scholarly journals A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: linking ecological, population genetics and evolutionary processes

2017 ◽  
Author(s):  
José M. Ponciano
Keyword(s):  
Population Genetics ◽  
Population Dynamics ◽  
Population Size ◽  
Environmental Stochasticity ◽  
Bayesian Nonparametric ◽  
Dynamics Modeling ◽  
Effective Population ◽  
Ecological Principles ◽  
Gp Model ◽  
Stochastic Population Dynamics

AbstractUsing a nonparametric Bayesian approach Palacios and Minin [1] dramatically improved the accuracy, precision of Bayesian inference of population size trajectories from gene genealogies. These authors proposed an extension of a Gaussian Process (GP) nonparametric inferential method for the intensity function of non-homogeneous Poisson processes. They found that not only the statistical properties of the estimators were improved with their method, but also, that key aspects of the demographic histories were recovered. The authors’ work represents the first Bayesian nonparametric solution to this inferential problem because they specify a convenient prior belief without a particular functional form on the population trajectory. Their approach works so well and provides such a profound understanding of the biological process, that the question arises as to how truly “biology-free” their approach really is. Using well-known concepts of stochastic population dynamics, here I demonstrate that in fact, Palacios and Minin’s GP model can be cast as a parametric population growth model with density dependence and environmental stochasticity. Making this link between population genetics and stochastic population dynamics modeling provides novel insights into eliciting biologically meaningful priors for the trajectory of the effective population size. The results presented here also bring novel understanding of GP as models for the evolution of a trait. Thus, the ecological principles foundation of Palacios and Minin [1]’s prior adds to the conceptual and scientific value of these authors’inferential approach. I conclude this note by listing a series of insights brought about by this connection with Ecology.

scholarly journals The population genetics of haplo-diploids and X-linked genes

1984 ◽  
Vol 44 (3) ◽  
pp. 321-341 ◽  
Author(s):  
P. J. Avery
Keyword(s):  
Population Genetics ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Disease Genes ◽  
Effective Population ◽  
Random Drift ◽  
Mutation Pressure ◽  
Electrophoretic Data ◽  
Fitness Parameters

SUMMARYFrom the available electrophoretic data, it is clear that haplodiploid insects have a much lower level of genetic variability than diploid insects, a difference that is only partially explained by the social structure of some haplodiploid species. The data comparing X-linked genes and autosomal genes in the same species is much more sparse and little can be inferred from it. This data is compared with theoretical analyses of X-linked genes and genes in haplodiploids. (The theoretical population genetics of X-linked genes and genes in haplodiploids are identical.) X-linked genes under directional selection will be lost or fixed more quickly than autosomal genes as selection acts more directly on X-linked genes and the effective population size is smaller. However, deleterious disease genes, maintained by mutation pressure, will give higher disease incidences at X-linked loci and hence rare mutants are easier to detect at X-linked loci. Considering the forces which can maintain balanced polymorphisms, there are much stronger restrictions on the fitness parameters at X-linked loci than at autosomal loci if genetic variability is to be maintained, and thus fewer polymorphic loci are to be expected on the X-chromosome and in haplodiploids. However, the mutation-random drift hypothesis also leads to the expectation of lower heterozygosity due to the decrease in effective population size. Thus the theoretical results fit in with the data but it is still subject to argument whether selection or mutation-random drift are maintaining most of the genetic variability at X-linked genes and genes in haplodiploids.

scholarly journals Effective population size for culturally evolving traits

2021 ◽  
Author(s):  
Dominik Deffner ◽  
Anne Kandler ◽  
Laurel Fogarty
Keyword(s):  
Population Genetics ◽  
Social Network ◽  
Cultural Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Network Structure ◽  
Cultural Exchange ◽  
Effective Size ◽  
Effective Population ◽  
Social Network Structure

