Genomic Coadaptation Research Articles

Allele-defined genome reveals biallelic differentiation during cassava evolution

Allele-defined genome reveals biallelic differentiation during cassava evolution

The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis.

Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct-1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.

Fluctuating Asymmetry of Human Populations: A Review

Fluctuating asymmetry, the random deviation from perfect symmetry, is a widely used population-level index of developmental instability, developmental noise, and robustness. It reflects a population’s state of adaptation and genomic coadaptation. Here, we review the literature on fluctuating asymmetry of human populations. The most widely used bilateral traits include skeletal, dental, and facial dimensions; dermatoglyphic patterns and ridge counts; and facial shape. Each trait has its advantages and disadvantages, but results are most robust when multiple traits are combined into a composite index of fluctuating asymmetry (CFA). Both environmental (diet, climate, toxins) and genetic (aneuploidy, heterozygosity, inbreeding) stressors have been linked to population-level variation in fluctuating asymmetry. In general, these stressors increase average fluctuating asymmetry. Nevertheless, there have been many conflicting results, in part because (1) fluctuating asymmetry is a weak signal in a sea of noise; and (2) studies of human fluctuating asymmetry have not always followed best practices. The most serious concerns are insensitive asymmetry indices (correlation coefficient and coefficient of indetermination), inappropriate size scaling, unrecognized mixture distributions, inappropriate corrections for directional asymmetry, failure to use composite indices, and inattention to measurement error. Consequently, it is often difficult (or impossible) to compare results across traits, and across studies.

A disproportionate role for mtDNA in Dobzhansky–Muller incompatibilities?

Evolution in allopatric populations can lead to incompatibilities that result in reduced hybrid fitness and ultimately reproductive isolation upon secondary contact. The Dobzhansky-Muller (DM) model nicely accounts for the evolution of such incompatibilities. Although DM incompatibilities were originally conceived as resulting of interactions between nuclear genes, recent studies have documented cases where incompatibilities have arisen between nuclear and mitochondrial genomes (mtDNA). Although mtDNA comprises only a tiny component (typically <<0.01%) of an organism's genetic material, several features of mtDNA may lead to a disproportionate contribution to the evolution of hybrid incompatibilities: (i) essentially all functions of mtDNA require interaction with nuclear gene products. All mtDNA-encoded proteins are components of the oxidative phosphorylation (OXPHOS) system and all mtDNA-encoded RNAs are part of the mitochondrial protein synthetic machinery; both processes require interaction with nuclear-encoded proteins for function. (ii) Transcription and replication of mtDNA also involve mitonuclear interactions as nuclear-encoded proteins must bind to regulatory motifs in the mtDNA to initiate these processes. (iii) Although features of mtDNA vary amongst taxa, metazoan mtDNA is typically characterized by high nucleotide substitution rates, lack of recombination and reduced effective population sizes that collectively lead to increased chance fixation of mildly deleterious mutations. Combined, these features create an evolutionary dynamic where rapid mtDNA evolution favours compensatory nuclear gene evolution, ultimately leading to co-adaptation of mitochondrial and nuclear genomes. When previously isolated lineages hybridize in nature or in the lab, intergenomic co-adaptation is disrupted and hybrid breakdown is observed; the role of intergenomic co-adaptation in hybrid breakdown and speciation will generally be most pronounced when rates of mtDNA evolution are high or when restricted gene flow results in significant population differentiation.

The nature of interactions that contribute to postzygotic reproductive isolation in hybrid copepods

Deleterious interactions within the genome of hybrids can lower fitness and result in postzygotic reproductive isolation. Understanding the genetic basis of these deleterious interactions, known as Dobzhansky-Muller incompatibilities, is the subject of intense current study that seeks to elucidate the nature of these deleterious interactions. Hybrids from crosses of individuals from genetically divergent populations of the intertidal copepod Tigriopus californicus provide a useful model in which to study Dobzhansky-Muller incompatibilities. Studies of the basis of postzygotic reproductive isolation in this species have revealed a number of patterns. First, there is evidence for a breakdown in genomic coadaptation between mtDNA-encoded and nuclear-encoded proteins that can result in a reduction in hybrid fitness in some crosses. It appears from studies of the individual genes involved in these interactions that although this coadaptation could lead to asymmetries between crosses, patterns of genotypic viabilities are not often consistent with simple models of genomic coadaptation. Second, there is a large impact of environmental factors on these deleterious interactions suggesting that they are not strictly intrinsic in nature. Temperature in particular appears to play an important role in determining the nature of these interactions. Finally, deleterious interactions in these hybrid copepods appear to be complex in terms of the number of genetic factors that interact to lead to reductions in hybrid fitness. This complexity may stem from three or more factors that all interact to cause a single incompatibility or the same factor interacting with multiple other factors independently leading to multiple incompatibilities.

