Lecture 13 Phylogeny:principles

Question 1

Systematics

Answer 1

Reconstructs Evolutionary Relationships

– Recognize what a phylogeny represents.
– Explain relationship between phenotypic similarity and evolutionary history.

Question 2

Cladistics

Answer 2

Focuses on Traits Derived from a Common Ancestor

– Differentiate between ancestral and derived characters.
– Contrast informative shared, derived characters from noninformative ones.

Question 3

Classification

Answer 3

Is a Labeling Process, Not an Evolutionary Reconstruction

– Differentiate among monophyletic, paraphyletic, and polyphyletic
– Discuss the phylogenetic species concept and its drawbacks

Question 4

Taxonomy

Answer 4

Attempts to Classify Organisms in an Evolutionary Context
– Explain how taxonomists name and group organisms.

Question 5

Domains

Answer 5

The Largest Taxons

– List examples showing that the three domains of life are monophyletic, but
the six kingdoms are not.

Question 6

How do biologist distinguish and categorize the millions of species on Earth

Answer 6

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Question 7

1. Phylogeny - evolutionary relationships

Answer 7

• Evolutionary history of a species or group of species
• A phylogeny of lizards and snakes - both glass lizards and
  snakes evolved from lizards with legs—but they evolved from
  different lineages of legged lizards
• It appears that their legless conditions evolved independently

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Question 8

Systematics

Answer 8

The inference of phylogenetic
relationships among species and the use of such information to classify species.

Question 9

Taxonomy

Answer 9

The identification, description,
classification and naming of species.

Question 10

Systematics- classifying organisms (Taxonomy)

Answer 10

• Taxonomy is a quest for identity and relationships

The science of classifying living things
* Linnaeus instituted the use of binomial descriptive names
– Genus (genera) Latin for “groups” - Always capitalized
– specific epithet - not capitalized
* Both written in italics
* for example, Homo sapiens
Can be abbreviated in text after first use
* Dinosaur Tyrannosaurus rex becomes T. rex.
* Bacteria Escherichia coli - E.coli
– hierarchical classification

Question 11

Common names

Answer 11

• Make poor labels.
• In North America, the common name “bear” brings a clear image to
  mind, but the image is very different for someone in Australia

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Question 12

Taxonomic hierarchy

Answer 12

The Linnaean hierarchy
* introduced a system for grouping species
in increasingly inclusive categories
* The taxonomic groups from broad to
narrow
– domain,
– kingdom,
– phylum (plural, phyla)
– class,
– order,
– family,
– genus,
– species
* A group at any level of hierarchy = taxon

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Question 13

Honeybee classification

Answer 13

Each taxon groups organisms by a set of characteristics
– For example, the European honeybee
* Species level: Apis mellifera, meaning honey-bearing bee
* Genus level: Apis, a genus of bees
* Family level: Apidae, a bee family. All members of this family are bees—some solitary,
some living in colonies as A. mellifera does.
* Order level: Hymenoptera, a grouping that includes bees, wasps, ants, and
sawflies—all of which have wings with membranes
* Class level: Insecta, a very large class that comprises animals with three major body
segments, three pairs of legs attached to the middle segment, and wings
* Phylum level: Arthropoda. Hard exoskeleton made of chitin and jointed appendages.
* Kingdom level: Animalia. Multicellular heterotrophs with cells that lack cell walls.

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Question 14

Linking Classification and Phylogeny

Answer 14

The evolutionary history of a group of organisms can be
represented in a branching diagram called a
phylogenetic tree

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Question 15

The connection between classification and phylogeny

Answer 15

Hierarchical
classification can reflect
the branching patterns
of phylogenetic trees. -
- relationships between
some of the taxa within
order Carnivora, itself a
branch of class
Mammalia

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Question 16

Cladograms: What We Can and Cannot Learn

Answer 16

Key to interpreting a cladogram
– Looks at how recently species share a common ancestor based on branches
– Does not look at the arrangement of species across the top of the tree

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Question 17

Parts of a Phylogenetic Tree

Answer 17

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Question 18

Parts of a phylogenetic tree

Answer 18

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Question 19

Alternative forms: Vertical, horizontal, diagonal

Answer 19

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Question 20

Rotating Around the branch points

Answer 20

• Rotation does not changing information on evolutionary relationships
• Order in which taxa appear at the branch tips is not significant
• The branching pattern signifies the order in which the lineages
  diverged from common ancestors
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Question 21

Branch Lengths vs genetic changes

Answer 21

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• In some trees, branch length reflects the number of genetic changes
  that have occurred in each lineage
• Lineages with shorter branches reflect fewer genetic changes than
  those with longer branches

Question 22

Branch Lengths vs time

Answer 22

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• In some trees, branch length is proportional to time
• Fossil data is used to place branch points in the context of geological time

Question 23

How do you read a phylogenetic tree?

Answer 23

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Question 24

Information we get

Answer 24

• Patterns of descent, not phenotypic similarity
• No information on when species evolved or
• No information on how much change occurred in a lineage
• DO not assume that a taxon evolved from the taxon next to it

Question: Why might a species be most phenotypically similar to a
species that is not its closest evolutionary relative?

