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  1. Article ; Online: Can heterosis and inbreeding depression explain the maintenance of outcrossing in a cleistogamous perennial?

    Soto, Tatyana Y / Rojas-Gutierrez, Juan Diego / Oakley, Christopher G

    American journal of botany

    2023  Volume 110, Issue 10, Page(s) e16240

    Abstract: Premise: What maintains mixed mating is an evolutionary enigma. Cleistogamy-the production of both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers on the same individual plant-is an excellent system to study the costs ... ...

    Abstract Premise: What maintains mixed mating is an evolutionary enigma. Cleistogamy-the production of both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers on the same individual plant-is an excellent system to study the costs of selfing. Inbreeding depression can prevent the evolution of greater selfing within populations, and heterosis in crosses between populations may further tip the balance in favor of outcrossing. Few empirical estimates of inbreeding depression and heterosis in the same system exist for cleistogamous species.
    Methods: We investigate the potential costs of selfing by quantifying inbreeding depression and heterosis in three populations of the cleistogamous perennial Ruellia humilis Nutt (Acanthaceae). We performed three types of hand-pollinations-self, outcross-within, and outcross-between populations-and measured seed number, germination, total flower production, and estimated cumulative fitness for the resulting progeny in a greenhouse experiment.
    Results: We found moderate inbreeding depression for cumulative fitness (<30%) in two populations, but outbreeding depression for crosses within a third population (-26%). For between-population crosses, there was weak to modest heterosis (11-47%) in two of the population combinations, but modest to strong outbreeding depression (-21 to -71%) in the other four combinations.
    Conclusions: Neither inbreeding depression nor heterosis was of sufficient magnitude to explain the continued production of chasmogamous flowers given the relative energetic advantage of cleistogamous flowers previously estimated for these populations. Outbreeding depression either within or between populations makes the maintenance of chasmogamous flowers even harder to explain. More information is needed on the genetic basis of cleistogamy to resolve this conundrum.
    MeSH term(s) Hybrid Vigor/genetics ; Inbreeding Depression ; Inbreeding ; Reproduction ; Pollination
    Language English
    Publishing date 2023-10-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2935-x
    ISSN 1537-2197 ; 0002-9122
    ISSN (online) 1537-2197
    ISSN 0002-9122
    DOI 10.1002/ajb2.16240
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Ecological genetics of local adaptation in Arabidopsis: An 8‐year field experiment

    Oakley, Christopher G. / Schemske, Douglas W. / McKay, John K. / Ågren, Jon

    Molecular Ecology. 2023 Aug., v. 32, no. 16 p.4570-4583

    2023  

    Abstract: There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic ... ...

    Abstract There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade‐offs? Here we address these questions in the self‐pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade‐offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8‐year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3‐year study, identifying one new genetic trade‐off and resolving one genetic trade‐off into two conditionally adaptive QTL.
    Keywords Arabidopsis thaliana ; annuals ; data collection ; ecological genetics ; ecology ; field experimentation ; quantitative traits ; seedlings ; self-pollination ; temporal variation ; Italy ; Sweden
    Language English
    Dates of publication 2023-08
    Size p. 4570-4583.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17045
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  3. Article ; Online: Can heterosis and inbreeding depression explain the maintenance of outcrossing in a cleistogamous perennial?

    Soto, Tatyana Y. / Rojas‐Gutierrez, Juan Diego / Oakley, Christopher G.

    American Journal of Botany. 2023 Oct., v. 110, no. 10 p.e16240-

    2023  

    Abstract: PREMISE: What maintains mixed mating is an evolutionary enigma. Cleistogamy—the production of both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers on the same individual plant—is an excellent system to study the costs of ...

