Molecular Phylogenetics Molecular Phylogenetics Basis of Phylogenetics Basis of Phylogenetics
Molecular PhylogeneticsMolecular Phylogenetics
Basis of Molecular PhylogeniesBasis of Molecular PhylogeniesOverviewOverview
Phylogenetics Definitions Phylogenetics Definitions
Genetic Variation and Evolution Genetic Variation and Evolution
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
Molecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary History
Morphology vs. MoleculesMorphology vs. Molecules
Molecular Tools Molecular Tools
Molecular Data Molecular Data
Which Gene to Use?Which Gene to Use?
Applications of Molecular PhylogeneticsApplications of Molecular Phylogenetics
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsPhylogenetics DefinitionsPhylogenetics Definitions
field of biology which does deal with field of biology which does deal with identifying and identifying and understanding the evolutionary relationshipsunderstanding the evolutionary relationships among the among the many different kinds of life on earth, both many different kinds of life on earth, both
living (living (extantextant) ) dead (dead (extinctextinct))
procedures for constructing procedures for constructing evolutionary treesevolutionary trees
a a phylogenyphylogeny describe the describe the historical relationships among historical relationships among lineages or organisms or their lineages or organisms or their parts (genes) parts (genes)
using trees to test hypothesesusing trees to test hypotheses
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsThe Evolution of Species orThe Evolution of Species or GenesGenes CanCan be be ModeledModeled as a as a BifurcatingBifurcating ProcessProcess
twotwo populations become reproductively isolated and populations become reproductively isolated and diverge due to random mutational diverge due to random mutational processesprocesses
overover time, this process may repeat itself, so that at any time, time, this process may repeat itself, so that at any time, each population can be said to be most closelyeach population can be said to be most closely--related related to some other population with which it shares a direct to some other population with which it shares a direct common common ancestorancestor
If genomes evolve the by accumulation of mutationsIf genomes evolve the by accumulation of mutations
the the amount of nucleotide sequence differenceamount of nucleotide sequence difference between a between a pair of genomes should indicate pair of genomes should indicate how recently those two how recently those two genomes shared a common ancestorgenomes shared a common ancestor
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsPhylogenetic DivergencePhylogenetic Divergence
consistsconsists of of changes in characterschanges in characters, such as amino acids in a , such as amino acids in a protein, or nucleotides in protein, or nucleotides in DNADNA
thethe longer two populations remain reproductively isolated, longer two populations remain reproductively isolated, the more divergence will the more divergence will occuroccur
GivenGiven the existence of the existence of homologous charactershomologous characters across a set of across a set of populations, it should be possible to populations, it should be possible to work backwards in timework backwards in time, , ascending the tree, until a ascending the tree, until a common ancestor of all populationscommon ancestor of all populationsin the set is in the set is reachedreached
How does genetic variation occur?How does genetic variation occur?
every organism posses a every organism posses a genomegenome that contains all the that contains all the biological information needed to construct and maintain a livingbiological information needed to construct and maintain a livingexample of that organismexample of that organism
The biological information contained in a genome is encoded in The biological information contained in a genome is encoded in the nucleotide sequence of its DNA or RNA molecules and is the nucleotide sequence of its DNA or RNA molecules and is divided into discrete units (divided into discrete units (genesgenes))
Genetic Variation Exists and Evolution Depends on ItGenetic Variation Exists and Evolution Depends on It
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
The information stored in a gene is The information stored in a gene is read by proteins, which attach to read by proteins, which attach to the genome and initiate a series of the genome and initiate a series of reactions reactions ((gene expressiongene expression))
DNA segments (large or small) can be DNA segments (large or small) can be
altered altered
duplicated duplicated
deleteddeleted
Genetic Variation Exists and Evolution Depends on ItGenetic Variation Exists and Evolution Depends on It
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
Point mutationsPoint mutations or other small changes (ex. or other small changes (ex. AA GG) generate a ) generate a new version of a gene (i.e. a new version of a gene (i.e. a new allelenew allele))
New lociNew loci are generated by gene are generated by gene duplication eventsduplication events
How does genetic variation occur?How does genetic variation occur?
