ArticleGenetics2012
Neutrality tests for sequences with missing data.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The missing data problem in population genomics and statistical methods to address them.G3 (Bethesda, Md.) · 2026Article
- Negative global-scale association between genetic diversity and speciation rates in mammals.Nature communications · 2025Article
- Genome-wide patterns of noncoding and protein-coding sequence variation in the major fungal pathogen Aspergillus fumigatus.G3 (Bethesda, Md.) · 2024Article
- Genome-wide patterns of non-coding sequence variation in the major fungal pathogenbioRxiv : the preprint server for biology · 2024Article
- Chromatin structure influences rate and spectrum of spontaneous mutations inGenome research · 2023Article
- Article
- Molecular genetic diversity and bioinformatic analysis of Leucocytozoon sabrazesi based on the mitochondrial genes cytb, coxI and coxIII and co-infection of Plasmodium spp.Parasite (Paris, France) · 2022Article
- Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions.Genetics, selection, evolution : GSE · 2021Article
- A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs.PLoS genetics · 2019Article
- Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides.Genome biology and evolution · 2019Article
- The Evolutionary Consequences of Transposon-Related Pericentromer Expansion in Melon.Genome biology and evolution · 2018Article
- The Site Frequency/Dosage Spectrum of Autopolyploid Populations.Frontiers in genetics · 2018Article
- Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations.Heredity · 2018Article
- A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia.G3 (Bethesda, Md.) · 2017Article
- Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families.Genome biology and evolution · 2016Article
- Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.PLoS neglected tropical diseases · 2015Article
- Characterization of the porcine nutrient and taste receptor gene repertoire in domestic and wild populations across the globe.BMC genomics · 2014Article
- Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.BMC bioinformatics · 2013Article
- SNP calling by sequencing pooled samples.BMC bioinformatics · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Missing data are common in DNA sequences obtained through high-throughput sequencing. Furthermore, samples of low quality or problems in the experimental protocol often cause a loss of data even with traditional sequencing technologies. Here we propose modified estimators of variability and neutrality tests that can be naturally applied to sequences with missing data, without the need to remove bases or individuals from the analysis. Modified statistics include the Watterson estimator θW, Tajima's D, Fay and Wu's H, and HKA. We develop a general framework to take missing data into account in frequency spectrum-based neutrality tests and we derive the exact expression for the variance of these statistics under the neutral model. The neutrality tests proposed here can also be used as summary statistics to describe the information contained in other classes of data like DNA microarrays.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.