Bioinformatics and Evolutionary Genomics The tree of life / HGT , origin of eukaryotes
Origin and Tree of Life
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Transcript of Origin and Tree of Life
11/28/2014
1
Early Earth and The Origin of Life
Timeline of Life on Earth
Timeline of Life on Earth
• Life on Earth is said to have originated 3.5 – 4.0 billion years ago
• Bacteria (prokaryotes) were the first organisms to inhabit Earth
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Miller-Urey Experiment
• In 1953, Miller and Urey did an experiment that simulated lab conditions that were similar to those of the early Earth
• After one week, they found a variety of organic compounds (including amino acids) that had been produced from inorganic material
Miller-Urey Experiment
Kingdoms of Life• Arranging the diversity of life into kingdoms is a
work in progress
• Early classification systems had two kingdoms: plants and animals
• Robert Whittaker proposed five kingdoms: Monera, Protista, Plantae, Fungi, and Animalia
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3
New information has revised our understanding of the tree of life
• Molecular data have provided insights into the deepest branches of the tree of life
• Early classification systems had two kingdoms:
plants and animals
• Robert Whittaker proposed five kingdoms:
Monera, Protista, Plantae, Fungi, and Animalia
Kingdoms of Life (R. Whittaker’s Classification)
Kingdoms of Life-Molecular data have provided insights into the deepest branches of the tree of life
-The five kingdom system has been replaced by three
domains: Archaea, Bacteria, and Eukarya
- Each domain has been split into kingdoms
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Pro
teo
ba
cte
ria
Ch
lam
yd
ias
Sp
iro
ch
ete
s
Cy
an
ob
ac
teri
a
Gra
m-p
os
itiv
e b
ac
teri
a
Ko
rarc
ha
eo
tes
Eu
rya
rch
ae
ote
s, c
ren
arc
ha
eo
tes
, na
no
arc
ha
eo
tes
Dip
lom
on
ad
s, p
ara
ba
sa
lid
s
Eu
gle
no
zo
an
s
Alv
eo
late
s (d
ino
fla
ge
lla
tes
, ap
ico
mp
lex
an
s, c
ilia
tes
)
Domain Archaea
Universal ancestor
Domain Bacteria
Domain Eukarya
Str
am
en
op
ile
s (w
ate
r m
old
s, d
iato
ms
, g
old
en
alg
ae
, b
row
n a
lga
e)
Ce
rco
zo
an
s, r
ad
iola
ria
ns
Re
d a
lga
e
Ch
loro
ph
yte
s
Ch
aro
ph
yc
ea
ns
Bry
op
hy
tes
(m
os
se
s, l
ive
rwo
rts
, ho
rnw
ort
s)
Plants
Fungi
Animals
Se
ed
les
s v
as
cu
lar
pla
nts
(fe
rns
)
Gy
mn
os
pe
rms
An
gio
sp
erm
s
Am
oe
bo
zo
an
s(a
mo
eb
as
, s
lim
e m
old
s)
Ch
ytr
ids
Zy
go
te fu
ng
i
Arb
us
cu
lar
my
co
rrh
iza
lfu
ng
i
Sa
c f
un
gi
Clu
b fu
ng
i
Ch
oa
no
fla
ge
lla
tes
Sp
on
ge
s
Cn
ida
ria
ns
(je
llie
s, c
ora
l)
Bilate
rally s
ym
metr
ical
an
imals
(an
nelid
s,
art
hro
po
ds,
mo
llu
scs
, ech
ino
derm
s,
vert
eb
rate
s)
Investigating the Tree of Life• Ex: Legless lizards have evolved independently in several
different groups
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• Phylogeny is the evolutionary history of a species or group of related species
• The discipline of systematics classifies organisms and determines their evolutionary relationships
• Systematists use fossil, molecular, and genetic data to infer evolutionary relationships
• Taxonomy is the ordered division and naming of organisms
Binomial Nomenclature
• In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
• Linnaean system is useful today: two-part names for species and hierarchical classification
• The two-part scientific name of a species is binomial:
-first part of the name is the genus
-second part, called the specific epithet (unique for each species within the genus)
• The first letter of the genus is capitalized, and the entire species name is italicized
• Both parts together name the species-its SCIENTIFIC NAME (not the specific epithet alone)
