces causing low genotypic correlation between line per se and testcross performance could not rule out a possible relevance of epistasis and suggested the presence of masking dominance effects.     

Parallel genotypic adaptation: when evolution repeats itself

Until recently, parallel genotypic adaptation was considered unlikely because phenotypic differences were thought to be controlled by many genes. There is increasing evidence, however, that phenotypic variation sometimes has a simple genetic basis and that parallel adaptation at the genotypic level may be more frequent than previously believed. Here, we review evidence for parallel genotypic adaptation derived from a survey of the experimental evolution, phylogenetic, and quantitative genetic literature. The most convincing evidence of parallel genotypic adaptation comes from artificial selection experiments involving microbial populations. In some experiments, up to half of the nucleotide substitutions found in independent lineages under uniform selection are the same. Phylogenetic studies provide a means for studying parallel genotypic adaptation in non-experimental systems, but conclusive evidence may be difficult to obtain because homoplasy can arise for other reasons. Nonetheless, phylogenetic approaches have provided evidence of parallel genotypic adaptation across all taxonomic levels, not just microbes. Quantitative genetic approaches also suggest parallel genotypic evolution across both closely and distantly related taxa, but it is important to note that this approach cannot distinguish between parallel changes at homologous loci versus convergent changes at closely linked non-homologous loci. The finding that parallel genotypic adaptation appears to be frequent and occurs at all taxonomic levels has important implications for phylogenetic and evolutionary studies. With respect to phylogenetic analyses, parallel genotypic changes, if common, may result in faulty estimates of phylogenetic relationships. From an evolutionary perspective, the occurrence of parallel genotypic adaptation provides increasing support for determinism in evolution and may provide a partial explanation for how species with low levels of gene flow are held together.     

Host‐associated genomic differentiation in congeneric butterflies: now you see it,now you do not

Ecotypic variation among populations may become associated with widespread genomic differentiation, but theory predicts that this should happen only under particular conditions of gene flow, selection and population size. In closely related species, we might expect the strength of host‐associated genomic differentiation (HAD) to be correlated with the degree of phenotypic differentiation in host‐adaptive traits. Using microsatellite and Amplified Fragment Length Polymorphism (AFLP) markers, and controlling for isolation by distance between populations, we sought HAD in two congeneric species of butterflies with different degrees of host plant specialization. Prior work on Euphydryas editha had shown strong interpopulation differentiation in host‐adapted traits, resulting in incipient reproductive isolation among host‐associated ecotypes. We show here that Euphydryas aurinia had much weaker host‐associated phenotypic differentiation. Contrary to our expectations, we detected HAD in Euphydryas aurinia, but not in E. editha. Even within an E. aurinia population that fed on both hosts, we found weak but significant sympatric HAD that persisted in samples taken 9 years apart. The finding of significantly stronger HAD in the system with less phenotypic differentiation may seem paradoxical. Our findings can be explained by multiple factors, ranging from differences in dispersal or effective population size, to spatial variation in genomic or phenotypic traits and to structure induced by past histories of host‐adapted populations. Other infrequently measured factors, such as differences in recombination rates, may also play a role. Our result adds to recent work as a further caution against assumptions of simple relationships between genomic and adaptive phenotypic differentiation.     

Phenotypic diversity,population structure and stress protein-based capacitoring in populations of Xeropicta derbentina,a heat-tolerant land snail species

The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.     

Replicability and recurrence in the experimental evolution of a group I ribozyme

In order to explore the variety of possible responses available to a ribozyme population evolving a novel phenotype, five Tetrahymena thermophila group I intron ribozyme pools were evolved in parallel for cleavage of a DNA oligonucleotide. These ribozyme populations were propagated under identical conditions and characterized when they reached apparent phenotypic plateaus; the populations that reached the highest plateau showed a near 100-fold improvement in DNA cleavage activity. A detailed characterization of the evolved response in these populations reveals at least two distinct phenotypic trajectories emerging as a result of the imposed selection. Not only do these distinct solutions exhibit differential DNA cleavage activity, but they also exhibit a very different correlation with a related, but unselected, phenotype: RNA cleavage activity. In turn, each of these trajectories is underwritten by differing genotypic profiles. This study underscores the complex network of possible trajectories through sequence space available to an evolving population and uncovers the diversity of solutions that result when the process of experimental evolution is repeated multiple times in a simple, engineered system.     