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Question 25

2. Information: morphological and molecular

Answer 25

Because phenotypic similarity may be misleading, most systematists consider two types of similarities: * Derived characteristic - inherited from the most recent common ancestor of an entire group * Ancestral characteristic - arose prior to the common ancestor of the group Only features resulting from common ancestry are useful for determining evolutionary relationships

Question 26

Derived characteristic

Answer 26

inherited from the most recent common ancestor of an entire group

Question 27

Ancestral characteristic

Answer 27

arose prior to the common ancestor of the group

Question 28

2. Information: morphological and molecular

Answer 28

Homologies - Phenotypic and genetic similarities due data to shared ancestry Organisms with similar morphology or DNA sequence are likely to be more closely related than those that vastly differ in structure and sequence Analogy is similarity due to convergent evolution

Question 29

Characters

Answer 29

* Characters can be any aspect of the phenotype – Morphology – Physiology – Behavior – DNA * Characters should exist in recognizable character states – Example: Character “teeth” in amniote vertebrates has two states: * present in most mammals and reptiles, * absent in birds and turtles

Question 30

Evaluating Molecular Homologies

Answer 30

* Sequence DNA * Align comparable sequences – Closely related species - differ at one or a few sites – Distantly related species - different bases at many sites * Insertions and deletions are point mutations that shift the entire DNA sequence following the mutation * Failure to take these mutations into account would overlook otherwise good sequence matches * Computer programs are used to identify such matches by testing possible sequence alignments Points of sequence similarity reflect homology, ● 11 of the original 12 bases have not changed since the species diverged. ● those portions of the sequences still align once the length is adjusted. ● Coincidental matches between unrelated organisms can occur ● Statistical tools distinguish between distant homologies and coincidental matches slide 26-27

Question 31

Shared characters used to construct trees

Answer 31

● Once homologous characters have been identified, they can be used to infer a phylogeny ● Cladogram - Depicts a hypothesis of evolutionary relationships ● A clade - group of species that includes an ancestral species and all its descendants Clades can be nested within larger clades slide 28

Question 32

Cladogram

Answer 32

Depicts a hypothesis of evolutionary relationships

Question 33

A clade

Answer 33

group of species that includes an ancestral species and all its descendants

Question 34

Systematics and Classification

Answer 34

monophyletic group (clade Paraphyletic group Polyphyletic group slide 29

Question 35

Monophyletic group (clade)

Answer 35

– Includes the most recent common ancestor of the group and all of its descendant

Question 36

Paraphyletic group

Answer 36

– Includes the most recent common ancestor of the group, not all its descendants

Question 37

Polyphyletic group

Answer 37

– Does not include the most recent common ancestor of all members of the group

Question 38

Ancestral vs. derived characters

Answer 38

– Presence of hair is a shared derived feature of mammals – Presence of lungs in mammals is an ancestral feature; also present in amphibians and reptiles – Shared, derived feature of hair suggests that all mammal species share a common ancestor that existed more recently than the common ancestor of mammals, amphibians, and reptiles The derived characters between the cladogram branch points are shared by all organisms above the branch points and are not present in any below them. The outgroup (in this case, the lamprey) does not possess any of the derived characters. slide 32

Question 39

3. Shared Ancestral and Shared Derived Characters

Answer 39

In comparison with its ancestor, an organism has both shared and different characteristics * Shared ancestral character: character that originated in an ancestor of the taxon (e.g. spine in all vertebrates) * Shared derived character - evolutionary novelty unique to a particular clade (e.g. both mammals and reptiles are vertebrates but fur is unique to mammals) can be used to group organisms into clades. Only shared derived characters are considered informative about evolutionary relationships slide 33

Question 40

Inferring Phylogenies Using Derived Characters

Answer 40

Outgroup - species or group of species closely related to, but not part of the group of species being studied (the ingroup) Compare each Ingroup species with the outgroup to differentiate between shared derived and shared ancestral characters Characters shared by the outgroup and ingroup are assumed to be ancestral

Question 41

Outgroup

Answer 41

species or group of species closely related to, but not part of the group of species being studied (the ingroup)

Question 42

Ingroup

Answer 42

species with the outgroup to differentiate between shared derived and shared ancestral characters

Question 43

Inferring Phylogenies Using Derived Characters

Answer 43

5 derived characters: hair, amnion, 4 limbs, hinged jaws and backbone 6 taxa: lancelet, lamprey, bass, frog, turtle and leopard slide 35

Question 44

Maximum Parsimony and Maximum Likelihood

Answer 44

Maximum parsimony assumes that the most likely tree is the one that requires the fewest evolutionary events (appearances of shared derived characters) In phylogenies based on DNA, the most parsimonious tree has the fewest base changes Maximum likelihood identifies the tree most likely to have produced a given set of DNA data based on probability rules about how DNA changes over time Probability rules could be based on the assumption that all nucleotide substitutions are equally likely

Question 45

Example: 4 taxa

Answer 45

Imagine that we want to figure out the evolutionary relationships among just four taxa: A, B, C, and D 15 different ways slide 37

Question 46

How to pick the best tree?

Answer 46

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Question 47

How to pick the best tree?

Answer 47

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Question 48

Example: The great apes

Answer 48

Let’s use orangutan as an outgroup as they are more distantly related to the others 3 species in the ingroup To build a phylogenetic tree between C, G, H using O as an outgroup, there only 3 possibilities slide 40

Question 49

Relationships in the 3 possible trees

Answer 49

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Question 50

Species concepts

Answer 50

* Biological species concept (BSC) – Defines species as groups of interbreeding populations that are reproductively isolated * Phylogenetic species concept (PSC) – groups of populations that have been evolving independently of other groups of populations – Species is a population or set of populations characterized by one or more shared derived characters

Question 51

Biological species concept (BSC)

Answer 51

– Defines species as groups of interbreeding populations that are reproductively isolated

Question 52

Phylogenetic species concept (PSC)

Answer 52

– groups of populations that have been evolving independently of other groups of populations

Question 53

PSC vs. BSC

Answer 53

* PSC solves 2 BSC problems – BSC cannot be applied to allopatric populations – would they interbreed? – PSC looks to the past to see if they have been separated long enough to develop their own derived characters * BSC can be applied only to sexual species – PSC can be applied to both sexual and asexual species