Genetic structure of lake and stream populations in a Pyrenean amphibian (Calotriton asper) reveals evolutionary significant units associated with paedomorphosis

Differences in environmental conditions such as those between lakes and streams can produce phenotypic variation and ultimately promote evolutionary diversification. Some species of newts and salamanders can occupy these habitats and express alternative phenotypes: metamorphs that lose gills at metamorphosis and paedomorphs that retain them at the adult stage. Whereas this process is facultative in some species, it is obligatory in others, thus suggesting that isolation and environmental pressures may have canalized developmental pathways. In this study, we focused our research on the Pyrenean brook newt, Calotriton asper, which is present in both lakes and streams, but whose fully aquatic paedomorphic individuals are only present in lakes. We aimed to determine the genetic structure and differentiation of two paedomorphic populations, including their surrounding stream and lake metamorphic populations, to test whether populations of paedomorphs can constitute evolutionary significant units. Although gene flow was identified between lakes and nearby stream populations, there was a low percentage of dispersers, and the paedomorphic populations were genetically differentiated from the populations of metamorphs. It is likely that the studied lakes have offered peculiar conditions that have allowed the development of a paedomorphic phenotype. These populations and phenotypes therefore constitute good models to understand local adaptations. As each of these populations of paedomorphs can be considered evolutionary significant units that cannot be replaced by other nearby populations in case of a population crash, conservation actions should be focused directly on them.     

BREAKDOWN OF DIOECY: MODELS WHERE MALES ACQUIRE COSEXUAL FUNCTIONS

We have reanalyzed models of the breakdown of dioecy involving modified males to investigate female frequencies in the resulting gynodioecious populations. We extend and simplify previous treatments to deal with biologically relevant factors including pollen limitation, partial selfing of modified males, and inbreeding depression, to highlight the different empirically detectable advantages that may be gained by modified males that can reproduce as cosexes (i.e., can produce some seeds); these include “inconstant males,” which can sometimes display some female function. Males reproducing wholly or occasionally as cosexual phenotypes can gain the transmission advantage of selfing, if partial self‐fertilization is possible, and from reproductive assurance when pollen is limiting. If, because of resource limitation, such cosexual phenotypes produce fewer ovules than females, their nonselfed ovules will require a lower pollen pool size for full seed‐set, compared with females. We investigate the conditions for these benefits to allow modified males to invade dioecious populations. Sometimes, such invasion leads to replacement of dioecy by the cosexual type, but sometimes the breakdown populations remain sexually polymorphic. When competition occurs between genotypes in the pollen load on a flower, high female frequencies can arise when Y chromosome‐bearing pollen competes poorly with X pollen.     

Epialleles via DNA methylation: consequences for plant evolution

In plants, naturally occurring methylation of genes can affect the level of gene expression. Variation among individuals in the degree of methylation of a gene, termed epialleles, produces novel phenotypes that are heritable across generations. To date, ecologically important genes with methylated epialleles have been found to affect floral shape, vegetative and seed pigmentation, pathogen resistance and development in plants. Currently, the extent to which epiallelic variation is an important common contributor to phenotypic variation in natural plant populations and its fitness consequences are not known. Because epiallele phenotypes can have identical underlying DNA sequences, response to selection on these phenotypes is likely to differ from expectations based on traditional models of microevolution. Research is needed to understand the role of epialleles in natural plant populations. Recent advances in molecular genetic techniques could enable population biologists to screen for epiallelic variants within plant populations and disentangle epigenetic from more standard genetic sources of phenotypic variance, such as additive genetic variance, dominance variance, epistasis and maternal genetic effects.     

Metabolic,ethnic, constitutional specificity of antibacterial immunity

Constitutional antibacterial immunity in different ethnic groups (populations) may be related to their genetically determined metabolic status—phenotypes of enzymatic reactions of metabolization (biotransformation) of xenobiotics—and expressed to different degrees depending on the frequency of the carriers of these phenotypes in populations; i.e., it may be ethnic-specific. The probability of the presence in different populations of the association of constitutional immunity to brucellosis, tuberculosis, and cholera with the oxidation and/or N-acetylation status, i.e., the ethnic dependence of the immunity, has been theoretically shown. Three variants of this dependence are presented. For revealing the ethnic dependence of constitutional immunity and predicting ethnic predisposition to bacterial infections, we need the “metabolic ethnic immunological data register” of the population. The results of such a study can be used in immunology for the assessment of the manifestation of metabolic ethnic constitutional antibacterial immunity and in epidemiology for the assessment of epidemiological situations in countries with the corresponding ethnic composition.     