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade‐offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.     

Evolutionary principles for general frequency-dependent two-phenotype models in sexual populations

The evolutionary dynamics in general two-sex two-phenotype frequency-dependent selection models are studied with respect to underlying multi-allele one-locus genetic systems. Two classes of equilibria come into play: genotypic equilibria, with equilibrium allelic frequencies independent of the phenotype, and phenotypic equilibria, which are characterized by equal mean phenotypic fitnesses. The exact conditions for genotypic equilibria to exist and be stable and for phenotypic equilibria to exist and be evolutionarily attractive are examined. Using adequate definitions of mean fitnesses in general contexts of frequency-dependent selection in dioecious populations, we show that two phenotypes, when they can coexist in the population, tend to balance their fitnesses as far as is allowed by the genetic system as more alleles responsible for phenotype determination are introduced into the population.     

Impact of genotyping strategy on the accuracy of genomic prediction in simulated populations of purebred swine

Single-step genomic BLUP (ssGBLUP) has been widely used in genomic evaluation due to relatively higher prediction accuracy and simplicity of use. The prediction accuracy from ssGBLUP depends on the amount of information available concerning both genotype and phenotype. This study investigated how information on genotype and phenotype that had been acquired from previous generations influences the prediction accuracy of ssGBLUP, and thus we sought an optimal balance about genotypic and phenotypic information to achieve a cost-effective and computationally efficient genomic evaluation. We generated two genetically correlated traits (h² = 0.35 for trait A, h² = 0.10 for trait B and genetic correlation 0.20) as well as two distinct populations mimicking purebred swine. Phenotypic and genotypic information in different numbers of previous generations and different genotyping rates for each litter were set to generate different datasets. Prediction accuracy was evaluated by correlating genomic estimated breeding values with true breeding values for genotyped animals in the last generation. The results revealed a negligible impact of previous generations that lacked genotyped animals on the prediction accuracy. Phenotypic and genotypic data, including the most recent three to four generations with a genotyping rate of 40% or 50% for each litter, could lead to asymptotic maximum prediction accuracy for genotyped animals in the last generation. Single-step genomic best linear unbiased prediction yielded an optimal balance about genotypic and phenotypic information to ensure a cost-effective and computationally efficient genomic evaluation of populations of polytocous animals such as purebred pigs.     

PHENOTYPIC VARIATION AND GENOTYPIC DIVERSITY IN A PLANKTONIC POPULATION OF THE TOXIGENIC MARINE DINOFLAGELLATE ALEXANDRIUM TAMARENSE (DINOPHYCEAE)1

Multiple clonal isolates from a geographic population of Alexandrium tamarense (M. Lebour) Balech from the North Sea exhibited high genotypic and phenotypic variation. Genetic heterogeneity was such that no clonal lineage was repeatedly sampled according to genotypic markers specified by amplified fragment length polymorphism (AFLP) and microsatellites. Subsampling of genotypic data from both markers showed that ordination of individuals by pair‐wise genetic dissimilarity indices was more reliable by AFLP (482 biallelic loci) than by microsatellites (18 loci). However, resulting patterns of pair‐wise genetic similarities from both markers were significantly correlated (Mantel test P < 0.005). The composition of neurotoxins associated with paralytic shellfish poisoning (PSP) was also highly diverse among these isolates and allowed clustering of toxin phenotypes based on prevalence of individual toxins. Correlation analysis of pair‐wise relatedness of individual clones according to PSP‐toxin profiles and both genotypic characters failed to yield close associations. The expression of allelochemical properties against the cryptophyte Rhodomonas salina (Wis?ouch) D. R. A. Hill et Wetherbee and the predatory dinoflagellate Oxyrrhis marina Dujard. manifested population‐wide variation of responses in the target species, from no visible effect to complete lysis of target cells. Whereas the high genotypic variation indicates high potential for adaptability of the population, we interpret the wide phenotypic variation as evidence for lack of strong selective pressure on respective phenotypic traits at the time the population was sampled. Population markers as applied here may elucidate the ecological significance of respective traits when followed under variable environmental conditions, thereby revealing how variation is maintained within populations.