Evolutionary processes (anagenesis and cladogenesis) produce a pattern
   phylogeny: the history of organismal evolution
      [cf. genealogy: the history of a single family]
   Diagrams of phylogeny resemble trees
      living species are the terminal twigs
      extinct species are the interior twigs
      genera, families, orders are successively older & more inclusive branches & limbs

Systematics: the science of organizing the history of organismal evolution
      science of ordering

   Identification: recognizing the place of an organisms in an existing classification
      E.g., use of dichotomous keys to identify organisms

   Taxonomy (Nomenclature): assigning scientific names according to legal rules
      E.g., use of ICZN Green Book in Zoology: Priority & Stability

   Classification: determining the evolutionary relationships of organisms
         A "Natural Classification" will accurately reflect phylogeny
            Classification should be a hypothesis of evolutionary relationships

      Alternative classifications are possible (and widely used): But
       An arbitrary classification cannot help us understand evolution
       Ex: If all 'marine mammals' combined in single Order,
                    implication that aquatic adaptations evolved only once
             If seals (Pinnipedia), toothed (Odontoceti), & baleen whales (Mysticeti) evolved separately,
                    understand differences in their physiology.

Traditional taxonomy emphasized analysis of similarity
Modern taxonomy (Phylogenetic Analysis) emphasizes cladistic ancestry
        Analysis of distribution of shared character states:
         Evolutionary Genetics provides protein & DNA sequence allelic variants

   Homologous characters 'similar' because of descent from common ancestor
      Therefore useful for classification
         bat wing vs. kangaroo arm: from Therapsid forelimb
         ostrich 'wing' vs. penguin 'wing': from Archeopteryx-like wing
       bat vs. bird forelimb from reptile forelimb (cf. analogous wing structures)

   INSIGHT: Homologous characters evolve over time =>
   ***Homologous characters need not look / function alike**
      Characters unchanged from ancestors: 'ancestral' or plesiomorphic
      Characters changed in descendants: 'derived' or apomorphic
          [Avoid 'primitive' and 'advanced': false connotations]

      Homologous characters of two types:
       Shared ancestral characters: similar to each other and ancestor
            'ordinary homologies': symplesiomorphic characters
                    Usual sense of 'homology" taught in introductory courses
               Ex.: scales in lizards & crocodiles evolved from Diapsida
       Shared derived characters: similar to each other & different from ancestor
             'special homologies': synapomorphic characters
              Ex.: carnassial pair (P⁴/M₁) a synapomorphy of Canidae & Felidae
                      derived from molariform teeth in Creodonta
 
       Characters unique to particular taxa: autapomorphic
         Ex.: wings in Chiroptera unique among mammals
         HOMEWORK: Are there such things as auto-plesiomorphic characters? Give an example.

   The nature of homology changes depending on the taxa under analysis
        Ex.: "Hair"
             Among turtle, lizard, bird, & cat:          unique character of Mammalia
             Among turtle, lizard, cat, & kangaroo: shared derived character of therian Synapsida
             Among kangaroo, bat, cat, & whale:    shared ancestral character of terrestrial non-cetaceans

       Also: wings an autapomorphy of the order Chiroptera [they evolved once]
             wings also a synapomorphy of suborders Mega- & Microchiroptera [they are related]

   Use of analogous characters lead to polyphyletic groups:
      loosely: groups that do not have a common ancestor
         [but everything has a common ancestor]
      Accurately: groups that do not include their common ancestor
       Ex.: Pinnipedia (marine carnivores) once thought polyphyletic
                    walruses & "eared" sea lions related to bears,
                    earless ("true") seals related to weasels
                    [This turns out not so]
         Polyphyletic groups often defined by "absence" characters
         Amphibia: scaleless tetrapods
                 Earliest terrestrial Tetrapoda (Devonian Amphibia) had scales
                 Modern Lissamphibia [salamanders (Caudata), frogs (Anura), & caecilians (Gymnophiona)
                        secondarily scaleless [adaptation for dermal respiration]
                        & possibly independent lineages
   Analogous characters & polyphyletic groups rejected as basis of taxonomy

