Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other ...(donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans‐species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non‐native ancestry in an endangered native salamander, are examined.
Inbreeding depression, the reduction of fitness caused by inbreeding, is a nearly universal phenomenon that depends on past mutation, selection, and genetic drift. Recent estimates suggest that its ...impact on individual fitness is even greater than previously thought. Genomic information is contributing to its detection and can enlighten important aspects of its genetic architecture. In natural populations, purging and genetic rescue mitigate fitness decline during inbreeding periods, and might be critical to population survival, thus, both mechanisms should be considered when assessing extinction risks. However, deliberate purging and genetic rescue involve considerable risk in the short and medium term, so that neither appears to be a panacea against high inbreeding depression.
Inbreeding is being estimated using genomic approaches in many more species that do not have pedigrees.
Pedigree inbreeding is being used in combination with genomic estimation of relationships. This partnering provides insight to what the pedigree has missed, such as inbred or related founders and inbreeding before the pedigree was initiated.
Specific loci determining inbreeding depression are being found using various approaches, such as candidate loci, homozygosity mapping or genome wide association, particularly for variants with large effects.
Inbreeding depression, purging and genetic rescue are recognized as essential elements to be considered in conservation programs, and genomic monitoring of genetic rescue and purging are being used or considered to plan and monitor management.
Recent genomic data have found that many genes show the signal of selection. How many of these genes are undergoing heterozygote advantage selection is only beginning to be known. Initial genomic ...surveys have suggested that only a small proportion of loci have polymorphisms maintained by heterozygote advantage and this is consistent with the few examples generated from other approaches within given species. Unless further studies provide large numbers of loci with heterozygote advantage, it appears that loci with heterozygote advantage must be considered only a small minority of all loci in a species. This is not to say that some heterozygote advantage loci do not have important adaptive functions, but that their role in overall evolutionary change might be more of an unusual phenomenon than a major player in adaptation.
Although FST is widely used as a measure of population structure, it has been criticized recently because of its dependency on within‐population diversity. This dependency can lead to difficulties in ...interpretation and in the comparison of estimates among species or among loci and has led to the development of two replacement statistics, F′ST and D. F′ST is the normal FST standardized by the maximum value it can obtain, given the observed within‐population diversity. D uses a multiplicative partitioning of diversity, based on the effective number of alleles rather than on the expected heterozygosity. In this study, we review the relationships between the three classes of statistics (FST, F′ST and D), their estimation and their properties. We illustrate the relationships between the statistics using a data set of estimates from 84 species taken from the last 4 years of Molecular Ecology. As with FST, unbiased estimators are available for the two new statistics D and F′ST. Here, we develop a new unbiased F′ST estimator based on GST, which we call G′′ST. However, F′ST can be calculated using any FST estimator for which the maximum value can be obtained. As all three statistics have their advantages and their drawbacks, we recommend continued use of FST in combination with either F′ST or D. In most cases, F′ST would be the best choice among the latter two as it is most suited for inferences of the influence of demographic processes such as genetic drift and migration on genetic population structure.
Scott
et al
. (Reports, 27 November 2020, p. 1086) suggest, on the basis of conclusions obtained from a desert tortoise reintroduction program, that higher genomic heterozygosity should be used to ...identify individuals for successful translocation. I contend that this recommendation is questionable given these relocated tortoises’ unknown origin, their high mortality, insufficient data on resident tortoises and other components of fitness, and potential allelic dropout.
The selective mechanisms for maintaining polymorphism in natural populations has been the subject of theory, experiments, and review over the past half century. Advances in molecular genetic ...techniques have provided new insight into many examples of balancing selection. In addition, new theoretical developments demonstrate how diversifying selection over environments may maintain polymorphism. Tests for balancing selection in the current generation, the recent past, and the distant past provide a comprehensive approach for evaluating selective impacts. In particular, sequenced-based tests provide new ways to evaluate the long-term impact of selection on particular genes and the overall genome in natural populations. Overall, there appear to be many loci exhibiting the signal of adaptive directional selection from genomic scans, but the present evidence suggests that the proportion of loci where polymorphism is maintained by environmental heterogeneity is low. However, as more molecular genetic details become available, more examples of polymorphism maintained by selection in heterogeneous environments may be found.
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation ...biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
Malaria is one of the leading causes of death worldwide and has been suggested as the most potent type of selection in humans in recent millennia. As a result, genes involved in malaria resistance ...are excellent examples of recent, strong selection. In 1949, Haldane initially suggested that infectious disease could be a strong selective force in human populations. Evidence for the strong selective effect of malaria resistance includes the high frequency of a number of detrimental genetic diseases caused by the pleiotropic effects of these malaria resistance variants, many of which are "loss of function" mutants. Evidence that this selection is recent comes from the genetic dating of the age of a number of these malaria resistant alleles to less than 5,000 years before the present, generally much more recent than other human genetic variants. An approach to estimate selection coefficients from contemporary case-control data is presented. In the situations described here, selection is much greater than 1%, significantly higher than generally observed for other human genetic variation. With these selection coefficients, predictions are generated about the joint change of alleles S and C at the β-globin locus, and for α-thalassaemia haplotypes and S, variants that are unlinked but exhibit epistasis. Population genetics can be used to determine the amount and pattern of selection in the past and predict selection in the future for other malaria resistance variants as they are discovered.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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