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193) is about four times lower than the genomic background (K = 0.0743). We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the species stopped forming fertile hybrids, thereby complementing the average portrait of divergence between species provided by genomic data.

Genomic changes at early stages of formation of allopolyploid Aegilops longissima × Triticum urartu

Using the model of synthetic allopolyploid Aegilops longissima TL05 x Triticum urartu TMU06 of the first generation, the degree and character of changes in subtelomeric, microsatellite and random amplified DNA sequences (RAPD) on early stage of polyploidization was estimated. Study of genome changes was performed by comparing of PCR spectra obtained while amplifying genome DNA of allopolyploid and its parental forms. For analysis of subtelomeric DNA, we used 66 pairs of primers composed of 11 singular primers designed for subtelomere DNA sequences of cereals. RAPD analysis was performed with usage of 38 primers, in microsatellite (SSR) analysis 23 primer pairs were used. RAPD analysis appeared to be a more effective PCR-based method to identify genome changes. Absence of some PCR fragments typical for parental genome in RAPD specters of allopolyploid TL05 x TMU06 was shown using 13 primers of 38 (34%), and with usage of subtelomere primers such changes in PSR specters were shown only for one of 66 pays of primers (1.5%). SSR loci were stable during the polyploidization process. Subsequent analysis of PCR fragments absent in specter of synthetic allopolyploid showed that high level of genome changes in RAPD analysis is probably connected with more effective ability of this method to reveal point mutations. Some data was found suggesting that not all genome changes observed in experimentally synthesized allopolyploids of the first generation are consequences of coadaptation of few genomes in one nucleus.

The Significance of Genomic Imprinting for Brain Development and Behaviour

Professor Barry Keverne FRS, FMedSci – Behavioural Neuroscience, King's College, Cambridge, described how genomic imprinting provides for co-adaptation of mother and fetus, for maternal provision and fetal use of resources. On the other hand it is open to genetic transmission of clinical disorders, for instance Prada-Willli syndrome leading to obesity, and Angelman's syndrome with mental retardation. Among vertebrates, genomic imprinting only evolved in mammals and the placenta is a primary target for expression of imprinted genes. There are certain autosomal genes in mammals that are only expressed if inherited from one parent rather than from the other. More often the paternal gene – allele – is expressed which means that the maternal allele is silenced, usually by methylation, bonding of a CH3 group. Genomic imprinting, distinct from epigenesis, occurs in germ-line cells, ensuring transgenerational effects. Epigenesis, in somatic cells, is usually restricted to one generation, although if it causes a change of behaviour – better mothering say – that can have consequences in the next generation by social transmission. Imprinting is reversible according to parent of origin and there is no change in the gene sequence, as occurs by mutation. Genomic imprinting acts primarily through key regulatory genes which in turn have a cascade effect through other genes. Possible effects vary widely, for instance the mother's food intake and weight gain; maternal fat and blood glucose; letdown of milk and post-natal pup growth. Other affects include her maternal behaviour, nest-building, and placental hormones, placental blood flow and nutrient transfer, fetal growth, and early weaning and puberty onset. In these ways the placenta enables the fetus to regulate its own destiny, mainly by genomic co-adaptation affecting hormonal action on receptors in the maternal hypothalamus. The two genomes, infant and maternal, are co-adaptive for infant wellbeing and reproductive success. Offspring that have extracted “good” maternal nurturing through imprinted genes will themselves be genetically predisposed towards good mothering. Through imprinting, a gene contributing to fitness is established in the population more quickly, especially when paternally expressed due to the greater reproductive fitness of males expressing this allele. Although genomic imprinting affects hormonal activity and nutrient metabolism, there is no evidence for hormones or nutrients affecting genomic imprinting. Hormones and nutrients can, particularly in early life, epigenetically affect the individual's future life for better or for worse, and significantly contribute to “foetal programming”.

