ArticleIntegrative and comparative biology2022
Simulation-Based Evaluation of Methods, Data Types, and Temporal Sampling Schemes for Detecting Recent Population Declines.
Article in Integrative and comparative biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The practice and promise of temporal genomics for measuring evolutionary responses to global change.Molecular ecology resources · 2025Pooled it
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Anthropocene genetic diversity loss in the marine tropics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Estimating the Effective Population Size Across Space and Time in the Critically Endangered Western Chimpanzee in Guinea-Bissau: Challenges and Implications for Conservation Management.Evolutionary applications · 2025Article
- Postglacial Echoes: Parasite Genomics Uncover Environmental Changes in Postglacial European Lakes.Molecular ecology · 2025Article
- Effective Population Size Estimation in Large Marine Populations: Considering Current Challenges and Opportunities When Simulating Large Data Sets With High-Density Genomic Information.Evolutionary applications · 2025Review
- Parallel genetic adaptation amid a background of changing effective population sizes in divergent yellow perch (Proceedings. Biological sciences · 2025Article
- Comparing GeneticEvolutionary applications · 2024Article
- Rapid genetic adaptation to a novel ecosystem despite a large founder event.Molecular ecology · 2024Article
- Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species.Evolutionary applications · 2024Article
- Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system.The Journal of heredity · 2024Article
- Impact of population structure in the estimation of recent historical effective population size by the software GONE.Genetics, selection, evolution : GSE · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding recent population trends is critical to quantifying species vulnerability and implementing effective management strategies. To evaluate the accuracy of genomic methods for quantifying recent declines (beginning <120 generations ago), we simulated genomic data using forward-time methods (SLiM) coupled with coalescent simulations (msprime) under a number of demographic scenarios. We evaluated both site frequency spectrum (SFS)-based methods (momi2, Stairway Plot) and methods that employ linkage disequilibrium information (NeEstimator, GONE) with a range of sampling schemes (contemporary-only samples, sampling two time points, and serial sampling) and data types (RAD-like data and whole-genome sequencing). GONE and momi2 performed best overall, with >80% power to detect severe declines with large sample sizes. Two-sample and serial sampling schemes could accurately reconstruct changes in population size, and serial sampling was particularly valuable for making accurate inferences when genotyping errors or minor allele frequency cutoffs distort the SFS or under model mis-specification. However, sampling only contemporary individuals provided reliable inferences about contemporary size and size change using either site frequency or linkage-based methods, especially when large sample sizes or whole genomes from contemporary populations were available. These findings provide a guide for researchers designing genomics studies to evaluate recent demographic declines.
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