Phylogeny and Systematics

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Phylogeny and Systematics

• Barbara Musolf
• Clayton State University
• AS Building G 110-G
• 678-466-4851

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Objectives

• What is the basis for phylogenies?
• How does phylogeny link Linnaean classification
  with evolutionary history?
• How are phylogenetic trees constructed?
• How is molecular biology used to determine
  ancestries and evolutionary history?

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Tree of Life Website

• Don't draw conclusions about the relative
  diversity of different groups of organisms.
• Don't interpret relative branch lengths as
  indicators of levels of evolutionary
  "advancement".
• No organism alive today represents the ancestor
  of any other living creature.

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Phylogeny genesis of the tribe

• Phylogeny seeks to determine the origin and
  history of species.
• The search for this history leads biologists to
  draw on the fossil record to seek a species
  ancestor.
• Systematics is the analytical tool used to
  examine morphological and molecular resemblances.

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The basis for phylogenies fossils

• Fossils provide an incomplete but historical
  record .
• Fossils favor organisms that
• Existed for a long time
• Were abundant and widespread
• Had a hard skeleton or shell that enabled them to
  be formed into fossils

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Origin of fossils in sandstone
Rivers carry sediment to the ocean.
Sedimentary rock layers containing fossils form
on the ocean floor.
Over time, new strata are deposited,
containing fossils from each time period.
As sea levels change and the seafloor is
pushed upward, sedimentary rocks are exposed.
Erosion reveals strata and fossils.
Younger stratum with more recent fossils
Older stratum with older fossils
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The basis for phylogenies morphological and
molecular homologies

• Morphological evidence Homologous structures
  strongly suggest descent from a common ancestor.
• Ex. Forelimbs of mammals
• Molecular homologies are a more reliable
  indicator of relatedness.
• Organisms that share homologous DNA but share
  little morphological homology
• Ex. Hawaiian silversword plants

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Homology vs Analogy

• Analogy is similarity caused by convergent
  evolution.
• The more points of resemblance between two
  species the more likely they are homologous.

Australian mole
North American mole
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Molecular homologies
1
2

• Beginning of divergence
• Mutations
• Lack of alignment
• Realignment using a computer program

Deletion
1
2
Insertion
1
2
1
2
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Molecular homoplasy

• This sequence of two organisms indicates they
  share 25 of their bases.
• Mathematical tools suggest this is a coincidence
  rather than homology.

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Linnaeus classification

• Linnaeus classification placed organisms into
  categories
• Used similarities and differences to sort
  categories.
• Introduced binomial nomenclature (genus and
  species) to identify organisms.
• Species name was unique for the organism
• Panthera pardus
• We still use Linnaeuss classification and
  binomial nomenclatureHomo sapiens

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Hierarchical Classification
Panthera pardus
Species
Panthera
Genus

• Linnaeus established broad categories that fit
  into a hierarchy.

Felidae
Family
Carnivora
Order
Mammalia
Class
Chordata
Phylum
Animalia
Kingdom
Eukarya
Animation Classification Schemes
Domain
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Binomial nomenclature

• Each organism is referred to using both genus and
  the species epithet
• Both genus and species are italicized and genus
  is capitalizedPanthera pardus
• The species name is always latinized.
• Ex Loriculus sclateri is a bird that was named
  by Wallace after a scientist named Sclater.

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Phylogenetic trees
Leopard
Domestic cat

• Root
• Node
• Branch

Common ancestor
Leopard
Domestic cat
Wolf
Common ancestor
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Phylogeny and classification

• Phylogeny shows the nesting of groups within more
  inclusive groups.
• Nodes lead to two-way branch points or
  dichotomies.
• Branches that are further removed from the root
  show greater divergence from the root or
  ancestor.
• Darwin co-opted Linnaeuss classification because
  it could show evolutionary relationships.
• Our classifications will come to be, as far as
  they can be so made, geneaologies.

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Species
Panthera pardus (leopard)
Mephitis mephitis (striped skunk)
Lutra lutra (European otter)
Canis familiaris (domestic dog)
Canis lupus (wolf)
Genus
Panthera
Mephitis
Lutra
Canis
Family
Felidae
Mustelidae
Canidae
Order
Carnivora
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Phylogenetic systematics

• A clade is made up of an ancestral species and
  its descendents.
• Valid clades are monophyletic.
• Incomplete clades
• Paraphyletic clades lack some of the descendents
• Polyphyletic clades lack the ancestor

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Grouping 1
Monophyletic
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Grouping 2
Paraphyletic
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LE 25-10c
Grouping 3
Polyphyletic
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Shared primitive vs shared derived characteristics

• Shared primitive characteristics are those shared
  beyond the taxon that is being defined.
• Example is the backbone in mammals
• Shared derived characteristics are unique to a
  clade.
• Example is presence of hair for thermoregulation
  in mammals.
• Outgroups are used to differentiate between
  shared primitive and shared derived
  characteristics.

