共查询到20条相似文献,搜索用时 0 毫秒
1.
Leandro Duarte;Gabriel Nakamura;Vanderlei Debastiani;Renan Maestri;Maria João Ramos Pereira;Marcus Cianciaruso;José Alexandre Felizola Diniz-Filho; 《Ecography》2023,2023(12):e06544
The imprint left by niche evolution on the variation of biological diversity across spatial and environmental gradients is still debated among ecologists. Furthermore, understanding to what extent dispersal limitation may reinforce or blur such imprint is still a gap in the ecological knowledge. In this article we introduce a simulation approach coupled to approximate Bayesian computation (ABC) that parameterizes both the adaptation rate of species' niche positions over the evolution of a monophyletic lineage and the intensity of dispersal limitation associated with the variation of species alpha diversity among assemblages distributed across spatial and environmental gradients. The analytical tool was implemented in the R package 'mcfly' (www.r-project.org). We evaluated the statistical performance of the analytical framework using simulated datasets, which confirmed the suitability of the analysis to estimate adaptation rate parameter but showed to be less precise in relation to the dispersal limitation parameter. Also, we found that increased dispersal limitation levels improved the parameterization of the adaptation rate of species' niche positions in simulated datasets. Further, we evaluated the role played by niche evolution and dispersal limitation on species alpha diversity variation of Phyllostomidae bats across the Neotropics. The framework proposed here shed light on the links between niche evolution, dispersal limitation and gradients of biological diversity, and thereby improved our understanding of evolutionary imprints on current biological diversity patterns. 相似文献
2.
The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine-learning literature. We consider different types of boosting and compare them to partial least-squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the reintroduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4Neu) and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate and find that most of the variation across loci of the ancestral mutation rate u is between 7.7 × 10−4 and 3.5 × 10−3 per locus per generation. The proportion of males with access to matings is estimated as , which is in good agreement with recent independent estimates. 相似文献
3.
Rosa María García-Martínez Irene de los Angeles Barriga-Sosa Benjamín López Omar Mejía 《Journal of fish biology》2020,97(4):1039-1050
In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico. 相似文献
4.
Frank SA 《Journal of evolutionary biology》2011,24(3):485-496
The consistency of the species abundance distribution across diverse communities has attracted widespread attention. In this paper, I argue that the consistency of pattern arises because diverse ecological mechanisms share a common symmetry with regard to measurement scale. By symmetry, I mean that different ecological processes preserve the same measure of information and lose all other information in the aggregation of various perturbations. I frame these explanations of symmetry, measurement, and aggregation in terms of a recently developed extension to the theory of maximum entropy. I show that the natural measurement scale for the species abundance distribution is log-linear: the information in observations at small population sizes scales logarithmically and, as population size increases, the scaling of information grades from logarithmic to linear. Such log-linear scaling leads naturally to a gamma distribution for species abundance, which matches well with the observed patterns. Much of the variation between samples can be explained by the magnitude at which the measurement scale grades from logarithmic to linear. This measurement approach can be applied to the similar problem of allelic diversity in population genetics and to a wide variety of other patterns in biology. 相似文献
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Alexander T. Xue Michael J. Hickerson 《Evolution; international journal of organic evolution》2020,74(5):808-830
Comparing divergences across multiple sister population pairs has been a focus in phylogeography since its inception. Initial approaches used organelle genetic data and involved qualitative comparisons of phylogenetic patterns to evaluate hypotheses of shared and variable evolutionary responses. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can exploit aggregated genomic-scale data within a unified analytical framework. To this end, we introduce the aggregate joint site frequency spectrum (ajSFS) by validating its use within a hierarchical Bayesian framework through several in silico experiments. Subsequently, we applied our method against two published restriction site–associated DNA marker datasets consisting of eight local replicates of a lamprey species pair and six co-distributed passerine taxon pairs, respectively, with the aim of inferring variability in co-divergence and co-migration histories. We found that the lamprey population pairs exhibited temporal synchrony in both co-divergence and collective secondary contact times, yet an idiosyncratic pattern in secondary migration intensities. In contrast, the bird population pairs displayed thoroughly asynchronous co-divergence histories. Our results demonstrate that the ajSFS can be exploited for complex and flexible co-demographic inference, opening up new possibilities for comparative phylogeography and population genomic studies. 相似文献
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S Pueyo 《Ecology and evolution》2012,2(5):988-993
An increasing number of authors agree in that the maximum entropy principle (MaxEnt) is essential for the understanding of macroecological patterns. However, there are subtle but crucial differences among the approaches by several of these authors. This poses a major obstacle for anyone interested in applying the methodology of MaxEnt in this context. In a recent publication, Frank (2011) gives some arguments why his own approach would represent an improvement as compared to the earlier paper by Pueyo et al. (2007) and also to the views by Edwin T. Jaynes, who first formulated MaxEnt in the context of statistical physics. Here I show that his criticisms are flawed and that there are fundamental reasons to prefer the original approach. 相似文献
8.
