---
_id: '14705'
abstract:
- lang: eng
text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s,
this lineage, and in particular the model species Artemia franciscana, has been
the subject of extensive research. However, our understanding of the genetic mechanisms
underlying various aspects of their reproductive biology, including sex determination,
are still lacking. This is partly due to the scarcity of genomic resources for
Artemia species and crustaceans in general. Here, we present a chromosome-level
genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake,
USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into
21 linkage groups using a previously published high-density linkage map. We performed
coverage and FST analyses using male and female genomic and transcriptomic reads
to quantify the extent of differentiation between the Z and W chromosomes. Additionally,
we quantified the expression levels in male and female heads and gonads and found
further evidence for dosage compensation in this species.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds
light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705
apa: Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:14705
chicago: Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.
ieee: M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation.’” Institute of Science and Technology
Austria, 2024.
ista: Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:14705.
mla: Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology
Austria, 2024, doi:10.15479/AT:ISTA:14705.
short: M.N. Elkrewi, (2024).
contributor:
- contributor_type: researcher
first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- contributor_type: project_member
first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- contributor_type: supervisor
first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- contributor_type: researcher
first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
date_created: 2023-12-22T13:40:48Z
date_published: 2024-01-02T00:00:00Z
date_updated: 2025-07-24T11:06:43Z
day: '02'
ddc:
- '576'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:14705
file:
- access_level: open_access
checksum: bdaf1392867786634ec5466d528c36ca
content_type: text/plain
creator: melkrewi
date_created: 2023-12-22T13:54:21Z
date_updated: 2023-12-22T13:54:21Z
file_id: '14707'
file_name: readme.txt.txt
file_size: 847
relation: main_file
success: 1
- access_level: open_access
checksum: 973e1cbdab923a71709782177980829f
content_type: application/x-zip-compressed
creator: melkrewi
date_created: 2023-12-22T14:14:06Z
date_updated: 2023-12-22T14:14:06Z
file_id: '14708'
file_name: data_artemia_franciscana_genome.zip
file_size: 343632753
relation: main_file
success: 1
file_date_updated: 2023-12-22T14:14:06Z
has_accepted_license: '1'
keyword:
- sex chromosome evolution
- genome assembly
- dosage compensation
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '15009'
relation: used_in_publication
status: public
retracted: '1'
status: public
title: Data from "Chromosome-level assembly of Artemia franciscana sheds light on
sex-chromosome differentiation"
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: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14850'
abstract:
- lang: eng
text: Elaborate sexual signals are thought to have evolved and be maintained to
serve as honest indicators of signaller quality. One measure of quality is health,
which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal
gecko that is often infested with ectoparasites in the wild, and males of this
species express visual (coloured gular patches) and chemical (femoral gland secretions)
traits that receivers could assess during social interactions. In this paper,
we tested whether ectoparasites affect individual health, and whether signal quality
is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite
level was negatively correlated with body condition in both sexes. Moreover, some
characteristics of both visual and chemical traits in males were strongly associated
with ectoparasite levels. Specifically, males with higher ectoparasite levels
had yellow gular patches with lower brightness and chroma, and chemical secretions
with a lower proportion of aromatic compounds. We then determined whether ectoparasite
levels in males influence female behaviour. Using sequential choice trials, wherein
females were provided with either the visual or the chemical signals of wild-caught
males that varied in ectoparasite level, we found that only chemical secretions
evoked an elevated female response towards less parasitised males. Simultaneous
choice trials in which females were exposed to the chemical secretions from males
that varied in parasite level further confirmed a preference for males with lower
parasites loads. Overall, we find that although health (body condition) or ectoparasite
load can be honestly advertised through multiple modalities, the parasite-mediated
female response is exclusively driven by chemical signals.
acknowledgement: "We thank Anuradha Batabyal and Shakilur Kabir for scientific discussions,
and help with sampling and colour analyses. We thank Muralidhar and the central
LCMS facility of the IISc for their technical support with the GCMS.\r\nResearch
funding was provided by the Department of Science and Technology Fund for Improvement
of S&T Infrastructure (DST-FIST), the Department of Biotechnology-Indian Institute
of Science (DBT-IISc) partnership program and a Science and Engineering Research
Board (SERB) grant to M.T. (EMR/2017/002228). Open Access funding provided by Indian
Institute of Science. Deposited in PMC for immediate release."
article_number: jeb246217
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Mihir
full_name: Joshi, Mihir
last_name: Joshi
- first_name: Maria
full_name: Thaker, Maria
last_name: Thaker
citation:
ama: Pal A, Joshi M, Thaker M. Too much information? Males convey parasite levels
using more signal modalities than females utilise. Journal of Experimental
Biology. 2024;227(1). doi:10.1242/jeb.246217
apa: Pal, A., Joshi, M., & Thaker, M. (2024). Too much information? Males convey
parasite levels using more signal modalities than females utilise. Journal
of Experimental Biology. The Company of Biologists. https://doi.org/10.1242/jeb.246217
chicago: Pal, Arka, Mihir Joshi, and Maria Thaker. “Too Much Information? Males
Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Journal
of Experimental Biology. The Company of Biologists, 2024. https://doi.org/10.1242/jeb.246217.
ieee: A. Pal, M. Joshi, and M. Thaker, “Too much information? Males convey parasite
levels using more signal modalities than females utilise,” Journal of Experimental
Biology, vol. 227, no. 1. The Company of Biologists, 2024.
ista: Pal A, Joshi M, Thaker M. 2024. Too much information? Males convey parasite
levels using more signal modalities than females utilise. Journal of Experimental
Biology. 227(1), jeb246217.
mla: Pal, Arka, et al. “Too Much Information? Males Convey Parasite Levels Using
More Signal Modalities than Females Utilise.” Journal of Experimental Biology,
vol. 227, no. 1, jeb246217, The Company of Biologists, 2024, doi:10.1242/jeb.246217.
short: A. Pal, M. Joshi, M. Thaker, Journal of Experimental Biology 227 (2024).
date_created: 2024-01-22T08:14:49Z
date_published: 2024-01-10T00:00:00Z
date_updated: 2024-01-23T12:13:08Z
day: '10'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1242/jeb.246217
external_id:
pmid:
- '38054353'
file:
- access_level: open_access
checksum: 136325372f6f45abaa62a71e2d23bfb6
content_type: application/pdf
creator: dernst
date_created: 2024-01-23T12:08:24Z
date_updated: 2024-01-23T12:08:24Z
file_id: '14877'
file_name: 2024_JourExperimBiology_Pal.pdf
file_size: 594128
relation: main_file
success: 1
file_date_updated: 2024-01-23T12:08:24Z
has_accepted_license: '1'
intvolume: ' 227'
issue: '1'
keyword:
- Insect Science
- Molecular Biology
- Animal Science and Zoology
- Aquatic Science
- Physiology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Biology
publication_identifier:
eissn:
- 0022-0949
issn:
- 1477-9145
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/arka-pal/Cnemaspis-SexualSignaling
status: public
title: Too much information? Males convey parasite levels using more signal modalities
than females utilise
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 227
year: '2024'
...
---
_id: '15020'
abstract:
- lang: eng
text: "This thesis consists of four distinct pieces of work within theoretical biology,
with two themes in common: the concept of optimization in biological systems,
and the use of information-theoretic tools to quantify biological stochasticity
and statistical uncertainty.\r\nChapter 2 develops a statistical framework for
studying biological systems which we believe to be optimized for a particular
utility function, such as retinal neurons conveying information about visual stimuli.
We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the
expected utility. We explore how such priors aid inference of system parameters
with limited data and enable optimality hypothesis testing: is the utility higher
than by chance?\r\nChapter 3 examines the ultimate biological optimization process:
evolution by natural selection. As some individuals survive and reproduce more
successfully than others, populations evolve towards fitter genotypes and phenotypes.
