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POB 2 > Lecture 13 Phylogeny:principles > Flashcards

Lecture 13 Phylogeny:principles Flashcards

1
Q

Systematics

A

Reconstructs Evolutionary Relationships

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

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2
Q

Cladistics

A

Focuses on Traits Derived from a Common Ancestor

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

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3
Q

Classification

A

Is a Labeling Process, Not an Evolutionary Reconstruction

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

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4
Q

Taxonomy

A

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

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5
Q

Domains

A

The Largest Taxons

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

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6
Q

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

A

slide 4

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7
Q
  1. Phylogeny - evolutionary relationships
A
  • 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

slide 5

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8
Q

Systematics

A

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

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9
Q

Taxonomy

A

The identification, description,
classification and naming of species.

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10
Q

Systematics- classifying organisms (Taxonomy)

A
  • 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

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11
Q

Common names

A
  • 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

slide 8

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12
Q

Taxonomic hierarchy

A

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

slide 9

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13
Q

Honeybee classification

A

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.

slide 10

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14
Q

Linking Classification and Phylogeny

A

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

slide 11

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15
Q

The connection between classification and phylogeny

A

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

slide 12

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16
Q

Cladograms: What We Can and Cannot Learn

A

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

slide 13

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17
Q

Parts of a Phylogenetic Tree

A

slide 14

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18
Q

Parts of a phylogenetic tree

A

slide 15

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19
Q

Alternative forms: Vertical, horizontal, diagonal

A

slide 16

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20
Q

Rotating Around the branch points

A
  • 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
    slide 17
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21
Q

Branch Lengths vs genetic changes

A

slide 18

  • 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
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22
Q

Branch Lengths vs time

A

slide 19

  • In some trees, branch length is proportional to time
  • Fossil data is used to place branch points in the context of geological time
23
Q

How do you read a phylogenetic tree?

A

slide 20

24
Q

Information we get

A
  • 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?

slide 21

25
Q
  1. Information: morphological and molecular
A

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

26
Q

Derived characteristic

A

inherited from the most recent
common ancestor of an entire group

27
Q

Ancestral characteristic

A

arose prior to the common
ancestor of the group

28
Q
  1. Information: morphological and molecular
A

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

29
Q

Characters

A
  • 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
30
Q

Evaluating Molecular Homologies

A
  • 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

31
Q

Shared characters used to construct trees

A

● 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

32
Q

Cladogram

A

Depicts a hypothesis of evolutionary relationships

33
Q

A clade

A

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

34
Q

Systematics and Classification

A

monophyletic group (clade

Paraphyletic group

Polyphyletic group

slide 29

35
Q

Monophyletic group (clade)

A

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

36
Q

Paraphyletic group

A

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

37
Q

Polyphyletic group

A

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

38
Q

Ancestral vs. derived characters

A

– 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

39
Q
  1. Shared Ancestral and Shared Derived Characters
A

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

40
Q

Inferring Phylogenies Using Derived Characters

A

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

41
Q

Outgroup

A

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

42
Q

Ingroup

A

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

43
Q

Inferring Phylogenies Using Derived Characters

A

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

slide 35

44
Q

Maximum Parsimony and Maximum Likelihood

A

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

45
Q

Example: 4 taxa

A

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

slide 37

46
Q

How to pick the best tree?

A

slide 38

47
Q

How to pick the best tree?

A

slide 39

48
Q

Example: The great apes

A

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

49
Q

Relationships in the 3 possible trees

A

slide 41-46

50
Q

Species concepts

A
  • 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

51
Q

Biological species concept (BSC)

A

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

52
Q

Phylogenetic species concept (PSC)

A

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

53
Q

PSC vs. BSC

A
  • 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

POB 2 (25 decks)

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