    Abstract PREMISE: What maintains mixed mating is an evolutionary enigma. Cleistogamy—the production of both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers on the same individual plant—is an excellent system to study the costs of selfing. Inbreeding depression can prevent the evolution of greater selfing within populations, and heterosis in crosses between populations may further tip the balance in favor of outcrossing. Few empirical estimates of inbreeding depression and heterosis in the same system exist for cleistogamous species. METHODS: We investigate the potential costs of selfing by quantifying inbreeding depression and heterosis in three populations of the cleistogamous perennial Ruellia humilis Nutt (Acanthaceae). We performed three types of hand‐pollinations—self, outcross‐within, and outcross‐between populations—and measured seed number, germination, total flower production, and estimated cumulative fitness for the resulting progeny in a greenhouse experiment. RESULTS: We found moderate inbreeding depression for cumulative fitness (<30%) in two populations, but outbreeding depression for crosses within a third population (–26%). For between‐population crosses, there was weak to modest heterosis (11–47%) in two of the population combinations, but modest to strong outbreeding depression (–21 to –71%) in the other four combinations. CONCLUSIONS: Neither inbreeding depression nor heterosis was of sufficient magnitude to explain the continued production of chasmogamous flowers given the relative energetic advantage of cleistogamous flowers previously estimated for these populations. Outbreeding depression either within or between populations makes the maintenance of chasmogamous flowers even harder to explain. More information is needed on the genetic basis of cleistogamy to resolve this conundrum.
    Keywords Ruellia ; cleistogamy ; evolution ; flowers ; germination ; greenhouse experimentation ; heterosis ; outcrossing ; progeny ; selfing
    Language English
    Dates of publication 2023-10
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 2935-x
    ISSN 1537-2197 ; 0002-9122
    ISSN (online) 1537-2197
    ISSN 0002-9122
    DOI 10.1002/ajb2.16240
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: A large-effect fitness trade-off across environments is explained by a single mutation affecting cold acclimation.

    Lee, Gwonjin / Sanderson, Brian J / Ellis, Thomas J / Dilkes, Brian P / McKay, John K / Ågren, Jon / Oakley, Christopher G

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 6, Page(s) e2317461121

    Abstract: Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a ... ...

    Abstract Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes of
    MeSH term(s) Arabidopsis/genetics ; Mutation ; Acclimatization/genetics ; Arabidopsis Proteins/genetics ; Transcription Factors/genetics ; Cold Temperature ; Genetic Fitness
    Chemical Substances Arabidopsis Proteins ; Transcription Factors
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2317461121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Ecological genetics of local adaptation in Arabidopsis: An 8-year field experiment.

    Oakley, Christopher G / Schemske, Douglas W / McKay, John K / Ågren, Jon

    Molecular ecology

    2023  Volume 32, Issue 16, Page(s) 4570–4583

    Abstract: There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic ... ...

    Abstract There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality versus genetic trade-offs? Here we address these questions in the self-pollinating, annual plant Arabidopsis thaliana. We used 400 recombinant inbred lines (RILs) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first 3 years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found 10 adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden, respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The 8-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous 3-year study, identifying one new genetic trade-off and resolving one genetic trade-off into two conditionally adaptive QTL.
    MeSH term(s) Arabidopsis/genetics ; Adaptation, Physiological/genetics ; Quantitative Trait Loci/genetics ; Acclimatization ; Genotype ; Seedlings/genetics
    Language English
    Publishing date 2023-06-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.17045
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: (with research data) Small effective size limits performance in a novel environment.

    Oakley, Christopher G

    Evolutionary applications

    2013  Volume 6, Issue 5, Page(s) 823–831

    Abstract: Understanding what limits or facilitates species' responses to human-induced habitat change can provide insight for the control of invasive species and the conservation of small populations, as well as an arena for studying adaptation to realistic novel ... ...

    Abstract Understanding what limits or facilitates species' responses to human-induced habitat change can provide insight for the control of invasive species and the conservation of small populations, as well as an arena for studying adaptation to realistic novel environments. Small effective size of ancestral populations could limit the establishment in, or response to, a novel or altered habitat because of low genetic variation for ecologically important traits, and/or because small populations harbor fixed deleterious mutations. I estimated the fitness of individuals from populations of the endangered plant
    Language English
    Publishing date 2013-04-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2405496-3
    ISSN 1752-4563 ; 1752-4571
    ISSN (online) 1752-4563
    ISSN 1752-4571
    DOI 10.1111/eva.12068
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  7. Article ; Online: Life-history trade-offs and the genetic basis of fitness in Arabidopsis thaliana.

