BI107 Chapter 22 Reconstructing and Using Phylogenies
Three assumptions in cladistics
1. any group of organisms are related by descent from a common ancestor 2. there is a bifurcating pattern of cladogenesis 3. change in characteristics occurs in lineages over time
why do biologists need cladistics?
1. cladistics is useful for creating systems of classification 2. cladistics predicts the properties of organisms 3. cladistics helps to elucidate mechanisms of evolution
linnean classification order
1. kindom 2. phyla 3. class 4. order 5 family 6. genus 7. species
sources of phylogenetic information include
1. morphology 2. patterns of development 3. the fossil record 4. behavioral traits 5. molecular traits such as DNA and protein sequences
the explicit mathematic models account for
1. multiple changes at a given position in a DNA sequence 2. different rates of change at different positions in a gene 3. rate of change at different positions in a codon 4. among different nucleotide
How do biologists use phylogenetic trees?
1. phylogenetic trees are used to make comparisons among living organisms 2. phylogenetic trees are used to reconstruct the past and to understand the origin of traits 3. biologists can use phylogenetic trees to reconstruct ancestral states 4. phylogenetic trees may include estimates of divergence times of lineages determined determined by molecular clock analysis
phylogenetic trees are used to 5 things
1. reconstruct past history of lineages 2. determine when and where traits arose 3. make biological comparisons among genes, populations and species 4. reconstruct ancestral traits 5. estimate the timing of evolutionary events
morphological approaches to phylogenetic analysis have limitations
1. some taxa exhibit little morphological diversity despite great species diversity 2. few morphological traits can be compared across distantly related species (earthworms and mammals) 3. some morphological variation has an environmental rather than a genetic basis and so must be excluded from phylogenetic analysis
phylogenies are constructed from many sources of data. types of data include 5 things
1. studies of morphology 2. development, 3. fossil record 4. behavioral traits 5. molecular traits ( DNA and protein sequences)
phylogenic trees can tell us two things
1. when ancestral lineages divided into descendant lineages 2. how related species are
Molecular Data
All heritable variation is encoded in DNA that can be used in phylogenetic analysis. In recent years, DNA sequences have become among the most widely sued sources of data for constructing phylogenetic trees
Monophyletic group
Archosaurian
Example of reversal:
Birds do not have claws on forelimbs, los in ancestor But Hoatzin does have claws on forelimbs selected for because of escape behavior mutation switched back on, nothing else was required
Independent evolution of similar character states in 2 different lineages; can be
DNA sequence, behavior, morphological feature
The true phylogeny and the ancestral DNA sequences were accurately reconstructed solely from the
DNA sequences of the viruses at the tips of the tree branches
homologous features may be any inheritable traits, including
DNA sequences, protein structure, anatomical structure, and even some behavior patterns
Paleontology
Fossil record shows where and when organisms lived in the past and gives us an idea of what they looked like. The fossil record does have limitations: few or no fossils have been found for some groups and the fossil record may be fragmentary
phylogenetic analysis have become important for studying the transmission of viruses such as
HIV and they are important for understanding the present global diversity of such viruses and for determining their origins in human populations
A broad phylogenetic analysis of immunodeficiency viruses show that human acquired these viruses from two different hosts:
HIV-1 from chimpanzees and HIV2 from sooty mangabeys
Given the phylogeny of HIV and SIV, what may explain why HIV-1 is more infective than HIV-2? A. RNA polymerases from HIV-1 are more efficient B. HIV-1 is derived from Chimpanzees which are our closest living relatives. C. HIV-2 is derived from Sootey Mangabeys, a more distantly related monkey. D. B & C above.
HIV-1 is more harmful to us than HIV2 because chimpanzees are our closest living relatives. D: B and C above
ingroup
In a phylogenetic study, the group of organisms of primary interest
outgroup
In phylogenetics, a group of organisms used as a point of reference for comparison with the group of primary interest (ingroup)
Why do many new influenza strains arise in large cities in Asia?
