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INVESTIGATING THE TREE
OF LIFE
Phylogeny
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What is evolutionary biology?
about both process and history
processes of evolution are naturalselection and other mechanisms thatchange the genetic composition ofpopulations and can lead to the evolutionof new species
major goal: to reconstruct the history oflife on earth
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Point to consider here is
how scientists trace phylogeny, theevolutionary history of a group oforganisms
to reconstruct phylogeny, scientists usesystematics, an analytical approach tounderstanding the diversity and
relationships of living and extinctorganisms
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Evidence used to reconstructphylogenies
can be obtained from the fossil record andfrom morphological and biochemicalsimilarities between organisms
in the past, systematists use comparisonsof nucleotide sequences in DNA and RNAto help identify evolutionary relationships
between individual genes or even entiregenomes
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Scientists are kept busy by
working to construct a universal tree oflife
will be refined as the database of DNA andRNA sequences grows
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Phylogenies are based oncommon ancestries inferred from
fossil, morphological, andmolecular evidence
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Sedimentary rocks are the richestsource of fossils
Fossils are the preserved remnants orimpressions left by organisms that lived inthe past.
In essence, they are the historicaldocuments of biology.
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Sedimentary rocks
form from layers of sand and silt that arecarried by rivers to seas and swamps,where the minerals settle to the bottom
along with the remains of organisms
as deposits pile up, they compress oldersediments below them into layers called
strata
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Fossil record
ordered array in which fossils appearwithin sedimentary rock strata
rocks record the passing of geological time
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Fossil record
fossils can be used to constructphylogenies only if their ages can bedetermined
fossil record is a substantial butincomplete, chronicle of evolutionarychange
majority of living things were not capturedas fossils upon their death
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Fossil record
geological processes destroyed manyfossils
only a fraction of existing fossils havebeen discovered
fossil record is biased in favor of speciesthat existed for a long time, wereabundant and widespread, and had hardshells or skeletons that fossilized readily
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Morphological and molecular similaritiesmay provide clues to phylogeny
similarities due to shared ancestry are calledhomologies
organisms that share similar morphologies orDNA sequences are more closely related thanorganisms without such similarities
morphological divergence between closelyrelated species can be small or great
morphological diversity may be controlled byrelatively few genetic differences
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Analogy
similarity due to convergent evolution
when two organisms from differentevolutionary lineages experience similarenvironmental pressures, natural selectionmay result in convergent evolution
similar analogous adaptations may evolvein such organisms
analogies are not due to shared ancestry
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Distinguishing homology from analogy iscritical in the reconstruction of phylogeny
both birds and bats have adaptations that allowthem to fly
a close examination of a batswing shows agreater similarity to a cats forelimb that to abirdswing
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Distinguishing homology from analogy iscritical in the reconstruction of phylogeny
fossil evidence documents that bat andbird wings arose independently fromwalking forelimbs of different ancestors
a bats wing is homologous to othermammalian forelimbs but analogous infunction to a birdswing
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Homoplasies
Analogous structures that have evolvedindependently
the more points of resemblance that twocomplex structures have, the less likely itis that they evolved independently
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For example
skulls of a human and a chimpanzee areformed by the fusion of many bones
two skulls match almost perfectly
highly unlikely to have separate origins
genes involved in the development of both
skulls were inherited from a commonancestor
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Species relationships
genes which are sequences of nucleotides
systematists compare long stretches ofDNA and even entire genomes to assessrelationships between species
if genes in two organisms have closelysimilar nucleotide sequences, it is highlylikely that the genes are homologous
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Molecular comparisons of nucleicacids
it may be difficult to carry out
first step is to align nucleic acid sequences fromthe two species being studied.
