Chapter 4:Evolutionary Biology

What is systemics?

study of biological diversity and evolutionary relationships of organisms made up of two fields taxonomy and phylogeny

Taxonomy

The science of classifying organisms by naming taxa and placing them in groups, there is no true classification classifications change as new data is discovered

Phylogeny

Evolutionary history of a species or group of species.

Taxon

species or genus or kingdom etc

Rules of Taxonomy

Formal rules that scientists must follow from the International union of zoological nomenclature

Carolus Linnaeus

Father of the modern classification system who published Systema Naturae he created a binomial nomenclature system and a hierarchical system of classification where each taxonomic level is nested within the level above it

What is the hierarchical order ?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species, Subspecies

Binomial nomenclature

Each species has unique name including a genus and species

How did Linnaeus group organisms?

His strategy was to classify organisms according to visible similarities and differences. Today scientist are correcting taxonomy to only group organisms that are related by shared evolutionary history convergence makes this difficult

Convergent evolution

The evolution of two unrelated organisms into similar morphologies (ie bats and birds)

Phylogeny

Hypothesis of evolutionary relationships

Phylogenetic tree

A graphical summary of evolutionary history, phylogeny is an estimate and a tree represents the best hypothesis of evolutionary relationships given the data available

Occams razor

William of Ockham logician and friar who said entities should not be multiplied unnecessarily which was restated by Issac newton who said we are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances aka keep it simple stupid

The simplest explanation is most likely to be true

Principle of parsimony

the belief that explanations of phenomena and events should remain simple until the simple explanations are no longer valid

Homology

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

Synapomorphy

Shared derived characters of all members of a group these are used to decide where branches should be on a phylogeny

Autapomorphy

Some traits are derived along a single lineage this is not useful for estimating relatedness

Plesiomorphy (symplesiomorphy)

Traits may also occur because they are retained from the ancestor

Homoplasy (analogous)

The same traits may be independently derived in different lineages, natural selection favors similar adaptations in similar habitats. Traits may revert to ancestral form because of mutation or selection this may destroy phylogenetic signal and lead to misleading reconstruction

Convergent evolution..

Produces homoplasies aka analogous structures (homoplasy is the cladistic term used in this class) Convergence and reversals are collectively known as homoplasy

How does homoplasy affect phylogenetic data?

Creates noise in the data and can give conflicting information about relationships, systematists try to minimize homoplasy in a data set (Occam's razor) they choose characters that evolve slowly relative to the age of taxa ( autapomorphies are uninformative)

Maximum Parsimony Method

Minimizes total amount of evolutionary change in a tree

Assumptions for phylogenetic analysis

1) Homology

2) Character states have genetic basis

3) Characters are independent

4) Character evolution reflects organismal phylogeny

Parsimony and phylogeny

Most closely related taxa should have the most traits in common

Characters

May be DNA sequence or absence of skeletal elements or floral parts, mode of embryonic development etc. Characters scored in different taxa must be homologous.

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

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 and bayesian analysis)

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

Cladistic methods

Techniques that identify monophyletic groups based on synapomorphies which define evolutionary branching points Autapomorphies and ancestral characters (plesiomorphies) do not. Must be able to identify homology of traits and direction of change through time.

What methods are used to identify polarity?

The outgroup method is commonly used where the character state of the target taxa is compared with that of a relative that diverged earlier, the outgroup represents the ancestral state and is identified from other phylogenetic studies or fossil data, can use several outgroups at once

Outgroup

A closely related taxon that is used to represent the ancestor, the outgroup tells us which characters are derived and which are ancestral

Maximum Parsimony Analysis

Considers tree with fewest evolutionary changes as most likely.

Cladogram

Tree made using synapomorphies is a cladogram

Clade

A monophyletic group

Monophyletic group

group that consists of a single ancestral species and all its descendants and excludes any organisms that are not descended from that common ancestor

Congruence

When no convergence or reversal occurs all synapomorphies are congruent, when all nodes are not congruent, goal is to minimize homoplasy

If methods are congruent you have more confidence in phylogenetic reconstructions

Nodes

Connecting points between branches that represent extinct taxa and bifurcating branching points

Bifurcation

Point where branches go in two directions

What ways can you draw a tree?

Slanted or rectangular

Phylogram

Rectangular with informative branch lengths

Polytomy

A branch point from which more than two descendant groups emerge this means the nodes are unresolved and their is uncertainty about their lineages

Monophyletic group

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

Paraphyletic group

A group that is monophyletic except that some of the descendents of the common ancestor have been left out

Polyphyletic group

Consisters of unrelated lineages each more closely related to other lineages not places in the taxon

Winged organisms are..