DNA replicationDNA replicationevery time a cell divides, it must make a complete copy of its every time a cell divides, it must make a complete copy of its genomegenome
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsGenetic Variation Exists and Evolution Depends on ItGenetic Variation Exists and Evolution Depends on It
How does genetic variation occur?How does genetic variation occur?
must be extremely accurate in order to avoid introducing must be extremely accurate in order to avoid introducing mutationsmutations, or changes in the nucleotide sequence of a short , or changes in the nucleotide sequence of a short region of the genomeregion of the genome
Inevitably, some mutations occur Inevitably, some mutations occur
errors in DNA replicationerrors in DNA replication
effects of chemical agents effects of chemical agents or radiationor radiation
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsGenetic Variation Exists and Evolution Depends on ItGenetic Variation Exists and Evolution Depends on It
How does genetic variation occur?How does genetic variation occur?
Silent mutationsSilent mutationsresult in a change that has result in a change that has no effectno effect on the functioning of the on the functioning of the genomegenomeinclude virtually include virtually all changes that happen in theall changes that happen in the noncodingnoncodingcomponents of genomescomponents of genomes
Mutations in somatic cellsMutations in somatic cellsimportant only for the organism in which it occurs and has important only for the organism in which it occurs and has no no potential evolutionary impactpotential evolutionary impact because a somatic cell does because a somatic cell does not pass on copies of its genome to the next generation not pass on copies of its genome to the next generation
Mutations in germ cellsMutations in germ cellscan be transmitted to the next generationcan be transmitted to the next generation and will then and will then be present in all the cells of an individual who inherits that be present in all the cells of an individual who inherits that mutationmutation
Genetic Variation Exists and Evolution Depends on ItGenetic Variation Exists and Evolution Depends on It
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
How does genetic variation occur?How does genetic variation occur?
two or more alleles for that two or more alleles for that gene are present in a populationgene are present in a population
each of these alleles has its own each of these alleles has its own alleleallele or or gene frequencygene frequency
Allele frequenciesAllele frequencies vary over time byvary over time by
natural selectionnatural selection
random driftrandom drift
New alleles appear in a population because of mutations that occNew alleles appear in a population because of mutations that occur ur in the reproductive cells of an organismin the reproductive cells of an organism
many genes are many genes are polymorphicpolymorphic
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
What What isis phylogenetic phylogenetic analysisanalysisandand
WhyWhy should we perform itshould we perform it??
Inferring a phylogeny is an attempt to produce a Inferring a phylogeny is an attempt to produce a best estimate of an evolutionary history based best estimate of an evolutionary history based upon incomplete informationupon incomplete information
we do not have direct information about the past we do not have direct information about the past
only access to contemporary species and moleculesonly access to contemporary species and molecules
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
What What isis phylogenetic phylogenetic analysisanalysisandand
WhyWhy should we perform itshould we perform it??
Phylogenetic analysis has two major componentsPhylogenetic analysis has two major components
PhylogenyPhylogeny InferenceInference or “or “TreeTree Building”Building”thethe inference of the branching orders, and inference of the branching orders, and ultimatelyultimately the the evolutionary evolutionary relationships betweenrelationships between ““taxataxa””
((entities such as genes, entities such as genes, species, populationsspecies, populations, , etc.)etc.)
CharacterCharacter and and RateRate AnalysisAnalysisusingusing phylogeniesphylogenies as analytical frameworks as analytical frameworks forfor rigorous rigorous understanding of theunderstanding of the evolution of evolution of variousvarious traitstraits or or conditions of interest conditions of interest
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
What What isis phylogenetic phylogenetic analysisanalysisandand
WhyWhy should we perform itshould we perform it??
