---
_id: '489'
abstract:
- lang: eng
text: 'Graph games of infinite length are a natural model for open reactive processes:
one player represents the controller, trying to ensure a given specification,
and the other represents a hostile environment. The evolution of the system depends
on the decisions of both players, supplemented by chance. In this work, we focus
on the notion of randomised strategy. More specifically, we show that three natural
definitions may lead to very different results: in the most general cases, an
almost-surely winning situation may become almost-surely losing if the player
is only allowed to use a weaker notion of strategy. In more reasonable settings,
translations exist, but they require infinite memory, even in simple cases. Finally,
some traditional problems becomes undecidable for the strongest type of strategies.'
alternative_title:
- EPTCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Julien
full_name: Cristau, Julien
last_name: Cristau
- first_name: Claire
full_name: David, Claire
last_name: David
- first_name: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Cristau J, David C, Horn F. How do we remember the past in randomised strategies?
In: Proceedings of GandALF 2010. Vol 25. Open Publishing Association; 2010:30-39.
doi:10.4204/EPTCS.25.7'
apa: 'Cristau, J., David, C., & Horn, F. (2010). How do we remember the past
in randomised strategies? In Proceedings of GandALF 2010 (Vol. 25, pp.
30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.25.7'
chicago: Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the
Past in Randomised Strategies?” In Proceedings of GandALF 2010, 25:30–39.
Open Publishing Association, 2010. https://doi.org/10.4204/EPTCS.25.7.
ieee: J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised
strategies?,” in Proceedings of GandALF 2010, Minori, Amalfi Coast, Italy,
2010, vol. 25, pp. 30–39.
ista: 'Cristau J, David C, Horn F. 2010. How do we remember the past in randomised
strategies? Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and
Formal Verification, EPTCS, vol. 25, 30–39.'
mla: Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?”
Proceedings of GandALF 2010, vol. 25, Open Publishing Association, 2010,
pp. 30–39, doi:10.4204/EPTCS.25.7.
short: J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing
Association, 2010, pp. 30–39.
conference:
end_date: 2010-06-18
location: Minori, Amalfi Coast, Italy
name: 'GandALF: Games, Automata, Logic, and Formal Verification'
start_date: 2010-06-17
corr_author: '1'
date_created: 2018-12-11T11:46:45Z
date_published: 2010-06-09T00:00:00Z
date_updated: 2026-06-18T18:51:53Z
day: '09'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4204/EPTCS.25.7
external_id:
arxiv:
- '1006.1404'
fulldoi: https://doi.org/10.4204/EPTCS.25.7
intvolume: ' 25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1006.1404
month: '06'
oa: 1
oa_version: Published Version
page: 30 - 39
publication: Proceedings of GandALF 2010
publication_status: published
publisher: Open Publishing Association
publist_id: '7332'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How do we remember the past in randomised strategies?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2010'
...
---
_id: '533'
abstract:
- lang: eng
text: Any programming error that can be revealed before compiling a program saves
precious time for the programmer. While integrated development environments already
do a good job by detecting, e.g., data-flow abnormalities, current static analysis
tools suffer from false positives ("noise") or require strong user interaction.
We propose to avoid this deficiency by defining a new class of errors. A program
fragment is doomed if its execution will inevitably fail, regardless of which
state it is started in. We use a formal verification method to identify such errors
fully automatically and, most significantly, without producing noise. We report
on experiments with a prototype tool.
article_processing_charge: No
author:
- first_name: Jochen
full_name: Hoenicke, Jochen
last_name: Hoenicke
- first_name: Kari
full_name: Leino, Kari
last_name: Leino
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Schäf, Martin
last_name: Schäf
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. Formal
Methods in System Design. 2010;37(2-3):171-199. doi:10.1007/s10703-010-0102-0
apa: Hoenicke, J., Leino, K., Podelski, A., Schäf, M., & Wies, T. (2010). Doomed
program points. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-010-0102-0
chicago: Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas
Wies. “Doomed Program Points.” Formal Methods in System Design. Springer,
2010. https://doi.org/10.1007/s10703-010-0102-0.
ieee: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program
points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp.
171–199, 2010.
ista: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points.