Population differentiation and genetic variation inform translocation decisions for Liatris scariosa var. novae- angliae, a rare New England grassland perennial

Augmentation of small rare species populations is sometimes suggested on genetic grounds. However, outbreeding depression via dilution of local adaptation or break-up of genomic coadaptation may occur. These effects depend on the causes of population divergence. Here, we compare genetic measures of population divergence in Liatris scariosa var. novae-angliae, a rare New England perennial. We measured G ST, neutral marker subdivision, and Q ST, quantitative subdivision of propagule and juvenile plant traits. G ST was relatively high. Q ST for leaf shape exceeded G ST, indicating local adaptation, while Q ST for other traits fell within or below the G ST range. Local adaptation appears low for juvenile traits, although the high G ST cautions against translocation because of potential coadaptation. If translocation is still required, however, donor populations should contain high quantitative genetic diversity. We assess population size and allozyme diversity as predictors of quantitative genetic variation, but find these poor proxies for direct measurement.

Recombination does not generate pinworm susceptibility during experimental crosses between two mouse subspecies.

The susceptibility to Aspiculuris tetraptera of European Mus musculus hybrids is thought to reflect the disruption of genomic co-adaptation through recombination of the parental genomes. Here, we compared the susceptibility to this parasite between parents and experimental hybrids (intersubspecific until F4, intrasubspecific F1, F2) to clarify the contributions of heterosis and subspecies incompatibility. F1 showed hybrid vigor. Unlike intrasubspecific F2, intersubspecific F2 were less resistant than F1, but revealed no increased susceptibility relative to the parents. Intersubspecific F3 and F4 showed the same hybrid vigor as F1. Heterosis contributed most to the resistance, but the differences between intra- and intersubspecific F2 suggested genomic incompatibilities between subspecies. However, the susceptibility did not increase through the recombination process, showing that disruption of co-adaptation does not directly affect resistance. Even if previous studies still support the selective role of parasites in the current hybrid zone, an alternative hypothesis on the origin of hybrid susceptibility is warranted.

Developmental stability in Brassica cretica: the effect of crossing distance on fluctuating asymmetry in cotyledon morphology

In the present investigation of Brassica cretica, a wild relative of the cultivated cabbage, B. oleracea, we performed an extensive crossing experiment, involving self-pollinations, random outcrosses within populations and hybridizations between populations or species, to evaluate the relationship between crossing distance and developmental stability, estimated as the absolute difference between the right and left lobe of the cotyledons. The frequency distribution of the right-minus-left scores had a narrower peak than expected for normally-distributed data, but there was no directional asymmetry or antisymmetry. Despite evidence for inbreeding depression in seedling biomass and cotyledon size, the type of cross had negligible influence on cotyledon asymmetry. Separate analyses of between-population hybrids revealed differences among progenies from different pairs of populations and a tendency for the F1 hybrid means to decrease with the geographic distance separating the parent populations, but only for the two size variables. Based on these and other observations, we propose that the degree of cotyledon asymmetry is unrelated to genome-wide characteristics, such as the level of heterozygosity and genomic co-adaptation, and that cotyledon asymmetry is unrelated to the level of genetic stress experienced by each individual. Hence, there is no reason to consider measures of asymmetry as more sensitive indicators of genetic health than conventional fitness variables.

Nonlocal transplantation and outbreeding depression in the subshrubLotus scoparius(Fabaceae)

The genetic background of transplants used to create or augment wild populations may affect the long-term success of restored populations. If seed sources are from differently adapted populations, then the relative performance of progeny from crosses among populations may decrease with an increase in genetic differences of parents and in the differences of parental environments to the transplant location. We evaluated the potential for such outbreeding depression by hybridizing individuals from six different populations of Lotus scoparius var. scoparius and L. s. var. brevialatus. We used allozyme data to calculate genetic distances between source populations, and compiled climatic data and measured soil traits to estimate environmental distances between source populations. We found significant outbreeding depression following controlled crosses. In the greenhouse, the success of crosses (seeds/flower × seedlings/seed) decreased with increasing genetic distance between populations revealing genetically based outbreeding depression unrelated to local adaptation. After outplanting to one native site (in situ common garden), field cumulative fitness of progeny (survival × fruit production) decreased significantly with mean environmental distance of the parental populations to the transplant site, but not with genetic distance between the crossed populations. This result is consistent with a disruption of local adaptation. At the second, ecologically contrasting common garden, where low survival reduced statistical power, field cumulative fitness (survival × progeny height) did not decrease significantly with either environmental distance or genetic distance. Overall, intervariety crosses were 40 and 50% as fit (seeds/flower × seedlings/seed × survival × fruits at the first garden or × height at the second) as intravariety crosses. These results suggest that the cumulative outbreeding depression was caused by a combination of genetically based ecological differences among populations and other genomic coadaptation. We conclude that mixing genetically differentiated seed sources of Lotus scoparius may significantly lower the fitness of augmented or restored populations. Genetic and environmental similarities of source populations relative to the transplant site should be considered when choosing source materials, a practice recommended by recent seed transfer policies. Geographic separation was not a good surrogate for either of these measures.