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsPremises to Phylogenetic InferencesPremises to Phylogenetic Inferences
TreeTree--like model of evolution (bifurcating process) like model of evolution (bifurcating process)
inheritance of ancestral charactersinheritance of ancestral characters
existence of an evolutionary history defined by existence of an evolutionary history defined by changes in these characterschanges in these characters
Phylogenetic analysis requires careful thoughtPhylogenetic analysis requires careful thought
phylogenetic analysis is frequently treated phylogenetic analysis is frequently treated
as a as a black boxblack box into which data are fed into which data are fed
(often gathered at considerable cost) and (often gathered at considerable cost) and
out of which out of which The Tree springsThe Tree springs
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
PrePre--Molecular ToolsMolecular ToolsPaleontological recordPaleontological record
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
PrePre--Molecular ToolsMolecular ToolsPaleontological recordPaleontological record
MorphologyMorphology
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
PrePre--Molecular ToolsMolecular ToolsPaleontological recordPaleontological record
MorphologyMorphology
BehaviourBehaviour
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
PrePre--Molecular ToolsMolecular ToolsPaleontological recordPaleontological record
MorphologyMorphology
BehaviourBehaviour
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
GeneticsGenetics
chromosomeschromosomesnumbernumberstructurestructure
gene frequenciesgene frequencies
Source of Information for Phyogenetic AnalysesSource of Information for Phyogenetic Analyses
PrePre--Molecular ToolsMolecular ToolsPaleontological recordPaleontological record
MorphologyMorphology
BehaviourBehaviour
GeneticsGenetics
chromosomeschromosomesnumbernumberstructurestructure
gene frequenciesgene frequencies
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics
Molecular ToolsMolecular Tools
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsMorphological trait comparisons work for finches Morphological trait comparisons work for finches and other macroorganisms...and other macroorganisms...
B. anthracisB. anthracis B. japonicumB. japonicum
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics...but does not work for bacteria...but does not work for bacteria
Previous viewPrevious view
bacteria and other microbes are “bacteria and other microbes are “living fossilsliving fossils” in the course ” in the course of evolutionof evolution
““Primitive” microbes as “Primitive” microbes as “evolutionary deadevolutionary dead--endsends””
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics...but does not work for bacteria...but does not work for bacteria
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of Phylogenetics...but does not work for bacteria...but does not work for bacteria
Today’s dominant viewToday’s dominant view
all organisms have evolved, and continue to evolve through all organisms have evolved, and continue to evolve through time along divergent linestime along divergent lines
Molecular PhylogeneticsMolecular Phylogenetics
Molecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary HistoryZuckerkandl & Pauling (1965)Zuckerkandl & Pauling (1965)
““We may ask the question where in the now We may ask the question where in the now living systems the greatest amount of living systems the greatest amount of information of their past historyinformation of their past history has has survived and how it can be extracted”survived and how it can be extracted”
““Best fit are the different types of Best fit are the different types of macromolecules (sequences) which carry macromolecules (sequences) which carry the the genetic informationgenetic information””
Basis of PhylogeneticsBasis of Phylogenetics
Molecular PhylogeneticsMolecular Phylogenetics
Molecular PhylogeneticsMolecular Phylogenetics
uses individual nucleotides or amino acids as uses individual nucleotides or amino acids as characterscharacters to reconstruct evolutionary historyto reconstruct evolutionary history
ZuckerkandlZuckerkandl & & PaulingPauling (1965)(1965)comparisoncomparison of hemoglobin of hemoglobin amino acidamino acid sequences from a sequences from a number of species number of species molecularmolecular clock hypothesisclock hypothesis
Fitch & Fitch & MargoliashMargoliash (1967)(1967)comparisoncomparison of of cytochrome cytochrome cc aminoamino acid acid sequencessequences from a from a number of species and phylogenetic reconstructionnumber of species and phylogenetic reconstruction
Wilson & Wilson & SarichSarich (1967)(1967)calibratecalibrate genetic distance derived from genetic distance derived from molecularmolecular similarity similarity with time span of fossil record and dated with time span of fossil record and dated human/chimphuman/chimpdivergence at 5 million yearsdivergence at 5 million years
Basis of PhylogeneticsBasis of PhylogeneticsMolecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary History
Molecular PhylogeneticsMolecular Phylogenetics
The rapid development and power of molecular techniques has The rapid development and power of molecular techniques has produced a produced a euphoria in evolutionary biologyeuphoria in evolutionary biology
because so many new problems can be addressed, it is a because so many new problems can be addressed, it is a commonly held commonly held misconceptionmisconception that that all evolutionary all evolutionary problems are solvable with molecular dataproblems are solvable with molecular data
