Module 2: Evidences for Evolution + Classification and Phylogeny

1. Fossil Records

2. Homology and Common Descent

3. Ontogeny

4. Branching Evolution

5. Vestigial Characters

6. Convergence

7. Suboptimal Designs

8. Biogeography

What are the 8 Evidences for Evolution?

Sedimentary Rocks

What rocks are used to look at the strata of different ages?

T

T or F: fossils in different strata have the different time period

T

T or F: The nearer the strata is to the surface, the younger the strata and the fossils located in it is.

There are gaps in evolutionary history. The more fossils are found, the less gaps there in the evolutionary history

What does incompleteness of fossil record mean?

Scientists discovered Archaefructus sinensis (ancient fruit) which was a specimen that shows intermediate characters between flowering plants and seed plants. It is NOT the ancestor of gymnosperms and angiosperms.

How were fossils utilized in explaining the evolutionary history of gymnosperms (seed plants) and angiosperms (flowering plants)?

T

T or F: intermediate forms allow us to understand connections between organisms. These fossils are not direct ancestors; instead they exist in parallel lineages.

T, it helps us understand when the characters appeared in evolution

T or F: fossils allows us to understand the chronical emergence of anatomical characters

1. When the characters arose

2. How the characters arose

Fossils are important in determining ___ and ___ the characters arose

Homology

This is when the structures look the same and share a common ancestor but they have different functions

Chiridian limb of dogs and birds.

• Dogs: running

• Birds: flying

Example of homology(dogs vs birds)

Ontogeny

Study of how organisms developed from early embryo stages

F, ontogeny does not summarize phylogeny. Just because we had tails and gills, does not mean that we were fish at one point. Ontogeny hints at a common ancestor when embryos of different species are homologous

T or F: Human embryo has similar characteristics to the embryos of other animals, e.g. the presence of gills and tails. That means that we were once a fish.

• Ontogeny: how characters are related among different organisms during embryonic stage

• Embryology: study of development of embryo at a particular lineage

Ontogeny vs Embryology

• Evolution does NOT occur in a linear manner.

• We can only infer the characters of ancestors but not the ancestors themselves.

What does it mean to have a branching evolution?

Vestigial Character

• A lost or reduced organ

• What is left of an evolution when an organism goes to a different lineage

• Whales have remnants of pelvic structure as evidence of land colonization in the past.

• Some lineages of snakes related to lizards have vestigial legs.

Examples of vestigial characters

Convergence

Presence of a trait that is similar in two different lineages and is a result of adaptations in similar environment

Artic foxes and birds have white coloration and have coverings that can insulate them. This is a result of being exposed to the same environment. They had they same survival strategy.

Example of convergence

T

T or F: Having suboptimal designs show that evolution is not always efficient. It also shows similarity in characters of different organisms, implying a common ancestor

Biogeography

Study of patterns of geographic distribution of organisms and the factors that determine those patterns

Phylogeny

• Phylo (phylum): lineages

• Geny (genesis): origin

It means origin of lineages

Phylogeny

It is the historical pattern of descent of organized beings

Phylogeny

It is a tree that illustrates the genesis of phyla. It is a graphic representation of evolutionary relationships between organisms.

Phylogeny

It is a tree that illustrates sister-group relationships, or “who is most closely related to whom“ or the degree of evolutionary relatedness

Phylogeny

It is a tree that provides secondary homologies

Hatch marks

Represents a homologous characteristic shared by all the groups to the right of the mark

T

T or F: there is not “TOP“ to a tree because a phylogenetic tree can be represented in multiple ways or directions. There is only temporal direction

Resolved tree

• A phylogenetic tree where there is resolution at each node.

• There are two branches at each node.

Ancestors

Nodes in phylogenetic trees represent ____

Polytomy (unresolved tree)

• A phylogenetic tree where there are more than two branches at a node.

• In this tree, we cannot know which lineages are closer to each other

3 Realms of Life:

• Archaea

• Bacteria

• Eukarya

Example of polytomy

Difference between genealogy and phylogeny

• Clade: Monophyletic Groups

• Grade: Paraphyletic Groups, Polyphyletic Groups

Clade vs Grade

Monophyletic group

A grouping that contains common ancestor and all of its descendants

Paraphyletic group

A grouping that contains ancestor and part of its descendants

Polyphyletic group

A grouping that does not contain common ancestor of all group members

Fish

What is a famous polyphyletic grouping system

Reptilia

What is a famous paraphyletic grouping

Systematics

The science of biological classification and of the evolutionary relationships among organisms

Cladistic

• A method of analyzing characters and attempts to determine evolutionary sequence of characters

• It determines while is plesiomorphic and apomorphic character states

Systematics

A phylogenetic classification expresses only the phylogenetic relationships among organisms determined using cladistic analysis

Character

• A set of attributes

• Anything that can be observed and measure in organisms

Character States

• Every possible form a character can potentially display

• Can be quantitative or qualitative

Plesiomorphic

Ancestral state of a character

Symplesiomorphic

Refers to a plesiomorphic character that is present in two or more taxa

Apomorphic

In a series of character state transformations, this is the derived state with reference to the ancestral state