in closely related species, sequences may differat only one or a few sites
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Molecular comparisons of nucleicacids
distantly related species may have manydifferences or sequences of differentmorphology
insertions and deletions accumulate,altering the lengths of the gene sequences
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Divergence
Deletions or insertions may shift theremaining sequences, making it difficult torecognize closely matching nucleotide
sequences
systematists use computer programs toanalyze comparable DNA sequences of
differing lengths and align themappropriately
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Divergence
molecules have diverged between species& does not tell us how long ago theircommon ancestor lived
molecular divergences betweenlineages with complete fossil recordscan serve as a molecular yardstick to
measure the appropriate time span ofvarious degrees of divergence
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Morphological characteristics
it is necessary to distinguish homology fromanalogy to determine the usefulness ofmolecular similarities for reconstruction of
phylogenies
closely similar sequences are most likelyhomologies
in distantly related organisms, identical bases indifferent sequences may simply be coincidentalmatches or molecular homoplasies
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Distant homologies
scientists have developed mathematical toolsthat can distinguishdistanthomologies fromcoincidental matches in divergent sequences
molecular analysis has provided proofs thathumans share a distant common ancestor withbacteria
scientists have sequenced more than 20 billionbases of nucleic acid data from thousands ofspecies
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Phylogenetic systematics connectsclassification with evolutionary history
In 1748
Carolus Linnaeus published SystemaNaturae, his classification of all plants andanimals known at the time
Taxonomy is an ordered division oforganisms into categories based onsimilarities and differences
Linnaeus's classification was based onresemblances between organisms
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Taxonomy employs a hierarchicalsystem of classification
The Linnaean system, first formallyproposed by Linnaeus in Systema naturaein the 18th century, has two main
characteristics:
Each species has a two-part name
Species are organized hierarchically into
broader and broader groups of organisms
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Under the binomial system
each species is assigned a two-part Latinizedbinomial name
the genus is the closest group to which aspecies belongs
the specific epithet refers to one species withineach genus
first letter of the genus is capitalized, italicizedand Latinized
Homo sapiens meanswiseman
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A hierarchical classification
groups species into increasingly broadtaxonomic categories
species that appear to be closely relatedare grouped into the same genus
the leopard, Panthera pardus, belongs to agenus that includes the African lion
(Panthera leo) and the tiger (Pantheratigris)
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Genera
grouped into family, order, class, phylum, kingdom,and domain
each taxonomic level is more comprehensive than the
previous one all species of cats are mammals, but not all mammals
are cats
named taxonomic unit at any level is called a taxon Panthera is a taxon at the genus level, and Mammalia
is a taxon at the class level
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Higher classification levels
not defined by some measurablecharacteristic, such as the reproductiveisolation that separates biological species
larger categories are not comparablebetween lineages
an order of snails does not necessarily
exhibit the same degree of morphologicalor genetic diversity as an order ofmammals
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Classification and phylogeny arelinked
systematists explore phylogeny byexamining various characteristics in livingand fossil organisms
- construct branching diagrams calledphylogenetic trees to depict theirhypotheses about evolutionary
relationships
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Branching of the tree
reflects the hierarchical classification of groupsnested within more inclusive groups
methods for tracing phylogeny began withDarwin, who realized the evolutionaryimplications of Linnaean hierarchy
- introduced phylogenetic systematics in On
the Origin of Specieswhen he wrote:Ourclassifications will come to be, as far as theycan be so made, genealogies.
