investigating the tree of life (2)

7/27/2019 Investigating the Tree of Life (2)

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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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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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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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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

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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

investigating the tree of life (2)

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