首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 0 毫秒
1.
2.
    
The recent advent of high-throughput sequencing and genotyping technologies makes it possible to produce, easily and cost effectively, large amounts of detailed data on the genotype composition of populations. Detecting locus-specific effects may help identify those genes that have been, or are currently, targeted by natural selection. How best to identify these selected regions, loci, or single nucleotides remains a challenging issue. Here, we introduce a new model-based method, called SelEstim, to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former. The underlying population genetic model is a diffusion approximation for the distribution of allele frequency in a population subdivided into a number of demes that exchange migrants. We use a Markov chain Monte Carlo algorithm for sampling from the joint posterior distribution of the model parameters, in a hierarchical Bayesian framework. We present evidence from stochastic simulations, which demonstrates the good power of SelEstim to identify loci targeted by selection and to estimate the strength of selection acting on these loci, within each deme. We also reanalyze a subset of SNP data from the Stanford HGDP–CEPH Human Genome Diversity Cell Line Panel to illustrate the performance of SelEstim on real data. In agreement with previous studies, our analyses point to a very strong signal of positive selection upstream of the LCT gene, which encodes for the enzyme lactase–phlorizin hydrolase and is associated with adult-type hypolactasia. The geographical distribution of the strength of positive selection across the Old World matches the interpolated map of lactase persistence phenotype frequencies, with the strongest selection coefficients in Europe and in the Indus Valley.  相似文献   

3.
A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info.  相似文献   

4.
5.
Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin’s exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate–aromatic interactions including CH–π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.  相似文献   

6.
    
Quantitative genetic models of sexual selection have generally failed to provide a direct connection to speciation and to explore the consequences of finite population size. The connection to speciation has been indirect because the models have treated only the evolution of male and female traits and have stopped short of modeling the evolution of sexual isolation. In this article we extend Lande's (1981) model of sexual selection to quantify predictions about the evolution of sexual isolation and speciation. Our results, based on computer simulations, support and extend Lande's claim that drift along a line of equilibria can rapidly lead to sexual isolation and speciation. Furthermore, we show that rapid speciation can occur by drift in populations of appreciable size ( Ne ≥ 1000). These results are in sharp contrast to the opinion of many researchers and textbook writers who have argued that drift does not play an important role in speciation. We argue that drift may be a powerful amplifier of speciation under a wide variety of modeling assumptions, even when selection acts directly on female mating preferences.  相似文献   

7.
    
In order to improve forecasting of pest epidemics, it is important to know the spatial scale at which specific forecasts are reliable. To investigate the spatial scale of aphid outbreaks, we have developed a spatio-temporal stochastic aphid population growth model and fitted the model to empirical spatial time series of aphid population data using a Bayesian hierarchical fitting procedure. Furthermore, detailed spatial data of the initial phases of population growth were investigated in semivariograms. Our results suggest that spatial variation is low in the initial occurrence probability at a spatial scale of 10 km. Consequently, the results support the hypothesis that initial aphid population sizes and outbreaks may be predicted in fields within a 10 km radius. For farmers, this may imply that they can rely their decision of whether to spray against aphids on observations made by other nearby farmers or by the consultancy service.  相似文献   

8.
    
Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the ‘temporal storage effect’ and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.  相似文献   

9.
    
Harbor porpoises, Phocoena phocoena, off California, comprise four recognized population stocks: Morro Bay (MOR), Monterey Bay (MRY), San Francisco-Russian River (SFRR), and Northern California-Southern Oregon (NCSO). The three southernmost stocks experienced substantial bycatch in gill net fisheries during the 1970s and 1980s. While the SFRR stock received full protection from gill nets in 1989, the MOR and MRY stocks continued to experience at least some bycatch through 2001–2002. We examined long-term population trends for these four harbor porpoise stocks, based on two sets of systematic, aerial line-transect surveys conducted off California during summer/fall of 1986–2017. We applied a Bayesian hierarchical framework to specify a process model of population density and an observation model of porpoise counts during line-transect surveys. Growth rates were estimated for periods with and without bycatch. Posterior distributions indicate the MOR, MRY, and SFRR stocks, respectively, grew at 9.6%, 5.8%, and 6.1% per year after gill nets were largely or fully eliminated for each stock. Abundance off northern California appears stable or slightly increasing. This study provides a first empirical estimate of maximum net reproductive rate for harbor porpoise (at least 9.6%), and demonstrates that porpoise populations can recover from substantial gill net impacts if bycatch is eliminated.  相似文献   

