Genetic variability in fallow deer, Dama dama L

Summary. Twelve blood proteins and enzymes were tested for polymorphism in a herd of fallow deer, Dama dama L., bred for meat production in Western Germany, to investigate the genetic constitution of the population. Although an enzyme polymorphism was detected (Catalase) for the first time in this species, electrophoretic variation is very low in comparison to other large ungulates. Possible explanations for this finding, such as recent inbreeding and a past genetic bottleneck, are given. The relationship between low genetic variation in biochemical marker systems and fitness is discussed.     

Evolution of balanced genetic polymorphism

Extreme genetic polymorphism maintained by balancing selection (so called because many alleles are maintained in a balance by a mechanism of rare allele advantage) is intimately associated with the important task of self/non-self-discrimination. Widely disparate self-recognition systems of plants, animals and fungi share several general features, including the maintenance of large numbers of alleles at relatively even frequency, and persistence of this variation over very long time periods. Because the evolutionary dynamics of balanced polymorphism are very different from those of neutral genetic variation, data on balanced polymorphism have been used as a novel source for inference of the history of populations. This review highlights the unique evolutionary properties of balanced genetic polymorphism, and the use of theoretical understanding in analysis and application of empirical data for inference of population history. However, a second goal of this review is to point out where current theory is incomplete. Recent observations suggest that entirely novel selective forces may act in concert with balancing selection, and these novel forces may be extremely potent in shaping genetic variation at self-recognition loci.     

A molecular isolation mechanism associated with high intra-specific diversity in rice

High levels of inter-specific diversity are expected due to genetic isolation, the reproductive or geographical barriers, which lead to the accumulation of nucleotide variation. However, high levels of genetic variation are repeatedly observed even within species, notably at loci of the human major histocompatability complex and of plant resistance genes. Are molecular isolations responsible for the high intra-specific variation? To address this issue, we performed a genome-wide survey of the relationship between the possible factors that could cause genetic isolation, and the level of polymorphism, based on two rice genome comparisons. Here, we show that the levels of polymorphism in rice genes are positively correlated with the proportions of non-alignable flanking sequences, and that the correlation is observed even in single-copy genes. The physical locations of the genes were also investigated, and a strong association between the asymmetric architecture of genomes and the levels of polymorphism was revealed. These results suggest that the flank heterogeneity and the asymmetric architecture between genomes serve as isolation mechanisms at the molecular level that result in accumulation of higher genetic variation. This mechanism is of fundamental importance to understand natural genetic variation within species.     

A sex-linked locus controls wing polymorphism in males of the pea aphid,Acyrthosiphon pisum (Harris)

Discrete variation in wing morphology is a very common phenomenon in insects and has been used extensively in the past 50 years as a model to study the ecology and evolution of dispersal. Wing morph determination can be purely genetic, purely environmental, or some combination of the two. The precise genetic determinants of genetically based wing morph variation are unknown. Here we explore the genetic basis of wing polymorphism in the pea aphid, which can produce either winged or wingless males. We confirm that three types of pea aphid clones coexist in natural populations, those producing winged males only, those producing wingless males only, and those producing a mixture of both. A Mendelian genetic analysis reveals that male wing polymorphism in pea aphids is determined by a single locus, two alleles system. Using microsatellite loci of known location, we show that this locus is on the X chromosome. The existence of a simple genetic determinism for wing polymorphism in a system in which genetic investigation is possible may help investigations on the physiological and molecular mechanisms of genetically-based wing morph variation. This locus could also be used in the search for genes involved in the wing polyphenism described in parthenogenetic females and to investigate the interplay between polymorphisms and polyphenisms.     

