Recent book reviews

In one of the earliest blog posts (Reviews of recent books) I provided links to some book reviews. Recently, a few have appeared for Dan Gusfield's book: ReCombinatorics: the algorithmics of ancestral recombination graphs and explicit phylogenetic networks (2014. The MIT Press, Cambridge, MA).

In addition to the three endorsements that appear as part of the publisher's blurb, a number of independent book reviews have appeared since its publication:

(2014) Computing Reviews Review#143064.

Michael Sanderson (2015) Quarterly Review of Biology 90: 344-345.

Luay Nakhleh (2015) SIAM Reviews 57: 638-642.

From the mathematical point of view, the reviews make it clear that this book is necessary because networks are very much part of the fringe of the computational sciences. Indeed, the challenge is to convince mathematicians that interesting mathematical problems exist with the the study of networks. In this sense, the main limitation of the book is its focus on the parsimony criterion for optimization, rather than statistical approaches to inference, which play such a large part in phylogenetic analyses.

From the biological point of view, the principal issue seems to be the reliance of the book on the infinite sites model, which does not currently have wide applicability in phylogenetics (eg. mostly in population studies such as haplotype inference and association mapping).

The ultimate goal for both computational end biological scientists is working out how to include recombination in the framework of other types of phylogenetic networks. A basic assumption of many phylogenetic analyses is that there has been no recombination. This is because recombination can destroy much of the evidence left by historically preceding processes, so that neither genotype nor phenotype data can reveal patterns and processes that pre-date the recombination events. In this sense, recombination becomes the reticulation process, rather than processes like hybridization or introgression.

More literature on trees and networks

In a previous blog post I listed some of the Books about the history of trees and networks. While I mentioned a review paper by Pascal Tassy, I did not list his earlier book on the subject, which actually pre-dates all of the books listed.

  

• Tassy, Pascal (1991) L'Arbre à Remonter le Temps. Paris: Christian Bourgois Éditeur. First edition. (1998) Paris: Diderot Éditeur. Second edition.

In French; paperback. A conceptual history of phylogenetics up to the end of the 20th century. Covers the development of ideas for the general public, with a few illustrations. Networks are barely mentioned.

In this context, there are also other sources that illustrate at least part of the history of trees and networks (along with textbooks covering systematics). These include:

Archibald, J. David (2009) Edward Hitchcock's pre-Darwinian (1840) "Tree of Life". Journal of the History of Biology 42: 561-592.

Bigoni, Francesca and Barsanti, Giulio (2011) Evolutionary trees and the rise of modern primatology: the forgotten contribution of St. George Mivart. Journal of Anthropological Sciences 89: 93-107.

Coggon, Jennifer (2002) Quinarianism after Darwin’s Origin: the circular system of William Hincks. Journal of the History of Biology 35: 5-42.

Gaffney, Eugene S. (1984) Historical analysis of theories of chelonian relationship. Systematic Zoology 33: 283-301.

Gontier, Nathalie (2011) Depicting the Tree of Life: the philosophical and historical roots of evolutionary tree diagrams. Evolution: Education and Outreach 4: 515-538.

Lam, Herman J. (1936) Phylogenetic symbols, past and present (being an apology for genealogical trees). Acta Biotheoretica 2: 153-194.

Nelson, Gareth and Platnick, Norman (1981) Systematics and Biogeography: Cladistics and Vicariance. Columbia Uni. Press, New York.

O’Hara, Robert J. (1988) Diagrammatic classifications of birds, 1819-1901: views of the natural system in 19th-century British ornithology. In: H. Ouellet (ed.) Acta XIX Congressus Internationalis Ornithologici, pp. 2746-2759. National Museum of Natural Sciences, Ottawa.

O’Hara, Robert J. (1991) Representations of the natural system in the nineteenth century. Biology and Philosophy 6: 255-274.

O'Hara, Robert J. (1996) Trees of history in systematics and philology. Memorie della Società Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano 27: 81-88.

Ragan, Mark A. (2009) Trees and networks before and after Darwin. Biology Direct 4: 43.

