Lecture 13 Phylogeny:principles Flashcards
Systematics
Reconstructs Evolutionary Relationships
– Recognize what a phylogeny represents.
– Explain relationship between phenotypic similarity and evolutionary history.
Cladistics
Focuses on Traits Derived from a Common Ancestor
– Differentiate between ancestral and derived characters.
– Contrast informative shared, derived characters from noninformative ones.
Classification
Is a Labeling Process, Not an Evolutionary Reconstruction
– Differentiate among monophyletic, paraphyletic, and polyphyletic
– Discuss the phylogenetic species concept and its drawbacks
Taxonomy
Attempts to Classify Organisms in an Evolutionary Context
– Explain how taxonomists name and group organisms.
Domains
The Largest Taxons
– List examples showing that the three domains of life are monophyletic, but
the six kingdoms are not.
How do biologist distinguish and categorize the millions of species on Earth
slide 4
- Phylogeny - evolutionary relationships
- 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
Systematics
The inference of phylogenetic
relationships among species and the use of such information to classify species.
Taxonomy
The identification, description,
classification and naming of species.
Systematics- classifying organisms (Taxonomy)
- 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
Common names
- 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
Taxonomic hierarchy
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
Honeybee classification
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
Linking Classification and Phylogeny
The evolutionary history of a group of organisms can be
represented in a branching diagram called a
phylogenetic tree
slide 11
The connection between classification and phylogeny
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
Cladograms: What We Can and Cannot Learn
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
Parts of a Phylogenetic Tree
slide 14
Parts of a phylogenetic tree
slide 15
Alternative forms: Vertical, horizontal, diagonal
slide 16
Rotating Around the branch points
- 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
Branch Lengths vs genetic changes
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
Branch Lengths vs time
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
How do you read a phylogenetic tree?
slide 20
Information we get
- 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
- Information: morphological and molecular
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
Derived characteristic
inherited from the most recent
common ancestor of an entire group
Ancestral characteristic
arose prior to the common
ancestor of the group
- Information: morphological and molecular
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
Characters
- 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
Evaluating Molecular Homologies
- 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
Shared characters used to construct trees
● 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
Cladogram
Depicts a hypothesis of evolutionary relationships
A clade
group of species that includes an ancestral species and all its descendants
Systematics and Classification
monophyletic group (clade
Paraphyletic group
Polyphyletic group
slide 29
Monophyletic group (clade)
– Includes the most recent common ancestor of the group and all of its descendant
Paraphyletic group
– Includes the most recent common ancestor of the group, not all its descendants
Polyphyletic group
– Does not include the most recent common ancestor of all members of the group
Ancestral vs. derived characters
– 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
- Shared Ancestral and Shared Derived Characters
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
Inferring Phylogenies Using Derived Characters
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
Outgroup
species or group of species closely related to, but not part of the group of species being studied (the ingroup)
Ingroup
species with the outgroup to differentiate between shared derived and shared ancestral
characters
Inferring Phylogenies Using Derived Characters
5 derived characters: hair, amnion, 4 limbs, hinged jaws and backbone
6 taxa: lancelet, lamprey, bass, frog, turtle and leopard
slide 35
Maximum Parsimony and Maximum Likelihood
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
Example: 4 taxa
Imagine that we
want to figure
out the
evolutionary
relationships
among just four
taxa:
A, B, C, and D
15 different ways
slide 37
How to pick the best tree?
slide 38
How to pick the best tree?
slide 39
Example: The great apes
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
Relationships in the 3 possible trees
slide 41-46
Species concepts
- 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
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
PSC vs. BSC
- 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