Formal Methods in System Design. 37(2–3), 171–199.
mla: Hoenicke, Jochen, et al. “Doomed Program Points.” Formal Methods in System
Design, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:10.1007/s10703-010-0102-0.
short: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in
System Design 37 (2010) 171–199.
corr_author: '1'
date_created: 2018-12-11T11:47:01Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2025-09-30T09:48:58Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/s10703-010-0102-0
external_id:
isi:
- '000286631700004'
fulldoi: https://doi.org/10.1007/s10703-010-0102-0
intvolume: ' 37'
isi: 1
issue: 2-3
language:
- iso: eng
month: '12'
oa_version: None
page: 171 - 199
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '7284'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Doomed program points
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2010'
...
---
_id: '5388'
abstract:
- lang: eng
text: "We present an algorithmic method for the synthesis of concurrent programs
that are optimal with respect to quantitative performance measures. The input
consists of a sequential sketch, that is, a program that does not contain synchronization
constructs, and of a parametric performance model that assigns costs to actions
such as locking, context switching, and idling. The quantitative synthesis problem
is to automatically introduce synchronization constructs into the sequential sketch
so that both correctness is guaranteed and worst-case (or average-case) performance
is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe
show that for worst-case performance, the problem can be modeled\r\nas a 2-player
graph game with quantitative (limit-average) objectives, and\r\nfor average-case
performance, as a 2 1/2 -player graph game (with probabilistic transitions). In
both cases, the optimal correct program is derived from an optimal strategy in
the corresponding quantitative game. We prove that the respective game problems
are computationally expensive (NP-complete), and present several techniques that
overcome the theoretical difficulty in cases of concurrent programs of practical
interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic
syn- thesis of programs that access a concurrent list. For certain parameter val-
ues, our method automatically synthesizes various classical synchronization schemes
for implementing a concurrent list, such as fine-grained locking or a lazy algorithm.
For other parameter values, a new, hybrid synchronization style is synthesized,
which uses both the lazy approach and coarse-grained locks (instead of standard
fine-grained locks). The trade-off occurs because while fine-grained locking tends
to decrease the cost that is due to waiting for locks, it increases cache size
requirements."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative
Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004
apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh,
R. (2010). Quantitative synthesis for concurrent programs. IST Austria.
https://doi.org/10.15479/AT:IST-2010-0004
chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna,
and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria,
2010. https://doi.org/10.15479/AT:IST-2010-0004.
ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative
synthesis for concurrent programs. IST Austria, 2010.
ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative
synthesis for concurrent programs, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs.
IST Austria, 2010, doi:10.15479/AT:IST-2010-0004.
short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative
Synthesis for Concurrent Programs, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-10-07T00:00:00Z
date_updated: 2025-04-15T08:12:00Z
day: '07'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2010-0004
file:
- access_level: open_access
checksum: da38782d2388a6fa32109d10bb9bad67
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5515'
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file_date_updated: 2020-07-14T12:46:42Z
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has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '24'
related_material:
record:
- id: '3366'
relation: later_version
status: public
status: public
title: Quantitative synthesis for concurrent programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5389'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the im- plementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria;
2010. doi:10.15479/AT:IST-2010-0003
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances.
IST Austria. https://doi.org/10.15479/AT:IST-2010-0003
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation
Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances.
IST Austria, 2010.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria,
24p.
mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria,
2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2026-06-18T18:41:23Z
day: '04'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0003
file:
- access_level: open_access
checksum: 284ded99764e32a583a8ea83fcea254b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5547'
file_name: IST-2010-0003_IST-2010-0003.pdf
file_size: 367246
relation: main_file
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has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '25'
related_material:
record:
- id: '4393'
relation: later_version
status: public
- id: '3249'
relation: later_version
status: public
status: public
title: Simulation distances
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5390'
abstract:
- lang: eng
text: The class of ω regular languages provide a robust specification language in
verification. Every ω-regular condition can be decomposed into a safety part and
a liveness part. The liveness part ensures that something good happens “eventually.”
Two main strengths of the classical, infinite-limit formulation of liveness are
robustness (independence from the granularity of transitions) and simplicity (abstraction
of complicated time bounds). However, the classical liveness formulation suffers
from the drawback that the time until something good happens may be unbounded.
