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  1. Article ; Online: Population genetic concerns related to the interpretation of empirical outliers and the neglect of common evolutionary processes.

    Jensen, Jeffrey D

    Heredity

    2023  Volume 130, Issue 3, Page(s) 109–110

    MeSH term(s) Genetics, Population ; Biological Evolution
    Language English
    Publishing date 2023-02-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-022-00575-5
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    In stock of ZB MED Cologne/Königswinter

    Ub I Zs.154: Show issues Location:
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  2. Article ; Online: Temporal challenges in detecting balancing selection from population genomic data.

    Soni, Vivak / Jensen, Jeffrey D

    G3 (Bethesda, Md.)

    2024  

    Abstract: The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human ...

    Abstract The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding inference, and the expected signatures of balancing selection additionally change in a temporal fashion. Here we use forward-in-time simulations to quantify expected statistical power to detect balancing selection using both site frequency spectrum (SFS)- and linkage disequilibrium (LD)-based methods under a variety of evolutionarily realistic null models. We find that whilst SFS-based methods have little power immediately after a balanced mutation begins segregating, power increases with time since the introduction of the balanced allele. Conversely, LD-based methods have considerable power whilst the allele is young, and power dissipates rapidly as the time since introduction increases. Taken together, this suggests that SFS-based methods are most effective at detecting long-term balancing selection (>25N generations since the introduction of the balanced allele) whilst LD-based methods are effective over much shorter timescales (<1N generations), thereby leaving a large time frame over which current methods have little power to detect the action of balancing selection. Finally, we investigate the extent to which alternative evolutionary processes may mimic these patterns, and demonstrate the need for caution in attempting to distinguish the signatures of balancing selection from those of both neutral processes (e.g., population structure and admixture) as well as of alternative selective processes (e.g., partial selective sweeps).
    Language English
    Publishing date 2024-03-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkae069
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  3. Article ; Online: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.

    Soni, Vivak / Terbot, John W / Jensen, Jeffrey D

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3240

    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Polymorphism, Genetic ; Genetics, Population
    Language English
    Publishing date 2024-04-16
    Publishing country England
    Document type Letter
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46261-4
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  4. Article ; Online: Extending use of levonorgestrel 52 mg intrauterine device to 8 years.

    Creinin, Mitchell D / Jensen, Jeffrey T

    American journal of obstetrics and gynecology

    2023  Volume 229, Issue 1, Page(s) 84

    MeSH term(s) Female ; Humans ; Levonorgestrel ; Intrauterine Devices ; Contraceptive Agents, Female ; Intrauterine Devices, Medicated ; Intrauterine Devices, Copper
    Chemical Substances Levonorgestrel (5W7SIA7YZW) ; Contraceptive Agents, Female
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 80016-8
    ISSN 1097-6868 ; 0002-9378
    ISSN (online) 1097-6868
    ISSN 0002-9378
    DOI 10.1016/j.ajog.2023.03.011
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  5. Article: Effects of Selection at Linked Sites on Patterns of Genetic Variability.

    Charlesworth, Brian / Jensen, Jeffrey D

    Annual review of ecology, evolution, and systematics

    2023  Volume 52, Page(s) 177–197

    Abstract: Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population ...

    Abstract Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill-Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.
    Language English
    Publishing date 2023-03-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2131661-2
    ISSN 1543-592X
    ISSN 1543-592X
    DOI 10.1146/annurev-ecolsys-010621-044528
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    In stock of ZB MED Bonn / Germany

    Z 78/721: Show issues
    Z 7956: Show issues

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  6. Article ; Online: The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects.

    Soni, Vivak / Pfeifer, Susanne P / Jensen, Jeffrey D

    Genome biology and evolution

    2024  Volume 16, Issue 2

    Abstract: Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavor; however, despite clear evidence that both mutation and ... ...

