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PubMed2026

Quantifying the Evolutionary Potential for Delta Smelt Persistence in a Warming Habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature. Using a pedigree and whole genome sequencing data, we characterized the genetic basis of CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size and degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait. We observed modest heritability for CTMax at rearing temperatures of 15°C and 18°C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (i.e., many loci detected with a GxE effect). This temperature-dependent genomic architecture is consistent with our finding that additive genetic variation for CTMax was reduced under warmer rearing conditions, indicating a potential constraint on adaptive evolutionary change. The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for captive management and may inform supplementation of fish to the wild in an ever-warming environment.

conservation physiology↗
PubMed2004

Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog.

Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipiens, over a 22-30 year time interval (11-15 generations). Genetic structure among the populations was very stable, suggesting that these populations were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) than toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Ne/Nc ratios in the range of 0.1-1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly.

Animals↗
PubMed1997

Random mating and selection in families against homozygotes for HLA in south Amerindians.

We have examined HLA-A and HLA-B in a large sample of families of South Amerindians for non-random mating and for Mendelian segregation in their progeny. The proportion of couples sampled for mating averaged over 50% of the total matings with progeny for 10 of the 11 tribes with 10 or more known matings. In nearly all cases, HLA-sharing proportions were very close to those expected from random mating, suggesting strong negative-assortative mating for MHC is not present in these South Amerindians. In progeny from these matings and others in 23 tribes, there was a large deficiency of homozygotes (excess of heterozygotes) compared with Mendelian expectations. In particular, there was a deficiency in all types of matings except when the female was a homozygote and the male shared one allele with her; the reciprocal mating showed no such deficiency. This non-reciprocity suggests the importance of some type of maternal-fetal interaction. A model to describe these results showed very surprising properties for two alleles: no change in allelic frequency like neutrality, an excess of heterozygotes like heterozygote advantage, and a minimum fitness at intermediate allelic frequency like heterozygote disadvantage. For three or more alleles, the model has the qualities of a traditional balancing selection model.

Adolescent↗
PubMed1967

Transferrin polymorphism and population differences in the genetic variability of chimpanzees.

Genetic divergencies between chimpanzee populations, not only.between Pan panicus and Pan troglodytes but also between different groups of the latter, are revealed by typing of transferrin. In particular, differences in the incidence of polymorphic transferrins occur between the groups formed by subdividing a large captive chimpanzee colony of heterogeneous geographic origins into racial types solely on the basis of morphological traits. Genetic variability is extremely high in one of these groups, intermediate in another, and relatively low in a third, with the pattern of changing frequencies of allelic genes at the T(f) locus following the pattern of geographic distribution of the actual conspecific populations or races for which the groups are named.

Animals↗
PubMed1975

Genetic analysis of a population of Tribolium. V. Viability of the unsaturated fatty acid sensitive mutant.

The viability pattern of the unsaturated fatty acid sensitive mutant (cos/cos) of Tribolium castaneum was examined with reference to the normal genotype from egg hatching through adult emergence. The beetles were cultured on diets with 0, 3, or 5% corn oil in growth chambers maintained at 33 +/- 1 degree C and either 42 +/- 6% or 75 +/- 3% relative humidity. The pattern of the mutant was altered during the larval stage and was dependent on both the concentration of dietary fatty acid and the relative humidity of the culture chamber. Values of the viability component of fitness were assigned to the cos/cos, +/-/cos and +/-/+/- genotypes for multiple environments based on the number of eggs surviving to pupation. In large, random mating populations segregating at this locus, a stable genetic polymorphism is forecast. Predicted rates of change of allele frequency are dependent upon the culture conditions.

Animals↗
PubMed1994

Somatic and heritable effects of environmental genotoxins and the emergence of evolutionary toxicology.

The genetic effects of environmental pollutants include mutations in somatic cells or germinal cells that are the direct result of exposure to toxicants. Biomarkers that detect such mutagenic effects have been developed and tested in field studies on wildlife populations. However, another class of genetic effects resulting from pollution exposure exists. Specifically, changes in allele frequencies of populations will occur as a result of population bottlenecks, inbreeding, or selection at loci critical for survival in polluted environments. We describe how such genetic alterations can be studied at the population level using the techniques of molecular genetics, and we predict the development of a new field, evolutionary toxicology, that will address such issues.

Animals↗
PubMed2004

How old is the most recent ancestor of two copies of an allele?

An important clue to the evolutionary history of an allele is the structure of the neighboring region of the genome, which we term the genomic background of the allele. Consider two copies of the allele. How similar we expect their genomic background to be is strongly influenced by the age of their most recent common ancestor (MRCA). We apply diffusion theory, first used by Motoo Kimura as a tool for predicting the changes in allele frequencies over time and developed by him in many articles in this journal, to prove a variety of new results on the age of the MRCA under the simplest demographic assumptions. In particular, we show that the expected age of the MRCA of two copies of an allele with population frequency f is just 2Nf generations, where N is the effective population size. Our results are a first step in running exact coalescent simulations, where we also simulate the history of the population frequency of an allele.