Variation in female mate choice within guppy populations: population divergence,multiple ornaments and the maintenance of polymorphism

The evolutionary significance of variation in mate choice behaviour is currently a subject of some debate and considerable empirical study. Here, I review recent work on variation within and among guppy (Poecilia reticulata) populations in female mate choice and mating preferences. Empirical results demonstrate that there is substantial variation within and among populations in female responsiveness and choosiness, and much of this variation is genetic. Evidence for variation in preference functions also exists, but this appears to be more equivocal and the relative importance of genetic variation is less clear cut. In the second half of this review I discuss the potential significance of this variation to three important evolutionary issues: the presence of multiple male ornaments, the maintenance of polymorphism and divergence in mate recognition among populations. Studies of genetic variation in mate choice within populations indicate that females have complex, multivariate preferences that are able to evolve independently to some extent. These findings suggest that the presence of multiple male ornaments may be due to multiple female mating preferences. The extreme polymorphism in male guppy colour patterns demands explanation, yet no single satisfactory explanation has yet emerged. I review several old ideas and a few new ones in order to identify the most promising potential explanations for future empirical testing. Among these are negative frequency dependent selection, environmental heterogeneity coupled with gene flow, and genetic constraints. Last, I review the relative extent of within and among-population variation in mate choice and mating preferences in order to assess why guppies have not speciated despite a history of isolation and divergence. I argue that variation within guppy populations in mate choice and enhanced mating success of new immigrants to a pool are major impediments to population divergence of the magnitude that would be required for speciation to occur.     

Polymorphism in Genes That Influence Sperm Displacement

Paternity of offspring of multiply inseminated females is in many organisms highly skewed, with an advantage generally going to the male that most recently mated. Variation in sperm competitive ability can result in strong natural selection, and one expects that a gene that offers an advantage in sperm displacement would, all else being equal, be rapidly fixed, leaving low equilibrium levels of variability in sperm competition. However, empirical studies have demonstrated genetic variation in sperm displacement, begging the question of how this variation can be maintained. Here we develop a population genetic model to find conditions that maintain polymorphism in alleles that influence sperm displacement. We consider a one-locus model in which allelic variants have pleiotropic effects on fecundity and mating ability in addition to sperm displacement. This model can admit more than one stable polymorphism, and we find conditions for protected polymorphism. Induced overdominance is not necessary for stable polymorphism. These results have direct bearing on the observed variation in the ability of resident sperm to defend against displacement.     

Spatiotemporal environmental heterogeneity and the maintenance of the tailspot polymorphism in the variable platyfish (Xiphophorus variatus)

Genetic variation is critical for adaptive evolution. Despite its importance, there is still limited evidence in support of some prominent theoretical models explaining the maintenance of genetic polymorphism within populations. We examined 84 populations of Xiphophorus variatus, a livebearing fish with a genetic polymorphism associated with physiological performance, to test: (1) whether niche differentiation explains broad‐scale maintenance of polymorphism, (2) whether polymorphism is maintained among populations by local adaptation and migration, or (3) whether heterogeneity in explicit environmental variables could be linked to levels of polymorphism within populations. We found no evidence of climatic niche differentiation that could generate or maintain broad geographic variation in polymorphism. Subsequently, hierarchical partitioning of genetic richness and partial mantel tests revealed that 76% of the observed genetic richness was partitioned within populations with no effect of geographic distance on polymorphism. These results strongly suggest a lack of migration‐selection balance in the maintenance of polymorphism, and model selection confirmed a significant relationship between environmental heterogeneity and genetic richness within populations. Few studies have demonstrated such effects at this scale, and additional studies in other taxa should examine the generality of gene‐by‐environment interactions across populations to better understand the dynamics and scale of balancing selection.     

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.     

Genetic variation affecting host-parasite interactions: different genes affect different aspects of sigma virus replication and transmission in Drosophila melanogaster

In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.     

Why is there so much genetic variation for wing dimorphism?

