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