We formalize this as accumulation of genetic information, and use population genetics
theory to study how much such information can be accumulated per generation and
maintained in the face of random mutation and genetic drift. We identify the population
size and fitness variance as the key quantities that control information accumulation
and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter
3, but from a different perspective: we ask how much genetic information organisms
actually need, in particular in the context of gene regulation. For example, how
much information is needed to bind transcription factors at correct locations
within the genome? Population genetics provides us with a refined answer: with
an increasing population size, populations achieve higher fitness by maintaining
more genetic information. Moreover, regulatory parameters experience selection
pressure to optimize the fitness-information trade-off, i.e. minimize the information
needed for a given fitness. This provides an evolutionary derivation of the optimization
priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information
between a signal and a communication channel output (such as neural activity).
Mutual information is an important utility measure for biological systems, but
its practical use can be difficult due to the large dimensionality of many biological
channels. Sometimes, a lower bound on mutual information is computed by replacing
the high-dimensional channel outputs with decodes (signal estimates). Our result
provides a corresponding upper bound, provided that the decodes are the maximum
posterior estimates of the signal."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
citation:
ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020
apa: Hledik, M. (2024). Genetic information and biological optimization.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020
chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute
of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.
ieee: M. Hledik, “Genetic information and biological optimization,” Institute of
Science and Technology Austria, 2024.
ista: Hledik M. 2024. Genetic information and biological optimization. Institute
of Science and Technology Austria.
mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute
of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.
short: M. Hledik, Genetic Information and Biological Optimization, Institute of
Science and Technology Austria, 2024.
date_created: 2024-02-23T14:02:04Z
date_published: 2024-02-23T00:00:00Z
date_updated: 2025-06-30T13:21:09Z
day: '23'
ddc:
- '576'
- '519'
department:
- _id: GradSch
- _id: NiBa
- _id: GaTk
doi: 10.15479/at:ista:15020
ec_funded: 1
file:
- access_level: open_access
checksum: b2d3da47c98d481577a4baf68944fe41
content_type: application/pdf
creator: mhledik
date_created: 2024-02-23T13:50:53Z
date_updated: 2024-02-23T13:50:53Z
file_id: '15021'
file_name: hledik thesis pdfa 2b.pdf
file_size: 7102089
relation: main_file
success: 1
- access_level: closed
checksum: eda9b9430da2610fee7ce1c1419a479a
content_type: application/zip
creator: mhledik
date_created: 2024-02-23T13:50:54Z
date_updated: 2024-02-23T14:20:16Z
file_id: '15022'
file_name: hledik thesis source.zip
file_size: 14014790
relation: source_file
file_date_updated: 2024-02-23T14:20:16Z
has_accepted_license: '1'
keyword:
- Theoretical biology
- Optimality
- Evolution
- Information
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '158'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication_identifier:
issn:
- 2663 - 337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7553'
relation: part_of_dissertation
status: public
- id: '7606'
relation: part_of_dissertation
status: public
- id: '12081'
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
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Genetic information and biological optimization
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '14613'
abstract:
- lang: eng
text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element
F - that likely predates their origin. Interestingly, the X has undergone turnover
in multiple fly species (Diptera) after being conserved for more than 450 MY.
The long evolutionary distance between Diptera and other sequenced insect clades
makes it difficult to infer what could have contributed to this sudden increase
in rate of turnover. Here, we produce the first genome and transcriptome of a
long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly
Panorpa cognata X-chromosome gene content, expression, and structure, to that
of several dipteran species as well as more distantly-related insect orders (Orthoptera
and Blattodea). We find high conservation of gene content between the mecopteran
X and the dipteran Muller F element, as well as several shared biological features,
such as the presence of dosage compensation and a low amount of genetic diversity,
consistent with a low recombination rate. However, the two homologous X chromosomes
differ strikingly in their size and number of genes they carry. Our results therefore
support a common ancestry of the mecopteran and ancestral dipteran X chromosomes,
and suggest that Muller element F shrank in size and gene content after the split
of Diptera and Mecoptera, which may have contributed to its turnover in dipteran
insects.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection,
and Tim Connallon for valuable comments and suggestions on earlier versions of the
manuscript. Computational resources and support were provided by the Scientific
Computing unit at the ISTA. This research was supported by grants from the Austrian
Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)."
article_number: msad245
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Clementine
full_name: Lasne, Clementine
id: 02225f57-50d2-11eb-9ed8-8c92b9a34237
last_name: Lasne
orcid: 0000-0002-1197-8616
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly
(Panorpa cognata) genome highlights conserved and derived features of the peculiar
dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245
apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &
Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved
and derived features of the peculiar dipteran X chromosome. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245
chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra
Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata)
Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.”
Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.
ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B.
Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived
features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution,
vol. 40, no. 12. Oxford University Press, 2023.
ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023.
The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12),
msad245.
mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights
Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular
Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press,
2023, doi:10.1093/molbev/msad245.
short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso,
Molecular Biology and Evolution 40 (2023).
date_created: 2023-11-27T16:14:37Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-02-21T12:18:35Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msad245
external_id:
pmid:
- '37988296'
file:
- access_level: open_access
checksum: 47c1c72fb499f26ea52d216b242208c8
content_type: application/pdf
creator: dernst
date_created: 2024-01-02T11:39:38Z
date_updated: 2024-01-02T11:39:38Z
file_id: '14727'
file_name: 2023_MolecularBioEvo_Lasne.pdf
file_size: 8623505
relation: main_file
success: 1
file_date_updated: 2024-01-02T11:39:38Z
has_accepted_license: '1'
intvolume: ' 40'
issue: '12'
keyword:
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
- _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3
grant_number: ESP39 49461
name: Mechanisms and Evolution of Reproductive Plasticity
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- description: News on ISTA webpage
relation: press_release
url: https://ista.ac.at/en/news/on-the-hunt/
record:
- id: '14614'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features
of the peculiar dipteran X chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2023'
...
---
_id: '14785'
abstract:
- lang: eng
text: Small cryptic plasmids have no clear effect on the host fitness and their
functional repertoire remains obscure. The naturally competent cyanobacterium
Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their
evolution with this species is supported by horizontal transfer remains understudied.
Here, we show that the small cryptic plasmid DNA is transferred in the population
exclusively by natural transformation, where the transfer frequency of plasmid‐encoded
genes is similar to that of chromosome‐encoded genes. Establishing a system to
follow gene transfer, we compared the transfer frequency of genes encoded in cryptic
plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations
of two Synechocystis sp. PCC 6803 labtypes (termed
Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends
on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake
in the Sevilla labtype ranged among the lowest detected transfer rates in our
experiments. Our study indicates that horizontal DNA transfer via natural transformation
is frequent in the evolution of small cryptic plasmids that reside in naturally
competent organisms. Furthermore, we suggest that the contribution of natural
transformation to cryptic plasmid persistence in Synechocystis is limited.
acknowledgement: "We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla,
Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab
of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful
discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann,
FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National
Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft,
Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber:
101043835"
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Fabian
full_name: Nies, Fabian
last_name: Nies
- first_name: Tanita
full_name: Wein, Tanita
last_name: Wein
- first_name: Dustin M.
full_name: Hanke, Dustin M.
last_name: Hanke
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Jaime
full_name: Alcorta, Jaime
last_name: Alcorta
- first_name: Claudia
full_name: Taubenheim, Claudia
last_name: Taubenheim
- first_name: Tal
full_name: Dagan, Tal
last_name: Dagan
citation:
ama: Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution
of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203
apa: Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim,
C., & Dagan, T. (2023). Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology
Reports. Wiley. https://doi.org/10.1111/1758-2229.13203
chicago: Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime
Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in
the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental
Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.
ieee: F. Nies et al., “Role of natural transformation in the evolution of
small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology
Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.
ista: Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T.
