---
_id: '9857'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- 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: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed
wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies
and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed
WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science
, 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.
ieee: T. Schmidt et al., “Supporting information concerning observed wMel
frequencies and analyses of habitat variables.” Public Library of Science , 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting
information concerning observed wMel frequencies and analyses of habitat variables,
Public Library of Science , 10.1371/journal.pbio.2001894.s015.
mla: Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies
and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:41:52Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s015
month: '05'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Supporting information concerning observed wMel frequencies and analyses of
habitat variables
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9858'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- 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: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities,
Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities,
Wolbachia Infection Status and Housing Characteristics.” Public Library of Science,
2017. https://doi.org/10.1371/journal.pbio.2001894.s016.
ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file
with data on mosquito densities, Wolbachia infection status and housing characteristics,
Public Library of Science, 10.1371/journal.pbio.2001894.s016.
mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia
Infection Status and Housing Characteristics. Public Library of Science, 2017,
doi:10.1371/journal.pbio.2001894.s016.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:47:07Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s016
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Excel file with data on mosquito densities, Wolbachia infection status and
housing characteristics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
file:
- access_level: open_access
checksum: 6d4c38cb1347fd43620d1736c6df5c79
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6329'
file_name: 2017_Evolution_Sachdeva_supplement.pdf
file_size: 625260
relation: main_file
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checksum: f1d90dd8831b44baf49b4dd176f263af
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
file_id: '6330'
file_name: 2017_Evolution_Sachdeva_article.pdf
file_size: 520110
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file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: '1478 - 1493 '
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-05-28T11:57:05Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T09:01:00Z
date_updated: 2019-08-13T09:01:00Z
file_id: '6811'
file_name: Novak_thesis.pdf
file_size: 3564901
relation: main_file
- access_level: open_access
checksum: 30808d2f7ca920e09f63a95cdc49bffd
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T13:42:47Z
date_updated: 2021-02-22T13:42:47Z
file_id: '9186'
file_name: 2016_Novak_Thesis.pdf
file_size: 2814384
relation: main_file
success: 1
file_date_updated: 2021-02-22T13:42:47Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
- access_level: closed
checksum: 66cb61a59943e4fb7447c6a86be5ef51
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T08:53:52Z
date_updated: 2019-08-13T08:53:52Z
file_id: '6810'
file_name: Tugrul_thesis_w_signature_page.pdf
file_size: 3695257
relation: main_file
- access_level: open_access
checksum: 293e388d70563760f6b24c3e66283dda
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:45:20Z
date_updated: 2021-02-22T11:45:20Z
file_id: '9182'
file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:45:20Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
record:
- id: '5554'
relation: research_data
status: public
- id: '1666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1631'
abstract:
- lang: eng
text: 'Ancestral processes are fundamental to modern population genetics and spatial
structure has been the subject of intense interest for many years. Despite this
interest, almost nothing is known about the distribution of the locations of pedigree
or genetic ancestors. Using both spatially continuous and stepping-stone models,
we show that the distribution of pedigree ancestors approaches a travelling wave,
for which we develop two alternative approximations. The speed and width of the
wave are sensitive to the local details of the model. After a short time, genetic
ancestors spread far more slowly than pedigree ancestors, ultimately diffusing
out with radius ## rather than spreading at constant speed. In contrast to the
wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the
local details of the models.'
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic
ancestry in spatially distributed populations. Theoretical Population Biology.
2016;108:1-12. doi:10.1016/j.tpb.2015.10.008
apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread
of pedigree versus genetic ancestry in spatially distributed populations. Theoretical
Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008
chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton.
“Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.”
Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.
ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree
versus genetic ancestry in spatially distributed populations,” Theoretical
Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.
ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus
genetic ancestry in spatially distributed populations. Theoretical Population
Biology. 108, 1–12.
mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially
Distributed Populations.” Theoretical Population Biology, vol. 108, Academic
Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.
short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population
Biology 108 (2016) 1–12.
date_created: 2018-12-11T11:53:08Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2015.10.008
ec_funded: 1
file:
- access_level: open_access
checksum: 6a65ba187994d4ad86c1c509e0ff482a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:12Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4865'
file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf
file_size: 1684043
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 108'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 12
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5524'
pubrep_id: '465'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spread of pedigree versus genetic ancestry in spatially distributed populations
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2016'
...
---
_id: '5550'
abstract:
- lang: eng
text: "We collected flower colour information on species in the tribe Antirrhineae
from taxonomic literature. We also retreived molecular data from GenBank for as
many of these species as possible to estimate phylogenetic relationships among
these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary
transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor
full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in
yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”,
Annals of Botany (in press)"
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34
apa: Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS)
files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34
chicago: Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS)
Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.
ieee: T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:34.
mla: Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS)
Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34.
short: T. Ellis, D. Field, (2016).
datarep_id: '34'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:49:54Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:34
file:
- access_level: open_access
checksum: 950f85b80427d357bfeff09608ba02e9
content_type: application/zip
creator: system
date_created: 2018-12-12T13:02:27Z
date_updated: 2020-07-14T12:47:00Z
file_id: '5594'
file_name: IST-2016-34-v1+1_tellis_flower_colour_data.zip
file_size: 4468543
relation: main_file
file_date_updated: 2020-07-14T12:47:00Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
publist_id: '5828'
related_material:
record:
- id: '1382'
relation: research_paper
status: public
status: public
title: Flower colour data and phylogeny (NEXUS) files
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5551'
abstract:
- lang: eng
text: "Data from array experiments investigating pollinator behaviour on snapdragons
in controlled conditions, and their effect on plant mating. Data were collected
as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a
total of 36 plants in a grid inside a closed organza tent, with a single hive
of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered
Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus,
at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn
how to deal with snapdragons, I observed pollinators foraging on plants, and recorded
the transitions between plants. Thereafter seeds on plants were allowed to develops.
A sample of these were grown to maturity when their flower colour could be determined,
and they were scored as yellow, magenta, or hybrid."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35
apa: Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35
chicago: Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.
ieee: T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:35.
mla: Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '35'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:27Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:35
file:
- access_level: open_access
checksum: aa3eb85d52b110cd192aa23147c4d4f3
content_type: application/zip
creator: system
date_created: 2018-12-12T13:05:12Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5640'
file_name: IST-2016-35-v1+1_array_data.zip
file_size: 32775
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Data on pollinator observations and offpsring phenotypes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5552'
abstract:
- lang: eng
text: "Data on pollinator visitation to wild snapdragons in a natural hybrid zone,
collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon
flowers have a mouth-like structure which pollinators must open to access nectar.
We placed 5mm cellophane tags in these mouths, which are held in place by the
pressure of the flower until a pollinator visits. When she opens the flower, the
tag drops out, and one can infer a visit. We surveyed plants over multiple days
in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic
variables which may be explanatory variables for pollinator visitation."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36
apa: Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:36
chicago: Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data.” Institute of Science and Technology Austria,
2016. https://doi.org/10.15479/AT:ISTA:36.
ieee: T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with
phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants,
with phenotypic and frequency data., Institute of Science and Technology Austria,
10.15479/AT:ISTA:36.
mla: Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants,
with Phenotypic and Frequency Data. Institute of Science and Technology Austria,
2016, doi:10.15479/AT:ISTA:36.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '36'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:40Z
day: '19'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:36
file:
- access_level: open_access
checksum: cbc61b523d4d475a04a737d50dc470ef
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:07Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5625'
file_name: IST-2016-36-v1+1_tag_assay_archive.zip
file_size: 44905
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic
and frequency data.
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5553'
abstract:
- lang: eng
text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
1127 open-pollinated progeny from a natural hybrid zone, collected as part of
Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
removed from this dataset.\r\n\r\nOther data were retreived from an online database
of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37
apa: Field, D., & Ellis, T. (2016). Inference of mating patterns among wild
snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:37
chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.
ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
2016.
ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
10.15479/AT:ISTA:37.
mla: Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology
Austria, 2016, doi:10.15479/AT:ISTA:37.
short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:14Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
- access_level: open_access
checksum: 4ae751b1fa4897fa216241f975a57313
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:02Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5620'
file_name: IST-2016-37-v1+1_paternity_archive.zip
file_size: 132808
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1398'
relation: research_paper
status: public
status: public
title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
in 2012
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5554'
abstract:
- lang: eng
text: "The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which
is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena
Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments
and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student
in Jon Bollback's group at IST Austria) performed the experiments and created
the data on lac promoter evolution."