Alleles↗
PubMed2004

Joint effects of self-fertilization and population structure on mutation load, inbreeding depression and heterosis.

Both the spatial distribution of organisms and their mode of reproduction have important effects on the change in allele frequencies within populations. In this article, we study the combined effect of population structure and the rate of partial selfing of organisms on the efficiency of selection against recurrent deleterious mutations. Assuming an island model of population structure and weak selection, we express the mutation load, the within- and between-deme inbreeding depression, and heterosis as functions of the frequency of deleterious mutants in the metapopulation; we then use a diffusion model to calculate an expression for the equilibrium probability distribution of this frequency of deleterious mutants. This allows us to derive approximations for the average mutant frequency, mutation load, inbreeding depression, and heterosis, the simplest ones being Equations 35-39 in the text. We find that population structure can help to purge recessive deleterious mutations and reduce the load for some parameter values (in particular when the dominance coefficient of these mutations is <0.2-0.3), but that this effect is reversed when the selfing rate is above a given value. Conversely, within-deme inbreeding depression always decreases, while heterosis always increases, with the degree of population subdivision, for all selfing rates.

Crosses, Genetic↗
PubMed2006

A clarification of the Hardy-Weinberg law.

C. C. Li showed that Hardy-Weinberg proportions (HWP) can be maintained in a large population by nonrandom mating as well as random mating. In particular he gave the mating matrix for the symmetric case in the most general form possible. Thus Li showed that, once HWP are attained, the same proportions can be maintained by what he called pseudorandom mating. This article shows that, starting from any genotypic distribution at a single locus with two alleles, the same in each sex, HWP can be reached in one round of nonrandom mating with no change in allele frequency. In the model that demonstrates this fact, random mating is represented by a single point in a continuum of nonrandom possibilities.

Alleles↗
PubMed2026

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat.

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15&#xb0;C and 18&#xb0;C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

conservation physiology↗
PubMed2002

The GP problem: quantifying gene-to-phenotype relationships.

In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem. Integrating information across levels of organization within a genotype-environment system is a major challenge in computational biology. However, resolving the GP problem is a fundamental requirement if we are to understand and predict phenotypes given knowledge of the genome and model dynamic properties of biological systems. Organisms are consequences of this integration, and it is a major property of biological systems that underlies the responses we observe. We discuss the E(NK) model as a framework for investigation of the GP problem and the prediction of system properties at different levels of organization. We apply this quantitative framework to an investigation of the processes involved in genetic improvement of plants for agriculture. In our analysis, N genes determine the genetic variation for a set of traits that are responsible for plant adaptation to E environment-types within a target population of environments. The N genes can interact in epistatic NK gene-networks through the way that they influence plant growth and development processes within a dynamic crop growth model. We use a sorghum crop growth model, available within the APSIM agricultural production systems simulation model, to integrate the gene-environment interactions that occur during growth and development and to predict genotype-to-phenotype relationships for a given E(NK) model. Directional selection is then applied to the population of genotypes, based on their predicted phenotypes, to simulate the dynamic aspects of genetic improvement by a plant-breeding program. The outcomes of the simulated breeding are evaluated across cycles of selection in terms of the changes in allele frequencies for the N genes and the genotypic and phenotypic values of the populations of genotypes.

Computer Simulation↗
PubMed1990

[Stabilizing selection and linkage disequilibrium].

An approach to the investigation of the evolution of quantitative traits on the basis of analysis of two-locus marginal systems dynamics has been developed. It has been shown that under stabilizing selection the "quasi-stationary" state is quickly reached and maintained continuously. The "quasi-stationary" state is characterized by small changes in allele frequencies and by linkage disequilibrium that significantly decreases genotypic variance. Equations defining the role of linkage disequilibrium in the stationary state of mutation-selection balance are derived.

Alleles↗
PubMed1988

[Macromutation and evolution: the fixation of Goldschmidt's macromutations as species and genus traits. Hairlessness mutations in mammals].

A brief survey of the development of concepts on the role of macromutations in evolution is given. Contrary to Iu. A. Filipchenko (1926, 1927), who introduced the "micro- and macromutation" terms and believed that regularities of macroevolution could not be reduced to microevolutionary processes, the majority of "synthetists" explained any form of evolution by changes in allele frequencies. From the studies of Drosophila homoeotic mutants R. Goldschmidt (1940) developed the concept of "hopeful monsters" and their role in macroevolution. However, the homoeotic mutants are of drastically reduced viability, which allows the gradualists to reject Goldschmidt's ideas. The distribution of hairlessness mutations (hairless, nude etc.) with the monogenic pattern of inheritance in mammals was studied. Hairless mutants are known in Peromyscus, Mus musculus, Rattus rattus, R. norvegicus, Canis familiaris, Ovis aries. Hairlessness as norm is found in 53 among contemporaneous 1037 mammalian genera. Part of these cases (hairlessness in all Cetacea and Sirenia) may be explained in terms of both macromutations and obligatory gradualism. There is no doubt as to the macromutational origin of hairlessness in the bat Cheiromeles and the rodent Heterocephalus (Bathyergidae); the genera systematically and ecologically close to these have normal pelage. It is quite possible that hairlessness of walrus (Odobenus) has the same origin. The appearance and fixation of single Goldschmidt's macromutation cannot yet be considered as a macroevolutionary process, though the possibility of fixation of a macromutation in nature as a species and genus character contradicts strongly the concept of obligatory gradualism of evolution.