A stronger formulation of liveness, so-called finitary liveness, overcomes this
drawback, while still retaining robustness and simplicity. Finitary liveness requires
that there exists an unknown, fixed bound b such that something good happens within
b transitions. In this work we consider the finitary parity and Streett (fairness)
conditions. We present the topological, automata-theoretic and logical characterization
of finitary languages defined by finitary parity and Streett conditions. We (a)
show that the finitary parity and Streett languages are Σ2-complete; (b) present
a complete characterization of the expressive power of various classes of automata
with finitary and infinitary conditions (in particular we show that non-deterministic
finitary parity and Streett automata cannot be determinized to deterministic finitary
parity or Streett automata); and (c) show that the languages defined by non-deterministic
finitary parity automata exactly characterize the star-free fragment of ωB-regular
languages.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: Chatterjee K, Fijalkow N. Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages. IST Austria; 2010. doi:10.15479/AT:IST-2010-0002
apa: Chatterjee, K., & Fijalkow, N. (2010). Topological, automata-theoretic
and logical characterization of finitary languages. IST Austria. https://doi.org/10.15479/AT:IST-2010-0002
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0002.
ieee: K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical
characterization of finitary languages. IST Austria, 2010.
ista: Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical
characterization of finitary languages, IST Austria, 21p.
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010, doi:10.15479/AT:IST-2010-0002.
short: K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2020-07-14T23:04:41Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2010-0002
file:
- access_level: open_access
checksum: 283d3604d76dd4d5161585d4c8625fbe
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:10Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5532'
file_name: IST-2010-0002_IST-2010-0002.pdf
file_size: 395662
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
fulldoi: https://doi.org/10.15479/AT:IST-2010-0002
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '26'
status: public
title: Topological, automata-theoretic and logical characterization of finitary languages
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5391'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each node consists an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
imple- mentation and proved that the corrected version is linearizable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking
of Linearizability of Concurrent List Implementations. IST Austria; 2010.
doi:10.15479/AT:IST-2010-0001
apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations. IST
Austria. https://doi.org/10.15479/AT:IST-2010-0001
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations.
IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001.
ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model
checking of linearizability of concurrent list implementations. IST Austria,
2010.
ista: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations, IST Austria, 27p.
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking
of Linearizability of Concurrent List Implementations, IST Austria, 2010.
date_created: 2018-12-12T11:39:04Z
date_published: 2010-04-19T00:00:00Z
date_updated: 2024-10-21T06:03:05Z
day: '19'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0001
file:
- access_level: open_access
checksum: 986645caad7dd85a6a091488f6c646dc
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:44Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5505'
file_name: IST-2010-0001_IST-2010-0001.pdf
file_size: 372286
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
fulldoi: https://doi.org/10.15479/AT:IST-2010-0001
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '27'
related_material:
record:
- id: '4390'
relation: later_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '9452'
abstract:
- lang: eng
text: Eukaryotic cytosine methylation represses transcription but also occurs in
the bodies of active genes, and the extent of methylation biology conservation
is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that
gene body methylation is conserved between plants and animals, whereas selective
methylation of transposons is not. We show that methylation of plant transposons
in the CHG context extends to green algae and that exclusion of histone H2A.Z
from methylated DNA is conserved between plants and animals, and we present evidence
for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant
DNA methylation systems are mosaics of conserved and derived features, and indicate
that gene body methylation is an ancient property of eukaryotic genomes.
article_processing_charge: No
article_type: original
author:
- first_name: 'Assaf '
full_name: 'Zemach, Assaf '
last_name: Zemach
- first_name: Ivy E.
full_name: McDaniel, Ivy E.
last_name: McDaniel
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis
of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
apa: Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide
evolutionary analysis of eukaryotic DNA methylation. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1186366
chicago: Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide
Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American
Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
ieee: A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary
analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American
Association for the Advancement of Science, pp. 916–919, 2010.
ista: Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary
analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.
mla: Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA
Methylation.” Science, vol. 328, no. 5980, American Association for the
Advancement of Science, 2010, pp. 916–19, doi:10.1126/science.1186366.
short: A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.
date_created: 2021-06-04T08:26:08Z
date_published: 2010-05-14T00:00:00Z
date_updated: 2021-12-14T08:35:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1126/science.1186366
extern: '1'
external_id:
pmid:
- '20395474 '
fulldoi: https://doi.org/10.1126/science.1186366
intvolume: ' 328'
issue: '5980'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa_version: None
page: 916-919
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide evolutionary analysis of eukaryotic DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 328
year: '2010'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
fulldoi: https://doi.org/10.1073/pnas.1009695107
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
fulldoi: https://doi.org/10.1016/j.cub.2010.07.007
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '9764'
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the
drift load. 2010. doi:10.1371/journal.pbio.1000429.s003
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010.
