---
_id: '14613'
abstract:
- lang: eng
  text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element
    F - that likely predates their origin. Interestingly, the X has undergone turnover
    in multiple fly species (Diptera) after being conserved for more than 450 MY.
    The long evolutionary distance between Diptera and other sequenced insect clades
    makes it difficult to infer what could have contributed to this sudden increase
    in rate of turnover. Here, we produce the first genome and transcriptome of a
    long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly
    Panorpa cognata X-chromosome gene content, expression, and structure, to that
    of several dipteran species as well as more distantly-related insect orders (Orthoptera
    and Blattodea). We find high conservation of gene content between the mecopteran
    X and the dipteran Muller F element, as well as several shared biological features,
    such as the presence of dosage compensation and a low amount of genetic diversity,
    consistent with a low recombination rate. However, the two homologous X chromosomes
    differ strikingly in their size and number of genes they carry. Our results therefore
    support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
    and suggest that Muller element F shrank in size and gene content after the split
    of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
    insects.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection,
  and Tim Connallon for valuable comments and suggestions on earlier versions of the
  manuscript. Computational resources and support were provided by the Scientific
  Computing unit at the ISTA. This research was supported by grants from the Austrian
  Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."
article_number: msad245
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Clementine
  full_name: Lasne, Clementine
  id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
  last_name: Lasne
  orcid: 0000-0002-1197-8616
- first_name: Marwan N
  full_name: Elkrewi, Marwan N
  id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
  last_name: Elkrewi
  orcid: 0000-0002-5328-7231
- first_name: Melissa A
  full_name: Toups, Melissa A
  id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
  last_name: Toups
  orcid: 0000-0002-9752-7380
- first_name: Lorena Alexandra
  full_name: Layana Franco, Lorena Alexandra
  id: 02814589-eb8f-11eb-b029-a70074f3f18f
  last_name: Layana Franco
  orcid: 0000-0002-1253-6297
- first_name: Ariana
  full_name: Macon, Ariana
  id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
  last_name: Macon
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly
    (Panorpa cognata) genome highlights conserved and derived features of the peculiar
    dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a
    href="https://doi.org/10.1093/molbev/msad245">10.1093/molbev/msad245</a>
  apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38;
    Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved
    and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology
    and Evolution</i>. Oxford University Press. <a href="https://doi.org/10.1093/molbev/msad245">https://doi.org/10.1093/molbev/msad245</a>
  chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra
    Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata)
    Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
    <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href="https://doi.org/10.1093/molbev/msad245">https://doi.org/10.1093/molbev/msad245</a>.
  ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B.
    Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived
    features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>,
    vol. 40, no. 12. Oxford University Press, 2023.
  ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023.
    The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
    of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12),
    msad245.
  mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights
    Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular
    Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press,
    2023, doi:<a href="https://doi.org/10.1093/molbev/msad245">10.1093/molbev/msad245</a>.
  short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso,
    Molecular Biology and Evolution 40 (2023).
date_created: 2023-11-27T16:14:37Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:18:35Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msad245
external_id:
  pmid:
  - '37988296'
file:
- access_level: open_access
  checksum: 47c1c72fb499f26ea52d216b242208c8
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-02T11:39:38Z
  date_updated: 2024-01-02T11:39:38Z
  file_id: '14727'
  file_name: 2023_MolecularBioEvo_Lasne.pdf
  file_size: 8623505
  relation: main_file
  success: 1
file_date_updated: 2024-01-02T11:39:38Z
has_accepted_license: '1'
intvolume: '        40'
issue: '12'
keyword:
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
  grant_number: F8810
  name: The highjacking of meiosis for asexual reproduction
- _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3
  grant_number: ESP39 49461
  name: Mechanisms and Evolution of Reproductive Plasticity
publication: Molecular Biology and Evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  link:
  - description: News on ISTA webpage
    relation: press_release
    url: https://ista.ac.at/en/news/on-the-hunt/
  record:
  - id: '14614'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
  of the peculiar dipteran X chromosome
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2023'
...
---
_id: '10167'
abstract:
- lang: eng
  text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic.
