© Draft materials. Do not circulate. Page 1 Rooting'and'outgroups'!Rooted!trees!contain!information!about!the!flow!of!time,!which!allows!them!to!tell!us!about!recency!of!common!ancestry!(monophyly)!and!the!direction!of!trait!evolution.!!Rooted!trees!are!therefore!essential!for!most!downstream!uses!of!phylogenies,!from!classification!to!studies!of!adaptation.!!However,!most!methods!of!phylogenetic!inference!do!not!directly!yield!rooted!trees,!but!unrooted!trees.!!While!you!can!read!much!of!the!secondary!phylogenetic!literature!only!understanding!rooted!trees,!it!is!essential!to!understand!unrooted!trees!(and!how!they!are!rooted)!if!you!plan!to!be!engaged!in!phylogenetic!research!or!if!you!want!to!be!able!to!critically!read!the!primary!phylogenetic!literature.!!At!one!level!rooting!is!simple:!there!are!just!a!handful!of!ways!to!root!trees!and!these!all!have!a!sound!logical!basis.!!Nonetheless,!perhaps!because!rooting!requires!a!certain!level!of!mental!gymnastics,!I!have!observed!that!even!professional!biologists!have!been!known!to!stumble!over!unrooted!trees!and!to!over‐interpret!rooted!trees.!!Therefore,!I!start!by!introducing!unrooted!trees!and!then!list!the!three!main!methods!for!converting!them!into!rooted!trees.!!I!end!by!visiting!some!of!the!common!mistakes!made!that!relate!to!rooting!and!provide!guidelines!as!to!how!to!avoid!these!errors.!!The'information'content'of'unrooted'trees!!An!unrooted!tree!is!simply!a!tree!that!lacks!a!defined!root.!!In!an!unrooted!tree!the!lines!represent!evolutionary!lineages,!but!unlike!a!rooted!tree,!we!do!not!know!which!way!evolution!preceded!along!the!lineage.!!Because!a!clade!is!an!ancestor!and!all!its!descendants!we!need!temporal!information!to!identify!clades.!!Thus,!the!internal!branches!of!an!unrooted!tree!do!not!define!clades!but!rather!split!the!taxa!into!two!sets!that!are!attached!(directly!or!indirectly)!to!the!two!ends!of!the!branch.!!Let’s!work!through!this.!!Start!by!considering!a!rooted!tree,!such!as!that!shown!for!select!Archosaurs.!After!removing!the!root!from!this!rooted!tree!it!is!possible!to!redraw!the!unrooted!tree!in!several!different!formats.!© Draft materials. Do not circulate. Page 2 !The!first!unrooted!tree!in!this!example!maintains!the!general!shape!of!the!rooted!tree!except!for!an!apparent!polytomy!in!the!position!that!used!to!correspond!to!the!root.!!Actually!this!is!not!a!polytomy,!just!the!correct!way!to!draw!this!unrooted!tree!when!the!root!node!has!been!removed.!!This!can!be!seen!because!the!third!tree!has!been!spread!out!to!avoid!even!an!impression!of!a!root.!!The!tree!is!binary!in!that!each!node!has!three!branches!–!one!corresponding!to!the!ancestral!lineage!and!two!to!descendent!lineages!(although!the!figure!doesn’t!specify!which!are!ancestral!and!which!derived).!!If!you!find!it!hard!to!see!that!the!second!and!third!trees!are!identical!in!content,!there!are!three!ways!to!proceed.!!!!(1)!You!could!use!mental!gymnastics!to!visualize!the!changes!in!shape!needed!to!get!from!one!tree!to!another.!!You!should!imagine!that!the!trees!are!made!of!string!