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.
2016. doi:10.15479/AT:ISTA:43
apa: Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43
chicago: Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.
ieee: M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA
Polymerase.” Institute of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.
mla: Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial
RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.
short: M. Tugrul, (2016).
contributor:
- contributor_type: researcher
first_name: Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
- contributor_type: researcher
first_name: Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
datarep_id: '43'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-05-12T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.15479/AT:ISTA:43
file:
- access_level: open_access
checksum: 1fc0a10bb7ce110fcb5e1fbe3cf0c4e2
content_type: application/zip
creator: system
date_created: 2018-12-12T13:03:08Z
date_updated: 2020-07-14T12:47:01Z
file_id: '5626'
file_name: IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip
file_size: 1123495
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- RNAP binding
- de novo promoter evolution
- lac promoter
month: '05'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1131'
relation: used_in_publication
status: public
status: public
title: Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1518'
abstract:
- lang: eng
text: The inference of demographic history from genome data is hindered by a lack
of efficient computational approaches. In particular, it has proved difficult
to exploit the information contained in the distribution of genealogies across
the genome. We have previously shown that the generating function (GF) of genealogies
can be used to analytically compute likelihoods of demographic models from configurations
of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
a simple, recursive form, the size of such likelihood calculations explodes quickly
with the number of individuals and applications of this framework have so far
been mainly limited to small samples (pairs and triplets) for which the GF can
be written by hand. Here we investigate several strategies for exploiting the
inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
can be decomposed into a set of equivalence classes that allows likelihood calculations
from nontrivial samples. Using this strategy, we automated blockwise likelihood
calculations for a general set of demographic scenarios in Mathematica. These
histories may involve population size changes, continuous migration, discrete
divergence, and admixture between multiple populations. To give a concrete example,
we calculate the likelihood for a model of isolation with migration (IM), assuming
two diploid samples without phase and outgroup information. We demonstrate the
new inference scheme with an analysis of two individual butterfly genomes from
the sister species Heliconius melpomene rosina and H. cydno.
acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project
and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on
an earlier version of this manuscript. This work was supported by funding from the\r\nUnited
Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant
from the European\r\nResearch Council (250152) (to N.H.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Simon
full_name: Martin, Simon
last_name: Martin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786.
doi:10.1534/genetics.115.183814
apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies
for calculating blockwise likelihoods under the coalescent. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.115.183814
chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient
Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics.
Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.
ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for
calculating blockwise likelihoods under the coalescent,” Genetics, vol.
202, no. 2. Genetics Society of America, pp. 775–786, 2016.
ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.
mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods
under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America,
2016, pp. 775–86, doi:10.1534/genetics.115.183814.
short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.
date_created: 2018-12-11T11:52:29Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2025-05-28T11:42:48Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
- _id: NiBa
doi: 10.1534/genetics.115.183814
ec_funded: 1
external_id:
pmid:
- '26715666'
file:
- access_level: open_access
checksum: 41c9b5d72e7fe4624dd22dfe622337d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:51Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5241'
file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf
file_size: 957466
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
page: 775 - 786
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5658'
pubrep_id: '561'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient strategies for calculating blockwise likelihoods under the coalescent
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1349'
abstract:
- lang: eng
text: Crossing fitness valleys is one of the major obstacles to function optimization.
In this paper we investigate how the structure of the fitness valley, namely its
depth d and length ℓ, influence the runtime of different strategies for crossing
these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist
nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis
algorithm. While the (1+1) EA has to jump across the valley to a point of higher
fitness because it does not accept decreasing moves, the non-elitist algorithms
may cross the valley by accepting worsening moves. We show that while the runtime
of the (1+1) EA algorithm depends critically on the length of the valley, the
runtimes of the non-elitist algorithms depend crucially only on the depth of the
valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial
in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of
small length. Moreover, we show that both SSWM and Metropolis can also efficiently
optimize a rugged function consisting of consecutive valleys.