Autapomorphic

• Refers to a derived state of a character that is unique to one of the two groups

• Not useful in classification since it only belongs to one lineage

Synapomorphic

Apomorphic character that is shared by two or more taxa or lineages

Homology

• Shows same fundamental organization and same essential connections with neighboring organs, despite variations in appearance of these structures

• Similarity among organs which is presumed to be inherited from a common ancestor

Homoplasy

A similarity among one or several species but this is not due to an inheritance from a common ancestor

• Convergence

• Parallelism

• Reversion

3 Types of Homoplasy

1. Resemblance due to secondary homology

• Resemblance is observed through phylogeny using implied parsimony analysis

2. Resemblance due to convergence

• 2 species sharing the same character state experienced 2 independent evolutionary events

• Transformation occurs in the same direction

3. Resemblance due to reversion

• Return to ancestral character

• Transformation occurs in a different direction

Explain the 3 Different Categories of Resemblance

Homology

• Similarly inherited from a common ancestor

  • EX: chiridian limb

Convergence

• Similar attributes that appeared independently in different taxa as a result of being subjected into similar environmental forces

• EX: dolphins and sharks’ hydrodynamic shape

Reversion

• Derived character that returned into its plesiomorphic state

• EX: Grasses, which emerged later in time, resemble woody plants rather than flowering plants since they can’t produce their own food

Classification

Construction of a meaningful link among objects that has the form of a hierarchical system.

The arrangement of living organisms into hierarchical groups according to a set of predefined groups

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

System of classification

T

T or F: Binomial Nomenclature of the Linnaean Classification System is still being used today

Taxon

Group of recognized organisms found within different categories of hierarchical classification

T

T or F: Any clade can be considered as a taxon

Taxonomy

• The science of the rules for classification of living organisms

  • The science of the theory and practice of classification (Mayr). It includes the recognition and identification of living organisms and their organization in a classification

• Parsimony

• Maximum Likelihood

• Bayesian Inference

• Neighbor Joining or Phenetic

4 Methods of Constructing Phylogenies

Construct its phylogenetic tree.

Occam

Parsimony was attributed to a 14th century monk named _____

Parsimony

It is a method of phylogeny construction that, given all possible dendrograms, retains the one with the lowest number of required evolutionary events.

Hypothesis 1

Which is more parsimonious out of the 2?

1. Cladogenesis and Anagenesis

2. Convergent and Parallel Evolution

3. Mosaic Evolution

4. Heterochrony

5. Exaptation

6. Adaptive Radiation

6 Patterns of Evolution

Cladogenesis

• Pattern of evolution that results in the formation of a new clade

• One or more species arising from one original species

Anagenesis

• Pattern of evolution that shows slow change within one species

• It does not result in speciation

T

T or F: Anagenesis leads to variation in character states within a species. Cladogenesis happens when a variation leads to the formation of new species.

Convergent Evolution

Shared organ that functions similarly in two different or very distant lineages that do not share common ancestry

Parallel Evolution

Shared organ that functions similarly in closely related lineages

T

T or F: both convergent and parallel evolution lead to homoplasy

Complex eye: molluscs and mammals

• The eye complex of octopus and human have same function but characters are not evolutionarily related

Digger limb: insect and mammals

• Presence of digger limbs in crickets and moles; but, they don’t come from same ancestry

Examples of convergent evolution

In mammals,

• Marsupial mammals: develop their young outside their bodies

• Placental mammals: develop their young from within their bodies

Example of parallel evolution

Parallel	Convergent
closely related taxa	distantly related taxa
homologous → orthologous	non-homologous genes
similar changes in gene » similar phenotype	different changes in same gene » similar phenotype

Differences between parallel and convergent evolution

Mosaic Evolution

This states that not all characters arise or change at the same time

T

T or F: The emergence of bipedalism did not happen in one instance or linearly. It went through several transitions + occurred in a branching manner

Heterochrony

• A change in the relative rate or timing of a developmental event in an organism relative to when that event in its ancestor

• Shows the impact of developmental genes in creation of new species

Neoteny or Paedomorphosis

It means retaining the juvenile characters of adulthood

HOX gene

Neoteny is a result of a mutation in the ___ ___ which does not allow some character traits to develop in adulthood

• Unlike chimpanzees, adult human skulls retained similarities fetus skulls allowing bipedalism

  • The insertion of spine in human skull allows optimal posture for walking upright

• Salamanders retain their gills (juvenile characteristic) allowing them to grow in bodies of water.

Examples of neoteny/paedomorphosis

Exaptation

Structures evolve for a particular context but are co-opted for another function

• Tiktaalik had fins for aquatic environment. Eventually, its fins were used to aid in walking on land. This is the chiridian limb.

• The feathers of bird were initially used for warmth. Now, some use it for flight.

Examples of exaptation

Adaptive Radiation

It occurs when organisms are able to rapidly diversify and adapt to different niches