(that!can!bend!or!change!length)!and!ask!yourself!whether!you!could!rearrange!the!second!tree!to!yield!the!third!without!having!to!cut!the!string!(the!answer!is!yes).!!!!!!(2)!You!could!list!the!tips!that!are!attached!to!each!node!and!see!if!the!same!set!of!nodes!are!present!in!each!case.!!The!table!lists!all!11!nodes!and!their!connected!tips.!!Because!the!list!is!the!same!for!both!unrooted!trees!(and!the!rooted!tree),!they!are!the!same.!!Bran ch!1!Bran ch!2!Bran ch!3!Stegosaurus!Ankylosau rus!Diplodocus,!Allosaurus,!Tyrannosaurus,!Veloci raptor,!Archaeopteryx,!Ostrich,!Rob in,!Rooted Unrooted Unrooted© Draft materials. Do not circulate. Page 3 Pterosaur,! Crocodile,!T ricerotops,!Iguanodon!Trice rotops!Iguanodon!Diplodocus,!Allosaurus,!Tyrannosaurus,!Veloci raptor,!Archaeopteryx,!Ostrich,!Rob in,!Pterosaur,! Crocodile,!Stegosaurus,!Ankylosau rus!Trice rotops,!Iguanodon!Stegosaurus,!Akylosaurus!Diplodocus,!Allosaurus,!Tyrannosaurus,!Veloci raptor,!Archaeopteryx,!Ostrich,!Rob in,!Pterosaur,! Crocodile!Pterosaur!Crocodile!Diplodocus,!Allosaurus,!Tyrannosaurus!Velociraptor,!Archaeopteryx,!Ostrich,!Robin,!Stegosaurus,!Akylosaurus,!Trice rotops,!Iguanodon!Pterosaur,! Crocodile!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon!Diplodocus,!Allosaurus,!Tyrannosaurus,!Veloci raptor,!Archaeopteryx,!Ostrich,!Rob in!Diplodocus!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile!Allosaurus ,!Tyrannosa urus,!Velociraptor,!Archaeopteryx,!Ostrich,!Robin!Allosaurus !Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile,!Diplodocus!Tyrannosaurus,!Veloci raptor,!Archaeopteryx,!Ostrich,!Rob in!Tyrannosaurus!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile,!Diplodocus,!Allosaurus!Velociraptor,!Archaeopteryx,!Ostrich,!Robin!Velociraptor!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile,!Diplodocus,!Allosaurus,!Tyrannosaurus!Archaeopteryx,!Ostrich,!Rob in!Archaeopteryx!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile,!Diplodocus,!Allosaurus,!Tyrannosaurus,!Velociraptor!Ostri ch,!Ro bin!Ostri ch!Robin!Stegosaurus,!Akylosaurus,!Tricerotops,!© Draft materials. Do not circulate. Page 4 Iguanodon,!Pterosaurus,!Crocodile,!Diplodocus,!Allosaurus,!Tyrannosaurus,!Veloci raptor,!Archaepteryx!!(3)!You!could!list!the!sets!of!taxa!separated! by!each!internal!branch,!the!set!of!splits.!!For!example,!one!internal!branch!(shown!to!the! right)!divides!Stegosaurus,!Akylosaurus,!Tricerotops,!Iguanodon,!Pterosaurus,!Crocodile!on!the!one!side!from!Diplodocus,!Allosaurus,!Tyrannosaurus,!Velociraptor,!Archaeopteryx,!Ostrich!and!Robin,!on!the! other.!!Because!there!are!an!odd!number!of!taxa!in! this!case,!we!can!define!each!split!by!just!listing!the!smaller!of!the!two!sets!of!taxa.!!Thus,!you!should!be!able!to!see!that!both!trees!are!composed!of!the!following!splits:!Stegosaurus,!Ankylosaurus!Iguanodon,!Triceroto ps!Stegosaurus,!Ankylosaurus,!Iguan odon,!Tricerotops!Pterosaur,!Crocodile!Stegosaurus,!Ankylosaurus,!Iguan odon,!Tricerotops,!Pterosaur,!Crocodile!Allosaurus,!Tyrannosaurus,!Velocirapt or,!Archaeopteryx,!Ostrich,!Robin!Tyrannosaurus,!Velociraptor,! Archaeopteryx,!O strich,!Robin!Velocira ptor,!Arc haeopteryx,!Ostrich,!Robin!Archaeopter yx,!Ostrich,!R obin