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms
elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary
Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909'
apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016).
When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings
of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170).
Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909'
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora
Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.”
In Proceedings of the Genetic and Evolutionary Computation Conference 2016
, 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism
outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic
and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp.
1163–1170.
ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism
outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and
Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation
conference, 1163–1170.'
mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing
Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference
2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.
short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings
of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.
conference:
end_date: 2016-07-24
location: Denver, CO, USA
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2016-07-20
date_created: 2018-12-11T11:51:31Z
date_published: 2016-07-20T00:00:00Z
date_updated: 2021-01-12T06:50:03Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2908812.2908909
ec_funded: 1
file:
- access_level: open_access
checksum: a1896e39e4113f2711e46b435d5f3e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:27Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5214'
file_name: IST-2016-650-v1+1_p1163-oliveto.pdf
file_size: 979026
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1163 - 1170
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 '
publication_status: published
publisher: ACM
publist_id: '5900'
pubrep_id: '650'
quality_controlled: '1'
scopus_import: 1
status: public
title: When non-elitism outperforms elitism for crossing fitness valleys
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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1356'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting
Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796
apa: Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and
the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796
chicago: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations
and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016.
https://doi.org/10.1534/genetics.115.184796.
ieee: N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the
‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America,
pp. 3–4, 2016.
ista: Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the
“Shifting Balance”. Genetics. 202(1), 3–4.
mla: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and
the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of
America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.
short: N.H. Barton, Genetics 202 (2016) 3–4.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-01-05T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1534/genetics.115.184796
file:
- access_level: open_access
checksum: 3562b89c821a4be84edf2b6ebd870cf5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:26Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4687'
file_name: IST-2017-769-v1+1_SewallWright1931.pdf
file_size: 112674
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 3 - 4
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5889'
pubrep_id: '769'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1357'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics.
2016;202(3):865-866. doi:10.1534/genetics.116.187542
apa: Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542
chicago: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent
Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.
ieee: N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,”
Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.
ista: Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. 202(3), 865–866.
mla: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.”
Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66,
doi:10.1534/genetics.116.187542.
short: N.H. Barton, Genetics 202 (2016) 865–866.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.187542
file:
- access_level: open_access
checksum: b2174bab2de1d1142900062a150f35c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:09Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5127'
file_name: IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf
file_size: 130779
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 865 - 866
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5888'
pubrep_id: '768'
quality_controlled: '1'
scopus_import: 1
status: public
title: Richard Hudson and Norman Kaplan on the coalescent process
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1358'
abstract:
- lang: eng
text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA
interactions. Limited specificity may lead to crosstalk: a regulatory state in
which a gene is either incorrectly activated due to noncognate TF–DNA interactions
or remains erroneously inactive. As each TF can have numerous interactions with
noncognate cis-regulatory elements, crosstalk is inherently a global problem,
yet has previously not been studied as such. We construct a theoretical framework
to analyse the effects of global crosstalk on gene regulation. We find that crosstalk
presents a significant challenge for organisms with low-specificity TFs, such
as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting
at equilibrium, including variants of cooperativity and combinatorial regulation.
Our results suggest that crosstalk imposes a previously unexplored global constraint
on the functioning and evolution of regulatory networks, which is qualitatively
distinct from the known constraints that act at the level of individual gene regulatory
elements.'
article_number: '12307'
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- 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: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to
gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016).
Intrinsic limits to gene regulation by global crosstalk. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms12307
chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and
Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature
Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic
limits to gene regulation by global crosstalk,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits
to gene regulation by global crosstalk. Nature Communications. 7, 12307.
mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”
Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2023-09-07T12:53:49Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
file:
- access_level: open_access
checksum: fe3f3a1526d180b29fe691ab11435b78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4919'
file_name: IST-2016-627-v1+1_ncomms12307.pdf
file_size: 861805
relation: main_file
- access_level: open_access
checksum: 164864a1a675f3ad80e9917c27aba07f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:02Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4920'
file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf
file_size: 1084703
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5887'
pubrep_id: '627'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Intrinsic limits to gene regulation by global crosstalk
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '1359'
abstract:
- lang: eng
text: "The role of gene interactions in the evolutionary process has long\r\nbeen
controversial. Although some argue that they are not of\r\nimportance, because
most variation is additive, others claim that\r\ntheir effect in the long term
can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions
under directional\r\nselection assuming no mutation or dominance, and that epistasis
is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can
be increased by selection and analyze two extreme\r\nregimes, in which either
drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios,
epistatic interactions affect\r\nthe long-term response to selection by modulating
the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson
A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument
to show that, for any form of epistasis, the total response\r\nof a haploid population
is proportional to the initial total genotypic\r\nvariance. In contrast, the total
response of a diploid population is\r\nincreased by epistasis, for a given initial
genotypic variance. When\r\nselection dominates, we show that the total selection
response can\r\nonly be increased by epistasis when s\r\nome initially deleterious
alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple
approximation for this effect and show that, in this regime, it is\r\nthe structure
of the genotype - phenotype map that matters and not\r\nthe variance components
of the population."
article_processing_charge: No
article_type: original
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Paixao T, Barton NH. The effect of gene interactions on the long-term response
to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
apa: Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on
the long-term response to selection. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1518830113
chicago: Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions
on the Long-Term Response to Selection.” PNAS. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1518830113.
ieee: T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term
response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences,
pp. 4422–4427, 2016.
ista: Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term
response to selection. PNAS. 113(16), 4422–4427.
mla: Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on
the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National
Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.
short: T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.
date_created: 2018-12-11T11:51:34Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2021-01-12T06:50:08Z
day: '19'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1073/pnas.1518830113
ec_funded: 1
external_id:
pmid:
- '27044080'
intvolume: ' 113'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/
month: '04'
oa: 1
oa_version: Published Version
page: 4422 - 4427
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5886'
quality_controlled: '1'
scopus_import: 1
status: public
title: The effect of gene interactions on the long-term response to selection
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1382'
abstract:
- lang: eng
text: Background and aims Angiosperms display remarkable diversity in flower colour,
implying that transitions between pigmentation phenotypes must have been common.
Despite progress in understanding transitions between anthocyanin (blue, purple,
pink or red) and unpigmented (white) flowers, little is known about the evolutionary
patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented
flowers. This study investigates the relative rates of evolutionary transitions
between different combinations of yellow- and anthocyanin-pigmentation phenotypes
in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on
anthocyanin and yellow floral pigmentation for 369 species across the tribe. We
then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative
methods to estimate transition rates among pigmentation phenotypes across the
phylogeny. Key Results In contrast to previous studies we found a bias towards
transitions involving a gain in pigmentation, although transitions to phenotypes
with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite
the dominance of yellow and anthocyanin-pigmented taxa, transitions between these
phenotypes are constrained to move through a white intermediate stage, whereas
transitions to double-pigmentation are very rare. The most abundant transitions
are between anthocyanin-pigmented and unpigmented flowers, and similarly the most
abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented
flowers. Conclusions Our findings show that pigment evolution is limited by the
presence of other floral pigments. This interaction between anthocyanin and yellow
pigments constrains the breadth of potential floral diversity observed in nature.
In particular, they suggest that selection has repeatedly acted to promote the
spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore,
the correlation between transition rates and polymorphism suggests that the forces
causing and maintaining variance in the short term reflect evolutionary processes
on longer time scales.
acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous
reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for
her efforts in tracking down the more obscure references.
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in
flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140.
doi:10.1093/aob/mcw043
apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin
pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany.
Oxford University Press. https://doi.org/10.1093/aob/mcw043
chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin
Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany.
Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.
ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae,” Annals of Botany, vol.
117, no. 7. Oxford University Press, pp. 1133–1140, 2016.
ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.
mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation
in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol.
117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.
short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.
date_created: 2018-12-11T11:51:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-02-21T13:49:53Z
day: '1'
department:
- _id: NiBa
doi: 10.1093/aob/mcw043
intvolume: ' 117'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 1133 - 1140
publication: Annals of Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5828'
quality_controlled: '1'
related_material:
record:
- id: '5550'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions
in the Antirrhineae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...