   Use of homologous characters results in monophyletic groups:
      loosely, groups descended from single common ancestor
      accurately, groups that include common ancestor of group

   Use of shared ancestral characters results in paraphyletic groups:
      a monophyletic group that includes ancestor and
      some but not all of its descendants.
        Grade: group defined by combination of shared ancestral & derived characters
                    describes level of biological organization
   Ex.: among traditional taxonomic Classes of Vertebrata
          Agnatha: jawless descendants of first vertebrates
                  Comprises hagfish (Myxiniformes) & lampreys (Petromyzontiformes)
                         [jawlessness may be secondary adaptation for parasitism]
                  gnathostomous (jawed) relatives of Craniata (Chondrichthyes, "fish") not included
          Osteicthyes: fish with bony skeletons
                  amniotic relatives of Sarcopterygia (lungfish) not included
          Reptilia: scaly tetrapod descendants of first amniotes
                  feathery diapsid & furry synapsid relatives not included

Paraphyletic groups rejected in modern Phylogenetic Taxonomy ("Cladistics")

  Classification should reflect relationship only, not similarity
          Relationship determined objectively, e.g., by molecular methods
            Organismal similarity & differences to be explained

   Grades subjective & perpetuate evolutionary myths
           Which characters important?
            'Scaly' reptiles leftover after removal of 'feathery' birds & 'hairy' mammals
                  Why not take out "finny" Icthyosauria (marine reptiles)?
            "Reptiles & lungfish aren't variable. Their body plans limited evolutionary possibilities."
            "Dinosaurs more like reptiles than birds. Dinosaurs are reptiles."
            "Teeth in modern mammals evolved from toothless edentate or insectivorous ancestors."

   *** Grades not useful units for evolutionary analysis ***

    Ex.: Evolution of pagophilic (ice-breeding) behavior in phocid seals (Perry et al. 1995; Carr & Perry 1997)
       Phoca vitulina (harbor seals) breed on land,
                 other seals (e.g., Phoca groenlandica & Halichoerus grypus) breed & nurse young on ice
       Traditional taxonomy suggests ice-breeding has evolved several times:
                     Separate explanations for each pagophilic species required:
                     e.g., ice-breeding a polar bear avoidance behavior
       Phylogenetic taxonomy (supported by molecular analysis) suggests ice-breeding is ancestral:
         Phoca groenlandica a separate genus Pagophilus groenlandicus,
                     & more closely related to ice-breeding seals like Cystophora
                  => Phoca shows recent evolutionary shift to terrestrial breeding,
                     special explanations for ancestral pagophilic behavior not required

  Exclusive use of shared derived characters results in holophyletic groups:
      monophyletic group that includes the ancestor and all of its descendants
      Clade: group defined by shared derived character (s)
                  describes complete ancestor-descendant lineage

   Ex.: Among traditional Classes of Vertebrata
         * Placodermi: gnathostomes with hinged craniovertebral joint in skull [*extinct]
           Chondricthyes: gnathostomes with hyostylic jaw suspension
           Mammalia: cynodont therapsids with dentary-squamosal jaw suspension & hair
           Aves: Archosauria with feathers
           Saurischia: amniotes with diapsid skull includes both Mammalia & Aves

      Holophyletic groups (called Monophyletic) are accepted by cladistic taxonomy,

       Contrast traditional versus cladistic taxonomies of Primates
                      Hominidae (Homo) separated from Pongidae (Pan, Gorilla, Pongo) (Great Apes)
                        perceived similarity of Apes & assumed distinctiveness of Homo emphasized,
                            relationship of Pan & Homo obscured
           Versus Homininae groups Homo, Pan, & Gorilla 
                       Homo & Pan grouped as Homini (or Panini)
                            relationship emphasized
                            Does this obscure ape similarities?

Text material © 2022 by Steven M. Carr