scholarly journals Inferring demographic history using two-locus statistics

2017 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Ryan N. Gutenkunst
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Composite Likelihood ◽  
Effective Population ◽  
Allele Frequency Spectrum ◽  
Variation Data ◽  
Population Genetic Inference ◽  
Genetic Inference ◽  
Population Demographic

AbstractPopulation demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are indeed more sensitive to demographic history than single-locus statistics such as the AFS. In particular, two-locus statistics escape the notorious confounding of depth and duration of a bottleneck, and they provide a means to estimate effective population size based on the recombination rather than mutation rate. We applied our approach to a Zambian population of Drosophila melanogaster. Notably, using both single– and two-locus statistics, we found substantially lower estimates of effective population size than previous works. Together, our results demonstrate the broad potential for two-locus statistics to enable powerful population genetic inference.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

scholarly journals Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis

2008 ◽  
Vol 90 (1) ◽  
pp. 119-128 ◽  
Author(s):  
STEPHEN I. WRIGHT ◽  
NARDIN NANO ◽  
JOHN PAUL FOXE ◽  
VAQAAR-UN NISA DAR
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Likelihood Estimation ◽  
Composite Likelihood ◽  
Nuclear Genes ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Arabidopsis Lyrata ◽  
Tests Of Neutrality ◽  
Low Levels

SummaryCytoplasmic genomes typically lack recombination, implying that genetic hitch-hiking could be a predominant force structuring nucleotide polymorphism in the chloroplast and mitochondria. We test this hypothesis by analysing nucleotide polymorphism data at 28 loci across the chloroplast and mitochondria of the outcrossing plant Arabidopsis lyrata, and compare patterns with multiple nuclear loci, and the highly selfing Arabidopsis thaliana. The maximum likelihood estimate of the ratio of effective population size at cytoplasmic relative to nuclear genes in A. lyrata does not depart from the neutral expectation of 0·5. Similarly, the ratio of effective size in A. thaliana is close to unity, the neutral expectation for a highly selfing species. The results are thus consistent with neutral organelle polymorphism in these species or with comparable effects of hitch-hiking in both cytoplasmic and nuclear genes, in contrast to the results of recent studies on gynodioecious taxa. The four-gamete test and composite likelihood estimation provide evidence for very low levels of recombination in the organelles of A. lyrata, although permutation tests do not suggest that adjacent polymorphic sites are more closely linked than more distant sites across the two genomes, suggesting that mutation hotspots or very low rates of gene conversion could explain the data.

scholarly journals Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo

2018 ◽  
Author(s):  
Amy Ko ◽  
Rasmus Nielsen
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Population Size ◽  
Effective Population Size ◽  
Simulated Data ◽  
Composite Likelihood ◽  
Joint Estimation ◽  
Pedigree Information ◽  
Effective Population

Pedigrees provide a fine resolution of the genealogical relationships among individuals and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of short-term effective population size (Ne), which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and Ne from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals with the use of composite likelihood, which significantly increases computational efficiency. We show on simulated data that our method is able to jointly estimate relationships up to first cousins and Ne with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.

scholarly journals Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

2017 ◽  
Author(s):  
Erik M. Volz ◽  
Xavier Didelot
Keyword(s):  
Growth Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Growth Rates ◽  
Sequence Data ◽  
Demographic History ◽  
Parametric Models ◽  
Effective Population ◽  
Epidemic Dynamics ◽  
Non Parametric

AbstractNon-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stationary stochastic processes which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

scholarly journals Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Song ◽  
Bin Gao ◽  
Peter Halvarsson ◽  
Yun Fang ◽  
Siegfried Klaus ◽  
...  
Keyword(s):  
Climate Change ◽  
Boreal Forest ◽  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Bird Species ◽  
Future Climate Change ◽  
Effective Population ◽  
Hazel Grouse ◽  
Chinese Grouse

Abstract Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.

scholarly journals Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

2019 ◽  
Author(s):  
Xi Wang ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Picea Abies ◽  
Population Size ◽  
Effective Population Size ◽  
Norway Spruce ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

scholarly journals An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9939
Author(s):  
Jessica F. McLaughlin ◽  
Kevin Winker
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Population Level ◽  
Sample Sizes ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Single Nucleotide ◽  
Population Demographic

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

scholarly journals Robust estimation of recent effective population size from number of independent origins in soft sweeps

2018 ◽  
Author(s):  
Bhavin S. Khatri ◽  
Austin Burt
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Demographic History ◽  
Population Sample ◽  
Natural Populations ◽  
Population History ◽  
Effective Population ◽  
Current Frequency ◽  
Population Size Estimate ◽  
Recurrent Mutations

Estimating recent effective population size is of great importance in characterising and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whilst methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward time theoretical framework, we show the mean number of origins is a function of θ = 2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants pre-existed before selection arose, and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared to time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6 × 107, and including seasonal demographic oscillations, a minimum effective population size greater than 6 × 106 and a maximum less than 3 × 109.

scholarly journals Recent evolution in Rattus norvegicus is shaped by declining effective population size

2015 ◽  
Author(s):  
Eva E Deinum ◽  
Daniel L Halligan ◽  
Rob W Ness ◽  
Yao-Hua Zhang ◽  
Lin Cong ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Rattus Norvegicus ◽  
Demographic History ◽  
Physical Distance ◽  
House Mice ◽  
Effective Population ◽  
Genome Sequences ◽  
Wild House Mice ◽  
Wild Rats

The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analysing genome sequences of 12 wild-caught brown rats from their ancestral range in NE China, along with the sequence of a black rat, R. rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (N_e) of this species = 1.24 x 10^5, based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse Mus musculus castaneus), which has a much larger N_e. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent (PSMC) analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements (CNEs). This leads to negative estimates of the rate of adaptive evolution (alpha) in proteins and CNEs, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.

scholarly journals Runs of homozygosity in killer whale genomes provide a global record of demographic histories

2021 ◽  
Author(s):  
Andy Foote ◽  
Rebecca Hooper ◽  
Alana Alexander ◽  
Robin Baird ◽  
Charles Baker ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Killer Whale ◽  
Demographic History ◽  
Population History ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
High Background ◽  
Genome Wide ◽  
Conservation Concern

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically the probability of inbreeding mediated by mating system and/or population demography. Here, we investigate whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global dataset of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstruct demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We find a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations and populations of known conservation concern, including a Scottish population, for which 37.8% of the autosomes comprised of ROH >1.5 Mb in length.

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