10.
Both genetic drift and natural selection cause the frequencies of alleles in a population to vary over time. Discriminating between these two evolutionary forces, based on a time series of samples from a population, remains an outstanding problem with increasing relevance to modern data sets. Even in the idealized situation when the sampled locus is independent of all other loci, this problem is difficult to solve, especially when the size of the population from which the samples are drawn is unknown. A standard χ2-based likelihood-ratio test was previously proposed to address this problem. Here we show that the χ2-test of selection substantially underestimates the probability of type I error, leading to more false positives than indicated by its P-value, especially at stringent P-values. We introduce two methods to correct this bias. The empirical likelihood-ratio test (ELRT) rejects neutrality when the likelihood-ratio statistic falls in the tail of the empirical distribution obtained under the most likely neutral population size. The frequency increment test (FIT) rejects neutrality if the distribution of normalized allele-frequency increments exhibits a mean that deviates significantly from zero. We characterize the statistical power of these two tests for selection, and we apply them to three experimental data sets. We demonstrate that both ELRT and FIT have power to detect selection in practical parameter regimes, such as those encountered in microbial evolution experiments. Our analysis applies to a single diallelic locus, assumed independent of all other loci, which is most relevant to full-genome selection scans in sexual organisms, and also to evolution experiments in asexual organisms as long as clonal interference is weak. Different techniques will be required to detect selection in time series of cosegregating linked loci.  相似文献   

11.
    
Neural networks are increasingly being used in science to infer hidden dynamics of natural systems from noisy observations, a task typically handled by hierarchical models in ecology. This article describes a class of hierarchical models parameterised by neural networks – neural hierarchical models. The derivation of such models analogises the relationship between regression and neural networks. A case study is developed for a neural dynamic occupancy model of North American bird populations, trained on millions of detection/non‐detection time series for hundreds of species, providing insights into colonisation and extinction at a continental scale. Flexible models are increasingly needed that scale to large data and represent ecological processes. Neural hierarchical models satisfy this need, providing a bridge between deep learning and ecological modelling that combines the function representation power of neural networks with the inferential capacity of hierarchical models.  相似文献   

12.
13.
    
The identification of genes influencing fitness is central to our understanding of the genetic basis of adaptation and how it shapes phenotypic variation in wild populations. Here, we used whole‐genome resequencing of wild Rocky Mountain bighorn sheep (Ovis canadensis) to >50‐fold coverage to identify 2.8 million single nucleotide polymorphisms (SNPs) and genomic regions bearing signatures of directional selection (i.e. selective sweeps). A comparison of SNP diversity between the X chromosome and the autosomes indicated that bighorn males had a dramatically reduced long‐term effective population size compared to females. This probably reflects a long history of intense sexual selection mediated by male–male competition for mates. Selective sweep scans based on heterozygosity and nucleotide diversity revealed evidence for a selective sweep shared across multiple populations at RXFP2, a gene that strongly affects horn size in domestic ungulates. The massive horns carried by bighorn rams appear to have evolved in part via strong positive selection at RXFP2. We identified evidence for selection within individual populations at genes affecting early body growth and cellular response to hypoxia; however, these must be interpreted more cautiously as genetic drift is strong within local populations and may have caused false positives. These results represent a rare example of strong genomic signatures of selection identified at genes with known function in wild populations of a nonmodel species. Our results also showcase the value of reference genome assemblies from agricultural or model species for studies of the genomic basis of adaptation in closely related wild taxa.  相似文献   

14.
Population monitoring of Atlantic salmon (Salmo salar L.) abundance is an essential element to understand annual stock variability and inform fisheries management processes. Smolts are the life stage marking the transition from the freshwater to the marine phase of anadromous Atlantic salmon. Estimating smolt abundance allows for subsequent inferences on freshwater and marine survival rates. Annual abundances of out-migrating Atlantic salmon smolts were estimated using Bayesian models and an 18-year capture–mark–recapture time series from two to five trapping locations within the Restigouche River (Canada) catchment. Some of the trapping locations were at the outlet of large upstream tributaries, and these sampled a portion of the total out-migrating population of smolts for the watershed, whereas others were located just above the head of tide of the Restigouche River and sampled the entire run of salmon smolts. Due to logistic and environmental conditions, not all trapping locations were operational each year. Additionally, recapture rates were relatively low (<5%), and the absolute number of recaptures was relatively few (most often a few dozen), leading to incoherent and highly uncertain estimates of tributary-specific and whole catchment abundance estimates when the data were modeled independently among trapping locations and years. Several models of increasing complexity were tested using simulated data, and the best-performing model in terms of bias and precision incorporated a hierarchical structure among years on the catchability parameters and included an explicit spatial structure to account for the annual variations in the number of sampled locations within the watershed. When the best model was applied to the Restigouche River catchment dataset, the annual smolt abundance estimates varied from 250,000 to 1 million smolts, and the subbasin estimates of abundance were consistent with the spatial structure of the monitoring programme. Ultimately, increasing the probabilities of capture and the absolute number of recaptures at the different traps will be required to improve the precision and reduce the bias of the estimates of smolt abundance for the entire basin and within subbasins of the watershed. The model and approach provide a significant improvement in the models used to date based on independent estimates of abundance by trapping location and year. Total abundance and relative production in discrete spawning, nesting, or rearing areas provide critical information to appropriately understand and manage the threats to species that can occur at subpopulation spatial scales.  相似文献   

15.
16.
    
Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium‐density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.  相似文献   

17.
We consider a stoichiometric population model of two producers and one consumer. Stoichiometry can be thought of as the tracking of food quality in addition to food quantity. Our model assumes a reduced rate of conversion of biomass from producer to consumer when food quality is low. The model is open for carbon but closed for nutrient. The introduction of the second producer, which competes with the first, leads to new equilibria, new limit cycles, and new bifurcations. The focus of this paper is on the bifurcations which are the result of enrichment. The primary parameters we vary are the growth rates of both producers. Secondary variable parameters are the total nutrients in the system, and the producer nutrient uptake rates. The possible equilibria are: no-life, one-producer, coexistence of both producers, the consumer coexisting with either producer, and the consumer coexisting with both producers. We observe limit cycles in the latter three coexistence combinations. Bifurcation diagrams along with corresponding representative time series summarize the behaviours observed for this model.  相似文献   

18.
We study a discrete-time system of equations for a structured ungulate population exploited by human harvesting or a dynamic predator. The population is divided into juveniles, and female and male adults. Harvesting is concentrated on adults (trophy hunting of males or population control measures on females), whereas predation occurs in juveniles. Though the model consists of four nonlinear equations, we find explicit expressions for the steady states. We use these explicit expressions to investigate harvesting rates that allow population persistence, rates that ensure population control, and optimal harvesting efforts. Several reductions of complexity allow for a detailed analysis of the dynamics of the model. Most notably, we find that even compensatory density dependence can lead to a period doubling bifurcation, that the model does not support consumer–resource cycles, and that an Allee effect can emerge from the interplay of stage-specific predation and density-dependent prey reproduction.  相似文献   

19.
    
Population viability analyses are useful tools to predict abundance and extinction risk for imperiled species. In southeastern North America, the federally threatened gopher tortoise (Gopherus polyphemus) is a keystone species in the diverse and imperiled longleaf pine (Pinus palustris) ecosystem, and researchers have suggested that tortoise populations are declining and characterized by high extinction risk. We report results from a 30-year demographic study of gopher tortoises in southern Alabama (1991–2020), where 3 populations have been stable and 3 others have declined. To better understand the demographic vital rates associated with stable and declining tortoise populations, we used a multi-state hierarchical mark-recapture model to estimate sex- and stage-specific patterns of demographic vital rates at each population. We then built a predictive population model to project population dynamics and evaluate extinction risk in a population viability context. Population structure did not change significantly in stable populations, but juveniles became less abundant in declining populations over 30 years. Apparent survival varied by age, sex, and site; adults had higher survival than juveniles, but female survival was substantially lower in declining populations than in stable ones. Using simulations, we predicted that stable populations with high female survival would persist over the next 100 years but sites with lower female survival would decline, become male-biased, and be at high risk of extirpation. Stable populations were most sensitive to changes in apparent survival of adult females. Because local populations varied greatly in vital rates, our analysis improves upon previous demographic models for northern populations of gopher tortoises by accounting for population-level variation in demographic patterns and, counter to previous model predictions, suggests that small tortoise populations can persist when habitat is managed effectively. © 2021 The Wildlife Society.  相似文献   

20.
    
Reciprocal selection between symbiotic organisms and their hosts can generate variations in local adaptation between them. Symbionts often form species complexes with lineages partially adapted to various hosts. However, it is unclear how interactions among these lineages influences geographic variation in the extent of host-symbiont local adaptation. We addressed this shortcoming with experiments on burying beetles Nicrophorus vespilloides and their specialist phoretic mite Poecilochirus carabi in two adjacent woodlands. Burying beetles transport these mites to vertebrate carrion upon which they both reproduce. P. carabi appears to be a species complex, with distinct lineages that specialise on breeding alongside different Nicrophorus species. We found that in one wood (Gamlingay Woods), N. vespilloides carries a mixture of mite lineages, with each lineage corresponding to one of the four Nicrophorus species that inhabits this wood. However, two burying beetle species coexist in neighbouring Waresley Woods and here N. vespilloides predominantly carries the mite lineage that favours N. vespilloides. Mite lineage mixing alters the degree of local adaptation for both N. vespilloides and the P. carabi mites, affecting reproductive success variably across different woodlands. In Gamlingay, mite lineage mixing reduced N. vespilloides reproductive success, while experimentally purifying mites lineage enhanced it. The near pure lineage of vespilloides mites negligibly affected Waresley N. vespilloides. Mite reproductive success varied with host specificity: Gamlingay mites had greatest reproductive success on Gamlingay beetles, and performed less well with Waresley beetles. By contrast, Waresley mites had consistent reproductive success, regardless of beetle's woodland of origin. We conclude that there is some evidence that N. vespilloides and its specific mite lineage have coadapted. However, neither N. vespilloides nor its mite lineage adapted to breed alongside other mite lineages. This, we suggest, causes variation between Waresley and Gaminglay Woods in the extent of local adaptation between N. vespilloides beetles and their P. carabi mites.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号