    Different parts of their ZW sex chromosomes have stopped recombining in distinct
    lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome
    is well characterized at the genomic and molecular level, the W-chromosome has
    remained largely unstudied from an evolutionary perspective, as only a few W-linked
    genes have been detected outside of the model species Schistosoma mansoni. Here,
    we characterize the gene content and evolution of the W-chromosomes of S. mansoni
    and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based
    pipeline to assemble around 100 candidate W-specific transcripts in each of the
    species. About half of them map to known protein coding genes, the majority homologous
    to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary
    strata present in the two species (including characterizing a previously undetected
    young stratum in S. japonicum) to infer patterns of sequence and expression evolution
    of W-linked genes at different time points after recombination was lost. W-linked
    genes show evidence of degeneration, including high rates of protein evolution
    and reduced expression. Most are found in young lineage-specific strata, with
    only a few high expression ancestral W-genes remaining, consistent with the progressive
    erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands
    out as a promising candidate for primary sex determination, opening new avenues
    for understanding the molecular basis of the reproductive biology of this group.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors thank IT support at IST Austria for providing an optimal
  environment for bioinformatic analyses. This work was supported by an Austrian Science
  Foundation FWF grant (Project P28842) to B.V.
article_processing_charge: No
article_type: original
author:
- first_name: Marwan N
  full_name: Elkrewi, Marwan N
  id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
  last_name: Elkrewi
  orcid: 0000-0002-5328-7231
- first_name: Mikhail A.
  full_name: Moldovan, Mikhail A.
  id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0
  last_name: Moldovan
  orcid: 0000-0002-8876-6494
- first_name: Marion A L
  full_name: Picard, Marion A L
  id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
  last_name: Picard
  orcid: 0000-0002-8101-2518
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform
    temporal dynamics of sex chromosome evolution and suggest candidate for sex determination.
    <i>Molecular Biology and Evolution</i>. 2021. doi:<a href="https://doi.org/10.1093/molbev/msab178">10.1093/molbev/msab178</a>
  apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021).
    Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
    and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>.
    Oxford University Press . <a href="https://doi.org/10.1093/molbev/msab178">https://doi.org/10.1093/molbev/msab178</a>
  chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz
    Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome
    Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and
    Evolution</i>. Oxford University Press , 2021. <a href="https://doi.org/10.1093/molbev/msab178">https://doi.org/10.1093/molbev/msab178</a>.
  ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome
    W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest
    candidate for sex determination,” <i>Molecular Biology and Evolution</i>. Oxford
    University Press , 2021.
  ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked
    genes inform temporal dynamics of sex chromosome evolution and suggest candidate
    for sex determination. Molecular Biology and Evolution.
  mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics
    of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular
    Biology and Evolution</i>, Oxford University Press , 2021, doi:<a href="https://doi.org/10.1093/molbev/msab178">10.1093/molbev/msab178</a>.
  short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology
    and Evolution (2021).
date_created: 2021-10-21T07:49:12Z
date_published: 2021-06-19T00:00:00Z
date_updated: 2023-08-14T08:03:06Z
day: '19'
ddc:
- '610'
department:
- _id: BeVi
doi: 10.1093/molbev/msab178
external_id:
  isi:
  - '000741368600009'
  pmid:
  - '34146097'
file:
- access_level: open_access
  checksum: 1b096702fb356d9c0eb88e1b3fcff5f8
  content_type: application/pdf
  creator: dernst
  date_created: 2022-05-06T09:47:18Z
  date_updated: 2022-05-06T09:47:18Z
  file_id: '11352'
  file_name: 2021_MolecularBiolEvolution_Elkrewi.pdf
  file_size: 1008594
  relation: main_file
  success: 1
file_date_updated: 2022-05-06T09:47:18Z
has_accepted_license: '1'
isi: 1
keyword:
- sex chromosomes
- evolutionary strata
- W-linked gene
- sex determining gene
- schistosome parasites
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28842-B22
  name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution
  and suggest candidate for sex determination
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '6089'
abstract:
- lang: eng
  text: Pleiotropy is the well-established idea that a single mutation affects multiple
    phenotypes. If a mutation has opposite effects on fitness when expressed in different
    contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
    the efficacy of selection by limiting the fixation of beneficial mutations through
    adaptation, and the removal of deleterious mutations through purifying selection.