2023. Role of natural transformation in the evolution of small cryptic plasmids
in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.
mla: Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small
Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology
Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.
short: F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim,
T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.
date_created: 2024-01-10T10:41:07Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2024-01-16T09:46:12Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1111/1758-2229.13203
external_id:
isi:
- '001080203100001'
pmid:
- '37794696'
file:
- access_level: open_access
checksum: d09ebb68fee61f4e2e09ec286c9cf1d3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:42:10Z
date_updated: 2024-01-16T09:42:10Z
file_id: '14810'
file_name: 2023_EnvirMicroBiolReports_Nies.pdf
file_size: 1518350
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:42:10Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '6'
keyword:
- Agricultural and Biological Sciences (miscellaneous)
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 656-668
pmid: 1
publication: Environmental Microbiology Reports
publication_identifier:
eissn:
- 1758-2229
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Role of natural transformation in the evolution of small cryptic plasmids in
Synechocystis sp. PCC 6803
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '14787'
abstract:
- lang: eng
text: Understanding the phenotypic and genetic architecture of reproductive isolation
is a long‐standing goal of speciation research. In several systems, large‐effect
loci contributing to barrier phenotypes have been characterized, but such causal
connections are rarely known for more complex genetic architectures. In this study,
we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward
an integrated understanding of speciation across a monkeyflower hybrid zone. Previous
work suggests that pollinator visitation acts as a primary barrier to gene flow
between two divergent red‐ and yellow‐flowered ecotypes ofMimulus
aurantiacus. Several candidate isolating traits and anonymous single
nucleotide polymorphism loci under divergent selection have been identified, but
their genomic positions remain unknown. Here, we report findings from demographic
analyses that indicate this hybrid zone formed by secondary contact, but that
subsequent gene flow was restricted by widespread barrier loci across the genome.
Using a novel, geographic cline‐based genome scan, we demonstrate that candidate
barrier loci are broadly distributed across the genome, rather than mapping to
one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals
that most floral traits are highly polygenic, with little evidence that QTL colocalize,
indicating that most traits are genetically independent. Finally, we find little
evidence that QTL and candidate barrier loci overlap, suggesting that some loci
contribute to other forms of reproductive isolation. Our findings highlight the
challenges of understanding the genetic architecture of reproductive isolation
and reveal that barriers to gene flow other than pollinator isolation may play
an important role in this system.
acknowledgement: We thank Julian Catchen for making modifications to Stacks to aid
this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and
Nicholas H. Barton provided advice, stimulating discussion and critical feedback.
The project was supported by National Science Foundation grant DEB-1258199.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Madeline A.
full_name: Chase, Madeline A.
last_name: Chase
- first_name: Hanna
full_name: McIntosh, Hanna
last_name: McIntosh
- first_name: Matthew A.
full_name: Streisfeld, Matthew A.
last_name: Streisfeld
citation:
ama: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and
bottom‐up approaches to understand the genetic architecture of speciation across
a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849
apa: Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023).
Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16849
chicago: Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld.
“Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture
of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley,
2023. https://doi.org/10.1111/mec.16849.
ieee: S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating
top‐down and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8.
Wiley, pp. 2041–2054, 2023.
ista: Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down
and bottom‐up approaches to understand the genetic architecture of speciation
across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.
mla: Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to
Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid
Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.
short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology
32 (2023) 2041–2054.
date_created: 2024-01-10T10:44:45Z
date_published: 2023-04-01T00:00:00Z
date_updated: 2024-01-16T10:10:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.16849
external_id:
isi:
- '000919244600001'
pmid:
- '36651268'
intvolume: ' 32'
isi: 1
issue: '8'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.01.28.478139
month: '04'
oa: 1
oa_version: Preprint
page: 2041-2054
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture
of speciation across a monkeyflower hybrid zone
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12159'
abstract:
- lang: eng
text: The term “haplotype block” is commonly used in the developing field of haplotype-based
inference methods. We argue that the term should be defined based on the structure
of the Ancestral Recombination Graph (ARG), which contains complete information
on the ancestry of a sample. We use simulated examples to demonstrate key features
of the relationship between haplotype blocks and ancestral structure, emphasizing
the stochasticity of the processes that generate them. Even the simplest cases
of neutrality or of a “hard” selective sweep produce a rich structure, often missed
by commonly used statistics. We highlight a number of novel methods for inferring
haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate
how they can be used to define haplotype blocks using an empirical data set. While
the advent of new, computationally efficient methods makes it possible to apply
these concepts broadly, they (and additional new methods) could benefit from adding
features to explore haplotype blocks, as we define them. Understanding and applying
the concept of the haplotype block will be essential to fully exploit long and
linked-read sequencing technologies.
acknowledgement: 'We thank the Barton group for useful discussion and feedback during
the writing of this article. Comments from Roger Butlin, Molly Schumer''s Group,
the tskit development team, editors and three reviewers greatly improved the manuscript.
Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg
Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant
P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society
and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- 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: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure
of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793
apa: Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023).
On the origin and structure of haplotype blocks. Molecular Ecology. Wiley.
https://doi.org/10.1111/mec.16793
chicago: Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and
Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular
Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.
ieee: D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the
origin and structure of haplotype blocks,” Molecular Ecology, vol. 32,
no. 6. Wiley, pp. 1441–1457, 2023.
ista: Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin
and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.
mla: Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.”
Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.
short: D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology
32 (2023) 1441–1457.
date_created: 2023-01-12T12:09:17Z
date_published: 2023-03-01T00:00:00Z
date_updated: 2023-08-16T08:18:47Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.16793
external_id:
isi:
- '000900762000001'
pmid:
- '36433653'
file:
- access_level: open_access
checksum: b10e0f8fa3dc4d72aaf77a557200978a
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T08:15:41Z
date_updated: 2023-08-16T08:15:41Z
file_id: '14062'
file_name: 2023_MolecularEcology_Shipilina.pdf
file_size: 7144607
relation: main_file
success: 1
file_date_updated: 2023-08-16T08:15:41Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '6'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1441-1457
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the origin and structure of haplotype blocks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2023'
...
---
_id: '12521'
abstract:
- lang: eng
text: Differentiated X chromosomes are expected to have higher rates of adaptive
divergence than autosomes, if new beneficial mutations are recessive (the “faster-X
effect”), largely because these mutations are immediately exposed to selection
in males. The evolution of X chromosomes after they stop recombining in males,
but before they become hemizygous, has not been well explored theoretically. We
use the diffusion approximation to infer substitution rates of beneficial and
deleterious mutations under such a scenario. Our results show that selection is
less efficient on diploid X loci than on autosomal and hemizygous X loci under
a wide range of parameters. This “slower-X” effect is stronger for genes affecting
primarily (or only) male fitness, and for sexually antagonistic genes. These unusual
dynamics suggest that some of the peculiar features of X chromosomes, such as
the differential accumulation of genes with sex-specific functions, may start
arising earlier than previously appreciated.
acknowledgement: We thank the Vicoso and Barton groups and ISTA Scientific Computing
Unit. We also thank two anonymous reviewers for their valuable comments. This work
was supported by the European Research Council under the European Union’s Horizon
2020 research and innovation program (grant agreements no. 715257 and no. 716117).
article_number: qrac004
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- 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: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
2023;7(1). doi:10.1093/evlett/qrac004'
apa: 'Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X:
Reduced efficiency of selection in the early stages of X chromosome evolution.
Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004'
chicago: 'Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso.
“Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome
Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.'
ieee: 'A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced
efficiency of selection in the early stages of X chromosome evolution,” Evolution
Letters, vol. 7, no. 1. Oxford University Press, 2023.'
ista: 'Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency
of selection in the early stages of X chromosome evolution. Evolution Letters.
7(1), qrac004.'
mla: 'Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the
Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no.
1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.'
short: A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).
date_created: 2023-02-06T13:59:12Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2023-08-16T11:44:32Z
day: '01'
ddc:
- '570'
department:
- _id: GradSch
- _id: BeVi
doi: 10.1093/evlett/qrac004
ec_funded: 1
external_id:
isi:
- '001021692200001'
pmid:
- '37065438'
file:
- access_level: open_access
checksum: a240a041cb9b9b7c8ba93a4706674a3f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:43:33Z
date_updated: 2023-08-16T11:43:33Z
file_id: '14068'
file_name: 2023_EvLetters_Mrnjavac.pdf
file_size: 2592189
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:43:33Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Slower-X: Reduced efficiency of selection in the early stages of X chromosome
evolution'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2023'
...