Wings and bristles: character specificity of the asymmetry phenotype in insecticide-resistant strains of Lucilia cuprina.

We investigated the hypothesis that observed higher levels of asymmetry displayed by insecticide-resistance genotypes of Lucilia cuprina are restricted to bristle characters, due to the action of resistance genes in bristle cell development, rather than through the disruption of genomic coadaptation. We compared the level of asymmetry of three bristle characters and three wing characters in non-modified and modified-resistance genotypes. Consistent with previous studies, resistance genotypes displayed greater levels of bristle asymmetry than either susceptible or modified genotypes. However, there were no differences among genotypes for any of the wing characters. To confirm that this result is attributable to the action of the resistance and modifier genes themselves, we also examined the responses of both bristle and wing characters to the more general developmental stress of extreme temperature. Sub-optimal temperature was shown to increase both bristle and wing asymmetry, suggesting that there are no underlying differences between the two character types which could, of themselves, explain the differential response observed in the resistance genotypes.

PLOIDY DOES NOT AFFECT FLUCTUATING ASYMMETRY IN THE CARPENTER BEE (HYMENOPTERA: ANTHOPHORIDAE)

Random deviations from perfect symmetry in bilateral traits, fluctuating asymmetry, are thought to reflect developmental stability: the ability of an individual to buffer against genetic and (or) environmental stress during development (Palmer and Strobeck 1986). Fluctuating asymmetry is often regarded as an indicator of individual quality or fitness (Møller and Swaddle 1997); however, factors underlying fluctuating asymmetry are not well understood (Markow 1995). It has been suggested that heterozygosity, ploidy, and genomic coadaptation (hybridization) are genetic factors affecting the magnitude of fluctuating asymmetry (Palmer and Strobeck 1986; Markow 1995; Møller and Swaddle 1997). Insects having a haplodiploid sex-determining mechanism present opportunities to examine the relationship between ploidy and fluctuating asymmetry. In hymenopterans, females are diploid and males haploid. Thus the effects of ploidy can be investigated by contrasting males and females within a population (e.g., Clarke 1997). Diploid females, in which deleterious recessives reducing developmental stability could be masked, may be expected to have smaller asymmetry than haploid males (e.g., Brückner 1976; Smithet al.1997). In this paper, we compare the level of fluctuating asymmetry in forewing venation of males to that of females in the carpenter beeXylocopa appendiculata circumvolansSmith.

Developmental instability in hybrids between Lychnis viscaria and Lychnis alpina (Caryophyllaceae)

Developmental instability shown by increased fluctuating asymmetry can be caused by either genetic or environmental stress. Genomic coadaptation and heterozygosity are the genetic factors that are commonly assumed to increase the level of developmental stability. Therefore, in hybrid populations the level of fluctuating asymmetry (FA) can be lower due to higher heterozygosity or higher due to disruption of coadapted gene complexes, depending on the degree of divergence between hybridizing taxa. Here I present data on FA in petals from hybrids between Lychnis viscaria (Caryophyllaceae) and Lychnis alpina and from parental species grown in a common garden environment. Petal asymmetry of hybrids was clearly higher than that of either parental species grown in common environment. Between the two parental species petal asymmetry did not differ. The mean size of the petals in hybrids was about the same as in L. viscaria, thus indicating no heterotic effect. Therefore, it seems that hybrids between L. viscaria and L. alpina do suffer from the disruption of coadapted gene complexes as indicated by higher developmental instability.

Evaluating the consequences of sexual size dimorphism—reply to Sodhi

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Competition between mitochondrial haplotypes in distinct nuclear genetic environments: Drosophila pseudoobscura vs. D. persimilis.

