It's the first of the month again, and Carnival of Evolution, #52 (the network edition) is now live at The Genealogical World of Phylogenetic Networks. The baton has been passed (from CoE #46) in nonlinear fashion [1]. That is to say that the hosts of Carnival of Evolution, #52 have expanded upon the phylogenetic-like results presented in CoE #46, The (tree) Structures of Life by presenting several examples of reticulating phylogenies [2]. They did a pretty good job.
Whereas phylogenetic trees are directed, acyclic graphs (DAGs), reticulating networks allow for possible recombination along the path from common ancestor to the taxonomic units under analysis. As a result, shared and derived traits among taxa in the graph (or network) cannot easily be traced back to a common origin. Here are two of my favorite features from CoE #52:
1) reticulating evolution as a cube (median graphs):
Median graphs are an instance of minimum spanning trees [3]. Using a distance metric, we are able to infer a graph topology based on distance between different taxa. Median networks are undirected because the center of a network (in this case embedded in a metric space) is based on the median value between all taxa under analysis. Thus, there is no clearly defined root nor independent evolutionary trajectories. This is not to be confused with the use of hypercubes in the study of evolvability and robustness [4].
2) Example of horizontal gene transfer (HGT) using blog posts about ENCODE:
Earlier this month, Nature featured a special edition full of papers released from the ENCODE project [5]. The goal of ENCODE is to use high-throughput techniques and bioinformatics to create a genome-wide library of functional elements [6]. This has stimulated much debate in the blogosphere regarding the true meaning behind results and interpretation offered by the study's authors [7] as well as the role of media hype in the scientific process. While I will not jump into the fray here, this debate/critique provides an excellent opportunity for the folks at CoE #52 to demonstrate how this evolutionary process (HGT) is represented in a phylogenetic context.
NOTES:
[1] Of course. I wouldn't have it any other way.
[2] These results are also based on non-replicating blog posts, and as such also have a neo-last common ancestor (neo-LCA). Also featured in CoE #52 is a post on single-organism oriented (e.g. genetic regulatory and physiological) networks from this blog entitled: Cascades in Common: biological network function in evolution.
[3] for an example from human genetics, please see: Bandelt, H-J., Forster, P., and Rohl, A. Median-Joining Networks for Inferring Intraspeciļ¬c Phylogenies. Molecular Biology and Evolution, 16(1):, 37–48 (1999).
YouTube tutorial on minimum spanning trees, presented by Steven Skiena, SUNY-Stonybrook.
[4] In this case, the networks are directed based on the numerical values (e.g. n-tuples) of individual nodes. For more information/examples, please see:
Wagner, A. Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B, 275 (1630), 91-100 (2008) AND Iordache, O. Self-evolvability for Biosystems. In Understanding Complex Systems, J.A.S. Kelso ed. pp. 101-134. Springer, Berlin (2012).
[5] They have organized all associated papers into a series of topical threads. This is a really innovative way to organize the primary literature.
[6] With all of the tea-leaf reading and going out on a limb that this entails. Keep in mind that this is the first such attempt since the draft sequence of the human genome was released.
[7] Is most of the genome functional, or is there a difference between explicit (causal) and implicit (merely associative) function? Is the criterion for "function" set forth by the ENCODE project a reasonable one? And just how relevant is this result to applications such as curing human disease or changing our understanding of evolution?
Whereas phylogenetic trees are directed, acyclic graphs (DAGs), reticulating networks allow for possible recombination along the path from common ancestor to the taxonomic units under analysis. As a result, shared and derived traits among taxa in the graph (or network) cannot easily be traced back to a common origin. Here are two of my favorite features from CoE #52:
1) reticulating evolution as a cube (median graphs):
2) Example of horizontal gene transfer (HGT) using blog posts about ENCODE:
NOTES:
[1] Of course. I wouldn't have it any other way.
[2] These results are also based on non-replicating blog posts, and as such also have a neo-last common ancestor (neo-LCA). Also featured in CoE #52 is a post on single-organism oriented (e.g. genetic regulatory and physiological) networks from this blog entitled: Cascades in Common: biological network function in evolution.
[3] for an example from human genetics, please see: Bandelt, H-J., Forster, P., and Rohl, A. Median-Joining Networks for Inferring Intraspeciļ¬c Phylogenies. Molecular Biology and Evolution, 16(1):, 37–48 (1999).
YouTube tutorial on minimum spanning trees, presented by Steven Skiena, SUNY-Stonybrook.
[4] In this case, the networks are directed based on the numerical values (e.g. n-tuples) of individual nodes. For more information/examples, please see:
Wagner, A. Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B, 275 (1630), 91-100 (2008) AND Iordache, O. Self-evolvability for Biosystems. In Understanding Complex Systems, J.A.S. Kelso ed. pp. 101-134. Springer, Berlin (2012).
[5] They have organized all associated papers into a series of topical threads. This is a really innovative way to organize the primary literature.
[6] With all of the tea-leaf reading and going out on a limb that this entails. Keep in mind that this is the first such attempt since the draft sequence of the human genome was released.
[7] Is most of the genome functional, or is there a difference between explicit (causal) and implicit (merely associative) function? Is the criterion for "function" set forth by the ENCODE project a reasonable one? And just how relevant is this result to applications such as curing human disease or changing our understanding of evolution?
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