    Although this has been widely discussed, in particular in the context of a putative
    “gender load,” it has yet to be systematically quantified. In this work, we empirically
    estimate to which extent different pleiotropic regimes impede the efficacy of
    selection in Drosophila melanogaster. We use whole-genome polymorphism data from
    a single African population and divergence data from D. simulans to estimate the
    fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
    of selection (DoS). After controlling for confounding covariates, we find that
    the different pleiotropic regimes have a relatively small, but significant, effect
    on selection efficacy. Specifically, our results suggest that pleiotropic sexual
    antagonism may restrict the efficacy of selection, but that this conflict can
    be resolved by limiting the expression of genes to the sex where they are beneficial.
    Intermediate levels of pleiotropy across tissues and life stages can also lead
    to maladaptation in D. melanogaster, due to inefficient purifying selection combined
    with low frequency of mutations that confer a selective advantage. Thus, our study
    highlights the need to consider the efficacy of selection in the context of antagonistic
    pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
  full_name: Fraisse, Christelle
  id: 32DF5794-F248-11E8-B48F-1D18A9856A87
  last_name: Fraisse
  orcid: 0000-0001-8441-5075
- first_name: Gemma
  full_name: Puixeu Sala, Gemma
  id: 33AB266C-F248-11E8-B48F-1D18A9856A87
  last_name: Puixeu Sala
  orcid: 0000-0001-8330-1754
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
citation:
  ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
    in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515.
    doi:<a href="https://doi.org/10.1093/molbev/msy246">10.1093/molbev/msy246</a>
  apa: Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates
    the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and
    Evolution</i>. Oxford University Press. <a href="https://doi.org/10.1093/molbev/msy246">https://doi.org/10.1093/molbev/msy246</a>
  chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
    Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular
    Biology and Evolution</i>. Oxford University Press, 2019. <a href="https://doi.org/10.1093/molbev/msy246">https://doi.org/10.1093/molbev/msy246</a>.
  ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
    of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>,
    vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
  ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
    of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
    500–515.
  mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
    in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36,
    no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href="https://doi.org/10.1093/molbev/msy246">10.1093/molbev/msy246</a>.
  short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
    (2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
  isi:
  - '000462585100006'
  pmid:
  - '30590559'
intvolume: '        36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28842-B22
  name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
  record:
  - id: '5757'
    relation: popular_science
    status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '5749'
abstract:
- lang: eng
  text: Parasitism creates selection for resistance mechanisms in host populations
    and is hypothesized to promote increased host evolvability. However, the influence
    of these traits on host evolution when parasites are no longer present is unclear.
    We used experimental evolution and whole-genome sequencing of Escherichia coli
    to determine the effects of past and present exposure to parasitic viruses (phages)
    on the spread of mutator alleles, resistance, and bacterial competitive fitness.
    We found that mutator alleles spread rapidly during adaptation to any of four
    different phage species, and this pattern was even more pronounced with multiple
    phages present simultaneously. However, hypermutability did not detectably accelerate
    adaptation in the absence of phages and recovery of fitness costs associated with
    resistance. Several lineages evolved phage resistance through elevated mucoidy,
    and during subsequent evolution in phage-free conditions they rapidly reverted
    to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this
    phenotypic reversion was achieved by additional genetic changes rather than by
    genotypic reversion of the initial resistance mutations. Insertion sequence (IS)
    elements played a key role in both the acquisition of resistance and adaptation
    in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions
    were not more frequent in mutator lineages. Our results provide a genetic explanation
    for rapid reversion of mucoidy, a phenotype observed in other bacterial species
    including human pathogens. Moreover, this demonstrates that the types of genetic
    change underlying adaptation to fitness costs, and consequently the impact of
    evolvability mechanisms such as increased point-mutation rates, depend critically
    on the mechanism of resistance.
acknowledgement: The authors thank three anonymous reviewers and the editor for helpful
  comments on the manuscript, as well as Dominique Schneider for feedback on an earlier
  draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was
  supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an
  EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824
  to S.W.).
article_processing_charge: No
author:
- first_name: Sébastien
  full_name: Wielgoss, Sébastien
  last_name: Wielgoss
- first_name: Tobias
  full_name: Bergmiller, Tobias
  id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
  last_name: Bergmiller
  orcid: 0000-0001-5396-4346
- first_name: Anna M.
  full_name: Bischofberger, Anna M.
  last_name: Bischofberger
- first_name: Alex R.
  full_name: Hall, Alex R.
  last_name: Hall
citation:
  ama: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites
    and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular
    Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href="https://doi.org/10.1093/molbev/msv270">10.1093/molbev/msv270</a>
  apa: Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016).
    Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
    bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a
    href="https://doi.org/10.1093/molbev/msv270">https://doi.org/10.1093/molbev/msv270</a>
  chicago: Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex
    R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator
    and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University
    Press, 2016. <a href="https://doi.org/10.1093/molbev/msv270">https://doi.org/10.1093/molbev/msv270</a>.
  ieee: S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation
    to parasites and costs of parasite resistance in mutator and nonmutator bacteria,”
    <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press,
    pp. 770–782, 2016.
  ista: Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites
    and costs of parasite resistance in mutator and nonmutator bacteria. Molecular
    Biology and Evolution. 33(3), 770–782.
  mla: Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite
    Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>,
    vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href="https://doi.org/10.1093/molbev/msv270">10.1093/molbev/msv270</a>.
  short: S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology
    and Evolution 33 (2016) 770–782.
date_created: 2018-12-18T13:18:10Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2023-09-05T13:46:05Z
day: '01'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1093/molbev/msv270
external_id:
  pmid:
  - '26609077'
file:
- access_level: open_access
  checksum: 47d9010690b6c5c17f2ac830cc63ac5c
  content_type: application/pdf
  creator: dernst
  date_created: 2018-12-18T13:21:45Z
  date_updated: 2020-07-14T12:47:10Z
  file_id: '5750'
  file_name: 2016_MolBiolEvol_Wielgoss.pdf
  file_size: 634037
  relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: '        33'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 770-782
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: Oxford University Press
pubrep_id: '587'
quality_controlled: '1'
related_material:
  record:
  - id: '9719'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Adaptation to parasites and costs of parasite resistance in mutator and nonmutator
  bacteria
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 33
year: '2016'
...
---
_id: '1902'
abstract:
- lang: eng
  text: In the 1960s-1980s, determination of bacterial growth rates was an important
    tool in microbial genetics, biochemistry, molecular biology, and microbial physiology.
    The exciting technical developments of the 1990s and the 2000s eclipsed that tool;
    as a result, many investigators today lack experience with growth rate measurements.
    Recently, investigators in a number of areas have started to use measurements
    of bacterial growth rates for a variety of purposes. Those measurements have been
    greatly facilitated by the availability of microwell plate readers that permit
    the simultaneous measurements on up to 384 different cultures. Only the exponential
    (logarithmic) portions of the resulting growth curves are useful for determining
    growth rates, and manual determination of that portion and calculation of growth
    rates can be tedious for high-throughput purposes. Here, we introduce the program
    GrowthRates that uses plate reader output files to automatically determine the
    exponential portion of the curve and to automatically calculate the growth rate,
    the maximum culture density, and the duration of the growth lag phase. GrowthRates
    is freely available for Macintosh, Windows, and Linux.We discuss the effects of
    culture volume, the classical bacterial growth curve, and the differences between
    determinations in rich media and minimal (mineral salts) media. This protocol
    covers calibration of the plate reader, growth of culture inocula for both rich
    and minimal media, and experimental setup. As a guide to reliability, we report
    typical day-to-day variation in growth rates and variation within experiments
    with respect to position of wells within the plates.
article_processing_charge: No
article_type: original
author:
- first_name: Barry
  full_name: Hall, Barry
  last_name: Hall
- first_name: Hande
  full_name: Acar, Hande
  id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
  last_name: Acar
  orcid: 0000-0003-1986-9753
- first_name: Anna
  full_name: Nandipati, Anna
  last_name: Nandipati
- first_name: Miriam
  full_name: Barlow, Miriam
  last_name: Barlow
citation:
  ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. <i>Molecular
    Biology and Evolution</i>. 2014;31(1):232-238. doi:<a href="https://doi.org/10.1093/molbev/mst187">10.1093/molbev/mst187</a>
  apa: Hall, B., Acar, H., Nandipati, A., &#38; Barlow, M. (2014). Growth rates made
    easy. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href="https://doi.org/10.1093/molbev/mst187">https://doi.org/10.1093/molbev/mst187</a>
  chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates
    Made Easy.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014.
    <a href="https://doi.org/10.1093/molbev/mst187">https://doi.org/10.1093/molbev/mst187</a>.
  ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” <i>Molecular
    Biology and Evolution</i>, vol. 31, no. 1. Oxford University Press, pp. 232–238,
    2014.
  ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular
    Biology and Evolution. 31(1), 232–238.
  mla: Hall, Barry, et al. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>,
    vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:<a href="https://doi.org/10.1093/molbev/mst187">10.1093/molbev/mst187</a>.
  short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution
    31 (2014) 232–238.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-06-07T11:08:13Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst187
external_id:
  pmid:
  - '24170494'
intvolume: '        31'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 232 - 238
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '5193'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth rates made easy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '3655'
abstract:
- lang: eng
  text: "The structural basis and distribution of variation in the ribosomal RNA multigene
    family ( rDNA) was studied in the X0 and neo-XY races of the Alpine grasshopper
    Podisma pedestris. Restriction-enzyme sites in the gene region of the rDNA repeat
    were identical in both races and homogeneous in the rDNA family. In contrast,
    sites for Hind111 and PvuII in the intergenic spacer (IGS) region showed racial
    divergence and variation within the rDNA family and within populations. A short
    insertion in the 28s gene region was present in a minority of repeats in both
    races. The distributions of four polymorphic IGS Hind111 fragments were surveyed
    at 43 locations in and around the hybrid zone. Two of these fragments appear to
    be distributed as clines, one of which is strongly associated with the neo-X chromosome.
    The other two fragments show considerable variation in both races and show negative
    association. It is proposed that the clinally distributed variants arise from
    processes of amplification and divergence of IGS sequence variants and that such
    \r\ndivergence may contribute to hybrid inviability. "
acknowledgement: 'We thank Dr. W. Kunz for providing the clones pLm6F4 and pLm4Bll
  and Dr. D. Glover for the clone pDm238. We thank Brian Curtis for his photographic
  assistance. '
article_processing_charge: No
article_type: original
author:
- first_name: John
  full_name: Dallas, John
  last_name: Dallas
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Gabriel
  full_name: Dover, Gabriel
  last_name: Dover
citation:
  ama: Dallas J, Barton NH, Dover G. Interracial rDNA variation in the grasshopper
    Podisma Pedestris. <i>Molecular Biology and Evolution</i>. 1988;5(6):660-674.
    doi:<a href="https://doi.org/10.1093/oxfordjournals.molbev.a040528">10.1093/oxfordjournals.molbev.a040528</a>
  apa: Dallas, J., Barton, N. H., &#38; Dover, G. (1988). Interracial rDNA variation
    in the grasshopper Podisma Pedestris. <i>Molecular Biology and Evolution</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/oxfordjournals.molbev.a040528">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>
  chicago: Dallas, John, Nicholas H Barton, and Gabriel Dover. “Interracial RDNA Variation
    in the Grasshopper Podisma Pedestris.” <i>Molecular Biology and Evolution</i>.
    Oxford University Press, 1988. <a href="https://doi.org/10.1093/oxfordjournals.molbev.a040528">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>.
  ieee: J. Dallas, N. H. Barton, and G. Dover, “Interracial rDNA variation in the
    grasshopper Podisma Pedestris,” <i>Molecular Biology and Evolution</i>, vol. 5,
    no. 6. Oxford University Press, pp. 660–674, 1988.
  ista: Dallas J, Barton NH, Dover G. 1988. Interracial rDNA variation in the grasshopper
    Podisma Pedestris. Molecular Biology and Evolution. 5(6), 660–674.
  mla: Dallas, John, et al. “Interracial RDNA Variation in the Grasshopper Podisma
    Pedestris.” <i>Molecular Biology and Evolution</i>, vol. 5, no. 6, Oxford University
    Press, 1988, pp. 660–74, doi:<a href="https://doi.org/10.1093/oxfordjournals.molbev.a040528">10.1093/oxfordjournals.molbev.a040528</a>.
  short: J. Dallas, N.H. Barton, G. Dover, Molecular Biology and Evolution 5 (1988)
    660–674.
date_created: 2018-12-11T12:04:28Z
date_published: 1988-07-01T00:00:00Z
date_updated: 2022-02-08T13:20:51Z
day: '01'
doi: 10.1093/oxfordjournals.molbev.a040528
extern: '1'
intvolume: '         5'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://academic.oup.com/mbe/article/5/6/660/1044340
month: '07'
oa: 1
oa_version: None
page: 660 - 674
publication: Molecular Biology and Evolution
publication_identifier:
  eissn:
  - 1537-1719
  issn:
  - 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '2728'
quality_controlled: '1'
status: public
title: Interracial rDNA variation in the grasshopper Podisma Pedestris
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 5
year: '1988'
...