Wing dimorphism appears in general to be determined either by a single locus, 2 allele system in which brachyptery is dominant, or by the additive action of numerous loci. In the latter case studies indicate that the heritability is typically quite large. It is generally postulated that wing dimorphism is under strong selection: why then is genetic variation not eroded? In this paper I consider three possible explanations. First, genetic variation may not be exposed to selection because environmental heterogeneity effectively makes heritability zero. Because wing dimorphisms are known to evolve it seems unlikely that this is the primary factor. Second, directional selection on a threshold trait may push the population almost to monomorphism but erodes genetic variance at a very slow rate. This mechanism cannot preserve variation but makes it possible for other factors to more easily maintain variability. Finally, I demonstrate that in a heterogeneous environment spatio-temporal variation in fitness will itself maintain a genetic polymorphism for wing dimorphism.     

GxG epistasis in growth and condition and the maintenance of genetic polymorphism in Gambusia holbrooki

Theory on indirect genetic effects (IGEs) indicates that variation in the genetic composition of social groups can generate GxG epistasis that may promote the evolution of stable polymorphisms. Using a livebearing fish with a genetic polymorphism in coloration and associated behavioral differences, we tested whether genotypes of social partners interacted with focal individual genotypes to influence growth and condition over 16 weeks of development. We found that IGEs had a significant influence on patterns of feeding, regardless of focal fish genotype. There was no influence of social environment on juvenile length, but there was significant GxG epistasis for body condition. Each focal juvenile was in better condition when its own genotype was not present in adult social partners. These data are consistent with negative frequency‐dependent selection in which each morph performs better when it is rare. Neither variation in feeding nor activity‐related behaviors explained variation in body condition, suggesting that GxG epistasis for condition was caused by physiological differences between the two genotypes. These findings indicate that GxG epistasis in a given polymorphism can generate fitness landscapes that contribute to the maintenance of that polymorphism and to maintenance of genetic variation for additional fitness‐related traits.     

苎麻叶绿体SSR引物筛选及分析

叶绿体微卫星标记为单亲遗传(除部分裸子植物外),有独立的进化路线,它在植物遗传多样性、群体遗传结构、系统发育分析及杂种鉴定等研究上用途广泛,是研究谱系地理的有效手段。苎麻的主产地和主要分布区均在我国,但其谱系地理研究目前尚未见有报道。该研究选择来自全国不同地区的52个苎麻样本,利用聚丙烯酰胺凝胶电泳法,在23对已知通用叶绿体SSR引物中筛选出适用于苎麻谱系地理研究的SSR引物,并利用筛选到的多态引物对52个苎麻样本进行聚类分析和单倍型网络图分析。结果表明:从23对通用引物中共筛选出16对适用于苎麻的多态引物,其平均多态信息含量为0.1053,虽然以上引物多态性较低,但能够用于野生苎麻的遗传分析研究;这52个苎麻样本聚为10支,分为8个单倍型,初步分析表明叶绿体SSR遗传变异速率较慢,不适用于苎麻种内的系统发育研究,但以上引物能够检测苎麻种内单倍型变异,可用于苎麻的谱系地理研究。     

Non-gradual variation in colour morphs of the strawberry poison frog Dendrobates pumilio: genetic and geographical isolation suggest a role for selection in maintaining polymorphism

The relative roles that geographical isolation and selection play in driving population divergence remain one of the central questions in evolutionary biology. We approached this question by investigating genetic and morphological variation among populations of the strawberry poison frog, Dendrobates pumilio, in the Bocas del Toro archipelago, Panama. We found significant population genetic structure and isolation by distance based on amplified fragment length polymorphism markers. Snout vent length (SVL), coloration and the extent and size of dorsal black spots showed large variation among the studied populations. Differences in SVL correlated with genetic distance, whereas black spot patterns and other coloration parameters did not. Indeed, the latter characters were observed to be dramatically different between contiguous populations located on the same island. These results imply that neutral divergence among populations may account for the genetic patterns based on amplified fragment length polymorphism markers and SVL. However, selective pressures need to be invoked in order to explain the extraordinary variation in spot size and coverage, and coloration. We discuss the possibility that the observed variation in colour morphs is a consequence of a combination of local variation in both natural selection on an aposematic signal towards visual predators and sexual selection generated by colour morph-specific mate preferences.     