Stevens, Peter F. (1984) Metaphors and typology in the development of botanical systematics 1690-1960, or the art of putting new wine in old bottles. Taxon 33: 169-211.

Tassy, Pascal (2011) Trees before and after Darwin. Journal of Zoological Systematics and Evolutionary Research 49: 89-101.

Willmann, Rainer (2003) From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe. Cladistics 19: 449–479.

Books about the history of trees and networks

The standard references for the conceptual history of phylogenetic trees and networks are:

• Ragan, Mark A. (2009) Trees and networks before and after Darwin. Biology Direct 4: 43.
• Tassy, Passcal (2011) Trees before and after Darwin. Journal of Zoological Systematics and Evolutionary Research 49: 89-101.

Over the past 20 years, a number of books have appeared that expand upon this topic, which it is worthwhile to list here.

• Barsanti, Giulio (1992) La Scala, la Mappa, l'Albero: Immagini e Classificazioni Della Natura Fra Sei e Ottocento. Firenze: Sansoni Editore.

In Italian. A conceptual history of classification up to the time of Haeckel, and the beginning of phylogenetics. Covers the development of ideas and images equally. Networks are treated as "maps".

This is expanded from a preceding review article: (1988) Le immagini della natura: scale, mappe, alberi 1700-1800. Nuncius 3(1): 55-125. 

• Stevens, Peter F. (1994) The Development of Biological Systematics: Antoine-Laurent de Jussieu, Nature, and the Natural System. New York: Columbia University Press.

A conceptual history of classification and phylogenetics, mainly as related to plants. Focuses on the early development of ideas within biosystematics, with accompanying illustrations. Networks are effectively treated as variants of trees.

• Pietsch, Theodore W. (2012) Trees of Life: a Visual History of Evolution. Baltimore: Johns Hopkins University Press.

A richly illustrated history of trees, with a few networks. Focuses on the illustrations, with some accompanying text. The best source to see what people have drawn in the way of trees, but weaker on networks.

• Minaka, Nobuhiro, and Sugiyama, Kunihiko (2012) Phylogeny Mandala: Chain, Tree, and Network. Tokyo: NTT Publishing.

In Japanese. Covers the development of the tree metaphor (with a few networks), as related to pedigrees, phylogenies, and knowledge representation in general. The breadth of the topic is indicated in the "mandala" of the title, which is "a generic term for any diagram, chart or geometric pattern that represents the cosmos metaphysically or symbolically".

• Archibald, J. David (2014) Aristotle's Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. New York: Columbia University Press.

A conceptual history of trees, with a few networks. Focuses on the development of the ideas, with accompanying illustrations. Starts with pedigrees, and proceeds from there to phylogenies. The best coverage of phylogeny concepts, but explicitly treats networks as "trees with reticulations".

See also this later post:
More literature on trees and networks

ReCombinatorics

This post is just to let everyone know that Dan Gusfield's long-awaited book on the interface between phylogenetics and population genetics is now available.

The book is targeted for mathematically inclined readers. It has a few contributions from Charles H. Langley, Yun S. Song and Yufeng Wu. The title is described as "a portmanteau word derived from the single-crossover recombination of the words 'recombination' and 'combinatorics'."

Hardcover 448 pp; ISBN: 9780262027526; $60.00 £30.95
More information is available from The MIT Press.

This new book joins these previous contributions to the genre:

Image from Celine Scornavacca.

Textbooks and phylogenetic networks

The question has been asked as to which of the current general books about phylogenetics actually cover phylogenetic networks. There are collections of essays where networks are covered, and there are specialist books, of course, but the question here is about general introductory books. While a number of books mention tree incongruence, and that this phenomenon could be represented using a reticulating graph, there appear to be only two books that specifically cover the topic of phylogenetic networks.

(1)
Barry G. Hall (2011) Phylogenetic Trees Made Easy: A How-To Manual, Fourth Edition. Sinauer Associates, Sunderland MA.

