Dating nodes in a phylogeny using inferred horizontal gene transfers
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers
Dating nodes in a phylogeny is an important problem in evolution and is typically performed by using molecular clocks and fossil age estimates . The manuscript by Chauve et al.  reports a novel method, which uses lateral gene transfers to help ordering nodes in a species tree. The idea is that a lateral gene transfer can only occur between two species living at the same time, which indirectly informs on node relative ages in a phylogeny: the donor species cannot be more recent than the recipient species. Horizontal gene transfers are increasingly recognized as frequent, even in eukaryotes, and especially in micro-organisms that have little fossil records [3-7]. Yet, such an important source of information has been very rarely used so far for inferring relative node ages in phylogenies. In this context, the method by Chauve et al.  represents an innovative and original approach to a difficult problem. An obvious limitation of the approach is that it relies on inferences of horizontal transfers, which detection is in itself a difficult problem. Incomplete taxon sampling, or the extinction of the true donor lineage may render patterns difficult to interpret in a temporary fashion. Yet, for clades with no fossils this may be the only piece of information we have at hand, and the growing amount of sequence data is likely to minimize issues derived from incomplete sampling.
The developed method, MaxTiC (for Maximal Time Consistency) , represents a very nice application of theoretical developments on the well-known « Feedback Arc Set » computer science problem to the evolutionary question of ordering nodes in a phylogeny. MaxTiC uses as input a species tree and a set of time constraints based on lateral gene transfers inferred using other softwares, and minimizes conflicts between node ordering and these time constraints. The application of MaxTiC on simulated datasets indicated that node ordering was fairly accurate . MaxTiC is implemented in a freely available software, which represents original and relevant contribution to the field of evolutionary biology.
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 Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szöllősi GJ, Daubin V and Tannier E. 2017. MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers. bioRxiv 127548, ver. 6 of 6th November 2017. doi: 10.1101/127548
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Tatiana Giraud and Toni Gabaldon (2017) Dating nodes in a phylogeny using inferred horizontal gene transfers. Peer Community in Evolutionary Biology, 100037. 10.24072/pci.evolbiol.100037
Revision round #227 Oct 2017
Decision round #2
I was pleased to see that this manuscript has been further carefully revised, and there remain only a few minor additional suggestions that should be addressed before the manuscript can be recommended by PCI
Reviewed by Mukul Bansal, 18 Oct 2017 03:44
Reviewed by anonymous reviewer, 07 Oct 2017 02:12
Revision round #109 Aug 2017
Decision round #1
The manuscript has been evaluated by two referees, who agree that this method using lateral gene transfers to help finding the temporal ordering (or ranking) of nodes in a given species tree is sound and should be of interest for scientists in evolutionary biology. The referees nevertheless raise concerns about the possible target journal, about lack of sufficient details and of clarity and suggest some improvements. I have to agree that, as it stands, the manuscript may not be readable for most biologists who could use this interesting method, which could prevent a wide use of the sofware. I would therefore recommend writing the abstract and introduction for a broader audience and explain there the method more intuitively. The conclusion does a better job in this regards than the abstract, but could still be improved. To sum up, there is potential for an interesting and relevant contribution to the field of evolutionary biology. However, the paper needs careful revision along the lines above. If you are able to accommodate these points, I would encourage resubmission to PCI Evol Biol.