ABSTRACTPopulation size has long been considered an important driver of cultural diversity and complexity. Results from population genetics, however, demonstrate that in populations with complex demographic structure or mode of inheritance, it is not the census population size, N, but the effective size of a population, Ne, that determines important evolutionary parameters. Here, we examine the concept of effective population size for traits that evolve culturally, through processes of innovation and social learning. We use mathematical and computational modeling approaches to investigate how cultural Ne and levels of diversity depend on (1) the way traits are learned, (2) population connectedness, and (3) social network structure. We show that one-to-many and frequency-dependent transmission can temporally or permanently lower effective population size compared to census numbers. We caution that migration and cultural exchange can have counter-intuitive effects on Ne. Network density in random networks leaves Ne unchanged, scale-free networks tend to decrease and small-world networks tend to increase Ne compared to census numbers. For one-to-many transmission and different network structures, effective size and cultural diversity are closely associated. For connectedness, however, even small amounts of migration and cultural exchange result in high diversity independently of Ne. Our results highlight the importance of carefully defining effective population size for cultural systems and show that inferring Ne requires detailed knowledge about underlying cultural and demographic processes.AUTHOR SUMMARYHuman populations show immense cultural diversity and researchers have regarded population size as an important driver of cultural variation and complexity. Our approach is based on cultural evolutionary theory which applies ideas about evolution to understand how cultural traits change over time. We employ insights from population genetics about the “effective” size of a population (i.e. the size that matters for important evolutionary outcomes) to understand how and when larger populations can be expected to be more culturally diverse. Specifically, we provide a formal derivation for cultural effective population size and use mathematical and computational models to study how effective size and cultural diversity depend on (1) the way culture is transmitted, (2) levels of migration and cultural exchange, as well as (3) social network structure. Our results highlight the importance of effective sizes for cultural evolution and provide heuristics for empirical researchers to decide when census numbers could be used as proxies for the theoretically relevant effective numbers and when they should not.

Predicting the effects of climate change on bird population dynamics

2019 ◽  
pp. 74-90
Author(s):  
Bernt-Erik Sæther ◽  
Steinar Engen ◽  
Marlène Gamelon ◽  
Vidar Grøtan
Keyword(s):  
Climate Change ◽  
Population Dynamics ◽  
Population Size ◽  
Environmental Stochasticity ◽  
Population Estimates ◽  
Parameter Estimates ◽  
Vital Rates ◽  
Statistical Sense ◽  
High Level ◽  
Avian Populations

Climate variation strongly influences fluctuations in size of avian populations. In this chapter, we show that it is difficult to predict how the abundance of birds will respond to climate change. A major reason for this is that most available time series of fluctuations in population size are in a statistical sense short, thus often resulting in large uncertainties in parameter estimates. We therefore argue that reliable population predictions must be based on models that capture how climate change will affect vital rates as well as including other processes (e.g. density-dependences) known to affect the population dynamics of the species in question. Our survey of examples of such forecast studies show that reliable predictions necessarily contain a high level of uncertainty. A major reason for this is that avian population dynamics are strongly influenced by environmental stochasticity, which is for most species, irrespective of their life history, the most important driver of fluctuations in population size. Credible population predictions must therefore assess the effects of such uncertainties as well as biases in population estimates.

scholarly journals Horseshoe‐based Bayesian nonparametric estimation of effective population size trajectories

Biometrics ◽  
2020 ◽  
Vol 76 (3) ◽  
pp. 677-690 ◽  
Author(s):  
James R. Faulkner ◽  
Andrew F. Magee ◽  
Beth Shapiro ◽  
Vladimir N. Minin
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Nonparametric Estimation ◽  
Bayesian Nonparametric ◽  
Effective Population ◽  
Bayesian Nonparametric Estimation

scholarly journals The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7216 ◽  
Author(s):  
Lucile Vigué ◽  
Adam Eyre-Walker
Keyword(s):  
Population Genetics ◽  
Gene Transfer ◽  
Neisseria Meningitidis ◽  
Population Size ◽  
Effective Population Size ◽  
Adaptive Evolution ◽  
Lateral Gene Transfer ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Effective Population

Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.

scholarly journals Genetic diversity and structure of two endangered mole salamander species of the Trans-Mexican Volcanic Belt

