Dataset Information

Estimating evolutionary and demographic parameters via ARG-derived IBD.

ABSTRACT: Inference of demographic and evolutionary parameters from a sample of genome sequences often proceeds by first inferring identical-by-descent (IBD) genome segments. By exploiting efficient data encoding based on the ancestral recombination graph (ARG), we obtain three major advantages over current approaches: (i) no need to impose a length threshold on IBD segments, (ii) IBD can be defined without the hard-to-verify requirement of no recombination, and (iii) computation time can be reduced with little loss of statistical efficiency using only the IBD segments from a set of sequence pairs that scales linearly with sample size. We first demonstrate powerful inferences when true IBD information is available from simulated data. For IBD inferred from real data, we propose an approximate Bayesian computation inference algorithm and use it to show that poorly-inferred short IBD segments can improve estimation precision. We show estimation precision similar to a previously-published estimator despite a 4 000-fold reduction in data used for inference. Computational cost limits model complexity in our approach, but we are able to incorporate unknown nuisance parameters and model misspecification, still finding improved parameter inference.

SUBMITTER: Huang Z

PROVIDER: S-EPMC10979897 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Estimating evolutionary and demographic parameters via ARG-derived IBD.

Huang Zhendong Z Kelleher Jerome J Chan Yao-Ban YB Balding David J DJ

bioRxiv : the preprint server for biology 20240313

Inference of demographic and evolutionary parameters from a sample of genome sequences often proceeds by first inferring identical-by-descent (IBD) genome segments. By exploiting efficient data encoding based on the ancestral recombination graph (ARG), we obtain three major advantages over current approaches: (i) no need to impose a length threshold on IBD segments, (ii) IBD can be defined without the hard-to-verify requirement of no recombination, and (iii) computation time can be reduced with ...[more]

PMID: 38559261

Similar Datasets

Project description:BackgroundThe Approximate Bayesian Computation (ABC) approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years.ResultsWe evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC.ConclusionsWe conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

Project description:Correlations between annual recovery and survival probabilities estimated from tag-recovery data have been used to quantify the demographic response of exploited populations to harvest. Deane et al. (2023) evaluated the bias and certainty of correlation parameters between recovery and survival probabilities estimated as random effects drawn from bivariate normal distributions relative to different prior distributions and sample size combinations. Riecke et al. (2024) observed that we incorrectly parameterized a precision matrix with Gamma priors and suggested using a Gamma(1,1) prior distribution for the standard deviations as an alternative. Riecke et al. (2024) provided results from tag-recovery models that estimate mortality hazard rates after fitting these models to tag-recovery datasets with large sample sizes. Here, we fit tag-recovery models to the data we previously simulated (Deane et al. 2023) while using Gamma(1,1) as the prior distribution for standard deviations while parameterizing these models to estimate recovery and survival in discrete time or to estimate cause-specific mortality as hazard rates. We compare our new results to previous results obtained while using Uniform(0,5) prior distribution for the standard deviations. When sample sizes were large, correlation estimates obtained with either prior distribution provided similarly reliable parameter recovery and inference, replicating results of Riecke et al. (2024). With smaller sample sizes similar to those available for most duck populations in North America, correlations estimated with either prior distribution were uncertain and ambiguous. With decreasing sample sizes, annual survival was estimated with increasing uncertainty when compared to annual recovery, likely contributing to the poor ability to estimate correlation. Consistent with the original interpretation of Deane et al. (2023) and previous literature, we found correlations were often estimated with high uncertainty such that the sign (+ or -) may be the only attribute of these parameters that can be reliably interpreted.

Project description:Effective management of wildlife populations rely on knowledge of their abundance, survival, and reproductive rates. Maintaining long-term studies capable of estimating demographic parameters for long-lived, slow-reproducing species is challenging. Insights into the effects of research intensity on the statistical power to estimate demographic parameters are limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes, and reproductive output of Indo-Pacific bottlenose dolphins (Tursiops aduncus), using a 3-year subsample of a long-term, capture-recapture study off Bunbury, Western Australia. Photo-identification on individual dolphins was collected following Pollock's Robust Design, where seasons were defined as "primary periods", each consisting of multiple "secondary periods." The full dataset consisted of 12 primary periods and 72 secondary periods, resulting in the study area being surveyed 24 times/year. We simulated reduced survey effort by randomly removing one, two, or three secondary periods per primary period. Capture-recapture models were used to assess the effect of survey intensity on the power to detect trends in population abundance, while individual dolphin sighting histories were used to assess the ability to conduct home range analyses. We used sighting records of adult females and their calving histories to assess survey effort on quantifying reproductive output. A 50% reduction in survey effort resulted in (a) up to a 36% decline in population abundance at the time of detection; (b) a reduced ability to estimate home range sizes, by increasing the time for individuals to be sighted on ≥30 occasions (an often-used metric for home range analyses) from 7.74 to 14.32 years; and (c) 33%, 24%, and 33% of annual calving events across three years going undocumented, respectively. Results clearly illustrate the importance of survey effort on the ability to assess demographic parameters with clear implications for population viability analyses, population forecasting, and conservation efforts to manage human-wildlife interactions.

Dataset Information

Estimating evolutionary and demographic parameters via ARG-derived IBD.

Publications

Estimating evolutionary and demographic parameters via ARG-derived IBD.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets