---
_id: '7652'
abstract:
- lang: eng
  text: Organisms cope with change by taking advantage of transcriptional regulators.
    However, when faced with rare environments, the evolution of transcriptional regulators
    and their promoters may be too slow. Here, we investigate whether the intrinsic
    instability of gene duplication and amplification provides a generic alternative
    to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations
    in Escherichia coli, we show that gene duplications and amplifications enable
    adaptation to fluctuating environments by rapidly generating copy-number and,
    therefore, expression-level polymorphisms. This amplification-mediated gene expression
    tuning (AMGET) occurs on timescales that are similar to canonical gene regulation
    and can respond to rapid environmental changes. Mathematical modelling shows that
    amplifications also tune gene expression in stochastic environments in which transcription-factor-based
    schemes are hard to evolve or maintain. The fleeting nature of gene amplifications
    gives rise to a generic population-level mechanism that relies on genetic heterogeneity
    to rapidly tune the expression of any gene, without leaving any genomic signature.
acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic
  and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help
  with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is
  a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences)
  Fellowship of the Austrian Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
  full_name: Tomanek, Isabella
  id: 3981F020-F248-11E8-B48F-1D18A9856A87
  last_name: Tomanek
  orcid: 0000-0001-6197-363X
- first_name: Rok
  full_name: Grah, Rok
  id: 483E70DE-F248-11E8-B48F-1D18A9856A87
  last_name: Grah
  orcid: 0000-0003-2539-3560
- first_name: M.
  full_name: Lagator, M.
  last_name: Lagator
- first_name: A. M. C.
  full_name: Andersson, A. M. C.
  last_name: Andersson
- first_name: Jonathan P
  full_name: Bollback, Jonathan P
  id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
  last_name: Bollback
  orcid: 0000-0002-4624-4612
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level
    gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. 2020;4(4):612-625.
    doi:<a href="https://doi.org/10.1038/s41559-020-1132-7">10.1038/s41559-020-1132-7</a>
  apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik,
    G., &#38; Guet, C. C. (2020). Gene amplification as a form of population-level
    gene expression regulation. <i>Nature Ecology &#38; Evolution</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41559-020-1132-7">https://doi.org/10.1038/s41559-020-1132-7</a>
  chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P
    Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level
    Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature,
    2020. <a href="https://doi.org/10.1038/s41559-020-1132-7">https://doi.org/10.1038/s41559-020-1132-7</a>.
  ieee: I. Tomanek <i>et al.</i>, “Gene amplification as a form of population-level
    gene expression regulation,” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no.
    4. Springer Nature, pp. 612–625, 2020.
  ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC.
    2020. Gene amplification as a form of population-level gene expression regulation.
    Nature Ecology &#38; Evolution. 4(4), 612–625.
  mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level
    Gene Expression Regulation.” <i>Nature Ecology &#38; Evolution</i>, vol. 4, no.
    4, Springer Nature, 2020, pp. 612–25, doi:<a href="https://doi.org/10.1038/s41559-020-1132-7">10.1038/s41559-020-1132-7</a>.
  short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik,
    C.C. Guet, Nature Ecology &#38; Evolution 4 (2020) 612–625.
date_created: 2020-04-08T15:20:53Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-25T23:30:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41559-020-1132-7
external_id:
  isi:
  - '000519008300005'
file:
- access_level: open_access
  checksum: ef3bbf42023e30b2c24a6278025d2040
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-09T09:56:01Z
  date_updated: 2020-10-09T09:56:01Z
  file_id: '8640'
  file_name: 2020_NatureEcolEvo_Tomanek.pdf
  file_size: 745242
  relation: main_file
  success: 1
file_date_updated: 2020-10-09T09:56:01Z
has_accepted_license: '1'
intvolume: '         4'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 612-625
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
  name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: Nature Ecology & Evolution
publication_identifier:
  issn:
  - 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/
  record:
  - id: '8155'
    relation: dissertation_contains
    status: public
  - id: '7383'
    relation: research_data
    status: public
  - id: '7016'
    relation: research_data
    status: public
  - id: '8653'
    relation: used_in_publication
    status: public
scopus_import: '1'
status: public
title: Gene amplification as a form of population-level gene expression regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '7146'
abstract:
- lang: eng
  text: Prevailing models of sex-chromosome evolution were largely inspired by the
    stable and highly differentiated XY pairs of model organisms, such as those of
    mammals and flies. Recent work has uncovered an incredible diversity of sex-determining
    systems, bringing some of the assumptions of these traditional models into question.
    One particular question that has arisen is what drives some sex chromosomes to
    be maintained over millions of years and differentiate fully, while others are
    replaced by new sex-determining chromosomes before differentiation has occurred.
    Here, I review recent data on the variability of sex-determining genes and sex
    chromosomes in different non-model vertebrates and invertebrates, and discuss
    some theoretical models that have been put forward to account for this diversity.
article_processing_charge: No
article_type: original
author:
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover.