https://doi.org/10.1371/journal.pbio.1000429.s003.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis
and the drift load.” Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis
and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.
mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.s003.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).
date_created: 2021-08-02T09:45:39Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2025-09-30T09:42:52Z
day: '20'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429.s003
fulldoi: https://doi.org/10.1371/journal.pbio.1000429.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '3779'
relation: used_in_publication
status: public
status: public
title: Heterosis and the drift load
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2010'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
article_processing_charge: No
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
corr_author: '1'
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2025-09-30T09:47:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
external_id:
isi:
- '000285297000025'
fulldoi: https://doi.org/10.1534/genetics.110.123240
intvolume: ' 186'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
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: '3337'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 186
year: '2010'
...
---
_id: '3604'
abstract:
- lang: eng
text: We investigated temporal changes in hybridization and introgression between
native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on
the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples
of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that
either the proportion of recent hybrids, or the levels of introgression had changed
over the study period. Nevertheless, in one population where the two species have
been in contact since ∼1970, 44% of individuals sampled during the study were
hybrids. This suggests that hybridization between these species can proceed fairly
rapidly. By analysing the number of alleles that have introgressed from polymorphic
red deer into the genetically homogenous sika population, we reconstructed the
haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization
events could account for all the recently hybridized sika-like individuals found
across a large section of the Peninsula. Although we demonstrate that low rates
of F1 hybridization can lead to substantial introgression, the progress of hybridization
and introgression appears to be unpredictable over the short timescales.
article_processing_charge: No
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- 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: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal
changes in hybridisation and introgression between invasive sika (Cervus nippon)
and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular
Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x
apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010).
Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x
chicago: Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine
Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010.
https://doi.org/10.1111/j.1365-294X.2009.04497.x.
ieee: H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,”
Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.
ista: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland.
Molecular Ecology. 19(5), 910–924.
mla: Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell,
2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.
short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology
19 (2010) 910–924.
date_created: 2018-12-11T12:04:12Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2025-09-30T09:47:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2009.04497.x
external_id:
isi:
- '000274550100008'
fulldoi: https://doi.org/10.1111/j.1365-294X.2009.04497.x
intvolume: ' 19'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 910 - 924
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2010'
...
---
_id: '3718'
abstract:
- lang: eng
text: Long-term depression (LTD) is a form of synaptic plasticity that may contribute
to information storage in the central nervous system. Here we report that LTD
can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing
low frequency stimulation with a modest postsynaptic depolarization. The induction
of LTD required the activation of both metabotropic glutamate receptors of the
mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and
N types, leading to the stimulation of intracellular inositol trisphosphate (IP3)
receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular
stores activated the protein phosphatase cascade involving calcineurin and protein
phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This
effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking
P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors
inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal
neurons. In addition, we show that the release of ATP under hypoxia is able to
inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data
suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation
of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD
in prefrontal cortex.
acknowledgement: " The financial support of the Deutsche Forschungsgemeinschaft (IL
20/12-1, KI 677/2-4) is gratefully acknowledged.\r\nWe thank B. H. Koller (Department
of Genetics and Molecular Biology, University of North Carolina at Chapel Hill,
NC, USA) for the generous supply of P2Y1−/− and P2Y2−/− mice. We are grateful to
Dr. A. Schulz for reanalysing the genotype of the P2Y1−/− mice. The authors thank
P. Jonas and U. Heinemann for many helpful comments and A-K. Krause, L Feige and
M. Eberts for their excellent technical support."
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Hartmut
full_name: Schmidt, Hartmut
last_name: Schmidt
- first_name: Heike
full_name: Franke, Heike
last_name: Franke
- first_name: Ute
full_name: Krügel, Ute
last_name: Krügel
- first_name: Jens
full_name: Eilers, Jens
last_name: Eilers
- first_name: Peter
full_name: Illes, Peter
last_name: Illes
- first_name: Zoltan
full_name: Gerevich, Zoltan
last_name: Gerevich
citation:
ama: Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression
in the prefrontal cortex. Neuropharmacology. 2010;59(6):406-415. doi:10.1016/j.neuropharm.2010.05.013
apa: Guzmán, J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., Illes, P., &
Gerevich, Z. (2010). P2Y1 receptors inhibit long-term depression in the prefrontal
cortex. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2010.05.013
chicago: Guzmán, José, Hartmut Schmidt, Heike Franke, Ute Krügel, Jens Eilers, Peter
Illes, and Zoltan Gerevich. “P2Y1 Receptors Inhibit Long-Term Depression in the
Prefrontal Cortex.” Neuropharmacology. Elsevier, 2010. https://doi.org/10.1016/j.neuropharm.2010.05.013.