---
_id: '11488'
abstract:
- lang: eng
text: Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic
medium (CGM) at high redshifts. In this work, we aim to explore the existence
of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters
(LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5,
and spectroscopic redshifts were assigned or constrained for all the sources thanks
to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit
Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes
21 galaxies that are purely F775W-magnitude selected within the redshift range
z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding
any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly
more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs
and four non-LAHs. We report the first individual detections of extended Lyα emission
around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which
is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected
galaxies generally have a large amount of hydrogen in their CGM. We derived the
mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections
and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint
redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding
gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz,
is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7.
Assuming that Lyα emission and absorption arise in the same gas, this suggests,
based on abundance matching, that LAHs trace the same gas as damped Lyα systems
(DLAs) and sub-DLAs.
acknowledgement: 'We thank the anonymous referee for constructive comments and suggestions.
We would like to express our gratitude to Edmund Christian Herenz, Leindert Boogard,
Miroslava Dessauges, Moupiya Maji, Valentin Mauerhofer, Charlotte Paola Simmonds
Wagemann, Masami Ouchi, Kazuhiro Shimasaku, Akio Inoue, and Rieko Momose for giving
insightful comments and suggestions. H.K. is grateful to Liam McCarney for useful
suggestions on English writing through the UniGE’s Tandems linguistiques. H.K. acknowledges
support from Swiss Government Excellence Scholarships and Japan Society for the
Promotion of Science (JSPS) Overseas Research Fellowship. H.K., F.L., and A.V. are
supported by the SNF grant PP00P2 176808. A.V. and T.G. are supported by the ERC
Starting Grant 757258“TRIPLE”. This work was supported by the Programme National
Cosmology et Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and
CNES. This work is based on observations taken by VLT, which is operated by European
Southern Observatory. This research made use of Astropy, which is a community-developed
core Python package for Astronomy (Astropy Collaboration 2013, 2018), and other
software and packages: MARZ, MPDAF (Piqueras et al. 2019), PHOTUTILS, Numpy (Harris
et al. 2020), Scipy (Virtanen et al. 2020), and matplotlib (Hunter 2007).'
article_number: A44
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Haruka
full_name: Kusakabe, Haruka
last_name: Kusakabe
- first_name: Anne
full_name: Verhamme, Anne
last_name: Verhamme
- first_name: Jérémy
full_name: Blaizot, Jérémy
last_name: Blaizot
- first_name: Thibault
full_name: Garel, Thibault
last_name: Garel
- first_name: Lutz
full_name: Wisotzki, Lutz
last_name: Wisotzki
- first_name: Floriane
full_name: Leclercq, Floriane
last_name: Leclercq
- first_name: Roland
full_name: Bacon, Roland
last_name: Bacon
- first_name: Joop
full_name: Schaye, Joop
last_name: Schaye
- first_name: Sofia G.
full_name: Gallego, Sofia G.
last_name: Gallego
- first_name: Josephine
full_name: Kerutt, Josephine
last_name: Kerutt
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Michael
full_name: Maseda, Michael
last_name: Maseda
- first_name: Themiya
full_name: Nanayakkara, Themiya
last_name: Nanayakkara
- first_name: Roser
full_name: Pelló, Roser
last_name: Pelló
- first_name: Johan
full_name: Richard, Johan
last_name: Richard
- first_name: Laurence
full_name: Tresse, Laurence
last_name: Tresse
- first_name: Tanya
full_name: Urrutia, Tanya
last_name: Urrutia
- first_name: Eloïse
full_name: Vitte, Eloïse
last_name: Vitte
citation:
ama: 'Kusakabe H, Verhamme A, Blaizot J, et al. The MUSE eXtremely Deep Field: Individual
detections of Lyα haloes around rest-frame UV-selected galaxies at z
≃ 2.9–4.4. Astronomy & Astrophysics. 2022;660. doi:10.1051/0004-6361/202142302'
apa: 'Kusakabe, H., Verhamme, A., Blaizot, J., Garel, T., Wisotzki, L., Leclercq,
F., … Vitte, E. (2022). The MUSE eXtremely Deep Field: Individual detections of
Lyα haloes around rest-frame UV-selected galaxies at z ≃ 2.9–4.4.
Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202142302'
chicago: 'Kusakabe, Haruka, Anne Verhamme, Jérémy Blaizot, Thibault Garel, Lutz
Wisotzki, Floriane Leclercq, Roland Bacon, et al. “The MUSE EXtremely Deep Field:
Individual Detections of Lyα Haloes around Rest-Frame UV-Selected Galaxies
at z ≃ 2.9–4.4.” Astronomy & Astrophysics. EDP Sciences, 2022.
https://doi.org/10.1051/0004-6361/202142302.'
ieee: 'H. Kusakabe et al., “The MUSE eXtremely Deep Field: Individual detections
of Lyα haloes around rest-frame UV-selected galaxies at z ≃ 2.9–4.4,”
Astronomy & Astrophysics, vol. 660. EDP Sciences, 2022.'
ista: 'Kusakabe H, Verhamme A, Blaizot J, Garel T, Wisotzki L, Leclercq F, Bacon
R, Schaye J, Gallego SG, Kerutt J, Matthee JJ, Maseda M, Nanayakkara T, Pelló
R, Richard J, Tresse L, Urrutia T, Vitte E. 2022. The MUSE eXtremely Deep Field:
Individual detections of Lyα haloes around rest-frame UV-selected galaxies
at z ≃ 2.9–4.4. Astronomy & Astrophysics. 660, A44.'
mla: 'Kusakabe, Haruka, et al. “The MUSE EXtremely Deep Field: Individual Detections
of Lyα Haloes around Rest-Frame UV-Selected Galaxies at z ≃ 2.9–4.4.”
Astronomy & Astrophysics, vol. 660, A44, EDP Sciences, 2022, doi:10.1051/0004-6361/202142302.'
short: H. Kusakabe, A. Verhamme, J. Blaizot, T. Garel, L. Wisotzki, F. Leclercq,
R. Bacon, J. Schaye, S.G. Gallego, J. Kerutt, J.J. Matthee, M. Maseda, T. Nanayakkara,
R. Pelló, J. Richard, L. Tresse, T. Urrutia, E. Vitte, Astronomy & Astrophysics
660 (2022).
date_created: 2022-07-05T14:27:26Z
date_published: 2022-04-07T00:00:00Z
date_updated: 2022-07-19T09:33:24Z
day: '07'
doi: 10.1051/0004-6361/202142302
extern: '1'
external_id:
arxiv:
- '2201.07257'
intvolume: ' 660'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology:
observations'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2201.07257
month: '04'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The MUSE eXtremely Deep Field: Individual detections of Lyα haloes
around rest-frame UV-selected galaxies at z ≃ 2.9–4.4'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 660
year: '2022'
...
---
_id: '11497'
abstract:
- lang: eng
text: "Context. The hydrogen Lyman α line is often the only measurable feature in
optical spectra of high-redshift galaxies. Its shape and strength are influenced
by radiative transfer processes and the properties of the underlying stellar population.