The first three editions (2001, 2004, 2008) discussed trees only, but the fourth edition has added a chapter on networks. Chapter 15 (pp. 219-248) explicitly notes that "The material presented here is drawn almost entirely from the new book Phylogenetic Networks: Concepts Algorithms and Applications", which is also noted was "made available to me in manuscript prior to its publication."

There are four sections in the chapter:
  Why Trees Are Not Always Sufficient
  Unrooted and Rooted Phylogenetic Networks
  Learn More about Phylogenetic Networks
  Using SplitsTree to Estimate Unrooted Phylogenetic Networks
  Using Dendroscope to Estimate Rooted Networks from Rooted Tree

The first three sections are theoretical introductions to the topic, and the final two sections proceed through a worked example (a different one each).

The book provides a basic introduction to phylogenetics, which is its intent. So, the network topics are presented in a straightforward manner, which makes them easy to grasp. The worked examples are cookbook style, intended solely to get you started using the two chosen computer programs.

The author is to be congratulated for producing not only the first, but so far the only, general book that covers evolutionary networks.

(2)
Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme (editors) (2009) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Second Edition. Cambridge Uni Press, Cambridge.

The first edition (2003) had a chapter on SplitsTree by Vincent Moulton, and this was revised in the current edition to Split Networks: a Tool for Exploring Complex Evolutionary Relationships in Molecular Data, Chapter 21 (pp. 631-653), by Vincent Moulton and Katharina Huber.

The chapter provides a general introduction to the theory of splits graphs and their uses; and the practical exercises use SplitsTree. This was the first general book on phylogenetics to include networks, although evolutionary networks are not covered.

Conclusion

The coverage of networks is the final topic in the book in both cases, so it can hardly be claimed to have an important place. Nevertheless, these books are at least one step ahead of their competitors.

All of these books are examples of the contemporary focus on congruent tree patterns in evolution, with reticulate relationships being almost an afterthought. There is nothing in the word "phylogeny" that specifies a shape for evolutionary history — it comes from the Greek phylon "race" + geneia "origin". Evolutionary groups may arise by either vertical or horizontal processes, and so evolution may be tree-like or it may not. The current focus almost exclusively on trees is therefore somewhat misplaced.

Amazon is trying to tell us something

If one goes to the Humour section of the Books department at www.amazon.co.uk, and does a search for "phylogeny", one gets the following search results:

Inferring Phylogenies by Joseph Felsenstein
Advances in Sponge Science: Phylogeny, Systematics, Ecology edited by Mikel Becerro
Mathematics of Evolution and Phylogeny edited by Olivier Gascuel

If one goes to the Humor & Entertainment section of the Books department at www.amazon.com, and performs the same search, one gets the following search results:

Computational Paleontology edited by Ashraf M.T. Elewa
Evolutionary Biology: Concepts, Molecular and Morphological Evolution edited by Pierre Pontarotti
Lecture Notes in Computer Science 1075 - Proceedings of CPM 1996
Lecture Notes in Bioinformatics 2066 - Proceedings of JOBIM 2000
Lecture Notes in Bioinformatics 2452 - Proceedings of WABI 2002
Lecture Notes in Bioinformatics 3678 - Proceedings of RECOMB-CG 2005
Lecture Notes in Bioinformatics 4205 - Proceedings of RECOMB-CG 2006
Lecture Notes in Bioinformatics 4751 - Proceedings of RECOMB-CG 2007
Lecture Notes in Bioinformatics 5267 - Proceedings of RECOMB-CG 2008
Lecture Notes in Bioinformatics 5817 - Proceedings of RECOMB-CG 2009
Lecture Notes in Bioinformatics 6398 - Proceedings of RECOMB-CG 2010

Lecture Notes in Bioinformatics 5542 - Proceedings of ISBRA 2009

Lecture Notes in Bioinformatics 7292 - Proceedings of ISBRA 2012

None of these books is in any way humorous (at least not intentionally), and so either (i) the cataloguing schemes used by the various Amazon stores leave something to be desired, or (ii) Amazon is telling us that we look funny to the rest of the world.

