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A rooted phylogeny resolves early bacterial evolution [article]

Gareth A Coleman, Adrián A Davín, Tara Mahendrarajah, Anja A. Spang, Philip Hugenholtz, Gergely J Szöllősi, Tom A Williams
2020 bioRxiv   pre-print
We predict that the last bacterial common ancestor was a free-living flagellated, rod-shaped cell featuring a double membrane with a lipopolysaccharide outer layer, a Type III CRISPR-Cas system, Type IV  ...  A rooted bacterial phylogeny provides a framework to interpret this diversity and to understand the nature of early life.  ...  Multiple hits corresponding to the i n d i v i d u a l d o m a i n s o f a p r o t e i n a r e r e p o r t e d u s i n g a c u s t o m s c r i p t (parse_IPRdomains_vs2_GO_2.py).  ... 
doi:10.1101/2020.07.15.205187 fatcat:olm3yng7qnc7jatdgq745ptz5i

Gene transfers, like fossils, can date the Tree of Life [article]

Adrian A. Davin, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szollosi
2017 bioRxiv   pre-print
Biodiversity has always been predominantly microbial and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life.  ...  Here we show that patterns of lateral gene transfer deduced from the analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the  ...  As a consequence, a transfer event can be used to establish a relative age constraint between nodes in a phylogeny independently of any molecular clock hypothesis: the ancestor node of the donor lineage  ... 
doi:10.1101/193813 fatcat:tpofgtu6erf5ppmit7qw4urche

Zombi: A simulator of species, genes and genomes that accounts for extinct lineages [article]

Adrian A. Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szollosi
2018 bioRxiv   pre-print
As a consequence, ignoring extinct lineages in evolutionary studies can lead to spurious conclusions.  ...  Here we present Zombi, a platform to simulate the evolution of species, genes and genomes taking extinct lineages into account.  ...  ,B) and ((B,C),A).  ... 
doi:10.1101/339473 fatcat:culuee67efhbjfu622rtwnbvkm

Gene transfers can date the tree of life

Adrián A. Davín, Eric Tannier, Tom A. Williams, Bastien Boussau, Vincent Daubin, Gergely J. Szöllősi
2018 Nature Ecology & Evolution  
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life.  ...  Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the  ...  As a consequence, a transfer event can be used to establish a relative age constraint 45 between nodes in a phylogeny independently of any molecular clock hypothesis: the ancestor node of the donor 46  ... 
doi:10.1038/s41559-018-0525-3 pmid:29610471 pmcid:PMC5912509 fatcat:gxmxlstdrjh6xiddqvdiu4gdq4

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers [article]

Cedric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely Szollosi, Vincent Daubin, Eric Tannier
2017 bioRxiv   pre-print
Here we propose a method, implemented in a software called MaxTiC (Maximum Time Consistency), which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal  ...  Hence, the detection of a transfer event can be translated into a time constraint between nodes of a phylogeny if the donor and recipient can be identified.  ...  A study of the full 40 leaf tree, along with comparisons with other domains of life, tests of the transfer dating methods with molecular clocks, can be found in a companion paper (Davin et al., 2017)  ... 
doi:10.1101/127548 fatcat:f4lwbd4arrh3ljgl2hf5oyyuze

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul S Bansal, Vincent Berry, Bastien Boussau, François Chevenet, Nicolas Comte, Adrián A Davín, Christophe Dessimoz, David Dylus (+10 others)
2018 Bioinformatics  
Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc-along with a mapping onto a species tree  ...  Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of  ...  a bifurcation due to a speciation; see Figure 1 B.  ... 
doi:10.1093/bioinformatics/bty389 pmid:29762653 fatcat:4x5yhdsxvzex5fe3vvc3mml6gy

Inhaled remdesivir reduces viral burden in a nonhuman primate model of SARS-CoV-2 infection

Meghan S. Vermillion, Eisuke Murakami, Bin Ma, Jared Pitts, Adrian Tomkinson, Davin Rautiola, Darius Babusis, Hammad Irshad, Dustin Siegel, Cynthia Kim, Xiaofeng Zhao, Congrong Niu (+14 others)
2021 Science Translational Medicine  
Analytes were separated on a Phenomenex Luna C18 HST column (50 × 2.0 mM, 2.5 μm) using a ternary pump system (Shimadzu Scientific), a flow rate of 0.35 mL/min, and a gradient of Mobile phase A (Water  ...  Analytes were separated on a Phenomenex Synergi Hydro-RP 30A column (150 × 2.0 mM, 4.0 μm) at 25°C using a Waters Acquity Ultra Performance LC (Waters Corporation), a flow rate of 0.26 mL/min, and a gradient  ... 
doi:10.1126/scitranslmed.abl8282 pmid:34968150 pmcid:PMC8961622 fatcat:r5tqefxizvce5c5gvhm6wsauou

