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10.1093/gbe/evy080 http://scihub22266oqcxt.onion/10.1093/gbe/evy080 C5928405!5928405!29718211     free     free     free Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Genome+Biol+Evol 2018 ; 10 (5): 1198-209 Nephropedia Template TP {{tp|p=29718211|t=2018. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication |pdf=|usr=}}{{29718211}} gab.com Text Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication JO: Genome Biol Evol http://www.kidney.de/pget.php?&tw=1&pmid=29718211 #FOAvip In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible. Twit Text FOAVip Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication ????Genome Biol Evol http://www.kidney.de/pget.php?&tw=1&pmid=29718211 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=29718211 #FOAvip English Wikipedia <ref>{{Cite pmid|29718211}}</ref> Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication #MMPMID29718211 Kapust N; Nelson-Sathi S; Schönfeld B; Hazkani-Covo E; Bryant D; Lockhart PJ; Röttger M; Xavier JC; Martin WF Genome Biol Evol 2018[May]; 10 (5): 1198-209 PMID29718211show ga In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible. äFailure to Recover Major Events of Gene Flux in Real Biological Data D(epmc).pdf DeepDyve Pubget Overpricing