Polyphyletic ex: birds and wasps

What groups are Non-monophyletic?

Fish, prokaryotes, Dicots

Paraphyletic taxa

Are common, reptiles are paraphyletic with respect to birds and bony fish are paraphyletic with respect to tetrapods

Polyphyletic taxa

Are less common and more worrisome if we wish to base our classifications on only monophyletic groups ( most systematists do now) it is important to know the phylogeny of groups in question, many classical classifications still need altered

Phylogeny of whales

Whales and dolphins are in order Cetacea synapomorphy is loss of posterior limbs since whales are highly evolved assigning relationships is hard phylogenetic studies have found whales are closely related to order Artiodactyla ( even toed ungulates) aka pigs, camels, hippos

Hippos and whales

Recent studies suggest that cetacean and hippo clade is more likely than artiodactyl and cetacean clade which suggests traits for aquatic life between hippos and whales are homologous and synapomorphies

Factors used to reconstruct phylogenies

Morphological characters (skeleton), Molecular changes ( allozymes, DNA sequences), for fossils only morphological characters can be used and taxonomic expert is needed, often best to use both types of characters

Phylogenetic tree scoring

Assign a value to indicate relatedness or quality of relationship for part of tree structure

Whale and hippo talus bone

Astragalus aka talus bone in ankle joint is important in mammal systemics. If whales are sister to hippos two evolutionary steps are needed because whales lack an astragalus, this means whale + hippo is less parsimonious

why are whales supported as artiodactyls?

Extinct whales with legs have features of astragalus similar to artiodactyls

Why is more than one character used for reconstructing trees?

Must minimize homoplasy over all characters, DNA sequence data supports whale + hippo clade, one synapomorphy supports whale + hippo must find the most parsimonious solution for entire tree

Bootstrapping

Statistically evaluates confidence in nodes repeated sampling is used to see if tree differs from chance, bootstrapping values are percentages of the number of times the same branch arose after repeated sampling, bootstrap support over 70% indicates that the correct relationship was likely found, usually values are reported if they are over 50%

What are other reconstruction methods for trees?

Unweighted Pair-Group Method (UPGMA), Neighbor Joining, Maximum likelihood, Bayesian Analysis

Distance methods

Includes neighbor joining and UPGMA methods, based on clustering technique and overall similarity this is not a cladistic method and uses differences (distances) among character states to group taxa

Species with the least genetic distance assumed to be close relatives

Pros and cons of distance methods

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 meaning the method is susceptible to lots of error if there is a lot of homoplasy

Maximum likelihood phylogenetic method

Assumes a particular probabilistic model of sequence evolution and then calculates for each tree the probability of the data given, calculates the likelihood statistic which helps estimate the topology of the tree uses all data even autapomorphies and invariant sites P(data/tree)

Pros of the maximum likelihood method

Allows us to account for complex patterns of nucleotide evolution across regions of genes that may evolve differently, ideally model will be complex enough to estimate the rates of evolution of the branches of the tree

Why is maximum likelihood one of the most accurate methods?

This method must estimate a model and work with simple data sets like DNA sequence data which can only have four states ( base pairs) Morphology has to many states and would be more difficult to model, ML is very computationally intensive will take a long time

Bayesian method

Helps solve time issue associated with ML used P(tree/data) very similar to maximum likelihood

Sine/Line

Non coding DNA inserted into genomes retrotransposons

Molecular clock

It is hypothesised that molecular change happens at a steady rate you can use known dates to calibrate a molecular clock and be able to discern the ages of branching events using fossils or geologic events

Clocks for taxa

Have been estimates for a variety of taxa and have estimated to tick at a rate of 2% sequence divergence per million years, used mitochondrial genes and different genes evolve at different rates

Difficulties with molecular clocks

Not as smooth as originally predicted Irregularities from natural selection where some DNA changes are favored over others, some estimates are older than the fossil record and have a high degree of uncertainty, use of multiple genes may improve estimates

Mapping character states

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, ecologists and behaviorists studying distribution of traits should always map character states on a phylogeny

How is mapping done?

Done by optimizing characters on a phylogeny then can see where on the phylogeny each character appeared can do multiple characters at the same time with computer program and compare the map

Turtle case study

Ultraconserved elements provide evidence that turtles are a sister group to archosaurs (birds and crocodiles) using morphology tree, DNA tree, and microRNA tree