Clans, clades and unrooted trees

A few years back, Mark Wilkinson at The Natural History Museum, London came up with the idea that we should really have a more precise language for groups that we can see on unrooted trees.

The problem stemmed from the fact that on an unrooted tree a clade is not defined.

A clade is a monophyletic group, a collection of organisms or taxa that can trace their roots to a single common ancestor.

Naturally this means that we have clades within clades within clades.

All cellular life might be considered a clade, but this seems a little trivial and uninformative.

We generally think that a clade should be defined in some way.  The most usual definition is that all members of a clade might share a 'uniquely derived' character or feature.  They would have what we call a synapomorphy for that feature - all members of the clade would have this feature and those organisms that lacked the feature could not be members of that clade.  Vertebrates, for instance, all have vertebrae and we consider that vertebrates all form a single clade.  Strawberries are not vertebrates, in part, because they lack vertebrae (also we might imagine there are other reasons).

However, one point to make is that a clade can really only be defined on a rooted phylogenetic tree. An unrooted tree cannot have clades because the direction of evolution is not defined.

A 'clan'

Therefore, Mark proposed that we use the word 'clan' in order to identify a group on an unrooted tree that might - given some particular rooting - be a clade if the tree was rooted.  Essentially a clan is defined by a split on the unrooted tree, as long as we ignore the trivial splits that separate the terminal taxa from the rest of the tree.

Then we had the issue of what to call the unrooted equivalent of a sister-group.  We settled on 'adjacent group', which seemed sensible.

So far there have been no objections to this new terminology and in fact it seems to have caught on a little.  At the end of this blog post I will put a few manuscripts that have explored this terminology a little further.

Please leave a comment.

 

 

Reference:

Of clades and clans: terms for phylogenetic relationships in unrooted trees Wilkinson Mark ; McInerney James O. ; Hirt Robert P. Foster, Peter G ; Embley T. Martin TRENDS IN ECOLOGY & EVOLUTION  Volume: 22   Issue: 3   Pages: 114-115   DOI: 10.1016/j.tree.2007.01.002   Published: MAR 2007

http://www.ncbi.nlm.nih.gov/pubmed/17239486

 

clan

Some further reading:

Of woods and webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli Beauregard-Racine Julie; Bicep Cedric; Schliep Klaus; et al. BIOLOGY DIRECT  Volume: 6     Article Number: 39   DOI: 10.1186/1745-6150-6-39   Published: JUL 20 2011

Telling the whole story in a 10,000-genome world Beiko Robert G. BIOLOGY DIRECT  Volume: 6     Article Number: 34   DOI: 10.1186/1745-6150-6-34   Published: JUN 30 2011

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe Triponez Y.;Buerki S.; Borer M.; et al. MOLECULAR ECOLOGY  Volume: 20   Issue: 11   Pages: 2442-2463   DOI: 10.1111/j.1365-294X.2011.05096.x   Published: JUN 2011

Clades, clans, and reciprocal monophyly under neutral evolutionary models Zhu Sha; Degnan James H.; Steel Mike THEORETICAL POPULATION BIOLOGY  Volume: 79   Issue: 4   Pages: 220-227   DOI: 10.1016/j.tpb.2011.03.002   Published: JUN 2011

Characterization of a regulatory unit that controls melanization and affects longevity of mosquitoes An Chunju; Budd Aidan; Kanost Michael R.; et al. CELLULAR AND MOLECULAR LIFE SCIENCES  Volume: 68   Issue: 11   Pages: 1929-1939   DOI: 10.1007/s00018-010-0543-z   Published: JUN 2011

Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees Schliep Klaus; Lopez Philippe; Lapointe Francois-Joseph; et al. MOLECULAR BIOLOGY AND EVOLUTION  Volume: 28   Issue: 4   Pages: 1393-1405   DOI: 10.1093/molbev/msq323   Published: APR 2011

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi Slot Jason C.; Rokas Antonis CURRENT BIOLOGY  Volume: 21   Issue: 2   Pages: 134-139   DOI: 10.1016/j.cub.2010.12.020   Published: JAN 25 2011

Evolution of Patchily Distributed Proteins Shared between Eukaryotes and Prokaryotes: Dictyostelium as a Case Study Andersson Jan O. JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY  Volume: 20   Issue: 2   Pages: 83-95   DOI: 10.1159/000324505   Published: 2011

On the need for integrative phylogenomics, and some steps toward its creation Bapteste Eric; Burian Richard M. BIOLOGY & PHILOSOPHY  Volume: 25   Issue: 4   Pages: 711-736   DOI: 10.1007/s10539-010-9218-2   Published: SEP 2010

Mitochondrial DNA variation in Arctic charr (Salvelinus alpinus (L.)) morphs from Loch Rannoch, Scotland: evidence for allopatric and peripatric divergence Verspoor E.; Knox D.; Greer R.; et al. HYDROBIOLOGIA  Volume: 650   Issue: 1   Pages: 117-131   DOI: 10.1007/s10750-010-0106-1   Published: AUG 2010

 

James McInerney
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