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18 Birder's Guide to Listing & Taxonomy | October 2015 Introduction to Phylogenies answer at this point. This is because their thought process is bumping into the num- ber two reason for incorrect responses to questions like this: they count the number of nodes they had to cross to connect the two taxa, thinking that fewer nodes equals closer relationships. But, and I'm sure you know what's coming here, the number of nodes between taxa is completely useless to tell us how closely related they are! The number of nodes between taxa is dependent only on what taxa are included in the tree. So, instead of looking at the closest taxon in the linear order or the number of nodes connecting taxa, what do we need to look at to answer our question about Species 2? How far back in time you must go to con- nect the two taxa! Remember that the phy- logeny is tracing relationships of taxa back through time. The longer ago taxa shared a common ancestor, the less related they are (i.e., the further away the node connecting two taxa is from the tips of the tree, the less related they are). Returning to our exam- ple, which traced line went furthest back in time on the phylogeny? The line con- necting Species 2 and Species 1! Thus, Species 2 and Species 7 share a more recent common ancestor and are more closely related. Voilà! Now you can read a phylog- eny! Well, okay, perhaps it will take a bit more practice, but now you know the basic procedure for interpreting the evolutionary relationships among taxa in a phylogeny: look only for the most recent common ancestor (i.e., node) connecting taxa, ignoring linear order and the number of nodes connecting taxa. And if you ever trace connections as above and fnd that the lines go an equal distance back in time, then you know that the taxon of interest is related equally to the taxa you connected it to (e.g., Species 2 is related equally to Spe- cies 3 and Species 7). How do phylogenies affect taxonomy? Okay, so what? What do these phylog- enies have to do with all the splits and lumps (particularly splits these days!) handed down by checklist committees, not to mention the seemingly ever- changing taxonomic order of species in most feld guides? Quite a lot! More than any other line of evidence—such as behav- ior, morphology, vocalizations, or ecology— I think it's safe to say that genes (and the phylogenies constructed from their DNA sequences) currently dominate taxonomic decision-making. But to connect phylog- enies to taxonomy, I need to introduce two concepts that are extremely important in the process: monophyly and paraphyly. A monophyletic group of taxa (also known as a clade) comprises a common ancestor and all of its descendants, whereas a paraphy- letic group is a common ancestor and only some of its descendants (Figure 3). As a general rule, avian taxonomists will make changes that eliminate paraphyletic taxa. This approach applies to all taxa, from species to orders. The genus of Calliope Hummingbird provides an excellent exam- ple of a decision that converted an instance of paraphyly to monophyly. Calliope Hum- mingbird previously was placed in its own genus, Stellula, but is now in Selasphorus. The impetus for this taxonomic change was a study that showed Calliope to be phylo- genetically embedded within all of the Se- lasphorus species (Figure 4), thus rendering Selasphorus paraphyletic (the group did not include all the descendants of its common ancestor) (McGuire et al., 2007, 2009). An- other way to describe it is that some spe- cies in Selasphorus were shown to be more closely related to Calliope than to other Se- lasphorus species. Amazingly, a more recent study with better sampling supports Allen's Hummingbird being more closely related to Calliope than to Rufous (McGuire et al. 2014)! Thus, if the taxonomy were not changed, we'd be left with the awkwardly correct statement that Selasphorus is more closely related to Stellula than to Selaspho- rus. You can probably see why paraphyly can start offending the sensibilities of picky, detail-oriented folks, which taxonomists tend to be! To avoid such an unforgivable offense, Calliope became a Selasphorus, re- storing monophyly to the avian realm (well, this one small corner of it at least). Although the Calliope example concerns a genus change, the same thought process is what infuences many species-level splits and lumps (i.e., the ones that affect our life Common ancestor of paraphyletic taxon W Common ancestor of monophyletic taxon Z W 1 W 2 X W 3 Y Z 1 Z 2 Z 3 ships can be presented with very different linear orders because every node in a phy- logeny can be rotated without changing the results (Figure 2). If you can learn to ignore the linear arrangement of taxa in a phylog- eny, then you'll be in great shape! Instead of looking at what taxa are found nearest each other in the linear order, fo- cus on connecting taxa via branches and nodes only. Early on, it often helps to trace the branches between two taxa of interest with a pencil until you train your eyes to automatically do the same thing. So let's re- turn to the earlier question about the closer relative of Species 2 and trace some lines in Figure 1. First, taking the shortest route possible via branches in the phylogeny, connect Species 2 to Species 1; then repeat the process with a different colored writing tool for Species 2 and Species 7. Have you changed your answer to the question yet? Many of my students that gave a wrong an- swer at frst still will not have changed their Figure 3. A phylogeny illustrating the concepts of paraphyly and monophyly. Taxon W comprises the most recent common ancestor of its extant popula- tions (W 1, W2, W3) but only some of that ancestor's descendants (i.e., W does not include Taxon X, although X is a descendant of W's common ances- tor), rendering W paraphyletic. Taxon Z comprises its common ancestor and all of that ancestor's descendants, making Z monophyletic.