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Phylogeny and Systematics

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What is the basis for phylogenies? How does phylogeny link Linnaean ... Amphibian. Bird. Human. Rat. Mouse. outgroup. Ultrametric tree. Branches show time. ... – PowerPoint PPT presentation

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Title: Phylogeny and Systematics


1
Phylogeny and Systematics
  • Barbara Musolf
  • Clayton State University
  • AS Building G 110-G
  • 678-466-4851

2
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?

3
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.

4
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.

5
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

6
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
7
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

8
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
9
Molecular homologies
1
2
  • Beginning of divergence
  • Mutations
  • Lack of alignment
  • Realignment using a computer program

Deletion
1
2
Insertion
1
2
1
2
10
Molecular homoplasy
  • This sequence of two organisms indicates they
    share 25 of their bases.
  • Mathematical tools suggest this is a coincidence
    rather than homology.

11
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

12
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
13
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.

14
Phylogenetic trees
Leopard
Domestic cat
  • Root
  • Node
  • Branch

Common ancestor
Leopard
Domestic cat
Wolf
Common ancestor
15
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.

16
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
17
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

18
Grouping 1
Monophyletic
19
Grouping 2
Paraphyletic
20
LE 25-10c
Grouping 3
Polyphyletic
21
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.

22
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

23
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
24
Cladogram
Leopard
Turtle
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram
25
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
26
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
27
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.

28
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
29
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.

30
Application of parsimony Fig 25.15
31
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.

32
LE 25-16
Lizard
Bird
Mammal
Four-chambered heart
Mammal-bird clade
Lizard
Bird
Mammal
Four-chambered heart
Four-chambered heart
Lizard-bird clade
33
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.

34
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

35
Orthologous and Paralogous genes
LE 25-17a
Ancestral gene
LE 25-17b
Speciation
Orthologous genes
Ancestral gene
Gene duplication
Paralogous genes
36
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.

37
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.

38
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
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