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Phylogenetic systematics informs
the construction of phylogenetictrees based on shared characters
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Cladogram
patterns of shared characteristics can bedepicted in a diagram
if shared characteristics are homologousand explained by common ancestry, thenthe cladogram forms the basis of a
phylogenetic tree
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Cladogram
a clade is defined as a group of speciesthat includes an ancestral species and allits descendants
the study of resemblances among cladesis called cladistics
each branch, or clade, can be nested
within larger clades
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Cladogram
a valid clade is monophyletic, consisting of an ancestralspecies and all its descendants
lack information about some members of a clade may
result to a paraphyletic grouping that consists ofsomeof the descendants
may also be several polyphyletic groupings that lack acommon ancestor
needs a reconstruction to uncover species that tiethese groupings together into monophyletic clades
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Cladogram
determining which similarities between species arerelevant to grouping the species in a clade is achallenge
it is important to distinguish similarities that arebased on shared ancestry or homology from thosethat are based on convergent evolution or analogy
systematists must sort the homologous features toseparate shared derived characters from sharedprimitive characters
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Cladogram
a character refers to any featurethat a particular taxon possesses
a shared derived character is uniqueto a particular clade
a shared primitive character is found
not only in the clade being analyzed,but also in older clades
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Cladogram
presence of hair is a good character to distinguish theclade of mammals from other tetrapods
a shared derived character that uniquely identifies
mammals presence of a backbone can qualify as a shared
derived character but distinguishes all vertebrates fromother mammals
backbone is a shared primitive character because itevolved in the ancestor common to all vertebrates
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Cladogram
shared derived characters are useful inestablishing a phylogeny, but sharedprimitive characters are not
status of a character shared derivedversus shared primitive may depend onthe level at which the analysis is being
performed
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Cladogram
A key step in cladistic analysis is out-groupcomparison, which is used to differentiateshared primitive characters from shared
derived ones
need to identify an out-group, a species orgroup of species closely related to the
species being studied but known to beless closely related than any members ofthe study group are to each other
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Cladogram
to study the relationships among an in-group of five vertebrates (a leopard, aturtle, a salamander, a tuna, and a
lamprey) on a cladogram, an animal calledthe lancelet is a good choice
lancelet is a small member of the Phylum
Chordata that lacks a backbone
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Cladogram
species making up the in-group display a mixtureof shared primitive and shared derived characters
In an out-group analysis, the assumption is that
any homologies shared by the in-group and out-group are primitive characters that were present inthe common ancestor of both groups
homologies present in some or all of the in-grouptaxa are assumed to have evolved after thedivergence of the in-group and out-group taxa
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Example
a notochord, present in lancelets and in theembryos of the in-group, is a shared primitivecharacter and not useful for sorting out
relationships between members of the in-group presence of a vertebral column, shared by all
members of the in-group but not the out-group, is
a useful character for the whole in-group presence of jaws, absent in lampreys and present
in the other in-group taxa, helps to identify theearliest branch in the vertebrate cladogram.
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Analyzing the taxonomic distribution ofhomologies enables us
to identify the sequence in which derived charactersevolved during vertebrate phylogeny
cladogram presents the chronological sequence of
branching during the evolution of a set of organisms chronology indicate only the groups to which they
belong
a particular species in an old group may haveevolved more recently than a second species thatbelongs to a newer group
A l d i t h l ti
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A cladogram is not a phylogenetictree
to convert it to a phylogenetic tree, moreinformation from fossil record can indicatewhen and in which groups the characters
first appeared any chronology represented by the
branching pattern of a phylogenetic tree is
relative (earlier versus later) rather somany millions of years ago
A l d i t h l ti
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A cladogram is not a phylogenetictree
some tree diagrams provide morespecific information about timing
in a phylogram, the length of abranch reflects the number of geneticchanges that have taken place in a
particular DNA or RNA sequence in alineage
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Phylogram
branches in a phylogram may havedifferent lengths, all the different survivinglineages descended from a common
ancestor humans and bacteria had a common
ancestor that lived more than 3 billion
years ago ancestor was a prokaryote and was like a
modern bacterium
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Ultrameric tree
equal amounts of chronological time arerepresented in an ultrameric tree
branching pattern is similar to a phylogram butthe branches can be traced from the commonancestor to the present of equal lengths
no information about different evolutionary
rates found in phylograms
draw on data from the past to place certainbranch points in the context of geological time
The principles of maximum parsimony and
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The principles of maximum parsimony andmaximum likelihood help systematists reconstructphylogeny
As available data about DNA sequencesincrease, it becomes more difficult to drawthe phylogenetic tree that best describes
evolutionary history. If you are analyzing data for 50 species,
there are 3 1076 different ways to form
a tree.