Markets with a high density of poetry, swine and humans increase the probability of cross species infection and viral recombination
Do crocodiles practice parental care?
YES, mother crocodiles help in egg hatching
taxon is
a biological species that was given a name
evolutionary reversal
a character may revert from a derived state back to an ancestral state. Ex: frog teeth that were gone but came back in south american species
A taxon that consists of an ancestor and all of its evolutionary descendants is called
a clade
a cladogram (tree)
a cladogram is constructed that clusters taxa based on distribution of synapomorphies( shared, derived character states) among taxa, and depicts hypothesis of evolutionary relationships
paraphyletic group
a group that does not include all the descendants of a common ancestor
polyphyletic
a group that does not include its common ancestor
systematic and taxonomy
a major goal of evolutionary biology is to reconstruct the history of life on earth and classify biodiversity into coherent groups
Each branching point (or node) in a phylogenetic tree represents
a point at which lineages diverged in the past
derived trait
a trait found in a descendant that differs from its ancestral form is a derived trait
ancestral trait
a trait that was present in the ancestor of a gorup
phylogenetic analysis of DNA sequences can
accurately reconstruct evolutionary history
plant family names end in
aceae
wings of bats and wings of birds are
adaptations for flight and are not homologous
Example of convergent evolution: Desert adapted Cactaeae and Euphorbiaceae
adapted to hot, dry conditions. both have (despite widely separated by time and space) modified spines to protect form herbivory leaves that drop in wet season or stems that can photosynthesis (have chlorophyll)
Tinkering of these character states are
adaptive and functional but use for new function (flight) small evolutionary changes (tinkering) with dinosaurs let rise to modern birds
What you strive fore is a clade or monophyletic group
an ancestral species and all its descendants
As a point of reference
an ingroup is compared with an outgroup
characters can be
anatomical, like in the case of wings, but can also be embryological, or molecular
biologists can use phylogenetic method to reconstruct the morphology, behavior, or nucleotide and amino acid sequences of
ancestral species
Whales are part of the artiodactyls's family due to synapomorphy of the
ankle bone!
homologous
any features shared by two or more species that have been inherited from a common ancestor
Clade
any taxon that consists of an ancestor and all of its evolutionary descendants
sister clades
any two clades that are each other's closest relatives
changed state of characteristics is called
apomorphic (derived)
molecular data is not precise and may
apply to some but not all molecules
Whales are part of the clade for
artiodactyls
Whales are just highly adapted
artiodactyls.
A molecular clock is the
average rate at which a given gene or protein accumulates changes, and this rate of change can be used to gauge the time of a particular split in the phylogeny
Why is HIV 1 more infective than HIV2?
because it comes from our closest relatives ( the chimpanzees) and it doesn't require many changes to go from chimps to humans
the order of nodes along the horizontal (time) axis has meaning but the vertical distance
between the branches does not. it is largely arbitrary
Linnaeus developed a naming system called
binomial nomenclature that has allowed scientists throughout the world to refer unambiguously to the same organisms by the same names
now we recognized the tree of life as the basis for
biological classification
molecular clocks are used not only to date ancient events but also to study the timing of comparatively recent events. For example,
biologists were able to use the observed changes in HIV-1 over the past several decades to extrapolate back to the common ancestor of a group of HIV1 samples and estimate when HIV1 first entered human populations from chimpanzees
convergence/homoplasy
birds and bats both evolved flight, but they evolved those traits independently
Example of convergent/homoplasy
cactus and euphorb
A true monophyletic group
can be removed from a phylogenetic tree by a single cut in the tree
The name of the genus is alway
capitalized
HIV-1 is the common form of the virus in human populations in
central Africa, where chimpanzees are hunted for food
the branches can be rotated around any node and this does not
change the meaning of the trees
animal mitochondrial DNA
changes more rapidly and so mitochondrial genes have been used extensively to study evolutionary relationships among closely related animal species
branches can be flipped around the node without
changing the meaning of the tree
Wing is a
character
orders are grouped into
classes
A genus is a group of
closely related species
root
common ancestor for the group, normally shown on left
parental care evolved in reptiles in the
common ancestor of crocodiles and dinosaurs
phylogenies allow us to
compare and contrast living organisms
knowledge of evolutionary relationships is essential for making
comparison among evolutionary lineages (genes, species, clades) inferences about how particular traits of interest evolved inferences about the traits of poorly known or extinct lineages
phylogenies can reveal
convergent evolution
Both Saber-toothe marsupials and Saber-toothed cats are found today. THESE SPECIES ARE NOT IN THE SAME TAXONOMIC GROUP
convergent evolution; meaning the do not have recent, common saber-toothed ancestors
convergent evolution
convergent evolutions the phenomenon of independently evolved traits subjected to similar selection pressure may become superficially similar.
