---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
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: 14
year: '2017'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2025-05-28T11:57:06Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '2410'
abstract:
- lang: eng
text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis,
isolated from soil in Austria. It is the first phage to be discovered that infects
this species. Here, we present the complete genome sequence of this podovirus. '
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Gertraud
full_name: Stift, Gertraud
id: 2DB195CA-F248-11E8-B48F-1D18A9856A87
last_name: Stift
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence
of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements.
2013;1(3). doi:10.1128/genomeA.00216-13
apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013).
Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis.
Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13
chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan
P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus
Weihenstephanensis.” Genome Announcements. American Society for Microbiology,
2013. https://doi.org/10.1128/genomeA.00216-13.
ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete
genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,”
Genome Announcements, vol. 1, no. 3. American Society for Microbiology,
2013.
ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome
sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome
Announcements. 1(3).
mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel
Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements,
vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.
short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements
1 (2013).
date_created: 2018-12-11T11:57:30Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2021-01-12T06:57:19Z
day: '13'
ddc:
- '576'
department:
- _id: JoBo
- _id: LifeSc
doi: 10.1128/genomeA.00216-13
file:
- access_level: open_access
checksum: 0751ec74b695567e0cdf02aaf9c26829
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:36Z
date_updated: 2020-07-14T12:45:40Z
file_id: '5291'
file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf
file_size: 130026
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Genome Announcements
publication_status: published
publisher: American Society for Microbiology
publist_id: '4516'
pubrep_id: '398'
quality_controlled: '1'
scopus_import: 1
status: public
title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
file:
- access_level: open_access
checksum: 8007815078dccac21ecd1cf73a269dc6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4980'
file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf
file_size: 1040765
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 94'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1331 - 1345
publication: Journal of Mammalogy
publication_status: published
publisher: Oxford University Press
publist_id: '7319'
pubrep_id: '940'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new species of tapir from the Amazon
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 94
year: '2013'
...
---
_id: '508'
abstract:
- lang: eng
text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen
species with microbicidal activity. It is composed of two membrane-spanning subunits,
gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic
subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively).
Mutations in any of these genes can result in chronic granulomatous disease, a
primary immunodeficiency characterized by recurrent infections. Using evolutionary
mapping, we determined that episodes of adaptive natural selection have shaped
the extracellular portion of gp91-phox during the evolution of mammals, which
suggests that this region may have a function in host-pathogen interactions. On
the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2,
and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of
European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the
pattern of CYBA diversity is compatible with balancing natural selection, perhaps
mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern
of diversity characterized by a differentiated haplotype structure. Our study
provides insight into the role of pathogen-driven natural selection in an innate
immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic
NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other
complex diseases.
author:
- first_name: Eduardo
full_name: Tarazona Santos, Eduardo
last_name: Tarazona Santos
- first_name: Moara
full_name: Machado, Moara
last_name: Machado
- first_name: Wagner
full_name: Magalhães, Wagner
last_name: Magalhães
- first_name: Renee
full_name: Chen, Renee
last_name: Chen
- first_name: Fernanda
full_name: Lyon, Fernanda
last_name: Lyon
- first_name: Laurie
full_name: Burdett, Laurie
last_name: Burdett
- first_name: Andrew
full_name: Crenshaw, Andrew
last_name: Crenshaw
- first_name: Cristina
full_name: Fabbri, Cristina
last_name: Fabbri
- first_name: Latife
full_name: Pereira, Latife
last_name: Pereira
- first_name: Laelia
full_name: Pinto, Laelia
last_name: Pinto
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Ben
full_name: Sestanovich, Ben
last_name: Sestanovich
- first_name: Meredith
full_name: Yeager, Meredith
last_name: Yeager
- first_name: Stephen
full_name: Chanock, Stephen
last_name: Chanock
citation:
ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of
the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications.
Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119'
apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett,
L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes
CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119'
chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen,
Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics
of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.”
Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.'
ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH
oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular
Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167,
2013.'
ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw
A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M,
Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB,
CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution.
30(9), 2157–2167.'
mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH
Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular
Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp.
2157–67, doi:10.1093/molbev/mst119.'
short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett,
A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich,
M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst119
external_id:
pmid:
- '23821607'
intvolume: ' 30'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/
month: '09'
oa: 1
oa_version: Submitted Version
page: 2157 - 2167
pmid: 1
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7310'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and
NCF4: Functional implications'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2013'
...
---
_id: '3247'
abstract:
- lang: eng
text: The Brazilian Merganser is a very rare and threatened species that nowadays
inhabits only a few protected areas and their surroundings in the Brazilian territory.