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Maximum Parsimony
we look for the simplest explanation that isconsistent with the facts
if a tree based on morphological characters, the
most parsimonious tree is the one that requires thefewest evolutionary events to have occurred in theform of shared derived characters
for phylograms based on DNA sequences, themost parsimonious tree requires the fewest basechanges in DNA
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Ultrameric tree
principle of maximum likelihood
given certain rules about how DNAchanges over time
a tree should reflect the most likelysequence of evolutionary events
Maximum likelihood methods are designedto use as much information as possible
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The Methods
Distance methods minimize the total ofall the percentage differences among allthe sequences.
Character-state methods minimize thetotal number of base changes or searchfor the most likely pattern of base changes
among all the sequences.
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Phylogenetic trees are hypotheses
any phylogenetic tree represents a hypothesisabout how the organisms in the tree are related
best hypothesis is the one that best fits all the
available data
hypothesis may be modified when new evidenceis compelling for revising the trees
many older phylogenetic hypotheses have beenchanged or rejected
Phylogenetic trees are
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Phylogenetic trees arehypotheses
four-chambered hearts of birds andmammals are analogous
less likely for analogy and morphology to
distort a phylogenetic tree if severalderived characters define each clade inthe tree
strongest phylogenetic hypotheses aresupported by multiple lines of molecularand morphological/fossil evidence
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Much of an organisms
evolutionary history isdocumented in its genome
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Molecular approach
molecular systematics is a valuable tool fortracing an organismsevolutionary history
helps to understand phylogenetic relationships
that cannot be measured by nonmolecularmethods
molecular systematics helps to uncover
evolutionary relationships between groups thathave no basis for morphologicalcomparison(mammals and bacteria)
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Molecular systematics
enables scientists to compare genetic divergencewithin a species
molecular biology helps to extend systematics to
evolutionary relationships above and below thespecies level
findings are sometimes inconclusive
ability of molecular trees includes short and longperiods of time from different genes evolving atdifferent rates & same evolutionary lineage
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For example
DNA that codes for ribosomal RNA (rRNA)changes relatively slowly so comparisons ofDNA sequences in these genes can be used to
sort out relationships between taxa thatdiverged hundreds of millions of years ago
mitochondrial DNA (mtDNA) evolved relatively
recently and can be used to explore recentevolutionary events, such as relationshipsbetween groups within a species
G d li ti h id d
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Gene duplication has providedopportunities for evolutionary change
GD increases the number of genes in thegenome, providing opportunities forevolutionary change
GD has resulted in gene families (groupsof related genes within an organismsgenome)
GD have a common genetic ancestor
2 types of homologous genes: orthologousgenes and paralogous genes
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GD
orthologous: homologous genes that arefound in different gene pools because ofspeciation
hemoglobin genes in humans and mice
paralogous: found in more than one copyin the same genome
olfactory receptor genes
humans and mice more than 1,000 of theparalogous genes
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Emerging facts
Orthologous genes are widespread andcan extend over enormous evolutionarydistances
99% of the genes of humans and mice aredemonstrably orthologous, and 50% ofhuman genes are orthologous with those ofyeast
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Emerging facts
all living things share many biochemical anddevelopment pathways
number of genes seems dont increase at the
same rate as phenotypic complexity
humans have only 5x as many genes as yeast
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Emerging facts
humans have a large, complex brain and abody that contains more than 200different types of tissues
human genes are more versatile thanyeast and can carry out a wide variety oftasks
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Molecular clocks help track
evolutionary time
The timing of evolutionary events has
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The timing of evolutionary events hasrested primarily on the fossil record
to understand the relationships among allliving organisms, including those with nofossil record
molecular clocks serve as yardsticks formeasuring the absolute time ofevolutionary change
based on the observation that someregions of the genome evolve at constantrates.
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Regions of genome
number of nucleotide substitutions inorthologous genes is proportional to thetime that has elapsed since the two
species last shared a common ancestor in the case of paralogous genes, the
number of substitutions is proportional to
the time since the genes becameduplicated
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What are paralogous gene?
