Genetic Change and Rates of Cladogenesis

Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn.     

ORPHANS BY DESIGN: THE FUTURE OF GENETIC PARENTHOOD

Establishing the nature of genetic parenthood is an important task. This is, firstly, because many people desire that relationship and it is in their interest to know what that is, and secondly, because there is a view that it may incur certain moral obligations between the genetic parent and their child. Many theorists have made attempts to define exactly what genetic parenthood is. I show that these definitions are deficient if they wish to fully capture all reproductive scenarios in ways that are intuitive and/or meaningful. Through a series of cases involving technologies such as cloning and genome editing, we see that in lieu of the traditional two parents, there are possible beings who have no genetic parents, one genetic parent, or many genetic parents. Establishing these cases complicates our understanding of genetic parenthood. From this, we must reconsider current definitions, as well as the usefulness of defining genetic parenthood in these complex cases. Here I do not aim to establish a new definition, but rather to suggest that this complexity makes it necessary to re‐assess the importance of the connection between genetic parenthood and parental obligations and authorities.     

A quantum-theoretic approach to genetic problems

A quantum-theoretic picture of the transfer of genetic information is described. The advantage of such an approach is that a number of genetic effects appear to be explicable on the basis of general microphysical laws, independent of any specific model (such as DNA-protein coding) for the transmission of genetic information. It is assumed that the genetic information is carried by a family of numerical observables belonging to a specific microphysical system; it is shown that a single observable is theoretically sufficient to carry this information. The various types of structure that this observable can possess are then described in detail, and the possible genetic effects which can airse from each such structure are discussed. For example, it is shown how the assumption that the genetic observable possesses degenerate eigenvalues may lead to a theory of allelism. To keep the treatment self-contained, the basic quantum-theoretical principles to be used are discussed in some detail. Finally, the relation of the present approach to current biochemical ideas and to earlier quantum-theoretic treatments of genetic systems is discussed.     

Genetic compatibility, mate choice and patterns of parentage: invited review

There is growing interest in the possibility that genetic compatibility may drive mate choice, including gamete choice, particularly from the perspective of understanding why females frequently mate with more than one male. Mate choice for compatibility differs from other forms of choice for genetic benefits (such as 'good genes') because individuals are expected to differ in their mate preferences, changing the evolutionary dynamics of sexual selection. Recent experiments designed to investigate genetic benefits of polyandry suggest that mate choice on the basis of genetic compatibility may be widespread. However, in most systems the mechanisms responsible for variation in compatibility are unknown. We review potential sources of variation in genetic compatibility and whether there is any evidence for mate choice driven by these factors. Selfish genetic elements appear to have the potential to drive mate compatibility mate choice, though as yet there is only one convincing example. There is abundant evidence for assortative mating between populations in hybrid zones, but very few examples where this is clearly a result of selection against mating with genetically less compatible individuals. There are also numerous cases of inbreeding avoidance, but little evidence that mate choice or differential fertilization success driven by genetic compatibility occurs between unrelated individuals. The exceptions to this are a handful of situations where both the alleles causing incompatibility and the alleles involved in mate choice are located in a chromosome region where recombination is suppressed. As yet there are only a few potential sources of genetic compatibility which have clearly been shown to drive mate choice. This may reflect limitations in the potential for the evolution of mate choice for genetic compatibility within populations, although the most promising sources of such incompatibilities have received relatively little research.     

UNPREDICTABILITY OF CORRELATED RESPONSE TO SELECTION: PLEIOTROPY AND SAMPLING INTERACT

Given a set of loci that contribute additive genetic variation for a trait being selected, the pleiotropic effects of these loci on a second trait may vary. I simulated selection on genetic systems having different combinations of pleiotropic effects to investigate the variability of correlated responses to selection. The simulation shows that there are many possible combinations of pleiotropic effects that are characterized by the same value of the genetic correlation; the genetic correlation does not uniquely determine a set of pleiotropic effects. Furthermore, for a given value of the genetic correlation, differences in pleiotropic effects have a substantial impact on the variation in correlated responses. Some combinations of pleiotropic effects constrain correlated response to a narrow range of possible values; others allow a wide range, including some correlated responses in a direction opposite the sign of the genetic correlation. The genetic correlation is not a reliable predictor of pleiotropic constraint. Whereas it has been previously established that genetic correlations are not necessarily constraints, the alternative is also true: correlated response can be strictly constrained despite a genetic correlation of zero. Given the frequency of correlated responses in a direction opposite to the one predicted by the genetic correlation, it follows that correlated response is not a reliable predictor of genetic correlation in the base population.     

The neutral theory in an infinite population

Selective substitutions at one locus induce stochastic dynamics at a linked neutral locus that resemble genetic drift even when the population size is infinite. This new stochastic force, which is called genetic draft, causes genetic variation at the neutral locus to decrease with population size and the rate of deleterious substitution to increase with population size. The fact that heterozygosities in natural populations are only weakly dependent on population size suggests that genetic draft may be a much more important stochastic force than genetic drift in natural populations. Some of the mathematical properties of genetic draft are explored.     

