• I. The Science Of Classification
• II. Working principles for constructing a phylogeny
• III. The challenge of reconstructing mammalian phylogenies
• IV. Tutorials and other relevant links

Systematics

How we make sense out of the whole group?
How do we decide what organisms to group together?

I. The Science Of Classification

1. Earliest approaches were simply to give everything a name.

   taxonomy=the science of naming and classifying organisms

   1. Common criteria for classifying
      1. Ways of life (aquatic, terrestrial, volant)
      2. Environmental adaptations (hooves, flippers, wings)
      3. Morphological traits (hierarchy based on shared structural features)

   2. Lower levels: widely shared features
      

   3. Higher levels: more unique features (eg, species specific)
      
      Simpson ( The principles of classification and a classification of mammals , 1945): A classification scheme for Eutherians

   Unguiculata	share many primitive features, evolutionarily ancient, diverse specializations	insectivores, bats, primates, dermopterans, edentates, etc.
   Glires		rodents, lagomorphs
   Mutica	aquatic	cetaceans
   Ferungulata		carnivores, aardvark, elephants, hyraxes, sirenians, perissodactyls and artiodactyls

   
   
   
2. Problems with this type of approach: Similarities among organisms can occur for a variety of reasons.
   • homology (shared traits are inherited from a recent shared ancestor; the two taxa share a common ancestor that also possesed the trait)
   • convergence (shared traits are independently derived; the most recent common ancestor lacked the trait)

3. A major development in classification was the use of evolution as the basis for the structure of the hierarchy.
   1. Species grouped together have more recent common ancestor
   2. Shared characteristics are explained on the basis of shared evolutionary history (homology)

4. The field is now called systematics or phylogenetics.

   systematics= the scientific study of the kinds and diversity of organisms and of any and all relationships among them

   phylogenetics=systematics, with the organizing principle being evolution

   1. Phylogeny
      1. Definition: A series of relationships between species; inferred based on their shared and unique characteristics; also called a tree
      2. Describes a series of evolutionary changes
      3. Branching points (nodes) are common ancestors
      4. "Trunk" is the common ancestor for the whole group
      5. "Leaves" are individual taxa
      6. Groups that are most closely related to each other are sister taxa
      7. Represents a monophyletic group, rather than a paraphyletic or polyphyletic group

   2. What kind of characters do we use to construct the tree?
      1. Choice of characters affects shape of tree
      2. Homologous traits are useful, convergent traits are not

   3. Types of characters that can be used
      1. Morphology e.g., skeletal features, soft tissue features)
      2. Molecules (e.g. proteins or DNA)

II. Working principles for constructing a phylogeny

1. No two species are identical

2. Common origin

3. Location of branching points approximates how long ago divergence occurred

4. Principle of conservation
   1. Definition: The degree of relatedness (and therefore how recent the time of divergence) is proportional to the number of shared homologous characters.
   2. Corollary: Widely shared traits are likely to be ancestral eg, mammary glands

5. Principle of irreversibility : Once specialized, a morphological structure doesn't wholly return to a markedly different ancestral condition.

	hair?	milk?	lay eggs?	livebearing?	placenta?
platypus	x	x	x
echidna	x	x	x
opossum	x	x		x
cat	x	x		x	x
elephant	x	x		x	x

6. Two basic ways to apply these rules
   1. Phenetics: based on overall similarity
      Used by Linnaeus and many, many others
      
      

   2. Cladistics: based on shared derived traits (synapomorphies)
      Devised by Willi Hennig (1956, 1966)
      

7. Major recent developments
   1. Use of molecular data
   2. Development of strict mathematical rules for constructing trees and for choosing amongst different trees
   3. Use of powerful computers has made it possible to increase both the number of characteristics being used and the number of species included in the analysis

   Think - Pair - Share

   
   
   
8. What kind of data should we use to construct mammalian phylogenies?
   
   
   1. Morphological data

      Advantages

      • Can get estimates of the time of divergence of lineages using fossil data and C14 dating
      • enables us to understand the morphology and ecology of extinct, ancestral species (or at least speculate about it)