Nobuyuki Kutsukake Hideki Innan 《Evolution; international journal of organic evolution》2013,67(2):355-367
Phylogenetic comparative methods (PCMs) have been used to test evolutionary hypotheses at phenotypic levels. The evolutionary modes commonly included in PCMs are Brownian motion (genetic drift) and the Ornstein–Uhlenbeck process (stabilizing selection), whose likelihood functions are mathematically tractable. More complicated models of evolutionary modes, such as branch‐specific directional selection, have not been used because calculations of likelihood and parameter estimates in the maximum‐likelihood framework are not straightforward. To solve this problem, we introduced a population genetics framework into a PCM, and here, we present a flexible and comprehensive framework for estimating evolutionary parameters through simulation‐based likelihood computations. The method does not require analytic likelihood computations, and evolutionary models can be used as long as simulation is possible. Our approach has many advantages: it incorporates different evolutionary modes for phenotypes into phylogeny, it takes intraspecific variation into account, it evaluates full likelihood instead of using summary statistics, and it can be used to estimate ancestral traits. We present a successful application of the method to the evolution of brain size in primates. Our method can be easily implemented in more computationally effective frameworks such as approximate Bayesian computation (ABC), which will enhance the use of computationally intensive methods in the study of phenotypic evolution. 相似文献
9.
Neuenschwander S Largiadèr CR Ray N Currat M Vonlanthen P Excoffier L 《Molecular ecology》2008,17(3):757-772
The present distribution of freshwater fish in the Alpine region has been strongly affected by colonization events occurring after the last glacial maximum (LGM), some 20 000 years ago. We use here a spatially explicit simulation framework to model and better understand their colonization dynamics in the Swiss Rhine basin. This approach is applied to the European bullhead ( Cottus gobio ), which is an ideal model organism to study fish past demographic processes since it has not been managed by humans. The molecular diversity of eight sampled populations is simulated and compared to observed data at six microsatellite loci under an approximate Bayesian computation framework to estimate the parameters of the colonization process. Our demographic estimates fit well with current knowledge about the biology of this species, but they suggest that the Swiss Rhine basin was colonized very recently, after the Younger Dryas some 6600 years ago. We discuss the implication of this result, as well as the strengths and limits of the spatially explicit approach coupled to the approximate Bayesian computation framework. 相似文献
10.
The ability of the site-frequency spectrum (SFS) to reflect the particularities of gene genealogies exhibiting multiple mergers of ancestral lines as opposed to those obtained in the presence of population growth is our focus. An excess of singletons is a well-known characteristic of both population growth and multiple mergers. Other aspects of the SFS, in particular, the weight of the right tail, are, however, affected in specific ways by the two model classes. Using an approximate likelihood method and minimum-distance statistics, our estimates of statistical power indicate that exponential and algebraic growth can indeed be distinguished from multiple-merger coalescents, even for moderate sample sizes, if the number of segregating sites is high enough. A normalized version of the SFS (nSFS) is also used as a summary statistic in an approximate Bayesian computation (ABC) approach. The results give further positive evidence as to the general eligibility of the SFS to distinguish between the different histories. 相似文献
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Lotte A. van Boheemen Eric Lombaert Kristin A. Nurkowski Bertrand Gauffre Loren H. Rieseberg Kathryn A. Hodgins 《Molecular ecology》2017,26(20):5421-5434
Admixture between differentiated populations is considered to be a powerful mechanism stimulating the invasive success of some introduced species. It is generally facilitated through multiple introductions; however, the importance of admixture prior to introduction has rarely been considered. We assess the likelihood that the invasive Ambrosia artemisiifolia populations of Europe and Australia developed through multiple introductions or were sourced from a historical admixture zone within native North America. To do this, we combine large genomic and sampling data sets analysed with approximate Bayesian computation and random forest scenario evaluation to compare single and multiple invasion scenarios with pre‐ and postintroduction admixture simultaneously. We show the historical admixture zone within native North America originated before global invasion of this weed and could act as a potential source of introduced populations. We provide evidence supporting the hypothesis that the invasive populations established through multiple introductions from the native range into Europe and subsequent bridgehead invasion into Australia. We discuss the evolutionary mechanisms that could promote invasiveness and evolutionary potential of alien species from bridgehead invasions and admixed source populations. 相似文献
12.
Parul Johri Kellen Riall Hannes Becher Laurent Excoffier Brian Charlesworth Jeffrey D. Jensen 《Molecular biology and evolution》2021,38(7):2986
Current procedures for inferring population history generally assume complete neutrality—that is, they neglect both direct selection and the effects of selection on linked sites. We here examine how the presence of direct purifying selection and background selection may bias demographic inference by evaluating two commonly-used methods (MSMC and fastsimcoal2), specifically studying how the underlying shape of the distribution of fitness effects and the fraction of directly selected sites interact with demographic parameter estimation. The results show that, even after masking functional genomic regions, background selection may cause the mis-inference of population growth under models of both constant population size and decline. This effect is amplified as the strength of purifying selection and the density of directly selected sites increases, as indicated by the distortion of the site frequency spectrum and levels of nucleotide diversity at linked neutral sites. We also show how simulated changes in background selection effects caused by population size changes can be predicted analytically. We propose a potential method for correcting for the mis-inference of population growth caused by selection. By treating the distribution of fitness effect as a nuisance parameter and averaging across all potential realizations, we demonstrate that even directly selected sites can be used to infer demographic histories with reasonable accuracy. 相似文献
13.