Hierarchical Classification
• Linnaeus also introduced a system for grouping species in increasingly broad categories
• The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
• A taxonomic unit at any level of hierarchy is called a taxon
• The broader taxa are not comparable between lineages• For example, an order of snails has less genetic
diversity than an order of mammals
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Figure 26.3
Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora
Class:
Mammalia
Phylum:
Chordata
Domain:
Bacteria
Kingdom:
Animalia Domain:
ArchaeaDomain:
Eukarya
Linking Classification and Phylogeny
• Systematists depict evolutionary relationships in branching phylogenetic trees
Figure 26.4Order Family
Pantherapardus(leopard)
Genus Species
Canislatrans(coyote)
Taxideataxus(Americanbadger)
Lutra lutra(Europeanotter)
Canislupus(gray wolf)
Fe
lida
e
Ca
rniv
ora
Pa
nth
era
Ta
xid
ea
Mu
ste
lida
e
Lu
tra
Ca
nid
ae
Ca
nis
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• Linnaean classification and phylogeny can differ from each other
• Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents
• A phylogenetic tree represents a hypothesis about evolutionary relationships
• Each branch point represents the divergence of two species
• Sister taxa are groups that share an immediate common ancestor
• A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
• A basal taxon diverges early in the history of a group and originates near the common ancestor of the group
• A polytomy is a branch from which more than two groups emerge
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Figure 26.5
Branch point:where lineages diverge
ANCESTRALLINEAGE
This branch pointrepresents thecommon ancestor oftaxa A–G.
This branch point forms apolytomy: an unresolvedpattern of divergence.
Sistertaxa
Basaltaxon
Taxon A
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
Taxon G
What We Can and Cannot Learn from Phylogenetic Trees
• Phylogenetic trees show patterns of descent, not phenotypic similarity
• Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage
• It should not be assumed that a taxon evolved from the taxon next to it
Applying Phylogenies
• Phylogeny provides important information about similar characteristics in closely related species
• A phylogeny was used to identify the species of whale from which “whale meat” originated
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Minke (Southern Hemisphere)
Unknowns #1a, 2, 3, 4, 5, 6, 7, 8
Minke (North Atlantic)
Humpback (North Atlantic)
Humpback (North Pacific)
Gray
Blue
Unknowns #10, 11, 12
Unknown #13
Unknown #1b
Unknown #9
Fin (Mediterranean)
Fin (Iceland)
RESULTS
Phylogenies are inferred from morphological and molecular data
• To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
EXAMPLE: New views of animal phylogeny are emerging from molecular data
• Zoologists recognize about three dozen animal phyla
• Phylogenies now combine morphological, molecular, and fossil data
• Current debate in animal systematics has led to the development of multiple hypotheses about the relationships among animal groups
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ANCESTRALCOLONIALFLAGELLATE D
eu
tero
sto
mia
Pro
tosto
mia
Bila
teria
Eu
meta
zo
a
Meta
zo
a
Porifera
Cnidaria
Ctenophora
Ectoprocta
Brachiopoda
Echinodermata
Chordata
Platyhelminthes
Rotifera
Mollusca
Annelida
Arthropoda
Nematoda
MODEL HYPOTHESIS 1. based
mainly on morphological and
developmental comparisons
ANCESTRALCOLONIALFLAGELLATE
Deu
tero
sto
mia Lo
ph
otro
ch
ozo
a
Bila
teria
Eu
meta
zo
a
Meta
zo
a
Ecd
yso
zo
a
Porifera
Ctenophora
Cnidaria
Acoela
Echinodermata
Chordata
Platyhelminthes
Rotifera
Ectoprocta
Brachiopoda
Mollusca
Annelida
Nematoda
Arthropoda
Figure 32.11
MODEL HYPOTHESIS 2.