Page 524 of Political Studies Vol. 32, Issue 3 [page]

1984 Political Studies  
TAYLor 385 The Use and Abuse of Political Violence Davin MILLER 401 The Protestant Work Ethic, Voting Behaviour and Attitudes to the Trade Unions ADRIAN FuRNHAM 420 The Problem of Fellowship in Communitarian  ...  Theory: William Morris and Peter Kropotkin CaroLinE McCuLLocH 437 Output Disaggregation and the Quest for the Impact of Local Politics Georce A.  ... 

Page 19 of Brooklyn Barrister Vol. 2, Issue 5 [page]

1951 Brooklyn Barrister  
The Committee believes that every member has a friend or office associate, or knows a lawyer in his building who is not a member and could be persuaded of the desirability of joining the Association.  ...  McMahon, Adrian P. Driggs Max J. Persuan, 16 Court St., Brooklyn 2, N. Y. Proposed by: August Zolotorofe, Julius Applebaum Err Resnikorr, 16 Court St., Brooklyn 2, N. Y. Proposed by: Frank J.  ... 

Page 364 of Journal of Sedimentary Petrology Vol. 41, Issue 1 [page]

1971 Journal of Sedimentary Petrology  
Dept., Adrian Col- lege, Adrian, Mich. 49221 (’69) Manprip-SoLts, ALEJANDRO, Box 577, Hidalgo, Tex. 78557 (’70) MaceE, JOHN J., Mobil House, 54-60 Victoria St., London, S.W.1, England (’58) *MaceE, Rospert  ...  ., Canada (64) MacLacuHian, Davin B., State Geol. Survey, Har- risburg, Pa. 17120 (’67) MacLacHian, Marjorie E., Geol. Names Comm., . Geol.  ... 

Page 254 of Radiology Vol. 4, Issue 3 [page]

1925 Radiology  
L.) 2 KuTzMANN, ApDoLpH A. (with Hrnan. FRANK, and Gipson, THomas FE.)....... 2 LAMBERT, ADRIAN V. S., and MILLER, James A.  ...  .-+ 2 Miuier, James A. (with Lampert, ADRIAN 1 ee ee er re reer er Morrison, Lawrie B. X-ray and Radium in the Treatment of Non-malignant Dis-_ eases of the Uterus .........6600ccce8 .  ... 

Page 329 of Journal of Sedimentary Petrology Vol. 43, Issue 1 [page]

1973 Journal of Sedimentary Petrology  
A.  ...  Dept., Adrian College, Adrian, Mich. 49221 (’67) HakeEs, WILLIAM G., Geol. Dept., Univ. of Kansas, Lawrence, Kan. 66044 (’71) Harzouty, Micuet T., The Michel T. Halbouty Bldg., 5111 Westheimer Rd.  ... 

Page 743 of Political Studies Vol. 41, Issue 4 [page]

1993 Political Studies  
PAnsasl), 557 McDermott, F.C., Autopsy of a Social and Economic Miracle (J.A. CHANDLER), 134 McGary, Joun see O'LEARY, BRENDAN McGrecor, Davin, Hegel, Marx and the English State (C.J.  ...  ., United Nations Peacekeeping and the Non-Use of Force (A.  ... 

Page 154 of The New England Historical and Genealogical Register Vol. 40, Issue [page]

1886 The New England Historical and Genealogical Register  
April 1, 1859; received a classical education at Adrian College, graduated 1880 and began the study of law in Adrian. P.O. wee Junction. vi. Davin E., b. Nov. 16, 1862. vii. Cora M., b.  ...  April 9, 1857; was educated at Adrian College, and in 1880 was a farmer at Palmyra, Mich. wx. Netson C., b.  ... 

Page 695 of Political Studies Vol. 34, Issue 4 [page]

1986 Political Studies  
(eds) Room Sor Manoeuvre( ADRIAN LEFTWICH) 332 CLEGG, HUGH ARMSTRONG. A History of British Trade Unions since 1889 (DaAvipD HOWELL) 330 CoaTes, D. AND HILLARD, J.  ...  Children of Mao (Davin S. G. GOODMAN) 509 CHANDLER, J. A. AND LAwLEss, P. Local Authorities and the Creation of Employment (EDWARD C. PAGE) 490 CHILDS, DAvip (ed.)  ... 
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