Chapter 4 UCF Evolutionary Biology (PCB 4683)

Systematics is made up of which two fields

taxonomy and phylogenetics

Taxonomy

classifying organisms in groups

Taxon

species or genus or kingdom

Phylogenetics

reconstruction of evolutionary relationships

Rules of taxonomy

international union of zoological nomenclature

international union for algae, fungi, and plants.

Carolus Linneaus (1707-1778)

Father of modern classification system

Published Systema Naturae in 1758 (10th edition)

Hierarchical System of Classification

Domain, Kingdom, Phylum (Division), Class, Order, Family, Genus, Species

binomial nomenclature

Each species has a unique name

Better than using common names because it is more exact

Worldwide

Genus species

Genus Species

Noun + Adjective

example: Rana catesbeiana (bullfrog)

Phylogeny

Hypothesis of evolutionary relationships

Only an estimate

phylogenetic tree

graphical summary of evolutionary history

principle of parsimony

explanation that makes the fewest new assumptions is the most likely to be true

Synapomorphy

shared derived character of all members of a group

used to determine where branches should be on a phylogeny

more common than convergence and reversals

Autopomorphy

some traits are derived along a single lineage.

not useful for estimating relatedness

Plesiomorphy (symplesiomorphy)

traits may also occur because they are retained from the ancestor.

Homoplasy

the same traits may be independently derived in different lineages

convergence and reversals

example: seal and penguin flippers, flight in birds, bees, and bats

convergent evolution

produces homoplasies aka analogous structures

Maximum Parsimony Method

minimizes total amount of evolutionary change in a tree

Parsimony and Phylogeny

most closely related taxa should have the most traits in common

Morphological characteristics

1.well-established

2.less expensive

3.lots of material

4.genetic basis often poorly understood, but effectively examining many "genes" at one time

5.can examine fossil taxa

6.can look at more individuals more often

molecular characteristics

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

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

Outgroup

closely related taxon that is used instead of the ancestor

tells us which are derived and which are ancestral

When no convergence or reversal occurs

all synapomorphies are congruent

When all nodes are not congruent

goal is to minimize homoplasy

Cladogram

tree made using synopomorphies

clade

monophyletic group

Monophyletic group

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

Paraphyletic group

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

Polyphyletic group

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

Paraphyletic taxa

common

reptiles with respect to birds

bony fishes with respect to tetrapods

Polyphyly

less common and more worrisome

Order Cetacea

whales and dolphins

Synapomorphies of cetacea

loss of posterior limbs

Order Artiodactyl

even-toed ungulates: pigs, camels, cattle, and hippos.

Morphological characters (Phylogeny of Whales)

skeleton

Molecular characters (Phylogeny of Whales)

Allozymes, RFLPs, DNA sequences

Astragalus

ankle joint bone

Fossil Whales

Ancient whale fossils share many characteristics with both extant whales and artiodactyls

Whale-like ear bones

Artiodactyl-like astragalus

How do we evaluate confidence in a tree?

Bootstrap 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 probably found

Investigators usually report any bootstrap value over 50%

Reconstruction Criteria (most used modern methods)

distance based methods (neighbor-joining)

maximum likelihood

Bayesian analysis

coalescent methods

Distance methods

are typically VERY fast and easy to use to estimate a phylogenetic tree

they are not cladistic because they do not look for synapomorphies, but rather overall similarity

susceptible to lots of error when a dataset has lots of homoplasy

are not often used except as a starting point for more rigorous analyses

When using distance methods to reconstruct

species with the LEAST genetic distance between them are assumed to be CLOSE relatives

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)

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

Models can be simple (like parsimony) or very complex, the data is used to estimate which model to use.

Bayesian Methods

P(tree|data)

Ask what the probability is of a particular tree being correct, given the data and a model of evolution.

Bayesian approaches are typically coupled with Monte Carlo (MC) approaches to search „tree-space‟ (e.g. MetropolisCoupled Markov Chain Monte Carlo, or MC3)

Excellent method of inference!

Coalescent Methods

Model genetic drift backward in time with birth-death processes until gene variants "coalesce" in common ancestors (each gene considered separately, then information combined)

Can incorporate recombination, selection, gene flow, many other evolutionary/demographic processes

SINE/LINE

Short/Long Interspersed Elements

Non-coding DNA inserted into genomes (retrotransposons)

Molecular Clock

It is hypothesized that molecular change happens at a steady rate

Clocks for a variety of taxa have been estimated to tick at a rate of 2% sequence divergence per million years

This used mitochondrial genes (different genes evolve at different rates)