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.
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.
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
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