High equivalent widths of several hundred Å are especially hard to explain by
models and could point towards unusual stellar populations, for example with low
metallicities, young stellar ages, and a top-heavy initial mass function. Other
aspects influencing equivalent widths are the morphology of the galaxy and its
gas properties.\r\nAims. The aim of this study is to better understand the connection
between the Lyman α rest-frame equivalent width (EW0) and spectral properties
as well as ultraviolet (UV) continuum morphology by obtaining reliable EW0 histograms
for a statistical sample of galaxies and by assessing the fraction of objects
with large equivalent widths.\r\nMethods. We used integral field spectroscopy
from the Multi Unit Spectroscopic Explorer (MUSE) combined with broad-band data
from the Hubble Space Telescope (HST) to measure EW0. We analysed the emission
lines of 1920 Lyman α emitters (LAEs) detected in the full MUSE-Wide (one hour
exposure time) and MUSE-Deep (ten hour exposure time) surveys and found UV continuum
counterparts in archival HST data. We fitted the UV continuum photometric images
using the Galfit software to gain morphological information on the rest-UV emission
and fitted the spectra obtained from MUSE to determine the double peak fraction,
asymmetry, full-width at half maximum, and flux of the Lyman α line.\r\nResults.
The two surveys show different histograms of Lyman α EW0. In MUSE-Wide, 20% of
objects have EW0 > 240 Å, while this fraction is only 11% in MUSE-Deep and ≈16%
for the full sample. This includes objects without HST continuum counterparts
(one-third of our sample), for which we give lower limits for EW0. The object
with the highest securely measured EW0 has EW0 = 589 ± 193 Å (the highest lower
limit being EW0 = 4464 Å). We investigate the connection between EW0 and Lyman
α spectral or UV continuum morphological properties.\r\nConclusions. The survey
depth has to be taken into account when studying EW0 distributions. We find that
in general, high EW0 objects can have a wide range of spectral and UV morphological
properties, which might reflect that the underlying causes for high EW0 values
are equally varied."
acknowledgement: We thank the referee for thoughtful and constructive comments that
have improved the quality of this manuscript. Based on observations collected at
the European Southern Observatory under ESO programme 1101.A-0127. This work made
use of v2.2.1 of the Binary Population and Spectral Synthesis (BPASS) models as
described in Eldridge et al. (2017) and Stanway & Eldridge (2018). A.F. acknowledges
the support from grant PRIN MIUR2017-20173ML3WW_001. T.N. acknowledges support from
Australian Research Council Laureate Fellowship FL180100060.
article_number: '183'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Kerutt, J.
last_name: Kerutt
- first_name: L.
full_name: Wisotzki, L.
last_name: Wisotzki
- first_name: A.
full_name: Verhamme, A.
last_name: Verhamme
- first_name: K. B.
full_name: Schmidt, K. B.
last_name: Schmidt
- first_name: F.
full_name: Leclercq, F.
last_name: Leclercq
- first_name: E. C.
full_name: Herenz, E. C.
last_name: Herenz
- first_name: T.
full_name: Urrutia, T.
last_name: Urrutia
- first_name: T.
full_name: Garel, T.
last_name: Garel
- first_name: T.
full_name: Hashimoto, T.
last_name: Hashimoto
- first_name: M.
full_name: Maseda, M.
last_name: Maseda
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: H.
full_name: Kusakabe, H.
last_name: Kusakabe
- first_name: J.
full_name: Schaye, J.
last_name: Schaye
- first_name: J.
full_name: Richard, J.
last_name: Richard
- first_name: B.
full_name: Guiderdoni, B.
last_name: Guiderdoni
- first_name: V.
full_name: Mauerhofer, V.
last_name: Mauerhofer
- first_name: T.
full_name: Nanayakkara, T.
last_name: Nanayakkara
- first_name: E.
full_name: Vitte, E.
last_name: Vitte
citation:
ama: Kerutt J, Wisotzki L, Verhamme A, et al. Equivalent widths of Lyman α emitters
in MUSE-Wide and MUSE-Deep. Astronomy & Astrophysics. 2022;659. doi:10.1051/0004-6361/202141900
apa: Kerutt, J., Wisotzki, L., Verhamme, A., Schmidt, K. B., Leclercq, F., Herenz,
E. C., … Vitte, E. (2022). Equivalent widths of Lyman α emitters in MUSE-Wide
and MUSE-Deep. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202141900
chicago: Kerutt, J., L. Wisotzki, A. Verhamme, K. B. Schmidt, F. Leclercq, E. C.
Herenz, T. Urrutia, et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide
and MUSE-Deep.” Astronomy & Astrophysics. EDP Sciences, 2022. https://doi.org/10.1051/0004-6361/202141900.
ieee: J. Kerutt et al., “Equivalent widths of Lyman α emitters in MUSE-Wide
and MUSE-Deep,” Astronomy & Astrophysics, vol. 659. EDP Sciences, 2022.
ista: Kerutt J, Wisotzki L, Verhamme A, Schmidt KB, Leclercq F, Herenz EC, Urrutia
T, Garel T, Hashimoto T, Maseda M, Matthee JJ, Kusakabe H, Schaye J, Richard J,
Guiderdoni B, Mauerhofer V, Nanayakkara T, Vitte E. 2022. Equivalent widths of
Lyman α emitters in MUSE-Wide and MUSE-Deep. Astronomy & Astrophysics. 659,
183.
mla: Kerutt, J., et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide and
MUSE-Deep.” Astronomy & Astrophysics, vol. 659, 183, EDP Sciences,
2022, doi:10.1051/0004-6361/202141900.
short: J. Kerutt, L. Wisotzki, A. Verhamme, K.B. Schmidt, F. Leclercq, E.C. Herenz,
T. Urrutia, T. Garel, T. Hashimoto, M. Maseda, J.J. Matthee, H. Kusakabe, J. Schaye,
J. Richard, B. Guiderdoni, V. Mauerhofer, T. Nanayakkara, E. Vitte, Astronomy
& Astrophysics 659 (2022).
date_created: 2022-07-06T08:17:27Z
date_published: 2022-03-25T00:00:00Z
date_updated: 2022-07-19T09:47:16Z
day: '25'
doi: 10.1051/0004-6361/202141900
extern: '1'
external_id:
arxiv:
- '2202.06642'
intvolume: ' 659'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology:
observations'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2202.06642
month: '03'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 659
year: '2022'
...
---
_id: '10604'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After
nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding
to an apparent equilibrium between immigration and selection, wMel rose to fixation
by 2018. Using analytic approximations and statistical analyses, we demonstrate
that the observed fixation of wMel at PE is consistent with both stochastic transition
past an unstable threshold frequency and deterministic transformation produced
by steady immigration at a rate just above the threshold required for deterministic
invasion. The indeterminacy results from a delicate balance of parameters needed
to produce the delayed transition observed. Our analyses suggest that once Wolbachia
transinfections are established locally through systematic introductions, stochastic
“threshold crossing” is likely to only minimally enhance spatial spread, providing
a local ratchet that slightly—but systematically—aids area-wide transformation
of disease-vector populations in heterogeneous landscapes.
acknowledgement: We thank S. O'Neill, C. Simmons, and the World Mosquito Project for
providing access to unpublished data. S. Ritchie provided valuable insights into
Aedes aegypti biology and the literature describing A. aegypti populations near
Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill,
S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on
an earlier draft. Comments from three reviewers greatly improved our presentation.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- 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: Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road?
Drift, deterministic dynamics, and disease control. Evolution Letters.
2022;6(1):92-105. doi:10.1002/evl3.270
apa: Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection
cross the road? Drift, deterministic dynamics, and disease control. Evolution
Letters. Wiley. https://doi.org/10.1002/evl3.270
chicago: Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.
ieee: M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control,” Evolution Letters,
vol. 6, no. 1. Wiley, pp. 92–105, 2022.
ista: Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1),
92–105.
mla: Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.
short: M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.
date_created: 2022-01-09T09:45:17Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-02T13:50:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.270
external_id:
isi:
- '000754412600008'
file:
- access_level: open_access
checksum: 7e9a37e3b65b480cd7014a6a4a7e460a
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T06:59:10Z
date_updated: 2022-07-29T06:59:10Z
file_id: '11689'
file_name: 2022_EvolutionLetters_Turelli.pdf
file_size: 2435185
relation: main_file
success: 1
file_date_updated: 2022-07-29T06:59:10Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
keyword:
- genetics
- ecology
- evolution
- behavior and systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 92-105
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '11686'
relation: research_data
status: public
status: public
title: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics,
and disease control
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2022'
...