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Taxon vs clade

• Taxon is a designated group of species
• Examples humans, primates, mammals, vertebrates
• Clade is a taxon that includes all the
  evolutionary descendents of a common ancestor.
• Two clades that are each others closest
  relatives are sister clades
• Sister species are two species that are closest
  relatives

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Character table
LE 25-11
TAXA
Lancelet (outgroup)
Salamander
Lamprey
Leopard
Turtle
Tuna
Hair
Amniotic (shelled) egg
Four walking legs
CHARACTERS
Hinged jaws
Vertebral column (backbone)
Character table
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Cladogram
Leopard
Turtle
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram
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Phylogram
LE 25-12
Drosophila
Fish
Lancelet
Amphibian

• Length of the branch reflects number of changes
  in a particular DNA sequencehedgehog gene

Rat
Bird
Human
Mouse
outgroup
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Ultrametric tree
Drosophila
Bird
Rat
Mouse
Lancelet
Fish
Human
Amphibian
Cenozoic

• Branches show time.
• Branches are of equal length for all organisms
  from the ancestor to the present

65.5
Mesozoic
251
Paleozoic
542
Neoproterozoic
Millions of years ago
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How to assemble a phylogenetic tree

• Principle of maximum parsimony
• If assembling a tree based on morphology choose
  the tree that requires the fewest evolutionary
  events
• If assembling a tree based on DNA sequences
  choose the one that requires the fewest base
  changes
• Principle of maximum likelihood
• Given rules that govern DNA changes, a tree can
  be assembled that reflects evolutionary events.

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LE 25-14
Human
Mushroom
Tulip
0
30
40
Human
0
40
Mushroom
0
Tulip
Percentage differences between sequences
25
15
15
20
15
10
5
5
Tree 1 More likely
Tree 2 Less likely
Comparison of possible trees
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Maximum likelihood decisions

• Computer programs take the DNA evidence and
  follow the two principles.
• Distance methods minimize the total of all the
  percentage differences.
• Complex character-state methods minimize total
  number of base changes or search for the mostly
  likely base changes among all sequences.

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Application of parsimony Fig 25.15
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Phylogenetic tree as hypotheses

• Presents an hypothesis that shows the
  relationship between different organisms.
• The best hypothesis is the one that best fits all
  the available data.
• Phylogenetic hypotheses have often been revised
  or rejected when new information becomes
  available.

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LE 25-16
Lizard
Bird
Mammal
Four-chambered heart
Mammal-bird clade
Lizard
Bird
Mammal
Four-chambered heart
Four-chambered heart
Lizard-bird clade
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Evolutionary history in the genome

• Molecular systematics enables scientists to
• Compare groups that have little in common.
• Used to help Carl Woese discover the Archea
  domain
• Study genetic divergence within a species
• Study organisms that left no fossil record.
• Investigate relationships between taxa that
  diverged hundreds of million years ago
• Study of rRNA sequences show that fungi are more
  closely related to animals than green plants.
• Explore recent evolutionary events such as human
  migrations.

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Gene families

• Gene duplication is an important gene mutation.
• Duplicated genes form families within an
  organisms genome.
• Two types of homologous genes
• Orthologous genes are passed in a straight line
  through generations but are found in different
  gene pools because of speciation.
• Paralogous genes are duplicated genes in the
  genome

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Orthologous and Paralogous genes
LE 25-17a
Ancestral gene
LE 25-17b
Speciation
Orthologous genes
Ancestral gene
Gene duplication
Paralogous genes
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Genomic evolution

• Orthologous genes are widespread and ubiquitous.
• The number of genes has not increased at the same
  rate as phenotypic complexity.
• Humans have only 5X as many genes as yeast.
• Human genes are more versatile than yeast and can
  carry out many more functions.

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Molecular measurements of time

• Measurement of time assumes that some genes and
  regions of the genome evolve at a constant rate.
• Focus on nucleotide substitutions
• Calibrate the measurement by graphing the number
  of nucleotide substitutions against a known
  series of evolutionary branch points
• Many of the changes are neutral and produce no
  effect on fitness.
• Harmful mutations are removed from the genetic
  pool.
• Molecular measurements are unreliable beyond the
  fossil record.

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Tree of Life

• Last common ancestor of living things.
• Fusion of bacteria and arachea to produce
  Eukaryotes?
• Symbiosis of mitochondria and eukaryote ancestors
• Symbiosis of chloropast with plant ancestor