Fixation Of Deleterious Alleles Research Articles

Does symmetry preclude the evolution of senescence? A comment on Pen and Flatt 2021

Does symmetry preclude the evolution of senescence? A comment on Pen and Flatt 2021

Genetic and phenotypic consequences of early domestication in black soldier flies (Hermetia illucens)

The black soldier fly, Hermetia illucens, is an emerging biotechnological agent with its larvae being effective converters of organic waste into usable bio-products including protein and lipids. To date, most operations use unimproved commercial populations produced by mass rearing, without cognisance of specific breeding strategies. The genetic and phenotypic consequences of these commercial practices remain unknown and could have a significant impact on long-term population viability and productivity. The aim of this study was thus to assess the genetic and phenotypic changes during the early phases of colony establishment and domestication in the black soldier fly. An experimental colony was established from wild founder flies and a new microsatellite marker panel was developed to assess population genetic parameters along with the phenotypic characteristics of each generational cohort under captive breeding. The experimental colony was characterised by a small effective population size, subsequent loss of genetic diversity and rapid genetic and phenotypic differentiation between the generational cohorts. Ultimately, the population collapsed by the fifth generation, most likely owing to the adverse effect of inbreeding depression following the fixation of deleterious alleles. Species with r-selected life history characteristics (e.g. short life-span, high fecundity and low larval survival) are known to pose particular challenges for genetic management. The current study suggests that sufficient genetic and phenotypic variations exist in the wild population and that domestication and strain development could be achieved with careful population augmentation and selection during the early stages of colony establishment.

Genetic diversity and population structure of founders from wildlife conservation management units and wild populations of critically endangered Dermatemys mawii

Many endangered freshwater turtle species are born in captivity for conservation and future reintroduction into the wild. However, in order to improve breeding programs, an assessment of the genetic diversity of the founder individuals is required to avoid genetic problems such as inbreeding, fixation of deleterious alleles, or loss of allelic diversity due to genetic drift. In this research, we assessed the genetic diversity of the founder individuals from three Wildlife Management Units (UMA) dedicated to the reproduction of Dermatemys mawii in southeast Mexico, and from three wild populations using ten microsatellite markers. Dermatemys mawii is a freshwater turtle that is critically endangered due principally to fragmentation, loss, degradation, and contamination of its habitat, in addition to hunting for human consumption. Furthermore, genetic relationships among UMAs and wild populations, as well as within each kind of group, were investigated by means of Bayesian analysis (Structure software) and discriminant analysis of principal component (DAPC). Genetic diversity in wild populations could be considered as medium, and are less than values observed for UMAs. Genetic diversity for UMAs and wild populations were discussed considering origin of individuals, translocation between UMAs, habitat quality among other factors. Genetic structure analysis highlighted an evident separation between UMAs and wild populations (Bayesian and DAPC analyses), and the hierarchical analysis of structure among UMAs reflected the origin and relationship among them, whereas geographical situation of wild populations is the best explanation for its hierarchical structure. In light of our results, some conservation and management recommendations are provided for this endangered freshwater turtle.

Inbreeding depression and drift load in small populations at demographic disequilibrium

Inbreeding depression is a major driver of mating system evolution and has critical implications for population viability. Theoretical and empirical attention has been paid to predicting how inbreeding depression varies with population size. Lower inbreeding depression is predicted in small populations at equilibrium, primarily due to higher inbreeding rates facilitating purging and/or fixation of deleterious alleles (drift load), but predictions at demographic and genetic disequilibrium are less clear. In this study, we experimentally evaluate how lifetime inbreeding depression and drift load, estimated by heterosis, vary with census (Nc ) and effective (estimated as genetic diversity, He ) population size across six populations of the biennial Sabatia angularis as well as present novel models of inbreeding depression and heterosis under varying demographic scenarios at disequilibrium (fragmentation, bottlenecks, disturbances). Our experimental study reveals high average inbreeding depression and heterosis across populations. Across our small sample, heterosis declined with He , as predicted, whereas inbreeding depression did not vary with He and actually decreased with Nc . Our theoretical results demonstrate that inbreeding depression and heterosis levels can vary widely across populations at disequilibrium despite similar He and highlight that joint demographic and genetic dynamics are key to predicting patterns of genetic load in nonequilibrium systems.