Genetic rescue guidelines with examples from Mexican wolves and Florida panthers

In populations or species with low fitness (high genetic load), a new management strategy called genetic rescue has been advocated to help avoid extinction. In this strategy, unrelated individuals from another population are introduced into the population with low fitness in an effort to reduce genetic load. Here we present ten guidelines that can be used to evaluate when genetic rescue is a good management option, the appropriate procedures for genetic rescue planning and management, and the potential negative genetic consequences of genetic rescue. These guidelines are then used to evaluate the genetic rescue aspects of the recovery programs for the Mexican wolf and the Florida panther.     

Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast'.

Earlier use of a metaphor in explaining genetic redundancy in a news article has triggered a commentary and a competing metaphor by Dr Stephen Cooper, who went on to conclude that genetic redundancies are relatively unimportant for microorganisms. We argue here that the new metaphor is flawed and that genetic redundancies are integral to buffering all organisms against environmental and genetic damage.     

Balancing selection response and rate of inbreeding by including genetic relationships in selection decisions

An iterative selection strategy, based on estimated breeding values (EBV) and average relationship among selected individuals, is proposed to optimise the balance between genetic response and inbreeding. Stochastic simulation was used to compare rates of inbreeding and genetic gain with those of other strategies. For a range of heritabilities, population sizes and mating ratios, the iterative strategy, denoted ADJEBV, outperforms other strategies, giving the greatest genetic gain at a given rate of inbreeding and the least breeding at a given genetic gain. Where selection is currently by truncation on the EBV, with a restriction on the number of full-sibs selected, it should be possible to maintain similar levels of genetic gain and inbreeding with a reduction in population size of 10–30%, by changing to the iterative strategy. If performance is measured by the reduction in cumulative inbreeding without losing more than a given amount of genetic gain relative to results obtained under truncation selection on the EBV, then with the EBV based on a family index, the performance of ADJEBV is greater at low heritability, and is generally greater than where EBV are based on individual records. When comparisons of genetic response and inbreeding are made for alternative breeding scheme designs, schemes which give higher genetic gain within acceptable inbreeding levels would usually be favoured. If comparisons are made on this basis, then the selection method used should be ADJEBV, which maximises the genetic gain for a given level of inbreeding. The results indicated that all selection strategies used to reduce inbreeding had very small effects on the variance of gain, and so differences in this respect are unlikely to affect choices among selection strategies. Selection criteria are recommended based on maximising a selection objective which specifies the desired balance between genetic gain and inbreeding.     

Genetic connectivity and diversity in inselberg populations of Acacia woodmaniorum,a rare endemic of the Yilgarn Craton banded iron formations

Historically rare plant species with disjunct population distributions and small population sizes might be expected to show significant genetic structure and low levels of genetic diversity because of the effects of inbreeding and genetic drift. Across the globe, terrestrial inselbergs are habitat for rich, often rare and endemic flora and are valuable systems for investigating evolutionary processes that shape patterns of genetic structure and levels of genetic diversity at the landscape scale. We assessed genetic structure and levels of genetic diversity across the range of the historically rare inselberg endemic Acacia woodmaniorum. Phylogeographic and genetic structure indicates that connectivity is not sufficient to produce a panmictic population across the limited geographic range of the species. However, historical levels of gene flow are sufficient to maintain a high degree of adaptive connectivity across the landscape. Genetic diversity indicates gene flow is sufficient to largely counteract any negative genetic effects of inbreeding and random genetic drift in even the most disjunct or smallest populations. Phylogeographic and genetic structure, a signal of isolation by distance and a lack of evidence of recent genetic bottlenecks suggest long-term stability of contemporary population distributions and population sizes. There is some evidence that genetic connectivity among disjunct outcrops may be facilitated by the occasional long distance dispersal of Acacia polyads carried by insect pollinators moved by prevailing winds.     

Breeding racehorses: what price good genes?

Horse racing is a multi-million pound industry, in which genetic information is increasingly used to optimize breeding programmes. To maximize the probability of producing a successful offspring, the owner of a mare should mate her with a high-quality stallion. However, stallions with big reputations command higher stud fees and paying these is only a sensible strategy if, (i) there is a genetic variation for success on the racecourse and (ii) stud fees are an honest signal of a stallion's genetic quality. Using data on thoroughbred racehorses, and lifetime earnings from prize money (LE) as a measure of success, we performed quantitative genetic analyses within an animal model framework to test these two conditions. Although LE is heritable (VA=0.299+/-0.108, Pr=0.002), there is no genetic variance for stud fee and the genetic correlation between traits is therefore zero. This result is supported by an absence of any relationship between stud fees for currently active stallions and the predicted LE for their (hypothetical) offspring. Thus, while there are good genes to be bought, a stallion's fees are not an honest signal of his genetic quality and are a poor predictor of a foal's prize winning potential.     

Quantitative genetics in conservation biology

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.     

