tag:blogger.com,1999:blog-10781944.post8924246978747603057..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: 'Danger and Evolution in the Twilight Zone': Guest post by Randen Patterson and Gaurav BhardwajJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-10781944.post-29522092175150072922012-05-23T12:29:25.478-07:002012-05-23T12:29:25.478-07:00which is why we need methods for separating conver...which is why we need methods for separating convergence. It is possible. Proteins that arise convergently should be able to be resolved through statistical evaluation. Our efforts in this area have led us to conclude that even for folds that have evolved many times (e.g. HAD domains), they can be separated and correctly annotated by family using the phylogenetic signals we can derive. This also appears to be true for the 4206 RNA viruses we have performed studies on. If you can separate convergent families with statistical reliability, what would the limits be? :o)Randenhttps://www.blogger.com/profile/03408915653529625361noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-16208574903078775402012-05-14T09:12:18.739-07:002012-05-14T09:12:18.739-07:00I am with you on this Larry - my biggest concern i...I am with you on this Larry - my biggest concern in many evolutionary studies of proteins with low levels of sequence similarity is convergent evolution ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-83984783818961606712012-05-14T08:21:20.935-07:002012-05-14T08:21:20.935-07:00Randen Patterson and Gaurav Bhardwaj said,
A fund...Randen Patterson and Gaurav Bhardwaj said,<br /><br /><i>A fundamental problem to phylogenetic inference in the “twilight zone” (<25% pairwise identity), let alone the “midnight zone” (<12% pairwise identity), is the inability to accurately assign evolutionary relationships at these levels of divergence with statistical confidence. This lack of resolution arises from difficulties in separating the phylogenetic signal from the random noise at these levels of divergence.</i><br /><br />I don't think this is quite right. The most fundamental problem is whether similarities in the twilight zone arise by chance or common ancestry. It is not good science to assume, without evidence, that the similarities are due to common descent and not accident or convergence (Doolittle 1981). The statement implies that false assumption because it assumes there's a "phylogenetic signal" that needs finding.<br /><br />As Doolittle (1987) points out, two completely unrelated amino acid sequences can be aligned to give 10-20% sequence identity. This does not mean they evolved from a common ancestor. <br /><br />The goal should be to prove that common descent is the correct explanation. You don't do this by ASSUMING common descent then looking for algorithms that confirm your assumption. <br /><br />Incidentally, the same problems exists when comparing protein domains that are structurally similar. Are they actually homologous or is that just an unproven conclusion that's automatically applied to any two similar structures? <br /><br />Doolitte, R. (1981) Similar Amino Acid Sequences: Chance or Common Ancestry? Science 214:149-159.<br /><br />Doolittle, R. (1987) "Of URFS and ORFS" University Science Books, Mill Valley California, USALarry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-41984029606903501972012-05-11T20:55:35.635-07:002012-05-11T20:55:35.635-07:00Summer 2013 not 2012 ;0)Summer 2013 not 2012 ;0)Randenhttps://www.blogger.com/profile/03408915653529625361noreply@blogger.com