---
_id: '12152'
abstract:
- lang: eng
text: ESCRT-III filaments are composite cytoskeletal polymers that can constrict
and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III
filaments undergo a series of dramatic composition and geometry changes in the
presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the
membrane morphology. We set out to understand the physical mechanisms involved
in translating the changes in ESCRT-III polymer composition into membrane deformation.
We have built a coarse-grained model in which ESCRT-III polymers of different
geometries and mechanical properties are allowed to copolymerise and bind to a
deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific
polymers, we identify mechanical regimes in which changes in filament composition
trigger the associated membrane transition from a flat to a buckled state, and
then to a tubule state that eventually undergoes scission to release a small cargo-loaded
vesicle. We then characterise how the location and kinetics of polymer loss affects
the extent of membrane deformation and the efficiency of membrane neck scission.
Our results identify the near-minimal mechanical conditions for the operation
of shape-shifting composite polymers that sever membrane necks.
acknowledgement: "A.S . received an award from European Research Council (https://erc.europa.eu,
“NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org,
UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences
Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award
from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open,
Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an
award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation,
Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc,
MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research
(https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and
an award from the European Research Council\r\nConsolidator (https://erc.europa.eu,
311536). The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript."
article_number: e1010586
article_processing_charge: No
article_type: original
author:
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Elene
full_name: Lominadze, Elene
last_name: Lominadze
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane
reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational
Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586
apa: Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K.,
Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged
polymerization of ESCRT-III filaments. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1010586
chicago: Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos,
Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela
Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.”
PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.
ieee: X. Jiang et al., “Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public
Library of Science, 2022.
ista: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze
E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.
mla: Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization
of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.
short: X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E.
Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).
date_created: 2023-01-12T12:08:10Z
date_published: 2022-10-17T00:00:00Z
date_updated: 2023-08-04T09:03:21Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1371/journal.pcbi.1010586
ec_funded: 1
external_id:
isi:
- '000924885500005'
file:
- access_level: open_access
checksum: bada6a7865e470cf42bbdfa67dd471d2
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:45:01Z
date_updated: 2023-01-24T10:45:01Z
file_id: '12359'
file_name: 2022_PLoSCompBio_Jiang.pdf
file_size: 2641067
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:45:01Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '10'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
grant_number: '96752'
name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sharonJXY/3-filament-model
scopus_import: '1'
status: public
title: Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '12166'
abstract:
- lang: eng
text: Kerstin Johannesson is a marine ecologist and evolutionary biologist based
at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated
in the beautiful Kosterhavet National Park on the Swedish west coast. Her work,
using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main
model systems, has made a remarkable contribution to marine evolutionary biology
and our understanding of local adaptation and its genetic underpinnings.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular
Ecology Prize. Molecular Ecology. 2022;32(1):26-29. doi:10.1111/mec.16779
apa: Westram, A. M., & Butlin, R. (2022). Professor Kerstin Johannesson–winner
of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779
chicago: Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner
of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2022. https://doi.org/10.1111/mec.16779.
ieee: A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the
2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley,
pp. 26–29, 2022.
ista: Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022
Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.
mla: Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of
the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley,
2022, pp. 26–29, doi:10.1111/mec.16779.
short: A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.
date_created: 2023-01-12T12:10:28Z
date_published: 2022-11-28T00:00:00Z
date_updated: 2023-08-04T09:09:15Z
day: '28'
department:
- _id: NiBa
doi: 10.1111/mec.16779
external_id:
isi:
- '000892168800001'
intvolume: ' 32'
isi: 1
issue: '1'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/mec.16779
month: '11'
oa: 1
oa_version: Published Version
page: 26-29
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '12234'
abstract:
- lang: eng
text: Hybrid speciation—the origin of new species resulting from the hybridization
of genetically divergent lineages—was once considered rare, but genomic data suggest
that it may occur more often than once thought. In this study, Noguerales and
Ortego found genomic evidence supporting the hybrid origin of a grasshopper that
is able to exploit a broader range of host plants than either of its putative
parents.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Digest: On the origin of a possible hybrid species. Evolution.
2022;76(11):2784-2785. doi:10.1111/evo.14632'
apa: 'Stankowski, S. (2022). Digest: On the origin of a possible hybrid species.
Evolution. Wiley. https://doi.org/10.1111/evo.14632'
chicago: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.”
Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.'
ieee: 'S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution,
vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.'
ista: 'Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution.
76(11), 2784–2785.'
mla: 'Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution,
vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.'
short: S. Stankowski, Evolution 76 (2022) 2784–2785.
date_created: 2023-01-16T09:50:48Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:35:48Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14632
external_id:
isi:
- '000855751600001'
file:
- access_level: open_access
checksum: 4c0f05083b414ac0323a1b9ee1abc275
content_type: application/pdf
creator: dernst
date_created: 2023-01-27T11:28:38Z
date_updated: 2023-01-27T11:28:38Z
file_id: '12425'
file_name: 2022_Evolution_Stankowski.pdf
file_size: 287282
relation: main_file
success: 1
file_date_updated: 2023-01-27T11:28:38Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2784-2785
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Digest: On the origin of a possible hybrid species'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '12247'
abstract:
- lang: eng
text: Chromosomal inversions have been shown to play a major role in a local adaptation
by suppressing recombination between alternative arrangements and maintaining
beneficial allele combinations. However, so far, their importance relative to
the remaining genome remains largely unknown. Understanding the genetic architecture
of adaptation requires better estimates of how loci of different effect sizes
contribute to phenotypic variation. Here, we used three Swedish islands where
the marine snail Littorina saxatilis has repeatedly evolved into two distinct
ecotypes along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic effects
in the remaining genome using a quantitative genetics framework. We confirmed
the importance of inversions but showed that contributions of loci outside inversions
are of similar magnitude, with variable proportions dependent on the trait and
the population. Some inversions showed consistent effects across all sites, whereas
others exhibited site-specific effects, indicating that the genomic basis for
replicated phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were significant
but minor compared to inversions and polygenic background. Overall, this integrated
approach provides insight into the multiple mechanisms contributing to parallel
phenotypic divergence.
acknowledgement: We thank everyone who helped with fieldwork, snail processing, and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson
for their contributions, with inversions and shell shape respectively. KJ was funded
by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B.
and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS).
R.K.B. was also funded by the Natural Environment Research Council and the Swedish
Research Council Vetenskapsrådet.
article_processing_charge: No
article_type: original
author:
- first_name: Eva L.
full_name: Koch, Eva L.
last_name: Koch
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
2022;76(10):2332-2346. doi:10.1111/evo.14602
apa: Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R.
K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina
saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602
chicago: Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger
K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina
Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.
ieee: E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic
architecture of repeated phenotypic divergence in Littorina saxatilis evolution,”
Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.
ista: Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture
of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution.
76(10), 2332–2346.
mla: Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence
in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022,
pp. 2332–46, doi:10.1111/evo.14602.
short: E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution
76 (2022) 2332–2346.
date_created: 2023-01-16T09:54:15Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:42:11Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14602
external_id:
isi:
- '000848449100001'
pmid:
- '35994296'
file:
- access_level: open_access
checksum: defd8a4bea61cf00a3c88d4a30e2728c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T08:45:35Z
date_updated: 2023-01-30T08:45:35Z
file_id: '12439'
file_name: 2022_Evolution_Koch.pdf
file_size: 2990581
relation: main_file
success: 1
file_date_updated: 2023-01-30T08:45:35Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '10'
keyword:
- General Agricultural and Biological Sciences
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 2332-2346
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '13066'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis
evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '12264'
abstract:
- lang: eng
text: Reproductive isolation (RI) is a core concept in evolutionary biology. It
has been the central focus of speciation research since the modern synthesis and
is the basis by which biological species are defined. Despite this, the term is
used in seemingly different ways, and attempts to quantify RI have used very different
approaches. After showing that the field lacks a clear definition of the term,
we attempt to clarify key issues, including what RI is, how it can be quantified
in principle, and how it can be measured in practice. Following other definitions
with a genetic focus, we propose that RI is a quantitative measure of the effect
that genetic differences between populations have on gene flow. Specifically,
RI compares the flow of neutral alleles in the presence of these genetic differences
to the flow without any such differences. RI is thus greater than zero when genetic
differences between populations reduce the flow of neutral alleles between populations.