      Disadvantages

      • Morphological characteristics are more likely to be convergent
      • Patterns of inheritance of morphological traits not always clear
      • The fossil record is spotty due to the scarcity of fossils in some environments and for small bodied species
      • There are less data to use
      • Different character states sometime hard to differentiate (subjective and arbitrary) except in the case of presence/absence of a trait
      
      
      
   2. Molecular data

      Advantages

      • There's more of it!
      • Patterns of inheritance are straightforward
      • Molecular traits are less susceptible to convergence because (1) the genetic code is redundant (there are multiple ways to get the same result, so phenotypic traits that appear identical may have different genetic bases (2) much of the genome consists of non-coding DNA that is not subject to natural selection, and (3) many regions of DNA are selectively neutral and not subject to natural selection
      • The number of potential point mutation differences between species is likely to be very large, so even if there are independent identical mutations (i.e., convergence in DNA sequence), those will be outweighed by the number of dissimilar mutations
      • The number of mutations can be used to measure time because we can calculate a rate of mutation. This allows us to estimate time of divergence for different lineages, even in the absence of fossil data.

      Disadvantages

      • Different character states are usually easy to measure (but alignment is a complicating issue...)
      • Provides no information about what extinct species were like, in terms of their morphology and ecology
      
      
      
   3. Mix and match?

      Advantages

      • More data points (use all available information)

      Disadvantages

      • If any of your data are correlated, then those data may have a disproportionate influence over the results (this is termed pseudoreplication)

III. The challenge of reconstructing mammalian phylogenies

1. Problems
   1. More than 4,000 mammalian species
   2. Many orders whose relationships need to be figured out (~26)
   3. Some orders are speciose (e.g., rodents and bats) while others consist of very small numbers of species (e.g., Tubulidentata)
   4. ~10²⁸ different possible trees but only one is correct

2. First attempts to reconstruct mammalian phylogeny led to "bushy" trees because
   • Speciation happened very rapidly ~65 MYA, also called the "Garden of Eden" hypothesis (the explanation favored by morphologists) OR
   • Data available at that time were inadequate to create a more refined tree (the explanation favored by geneticists)

3. Later attempts (2001-2003) using molecular data produce more refined trees, but the trees vary widely
   • Murphy et. al (2001)
     Used 16.4 kilobase sequence of molecular data (19 nuclear and 3 mitochondrial genes)
     Notable features:
     • Basal split is between Afrotheria and all the rest (this split corresponds with when the African continent separated from South America)
     • Splits the old order Insectivora into separate orders (meaning the former Insectivora was polyphyletic)
     • Moves Chiroptera (but recognizes it as monophyletic)
     • Cetacea and Artiodactyla as sister taxa
     • Carnivora and Pholidota as sister taxa

   • Liu et al (2001) supertree
     Uses information from trees derived from molecular and morphological data
     Notable features:
     • Basal split is between Xenarthra (sloths, anteaters, armadillos) and everything else
     • Insectivora is monophyletic

   • Madsen et al (2001)
     Notable features:
     • Pholidota groups with insectivores and bats
     • Groups Xenarthra (sloths, anteaters, armadillos) with Afrotheria

   • Madsen et al (2002)
     Uses a single nuclear gene (1,175 base pairs)
     Notable features:
     • Basal split is between Xenarthra and everything else
     • Groups hedgehogs with Artiodactyla/Cetacea
     • Groups Lagomorpha with Scandentia

   • Aranson et al (2002)
     Uses mitochondrial DNA (9.882 kilobase sequence)
     Notable features:
     • Basal split is between hedgehogs and everything else
     • Groups Xenarthra with Sirenia/Proboscidea/Tubulidentata etc. (i.e. "Afrotheria")
     • Splits Lagomorpha and Rodentia

V. Tutorials and other relevant links

• Glossary of phylogenetic terms from University of California at Berkeley
• A cladistics tutorial from University of California at Berkeley
• The Tree of Life, depicting the diversity and phylogenetic history of life, from University of Arizona