ieee: J. Guzmán et al., “P2Y1 receptors inhibit long-term depression in the
prefrontal cortex.,” Neuropharmacology, vol. 59, no. 6. Elsevier, pp. 406–415,
2010.
ista: Guzmán J, Schmidt H, Franke H, Krügel U, Eilers J, Illes P, Gerevich Z. 2010.
P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology.
59(6), 406–415.
mla: Guzmán, José, et al. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal
Cortex.” Neuropharmacology, vol. 59, no. 6, Elsevier, 2010, pp. 406–15,
doi:10.1016/j.neuropharm.2010.05.013.
short: J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich,
Neuropharmacology 59 (2010) 406–415.
corr_author: '1'
date_created: 2018-12-11T12:04:47Z
date_published: 2010-11-01T00:00:00Z
date_updated: 2025-09-30T09:46:27Z
day: '01'
department:
- _id: PeJo
doi: 10.1016/j.neuropharm.2010.05.013
external_id:
isi:
- '000283453300006'
fulldoi: https://doi.org/10.1016/j.neuropharm.2010.05.013
intvolume: ' 59'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa_version: None
page: 406 - 415
publication: Neuropharmacology
publication_status: published
publisher: Elsevier
publist_id: '2512'
quality_controlled: '1'
scopus_import: '1'
status: public
title: P2Y1 receptors inhibit long-term depression in the prefrontal cortex.
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 59
year: '2010'
...
---
_id: '3719'
abstract:
- lang: eng
text: The induction of a signaling pathway is characterized by transient complex
formation and mutual posttranslational modification of proteins. To faithfully
capture this combinatorial process in a math- ematical model is an important challenge
in systems biology. Exploiting the limited context on which most binding and modification
events are conditioned, attempts have been made to reduce the com- binatorial
complexity by quotienting the reachable set of molecular species, into species
aggregates while preserving the deterministic semantics of the thermodynamic limit.
Recently we proposed a quotienting that also preserves the stochastic semantics
and that is complete in the sense that the semantics of individual species can
be recovered from the aggregate semantics. In this paper we prove that this quotienting
yields a sufficient condition for weak lumpability and that it gives rise to a
backward Markov bisimulation between the original and aggregated transition system.
We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
acknowledgement: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL
ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National
Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support
from SystemsX.ch, the Swiss Initiative in Systems Biology.
alternative_title:
- EPTCS
arxiv: 1
author:
- first_name: Jérôme
full_name: Feret, Jérôme
last_name: Feret
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based
systems. In: Vol 40. Open Publishing Association; 2010:142-161.'
apa: 'Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2010). Lumpability
abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC:
Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open
Publishing Association.'
chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
ieee: 'J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically
Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.'
ista: 'Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions
of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process
Calculi, EPTCS, vol. 40, 142–161.'
mla: Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems.
Vol. 40, Open Publishing Association, 2010, pp. 142–61.
short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association,
2010, pp. 142–161.
conference:
end_date: 2010-08-23
location: Jena, Germany
name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi'
start_date: 2010-08-23
date_created: 2018-12-11T12:04:47Z
date_published: 2010-10-30T00:00:00Z
date_updated: 2026-06-18T18:39:27Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
arxiv:
- '1011.0496'
file:
- access_level: open_access
checksum: eaaba991a86fff37606b0eb5196878e8
content_type: application/pdf
creator: kschuh
date_created: 2019-01-31T12:09:09Z
date_updated: 2020-07-14T12:46:14Z
file_id: '5904'
file_name: Lumpability_abstractions_of_rule-based_systems.pdf
file_size: 907155
relation: main_file
file_date_updated: 2020-07-14T12:46:14Z
has_accepted_license: '1'
intvolume: ' 40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 142-161
publication_status: published
publisher: Open Publishing Association
publist_id: '2511'
quality_controlled: '1'
related_material:
record:
- id: '3168'
relation: later_version
status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule-based systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2010'
...