    Abstract Disentangling the effects of demography and selection has remained a focal point of population genetic analysis. Knowledge about mutation and recombination is essential in this endeavor; however, despite clear evidence that both mutation and recombination rates vary across genomes, it is common practice to model both rates as fixed. In this study, we quantify how this unaccounted for rate heterogeneity may impact inference using common approaches for inferring selection (DFE-alpha, Grapes, and polyDFE) and/or demography (fastsimcoal2 and δaδi). We demonstrate that, if not properly modeled, this heterogeneity can increase uncertainty in the estimation of demographic and selective parameters and in some scenarios may result in mis-leading inference. These results highlight the importance of quantifying the fundamental evolutionary parameters of mutation and recombination before utilizing population genomic data to quantify the effects of genetic drift (i.e. as modulated by demographic history) and selection; or, at the least, that the effects of uncertainty in these parameters can and should be directly modeled in downstream inference.
    MeSH term(s) Selection, Genetic ; Demography ; Mutation ; Genetic Drift ; Recombination, Genetic ; Models, Genetic
    Language English
    Publishing date 2024-01-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evae004
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  7. Article ; Online: Some complexities in interpreting apparent effects of hitchhiking: A commentary on Gompert et al. (2022).

    Charlesworth, Brian / Jensen, Jeffrey D

    Molecular ecology

    2022  Volume 31, Issue 17, Page(s) 4440–4443

    Abstract: We write to address recent claims by regarding the potentially important and underappreciated phenomena of "indirect selection," the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon-generally known ...

    Abstract We write to address recent claims by regarding the potentially important and underappreciated phenomena of "indirect selection," the observation that neutral regions may be affected by natural selection. We argue both that this phenomenon-generally known as genetic hitchhiking-is neither new nor poorly studied, and that the patterns described by the authors have multiple alternative explanations.
    MeSH term(s) Models, Genetic ; Selection, Genetic
    Language English
    Publishing date 2022-07-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.16573
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    In stock of ZB MED Bonn / Germany

    Z 2005/723: Show issues

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  8. Article ; Online: Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana.

    Charlesworth, Brian / Jensen, Jeffrey D

    Molecular biology and evolution

    2022  Volume 40, Issue 2

    Abstract: ... between gene bodies and less selectively constrained sequences in the magnitude of Tajima's D ...

    Abstract It has recently been proposed that lower mutation rates in gene bodies compared with upstream and downstream sequences in Arabidopsis thaliana are the result of an "adaptive" modification of the rate of beneficial and deleterious mutations in these functional regions. This claim was based both on analyses of mutation accumulation lines and on population genomics data. Here, we show that several questionable assumptions were used in the population genomics analyses. In particular, we demonstrate that the difference between gene bodies and less selectively constrained sequences in the magnitude of Tajima's D can in principle be explained by the presence of sites subject to purifying selection and does not require lower mutation rates in regions experiencing selective constraints.
    MeSH term(s) Arabidopsis/genetics ; Mutation Rate ; Genetics, Population ; Genomics ; Mutation ; Selection, Genetic
    Language English
    Publishing date 2022-12-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msac275
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    Zs.A 2137: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: How Can We Resolve Lewontin's Paradox?

    Charlesworth, Brian / Jensen, Jeffrey D

    Genome biology and evolution

    2022  Volume 14, Issue 7

    Abstract: We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of ... ...

    Abstract We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
    MeSH term(s) Genetic Variation ; Genetics, Population ; Models, Genetic ; Population Density ; Selection, Genetic
    Language English
    Publishing date 2022-06-15
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evac096
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  10. Article: Developing an evolutionary baseline model for humans: jointly inferring purifying selection with population history.

    Johri, Parul / Pfeifer, Susanne P / Jensen, Jeffrey D

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics - including quantifying the relative contributions of adaptive vs. non-adaptive processes - but ... ...

    Abstract Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics - including quantifying the relative contributions of adaptive vs. non-adaptive processes - but it is also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (
    Language English
    Publishing date 2023-04-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.11.536488
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