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
      the science of ordering

   Identification: recognizing the place of an organisms in an existing classification
      Use of dichotomous keys to identify organisms

   Taxonomy (Nomenclature): assigning scientific names according to legal rules
      Recall discussion of ICZN Green Book (see also Phylocode homepage)

   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' are combined in a single order Cetacea,
                    this implies that aquatic adaptations have evolved only once.
                 If we understand that seals (Pinnipedia),
                    toothed whales (Odontoceti), & baleen whales (Mysticeti) evolved separately,
                    we will understand the differences in their physiology.

Traditional Taxonomy has emphasized analysis of similarity
Phylogenetic Analysis considers cladistic patterns of common ancestry
    Analysis of distribution of shared character states:
       Character: any morphological, molecular, behavioral, ecological, etc. attribute of an organism
       Character State: alternative forms of a Character [cf. "gene" and "allele"]
    Similarity of characters [character states] may occur for either of two reasons

   Analogous characters are 'similar' because of convergence from dissimilar ancestors
      These do not indicate common ancestry => not useful for classification
         bat wing vs. butterfly wing: embryologically dissimilar
       aquatic habit of whales and pinnipeds
         cow horn vs. deer antler: anatomically dissimilar
         legless lizard vs. snake: common ancestor had legs
       bat wing vs. bird wing: common ancestor was flightless reptile

   Homologous characters are 'similar' because of descent from common ancestor
      These are therefore useful for classification
         bat wing vs. kangaroo arm: from Therapsid forelimb
         ostrich 'wing' vs. penguin 'wing': from Archeopteryx-like wing
       bat forelimb vs. bird forelimb: from reptile forelimb

   Homologous characters will evolve over time =>
   Homologous characters need not look alike or function alike
      Characters that are unchanged from those of the ancestors
         are called 'ancestral' or plesiomorphic
      Characters that are changed in the descendants
         are called 'derived' or apomorphic
      [Avoid the terms 'primitive' and 'advanced': they have false connotations]

      Homologous characters are of two types:
       Shared ancestral characters: similar to each other, and to their ancestor
            also called 'ordinary homologies' or symplesiomorphic characters
                    This is the usual sense of 'homology" taught in introductory courses
               Ex.: scales in lizards & crocodiles are an inheritance from Diapsida
       Shared derived characters: similar to each other, and different from their ancestor
            also called 'special homologies' or synapomorphic characters
            Ex.: carnassial pair (P⁴/M₁) is a synapomorphy of dogs & cats
                      derived from molariform teeth in Creodonta
 
       Characters unique to particular taxa called autapomorphic characters
         Ex.: wings in Chiroptera are unique among mammals

   The nature of homology changes depending on the taxa under analysis
  Ex.: "Hair"
             Among turtle, lizard, bird, and cat:           a unique character of Mammalia
             Among turtle, lizard, cat, and kangaroo: a shared derived character of therian Synapsida
             Among kangaroo, bat, cat, and whale:    a 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 results in polyphyletic groups:
      loosely, groups that do not have a common ancestor
         [but everything has a common ancestor]
      accurately, groups that do not include the common ancestor of the group
       Ex.: Pinnipedia (marine carnivores) were once thought to be polyphyletic
                    walruses & 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 tetrapods (Devonian Amphibia) had scales
                 Modern Lissamphibia [salamanders (Caudata), frogs (Anura), & caecilians (Gymnophiona)
                        are secondarily scaleless [an adaptation for dermal respiration
                        & probably  independent lineages
        Edentata: toothless mammals
                    Jurassic mammals had teeth
                    anteaters (Xenarthra) and pangolins (Pholidota) secondarily toothless

   Polyphyletic groups are rejected by all modern taxonomists
         No 'evolutionary implications'
                 'edentate' [toothless] taxa evolved under distinct ecological conditions
       Ex.: "Insectivora" a  'garbage can'  taxon:
                any "primitive" insect-eating animal that doesn't fit elsewhere

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

   Monophyletic groups are of two kinds:

   Use of shared ancestral characters results in paraphyletic groups:
      a monophyletic group that includes ancestor and
      some but not all of its descendants. This creates a

      Grade: a group defined by a combination of shared ancestral & derived characters
         describes a level of biological organization

   Ex.: among traditional taxonomic Classes of Vertebrata
     Agnatha: jawless descendants of first vertebrates
             Comprises hagfish (Myxiniformes) & lampreys (Petromyzontiformes)
     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 accepted by traditional ("Evolutionary") taxonomists,
                                   rejected by 'Phylogenetic' taxonomists ("Cladists")

Note: Phylogenetic (Cladistic) taxonomy has replaced "traditional" taxonomy

Phylogenetic taxonomists make the following arguments

  Classification should reflect only relationship, not similarity
  Relationship can be determined objectively, e.g., by molecular methods
            Organismal similarity & differences are what we are trying to explain

   Grades are subjective
  Which character is more important?
            'Scaly' reptiles what's left when you take out 'feathery' birds & 'hairy' mammals
            Why not take out "finny" Icthyosauria (marine reptiles)?

   Grades perpetuate biological & evolutionary myths     
            "Reptiles & lungfish aren't variable.
                Their body plans limited evolutionary possibilities."
            "Dinosaurs more like reptiles than birds."
            "Teeth in modern mammals evolved from edentate ancestors."

   *** Grades are 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 behaviour
       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 behaviour 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 one or more shared derived characters
                  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 a diapsid skull includes both Mammalia & Aves

      Holophyletic groups are accepted by all modern taxonomists,
         'Phylogenetic' taxonomists use them exclusively [but don't like the term]
         'Traditional' taxonomists regard reliance solely on clades as misguided

Evolutionary taxonomists make the following arguments:

   Classification should reflect similarity as well as ancestry
        E.g., Commonly understood that turtles, lizards, & crocodiles are more similar than different,
                    and quite distinct from birds
       [Is this true? Depends on the features examined]

    Clades obscure biological distinctiveness
       Inclusion of Birds as Dinosauria obscures their differences
                Are they that different? Note hip structure & bipedalism
                Since "Jurassic Park": dinosaurs are "more like" birds: NOT

   Clades overemphasize minor differences
               Classification of amniotes by temporal openings "over-splits" group
               Are these differences so minor?

   Classification by clade leads to unfamiliar names
       Gnathostomata, Amniota, Sauropsida, etc.
                    But these correspond to major evolutionary innovations:
                        Jaws, amniotic egg, & water-impermeable skin
       "Need to Name" every branch leads to proliferation of categories
                (legion, tribe, cohort, etc.)
                    & prefixes (super-, sub-, infra-)
                    & suffixes (-oidea, -idae, -inae, -ini)
                        for superfamilies, families, subfamilies, tribes, respectively
                    Is this necessarily bad?

       Ex.: In the traditional taxonomy of Primates
                      Hominidae (Homo) separated from Pongidae (Pan, Gorilla, Pongo) (great apes)
                       => perceived similarity of apes & distinctiveness of Homo emphasized,
                            relationship of Pan & Homo obscured
               In a cladistic taxonomy of Primates
                       Homo, Pan, & Gorilla grouped as Homininae
                      Homo & Pan grouped as Homini (or Panini)
                       relationship emphasized
               Does this obscure ape similarities?

Text material © 2020 by Steven M. Carr