the evolution of morphological characters associated with flight is a classic example of the principle of
cooption: traits often evolved for some function other than their current function and have been coopted for their current function.
Parental care evolved in the common ancestor to
crocodiles and dinosaurs
Various taxa in caves lost eye and body pigmentation. Why?
dark environment, eyes and body pigmentation not needed energy can be used elsewhere, for reproduction repeated evolution of blind, albinao species
the molecular clock is used to
date evolutionary events
A particular trait may be ancestral or derived
depending on our phylogenic point of reference. Ex: feathers are an ancestral trait for any group of modern birds. However, if we were reconstructing the phylogeny of all vertebrates, the presence of feathers would be a derived trait that informs us about the close evolutionary relationships between birds and their extinct theropod dinosaur relatives
synapomorphies
derived traits that are shared among a group of organisms and are viewed as evidence of the common ancestry of that group are called synapomorphies
traits that are present only in some members of the in-group must be
derived traits within that ingroup
explicit mathematical models have been developed to
describe how DNA sequences change over time
Ex of paraphyletic group
dinosauria excluding birds
you can use fossils to estimate
divergence times
paraphyletic group
does not include all the relevant information does not include all the descendant
Monophyletic group or clade
encompasses one lineage and all descendats dinosauria include birds as they are descendants
Butterfly eyespots on wings is controlled by both
engrailed and modified Distalless
in many cases, investigators are interested in how the evolution of a trait depends on
environmental conditions or selection pressure
Phylogeny can be used to estimate
epidemiology
convergence
evolution of similar form and function not due to common descent
all life is connected through
evolutionary history
comparisons among species require an
evolutionary perspective
phylogenetic trees are depictions of
evolutionary relationships. Hypothesis of lineages Root to tip: past to present
New technological tools, such as electron microscope and computed tomography (CT) scans enables systematists to
examine and analyze the structure of organisms at much finer scales than was formerly possible
maximum likelihood methods incorporate more
explicit mathematical models of evolutionary change to reconstruct evolutionary history
the taxon above the genus in the linnaean system is the
family.
in-group all share that
first derived trait
outgroup does not have the
first derived trait (lamprey lacks jaws)
the valid name is the
first name that was proposed
the phylogenetic tree in the book depict time
flowing from the left (earliest) to right (most recent)
Fossil record support parental care in dinosaur
fossils found of dinosaurs practicing parental care, bones among nests
transitions occur more
frequently than transversions
Why can't you treat athlete's foot with anti-fungal medicine?
fungus too close to us phylogenetically as compared to bactera
character
general category and organisms manifest different states
Family names are based on the name of a member
genus but are not italicized
Mathematical models can be used to compute how a tree might evolve
given the observed data
phylogenetic tree
graphic representation of these lines of evolutionary descent. phylogenetic tree is a diagram that portrays a reconstruction of that history
phylogeny is the
history of evolutionary relationships among organisms or their genes.
