What is an archaeon and are the Archaea really unique?

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What is an archaeon and are the Archaea really unique? published as: https://t.co/4BgLgJP7Kn @thePeerJ #biorxiv
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2143 days ago
A thorough discussion as to why the phylogeny is NOT confounded by horizontal gene transfers can be found here https://t.co/aIk5KepvB1 and here Phylogenomics of protein structures https://t.co/U96LRi1XUB (let me know if you need a pdf).
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2143 days ago
A thorough discussion as to why the phylogenies are NOT confounded by horizontal gene transfers can be found here https://t.co/aIk5KepvB1 and here Phylogenomics of protein structures https://t.co/U96LRi1XUB (let me know if you need a pdf).
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RT @protevol: Happy to share my latest https://t.co/aIk5KepvB1. Dealing with the 3rd reviewer (opposing) was both fun and frustrating at…
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RT @protevol: Happy to share my latest https://t.co/aIk5KepvB1. Dealing with the 3rd reviewer (opposing) was both fun and frustrating at…
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Even the best-fitting amino-acid evolution models cannot resolve the archaeal radiation despite employing thousands of genes - @protevol https://t.co/C8oqkYFnkp https://t.co/7u9PuHoHGi
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2160 days ago
@PatrickForterre Correct. In this paper I show that such problems can be overcome by using "genomic characters" and "directional-evolution models". https://t.co/aIk5KepvB1
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2200 days ago
RT @protevol: @zhuqiyun @KaHochberg @PatrickForterre Rooting is a Hard problem! The major focus of our recent works is about assessing the…
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2210 days ago
@zhuqiyun @KaHochberg @PatrickForterre Rooting is a Hard problem! The major focus of our recent works is about assessing the root! The following assessment does not include Asgards https://t.co/NcDKnP8Qaf. But a more recent work includes Asgards and other new archaea https://t.co/aIk5KepvB1 https://t.co/4SusndL4kU
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2211 days ago
@zhuqiyun @PatrickForterre @WvSchaik @R_H_Ebright @Tanai_Cardona Worth repeating: gene tree conflicts != HGT. For more discussion pls see & "Untangling data bias, model bias, and interpretation bias (prior beliefs)" in Harish-2018 https://t.co/84oNtLVatS & see Eisen-2001 https://t.co/imFrYVkoBq
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2212 days ago
@WvSchaik @R_H_Ebright @NatureRevMicro @KnightLabNews @NatureComms Thanks. A quick note: gene tree conflicts =! HGT. For a thorough, incisive analysis & discussion pls see Eisen-2001 https://t.co/imFrYVkoBq & "Untangling data bias, model bias, and interpretation bias (prior beliefs)" in Harish-2018 https://t.co/PCkXFLVHYM
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2213 days ago
@merenbey @PatrickForterre One of the issues is infact what to put into these tools. Some common questions/objections were raised by Reviewer-3, which are also available here https://t.co/AP18s3YkpA
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2213 days ago
@merenbey @PatrickForterre Indeed, we'll get a tree from a tree-building tool just as we'll get a network from a network-building tool. I've explored both here. I'll appreciate your opinion/critique. https://t.co/aIk5KepvB1
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2213 days ago
@PatrickForterre If the logic is to compare proximity based on homologous genes/loci instead of substitution mutations in A, B, E species, then E species are further apart from both A and B! https://t.co/aIk5KepvB1 https://t.co/jQlAOBv0B3
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2214 days ago
@afuckingnavyrdi @R_H_Ebright @NatureRevMicro @WvSchaik @KnightLabNews @NatureComms Sure, I was going to anyway, in response to the previous message. This study explores why we get different trees and how we can resolve the differences https://t.co/aIk5KepvB1 Also the reviewer comments & responses here https://t.co/AP18s3YkpA
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2214 days ago
@afuckingnavyrdi @R_H_Ebright @NatureRevMicro @WvSchaik @KnightLabNews @NatureComms Sure, I was going to anyway, in response to the previous message. This study explores why we get different trees and how we can resolve the differences https://t.co/aIk5KepvB1 Also the reviewer comments & responses here https://t.co/AP18s3YkpA
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2215 days ago
@NatureRevMicro @KnightLabNews @NatureComms So does another view: A tertiary structure-based view of tree of life rather than the primary sequence-based view. https://t.co/aIk5KepvB1
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2215 days ago
@R_H_Ebright @NatureRevMicro @WvSchaik @KnightLabNews @NatureComms So does another view: A tertiary structure-based tree of life rather than the primary sequence-based tree of life! https://t.co/aIk5KepvB1
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2215 days ago
@Tanai_Cardona @Jwestrob @jongsanders There are many examples for both cases, but some recent ones: for (1) see Fig. 4 and discussiins on data quality (i.e. phylogenetic signal quality) https://t.co/aIk5KepvB1
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2216 days ago
@jongsanders Just so I don't interrupt your original thread. I guess including eukaryotes reduces the number of marker genes that can be used? https://t.co/aIk5KepvB1
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2216 days ago
Whoa!! Congrats. Many cool things, including graphics. I'm curious why no eukaryotes were included. @jongsanders Interested in your opinion about this https://t.co/aIk5KepvB1 https://t.co/1lQi1cu2oy
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2297 days ago
@jakeberv @burkhard_mstern btw, reviewer comments are OA too. Dealing with the proverbial 3rd reviewer, was both fun and frustrating at the same time!! https://t.co/AP18s3YkpA
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2297 days ago
RT @protevol: @jakeberv @burkhard_mstern We get a similar big picture with a model based 'genome phylogeny', i.e. Archaea and Bacteria are…
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2298 days ago
@jakeberv @burkhard_mstern We get a similar big picture with a model based 'genome phylogeny', i.e. Archaea and Bacteria are sister clades https://t.co/aIk5KepvB1
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2320 days ago
RT @protevol: @hhollandmoritz @Tanai_Cardona May be one solution to minimize sequence(ing) anomalies is to look beyond primary sequences? h…
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