Technological advancesTechnological advances have made possible for evolutionary have made possible for evolutionary biologists to easily obtain DNA sequences for phylogenetic biologists to easily obtain DNA sequences for phylogenetic pourposespourposes
PCRPCR (Polymerase Chain Reaction) technology(Polymerase Chain Reaction) technologyDNA sequencingDNA sequencing has become a common laboratory has become a common laboratory procedureprocedureComputer Computer hardwarehardware and and softwaresoftware development development
Rapid accumulation of phylogenetic dataRapid accumulation of phylogenetic data encompassing a encompassing a broad range of topics and applicationsbroad range of topics and applications
Basis of PhylogeneticsBasis of PhylogeneticsMolecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary History
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsMolecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary History
New journalsNew journals emphasizing the role of emphasizing the role of molecular studies in molecular studies in phylogenetic inferencephylogenetic inference
Molecular PhylogeneticsMolecular Phylogenetics
Basis of PhylogeneticsBasis of PhylogeneticsBasis of PhylogeneticsBasis of PhylogeneticsMolecules As Documents of Evolutionary HistoryMolecules As Documents of Evolutionary History
Books and ManualsBooks and Manuals
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
When we study DNA, we are looking directly at When we study DNA, we are looking directly at the genetic materialthe genetic material
we know that what we are looking atwe know that what we are looking at
is inheritedis inherited
DNA in modern organisms has been DNA in modern organisms has been
passed down ancestral organismspassed down ancestral organisms
DNA should reflect ancestryDNA should reflect ancestry and be and be
reliable for studying phylogenetic reliable for studying phylogenetic
relationshipsrelationships
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
we don't know exactly how it is inheritedwe don't know exactly how it is inherited
some aspects of the structure may some aspects of the structure may depend on direct depend on direct environmental environmental influencesinfluences and not be inherited at alland not be inherited at all
since we want to study inherited since we want to study inherited characteristics to reconstruct characteristics to reconstruct phylogenetic relationships, this could phylogenetic relationships, this could make morphology less reliable for make morphology less reliable for phylogenetic studiesphylogenetic studies
When we look at a structure of an organismWhen we look at a structure of an organism
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Existence of VariationExistence of VariationOne of the problems with studies of morphology is that we may beOne of the problems with studies of morphology is that we may belooking at a group of species that are extremely morphologicallylooking at a group of species that are extremely morphologicallysimilar similar
amphibiansamphibians are are highly conservedhighly conserved in terms of skeletal in terms of skeletal structure, muscles, organs, etc.structure, muscles, organs, etc.
Bufo fowleriBufo fowleri Bufo mauritanicusBufo mauritanicus Bufo viridisBufo viridis
Difficult to find a large enough number of characters to do a Difficult to find a large enough number of characters to do a reliable study of systematics (we need a large number of reliable study of systematics (we need a large number of characters because some may show convergent evolution)characters because some may show convergent evolution)
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Existence of VariationExistence of Variation
DNA sequencesDNA sequences have turned have turned out to be variable among species out to be variable among species
It is generally possible to find a It is generally possible to find a large number of characters large number of characters (base pair positions) that have(base pair positions) that have
phylogenetically phylogenetically
informative informative variationvariation
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
CostCostIt is much It is much less expensive less expensive to study morphologyto study morphology than than DNA DNA
for the same cost we may for the same cost we may be able to study more be able to study more aspects of body structure aspects of body structure than we can genesthan we can genes
DNA technology becomes less expensive and faster DNA technology becomes less expensive and faster all the all the time, so this disadvantage to morphology is becoming less time, so this disadvantage to morphology is becoming less importantimportant
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
The Fossil RecordThe Fossil RecordWe can include fossil species in studies We can include fossil species in studies based on morphologybased on morphology, , but, with very rare exceptions, we can not get DNA from fossilsbut, with very rare exceptions, we can not get DNA from fossils
Studies based on morphology Studies based on morphology
may allow us to find may allow us to find outgroupsoutgroups that that are more closely related to the are more closely related to the ingroup and therefore more reliable, ingroup and therefore more reliable, and to have a better representation of and to have a better representation of the ingroupthe ingroup
can be superior to those based on can be superior to those based on molecules, if we are looking at a molecules, if we are looking at a group for which a good fossil record group for which a good fossil record existsexists