Homo sapiens
homo is the genus to which the species belongs and sapiens identifies the particular species in the genus Homo
wing bones of bat and birds are
homologous
vertebral column is judged to be
homologous in all vertebrates
homoplasy results from
homoplasy results from convergent evolution or evolutionary reversal and usually reflect adaptation evolution in response to similar natural selection
Hoatzin have
homoplasy with species that have claws on forelimbs (but again, no evolutionary history, evolved independently by mutation)
phylogenetic trees
hypotheses of the hierarchical, evolutionary relationships of organisms, genes of population
the names of animal families end in the suffix
idae
Phylogenetics on trial
in court: phylogenetic evidence supported that man injected former girlfriend with HIV Girlfriend's HIV was used in the man's HIV clade, rather than someone from the community
any trait that is present in both the in-group and the outgroup must have evolved before the origin of the
in-groups and thus, must must be ancestral for the ingroup
all taxonomists now agree that polyphyletic and paraphyletic groups are
inappropriate as taxonomic units because they do not reflect evolutionary history
molecular clocks must be calibrated using
independent data, including fossil record, known times of divergence, or biogeographic dates ( such as the dates for separation of continents).
the root of the tree is located between the
ingroup and outgroup
Experiment to test accuracy of phylogenetic method
initial culture was split into two separate lineages, one became the in-group for analysis and the other lineage became the outgrip used for rooting the tree. Mutagens were added to the cultures to increase the mutation rate and the lineages in the in-group were split into two after every 400 generations and samples of the virus were saved for analysis at each of these branching points They they sequenced the samples from the end point of the eight lineages and give it to investigator to analyze without revealing the known history of the lineages or the sequences of the ancestral viruses
Both names are
italicized
and phyla into
kingdom
What character states were involved in power flights in birds?
light bones chest bone wish bone long arms highly mobile wrist long aerodynamic feather arms longer than legs After reconstruction, all of these character states evolved prior to power flight
viruses recombine across
lineages (horizontal gene transfer)
the name identifying the species is always
lowercased
maximum likelihood
mathmatical explanation of development of traits
phylogenetic trees can be constructed with
maximum likelihood method, which find the tree most likely to have generated the observed data
applying the parsimony principle to the construction of phylogenetic trees entails
minimizing the number of evolutionary changes that need to be assumed over all characters in all taxa in the tree
Evolutionary history is the basis for
modern biological classification
gene function as
molecular clocks, assisting with dating evolutionary events
maximum likelihood method are most often used with
molecular data
taxa are expected to be
monophyletic
taxa in modern classification are expected to be
monophyletic groups. paraphyletic and polyphyletic groups are not considered appropriate taxonomic units
biologist organize and classify life by identifying and naming
monophyletic groups. several sets of rules govern the use of scientific names so that each species and the higher taxon can be identified and named unambiguously.
taxa that share synapomorphies should be
more closely related to each other than to taxa lacking those character states
Example of convergent evolution
multiple lineages of cavefish without eyes evolved independently (seen in phylogeny)
HIV invaded human population on
multiple occasions; either 4 to 5 times; originated from the simian IV
Descendent with modification (natural selection) results in a
natural hierarchy of life, a phylogenic tree, or phylogeny
The timing of a splitting event in a lineage is shown by the position of a
node on the time axis, sometimes called the divergence axis
All vertebrate animals have a
notochord at some point during their development
the splits of the time axis represents events in which
one lineage diverged into two, such as a speciation event (for a tree of species), a gene duplication event (for a tree of genes), or a transmission event (for a tree of viral lineages transmitted through a host population)
Linnaeus gave each species two names
one name identifying species itself and the other the genus to which it belongs
how do we determine which traits are synapomorphies and which are homoplasies?
one way is to invoke the principle of parsimony
families are grouped into
orders
What can we infer, using the principle of parsimony for parental care?