Animals↗
PubMed2006

Ovis aries POU1F1 gene: cloning, characterization and polymorphism analysis.

POU1F1 (PIT-1/GHF-1) is a transcription factor with critical role in the transcriptional regulation of multiple genes in the pituitary and also important for the survival, differentiation and proliferation of three pituitary cell types. To understand the regulation of POU1F1 gene in Ovis aries we report its cloning, sequencing and characterization. The sequenced 5787 bp included six exons and two complete introns. Ovine POU1F1 gene has a high level of conservation with its bovine, human and rat counterparts showing 98.2%, 91.2% and 86.2% of similarity at the coding level, respectively. All six exons were analyzed for polymorphism detection in 100 animals of the Portuguese indigenous ovine breed 'Churra da Terra Quente'. One polymorphism was found at codon 58 in exon 2, in one allele of 4 animals leading to a change from cysteine to tyrosine (2% allelic frequency). In exon 3 two polymorphisms were detected: a G to A transition altering a glycine to an asparagine at codon 89 in one allele of one animal (0.5% allelic frequency) and another G to A transition at codon 105 converting an alanine into a threonine in one allele of 3 animals (1.5% allelic frequency). These polymorphisms might change the structure of the POU1F1 protein and modify gene-expression. In intron 4, an A to G transition was detected in one allele of six animals (3% allelic frequency). Exons 1, 4 and 6 showed no polymorphisms.

Animals↗
PubMed1997

Effects of apolipoprotein E on dementia and aging in the Shanghai Survey of Dementia.

We investigated the status of the apolipoprotein E allele in 538 participants in the incidence phase of the ongoing Shanghai Survey of Dementia, including 103 demented subjects, 72 with mild cognitive impairment and 363 cognitively normal. The apo E epsilon 4 allele was present in 10.2% of control subjects and the allelic frequency did not change between ages 60 to 96 years. The apo E epsilon 4 allelic frequency was increased both in those wiht Alzheimer's disease (AD) (25.4%) and those with vascular dementia (VaD) (22.2%), but not in those with other dementing illnesses or the cognitively impaired. All of the subjects homozygous for apo E epsilon 4 were demented, three were diagnosed as having AD, and three met NINDS/AIREN criteria for VaD. The increased apo E epsilon 4 allelic frequency in clinically diagnosed VaD patients suggests that some of the infarcts are secondary to congophilic angiopathy. The adjusted odds ratio of developing AD in this community-derived study for persons with at least one apo E epsilon 4 allele was 4.1 (95% CI: 2.2, 7.7). Thus, the apo E epsilon 4 risk of developing AD in this Chinese cohort is similar to that in western community studies.

Age Factors↗
PubMed1996

Molecular biology of APO E alleles in Alzheimer's and non-Alzheimer's dementias.

Current research into the aetiology of the dementias is focused upon genetic factors which give rise to the disease process. Recently the Apolipoprotein E gene (APO E) and in particular the epsilon 4 allele has been shown to be a risk factor for late onset Alzheimer's disease (AD) where there is an increased frequency of the epsilon 4 allele. The epsilon 4 allele has also been shown to reduce the age at onset of dementia in AD in a dose dependent manner, with the epsilon 2 allele having an opposing effect. We have genotyped a large series of clinically and neuropathologically confirmed cases of AD and found the expected increase in the Apolipoprotein epsilon 4 allele frequency when compared to a control population. Similarly, in Lewy Body Dementia (LBD) an increased epsilon 4 frequency is also found though a normal epsilon 2 frequency exists, unlike in AD where the epsilon 2 frequency is reduced. No changes in APO E allele frequencies were found in presenile AD, Parkinson's disease with or without dementia, or in Down's syndrome. No association was found between any of the APO E alleles and the histopathological indices of AD, cortical senile plaques and neurofibrillary tangles, in any disease category. Neurochemical indicators of AD, loss of choline acetyltransferase activity was also unaffected by APO E genotype. Whilst their appears to be a strong association between the APO E allele and AD and also in LBD, other related neurodegenerative disorders associated with dementia do not show such a linkage. Changes in the epsilon 2 allele frequency may indicate a genetic difference between AD and LBD. The epsilon 4 allele does not appear to influence the burden of AD type pathology and this is particularly relevant given the relative lack of NFT in LBD indicating that factors other than SP or NFT may govern the onset of dementia.

Alleles↗
PubMed2003

Estimating effective population size and migration rates from genetic samples over space and time.

In the past, moment and likelihood methods have been developed to estimate the effective population size (N(e)) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of N(e) if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N(e) and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N(e), respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N(e) and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

Computer Simulation↗
PubMed2025

Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae.

As organisms adapt to environmental changes, natural selection modifies the frequency of nonneutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae, a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.

Animals↗