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Phylogeny and Classification


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Phylogeny = Pattern of evolutionary history among species
Phylo- from phylum (Greek – tribe) and –genetic (from origin or genesis)
taxon (plural – taxa) - taxonomic group at any hierarchical level (could be a species,
genus, family, etc.)
Phylogenetic classification
Phylogenetic classification = hierarchical ordering of taxa according to phylogenetic
relationships consisting of a nested set of ever more inclusive groups. A more explicit
term than “natural” classification.
Phylogenetic reconstruction
Phylogeny reconstruction (cladistics) – the process by which we determine
relationships (from the present diversity to the pattern of evolutionary relationships)
Phylogenetic tree
Phylogenetic tree. Diagram show phylogenetic relations ships. The tips of the branches represent taxa living today.
Existing (vs. Extinct) - the tips of the branches
Shared derived similarity. Character states that have arisen in the ancestor of the group and are present in all of its members.
Example: Feathers on birds - these evolved at the time birds first appeared
Shared ancestral similarity
Example: keratin scales on reptiles - these are transformed into feathers in birds
In these examples, feathers are evidence of monophyly in birds, but scales are NOT
evidence of monophyly in reptiles.
Convergent similarity - similarity due to evolution in parallel in two different
organisms – convergent evolution
Example: wings on birds and bats - another term for this is Parallel evolution
Monophyletic group
Monophyletic group - a group of spp. that includes an ancestral sp. and all of its
descendants (identified by synapomorphies = homologies)
Paraphyletic group
Paraphyletic group - ancestor and some, but not all, descendants
Polyphyletic group
Polyphyletic group - a group of spp. in which the common ancestor does not belong to
the group
shared derived -->
shared ancestral -->
convergent -->
shared derived --> monophyly
shared ancestral --> paraphyly
convergent --> polyphyly
Similarities such as flower color
a character that arose with the evolution of the group and is shared
due to common ancestry. similarity in two or more organisms that can be traced back to the same
feature in the common ancestor of those organisms.
Example: wings on birds, also wings on bats, but NOT wings on birds AND bats
The different forms a character can take, such as different flower colors.
Monophyletic group
Polarity (= evolutionary direction)
Name 5 ways to assess polarity that are problematic and explain
1) fossil record - oldest is ancestral (primitive)
- works sometimes, but fossil record is notoriously incomplete!
e.g., simple leaves  compound leaves
2) simple to complex - evolutionary trends tend to be parallel between groups
- enough reversals that this is not reliable (evolution often ‘streamlines’
e.g., cave fish, parasitic plants
3) correlation - primitive states tend to occur together in organisms, or, if organism
has many derived characters, chances are, it has other derived characters.
- not always true, retention of ancestral characters is common.
4) common is primitive - ingroup analysis
- key innovation can make derived state more common than ancestral state
e.g., perennial habit in Castilleja – draw tree
5) Ontogeny - developmentally early stages are primitive, developmentally later
stages are derived.
- similar problems as ‘simple to complex’…evolution can do crazy things…
e.g., tails in tadpoles and juvenile fish – tails are primitive state. However,
some salamanders mature in the juvenile state…so tailed adults are the
derived condition!
The most useful tool for determining polarity and how it works
Outgroup comparison - inference from distribution of character states in sister
group. This is most commonly used approach today
- *requires related group/sp. for comparison
Outgroup, Ingroup, and Sister group
Ingroup - study group (putatively monophyletic)
Sister group - closest outgroup - special case of outgroup
Classification - the sorting of things into groups and the assigning of names to those
Classification – (for biology) The grouping of organisms into categories based on shared
characteristics or traits. the way we communicate about biological diversity
Historical source and methodology for current scientific classification
Greeks, based on morphology
Explain the Linneaus classification system
Linnaeus system “Species Plantarum” (1753)
Carol von Linne (Swedish botanist) – came up with a simple scheme which
immediately became very popular. He used just two words to describe the
binomial nomenclature - Each species has a two word Latin name
consisting of its genus and species names. These words are always
underlined or italicized when written.
Example: Thuja plicata – western red cedar to us in the PNW
hierarchical system - groups nested in larger groups
For example: Sitka Spruce
Kingdom Plantae
Phylum (Division) Coniferophyta
Class Coniferopsida
Order Coniferales
Family Cupressaceae
Genus Thuja
Species Thuja plicata.
Linnaeus called his system the “Sexual System”, because he used the presence or absence
and number of sexual parts as the basis for classification.
Artificial classification
Artificial classification - with no regard for evolutionary relationships (e.g., any
classification of things other than living things would have to be artificial).
However, evolutionary relationships make biological classification inherently different
than other classifications (i.e., the tree of life⬦)
Natural classification
Natural, or Phylogenetic, classification - reflecting evolutionary relationships.
Darwin (1859 – On the Origin of Species)
was the first to suggest that any classification of life should be “genealogical” and
would naturally be hierarchical; now we call this “phylogenetic”
Cladistic Analysis
- grouping species by shared derived states of characters
parsimony - (Occam's Razor) - the principle that the explanation requiring the
least change is preferred. Useful in resolving confusions from convergence

Describe the main branches of the angiosperms and the characteristics that separate different clades

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