Perhaps the difference between the two lists has something to do with the British Amazon insisting that "Humour" is also "Entertainment"? I guess that we should be grateful that there are not more books on these lists.

Book covers

Here is something for you to ponder. Of the three book covers that I know about that illustrate phylogenetic networks, the two by computational scientists have stylized "trees" with straight edges, such as one sees in graphs, while the one from a biologist has curved branches, such as one sees in nature. Who says that you can't judge a book by its cover?

Reviews of recent books

The first book to make an appearance that explicitly deals with phylogenetic networks was:

D. H. Huson, R. Rupp and C. Scornavacca (2011) Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press. [Dated 2010 but published January 17 2011] Available in hardback ISBN:978-0-521-75596-2 and as an eBook ISBN:978-0-511-92242-8.

In addition to the three reviews that appear as part of the publisher's blurb, a number of independent book reviews have appeared since its publication:

Tiratha Raj Singh (2011) Current Science 100: 1570-1571.

Paul Cull (2011) Computing Reviews Review#139416.

Steven Kelk (2012) Systematic Biology 61: 174-175.

Jim Whitfield (2012) Systematic Biology 61: 176-177.

These are all worth reading, but I wish to comment here on one particular review, the one by Steven Kelk. This review makes two points about current network methods that seem to me not to have been sufficiently emphasized in other publications. The review itself is thus an important contribution to the literature on phylogenetic networks.

(1) Rooted networks based on a "hybridization" model can be derived by combining clusters, triplets or trees. [Note: combining characters usually leads to a "recombination" model.] However, only by combining trees do the reticulation vertices in the resulting network explicitly model reticulate evolutionary events (e.g. hybridization or horizontal gene transfer); for clusters and triplets the reticulation vertices can be abstract. This has important practical consequences for biologists, who routinely interpret rooted networks as though all of the vertices (nodes) represent inferred ancestors undergoing "descent with modification" (as Charles Darwin called it). There has been insufficient attention paid to this point in the literature on cluster and triplet methods.

Note that this point does not deny any intrinsic mathematical interest in clusters and triplets (which Steven, himself, emphasizes in his own research work). Nor does it deny any possible use of them in practical network methods; indeed, I have seen them work quite well in practice. The point is simply that the tree model explicitly provides something that biologists find valuable, and which (I would argue) has been principally responsible for the widespread use of that model in phylogenetics. One can even argue that phylogenetic analysis is the inference of vertices in a tree/network. (If you look at Darwin’s only published tree you will note that it is the vertices of his tree that are missing, indicating his explicit doubt about the feasibility of inferring them.)

(2) Great attention has been paid in the literature to certain topologically restricted sub-families of rooted networks (such as galled networks, level-k networks, etc). These theoretical classes have been chosen because of concerns about computational tractability, rather than anything to do with the priorities of biological modeling. Unfortunately, little attention has been paid to how likely these networks are from the biological viewpoint. Perhaps the only other unequivocal publication on this topic is that of (M. Arenas, M. Patricio, D. Posada, G. Valiente. 2010. Characterization of phylogenetic networks with NetTest. BMC Bioinformatics 11: 268) More work needs to be done to address this uncertain applicability.

Steven's review appeared in Systematic Biology, which actually has a long tradition of original book reviews that are worth citing in formal research publications. For example, one of the more highly cited papers in the journal is the book review in which Don Colless published his tree-imbalance formula (D.H. Colless. [Review of] Phylogenetics: the Theory and Practice of Phylogenetic Systematics. Systematic Zoology 1982, 31:100-104), which receives continual citation because the formula is still commonly used today. Not everyone publishes original research in their book reviews!

Declaration of potential competing interest: I am currently the Book Review Editor for Systematic Biology, and so I am the one who commissioned Steven's review. However, I take no credit for the contents of the review! The numerous reviewers I have dealt with over the years have produced reviews that varied from excellent through mediocre to ones that needed extensive revision, and on to two that I wrote myself when the original reviewer failed to deliver.