Francesco Montinaro Vasili Pankratov Burak Yelmen Luca Pagani Mayukh Mondal 《American journal of human genetics》2021,108(11):2037-2051
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应用最大似然法(ML)、贝叶斯推论(BI)、邻接法(NJ)和似然比检验(hLRTs)进行泽泻目分子系统学研究。所用的rbcL基因序列代表了泽泻目14科46属以及作为外类群的6相关属。研究结果表明,*等级制似然比检验表明泽泻目rbcL序列最适合的DNA进化模型为GTR+I+G,最大似然法、贝叶斯法和邻接法构建的系统发育树拓扑结构相似,没有显著的差异,但贝叶斯树支持率较高;泽泻目为一单系类群,由两个主要谱系分支构成,深层分布格局由5个主要分支构成。基于分子系统发育树,文中对泽泻目科间、水鳖科+茨藻科、泽泻科+花蔺科+黄花蔺科、和\"Cymodoeaceae complex\"的系统发育关系进行了讨论。研究结果还表明,泽泻目系统发育关系可能还需要更多的证据进一步的澄清。 相似文献
15.
Why does the neutral theory, which is based on unrealistic assumptions, predict diversity patterns so accurately? Answering questions like this requires a radical change in the way we tackle them. The large number of degrees of freedom of ecosystems pose a fundamental obstacle to mechanistic modelling. However, there are tools of statistical physics, such as the maximum entropy formalism (MaxEnt), that allow transcending particular models to simultaneously work with immense families of models with different rules and parameters, sharing only well‐established features. We applied MaxEnt allowing species to be ecologically idiosyncratic, instead of constraining them to be equivalent as the neutral theory does. The answer we found is that neutral models are just a subset of the majority of plausible models that lead to the same patterns. Small variations in these patterns naturally lead to the main classical species abundance distributions, which are thus unified in a single framework. 相似文献
16.
Heiko Götte Marietta Kirchner Meinhard Kieser 《Biometrical journal. Biometrische Zeitschrift》2020,62(3):627-642
Defining the target population based on predictive biomarkers plays an important role during clinical development. After establishing a relationship between a biomarker candidate and response to treatment in exploratory phases, a subsequent confirmatory trial ideally involves only subjects with high potential of benefiting from the new compound. In order to identify those subjects in case of a continuous biomarker, a cut-off is needed. Usually, a cut-off is chosen that resulted in a subgroup with a large observed treatment effect in an exploratory trial. However, such a data-driven selection may lead to overoptimistic expectations for the subsequent confirmatory trial. Treatment effect estimates, probability of success, and posterior probabilities are useful measures for deciding whether or not to conduct a confirmatory trial enrolling the biomarker-defined population. These measures need to be adjusted for selection bias. We extend previously introduced Approximate Bayesian Computation techniques for adjustment of subgroup selection bias to a time-to-event setting with cut-off selection. Challenges in this setting are that treatment effects become time-dependent and that subsets are defined by the biomarker distribution. Simulation studies show that the proposed method provides adjusted statistical measures which are superior to naïve Maximum Likelihood estimators as well as simple shrinkage estimators. 相似文献
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Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression—the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a “soft sweep,” which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci. 相似文献
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Continuous progress in empirical population genetics based on the whole‐genome polymorphism data requires the theoretical analysis of refined models in order to interpret the evolutionary history of populations with adequate accuracy. Recent studies focus prevalently on the aspects of demography and adaptation, whereas age structure (for example, in plants via the maintenance of seed banks) has attracted less attention. Germ banking, that is, seed or egg dormancy, is a prevalent and important life‐history trait in plants and invertebrates, which buffers against environmental variability and modulates species extinction in fragmented habitats. Within this study, we investigate the combined effect of germ banking and time‐varying population size on the neutral coalescent and particularly derive the allele frequency spectrum under some simplifying assumptions. We then perform an ABC analysis using two simple demographic scenarios—a population expansion and an instantaneous decline. We demonstrate the appreciable influence of seed banks on the estimation of demographic parameters depending on the germination rate with biases scaled by the square of the germination rate. In the more complex case of a population bottleneck, which comprises an instantaneous decline and an expansion phase, ignoring information on the germination rate denies reliable estimates of the bottleneck parameters via the allelic spectrum. In particular, when seeds remain in the bank over several generations, recent expansions may remain invisible in the frequency spectrum, whereas ancient declines leave signatures much longer than in the absence of seed bank. 相似文献