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Abstract <p>This study investigates the accuracy of the Sequentially Markov Coalescent (SMC’) approximation in modeling the coalescent with recombination for structured populations. By comparing the total variation (TV) between the full coalescent with recombination model and its SMC’ approximation, we analyze the impact of migration rates, population structure, and bottlenecks. The results show that the TV between the full model and its SMC’ approximation in the case of structured coalescence differ most from the panmictic model at mid-range migration rates. Surprisingly, under high migration rates, a panmictic SMC’ model with historical effective population size outperforms the SMC’ approximation, suggesting that in some cases simpler models may be sufficient. In addition, our study presents an augmented structured model of SMC’ (as-SMC’), which includes information about the most recent common ancestor of the population, allowing for slightly improved accuracy in certain scenarios.</p>

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Evaluating the Accuracy of Sequentially Markov Coalescent Approximations for Structured Population Models

  • 期刊论文

  • 发表日期：

    2025年7月1日

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  • A. V. Dudkovskaia,
  • M. A. Shishkin

摘要

Abstract

This study investigates the accuracy of the Sequentially Markov Coalescent (SMC’) approximation in modeling the coalescent with recombination for structured populations. By comparing the total variation (TV) between the full coalescent with recombination model and its SMC’ approximation, we analyze the impact of migration rates, population structure, and bottlenecks. The results show that the TV between the full model and its SMC’ approximation in the case of structured coalescence differ most from the panmictic model at mid-range migration rates. Surprisingly, under high migration rates, a panmictic SMC’ model with historical effective population size outperforms the SMC’ approximation, suggesting that in some cases simpler models may be sufficient. In addition, our study presents an augmented structured model of SMC’ (as-SMC’), which includes information about the most recent common ancestor of the population, allowing for slightly improved accuracy in certain scenarios.