---
_id: '3772'
article_number: e1000987
article_processing_charge: No
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. Understanding adaptation in large populations. PLoS Genetics.
2010;6(6). doi:10.1371/journal.pgen.1000987
apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987
chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.
ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics,
vol. 6, no. 6. Public Library of Science, 2010.
ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics.
6(6), e1000987.
mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.
short: N.H. Barton, PLoS Genetics 6 (2010).
corr_author: '1'
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2025-09-30T09:45:21Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
external_id:
isi:
- '000279805200002'
file:
- access_level: open_access
checksum: 5c14de2680ab483cb835096c99ee734d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:24Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5075'
file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF
file_size: 349965
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
fulldoi: https://doi.org/10.1371/journal.pgen.1000987
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '2454'
pubrep_id: '524'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Understanding adaptation in large 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6
year: '2010'
...
---
_id: '3773'
abstract:
- lang: eng
text: If distinct biological species are to coexist in sympatry, they must be reproductively
isolated and must exploit different limiting resources. A two-niche Levene model
is analysed, in which habitat preference and survival depend on underlying additive
traits. The population genetics of preference and viability are equivalent. However,
there is a linear trade-off between the chances of settling in either niche, whereas
viabilities may be constrained arbitrarily. With a convex trade-off, a sexual
population evolves a single generalist genotype, whereas with a concave trade-off,
disruptive selection favours maximal variance. A pure habitat preference evolves
to global linkage equilibrium if mating occurs in a single pool, but remarkably,
evolves to pairwise linkage equilibrium within niches if mating is within those
niches--independent of the genetics. With a concave trade-off, the population
shifts sharply between a unimodal distribution with high gene flow and a bimodal
distribution with strong isolation, as the underlying genetic variance increases.
However, these alternative states are only simultaneously stable for a narrow
parameter range. A sharp threshold is only seen if survival in the 'wrong' niche
is low; otherwise, strong isolation is impossible. Gene flow from divergent demes
makes speciation much easier in parapatry than in sympatry.
acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish
Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He
also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n"
article_processing_charge: No
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. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001
apa: Barton, N. H. (2010). What role does natural selection play in speciation?
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001
chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.
ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.
ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547),
1825–1840.
mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1825–1840.
corr_author: '1'
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2025-09-30T09:45:54Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
isi:
- '000277208600009'
pmid:
- '20439284'
fulldoi: https://doi.org/10.1098/rstb.2010.0001
intvolume: ' 365'
isi: 1
issue: '1547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20439284
month: '06'
oa: 1
oa_version: Submitted Version
page: 1825 - 1840
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2455'
quality_controlled: '1'
scopus_import: '1'
status: public
title: What role does natural selection play in speciation?
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 365
year: '2010'
...
---
_id: '3774'
abstract:
- lang: eng
text: 1. Hybridisation with an invasive species has the potential to alter the phenotype
and hence the ecology of a native counterpart. 2. Here data from populations of
native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland
is used to assess the extent to which hybridisation between them is causing phenotypic
change. This is done by regression of phenotypic traits against genetic hybrid
scores. 3. Hybridisation is causing increases in the body weight of sika-like
deer and decreases in the body weight of red-like females. Hybridisation is causing
increases in jaw length and increases in incisor arcade breadth in sika-like females.
Hybridisation is also causing decreases in incisor arcade breadth in red-like
females. 4. There is currently no evidence that hybridisation is causing changes
in the kidney fat weight or pregnancy rates of either population. 5. Increased
phenotypic similarity between the two species is likely to lead to further hybridisation.
The ecological consequences of this are difficult to predict.
acknowledgement: "This project was funded through a NERC studentship to HVS which
was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission
Scotland rangers for all their help with providing the larder data for and samples
from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice
and Steve Albon for helpful comments on the manuscript."
article_processing_charge: No
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- 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: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal
Ecology. 2010;79(2):414-425. doi:10.1111/j.1365-2656.2009.01633.x
apa: Senn, H., Swanson, G., Goodman, S., Barton, N. H., & Pemberton, J. (2010).
Phenotypic correlates of hybridisation between red and sika deer (genus Cervus).