Microsatellite variation and recombination rate in the human genome

Background (purifying) selection on deleterious mutations is expected to remove linked neutral mutations from a population, resulting in a positive correlation between recombination rate and levels of neutral genetic variation, even for markers with high mutation rates. We tested this prediction of the background selection model by comparing recombination rate and levels of microsatellite polymorphism in humans. Published data for 28 unrelated Europeans were used to estimate microsatellite polymorphism (number of alleles, heterozygosity, and variance in allele size) for loci throughout the genome. Recombination rates were estimated from comparisons of genetic and physical maps. First, we analyzed 61 loci from chromosome 22, using the complete sequence of this chromosome to provide exact physical locations. These 61 microsatellites showed no correlation between levels of variation and recombination rate. We then used radiation-hybrid and cytogenetic maps to calculate recombination rates throughout the genome. Recombination rates varied by more than one order of magnitude, and most chromosomes showed significant suppression of recombination near the centromere. Genome-wide analyses provided no evidence for a strong positive correlation between recombination rate and polymorphism, although analyses of loci with at least 20 repeats suggested a weak positive correlation. Comparisons of microsatellites in lowest-recombination and highest-recombination regions also revealed no difference in levels of polymorphism. Together, these results indicate that background selection is not a major determinant of microsatellite variation in humans.     

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP

We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.     

Microsatellite evidence for obligate autogamy,but abundant genetic variation in the herbaceous monocarp Lobelia inflata (Campanulaceae)

Although high levels of self‐fertilization (>85%) are not uncommon in nature, organisms reproducing entirely through selfing are extremely rare. Predominant selfers are expected to have low genetic diversity because genetic variation is distributed among rather than within lineages and is readily lost through genetic drift. We examined genetic diversity at 22 microsatellite loci in 105 individuals from a population of the semelparous herb Lobelia inflata L. and found (i) no evidence of heterozygosity through outcrossing, yet (ii) high rates of genetic polymorphism (2–4 alleles per locus). Furthermore, this genetic variation among lineages was associated with phenotypic traits (e.g. flower colour, size at first flower). Coupled with previous work characterizing the fitness consequences of reproductive timing, our results suggest that temporal genotype‐by‐environment interaction may maintain genetic variation and, because genetic variation occurs only among lineages, this simple system offers a unique opportunity for future tests of this mechanism.     

MHC DQB-1 polymorphism in the Gulf of California fin whale (Balaenoptera physalus) population

One of the most isolated populations of fin whales occurs in the Gulf of California (GOC) with 400-800 individuals. This population shows reduced neutral genetic variation in comparison to the North Pacific population and thus might also display limited adaptive polymorphism. We sampled 36 fin whales from the GOC and assessed genetic variation at exon 2 of the major histocompatibility complex class II DQB-1 genes responsible for eliciting immune responses. Three divergent alleles were found with higher nonsynonymous than synonymous substitution rates within the peptide-binding region positions as well as the likely retention of ancient alleles, indicating that positive selection has shaped diversity in this species. Limited levels of nonneutral polymorphism, in addition to previously described low levels of neutral polymorphism, are consistent with the results of previous studies on vertebrate populations that have remained small and demographically stable for a very long time. Such low genetic variation in the GOC fin whales could be explained by 2 demographic scenarios: an ancient isolated population with limited gene flow or a more recent founder event after the last glacial maximum with very restricted gene flow.     

A Quantitative Test of the Neutral Theory Using Pooled Allozyme Data

Neutral theory predicts a positive correlation between the amount of polymorphism within species and evolutionary rate. Previous tests of this prediction using both allozyme and DNA data have led to conflicting conclusions about the influence of selection and mutation drift. It is argued here that quantitative conclusions about the adequacy of neutral theory can be obtained by analyzing genetic data pooled from many sources. Using this approach, a large database containing information on allozyme variation in over 1500 species is used to examine the relationship between heterozygosity and genetic distance. The results provide support for the hypothesis that a major percentage of protein variation can be explained by variation in neutral mutation rate, and a minor percentage by strong selection.