i need help with bio exam
has1mohammad
20b_phylogeny.pptxI think this is from “The Far Side” but not sure anymore.
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Phylogeny is the evolutionary history of a species or group of related species
The discipline of systematics classifies organisms according to their phylogenies
Fossil, molecular, and genetic techniques are used to reconstruct evolutionary relationships, often using a “family tree” approach
Is it the same as regular family tree of people?
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Phylogeny and the Tree of Life
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From Darwin’s notebook on The Beagle: His handwriting is almost as bad as mine!
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Binomial Nomenclature
Taxonomy is the ordered grouping (classification) and naming of organisms
In the 18th century, Carl “Carolus” Linnaeus published a system of taxonomy based on resemblances
Two key features of his system remain useful today: two-part names for species and hierarchical classification
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The two-part scientific name of a species is called a binomial. The first part of the name is the genus
The second, called the specific epithet, is only unique for a species within each genus. This is usually descriptive in Latin or Greek, and is the only rank that is not a proper noun.
Thus, only both parts uniquely name the species, not the specific epithet alone.
The first letter of the genus is capitalized, and both parts are italicized when typing or underlined when writing, e.g., Homo sapiens (What is the translation?)
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Fig. 26-3
Species:
Panthera
pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
Archaea
Domain: Eukarya
Bacteria
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Hierarchical Classification
Linnaeus also introduced a system for grouping species in increasingly broad categories
The main taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
Did King Philip Come Over For Good Soup?
A taxonomic unit at any level of hierarchy is known as a taxon (plural = taxa)
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A phylogenetic tree represents a hypothesis about evolutionary relationships, which may or may not align with Linnaean taxonomy
Each node represents the divergence of a lineage into 2+ lineages, i.e., speciation (?)
Sister taxa are groups that share an immediate common ancestor. There can be ties in degree of relatedness.
A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
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Linking Classification and Phylogeny
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Fig. 26-5
Sister
taxa
ANCESTRAL
LINEAGE
Taxon A
Polytomy
Common ancestor of
taxa A–F
Branch point
(node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
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Sorting Homology from Analogy
Organisms with similar morphologies or DNA sequences are generally more closely related than those with different structures/sequences
However, we must distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry, thus is the type properly used for constructing phylogenetic trees
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Humerus
Radius
Ulna
Carpals
Metacarpals
Phalanges
Human
Whale
Cat
Bat
Fig. 22-17
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Analogy is similarity NOT due to shared ancestry (convergent evolution, molecular and other coincidences)
Convergent evolution occurs when selection in similar environmental contexts produces similar features in different lineages
Such similarities obscure ancestry, thus should be omitted when constructing phylogenies
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Marsupial (above) and placental (below) moles separately evolved to burrow. Their similarities are therefore a mixture of analogies for digging and homologies inherited from the common ancestor of all mammals.
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Cladistics
Cladistics, the primary technique in use today, seeks to group organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants
Clades can be nested within larger clades, but must correspond to a separate and complete unit of ancestry
When using this approach, trees may be called cladograms (I just stick with “phylogeny”)
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A valid clade is deemed monophyletic (one history): it incorporates all descendants of a common ancestor, that ancestor often being extinct or unknown.
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Archosaurs
Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
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A paraphyletic grouping consists of an some, but not all, descendants. (?)The purple group plus turtles and crocodilians represents reptiles and is also paraphyletic. Thus, many argue for revision of bird-reptile taxonomy.
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Dinosaurs
Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
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A polyphyletic group contains various taxa with different most recent ancestors. (?)The purple grouping is based on having wings, but they are analogous. Throw in winged insects and you have a legendary example of how NOT to make a .
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Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
Flying Vertebrates
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Fig. 26-10
A
A
A
B
B
B
C
C
C
D
D
D
E
E
E
F
F
F
G
G
G
Group III
Group II
Group I
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group
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“Cladists” argue that taxonomy should be overhauled to be based on clades (i.e., discrete evolutionary units) rather than arbitrary similarities or convention. They used to be nasty but dialed it down once they beat out (or subsumed) the other approaches.
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In comparison with an ancestor, each organism has both shared and different characteristics
A shared ancestral character is a trait that originated in an ancestor of the taxon
A shared derived character represents an evolutionary novelty unique to a clade
Like homology/analogy, a trait can be either ancestral or derived, depending on which groups are being compared
Inferring Phylogenies Using Derived Characters
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Fig. 26-11
TAXA
Lancelet
(outgroup)
Lamprey
Salamander
Leopard
Turtle
Tuna
Vertebral column
(backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg
CHARACTERS
Hair
(a) Character table
Hair
Hinged jaws
Vertebral
column
Four walking legs
Amniotic egg
(b) Phylogenetic tree
Salamander
Leopard
Turtle
Lamprey
Tuna
Lancelet
(outgroup)
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
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Phylogenetic Trees as Hypotheses
The best hypothesis for a phylogenetic tree fits the most data: morphological, molecular, fossil
Phylogenetic bracketing exemplifies how trees can be used for further inquiry, sometimes allowing us to reconstruct features of an ancestor from its descendants
This has been applied to infer dinosaur nesting behavior from their closest living relatives, birds and crocodiles
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Eggs
Front limb
Hind limb
(a) Fossil remains of Oviraptor
and eggs
(b) Artist’s reconstruction of the dinosaur’s posture
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Fossils of dinosaurs have been found on fossilized nests. Does this mean they brooded their eggs on the nest, or perhaps just coincidence? Phylogenies may be brought to bear on other research questions.
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Common
ancestor of
crocodilians,
dinosaurs,
and birds
Birds
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Saurischian
dinosaurs
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Dinosaurs are bracketed by living groups that brood eggs in nests. This suggests that dinosaurs did as well, (?) otherwise brooding would have evolved or been lost multiple times. All else equal, this is less probable.
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From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Five kingdoms were later recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
Recently, a three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes (esp. rRNA)
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Fig. 26-21
Fungi
EUKARYA
Trypanosomes
Green algae
Land plants
Red algae
Forams
Ciliates
Dinoflagellates
Diatoms
Animals
Amoebas
Cellular slime molds
Leishmania
Euglena
Green nonsulfur bacteria
Thermophiles
Halophiles
Methanobacterium
Sulfolobus
ARCHAEA
COMMON
ANCESTOR
OF ALL
LIFE
BACTERIA
(Plastids, including
chloroplasts)
Green
sulfur bacteria
(Mitochondrion)
Cyanobacteria
Chlamydia
Spirochetes
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There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer complicates efforts to build a tree of life
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Fig. 26-22
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Archaea
Bacteria
Eukarya
Billions of years ago
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2
1
0
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Because the earliest organisms exchanged substantial amounts of DNA, perhaps we should change the tree of life to the ring of life.
One ring to rule them all…
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