Neandertal, Saccopastore (Italy) Neandertal, Saccopastore (Italy)
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Determination of HomologyDetermination of HomologyMorphological CharactersMorphological Characters
Similar looking structures may be considered homologous, when Similar looking structures may be considered homologous, when they are really coded by different genes they are really coded by different genes
this make the phylogeny unreliablethis make the phylogeny unreliable
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Determination of HomologyDetermination of Homology
AAAACCGG--GGTTAATTGGCC
AATTCCGGGGGGTT--TTGGCC
Alignment ProblemAlignment Problem
there are often insertions or deletions of there are often insertions or deletions of several base pairs into a gene so that the several base pairs into a gene so that the same gene in different species has different same gene in different species has different lengthlength
Gene DuplicationGene Duplication
duplicated copies of the gene both evolve duplicated copies of the gene both evolve
we might compare the original form of the we might compare the original form of the gene in one species with the duplicate gene in one species with the duplicate form of the gene in another species form of the gene in another species
paraloguos genesparaloguos genes
Similar problems can arise with DNASimilar problems can arise with DNA
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Convergent evolutionConvergent evolutionConvergent evolution Convergent evolution suggests thatsuggests that species may be relatedspecies may be related, , because they have similar characteristics, because they have similar characteristics, when in fact those when in fact those species are NOT relatedspecies are NOT related
When species independently occur in When species independently occur in similar environments, they are likely to similar environments, they are likely to evolve similar morphological traits through evolve similar morphological traits through natural selectionnatural selection
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Convergent evolutionConvergent evolutionThe Neutral Theory of Molecular Evolution The Neutral Theory of Molecular Evolution (Motoo Kimura, 1968)(Motoo Kimura, 1968)
Discovery of ubiquitous genic polymorphisms in natural Discovery of ubiquitous genic polymorphisms in natural populations brought about a great deal of debate over the populations brought about a great deal of debate over the significance of the variationsignificance of the variation
Kimura’s theoryKimura’s theory
the greatthe great majority of the majority of the differences in macromolecular differences in macromolecular structuresstructures observed between observed between individuals in a population are ofindividuals in a population are ofno adaptive significanceno adaptive significance and and have no impact on the have no impact on the reproductive success of the reproductive success of the individual in which they ariseindividual in which they arise
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
mutations subject to convergence because there mutations subject to convergence because there are only four possible bases (are only four possible bases (AA,,TT,,CC, , andand GG) )
it is not unlikely that by chance, different it is not unlikely that by chance, different species independently evolve the same base species independently evolve the same base pair at the same sitepair at the same site
Convergent evolutionConvergent evolutionThe Neutral Theory of Molecular Evolution The Neutral Theory of Molecular Evolution agrees with agrees with
the mutational molecular substitution rate observedthe mutational molecular substitution rate observed
the fact that the rate of the substitutions for the less the fact that the rate of the substitutions for the less biologically important part of macromolecules is greater than biologically important part of macromolecules is greater than for the active macromolecule domainsfor the active macromolecule domains
but...but...
DNA data can show convergent evolution just by chanceDNA data can show convergent evolution just by chance
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
Genes vs. SpeciesGenes vs. SpeciesRelationships calculated from sequence data represent the Relationships calculated from sequence data represent the relationships between genesrelationships between genes, this is not necessarily the same , this is not necessarily the same as relationships between as relationships between speciesspecies
youryour sequence data may not have the same phylogenetic sequence data may not have the same phylogenetic history as the species from which they were isolatedhistory as the species from which they were isolated
Different genes evolve at different speedsDifferent genes evolve at different speeds, and there is , and there is always the possibility of horizontal gene transfer (hybridizatioalways the possibility of horizontal gene transfer (hybridization, n, vector mediated DNA movement, or direct uptake of DNAvector mediated DNA movement, or direct uptake of DNA))
Molecular PhylogeneticsMolecular Phylogenetics
Morphology vs. MoleculesMorphology vs. Molecules
There are advantages and disadvantages to both There are advantages and disadvantages to both morphological and molecular studies of phylogenymorphological and molecular studies of phylogeny
Many people currently argue that to really know the phylogeneticMany people currently argue that to really know the phylogenetictree of life, tree of life, we need to study both kinds of characteristicwe need to study both kinds of characteristic