Class II antigen-specific murine cytolytic T lymphocytes (CTL). I. Analysis of bulk populations and establishment of Lyt-2+L3T4- and Lyt-2-L3T4+ bulk CTL lines

Murine allogeneic cytolytic T lymphocytes (CTLs), including long-term bulk CTL lines, were induced in I-region-incompatible combinations of strains in vitro in order to study the phenotypes of class II major histocompatibility complex (MHC) antigen-specific CTLs, as well as the possible functional involvement of accessory cell interaction molecules such as Lyt-2 and L3T4. This report shows that class II-specific allogeneic CTL populations consist of two types of T cells. Lyt-2+L3T4- (2+4-) and Lyt-2-L3T4+ (2-4+), in variable proportions depending on the strain combination, that in vitro bulk CTL lines with each of these phenotypes can be established, that the killing function of 2-4+ CTL is sensitive to the blocking effect of anti-L3T4 antibodies, suggesting functional involvement of this molecule in the CTL-target interaction, that anti-Lyt-2 antibodies fail to block killing by 2+4- cells, suggesting that such CTLs do not utilize this molecule in their killing function, and that while I-A-specific CTLs of both phenotypes are detectable, 2-4+ cells could not be detected among I-E-specific CTL populations.     

Genomics,environment and balancing selection in behaviourally bimodal populations: The caribou case

Selection forces that favour different phenotypes in different environments can change frequencies of genes between populations along environmental clines. Clines are also compatible with balancing forces, such as negative frequency‐dependent selection (NFDS), which maintains phenotypic polymorphisms within populations. For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioural trait prominent in species where only a fraction of the population seasonally migrates. Overall, NFDS is believed to be a common phenomenon in nature, yet a scarcity of studies were published linking naturally occurring allelic variation with bimodal or multimodal phenotypes and balancing selection. We applied a Pool‐seq approach and detected selection on alleles associated with environmental variables along a North–South gradient in western North American caribou, a species displaying partially migratory behaviour. On 51 loci, we found a signature of balancing selection, which could be related to NFDS and ultimately the maintenance of the phenotypic polymorphisms known within these populations. Yet, remarkably, we detected directional selection on a locus when our sample was divided into two behaviourally distinctive groups regardless of geographic provenance (a subset of GPS‐collared migratory or sedentary individuals), indicating that, within populations, phenotypically homogeneous groups were genetically distinctive. Loci under selection were linked to functional genes involved in oxidative stress response, body development and taste perception. Overall, results indicated genetic differentiation along an environmental gradient of caribou populations, which we found characterized by genes potentially undergoing balancing selection. We suggest that the underlining balancing force, NFDS, plays a strong role within populations harbouring multiple haplotypes and phenotypes, as it is the norm in animals, plants and humans too.     

New approaches to disease mapping in admixed populations

Admixed populations such as African Americans and Hispanic Americans are often medically underserved and bear a disproportionately high burden of disease. Owing to the diversity of their genomes, these populations have both advantages and disadvantages for genetic studies of complex phenotypes. Advances in statistical methodologies that can infer genetic contributions from ancestral populations may yield new insights into the aetiology of disease and may contribute to the applicability of genomic medicine to these admixed population groups.     

Epigenetic memory transmission through mitosis and meiosis in plants

Gene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. The mechanisms that control epigenetic marks have recently been uncovered using model organisms, such as the flowering plant Arabidopsis thaliana. In Arabidopsis, perturbation of epigenetic gene activity often results in heritable developmental phenotypes. Stable, but potentially reversible, changes in epigenetic status can also be sources for phenotypic variations in natural plant populations.     