parental care probably did not evolve twice
the node in the case of species, these split represent
past speciation events, when one lineage divided into two
and classed are grouped into
phyla (phylum)
reconstruction of ancient DNA sequences can also provide information about the biology of long-extinct organisms. For example,
phylogenetic analysis was used to reconstruct an opsin protein found in the ancestral archosaur. the investigators inferred the sequence and found that there was shift toward red end of the spectrum in light sensitivity compared to modern opsin. This means the ancestral archosaurs might have been active at night
Mathematical models expand the power of
phylogenetic reconstruction
The chloroplast genome is used extensively in
phylogenetic studies of plants, has changed slowly over evolutionary time, so it is often used to study relatively ancient phylogenetic relationships
groups of evolutionarily related species are represented as branches in a
phylogenetic tree
Phylogeny of dinosaurs
phylogeny of dinosaurs is based on bony characters clade away from outgroup have lighter bones. Dinosaurs were bipedal(lighter bodies for running and chasing food)
Example of why phylogenetic analysis is important
physician who purposefully injected blood from one of his HIV positive patients into his former girlfriend in attempt to kill her. The phylogenetic analysis supported viral transmission from the physician's patient to the victim
clades can be identified by
picking any point on a phylogenetic tree and then tracing all the descendant lineages to the tips of the terminal branches
original state of a characteristic is called
plesiomorphic (primitive)
groups that are not clades
polyphyletic or paraphyletic are not natural groups
parsimony states
preferred explanation of our observations is the simplest explanation
A and G are
purines
C and T are
pyrimidines
evolutionary reversal example
reduced eyes and pigmentation in cave fish
Molecular data: presence of LINEs and SINEs in whales and hippies suggest that they are most
related to each other than other mammals
The best hypothesis under the parsimony principle is the one that
requires the fewest homoplasies
The common ancestor of all the organisms in the tree forms the
root of the tree
Example of phylogeny reveals convergent evolution
self compatibility apparently evolved independently among these species of the plant genus Leptosiphon. Because the appearance and the structure of the flowers converged in the three selfing lineages, taxonomists mistakenly thought they were varieties of the same species.
synapomorphies
shared, derived character states
characters that have evolved similar states independently in 2 or more taxa are often associated with a
similar functional adaptation
characters that have evolved similar states independently in tow or more taxa are often associated with a
similar functional adaptation
homoplasties or homoplastic traits
similar traits in distantly related taxa generated by convergent evolution or evolutionary reversals
homologies are
similar traits that have been inherited from a common ancestor
Development
similarities in developmental patterns may reveal evolutionary relationships. some organism exhibit similarities in early developmental stages only. EX: the notochord of the sea squirts disappears as the larvae develop into adults
Parsimony provides the
simplest explanation for phylogenetic data
Parsimony is one way of choosing a phylogenetic tree (hypotheses)
simplest explanation for the pattern in the data is the preferred hypothesis (occam's razor) requires the fewest number of evolutionary changes
phylogenetic trees can be constructed by using parsimony principle to find the
simplest explanation for the phylogenetic data
variations occurs in character states
single nucleotide change
Behavior
some behavioral traits are culturally transmitted and some are inherited. Bird songs are culturally transmitted and is inappropriate traits for phylogenetic analysis. Frog calls are genetically determined and appear to be acceptable sources of information for reconstructing phylogenies
HIV-2 is the common form in human populations in western Africa where
sooty mangabeys are hunted for food.
group=
species
node
split in branch that indicate a division of one lineage into two
Linnean classification is
subjective
Transition
swapping between pyrimidines (CT)or purines(AG)
transversion
swapping for purines from pyrimidine
phylogenetic trees can be constructed from
synapmorphies using the logic of parsimony
a derived trait that is shared by two or more taxa and is interrupted from their common ancestor is called
synapomorphy
vertebral column is considered a
synapomorphy: a shared derived trait of the vertebrates
named species and groups of species are called
taxa
any group of organisms that is treated as a unit in a biological classification system, such as the genus Drosophila or all insects is called a
taxon
phylogenetic systematics
taxonomy that reflects relationship
The accuracy of phylogenetic methods can be
tested
convergent evolution and evolutionary reversals give rise to traits
that do not result from common ancestry called homoplasies
cladistics
the approach to inferring phylogenetic relationships based on the distribution of derived character states among taxa
Molecular clock hypothesis
the approximately constant rate of divergence of macromolecules from one another over evolutionary time; used to data past events in evolutionary history
Occam's razor
the best explanation is the one that fits the data the best while making the fewest assumptions
a phylogenetic tree may be used to portray
the evolutionary history of all life forms; of a major evolutionary group; of a small group of closely related specie; or in some cases, even of individuals, populations or genes within a species.
