Long Branches and Their Biological Meaning
An avowed objective of conservation is the maintenance of maximum evolutionary potential (Avise 2005). But as it is not feasible to confidently predict which lineages will be successful in the future, not least because much that happens in biology is subject to stochasticism. Retaining maximum evolutionary history might be an alternative and better, or at least achievable strategy. In this context, taxa at the tips of long branches attract special attention although a similar level of investment in representatives of speciose clades is also required to conserve the history represented by those lineages too.
On the face of it taxa on long branches appear to represent long evolutionary history. But what is a long branch and what information does it carry (or not carry) about the past?
Long branches on phylogenetic trees result from one of three processes:
1. The lineage might have evolved without lineage splitting increasing species diversity. This would involve each new species replaces its immediate ancestor in succession.
2. The branch/lineage experienced an accelerated rate of molecular evolution in relation to all others, at the locus providing the (presumed) phylogenetic signal.
3. The clade that includes the taxon in question has been extensively pruned so that near relatives have been removed.
Processes 1 and 2 could in themselves constitute evidence of distinctive unusual evolutionary mechanisms that demand conservation; however this would depend on verification. For 1, a detailed fossil record would be required to refute the alternative and more likely hypothesis that the lineage evolved via lineage splitting (Gould and Eldredge 1993) but has been subject to extinction (as in 3) (Vaux et al. 2015). For 2, analysis of other gene sequences would be needed to identify if rate variation was consistent across the genome or was due to gene-specific positive selection. If rate variation is locus-specific it is highly likely that resulting data are not tree-like, and hence phylogenetically misleading though interesting in other ways.
Process 3 can be further subdivided by the cause of the deficiency of closely related taxa. The absence of close relatives could result simply from experimental failure to sample extant species that are more closely related, or might represent extinction of other members of the clade at any time in the past. These alternatives can be readily tested by inclusion of all plausible extant relatives in phylogenetic analyses. Where a “clade” is truly represented by a singleton (i.e. no closer relatives exist on the planet), then the sister group corollary has to be considered. Every lineage exists as a sister to another lineage or clade so that taxa at the tips of long branches are not intrinsically more important in evolutionary terms than those on short branches. This can be readily demonstrated by the simple expedient of pruning an existing data set (Fig. 1a).
The role of variation in rates of molecular evolution in producing long branches can be determined from the underlying data. In ideal circumstances, if phylogenetic reconstruction has used appropriate models of DNA evolution and informative outgroups, trees with long branches resulting from rate acceleration are expected to look quite different from those that simply lack near relatives (Fig. 1b). Phylogenetic trees inferred from molecular data use sampling at time zero (the present) so it is expected that sequences will change subject to some local rate variation around a mean for a given taxon group, gene etc. with a relatively small variance (see Bromham and Penny 2003). Thus, typically, a phylogeny that is subject to local rate variation will appear unbalanced; branch tips will not be adjacent or nearly so (Fig. 1b). An obvious situation in which local branch rate might result in a long branch and/or phylogenetic misplacement of the node, exists when genes used for tree estimation are under positive/diversifying selection in some taxa, but are constrained in others.
The relative length of a branch in a phylogenetic tree might be used to direct conservation strategy in three distinct ways.
1. Species on long naked branches in phylogenies that include the appropriate sample of extant taxa can be taken as important representation of groups that were once more diverse, and that represent evolutionary potential that is different from the sister clade.
2. Species on long branches for which there is phylogenetic evidence of lineage specific acceleration of molecular evolution can be taken as representing interesting genomes with unusual genetic properties. A long branch of this type might result from genome-wide rate increase (compared to sister group) or locusspecific effects and represent specific adaptive traits.
Fig. 1 Phylogenetic trees illustrate the evolutionary relationships of species. a Influence of sampling on apparent cladogenesis. Pruning branches (grey) from the top phylogeny results in an apparent long branch for the remaining clade singleton (bottom). b Long branches where (top) unbalanced branch lengths result from different rates of molecular evolution at the gene used to make the tree (or wrong outgroup), and (bottom) equal rates of molecular evolution but different rates of speciation
3. Taxa on short branches nested within a clade, but accompanied by other character information on their distinctiveness (morphology, behaviour, habitat type) could be important representatives of evolutionarily innovative lineages.
For large organisms such as birds and mammals and many plant groups it is relatively easy to know how complete is taxon sampling amongst extant biota. In most cases existing taxonomy and checklists provide strong indicators. However, for smaller organisms, classification is often incomplete, taxa are not described and there are many instances of misclassification because character analysis has been lacking. Thus the significance of branch length is tempered by other information and the most phylogenetically diverse types of life on earth are severely under-represented.