Reduced population size can induce quick evolution of inbreeding depression in the invasive ladybird Harmonia axyridis

Understanding biological invasion is currently one of the main scientific challenges for ecologists. The introduction process is crucial for the success of an invasion, especially when it involves a demographic bottleneck. A small introduced population is expected to face a higher risk of extinction before the first stage of invasion is complete if inbreeding depression, caused by the expression of deleterious alleles, is important. Changes in mating regimes or in population size can induce the evolution of deleterious allele frequencies, either by selection or by drift, possibly resulting in the purging or the fixation of such alleles within the population. The harlequin ladybird Harmonia axyridis became invasive on several continents following a scenario including at least one event of demographic bottleneck. Although native populations suffered from severe inbreeding depression, it was greatly reduced in invasive ones suggesting that deleterious alleles were purged during the invasion process. In this study, we performed an experiment designed to manipulate the effective population size of H. axyridis across successive generations to mimic contrasting introduction events. We used the measurement of two fitness-related phenotypic traits in order to test (1) if inbreeding depression can evolve at the time-scale of an invasion; and (2) if the changes in inbreeding depression following a bottleneck in laboratory conditions are compatible with the purging of deleterious alleles observed in this species. We found that two generations of very low population size are enough to induce a substantial change in inbreeding depression. Although the genetic changes mostly consisted in fixation of deleterious alleles, purging did also occur, sometimes simultaneously with fixation.

Assessment of demographic bottleneck in Indian horse and endangered pony breeds.

Bottleneck study of any continuously decreasing population is important and crucial issue in its conservation strategies including the analysis of simulated and real populations (Williamson-Natesan 2005; Busch et al. 2007). A bottleneck in a population can increase the rate of inbreeding, loss of genetic variation, fixation of deleterious alleles, thereby reducing evolutionary potential of animals to adapt to new selective pressures, such as climatic change or shift in available resources and increasing the probability of population extinction (Frankham 1995). The genetic changes caused by a bottleneck in a population’s effective size can lower the possibility of population’s persistence (Vrijenhoek 1994; Newman and Pilson 1997). Various endangered or threatened populations have been reported to have low levels of genetic variations (Vrijenhoek 1994; Gibbs et al. 1998). However, all the populations that have been reduced in size did not show quantifiable lower levels of genetic diversity (Waldman et al. 1998) which also necessitates the assessment of bottlenecks with molecular marker for their conservation and evolutionary genetics. India is bestowed with a rich biodiversity of equids in the form of two horses (Marwari and Kathiawari) and four endangered pony breeds (Bhutia, Spiti, Manipuri and Zanskari) besides indigenous donkeys and wild asses (Gupta et al. 2012a,b; 2014). Overall population of these breeds, specially endangered pony breeds has declined in most of the pockets in their home tracts (less than 1000) which is due to their decreased utility and increased modernization of transport system even in hilly and difficult terrains (Gupta et al. 2012a, b). It is expected that bottleneck might have taken

A long-term genetic study reveals complex population dynamics of multiple-source plant reintroductions

A major challenge of using multiple-source populations in reintroductions for restoration and species conservation is to adequately assess the trade-off between the benefits of counteracting inbreeding depression via heterosis, and the risks of maladaptation and reduced fitness through outbreeding depression. In the 1990s, populations of the perennial plant Arenaria grandiflora rapidly declined and were nearing extinction in the Fontainebleau forest, France. This was likely due to inbreeding depression and/or fixation of deleterious alleles. To restore A. grandiflora in the Fontainebleau forest, a reintroduction experiment was conducted in 1999 using transplants from both local and non-local populations. Eight and twelve years later, we carried out a genetic study using microsatellite markers to assess the temporal dynamics of the genetic composition of reintroduced populations. We show that genetic diversity increased significantly in the reintroduced populations compared to the local-source population and that this increased diversity has been maintained for over ten years, highlighting the benefits of mixing individuals of multiple-source populations for restoration of small and inbred populations. Our results also suggest that the level of individual admixture between local and non-local genetic sources might affect individual fitness, which is influenced by the opposing effects of heterosis, inbreeding and outbreeding depressions and local adaptation.