Journal of Animal Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2656.2009.01633.x
chicago: Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine
Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus
Cervus).” Journal of Animal Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-2656.2009.01633.x.
ieee: H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic
correlates of hybridisation between red and sika deer (genus Cervus),” Journal
of Animal Ecology, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.
ista: Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates
of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology.
79(2), 414–425.
mla: Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and
Sika Deer (Genus Cervus).” Journal of Animal Ecology, vol. 79, no. 2, Wiley-Blackwell,
2010, pp. 414–25, doi:10.1111/j.1365-2656.2009.01633.x.
short: H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal
Ecology 79 (2010) 414–425.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2025-09-30T09:44:45Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-2656.2009.01633.x
external_id:
isi:
- '000274321200014'
pmid:
- '20002231'
fulldoi: https://doi.org/10.1111/j.1365-2656.2009.01633.x
intvolume: ' 79'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
page: 414 - 425
pmid: 1
publication: Journal of Animal Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2453'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 79
year: '2010'
...
---
_id: '3776'
abstract:
- lang: eng
text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling
questions in biology. The most compelling general explanation is that recombination
facilitates selection by breaking down the negative associations generated by
random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of
HRI owing to: deleterious mutation, balancing selection and selective sweeps on:
neutral diversity, rates of adaptation and the mutation load. These effects are
mediated primarily by the density of deleterious mutations and of selective sweeps.
Sequence polymorphism and divergence suggest that these rates may be high enough
to cause significant interference even in genomic regions of high recombination.
However, neither seems able to generate enough variance in fitness to select strongly
for high rates of recombination. It is plausible that spatial and temporal fluctuations
in selection generate much more fitness variance, and hence selection for recombination,
than can be explained by uniformly deleterious mutations or species-wide selective
sweeps.'
acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would
like to thank Brian Charlesworth and Sally Otto for their helpful comments."
article_processing_charge: No
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. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569.
doi:10.1098/rstb.2010.0106
apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2010.0106
chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.
ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1552. Royal Society, pp. 2559–2569, 2010.
ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.
mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 2559–2569.
corr_author: '1'
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2025-09-30T09:43:27Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
external_id:
isi:
- '000280097000016'
file:
- access_level: open_access
checksum: 4d8aade10db030124ab158b622e337e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:40Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5093'
file_name: IST-2016-555-v1+1_RS2009_revised.pdf
file_size: 250255
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
fulldoi: https://doi.org/10.1098/rstb.2010.0106
has_accepted_license: '1'
intvolume: ' 365'
isi: 1
issue: '1552'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 2559 - 2569
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2450'
pubrep_id: '555'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic linkage and natural selection
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 365
year: '2010'
...
---
_id: '3777'
abstract:
- lang: eng
text: 'Under the classical view, selection depends more or less directly on mutation:
standing genetic variance is maintained by a balance between selection and mutation,
and adaptation is fuelled by new favourable mutations. Recombination is favoured
if it breaks negative associations among selected alleles, which interfere with
adaptation. Such associations may be generated by negative epistasis, or by random
drift (leading to the Hill-Robertson effect). Both deterministic and stochastic
explanations depend primarily on the genomic mutation rate, U. This may be large
enough to explain high recombination rates in some organisms, but seems unlikely
to be so in general. Random drift is a more general source of negative linkage
disequilibria, and can cause selection for recombination even in large populations,
through the chance loss of new favourable mutations. The rate of species-wide
substitutions is much too low to drive this mechanism, but local fluctuations
in selection, combined with gene flow, may suffice. These arguments are illustrated
by comparing the interaction between good and bad mutations at unlinked loci under
the infinitesimal model.'
acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this
special issue, and the Royal Society and Wolfson Foundation for their support. Also,
A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.
article_processing_charge: No
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. Mutation and the evolution of recombination. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294.
doi:10.1098/rstb.2009.0320
apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2009.0320
chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.
ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.
ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544),
1281–1294.
mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1281–1294.
corr_author: '1'
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2025-09-30T09:44:03Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
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issue: '1544'
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main_file_link:
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url: http://www.ncbi.nlm.nih.gov/pubmed/20308104
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page: 1281 - 1294
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2451'
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title: Mutation and the evolution of recombination
type: journal_article
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year: '2010'
...
---
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abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2025-09-30T09:42:52Z
day: '20'
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department:
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doi: 10.1371/journal.pbio.1000429
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