What is phylogeny
the history of evolutionary relationships among genes, species, or higher taxa
phylogeny
the history of evolutionary relationships among organisms or their genes.
why study rats and mice and relate it to human behavior?
the model works; mice and rats are similar enough to use phylogenetically
morphology
the presence, size, shape, and other attributes of body parts
What is the principal advantages of maximum likelihood?
the principal advantages of maximum likelihood analyses are that they incorporate more information about the evolutionary change than do parsimony methods, and they are easier to rate in statistical framework
What are the principal disadvantages of maximum likelihood?
the principal disadvantages are that they are computationally intensive and require explicit mathematical models of evolutionary change
evolutionary reversal
the reversion to a primitive state
Occam's razor
the simplest explanation for the data is the preferred hypothesis
systematics
the study and classification of biodiversity
The origin of a sexually selected trait Sensory exploitation hypothesis
the tail extension of male swordtails apparently evolved through sexual selection, as females mated preferentially with males that had long swords phylogenetic analysis reveals that the platy fishes split from the swordtails before the evolution of the sword. The independent finding that female platyfish prefer male platyfish with an artificial sword further supports the idea that this appendage evolved as a result of a preexisting preference in females
monophyletic means
the taxon contains an ancestor and all descendants of that ancestor and no other organisms; in other words, taxon should be a complete branch on the tree of life (a clade)
Characters are
the thing that is shared among all of the taxa
the positions of the nodes on the time scale indicate
the times of the corresponding speciation events
several codes of biological nomenclature govern the use of scientific names. the rules of biological nomenclature are designed so that
there is only one correct scientific name for any single recognized taxon and so that a given scientific name applies only to a single taxon.
we infer sea squirts are more closely related to vertebrates because
they have a notochord during their early development
Green Fluorescent was discovered when the protein was extracted from the
tissues of bioluminescent jellyfish Aequorea Victoria
maximum likelihood identify the tree that is most likely
to have produced the observed data, given the assumptions of the model
transitions(changes between two purines or between two pyrimidines) are usually more likely than are
transversions (changes between a purine and pyrimidine)
the complete evolutionary history of life is known as the
tree of life
sister species
two species that are each other's closest relatives
polyphyletic group would be to put the
two together superficially
systematists
use explicit criteria to determine which hypothesis of relationships (trees) are most consistent with the data
GFP can be used for
visualizing gene expression
We are fish and we are primates
we are 1 lineage with mammals, but 1 lineage with fish too. lungfish share a more recent common ancestor to all tetrapods(us) than other firsh
by combining information about the various synapomorphies,
we can construct a phylogenetic tree
A group of jawless fishes called the lamprey is thought to have separated from the lineage leading to the other vertebrates before the jaw arose
we include the lamprey as the outgroup for our analysis. Because derived traits are traits acquired by other members of the vertebrate lineage after they diverged from the outgroup, any trait that is present in both the lamprey and the other vertebrates is judged to be ancestral
Parsimony
which tree is used? the tree that minimizes the number of evolutionary changes ( or changes in character state) is the preferred hypothesis
character state can be
wing is long, reduced or absent
Example of polyphyletic group
winged tetrapods
example of polyphyletic group
winged tetrapods (grouping by superficial characteristics that do not have evolutionary history
Do birds practice parental care?
yes