Interpopulation variation in mating system and late‐stage inbreeding depression in Magnolia stellata

Inbreeding has the potential to cause evolutionary changes in populations, although these changes are likely to drive populations to extinction through inbreeding depression and reductions in genetic diversity. We investigated the mating system and late-stage inbreeding depression (delta) in 10 populations of Magnolia stellata using nine microsatellite markers and evaluated the effects of population size and the degree of population isolation through inbreeding and inbreeding depression on the persistence of populations. The outcrossing rates were very similar (approximately 0.7) among populations, but the correlations of paternity, fractions of biparental inbreeding and inbreeding coefficients at the seed stage (F(S)) varied among populations, suggesting that the level of outcrossing was similar among populations, while the quality of it was not. A significant negative correlation was detected between F(S) and population size. The average value of delta was 0.709, and the values in six of the 10 populations were significant. The values of delta differed among populations, although clear relationships with population size and the degree of population isolation were not detected. However, in one population, which was very small and located in the edge of the species' range, we obtained a very low value of delta (-0.096), which may be indicative of purging or the fixation of deleterious alleles. Existing M. stellata populations that are small (and thus might be expected to have higher frequencies of inbreeding) and have large values of delta may be in danger of declining, even if the populations are located within the central region of the species' range.

Effects of population size on performance and inbreeding depression in Lupinus perennis

We investigated the relationships among population size, offspring performance, and inbreeding depression (delta) in Lupinus perennis by examining the effect of population size category (large vs. small) on seed production and offspring performance for three pollination treatments (open pollination, hand crossing and hand selfing). In each of our four pairs of populations, one member of the pair was substantially larger than the other. We then grew seeds from this factorial design (2 sizes x 4 pairs x 3 pollination treatments) in the greenhouse to investigate whether population size affects offspring performance in a common environment, and how small size affects purging of the inbreeding load. Multiplicative performance across four early life-stage components (seed production, seedling emergence, seedling survival and seedling growth) of smaller populations was not significantly lower, although biomass of seedlings declined in smaller populations. Self-pollination reduced seed production, seedling emergence and seedling growth, reflecting substantial inbreeding depression (delta = 0.404 +/- 0.043). Population size categories did not consistently differ in levels of inbreeding depression, suggesting that purging of genetic load in smaller populations has been limited, and that all populations still harbor inbreeding load. We also found a significant decrease in log performance with increases in the population inbreeding coefficient. These results indicate that even in seemingly large populations, lupines are susceptible to considerable fitness declines through both inbreeding load within populations, and drift load via genetic erosion and fixation of deleterious alleles between populations.

Role of inbreeding depression and purging in captive breeding and restoration programmes

Inbreeding depression is a major force affecting the evolution and viability of small populations in captive breeding and restoration programmes. Populations that experience small sizes may be less susceptible to future inbreeding depression because they have been purged of deleterious recessive alleles. We review issues related to purging, as they apply to the management of small populations, and discuss an experiment we conducted examining purging in populations of mosquitofish (Gambusia affinis). Purging is an important process in many small populations, but the literature contains a diversity of responses to purging both within and among studies. With the exception that slow inbreeding results in more purging and less threat to population viability, there seem to be few consistent trends that aid in prediction of how a purging event will affect a population. In our examination of purging on population viability in mosquitofish, single or multiple bottlenecks do not appear to have resulted in any purging of the influence of genetic load on population growth. Rather, serial bottlenecks resulted in a marked decline in population growth and an increase in extinction. Our results, taken together with those of reviewed studies, suggest that in small populations there is great uncertainty regarding the success of any single purging event in eliminating inbreeding depression, together with the high likelihood that purging will depress population viability through the fixation of deleterious alleles. In management of captive breeding and restoration programmes, the common practice of avoiding inbreeding and small population sizes should be followed whenever possible.