    Ellis, Thomas James / Postma, Froukje M / Oakley, Christopher G / Ågren, Jon

    Molecular ecology

    2021  Volume 30, Issue 12, Page(s) 2846–2858

    Abstract: Resources allocated to survival cannot be used to increase fecundity, but the extent to which this trade-off constrains adaptation depends on overall resource status. Adaptation to local environmental conditions may therefore entail the evolution of ... ...

    Abstract Resources allocated to survival cannot be used to increase fecundity, but the extent to which this trade-off constrains adaptation depends on overall resource status. Adaptation to local environmental conditions may therefore entail the evolution of traits that increase the amount of resources available to individuals (their resource status or 'condition'). We examined the relative contribution of trade-offs and increased condition to adaptive evolution in a recombinant inbred line population of Arabidopsis thaliana planted at the native sites of the parental ecotypes in Italy and Sweden in 2 years. We estimated genetic correlations among fitness components based on genotypic means and explored their causes with QTL mapping. The local ecotype produced more seeds per fruit than did the non-local ecotype, reflected in stronger adaptive differentiation than was previously shown based on survival and fruit number only. Genetic correlations between survival and overall fecundity, and between number of fruits and number of seeds per fruit, were positive, and there was little evidence of a trade-off between seed size and number. Quantitative trait loci for these traits tended to map to the same regions of the genome and showed positive pleiotropic effects. The results indicate that adaptive differentiation between the two focal populations largely reflects the evolution of increased ability to acquire resources in the local environment, rather than shifts in the relative allocation to different life-history traits. Differentiation both in phenology and in tolerance to cold is likely to contribute to the advantage of the local genotype at the two sites.
    MeSH term(s) Adaptation, Physiological/genetics ; Arabidopsis/genetics ; Genetic Fitness ; Humans ; Italy ; Quantitative Trait Loci ; Sweden
    Language English
    Publishing date 2021-05-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.15941
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Genome‐wide association analysis of freezing tolerance in soft red winter wheat

    Rojas‐Gutierrez, Juan Diego / Lee, Gwonjin / Sanderson, Brian J / Jameel, M. Inam / Oakley, Christopher G.

    Crop science. 2022 Mar., v. 62, no. 2

    2022  

    Abstract: Freezing tolerance is likely to be an important adaptation for both natural populations and crop cultivars like winter wheat (Triticum aestivum L.). In the United States, winter wheat represents 80% of the total wheat production. Understanding the ... ...

    Abstract Freezing tolerance is likely to be an important adaptation for both natural populations and crop cultivars like winter wheat (Triticum aestivum L.). In the United States, winter wheat represents 80% of the total wheat production. Understanding the genetic basis of freezing tolerance in wheat furthers our knowledge of abiotic stress tolerance in plants and may inform breeding programs aimed at adjusting the level of freezing tolerance for a given region. We examined freezing tolerance in a 267‐line panel of elite soft red winter wheat that has previously been used for genome‐wide association study (GWAS) on agronomically important traits. We were specifically interested in determining the extent of genetic variation for freezing tolerance within the panel, what the genetic basis of that variation is, and if there are correlations between freezing tolerance and other agronomically important traits. We found significant variation in freezing tolerance among the lines, measured as survival through three total days at −8 °C. We performed a GWAS on freezing tolerance and identified 13 candidate loci, with nearby candidate genes involved in different functions potentially associated with freezing tolerance. In addition, we found significant correlations between freezing tolerance and seven previously published yield related traits. In summary, we found considerable variation in freezing tolerance in this panel that is associated with yield related traits. Thus, these lines may be useful for breeding programs seeking to optimize freezing tolerance for present and future climatic conditions.
    Keywords Triticum aestivum ; abiotic stress ; cultivars ; genetic variation ; genome-wide association study ; soft red winter wheat ; stress tolerance ; winter wheat
    Language English
    Dates of publication 2022-03
    Size p. 637-647.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 410209-5
    ISSN 0011-183X
    ISSN 0011-183X
    DOI 10.1002/csc2.20682
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  9. Article: Life‐history trade‐offs and the genetic basis of fitness in Arabidopsis thaliana

    Ellis, Thomas James / Postma, Froukje M / Oakley, Christopher G / Ågren, Jon

    Molecular ecology. 2021 June, v. 30, no. 12

    2021  

    Abstract: Resources allocated to survival cannot be used to increase fecundity, but the extent to which this trade‐off constrains adaptation depends on overall resource status. Adaptation to local environmental conditions may therefore entail the evolution of ... ...

