Evo Bio Ch. 4 Estimating Evolutionary Trees

Three principles of cladistics

1. Any group of organisms is related by descent from a common ancestor 2. There is a bifurcating pattern of cladogenesis 3. Change in characteristics occurs in lineages over time

What are the assumptions regarding characters for phylogenetic analysis?

1. Homology 2. Character states have genetic basis 3. Characters are independent 4. Character evolution reflects organismal phylogeny

Other Phylogenetic methods (2)

1. Maximum Likelihood 2. Bayesian Markov Chain Monte Carlo (BMCMC)

Phylogeny of Whales Reconstructing the correct phylogeny of cetacean + hippo clade Which characters should be used to reconstruct the correct phylogeny? (2) Which one can only be used for fossils? Why are these characters difficult to use? Can they be scored rapidly?

1. Morphological characters -Skeleton 2. Molecular characters -Allozymes, RFLPs, DNA sequences Morphological characters can be used -Morphological characters difficult to use because taxonomic expert needed Many molecular characters can be scored rapidly Homoplasy difficult to identify Only four bases: G, A, T, C *Often best to use both types of characters*

Cladistic methods Several methods used to identify polarity: (5)

1. Most commonly used is the outgroup method 2. The character state of the target taxa is compared with that of a relative that diverged earlier 3. Outgroup represents the ancestral state 4. Identify outgroup from other phylogenetic studies or fossil data 5. Good to use several outgroups at once

Phylogeny of Whales Other reconstruction methods *Distance methods* (5)

1. Neighbor joining and UPGMA 2. Based on clustering technique 3. Based on overall similarity 4. Not a cladistic method 5. Uses differences (distances) among character states to group taxa

Phylogeny of Whales Other reconstruction methods (4) -Parsimony is not the only criterion for reconstructing phylogenies

1. UPGMA (Unweighted Pair-Group Method using arithmetic Averages) 2. Neighbor Joining 3. Maximum Likelihood 4. Bayesian Analysis

Molecular characters

1. huge number of characters 2. closer to real genetic basis 3. better models of how characters evolve 4. more amenable to certain analyses -Maximum likelihood -Bayesian Analysis

Morphological characters

1. well-established characters 2. lots of material 3. less expensive 4. genetic basis often poorly understood but may examine many "genes" at one time 5. can examine fossil taxa 6. can look at more individuals more often

Phylogeny of Whales Of the molecular data set some characters are parsimony informative, some are autapomorphic and some are invariant -Only synapomorphies used -Most synapomorphies support the overall phylogeny but one does not -One synapomorphy supports whale + hippo clade -Find most parsimonious solution for entire tree

142 - symplisiomorphy ( shared because its ancestral) 192 - otapomorphy 162 - synapomorphy that links cow, deer, whale, and hippo 166 - synapomorphy links whales and hippos 177- synapomorphy that links whale, hippo, pig, and peccary

What is the goal of mapping character states? What can you see after mapping is done? Ecologists and behaviorists studying the distribution of traits among species should always map the character states on a ______

Goal is to trace the evolution of a phenotypic trait along a phylogeny Can see if a trait is found within certain clades or if it has independently evolved multiple times phylogeny

Maximum Likelihood _____ Likelihood is the best.

Highest

Phylogenetic Method traits that are similar because they are derived from a common ancestor = ______

Homology

The same traits may be independently derived in different lineages (*character shared by a set of species but not present in their common ancestor*) Ex: Seal and penguin flippers, Flight in birds, bees and bats *ANALOGOUS STRUCTURES*

Homoplasy

Using Distance Methods to Reconstruct Phylogenetic Relationships

Species with the LEAST genetic distance (or other distance) between them are assumed to be CLOSE relatives

Cladistic methods _____ = a closely related taxon that is used to represent the ancestor Of course, one living species cannot be the ancestor of another, but we use the ______ to represent the ancestor tells us which characters are ____ and which are _____

Outgroup (2) derived ancestral

Phylogenetic Tree Terms Group that is monophyletic except that some descendents of the common ancestor have been left out

Paraphyletic Group

________ = graphical summary of evolutionary history Phylogeny is only an _____ A tree represents the _____ of evolutionary relationships given the data available

Phylogenetic tree estimate best hypothesis

Phylogeny of Whales Explain process using controversial example of the relationship of cetaceans to ungulates part 2

Recent molecular studies suggest that *cetacean + hippo clade is more likely* (a) than artiodactyl + cetacean clade (b) Suggests that some traits for aquatic life shared among hippos and whales are not convergent but homologous *Synapomorphies * Must test which phylogeny is more correct

Non-coding DNA inserted into genomes (retrotransposons)

SINE/LINE (whale and hippo share the # 1 code in locus 4,5,6)

How does Maximum Likelihood calculate the probability of the data given the tree. P(data|tree)?

Calculates the Likelihood statistic, which helps estimate the topology of the tree Uses all data, even autapomorphies and invariant sites Uses a particular model of evolution to help estimate the topology (tree shape) and branch lengths of the tree

Phylogeny of Whales How do we evaluate confidence in a tree? Is whale + hippo tree substantially better than whale + artiodactyl tree?

