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Background <p>While advances in high-throughput sequencing have facilitated the production of genome-wide data to illuminate genetic and phenotypic diversity and to inform management, conservation, and domestication of natural resources, the generation and processing of genome-wide variants obtained via high-throughput sequencing are prone to errors. Data filtering is an effective approach to improving data quality, but optimal filtering strategies have not been thoroughly investigated across species, especially for non-model aquatic invertebrates, such as bivalves, despite their high ecological and economic values. Given that bivalves have complex genomic architecture, exhibit special life history traits, and frequently experience drastic demographic changes, a comprehensive understanding of effects of variant filtering on downstream inferences is particularly needed.</p> Results <p>Using whole genome sequencing data, we create a collection of filtered data sets representing a full range of filtering for mapping quality, read depth, genotyping quality, missing data, and minor allele frequency to conduct population genetic and demographic analyses for six representative natural stocks of an ecologically and economically important marine bivalve, Zhikong scallop <i>Chlamys farreri</i>. While population structure evaluation is robust to various filtering choices, different filtering strategies apply to assessments of individual inbreeding, genetic diversity, and demographic trajectory. For inbreeding estimation, we suggest adopting higher filtering thresholds for minor allele frequency while keeping filtering criteria for other parameters relatively relaxing. For genetic diversity calculation, we recommend systematically testing both data sets that include and exclude invariants within a sample site and clearly reporting the sets of loci included for evaluation. For demographic history reconstruction, filtering options that maximize the number of reliable variants are more appropriate.</p> Conclusions <p>Findings from this study not only offer a reference for parameter settings in variant filtering for natural scallop stocks but also demonstrate a practical framework for how to navigate tradeoffs between data quality and quantity for other similar bivalves, such as oyster, clam, and mussel. Overall, our study provides a promising guideline for obtaining reliable genome-wide variants to instruct management, conservation, and domestication programs for non-model aquatic invertebrates.</p>

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Navigating tradeoffs in variant filtering for population genetic and demographic inferences to inform management, conservation, and domestication in non-model marine bivalves: a case study in scallop

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月14日

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  • Xiaoshen Yin,
  • Shiyun Duan,
  • Zhenmin Bao,
  • Xiaoli Hu

摘要

Background

While advances in high-throughput sequencing have facilitated the production of genome-wide data to illuminate genetic and phenotypic diversity and to inform management, conservation, and domestication of natural resources, the generation and processing of genome-wide variants obtained via high-throughput sequencing are prone to errors. Data filtering is an effective approach to improving data quality, but optimal filtering strategies have not been thoroughly investigated across species, especially for non-model aquatic invertebrates, such as bivalves, despite their high ecological and economic values. Given that bivalves have complex genomic architecture, exhibit special life history traits, and frequently experience drastic demographic changes, a comprehensive understanding of effects of variant filtering on downstream inferences is particularly needed.

Results

Using whole genome sequencing data, we create a collection of filtered data sets representing a full range of filtering for mapping quality, read depth, genotyping quality, missing data, and minor allele frequency to conduct population genetic and demographic analyses for six representative natural stocks of an ecologically and economically important marine bivalve, Zhikong scallop Chlamys farreri. While population structure evaluation is robust to various filtering choices, different filtering strategies apply to assessments of individual inbreeding, genetic diversity, and demographic trajectory. For inbreeding estimation, we suggest adopting higher filtering thresholds for minor allele frequency while keeping filtering criteria for other parameters relatively relaxing. For genetic diversity calculation, we recommend systematically testing both data sets that include and exclude invariants within a sample site and clearly reporting the sets of loci included for evaluation. For demographic history reconstruction, filtering options that maximize the number of reliable variants are more appropriate.

Conclusions

Findings from this study not only offer a reference for parameter settings in variant filtering for natural scallop stocks but also demonstrate a practical framework for how to navigate tradeoffs between data quality and quantity for other similar bivalves, such as oyster, clam, and mussel. Overall, our study provides a promising guideline for obtaining reliable genome-wide variants to instruct management, conservation, and domestication programs for non-model aquatic invertebrates.