Genetic stochasticity, mean fitness of individuals and population dynamics

Keller, Biebach & Hoeck (2007) and McGowan, Wright & Hunt (2007) both emphasize the need for further research aimed at gaining a greater understanding of the relationship between inbreeding levels and population dynamics, as well as the implications of that relationship for conservation efforts. We fully agree with them that further study is needed and we thank them for their kind words suggesting that our research (Reed, Nicholas & Stratton, 2007a) is an excellent step towards a better understanding of how genetic factors interact with the environment to influence the risk of extinction in wild populations. Our data suggest that inbreeding stress interactions lower the mean fitness of individuals in more inbred populations, exacerbating the dangerous part of population fluctuations and increasing the risk of extinction. It has been demonstrated that smaller populations, as indicated through estimates of decreased genetic variation or through direct counts of individuals, have decreased values for numerous components of fitness relative to larger populations (Reed & Frankham, 2003; Reed, 2005, 2007). This is not surprising as population size and breeding structure influence fitness through several mechanisms: efficiency of selection, inbreeding depression, fixation of deleterious alleles and the loss of potentially adaptive alleles through drift, and the input of beneficial mutations (Reed, 2005, 2007). In the populations of spiders used in this study, we demonstrated directly that fecundity is lower in smaller populations (Reed, Nicholas & Stratton, 2007b) and, therefore, the potential growth rate is lower. We purposely shied away from using the terms inbreeding depression and random genetic drift, even though it seems obvious that is what is going on. Instead we used the term genetic quality. The term is not nebulous and does not rely on comparing individuals to some local optimum as stated by Brodie (2007). We define genetic quality precisely as a decrease in the mean fitness of an individual and fitness is measured relative to the other populations in the study. We chose this term specifically because, in practical terms, that is what matters to the central question we sought to answer: Does reduced mean fitness of individuals lead to changes in population dynamics that make those populations more vulnerable to extinction despite density-dependent mortality? The fact that the fate of alleles is more stochastic in smaller populations means that, all else being equal, smaller populations will be composed of individuals of lower average genetic quality. Brodie (2007) suggests that it is important to distinguish inbreeding from loss of genetic diversity. In our data, expected and observed heterozygosity are both excellent predictors of population fitness and the correlation between them is extremely high (r=0.99). It makes no difference which of these two variables is used in the models. Thus, whatever nonrandom mating is occurring within populations, it is almost identical among populations. The statistical techniques we used can only differentiate among independent variables that differ among populations; hence, we cannot comment on the effects of nonrandom mating on fitness in these populations. However, we can say that the differences in expected heterozygosity among these populations are almost certainly due to differential amounts of random genetic drift and therefore the differences in fitness are also due mostly to drift. Allelic richness, on the other hand, is a rather poor predictor of population fitness relative to expected heterozygosity levels (Table 1). Some believe that allelic richness is very important for the evolutionary potential of populations because the limit of selection response, over time frames where mutation is negligible, may be determined by the initial number of alleles (James, 1971; Hill & Rasbash, 1986). Nonetheless, because the rare alleles are mostly deleterious, it is not surprising that allelic richness is strongly correlated with expected heterozygosity (r=0.95), but that expected heterozygosity has much stronger support than models using allelic richness. Brodie (2007) also suggests that the most important aspect of many real-world conservation problems is the

Introduction of Trojan sex chromosomes to boost population growth

Conservation programs that deal with small or declining populations often aim at a rapid increase of population size to above-critical levels in order to avoid the negative effects of demographic stochasticity and genetic problems like inbreeding depression, fixation of deleterious alleles, or a general loss of genetic variability and hence of evolutionary potential. In some situations, population growth is determined by the number of females available for reproduction, and manipulation of family sex ratios towards more daughters has beneficial effects. If sex determination is predominantly genetic but environmentally reversible, as is the case in many amphibia, reptiles, and fish, Trojan sex chromosomes could be introduced into populations in order to change sex ratios towards more females. We analyse the possible consequences for the introduction of XX-males (XX individuals that have been changed to phenotypic males in a XY/XX sex determination system) and ZW males, WW males, or WW females (in a ZZ/ZW sex determination system). We find that the introduction of WW individuals can be most effective for an increase of population growth, especially if the induced sex change has little or no effect on viability.