Can view slightly suboptimal trees (less parsimonious) to see how much difference there is Bootstrapping statistically evaluates confidence in nodes -Repeated sampling to see if tree differs from chance

Father of the modern classification system (lived 1707-1778) Published Systema Naturae in 1758 (10th edition) *Binomial nomenclature system* _____ system of classification -Each taxonomic level is nested within the level above it -Kingdom, Phylum (Division), Class, Order, Family, Genus, Species

Carolus Linneaus (Carl von Linné) Hierarchical

Tree terminology a monophyletic group

Clade

Techniques that identify monophyletic groups based on synapomorphies

Cladistic Method

Rules of Taxonomy _____ is governed by formal rules that scientists must follow -International Union of Zoological Nomenclature Naming conventions, native classifications, etc. -People of all cultures classify the organisms they encounter into groups

Classification

Non-Monophyly and Classification Are paraphyletic taxa common or uncommon? -Reptiles are paraphyletic with respect to _____ -Bony fishes are paraphyletic with respect to _____ ______ is less common and more worrisome If we wish to base our classifications on only monophyletic groups (as most systematists do now), it is important to know what? -Based on this criterion, many classical classifications should be altered

Common birds tetrapods Polyphyly The phylogeny of the groups in question before constructing the classification

Using Phylogenies to Answer Questions Difficulties with Molecular Clock

The molecular clock does not run as smoothly as originally predicted Irregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes may improve estimates

Parsimony and Phylogeny Most closely related taxa should have the most traits in _____ Characters -May be DNA sequence, presence or absence of skeletal elements or floral parts, mode of embryonic development, etc. -Characters scored in different taxa must be ____

common homologous

Cladistic Methods When no convergence or reversal occurs, all synapomorphies are ______ When all nodes are not congruent, goal is to minimize _____ Tree made using synapomorphies is a _____ _____ is a monophyletic group

congruent homoplasy cladogram Clade

Phylogeny of Whales Why is the Astragalus (a.k.a. talus; bone in ankle joint) an important character in mammal systematics?

Divides artiodactyls from perissodactyls If whales are sister to all artiodactyls, specialized astragalus evolved only once If whales are sister to hippos, two evolutionary steps are needed -Whales lack an astragalus Whale + hippo is less parsimonious

Mapping How is mapping done? What can you see after mapping is done? Can do multiple characters at the same time with a computer program and compare the map

Done by optimizing characters on a phylogeny Can then see where on the phylogeny each character has appeared

In Phylogenetic Methods, It is useful to use a variety of tree _____ methods If methods are congruent you have _____ confidence in your reconstructions

reconstruction more

Homoplasy Natural selection favors _______ in similar _____ Convergent evolution produces homoplasies a.k.a. ______ structures Homoplasy is the cladistic term we will use

similar adaptations habitats analogous

Using Phylogenies to Answer Questions Phylogenetic systematics can aid in classification of ____ Phylogenetic and evolutionary species concepts require that taxa be ______ Many traditional classifications are not based on _____ -Order Artiodactyla is not monophyletic -Order Cetacea should be sunk to family level

taxa monophyletic monophyly

How to Group Organisms? Linneaus and most taxonomists after him grouped taxa based on overall similarity without regard to _____ Today our challenge is correcting the taxonomy to only group organisms that are related by shared evolutionary history, regardless of outward _____ What makes this difficult?

Evolutionary relationships Similarity Convergence

What is the Phylogenetic Method?

Evolutionary relationships should only be reconstructed from traits that are similar because they are derived from a common ancestor

Binomial Nomenclature Each species has a unique name composed of ______ Better than just using common names because it is more ___ -Many obscure organisms don't have common name Linneaus' system is still in use by all biologists worldwide today Ex: Rana catesbeiana (bullfrog)

*Genus and species* exact

Phylogeny of Whales Extinct whales with legs have features of astragalus similar to who's? What does this statement support? Systematists use more than one ______ when reconstructing trees -Must minimize homoplasy over all characters -DNA sequence data supports whale + hippo clade

Artiodactyls Support for whales as artiodactyls character

Parsimony and Phylogeny Some traits are derived along a single lineage (*derived trait that is unique to one group*) Not useful for estimating relatedness

Autapomorphy

New likelihood methods employing Bayesian statistics along with Marcov Chain Monte Carlo algorithms are helping to solve time problem and are the cutting edge of phylogeny reconstruction these days... Similar to likelihood except P(tree|data) not P(data|tree) Ask what the probability is of a particular tree being correct, given the data and a model of evolution Excellent methods of *inference*

Bayesian Markov Chain Monte Carlo (BMCMC)

Homoplasy In homoplasy, why would a train revert to ancestral form? -What happens after? What two terms are collectively known as homoplasy? -What do those terms mean? Ex:Phrynosoma and Moloch -Desert dwelling ant specialists from two different families

Because of mutation or selection -This may destroy phylogenetic signal and lead to reconstruction of misleading relationships -Reversal Convergence and reversals -*similarity that does NOT arise from common ancestry*

Phylogeny of Whales _____ values are percentages of the number of times the same branch arose after repeated sampling What does support over 70% indicate? Investigators usually report any of its value over 50%

Bootstrap That the correct relationship was probably found

Distance-Based Methods (UPGMA, Neighbor Joining, etc..)