ADAPTIVE STRATEGIES OF COLONIZING ANIMAL SPECIES

1. An understanding of the adaptive strategies of colonizing animal species depends upon an integration of population genetics and ecology, but behavioural components should not be ignored especially higher in the phylogenetic series than insects. 2. An ecologically marginal habitat from which colonists are derived can be regarded as one in which physical stresses of climatic origin tend to be variable and extreme, so that resources are unpredictable and short lived. Prerequisites for genetic analysis are therefore phenotypes relatable to the r K continuum of adaptive strategies. These can be called ‘ecological phenotypes’. 3. Ecological phenotypes include tolerances to environmental stresses, development time, and resource utilization variability. Such phenotypes enable distinctions to be made between colonizing species and non-colonists. For example, colonizing species have ecological phenotypes incorporating high resistance to physical stress, rapid development time, and the exploitation of an array of food resources. They are ecologically versatile generalists. This includes the use of ethanol as a resource in Drosophila. 4. There is a substantial literature on variation in central and marginal populations based upon gene and chromosome polymorphisms. Most data show a reduction of chromosome polymorphisms and of lethals and semilethals towards the margins, but no equivalent reduction in enzyme polymorphisms. Widespread species tend to have low levels of chromosome polymorphisms as in marginal populations, but enzyme polymorphism levels vary too much among species for meaningful interpretations. Since these are genotypic assessments not directly relatable to the field situation, the somewhat unsatisfactory nature of these data from the interpretative point of view is understandable. In addition, the fundamental issue is not the variability of the genome, but the nature and role of loci controlling ecological phenotypes. 5. Ecological phenotypes can be analyzed at the population level with isofemale strains as the starting material. In theory, genetic activity can then be localized to the chromosomal and even genic levels in a species such as D. melanogaster. Isofemale strain studies in D. melanogaster are interpretable in terms of the r K continuum, and so reflect adaptive strategies in nature. 6. It is highly likely that the genetic architecture of ecological phenotypes of marginal populations mainly comprises a few additive genes of relatively large effect. This is an architecture permissive of rapid adaptation to new habitats, provided that the appropriate genes are present. Discussions of speciation via the founder principle, a colonization event in itself, have invoked a similar explanation.     

Spatio-temporal dynamics of alternative male phenotypes in coho salmon populations in response to ocean environment

1. The coexistence of alternative reproductive phenotypes will probably be shaped by spatial and temporal variability in the environment. However, the effects of such variability on coexistence and the scale at which it operates are seldom understood. 2. To quantify such effects, we examined spatial and temporal dynamics in the abundance and frequency of alternative phenotypes of male coho salmon, Oncorhynchus kisutch Walbaum, which mature as either large fighters (age-3 'hooknoses') or small sneakers (age-2 'jacks'). Using over 20 years of data on coded-wire tagged fish released from nine Oregon hatcheries, we tested for the effects of ocean environment independent of those due to freshwater rearing. 3. Annual fluctuations of the abundance of jack and hooknose males within populations were correlated strongly by brood year (cohort) but not by return year (breeding group). This occurred independently of significant effects of release practice (i.e. the number of fish released, body size at release and date of release), indicating that a synchronized fluctuation in mortality during the first year at sea was the predominant cause. As a result, the annual frequency of the alternative phenotypes at breeding varied considerably within populations. 4. Spatial patterns in the annual fluctuations of the two phenotypes were similar (i.e. synchronous among populations), except that jacks showed local spatial structure (decreased synchrony with distance) not evident among hooknoses. This suggests that oceanic processes affecting the two phenotypes operate at different spatial scales. Despite effects on salmon abundance, the ocean environment had little influence through its effects on salmon growth on the relative frequencies of the alternative phenotypes within and among populations. 5. The results provide insight into the evolutionary dynamics of alternative phenotypes, including an intragenerational time lag that increases annual variability in phenotype frequencies at breeding (return years) and the significance of local freshwater processes, rather than oceanic processes, on phenotype expression. Freshwater processes, such as juvenile growth, timing of migration and breeding competition, operating at evolutionary and intragenerational time-scales, are probably the predominant forces affecting phenotype frequency.     

