Population Genetic Concerns Related to the Interpretation of Empirical Outliers and the Neglect of Common Evolutionary Processes

Overview

Journal Heredity (Edinb)

Specialty Genetics

Date 2023 Feb 24

PMID 36829044

Authors

Jeffrey D Jensen

Affiliations

Soon will be listed here.

Citing Articles

Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.

Terbot Ii J, Terbot 2nd J, Soni V, Versoza C, Pfeifer S, Jensen J Genome Biol Evol. 2025; 17(1).

PMID: 39749927 PMC: 11746965. DOI: 10.1093/gbe/evae281.

Inferring the demographic history of aye-ayes () from high-quality, whole-genome, population-level data.

Terbot 2nd J, Soni V, Versoza C, Pfeifer S, Jensen J bioRxiv. 2024; .

PMID: 39605532 PMC: 11601231. DOI: 10.1101/2024.11.08.622659.

A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes () utilizing a well-fit evolutionary baseline model.

Soni V, Terbot 2nd J, Versoza C, Pfeifer S, Jensen J bioRxiv. 2024; .

PMID: 39605496 PMC: 11601216. DOI: 10.1101/2024.11.08.622667.

Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.

Soni V, Jensen J bioRxiv. 2024; .

PMID: 39605418 PMC: 11601476. DOI: 10.1101/2024.09.19.613979.

The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects.

Soni V, Pfeifer S, Jensen J Genome Biol Evol. 2024; 16(2).

PMID: 38207127 PMC: 10834165. DOI: 10.1093/gbe/evae004.

References

Charlesworth B, Jensen J . Effects of Selection at Linked Sites on Patterns of Genetic Variability. Annu Rev Ecol Evol Syst. 2023; 52:177-197. PMC: 10120885. DOI: 10.1146/annurev-ecolsys-010621-044528. View

Harris R, Sackman A, Jensen J . On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses. PLoS Genet. 2018; 14(12):e1007859. PMC: 6336318. DOI: 10.1371/journal.pgen.1007859. View

Johri P, Aquadro C, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A . Recommendations for improving statistical inference in population genomics. PLoS Biol. 2022; 20(5):e3001669. PMC: 9154105. DOI: 10.1371/journal.pbio.3001669. View

Charlesworth B, Jensen J . Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana. Mol Biol Evol. 2022; 40(2). PMC: 9907473. DOI: 10.1093/molbev/msac275. View

Zhong L, Zhu Y, Olsen K . Hard versus soft selective sweeps during domestication and improvement in soybean. Mol Ecol. 2022; 31(11):3137-3153. DOI: 10.1111/mec.16454. View

Johri P, Eyre-Walker A, Gutenkunst R, Lohmueller K, Jensen J . On the prospect of achieving accurate joint estimation of selection with population history. Genome Biol Evol. 2022; 14(7). PMC: 9254643. DOI: 10.1093/gbe/evac088. View

Johri P, Charlesworth B, Jensen J . Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection. Genetics. 2020; 215(1):173-192. PMC: 7198275. DOI: 10.1534/genetics.119.303002. View

Chikhi L, Rodriguez W, Grusea S, Santos P, Boitard S, Mazet O . The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity (Edinb). 2017; 120(1):13-24. PMC: 5837117. DOI: 10.1038/s41437-017-0005-6. View

Garud N, Messer P, Petrov D . Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data. PLoS Genet. 2021; 17(2):e1009373. PMC: 7946363. DOI: 10.1371/journal.pgen.1009373. View

10.

Jensen J . On reconciling single and recurrent hitchhiking models. Genome Biol Evol. 2010; 1:320-4. PMC: 2817426. DOI: 10.1093/gbe/evp031. View

11.

Johri P, Riall K, Becher H, Excoffier L, Charlesworth B, Jensen J . The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects. Mol Biol Evol. 2021; 38(7):2986-3003. PMC: 8233493. DOI: 10.1093/molbev/msab050. View

12.

Thornton K, Jensen J . Controlling the false-positive rate in multilocus genome scans for selection. Genetics. 2006; 175(2):737-50. PMC: 1800626. DOI: 10.1534/genetics.106.064642. View

13.

Johri P, Stephan W, Jensen J . Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers. PLoS Genet. 2022; 18(2):e1010022. PMC: 8870509. DOI: 10.1371/journal.pgen.1010022. View

14.

Barrett S, Arunkumar R, Wright S . The demography and population genomics of evolutionary transitions to self-fertilization in plants. Philos Trans R Soc Lond B Biol Sci. 2014; 369(1648). PMC: 4071518. DOI: 10.1098/rstb.2013.0344. View

15.

Smith J, Haigh J . The hitch-hiking effect of a favourable gene. Genet Res. 1974; 23(1):23-35. View

16.

Tajima F . Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989; 123(3):585-95. PMC: 1203831. DOI: 10.1093/genetics/123.3.585. View