我国人类遗传资源采集活动现状分析与对策建议*

人类遗传资源是指含有人体基因组、基因等遗传物质的器官、组织、细胞等遗传材料及其产生的数据等资料。我国人类遗传资源极其丰富,合理利用人类遗传资源对推动我国生命科学、生物医药和临床研究具有重要意义。为有效保护、管理和利用我国人类遗传资源,管理部门严格依法依规开展人类遗传资源行政审批。通过梳理2021年我国人类遗传资源采集活动行政许可情况,结合工作实际,对存在问题进行分析,并提出对策建议。     

Prokaryotic species are sui generis evolutionary units

Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources). HGT-based genetic conversions therefore causes homogenization, while genetic introductions drive divergence of populations upon fixation of genetic variants. The impact of HGT in different prokaryotic species may vary substantially and can range from very low levels to rampant HGT, producing chimeric groups of isolates. Combined with other evolutionary processes, these varying levels of HGT causes diversity space to be occupied by unique groups that are mostly incomparable in terms of genetic similarity, genomic cohesion and evolutionary age. As a result, the conventional, cut-off based metrics for species delineation are not adequate. Rather, a pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokaryotic species. Following this approach, all prokaryotic species may be regarded as unique and each of their own kind (sui generis). Taxonomic decisions thus require evolutionary information that integrates vertical inheritances with all possible sources of genetic heterogeneity to ultimately produce robust and biologically meaningful classifications.     

How is life history variation generated from the genetic resource allocation?

A simple quantitative genetic model is proposed to explain the observed genetic correlation structure of a bruchid beetleCallosobruchus chinensis in terms of two underlying variables: the resource acquisition and the resource allocation. Heritabilities and genetic correlations among age-specific, fecundities are regarded as consequences of genetic variations of the two variables. Genetic correlations are predominantly positive in both predictions and observations. Nonetheless, comparison between observed and predicted values in heritabilities, genetic correlations, and genetic principal components suggested significant genetic variances both of the resource allocation and the resource acquisition. The prediction of the model is discussed in relation, to experimental tests of trade-off in life history evolution.     

EPISTASIS AND THE EFFECT OF FOUNDER EVENTS ON THE ADDITIVE GENETIC VARIANCE

Models of founder events have focused on the reduction in the genetic variation following a founder event. However, recent work (Bryant et al., 1986; Goodnight, 1987) suggests that when there is epistatic genetic variance in a population, the total genetic variance within demes may actually increase following a founder event. Since the additive genetic variance is a statistical property of a population and can change with the level of inbreeding, some of the epistatic genetic variance may be converted to additive genetic variance during a founder event. The model presented here demonstrates that some of the additive-by-additive epistatic genetic variance is converted to additive genetic variance following a founder event. Furthermore, the amount of epistasis converted to additive genetic variance is a function of the recombination rate and the propagule size. For a single founder event of two individuals, as much as 75% of the epistatic variance in the ancestral population may become additive genetic variance following the founder event. For founder events involving two individuals with free recombination, the relative contribution of epistasis to the additive genetic variance following a founder event is equal to its proportion of the total genetic variance prior to the founder event. Traits closely related to fitness are expected to have relatively little additive genetic variance but may have substantial nonadditive genetic variance. Founder events may be important in the evolution of fitness traits, not because they lead to a reduction in the genetic variance, but rather because they lead to an increase in the additive genetic variance.     

Rarity and genetic diversity in Indo-Pacific Acropora corals

Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo-Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome.     

Genetic analysis of life-history constraint and evolution in a wild ungulate population

Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.     

INTERACTING PHENOTYPES AND THE EVOLUTIONARY PROCESS: I. DIRECT AND INDIRECT GENETIC EFFECTS OF SOCIAL INTERACTIONS

Interacting phenotypes are traits whose expression is affected by interactions with conspecifics. Commonly-studied interacting phenotypes include aggression, courtship, and communication. More extreme examples of interacting phenotypes—traits that exist exclusively as a product of interactions—include social dominance, intraspecific competitive ability, and mating systems. We adopt a quantitative genetic approach to assess genetic influences on interacting phenotypes. We partition genetic and environmental effects so that traits in conspecifics that influence the expression of interacting phenotypes are a component of the environment. When the trait having the effect is heritable, the environmental influence arising from the interaction has a genetic basis and can be incorporated as an indirect genetic effect. However, because it has a genetic basis, this environmental component can evolve. Therefore, to consider the evolution of interacting phenotypes we simultaneously consider changes in the direct genetic contributions to a trait (as a standard quantitative genetic approach would evaluate) as well as changes in the environmental (indirect genetic) contribution to the phenotype. We then explore the ramifications of this model of inheritance on the evolution of interacting phenotypes. The relative rate of evolution in interacting phenotypes can be quite different from that predicted by a standard quantitative genetic analysis. Phenotypic evolution is greatly enhanced or inhibited depending on the nature of the direct and indirect genetic effects. Further, unlike most models of phenotypic evolution, a lack of variation in direct genetic effects does not preclude evolution if there is genetic variance in the indirect genetic contributions. The available empirical evidence regarding the evolution of behavior expressed in interactions, although limited, supports the predictions of our model.