    <i>Nature Ecology &#38; Evolution</i>. 2019;3(12):1632-1641. doi:<a href="https://doi.org/10.1038/s41559-019-1050-8">10.1038/s41559-019-1050-8</a>
  apa: Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome
    turnover. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href="https://doi.org/10.1038/s41559-019-1050-8">https://doi.org/10.1038/s41559-019-1050-8</a>
  chicago: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
    Turnover.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41559-019-1050-8">https://doi.org/10.1038/s41559-019-1050-8</a>.
  ieee: B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,”
    <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12. Springer Nature, pp. 1632–1641,
    2019.
  ista: Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome
    turnover. Nature Ecology &#38; Evolution. 3(12), 1632–1641.
  mla: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome
    Turnover.” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12, Springer Nature,
    2019, pp. 1632–41, doi:<a href="https://doi.org/10.1038/s41559-019-1050-8">10.1038/s41559-019-1050-8</a>.
  short: B. Vicoso, Nature Ecology &#38; Evolution 3 (2019) 1632–1641.
date_created: 2019-12-04T16:05:25Z
date_published: 2019-11-25T00:00:00Z
date_updated: 2023-09-06T11:18:59Z
day: '25'
department:
- _id: BeVi
doi: 10.1038/s41559-019-1050-8
ec_funded: 1
external_id:
  isi:
  - '000500728800009'
intvolume: '         3'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa_version: None
page: 1632-1641
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715257'
  name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Nature Ecology & Evolution
publication_identifier:
  issn:
  - 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular and evolutionary dynamics of animal sex-chromosome turnover
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 3
year: '2019'
...
---
_id: '7725'
abstract:
- lang: eng
  text: Phenotypic plasticity is the ability of an individual genotype to alter aspects
    of its phenotype depending on the current environment. It is central to the persistence,
    resistance and resilience of populations facing variation in physical or biological
    factors. Genetic variation in plasticity is pervasive, which suggests its local
    adaptation is plausible. Existing studies on the adaptation of plasticity typically
    focus on single traits and a few populations, while theory about interactions
    among genes (for example, pleiotropy) suggests that a multi-trait, landscape scale
    (for example, multiple populations) perspective is required. We present data from
    a landscape scale, replicated, multi-trait experiment using a classic predator–prey
    system centred on the water flea Daphnia pulex. We find predator regime-driven
    differences in genetic variation of multivariate plasticity. These differences
    are associated with strong divergent selection linked to a predation regime. Our
    findings are evidence for local adaptation of plasticity, suggesting that responses
    of populations to environmental variation depend on the conditions in which they
    evolved in the past.
article_processing_charge: No
article_type: original
author:
- first_name: Julia
  full_name: Reger, Julia
  last_name: Reger
- first_name: Martin I.
  full_name: Lind, Martin I.
  last_name: Lind
- first_name: Matthew Richard
  full_name: Robinson, Matthew Richard
  id: E5D42276-F5DA-11E9-8E24-6303E6697425
  last_name: Robinson
  orcid: 0000-0001-8982-8813
- first_name: Andrew P.
  full_name: Beckerman, Andrew P.
  last_name: Beckerman
citation:
  ama: Reger J, Lind MI, Robinson MR, Beckerman AP. Predation drives local adaptation
    of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>. 2017;2:100-107.
    doi:<a href="https://doi.org/10.1038/s41559-017-0373-6">10.1038/s41559-017-0373-6</a>
  apa: Reger, J., Lind, M. I., Robinson, M. R., &#38; Beckerman, A. P. (2017). Predation
    drives local adaptation of phenotypic plasticity. <i>Nature Ecology &#38; Evolution</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41559-017-0373-6">https://doi.org/10.1038/s41559-017-0373-6</a>
  chicago: Reger, Julia, Martin I. Lind, Matthew Richard Robinson, and Andrew P. Beckerman.
    “Predation Drives Local Adaptation of Phenotypic Plasticity.” <i>Nature Ecology
    &#38; Evolution</i>. Springer Nature, 2017. <a href="https://doi.org/10.1038/s41559-017-0373-6">https://doi.org/10.1038/s41559-017-0373-6</a>.
  ieee: J. Reger, M. I. Lind, M. R. Robinson, and A. P. Beckerman, “Predation drives
    local adaptation of phenotypic plasticity,” <i>Nature Ecology &#38; Evolution</i>,
    vol. 2. Springer Nature, pp. 100–107, 2017.
  ista: Reger J, Lind MI, Robinson MR, Beckerman AP. 2017. Predation drives local
    adaptation of phenotypic plasticity. Nature Ecology &#38; Evolution. 2, 100–107.
  mla: Reger, Julia, et al. “Predation Drives Local Adaptation of Phenotypic Plasticity.”
    <i>Nature Ecology &#38; Evolution</i>, vol. 2, Springer Nature, 2017, pp. 100–07,
    doi:<a href="https://doi.org/10.1038/s41559-017-0373-6">10.1038/s41559-017-0373-6</a>.
  short: J. Reger, M.I. Lind, M.R. Robinson, A.P. Beckerman, Nature Ecology &#38;
    Evolution 2 (2017) 100–107.
date_created: 2020-04-30T10:46:02Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2021-01-12T08:15:07Z
day: '27'
doi: 10.1038/s41559-017-0373-6
extern: '1'
intvolume: '         2'
language:
- iso: eng
month: '11'
oa_version: None
page: 100-107
publication: Nature Ecology & Evolution
publication_identifier:
  issn:
  - 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Predation drives local adaptation of phenotypic plasticity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...