Herpetozoa ◽  
2019 ◽  
Vol 32 ◽  
pp. 237-248 ◽  
Author(s):  
Octavio Monroy-Vilchis ◽  
Rosa-Laura Heredia-Bobadilla ◽  
Martha M. Zarco-González ◽  
Víctor Ávila-Akerberg ◽  
Armando Sunny
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Size ◽  
Effective Population Size ◽  
Volcanic Belt ◽  
Population Declines ◽  
Effective Population ◽  
Mexican Volcanic Belt ◽  
Genetic Diversity And Structure ◽  
Trans Mexican Volcanic Belt

The most important factor leading to amphibian population declines and extinctions is habitat degradation and destruction. To help prevent further extinctions, studies are needed to make appropriate conservation decisions in small and fragmented populations. The goal of this study was to provide data from the population genetics of two micro-endemic mole salamanders from the Trans-Mexican Volcanic Belt. Nine microsatellite markers were used to study the population genetics of 152 individuals from two Ambystoma species. We sampled 38 individuals in two localities for A. altamirani and A. rivualre. We found medium to high levels of genetic diversity expressed as heterozygosity in the populations. However, all the populations presented few alleles per locus and genotypes. We found strong genetic structure between populations for each species. Effective population size was small but similar to that of the studies from other mole salamanders with restricted distributions or with recently fragmented habitats. Despite the medium to high levels of genetic diversity expressed as heterozygosity, we found few alleles, evidence of a genetic bottleneck and that the effective population size is small in all populations. Therefore, this study is important to propose better management plans and conservation efforts for these species.

scholarly journals Inferring population size history from large samples of genome wide molecular data - an approximate Bayesian computation approach

2016 ◽  
Author(s):  
Simon Boitard ◽  
Willy Rodriguez ◽  
Flora Jay ◽  
Stefano Mona ◽  
Frederic Austeritz
Keyword(s):  
Population Genetics ◽  
Population Size ◽  
Effective Population Size ◽  
Approximate Bayesian Computation ◽  
Recent Common Ancestor ◽  
Bayesian Computation ◽  
Effective Population ◽  
Wide Range ◽  
Complete Genomes ◽  
Approximate Bayesian

Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

scholarly journals Phenotypic plasticity and population viability: the importance of environmental predictability

2010 ◽  
Vol 277 (1699) ◽  
pp. 3391-3400 ◽  
Author(s):  
Thomas E. Reed ◽  
Robin S. Waples ◽  
Daniel E. Schindler ◽  
Jeffrey J. Hard ◽  
Michael T. Kinnison
Keyword(s):  
Population Dynamics ◽  
Phenotypic Plasticity ◽  
Population Size ◽  
Environmental Variability ◽  
Environmental Variation ◽  
Population Viability ◽  
Environmental Stochasticity ◽  
Demographic Models ◽  
Explicit Consideration ◽  
Population Viability Analyses

Phenotypic plasticity plays a key role in modulating how environmental variation influences population dynamics, but we have only rudimentary understanding of how plasticity interacts with the magnitude and predictability of environmental variation to affect population dynamics and persistence. We developed a stochastic individual-based model, in which phenotypes could respond to a temporally fluctuating environmental cue and fitness depended on the match between the phenotype and a randomly fluctuating trait optimum, to assess the absolute fitness and population dynamic consequences of plasticity under different levels of environmental stochasticity and cue reliability. When cue and optimum were tightly correlated, plasticity buffered absolute fitness from environmental variability, and population size remained high and relatively invariant. In contrast, when this correlation weakened and environmental variability was high, strong plasticity reduced population size, and populations with excessively strong plasticity had substantially greater extinction probability. Given that environments might become more variable and unpredictable in the future owing to anthropogenic influences, reaction norms that evolved under historic selective regimes could imperil populations in novel or changing environmental contexts. We suggest that demographic models (e.g. population viability analyses) would benefit from a more explicit consideration of how phenotypic plasticity influences population responses to environmental change.

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