A test for coadaptation of nuclear and mitochondrial genomes was performed using the sibling species, Drosophila pseudoobscura and D. persimilis. Two lines of flies with "disrupted" cytonuclear genotypes were constructed by repeated backcrossing of males from one species to females carrying mitochondrial DNA (mtDNA) from the other species. Each "disrupted" strain was competed in population cages with the original stock of each species from which the recurrent males were obtained during the backcrossing. As such, the two species' mitochondrial types were competed reciprocally in the nuclear genetic environments of each species. The trajectories of mtDNA haplotypes were followed in discrete-generation population cages using a PCR-four-cutter approach. A significant increase in the frequency of D. pseudoobscura mtDNA was observed in each of four replicate cages with a D. pseudoobscura nuclear background. In the D. persimilis nuclear background, one cage actually showed an increase in frequency of D. pseudoobscura mtDNA, although together the four replicate cages show little change in frequency. These results were repeated after frequency perturbations and reinitiation of each cage. An analysis of fitness components revealed that fertility selection greatly outweighed viability selection in these cytonuclear competition experiments. The asymmetry of the fitnesses of the mtDNA haplotypes on the two genetic backgrounds is consistent in direction with the previously reported asymmetry of female fertility in backcrosses between these two species. While our experiments do not allow us to identify mtDNA as the sole source of fitness variation, at a minimum the data indicate a fitness association between nuclear fertility factors and the D. pseudoobscura mtDNA on its own genetic background.

Evolutionary Ecology and Developmental Instability

The past decade has seen a resurgence of interest in developmental instability, reflected in fluctuating asymmetry, as a concept in evolutionary ecology. Many investigations interpret fluctuating asymmetry in populations or subsets of populations as reflecting the existence of, or at least the potential for, natural or sexual selection. However, the biological and nonbiological factors underlying the appearance of developmental instability are not well understood. For example, the ability of heterozygosity vs genomic coadaptation to have an impact on development and cause fluctuating asymmetry is still debated, though each will have important, but different, implications for the genetic structure of populations and genetic architecture of various traits. These and other issues reviewed in this chapter must be clarified in order for the concept of developmental instability to be meaningful in evolutionary and ecological studies.

Fluctuating asymmetry in the Mus musculus hybrid zone: a heterotic effect in disrupted co-adapted genomes.

Developmental stability reflects the organism's ability to buffer minor developmental accidents and is often estimated by measuring the fluctuating asymmetry. Either implicitly or explicitly, numerous authors have assumed that developmental stability is correlated with overall fitness. If this is the case, changes in morphological asymmetry across a hybrid zone could be used as a measure of the selection on hybrid genomes. Developmental stability in hybrid populations is theoretically related to the genetic distance between hybridizing taxa, and results from a balance between the stabilizing effect due to increased heterozygosity and the disruptive effect caused by breakdown of genomic co-adaptation. Here we have compared the amount of fluctuating asymmetry across a transect of the hybrid zone between the two European subspecies of the house mouse (Mus musculus domesticus and M. m. musculus) in Denmark. For the first time in any natural hybrid zone we found an increased developmental stability in the populations with mixed genomes. Moreover, the apparently beneficial effect of hybridization on the developmental stability of the hybrid mice contrasts with the results of both genetic and parasitological studies which show that hybrid dysgenesis occurs in this zone. Our results suggest that the barrier to gene flow in the Mus musculus hybrid zone may result from the disruption of relatively few gene systems. They also lead us to reassess the relation between developmental stability expressed as fluctuating asymmetry, co-adaptation and overall fitness.

Evaluating the fate of genetically modified microorganisms in the environment: are they inherently less fit?

Genetically modified microorganisms hold great promise for environmental applications. Nonetheless, some may have unintended adverse effects. Of particular concern for risk assessment is the simple fact that microorganisms are self-replicating entities, so that it may be impossible to control an adverse effect simply by discontinuing further releases of the organism. It has been suggested, however, that genetically modified microorganisms will be poor competitors and therefore unable to persist in the wild due to energetic inefficiency, disruption of genomic coadaptation, or domestication. Many studies support the hypothesis that genetically modified microorganisms are less fit than their progenitors, but there are a few noteworthy counter-examples in which genetic modifications unexpectedly enhance competitive fitness. Furthermore, subsequent evolution may eliminate the maladaptive effects of some genes, increasing the likelihood that a modified organism or its engineered genes will persist. Evaluating the likelihood that a genetically modified microorganism or its engineered genes will persist is a complex ecological and evolutionary problem. Therefore, an efficient regulatory framework would require such evaluations only when there are plausible scenarios for significant adverse environmental effects.