based mainly on
molecular data
Points of Agreement
1. All animals share a common ancestor colonial flagellate
2. Sponges are basal animals
3. Eumetazoa is a clade of animals (eumetazoans) with true tissues
4. Most animal phyla belong to the clade Bilateria, and are called bilaterians
5. Chordates and some other phyla belong to the clade Deuterostomia
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11
Body Symmetry• Animals can be categorized according to the symmetry of their bodies, or
lack of it
• Some animals have radial symmetry, with no front and back, or left and right
• Two-sided symmetry is called bilateral symmetry
• Bilaterally symmetrical animals have
• A dorsal (top) side and a ventral (bottom) side
• A right and left side
• Anterior (head) and posterior (tail) ends
• Cephalization, the development of a head
RADIALLY SYMMETRICAL: often sessile ex:
Hydra, sea anemone, coral polyp or planktonic
(drifting or weakly swimming) ex: jellyfish, comb
jellies
Bilateral animals often move actively w/ a
central nervous system ex: insects, man
Tissues
• Animal body plans also vary according to the organization of the animal’s tissues
• Tissues are collections of specialized cells isolated from other tissues by membranous layers
- Sponges lack true tissues
• During development, three germ layers give rise to the tissues and organs of the animal embryo
• Ectoderm is the germ layer covering the embryo’s surface
• Endoderm is the innermost germ layer and lines the developing digestive tube, called the archenteron
• Mesoderm – intervening layer
• Diploblastic animals have ectoderm and endoderm• These include cnidarians and comb jellies
• Triploblastic animals also have an intervening mesoderm layer; these include all bilaterians
• These include flatworms, arthropods, vertebrates, and others
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Muscle Tissue
Skeletal muscle
Nuclei
Musclefiber
Sarcomere
100 m
Smooth muscle Cardiac muscle
Nucleus Muscle fibers 25 m Nucleus Intercalated disk 50 m
Body Cavities
• Most triploblastic animals possess a body cavity• A true body cavity is called a coelom and is derived from
mesoderm• Coelomates are animals that possess a true coelom• A pseudocoelom is a body cavity derived from the
mesoderm and endoderm• Triploblastic animals that possess a pseudocoelom are called
pseudocoelomates• Triploblastic animals that lack a body cavity are called
acoelomates
© 2011 Pearson Education, Inc.
(a) Coelomate
Coelom
Digestive tract(from endoderm)
Body covering(from ectoderm)
Tissue layerlining coelomand suspendinginternal organs(from mesoderm)
(b) Pseudocoelomate
Body covering(from ectoderm)
Pseudocoelom Muscle layer(frommesoderm)
Digestive tract(from endoderm)
(c) Acoelomate
Body covering(from ectoderm)
Wall of digestive cavity(from endoderm)
Tissue-filled region(frommesoderm)
Figure 32.8
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Protostome and Deuterostome Development
• Based on early development, many animals can be categorized as having protostome development or deuterostome development
Cleavage
• In protostome development, cleavage is spiral and determinate
• In deuterostome development, cleavage is radial and indeterminate
- indeterminate cleavage, each cell in the early stages of
cleavage retains the capacity to develop into a
complete embryo
- makes possible identical twins, and embryonic stem
cells
(a) Cleavage
(b) Coelom formation
(c) Fate of the blastopore
Key
Ectoderm
Mesoderm
Endoderm
Protostome development(examples: molluscs,
annelids)
Deuterostome development(examples: echinoderms,
chordates)
Eight-cell stage Eight-cell stage
Spiral and determinate Radial and indeterminate
Archenteron
Coelom
Coelom
Blastopore BlastoporeMesoderm Mesoderm
Folds of archenteronform coelom.
Solid masses of mesodermsplit and form coelom.
Anus
Anus
Mouth
Mouth
Digestive tube
Mouth develops from blastopore. Anus develops from blastopore.
Figure 32.9
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Progress in Resolving Bilaterian Relationships• The morphology-based tree divides bilaterians into two
clades: deuterostomes and protostomes
• In contrast, recent molecular studies indicate three bilaterian clades: Deuterostomia, Ecdysozoa, and Lophotrochozoa
• Ecdysozoans shed their exoskeletons through a process called ecdysis
• Some lophotrochozoans have a feeding structure called a lophophore
• Others go through a distinct developmental stage called the trochophore larva
Future Directions in Animal Systematics
• Phylogenetic studies based on larger databases will likely provide further insights into animal evolutionary history