We show how RI can be quantified in a range of scenarios. A key conclusion is
that RI depends strongly on circumstances—including the spatial, temporal and
genomic context—making it difficult to compare across systems. After reviewing
methods for estimating RI from data, we conclude that it is difficult to measure
in practice. We discuss our findings in light of the goals of speciation research
and encourage the use of methods for estimating RI that integrate organismal and
genetic approaches.
acknowledgement: 'We are grateful to the participants of the ESEB satellite symposium
‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger
Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments
on this manuscript. We are also very grateful to Roger Butlin and the Barton Group
for the continued conversa-tions about RI. In addition, we thank all participants
of the speciation survey. Part of this work was funded by the Austrian Science Fund
FWF (grant P 32166)'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- 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: Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation?
Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005
apa: Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
What is reproductive isolation? Journal of Evolutionary Biology. Wiley.
https://doi.org/10.1111/jeb.14005
chicago: Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H
Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology.
Wiley, 2022. https://doi.org/10.1111/jeb.14005.
ieee: A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is
reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no.
9. Wiley, pp. 1143–1164, 2022.
ista: Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive
isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.
mla: Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary
Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1143–1164.
date_created: 2023-01-16T09:59:24Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:40Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14005
external_id:
isi:
- '000849851100002'
pmid:
- '36063156'
file:
- access_level: open_access
checksum: f08de57112330a7ee88d2e1b20576a1e
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:05:31Z
date_updated: 2023-01-30T10:05:31Z
file_id: '12448'
file_name: 2022_JourEvoBiology_Westram.pdf
file_size: 3146793
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:05:31Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1143-1164
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12265'
relation: other
status: public
scopus_import: '1'
status: public
title: What is reproductive isolation?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12265'
acknowledgement: We are very grateful to the authors of the commentaries for the interesting
discussion and to Luke Holman for handling this set of manuscripts. Part of this
work was funded by the Austrian Science Fund FWF (grant P 32166).
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- 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: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205.
doi:10.1111/jeb.14082'
apa: 'Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022).
Reproductive isolation, speciation, and the value of disagreement: A reply to
the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.14082'
chicago: 'Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas
H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement:
A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of
Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.'
ieee: 'A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive
isolation, speciation, and the value of disagreement: A reply to the commentaries
on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology,
vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.'
ista: 'Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation,
speciation, and the value of disagreement: A reply to the commentaries on ‘What
is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.'
mla: 'Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value
of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’”
Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05,
doi:10.1111/jeb.14082.'
short: A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary
Biology 35 (2022) 1200–1205.
date_created: 2023-01-16T09:59:37Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2023-08-04T09:53:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/jeb.14082
external_id:
isi:
- '000849851100009'
file:
- access_level: open_access
checksum: 27268009e5eec030bc10667a4ac5ed4c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T10:14:09Z
date_updated: 2023-01-30T10:14:09Z
file_id: '12449'
file_name: 2022_JourEvoBiology_Westram_Response.pdf
file_size: 349603
relation: main_file
success: 1
file_date_updated: 2023-01-30T10:14:09Z
has_accepted_license: '1'
intvolume: ' 35'
isi: 1
issue: '9'
keyword:
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1200-1205
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: The maintenance of alternative adaptive peaks in snapdragons
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '12264'
relation: other
status: public
scopus_import: '1'
status: public
title: 'Reproductive isolation, speciation, and the value of disagreement: A reply
to the commentaries on ‘What is reproductive isolation?’'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 35
year: '2022'
...
---
_id: '12280'
abstract:
- lang: eng
text: 'In repeated interactions, players can use strategies that respond to the
outcome of previous rounds. Much of the existing literature on direct reciprocity
assumes that all competing individuals use the same strategy space. Here, we study
both learning and evolutionary dynamics of players that differ in the strategy
space they explore. We focus on the infinitely repeated donation game and compare
three natural strategy spaces: memory-1 strategies, which consider the last moves
of both players, reactive strategies, which respond to the last move of the co-player,
and unconditional strategies. These three strategy spaces differ in the memory
capacity that is needed. We compute the long term average payoff that is achieved
in a pairwise learning process. We find that smaller strategy spaces can dominate
larger ones. For weak selection, unconditional players dominate both reactive
and memory-1 players. For intermediate selection, reactive players dominate memory-1
players. Only for strong selection and low cost-to-benefit ratio, memory-1 players
dominate the others. We observe that the supergame between strategy spaces can
be a social dilemma: maximum payoff is achieved if both players explore a larger
strategy space, but smaller strategy spaces dominate.'
acknowledgement: "This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG
863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant
850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript."
article_number: e1010149
article_processing_charge: No
article_type: original
author:
- first_name: Laura
full_name: Schmid, Laura
id: 38B437DE-F248-11E8-B48F-1D18A9856A87
last_name: Schmid
orcid: 0000-0002-6978-7329
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals
that use different strategy spaces. PLOS Computational Biology. 2022;18(6).
doi:10.1371/journal.pcbi.1010149
apa: Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity
between individuals that use different strategy spaces. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149
chicago: Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak.
“Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS
Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149.
ieee: L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between
individuals that use different strategy spaces,” PLOS Computational Biology,
vol. 18, no. 6. Public Library of Science, 2022.
ista: Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between
individuals that use different strategy spaces. PLOS Computational Biology. 18(6),
e1010149.
mla: Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different
Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.
short: L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology
18 (2022).
date_created: 2023-01-16T10:02:51Z
date_published: 2022-06-14T00:00:00Z
date_updated: 2025-07-14T09:09:49Z
day: '14'
ddc:
- '000'
- '570'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1010149
ec_funded: 1
external_id:
isi:
- '000843626800031'
pmid:
- '35700167'
file:
- access_level: open_access
checksum: 31b6b311b6731f1658277a9dfff6632c
content_type: application/pdf
creator: dernst
date_created: 2023-01-30T11:28:13Z
date_updated: 2023-01-30T11:28:13Z
file_id: '12460'
file_name: 2022_PlosCompBio_Schmid.pdf
file_size: 3143222
relation: main_file
success: 1
file_date_updated: 2023-01-30T11:28:13Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '6'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: PLOS Computational Biology
publication_identifier:
eissn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Direct reciprocity between individuals that use different strategy spaces
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2022'
...
---
_id: '10838'
abstract:
- lang: eng
text: Combining hybrid zone analysis with genomic data is a promising approach to
understanding the genomic basis of adaptive divergence. It allows for the identification
of genomic regions underlying barriers to gene flow. It also provides insights
into spatial patterns of allele frequency change, informing about the interplay
between environmental factors, dispersal and selection. However, when only a single
hybrid zone is analysed, it is difficult to separate patterns generated by selection
from those resulting from chance. Therefore, it is beneficial to look for repeatable
patterns across replicate hybrid zones in the same system. We applied this approach
to the marine snail Littorina saxatilis, which contains two ecotypes, adapted
to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous
hybrid zones between ecotypes offered the opportunity to test for the repeatability
of genomic architectures and spatial patterns of divergence. We sampled and phenotyped
snails from seven replicate hybrid zones on the Swedish west coast and genotyped
them for thousands of single nucleotide polymorphisms. Shell shape and size showed
parallel clines across all zones. Many genomic regions showing steep clines and/or
high differentiation were shared among hybrid zones, consistent with a common
evolutionary history and extensive gene flow between zones, and supporting the
importance of these regions for divergence. In particular, we found that several
large putative inversions contribute to divergence in all locations. Additionally,
we found evidence for consistent displacement of clines from the boulder–rock
transition. Our results demonstrate patterns of spatial variation that would not
be accessible without continuous spatial sampling, a large genomic data set and
replicate hybrid zones.
acknowledgement: "We thank everyone who helped with fieldwork, snail processing and
DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise
Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to
Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark
Ravinet for helpful discussions, and to three anonymous reviewers for their constructive
comments. This work was supported by the Natural Environment Research Council (NE/K014021/1),
the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas
and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary
Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628),
and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017).
