Lecture 05: Phylogenetics

Question 1

Why is phylogeny important?

Answer 1

1. Understanding and classifying the diversity of life on Earth
2. Testing evolutionary hypotheses:
   * trait evolution, coevolution, mode and pattern of speciation, correlated trait evolution, biogeography, geographic origins, age of different taxa, nature of molecular evolution, disease epidemiology

…and many more applications!

Question 2

Phylogeny

Answer 2

Branching diagram showing relationships between species (or higher taxa) based on their shared common ancestors

Question 3

Hierarchy (Phylogeny vs. classification)

Answer 3

• taxonomic classifications are hierarchical (Class, Order, Family, Genus, Species)
• Phylogenetic (cladistic) classification reflects evolutionary history
• The only objective form of classification – organisms share a true evolutionary history regardless of our arbitrary decisions of how to classify them

-> Classification is not as precise as phylogeny

Question 4

Phylogenetic Systematics

Answer 4

• German Entomologist Willi Hennig established that monophyletic groups (=clades) must be diagnosed by advanced (=derived) characters.
• Under the law of parsimony, taxa are grouped into clades based on minimizing the number of character changes.

Question 5

Phylognetic Vocabulary

Answer 5

• Apomorphy: an advanced (derived) state
• Autapomorphy: an apomorphy present in only a single taxon (parsimony-uninformative)
• Synapomorphy: shared derived character (parsimony-informative) (gemeinsames abgeleitetes Merkmal)
• Plesiomorphy: a retained (ancestral or ‘primitive’) state
• Symplesiomorphy: shared ancestral characters (uninformative) (Gemeinsames Vorläufermerkmal)
• Homology: when characters have a common origin in a common ancestor -> structures share a common structural and developmental (and genetic) pattern
• Homoplasy: when characters are independently evolved (uninformative)

homologie gegenteil: Analogie

Question 6

Monophyletic group

Answer 6

• Only group (clade) that is recognized in cladistic classification!
• Includes an ancestor and **all of its descendants (= a clade)

Example: Canids (Canidae, dogs) are a monophyletic clade within Mammalia
-> Each of the colored lineages within canids is also a monophyletic clade

Question 7

Paraphyletic group

Answer 7

• Includes ancestor and some, but not all of its descendants
• Taxon A is highly derived and looks very different from B, C, and ancestor

Example 1: Reptilia is a paraphyletic group unless it includes Aves
* Birds are more closely related to crocodilians than to other extant vertebrates
* Archosauria = Birds + Crocs
* We think of reptiles as turtles, lizards, snakes, and crocodiles

Example 2: ‘Dinosauria’ is a paraphyletic group unless it includes Aves (Birds are dinosaurs!).

Question 8

Polyphyletic group

Answer 8

• Includes two convergent descendants but not their common ancestor
• Taxon A and C share similar traits through convergent evolution

Example: Dolphins and sharks (Fins)

Question 9

How are phylogenies constructed?
Part 1: Sources of Data

Answer 9

1. Morphological Data
2. Molecular Data
   3.Supertree vs. Supermatrix

Question 10

Morphological Data/Morphological Characters

Answer 10

Character polarity
1. Criterion of position (Position of the pelvis in some snakes and humans )
2. Criterion of specific quality (Prostomial sensual organs in two polychaetes)
3. Criterion of intermediate forms (primary and secindary jaws Bony fish -> reptile -> mammal)

Question 11

Skeletal evidence

Answer 11

• Skeletons contain strong evidence of
  shared ancestry for all vertebrate
• Skeletal evidence can be assessed in
  both extant (living) and extinct (fossil)
  species

Question 12

Foosil records

Answer 12

1. Fossil discoveries show how early tetrapods evolved from fish (Upper Devonian (~360 Ma): Lungs & limbs, fishlike tail, gills, amphibian-like skull)
2. Fossil record also clearly shows the transition to early synapsids (mammal ancestors, Lycaenops - a carnivorous therapsid, mid-late Permian (~260 Ma))
3. Vestigial bones also provide more evidence of common ancestry among vertebrates
   * Remnants of structures with important functions in ancestors but no longer used
   * Pelvic girdle in some snakes, tailbone in humans
   * Vestigial pelvic bones in whales – their ancestors had legs

4 Homologous structures in mammal skeletons demonstrates common ancestry

Question 13

Molecular Data/Ancient data
Percentages of Genes from other organisms that also occure in *H.sapiens

Answer 13

Only comparison of larger parts of genome makes sense because of deep genetic homologies
* Mouse - 86%
* Fruit fly - 44%
* Yeast - 30%
* Nematode worm - 25%
* Amoeba - 22%
* Mustard (plant) - 19%
* E. coli (bacterium) - 9%

Ancient DNA - extinct human lineages (Example:Tooth from Denisova cave in Siberia 50,000-30,000 years old) -> shows that ancient humans were better adapted to high altitude

Question 14

Supertree & Supermatrix

Answer 14

Total-evidence analysis
brings together data from as many fields as possible to understand and map out the history of life on Eart

Question 15

Methods of Analysis: Parsimony

Answer 15

Parsimony
* the simplest solution is the preferred one
* Simplicity as a criterion for choosing among competing hypotheses -> known as Occam’s razor
* Constructing trees with parsimony: Outgroup:
When constructing a phylogeny for a group
of organisms, we need to employ an outgroup (or
several), which is not part of the group of interest
the ingroup ), but also not too distantly related to it.
The outgroup is used to polarize the character states: the character state possessed by the outgroup is defined a priori as ancestral (pleisiomorphic).