Fisherian and Wrightian theories of speciation

Fisher's theory of sexual selection, Wright's shifting-balance theory, and recent models based on them are reviewed as mechanisms of animal speciation. The joint evolution of mating preferences and secondary sexual characters can cause rapid nonadaptive phenotypic divergence and premating isolation between geographically separated populations, or along a cline. Extensive comparative data on Drosophila species support the suggestion of R. A. Fisher and T. Dobzhansky that the evolution of mating preferences can reinforce partial postmating isolation between sympatric populations. The interaction of natural selection and random genetic drift in local populations with a small effective size can produce a rapid transition between relatively stable phenotypes separated by an adaptive valley, or between chromosomal rearrangements with a heterozygote disadvantage. Large demographic fluctuations, such as frequent random local extinction and colonization, are required for the rapid spread of new adaptations (or karyotypes) when intermediate phenotypes (or rearrangement heterozygotes) are selected against.     

Sex ratio variation in gynodioecious Lobelia siphilitica: effects of population size and geographic location

Variation in population sex ratio can be influenced by natural selection on alternate sex phenotypes as well as nonselective mechanisms, such as genetic drift and founder effects. If natural selection contributes to variation in population sex ratio, then sex ratio should covary with resource availability or herbivory. With nonselective mechanisms, sex ratio should covary with population size. We estimated sex ratio, resource availability, herbivory and size of 53 populations of gynodioecious Lobelia siphilitica. Females were more common in populations with higher annual temperatures, lower soil moisture and lower predation on female fruits, consistent with sex-specific selection. Females were also more common in small populations, consistent with drift, inbreeding or founder effects. However, small populations occurred in areas with higher temperatures than large populations, suggesting that female frequencies in small populations could be caused by sex-specific selection. Both selective and nonselective mechanisms likely affect sex ratio variation in this gynodioecious species.     

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.     

Female frequencies and fitness components between sex phenotypes among gynodioecious populations of the colonizing species Trifolium hirtum All. in California

Summary Male sterility has been recently discovered in Californian populations of rose clover (Trifolium hirtum). This study describes the frequency distribution of male sterility in Turkish and Californian populations, and compares fitness components of hermaphrodites and females. As male-steriles were found in Turkey, it is likely that they were introduced to California during the 1940's with the original material derived from Turkey. The spread of male-sterile genotypes in California has given rise to an asymmetrical frequency distribution of male sterility with positive skewness. The frequency of females has not exceeded fifty percent and it appears to be temporally stable in most of the Californian populations. The hypothesis that female frequencies and fitness differences between phenotypes are correlated was tested by comparing sex phenotypes in seven populations with contrasting levels of male sterility. The analysis of those populations showed no evidence for such a correlation as no significant differences were found between sex phenotypes for fecundity and seed germination. The hypothesis that females are maintained due to fitness differences in the progeny of hermaphrodites and females was experimentally tested in the population with maximum frequency of male-steriles. The results showed no significant differences in the demographic performance of the progenies of hermaphrodites and females. The present results are discussed in terms of the possible mechanism of maintenance of gynodioecy in rose clover.     

Root architecture,plant size and soil nutrient variation in natural populations of <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Phenotypic variation in ecologically important traits may vary at large and small geographic scales, and may be shaped by natural selection. Here our explicit aim is to evaluate phenotypic differentiation among local populations and examine its relationship with ecological edaphic and climatic features that could lead to local adaptation. We characterized six populations of the model plant Arabidopsis thaliana over 3 years in the field in its native range. At each site, we measured edaphic conditions and aboveground and belowground phenotypes. In addition, we grew plants from the six characterized populations in a common greenhouse along with an additional fifteen populations from the Iberian Peninsula to examine evolutionary and ecological differentiation among populations, and relationships between geographic and ecological distance to phenotypic differences among populations. Significant differences in aboveground and belowground traits, population density, and micro- and macro-nutrient soil concentrations were found among the field populations. In particular, root architectural traits differed significantly among field populations. Complex patterns of ecological differences among population and plant phenotypes emerged when examining edaphic conditions in the Extremadura region, and geographic and climate variables at a broader scale of the Iberian Peninsula. We report levels of phenotypic variation at the local scale comparable to those found at broad geographic scales and report that local edaphic conditions contribute to population-level phenotypic variation in root and shoot traits. To our knowledge, these are the first reports of among population root architectural variation from natural field populations for this model organism. We demonstrate how ecological features, such as soil nutrients, can be associated with the phenotypic variation of A. thaliana measured in natural populations and may contribute to adaptive differentiation at a local scale.     