Distance methods are typically very very fast and easy to use to estimate a phylogenetic tree However, they are *not cladistic* because they do not look for *synapomorphies*, but rather overall similarity... -This means this method is also susceptible to lots of error when a dataset has lots of homoplasy...

Using Phylogenies to Answer Questions Molecular Clock

It is hypothesized that molecular change happens at a steady rate If this is so, you should be able to use known dates to calibrate a molecular clock and be able to discern the ages of branching events -Calibrate with fossils or geologic events Clocks for a variety of taxa have been estimated to tick at a rate of 2% sequence divergence per million years Used mitochondrial genes -Different genes evolve at different rates Other scientists have challenged the clock and found that molecular change does not always happen in a clocklike fashion

Allows us to account for complex patterns of nucleotide evolution across regions of genes that may evolve very differently (thus, not all types of changes are weighted evenly in determining the phylogeny...) Models can be simple (like parsimony) or very complex Ideally, the model will be complex enough to actually estimate the rates of evolution of the branches of the tree

Maximum Likelihood

assumes a particular probabilistic model of sequence evolution and then calculates for each tree *the probability of the data given the tree. P(data|tree)*

Maximum Likelihood

are among the most accurate methods to reconstruct phylogenies Because this method must estimate a model, it must work with simple data sets like DNA sequence data -DNA sequence data is simple because each character can only have one of four states A, T, C, G Morphology has too many possible states and would be too hard to model *ML is VERY VERY computationally intensive* - a tree with 30 species may take several days, with 100 species may take several months!

Maximum Likelihood Method

Parsimony and Phylogeny ________ method minimizes total amount of evolutionary change in a tree ________ are usually more common than convergence and reversal Most parsimonious trees minimize ______ to give best estimate of phylogeny

Maximum Parsimony Synapomorphies homoplasy

Phylogenetic Tree Terms All members are believed to stem from a single common ancestor, and the group includes this common ancestor

Monophyletic Group

In taxonomy, is there a one "true" classification? How is taxonomy decided? In taxonomy, what changes as new data are discovered?

NO By the opinions of biologists Classifications

Tree terminology represent extinct taxa and bifurcating branching points

Node

Hypothesis of evolutionary relationships

Phylogeny

Reconstructing evolutionary relationships

Phylogeny

Rectangular tree with informative branch lengths

Phylogram

Parsimony and Phylogeny Traits may also occur because they are retained from the ancestor (*primitive or ancestral trait*)

Pleisiomorphy (Sympleisiomorphy)

Phylogenetic Tree Terms consisting of unrelated lineages, each more closely related to other lineages not placed in the taxon

Polyphyletic Group

Bayesian Markov Chain Monte Carlo (BMCMC) Equation: *P(treeIdata) = P(dateItree)P(tree)/P(data)

Posterior Probability = Likelihood of tree x Prior probability of tree / Prior probability of data

The simplest explanation is the most likely to be true Occam's razor

Principle of parsimony

Phylogenetic Method are used to decide where branches should be on a phylogeny (*derived trait shared by two or more groups*)

Synapomorphies

In Cladistic Method _______ define evolutionary branching points _____ and ______ do not define evolutionary branching points Must be able to identify homology of traits and direction of change through time

Synapomorphies Autapomorphies and ancestral characters (plesiomorphies)

Phylogenetic Method Shared derived characters of all members of a group = _____

Synapomorphy

Study of biological diversity and evolutionary relationships of organisms

Systematics

Classifying organisms in groups

Taxonomy

Two fields of systematics

Taxonomy Phylogeny

The science of naming taxa and placing them into groups ______ = species or genus or kingdom, etc. The science of classifying organisms

Taxonomy Taxon

Phylogeny of Whales Explain process using controversial example of the relationship of cetaceans to ungulates part 1

Whales and dolphins are in order Cetacea -Synapomorphy is loss of posterior limbs Because whales are highly evolved for aquatic life, assigning relationships with other mammals is difficult Phylogenetic studies have found that *whales are closely related to order Artiodactyla (even-toed ungulates: pigs, camels, cattle, hippos)* -Whale fossils with hind limbs

Phylogeny of Whales How do we find the best tree?

With a small number of taxa you can evaluate all possible trees -Exhaustive search With more taxa the amount of possible trees increase exponentially For 8 taxa in artiodactyl tree there are 10,395 possibilities Must use a shortcut method to evaluate trees

Homoplasy Does homoplasy create noise in the data? Some characters give ______ information about relationships Systematists try to _____ homoplasy in a data set (Occam's razor) Choose characters that evolve slowly relative to age of taxa = autapomorphies are ______

YES conflicting minimize uninformative