Example: No food in fridge.. (which hypotheses requires the fewest assumptions)

Question 16

Whale evolution (Parsimony)

Answer 16

• Artiodactyla: The artiodactyla are a group of hoofed mammals that possess an even number of toes, and includes camels, pigs, peccaries, deer, the hippopotamus, cattle and giraffes.
• Cetacea: Cetaceans are mammals that are highly specialized for life in the water, with streamlined bodies, dorsal fins, a tail with two flukes, nostrils located on the top of the head, forelimbs as flippers, hind limbs and pelvis extremely reduced.
  -> What is the phylogenetic relationship between artiodactyls and whales?
  -> common ancestor with hippos (Cetartiodactyla today) or common ancestor with all (Artiodactyla previously)
• Parsimony using morphology of double trochleated astragalus -> 47 Ma whale fossils possess artiodactyl synapomorphy

Parsimony using genetics: As there is a conflict between sites 162 and 166 (Synapomorphies between cow, deer, whale, hippo) and 177 (synapomorphy between whale, hippo, pig and peccary)
- there must be a homoplasy in the data set
- Most parsimonious tree -> the least possible nucleotide changes
Possibility 1) whales evolved early (was assumed earlier)  47 nt changes
Possibility 2) whales evolved late  41 nt changes
- As you can make over 34,000,000 possible trees of 10 taxa max. -> parsimony has to be computed

Homoplasy: Wings in bats and birds; fins in sharks and dolphins. Different genetic and developmental pathways.

Question 17

Methods of Analysis: Likelihood methods

Answer 17

• Sometimes parsimony is violated during evolution, especially considering
  molecular data -> Specifically molecular (ATCG) data.
• So, to help direct our phylogenetic analysis we’re going to add some conditional probabilities.
  -> This, of course, makes things even more complicated to compute… (definitely need a powerful computer)

Question 18

The Bayes Theorem

Answer 18

probability of event A happening, given that data B is true

Example: Plain crash in Amazon

• 1% of fruit are poisonous
• 90% of poisonous fruit are red 40% of non-poisonous fruit are red
• Should you despair? Bayes theorem says probably not:

P(poisonous | red) = P(red | poisonous) * P(poisonous) / P(red)= 0.90 * 0.01 / (0.90 * 0.01 + 0.40 * 0.99)= 0.0222

Question 19

Time trees

Answer 19

• According to the molecular clock
  hypothesis, two taxa that shared a
  common ancestor t years ago should
  have accumulated more or less the
  same number of substitutions during
  time t. In most cases, however, the
  ancestor is unknown and there is no
  possibility to directly test the constancy
  of the evolutionary rate.
• In reality, we know rates are not
  constant, and we use calibrations
  (usually fossil) to help determine rates
  of evolution in different parts of the
  tree.
  Example: Using phylogenetics to chart the evolution and geographic spread of Ebola

Fossil Calibration of Nodes
* Here, a tree of mammals is constructed using molecular data from extant taxa.
* Age constraints for are assigned for nodes across the tree based on specialist knowledge of the fossil record.
* Molecular distances are then time calibrated and a timescale for the whole tree is generated

Example: Case Study- The Age of Origin of Placental Mammals (Rocks vs. Clocks)

Question 20

Coevoultion def.

Answer 20

Two (or more) species:
1) exert selective pressures on each other, and
2) evolve in response to each other -> Because each species is evolving in response to the other, one important feature of coevolution is that the selective environment is constantly changing

Question 21

Fig- wasp mutualism (Coevolution)

Answer 21

• Fig trees (Ficus)~750 tropical species, all of which depend entirely on wasps for pollination
• Figs are not fruits – they are specialized inflorescences with hundreds of unisexual flowers
  Fig wasps (Agaonidae)
• Males: suited only for boring holes and mating
• Females: adaptated for flying, burrowing into figs, and laying eggs in fig oocytes
  Coadaptations
• Receptive figs produce scents that are specific to a particular pollinator species
• Shape of ostiole specific to head shape of particular wasp species (lock-and-key)
• Morphology of individual flowers specialized to a particular wasp species

1. Female wasp enters via ostiole and oviposits in female flowers
2. Flower styles are different lengths – wasps only oviposit in ones w/ short styles

Cophylogeny:
Congruent phylogenies due to cospeciation – strong evidence for coevolution

Cospeciation
* Figs and pollinator wasps show a very high degree of cospeciation
* Despite pressure from parasitic wasps, fig – pollinator specificity is maintained
-> Indicates a very tight ecological relationship