    Abstract Resources allocated to survival cannot be used to increase fecundity, but the extent to which this trade‐off constrains adaptation depends on overall resource status. Adaptation to local environmental conditions may therefore entail the evolution of traits that increase the amount of resources available to individuals (their resource status or ‘condition’). We examined the relative contribution of trade‐offs and increased condition to adaptive evolution in a recombinant inbred line population of Arabidopsis thaliana planted at the native sites of the parental ecotypes in Italy and Sweden in 2 years. We estimated genetic correlations among fitness components based on genotypic means and explored their causes with QTL mapping. The local ecotype produced more seeds per fruit than did the non‐local ecotype, reflected in stronger adaptive differentiation than was previously shown based on survival and fruit number only. Genetic correlations between survival and overall fecundity, and between number of fruits and number of seeds per fruit, were positive, and there was little evidence of a trade‐off between seed size and number. Quantitative trait loci for these traits tended to map to the same regions of the genome and showed positive pleiotropic effects. The results indicate that adaptive differentiation between the two focal populations largely reflects the evolution of increased ability to acquire resources in the local environment, rather than shifts in the relative allocation to different life‐history traits. Differentiation both in phenology and in tolerance to cold is likely to contribute to the advantage of the local genotype at the two sites.
    Keywords Arabidopsis thaliana ; cold tolerance ; ecotypes ; evolutionary adaptation ; fecundity ; fruits ; genome ; inbred lines ; life history ; phenology ; quantitative traits ; seed size ; Italy ; Sweden
    Language English
    Dates of publication 2021-06
    Size p. 2846-2858.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note NAL-AP-2-clean ; JOURNAL ARTICLE
    ZDB-ID 1126687-9
    ISSN 1365-294X ; 0962-1083
    ISSN (online) 1365-294X
    ISSN 0962-1083
    DOI 10.1111/mec.15941
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  10. Article ; Online: Heterosis is common and inbreeding depression absent in natural populations of Arabidopsis thaliana.

    Oakley, Christopher G / Lundemo, Sverre / Ågren, Jon / Schemske, Douglas W

    Journal of evolutionary biology

    2019  Volume 32, Issue 6, Page(s) 592–603

    Abstract: The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter-population crosses may therefore exhibit ... ...

    Abstract The importance of genetic drift in shaping patterns of adaptive genetic variation in nature is poorly known. Genetic drift should drive partially recessive deleterious mutations to high frequency, and inter-population crosses may therefore exhibit heterosis (increased fitness relative to intra-population crosses). Low genetic diversity and greater genetic distance between populations should increase the magnitude of heterosis. Moreover, drift and selection should remove strongly deleterious recessive alleles from individual populations, resulting in reduced inbreeding depression. To estimate heterosis, we crossed 90 independent line pairs of Arabidopsis thaliana from 15 pairs of natural populations sampled across Fennoscandia and crossed an additional 41 line pairs from a subset of four of these populations to estimate inbreeding depression. We measured lifetime fitness of crosses relative to parents in a large outdoor common garden (8,448 plants in total) in central Sweden. To examine the effects of genetic diversity and genetic distance on heterosis, we genotyped parental lines for 869 SNPs. Overall, genetic variation within populations was low (median expected heterozygosity = 0.02), and genetic differentiation was high (median F
    MeSH term(s) Arabidopsis/genetics ; Genetic Fitness ; Hybrid Vigor ; Inbreeding Depression
    Language English
    Publishing date 2019-04-02
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1465318-7
    ISSN 1420-9101 ; 1010-061X
    ISSN (online) 1420-9101
    ISSN 1010-061X
    DOI 10.1111/jeb.13441
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