In order to estimate the remaining genetic diversity and population structure
in this species, two mitochondrial genes were sequenced in 39 individuals belonging
to two populations and in one individual collected in Argentina in 1950. We found
a highly significant divergence between two major remaining populations of Mergus
octosetaceus, which suggests a historical population structure in this species.
Furthermore, two deeply divergent lineages were found in a single location, which
could due to current or historical secondary contact. Based on the available genetic
data, we point out future directions which would contribute to design strategies
for conservation and management of this threatened species.
acknowledgement: "The present study received grants from FAPEMIG, CNPq, Petrobras
Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all
ethical guidelines and legal requirements of Brazil for sampling and studying an
endangered species.\r\nWe thank the Specialist Work Group for the Conservation of
Brazilian Merganser for valuable discussions and opinions on this manuscript. We
also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz
and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada
dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing
the samples from Argentina, Bradley C. Livezey for sending copies of his papers,
and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly
improved this manuscript."
author:
- first_name: Sibelle
full_name: Vilaça, Sibelle
last_name: Vilaça
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Lívia
full_name: Lins, Lívia
last_name: Lins
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity
in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298.
doi:10.1007/s10592-011-0262-5
apa: Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining
genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation
Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5
chicago: Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício
Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).”
Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5.
ieee: S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics,
vol. 13, no. 1. Springer, pp. 293–298, 2012.
ista: Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic
diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics.
13(1), 293–298.
mla: Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser
(Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer,
2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.
short: S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics
13 (2012) 293–298.
date_created: 2018-12-11T12:02:15Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T07:42:05Z
day: '01'
department:
- _id: JoBo
doi: 10.1007/s10592-011-0262-5
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 293 - 298
publication: Conservation Genetics
publication_status: published
publisher: Springer
publist_id: '3420'
quality_controlled: '1'
scopus_import: 1
status: public
title: Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2012'
...
---
_id: '3770'
abstract:
- lang: eng
text: 'The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon
and Orinoco basins, covering an area of approximately 7 million km2. Previous
morphological and genetic studies have proposed the existence of at least two
evolutionary significant units: one distributed across the Orinoco and Amazon
basins and another confined to the Bolivian Amazon. The presence of barriers in
the riverine environment has been suggested to play a significant role in shaping
present-day patterns of ecological and genetic structure for this species. In
the present study, we examined the phylogeographic structure, lineage divergence
time and historical demography using mitochondrial (mt)DNA sequences in different
pink dolphin populations distributed in large and small spatial scales, including
two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis
revealed that the Brazilian haplotypes occupy an intermediate position compared
to three previously studied geographic locations: the Colombian Amazon, the Colombian
Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern
of maternal isolation between two neighbouring populations from Brazil. Six mtDNA
CR haplotypes were identified in Brazil with no sharing between the two populations,
as well as specific cytochrome b (cyt b) haplotypes identified in each locality.
In addition, we analyzed autosomal microsatellites to investigate male-mediated
gene flow and demographic changes within the study area in Brazil. Data analysis
of 14 microsatellite loci failed to detect significant population subdivision,
suggesting that male-mediated gene flow may maintain homogeneity between these
two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic
collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of
mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages
through time, whereas a population decline was demonstrated in the Colombian Orinoco
lineage. Moreover, BSP and Tajima''s D and Fu''s Fs tests revealed a recent population
expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification
of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and
continued throughout the Pleistocene.'
article_processing_charge: No
author:
- first_name: Claudia
full_name: Hollatz, Claudia
last_name: Hollatz
- first_name: Sibelle
full_name: Vilaça, Sibelle
last_name: Vilaça
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Míriam
full_name: Marmontel, Míriam
last_name: Marmontel
- first_name: Cyndi
full_name: Baker, Cyndi
last_name: Baker
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F.
The Amazon River system as an ecological barrier driving genetic differentiation
of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society.
2011;102(4):812-827. doi:10.1111/j.1095-8312.2011.01616.x
apa: Hollatz, C., Vilaça, S., Fernandes Redondo, R. A., Marmontel, M., Baker, C.,
& Santos, F. (2011). The Amazon River system as an ecological barrier driving
genetic differentiation of the pink dolphin (Inia geoffrensis). Biological
Journal of the Linnean Society. Wiley. https://doi.org/10.1111/j.1095-8312.2011.01616.x
chicago: Hollatz, Claudia, Sibelle Vilaça, Rodrigo A Fernandes Redondo, Míriam Marmontel,
Cyndi Baker, and Fabrício Santos. “The Amazon River System as an Ecological Barrier
Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological
Journal of the Linnean Society. Wiley, 2011. https://doi.org/10.1111/j.1095-8312.2011.01616.x.
ieee: C. Hollatz, S. Vilaça, R. A. Fernandes Redondo, M. Marmontel, C. Baker, and
F. Santos, “The Amazon River system as an ecological barrier driving genetic differentiation
of the pink dolphin (Inia geoffrensis),” Biological Journal of the Linnean
Society, vol. 102, no. 4. Wiley, pp. 812–827, 2011.
ista: Hollatz C, Vilaça S, Fernandes Redondo RA, Marmontel M, Baker C, Santos F.