A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and
innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno.
754411/797747 and no. 706376, respectively."
article_processing_charge: No
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones
to understand the genomic basis of adaptive divergence. Molecular Ecology.
2021;30(15):3797-3814. doi:10.1111/mec.15861
apa: Westram, A. M., Faria, R., Johannesson, K., & Butlin, R. (2021). Using
replicate hybrid zones to understand the genomic basis of adaptive divergence.
Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15861
chicago: Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using
Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.”
Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15861.
ieee: A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid
zones to understand the genomic basis of adaptive divergence,” Molecular Ecology,
vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.
ista: Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid
zones to understand the genomic basis of adaptive divergence. Molecular Ecology.
30(15), 3797–3814.
mla: Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic
Basis of Adaptive Divergence.” Molecular Ecology, vol. 30, no. 15, Wiley,
2021, pp. 3797–814, doi:10.1111/mec.15861.
short: A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021)
3797–3814.
date_created: 2022-03-08T11:28:32Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2023-09-05T16:02:19Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/mec.15861
external_id:
isi:
- '000669439700001'
pmid:
- '33638231'
file:
- access_level: open_access
checksum: d5611f243ceb63a0e091d6662ebd9cda
content_type: application/pdf
creator: dernst
date_created: 2022-03-08T11:31:30Z
date_updated: 2022-03-08T11:31:30Z
file_id: '10839'
file_name: 2021_MolecularEcology_Westram.pdf
file_size: 1726548
relation: main_file
success: 1
file_date_updated: 2022-03-08T11:31:30Z
has_accepted_license: '1'
intvolume: ' 30'
isi: 1
issue: '15'
keyword:
- Genetics
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 3797-3814
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using replicate hybrid zones to understand the genomic basis of adaptive 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 30
year: '2021'
...
---
_id: '11524'
abstract:
- lang: eng
text: We measure the evolution of the rest-frame UV luminosity function (LF) and
the stellar mass function (SMF) of Lyman-α (Ly α) emitters (LAEs) from z ∼ 2 to
z ∼ 6 by exploring ∼4000 LAEs from the SC4K sample. We find a correlation between
Ly α luminosity (LLy α) and rest-frame UV (MUV), with best fit MUV=−1.6+0.2−0.3log10(LLyα/ergs−1)+47+12−11
and a shallower relation between LLy α and stellar mass (M⋆), with best fit log10(M⋆/M⊙)=0.9+0.1−0.1log10(LLyα/ergs−1)−28+4.0−3.8.
An increasing LLy α cut predominantly lowers the number density of faint MUV and
low M⋆ LAEs. We estimate a proxy for the full UV LFs and SMFs of LAEs with simple
assumptions of the faint end slope. For the UV LF, we find a brightening of the
characteristic UV luminosity (M∗UV) with increasing redshift and a decrease of
the characteristic number density (Φ*). For the SMF, we measure a characteristic
stellar mass (M∗⋆/M⊙) increase with increasing redshift, and a Φ* decline. However,
if we apply a uniform luminosity cut of log10(LLyα/ergs−1)≥43.0, we find much
milder to no evolution in the UV and SMF of LAEs. The UV luminosity density (ρUV)
of the full sample of LAEs shows moderate evolution and the stellar mass density
(ρM) decreases, with both being always lower than the total ρUV and ρM of more
typical galaxies but slowly approaching them with increasing redshift. Overall,
our results indicate that both ρUV and ρM of LAEs slowly approach the measurements
of continuum-selected galaxies at z > 6, which suggests a key role of LAEs in
the epoch of reionization.
acknowledgement: This research made use of Astropy, a community developed core Python
package for Astronomy (Astropy Collaboration et al. 2013). topcat, a graphical tool
for manipulating tabular data, was also utilized in this analysis (Taylor 2005).
SG would like to thank Nastasha Wijers for the discussion on the column density
distribution in EAGLE. SC gratefully acknowledges support from Swiss National Science
Foundation grants PP00P2 163824 and PP00P2 190092, and from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
grant agreement No 864361. GP acknowledges support from the Swiss National Science
Foundation (SNF) and from the Netherlands Research School for Astronomy (NOVA).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: S
full_name: Santos, S
last_name: Santos
- first_name: D
full_name: Sobral, D
last_name: Sobral
- first_name: J
full_name: Butterworth, J
last_name: Butterworth
- first_name: A
full_name: Paulino-Afonso, A
last_name: Paulino-Afonso
- first_name: B
full_name: Ribeiro, B
last_name: Ribeiro
- first_name: E
full_name: da Cunha, E
last_name: da Cunha
- first_name: J
full_name: Calhau, J
last_name: Calhau
- first_name: A A
full_name: Khostovan, A A
last_name: Khostovan
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: P
full_name: Arrabal Haro, P
last_name: Arrabal Haro
citation:
ama: Santos S, Sobral D, Butterworth J, et al. The evolution of the UV luminosity
and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6. Monthly
Notices of the Royal Astronomical Society. 2021;505(1):1117-1134. doi:10.1093/mnras/stab1218
apa: Santos, S., Sobral, D., Butterworth, J., Paulino-Afonso, A., Ribeiro, B., da Cunha,
E., … Arrabal Haro, P. (2021). The evolution of the UV luminosity and stellar
mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6. Monthly Notices of
the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stab1218
chicago: Santos, S, D Sobral, J Butterworth, A Paulino-Afonso, B Ribeiro, E da Cunha,
J Calhau, A A Khostovan, Jorryt J Matthee, and P Arrabal Haro. “The Evolution
of the UV Luminosity and Stellar Mass Functions of Lyman-α Emitters from z ∼ 2
to z ∼ 6.” Monthly Notices of the Royal Astronomical Society. Oxford University
Press, 2021. https://doi.org/10.1093/mnras/stab1218.
ieee: S. Santos et al., “The evolution of the UV luminosity and stellar mass
functions of Lyman-α emitters from z ∼ 2 to z ∼ 6,” Monthly Notices of the
Royal Astronomical Society, vol. 505, no. 1. Oxford University Press, pp.
1117–1134, 2021.
ista: Santos S, Sobral D, Butterworth J, Paulino-Afonso A, Ribeiro B, da Cunha E,
Calhau J, Khostovan AA, Matthee JJ, Arrabal Haro P. 2021. The evolution of the
UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼
6. Monthly Notices of the Royal Astronomical Society. 505(1), 1117–1134.
mla: Santos, S., et al. “The Evolution of the UV Luminosity and Stellar Mass Functions
of Lyman-α Emitters from z ∼ 2 to z ∼ 6.” Monthly Notices of the Royal Astronomical
Society, vol. 505, no. 1, Oxford University Press, 2021, pp. 1117–34, doi:10.1093/mnras/stab1218.
short: S. Santos, D. Sobral, J. Butterworth, A. Paulino-Afonso, B. Ribeiro, E. da Cunha,
J. Calhau, A.A. Khostovan, J.J. Matthee, P. Arrabal Haro, Monthly Notices of the
Royal Astronomical Society 505 (2021) 1117–1134.
date_created: 2022-07-07T10:02:59Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2022-08-18T10:51:47Z
day: '01'
doi: 10.1093/mnras/stab1218
extern: '1'
external_id:
arxiv:
- '2105.00007'
intvolume: ' 505'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: evolution'
- 'galaxies: high-redshift'
- 'galaxies: luminosity function'
- mass function
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2105.00007
month: '07'
oa: 1
oa_version: Preprint
page: 1117-1134
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters
from z ∼ 2 to z ∼ 6
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 505
year: '2021'
...