Describing homologous
genes that have arisenby duplication of anancestral gene
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Calibrating molecular clock
graph the number of nucleotide differences vstiming of a series of evolutionary branchpoints based from fossil records
slope of the best line through the pointsrepresents the evolution rate of molecularclock
rate can be used to estimate the absolutedate of evolutionary events without fossilrecord
No molecular clock is completely
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No molecular clock is completelyaccurate
genes that make good molecular clocks havefairly smooth average rates of change
no genes mark time with a precise tic-tac
accuracy in the rate of base changes
over time there may be chance deviationsabove and below the average rate
rates of change of various genes vary greatly
some genes evolve a million times faster thanothers
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Molecular clock approach
assumes that much of the change in DNAsequences is due to genetic drift and isselectively neutral
neutral theory suggests that muchevolutionary change in genes and proteins hasno effect on fitness and is not influenced by
Darwinian selection
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Molecular clock approach
many new mutations are harmful and areremoved quickly
if most of the rest are neutral and have
little or no effect on fitness, the rate ofmolecular change should be clocklike intheir regularity
Differences in the rates of change of specific genes
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Differences in the rates of change of specific genesare a function of the importance of the gene
if the exact sequence of amino acidsspecified by a gene is essential tosurvival, most mutations will be harmful
and will be removed by natural selection if the sequence of genes is less critical,
more mutations will be neutral, and
mutations will accumulate more rapidly
Some DNA changes are favored
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Some DNA changes are favoredby natural selection
lead some scientists to question the accuracy andutility of molecular clocks for timing evolution
almost 50% of the amino acid differences in proteins
of 2 Drosophila species have resulted fromdirectional natural selection
fluctuations in the rate of accumulation of mutationsdue to natural selection may even out
even genes with irregular clocks can mark elapsedtime
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Biologists: Skeptics
of conclusions derived from molecular clocksthat have been extrapolated to time spansbeyond the calibration in the fossil record
few fossils are older than 550 million years old
estimates for evolutionary divergences beforethat time may assume that molecular clocks
have been constant over billions of years estimates have a high degree of uncertainty
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Molecular clock approach
has been used to date the rise of the HIV virus from SIVviruses that infect chimpanzees and other primates tohumans
virus has spread to humans more than once multiple origins of HIV are reflected in the variety of strains
of the virus
HIV-1 M is the most common HIV strain
molecular clock has been calibrated for the virus bycomparing samples of the virus collected at various times
HIV-1 M strain invaded humans in the 1930s
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Molecular clock approach
HIV-1 M is the most common HIV strain
molecular clock has been calibrated forthe virus by comparing samples of the
virus collected at various times
HIV-1 M strain invaded humans in the1930s
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There is a universal tree of life
genetic code is universal in all forms of life
researchers infer that all living things havea common ancestor
researchers are working to link allorganisms into a universal tree of life
2 criteria identify regions of DNA that can
be used to reconstruct the branchingpattern of the tree
f
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Regions of DNA
regions must be able to be sequenced
must have evolved slowly, so that evendistantly related organisms show evidence
of homologies in these regions
rRNA genes, coding for the RNAcomponent of ribosomes, meet these
criteria
Two points have emerged from
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Two points have emerged fromthis effort
1. The tree of life consists of three greatdomains: Bacteria, Archaea, and Eukarya
Most prokaryotes belong to Bacteria
Archaea: a diverse group of prokaryotesthat inhabit many different habitats
Eukarya: all organisms with true nuclei,
including many unicellular organisms aswell as the multicellular kingdoms
Two points have emerged from
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Two points have emerged fromthis effort
2. Unclear early history of the domains
Early in the history of life, there weremany interchanges of genes between
organisms in the different domains
a. horizontal gene transfer, in which genesare transferred from one genome to
another by transposable elements
Unclear early history of the
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Unclear early history of thedomains
different organisms fused to produce new,hybrid organisms
first eukaryote arose through fusion
between an ancestral bacterium and anancestral archaean
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DONT BE CHOOSY!!!
R f
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References
www.course-notes.org
www.ccis.edu
www.griffith.edu.au
www.doctortee.com
www.slideshare.net
programspec.unimas.my www.indiana.edu