Genetic architecture of survival and fitness-related traits in two populations of Atlantic salmon

The additive genetic effects of traits can be used to predict evolutionary trajectories, such as responses to selection. Non-additive genetic and maternal environmental effects can also change evolutionary trajectories and influence phenotypes, but these effects have received less attention by researchers. We partitioned the phenotypic variance of survival and fitness-related traits into additive genetic, non-additive genetic and maternal environmental effects using a full-factorial breeding design within two allopatric populations of Atlantic salmon (Salmo salar). Maternal environmental effects were large at early life stages, but decreased during development, with non-additive genetic effects being most significant at later juvenile stages (alevin and fry). Non-additive genetic effects were also, on average, larger than additive genetic effects. The populations, generally, did not differ in the trait values or inferred genetic architecture of the traits. Any differences between the populations for trait values could be explained by maternal environmental effects. We discuss whether the similarities in architectures of these populations is the result of natural selection across a common juvenile environment.     

On the standardization of fitness and traits in comparative studies of phenotypic selection

Comparisons of the strength and form of phenotypic selection among groups provide a powerful approach for testing adaptive hypotheses. A central and largely unaddressed issue is how fitness and phenotypes are standardized in such studies; standardization across or within groups can qualitatively change conclusions whenever mean fitness differs between groups. We briefly reviewed recent relevant literature, and found that selection studies vary widely in their scale of standardization, but few investigators motivated their rationale for chosen standardization approaches. Here, we propose that the scale at which fitness should be relativized should reflect whether selection is likely to be hard or soft; that is, the scale at which populations (or hypothetical populations in the case of a contrived experiment) are regulated. We argue that many comparative studies of selection are implicitly or explicitly focused on soft selection (i.e., frequency and density‐dependent selection). In such studies, relative fitness should preferably be calculated using within‐group means, although this approach is taken only occasionally. Related difficulties arise for the standardization of phenotypes. The appropriate scale at which standardization should take place depends on whether groups are considered to be fixed or random. We emphasize that the scale of standardization is a critical decision in empirical studies of selection that should always warrant explicit justification.     

Molecular polymorphism distribution in phenotypically distinct populations of wine yeast strains.

Electrophoretic karyotyping and mitochondrial DNA restriction analysis were used to analyze natural yeast populations from fermenting musts in El Penedès, Spain. Both analyses revealed a considerable degree of polymorphism, indicating heterogeneous natural populations. By specifically designed genetic selection protocols, strains showing potentially interesting phenotypes, such as high tolerance to ethanol and temperature or the ability to grow and to ferment in wine-water-sugar mixtures, were isolated from these natural populations. Genetic analysis showed a strong correlation between the selected phenotypes and mitochondrial DNA polymorphisms. Karyotype analysis revealed several genetically similar yeast lineages in the natural yeast microflora, which we interpret as genetically isolated subpopulations of yeast strains with distinct genetic traits, which may correspond to specific microenvironments. Thus, molecular polymorphism analysis may be useful not only to study the geographical distribution of natural yeast strains but also to identify strains with specific phenotypic properties.     

Color vision pigment frequencies in wild tamarins (Saguinus spp.)

The adaptive importance of polymorphic color vision found in many New World and some prosimian primates has been discussed for many years. Polymorphism is probably maintained in part through a heterozygote advantage for trichromatic females, as such individuals are observed to have greater foraging success when selecting ripe fruits against a background of forest leaves. However, recent work also suggests there are some situations in which dichromatic individuals may have an advantage, and that variation in color vision among individuals possessing different alleles may also be significant. Alleles that confer a selective advantage to individuals are expected to occur at a higher frequency in populations than those that do not. Therefore, analyzing the frequencies of color vision alleles in wild populations can add to our understanding of the selective advantages of some color vision phenotypes over others. With this aim, we used molecular techniques to determine the frequencies of color vision alleles in 12 wild tamarin groups representing three species of the genus Saguinus. Our results show that allele frequencies are not equal, possibly reflecting different selective regimes operating on different color vision phenotypes.     

Transgressive Hybrids as Hopeful Monsters

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt’s infamous “hopeful monster”. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, “monstrous” phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts “hopeless” monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts “hopeful” monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant “hopeful monsters” will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.