2011. The Amazon River system as an ecological barrier driving genetic differentiation
of the pink dolphin (Inia geoffrensis). Biological Journal of the Linnean Society.
102(4), 812–827.
mla: Hollatz, Claudia, et al. “The Amazon River System as an Ecological Barrier
Driving Genetic Differentiation of the Pink Dolphin (Inia Geoffrensis).” Biological
Journal of the Linnean Society, vol. 102, no. 4, Wiley, 2011, pp. 812–27,
doi:10.1111/j.1095-8312.2011.01616.x.
short: C. Hollatz, S. Vilaça, R.A. Fernandes Redondo, M. Marmontel, C. Baker, F.
Santos, Biological Journal of the Linnean Society 102 (2011) 812–827.
date_created: 2018-12-11T12:05:04Z
date_published: 2011-04-01T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '01'
doi: 10.1111/j.1095-8312.2011.01616.x
extern: '1'
intvolume: ' 102'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 812 - 827
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley
publist_id: '2457'
status: public
title: The Amazon River system as an ecological barrier driving genetic differentiation
of the pink dolphin (Inia geoffrensis)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2011'
...
---
_id: '3771'
abstract:
- lang: eng
text: The small-sized frugivorous bat Carollia perspicillata is an understory specialist
and occurs in a wide range of lowland habitats, tending to be more common in tropical
dry or moist forests of South and Central America. Its sister species, Carollia
brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic
study proposed a hypothesis of origin and subsequent diversification for C. perspicillata
along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric
clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene
sequences and a more extensive sampling to test hypotheses related to the origin
and diversification of C. perspicillata plus C. brevicauda clade in South America.
The results obtained indicate that there are two sympatric evolutionary lineages
within each species. In C. perspicillata, one lineage is limited to the Southern
Atlantic Forest, whereas the other is widely distributed. Coalescent analysis
points to a simultaneous origin for C. perspicillata and C. brevicauda, although
no place for the diversification of each species can be firmly suggested. The
phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene
refugia hypothesis as a likely vicariant phenomenon shaping the present distribution
of its intraspecific lineages.
author:
- first_name: Ana
full_name: Pavan, Ana
last_name: Pavan
- first_name: Felipe
full_name: Martins, Felipe
last_name: Martins
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
- first_name: Albert
full_name: Ditchfield, Albert
last_name: Ditchfield
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
citation:
ama: 'Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns
of diversification in two species of short-tailed bats (Carollia Gray, 1838):
the effects of historical fragmentation of Brazilian rainforests. Biological
Journal of the Linnean Society. 2011;102(3):527-539. doi:10.1111/j.1095-8312.2010.01601.x'
apa: 'Pavan, A., Martins, F., Santos, F., Ditchfield, A., & Fernandes Redondo,
R. A. (2011). Patterns of diversification in two species of short-tailed bats
(Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.
Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2010.01601.x'
chicago: 'Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo
A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed
Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian
Rainforests.” Biological Journal of the Linnean Society. Wiley-Blackwell,
2011. https://doi.org/10.1111/j.1095-8312.2010.01601.x.'
ieee: 'A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo,
“Patterns of diversification in two species of short-tailed bats (Carollia Gray,
1838): the effects of historical fragmentation of Brazilian rainforests.,” Biological
Journal of the Linnean Society, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539,
2011.'
ista: 'Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns
of diversification in two species of short-tailed bats (Carollia Gray, 1838):
the effects of historical fragmentation of Brazilian rainforests. Biological Journal
of the Linnean Society. 102(3), 527–539.'
mla: 'Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed
Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian
Rainforests.” Biological Journal of the Linnean Society, vol. 102, no.
3, Wiley-Blackwell, 2011, pp. 527–39, doi:10.1111/j.1095-8312.2010.01601.x.'
short: A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological
Journal of the Linnean Society 102 (2011) 527–539.
date_created: 2018-12-11T12:05:05Z
date_published: 2011-02-10T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '10'
department:
- _id: FyKo
doi: 10.1111/j.1095-8312.2010.01601.x
intvolume: ' 102'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 527 - 539
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2456'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Patterns of diversification in two species of short-tailed bats (Carollia
Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2011'
...