Phylogeny and Systematics

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Chapter 25 Phylogeny and Systematics
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Phylogeny is the evolutionary history of a
species or group of related species.   A.  Fossil
record and geologic time             1. 
Sedimentary rocks are the richest source of
fossils                         a.  The fossil
record refers to the order in which fossils
appear within layers of rock that mark the
passing of geologic time.                        
b.  Organic substances in dead organisms
typically decay rapidly.  Parts that are rich in
minerals (eg. teeth, bones) may become
fossils.                           Figure 25.4
(p. 493) A gallery of fossils
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3.  The fossil record is substantial, but does
not provide a complete evolutionary
history                         a.  The fossil
record usually tells us about abundant,
widespread organisms with hard shells or
skeletons.   4.  Phylogeny has a biogeographic
basis in continental drift                        
a.  Moving continents isolate populations,
allowing for evolution to occur.   b.  250
million years ago all continents were connected
as Pangaea.   c.  Pangaea broke apart about 180
million years ago.   Figure 25.4 (p. 490) The
history of continental drift
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            5.  History is punctuated by mass
extinctions                         a.  There has
been a general increase in species diversity over
time.                                            
     Figure 25.5 (p. 491) Diversity of life and
periods of mass extinctions.
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                        b.  Permian
extinction                                    
i.  90 of marine species went extinct            
                           ii.  Pangaea formed
and some species began competing with each other
for the first time.                               
        iii.  Mass extinction was caused by
volcanic eruptions and climate changes            
                                     c. 
Cretaceous extinction                             
        i.  Dinosaurs went extinct                
                       ii.  An asteroid (or
comet) hit the earth and created a cloud of
debris that blocked out sunlight for months.
 Temperatures dropped and plants died.
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B.  Systematics  Connecting classification to
phylogeny             ? Systematics the study
of biological diversity in an evolutionary
context, including taxonomy and
phylogenetics.   1.  Taxonomy uses a hierarchical
classification system a.  Review the Linnaean
(binomial) system of classification  genus and
species.   b.  Review hierarchical
classfication  Kingdom, Phylum, Class, Order,
Family, Genus, Species                            
         - A named taxonomic unit at any level
is called a taxon.    Figure 25.7 (p. 493)
Hierarchical classification.
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                        c.  Phylogenetic trees
are used to place different taxonomic schemes
together, and to show connection between
classification and phylogeny.                    
        Figure 25.8 (p. 494) The connection
between classification and phylogeny.
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2.  Modern phylogenetic systematics are based on
cladistic analysis a.  A phylogenetic diagram
(tree) is also called a cladogram.    b.  Each
branch in the tree is called a clade.    c. 
Monophyletic pertains to a taxon that is derived
from a single ancestral species. ? only
legitimate cladogram type!   d.  Polyphyletic
pertains to a taxon whose members were derived
from two or more ancestors not common to all
members.   e.  Paraphyletic pertains to a taxon
that excludes some members that share a common
ancestor with members included in the
taxon.  ?Figure 25.9 (p. 495) Monophyletic
versus paraphyletic and polyphyletic groups.
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            3.  Constructing cladograms           
              a.  Identify homologies à shared
characteristics derived from one ancestor. NOTE
Analogous structures may look similar to one
another, but are not derived from a common
ancestor. These are in contrast to homologous
structures.   Fig. 25.10 is an example of an
analogous structure in two distantly related
plants. When two organisms have analogous
structures, this is an example of convergent
evolution ? Independent development of
similarity between species due to similar
selection pressures.
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• b.  When constructing a cladogram, the greater
  the number of homologous parts between two
  organisms, the more closely related they are.
• c.  The classification scheme must reflect these
  similarities.
• These similarities can be either
• Shared primitive characters, I.e. homologous
  characters that are shared by more than one
  taxon, e.g. backbone is shared by mammals and
  reptiles.
• Shared derived characters, I.e. an evolutionary
  novelty that is unique for a particular clade.
  The more derived characters that a species has,
  the more evolutionarily unique it is.

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Example of how to construct a cladogram 1.
Select your species for which you want to make a
cladogram. These are called the ingroup. They
have shared primitive and derived characters. 2.
Select an outgroup ? a species that is closely
related to the species under study, the outgroup
has a shared primitive character that is common
to all species. 3. Construct a character table
and tabulate the data. ? The more shared
characters, the more closely related are the
species. 4. Construct a cladogram based on the
number of shared characters. For
example Figure 25.11 (p. 497) Constructing a
cladogram. The outgroup here, the lancelet has a
notochord, the shared primitive character. The
ingroup is five vertebrates.
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The clade pattern can be used to structure a
hierarchy for the higher taxa, for
example Figure 25.12 (p. 498) Cladistics and
taxonomy.
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4.  Phylogeny can be inferred also from molecular
data                         a.  DNA and RNA
sequences of nucleic acids can be compared to
determine phylogeny. ? Example to follow. Note
that each change in a nucleic acid one
evolutionary event! The more events, the more
distantly related are the species. Fewer events
means that a species is more closely related.
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5.  The principle of parsimony helps systematists
reconstruct phylogeny a.  Phylogenies can be
extremely complicated.   b.  The principle of
parsimony states that a theory about nature
should be the simplest explanation that is
consistent with facts.                            
         - Keep it simple.                      
               - Sometimes called Occams
Razor.   c.  A phylogenetic tree is a
hypothesis.  There may be many possible trees,
but the simplest one is probably the most
accurate. Figure 25.14 (p. 500) Simplified
version of a four-species problem in
phylogenetics. Figure 25.15 (p. 500-501)
Parsimony and molecular systematics.
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Figure 25.16 (p. 502) -  Parsimony and the
analogy-versus-homology pitfall.  
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6.  Modern systematics is flourishing with
debate                         Example
demonstrates that the class reptilia is
paraphyletic and not monophyletic.
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a.  Lots of debate when comparing major
groups                                     -
Orders of mammals   Figure 25.19 (p. 505) When
did most major mammalian orders originate?
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