Fixation of deleterious alleles, evolution and human aging

Human aging, like everything else in biology, only makes sense in the context of evolution. There is substantial agreement among evolutionary geneticists regarding the evolutionary underpinnings of one of the main questions of human aging i.e. ‘Why do we age?’, which involves the higher rate of fixation of alleles that cause deleterious post-reproductive phenotypes vs. alleles that cause deleterious pre-reproductive phenotypes. Even higher rates of fixation of deleterious mutations are predicted to occur on population genetic grounds in two non-recombinant genomes in humans i.e. the Y chromosome, and the mitochondrial genome. The added burden of deleterious mutations on the Y may explain the reduced average lifespan of males vs. females. A high predicted fixation rate of the mitochondrial genome may explain its fast rate of evolution, and the high frequency of mitochondrial disease in relationship to this genomes’ small size, and may underlie the transfer of mitochondrial genes over evolutionary time to the nucleus. Thus a molecular evolutionary model of aging which focuses on increased fixation rates of (1) nuclear alleles which only have deleterious effects post-reproduction, (2) deleterious genes on the Y chromosome, and (3) deleterious genes on the mitochondrial genome, makes multiple testable predictions about the causes and mechanisms of aging.

Population type can influence the magnitude of inbreeding depression in Clarkia concinna (Onagraceae)

Fragmented populations may face high risk of extinction due to the deleterious consequences of increased inbreeding or of genetic drift in small and isolated populations. Theories on the mechanisms of inbreeding depression predict that the severity of inbreeding depression can eventually decrease in populations that persistently inbreed, and hence populations that are isolated through habitat fragmentation might experience a decrease in inbreeding depression over time. In this study, we tested this hypothesis using the patchily distributed, outcrossing annual plant, Clarkia concinna concinna (Onagraceae), which naturally experiences many fragmentation effects. We collected seeds from isolated and central subpopulations and created artificially inbred and outcrossed lines. Progeny from these crosses were planted into the field and greenhouse and assayed for fitness traits over the course of a growing season. Overall, inbreeding depression was substantial, ranging as high as 0.76 (for cumulative fitness in the field), and significant for plant height, fecundity, and above-ground biomass in all experiments. No inbreeding depression was detected for germination or survival rates in the greenhouse experiments, but in the field, survival was significantly depressed for inbred progeny. There was no evidence to support our hypothesis that increased inbreeding in isolated populations would lead to the purging of deleterious alleles and a decrease in the severity inbreeding depression. The most likely hypothesis to explain our results is that purging is not occurring more strongly in the isolated populations due to details of a number of genetic factors (e.g., selection against deleterious alleles is inconsistent or insufficient, or drift has caused fixation of deleterious alleles in these populations). This study supports the view that even when inbreeding depression is predicted to be less problematic, it may still be an important force influencing the fitness of populations.

An adaptive hypothesis for the evolution of the Y chromosome.

Population geneticists remain unsure of the forces driving the evolution of Y chromosomes. Here we consider the possibility that the degeneration of the Y reflects its inability to evolve adaptively. Because the overwhelming majority of favorable mutations on a nonrecombining proto-Y suffer a zero probability of fixation, the fitness of the Y must lag far behind that of the recombining X. At some point, this disparity will grow so large that selection favors an increase in the expression of (fit) X-linked alleles and a decrease in the expression of (unfit) Y-linked alleles. Our calculations suggest that this process acts far more rapidly than hitchhiking-induced erosion of the Y and at least as rapidly as the fixation of deleterious alleles on the Y by background selection. Most important, this hypothesis can explain the evolution of Y chromosomes in taxa such as Drosophila that have very large population sizes.