Classification & Phylogeny I (8)

Darwin described evolution with the phrase “descent with modification.” What did he mean?

A. Evolution takes a long time—it is not an instantaneous process.

B. Evolution is not “exceptional”—it is a natural phenomenon that is going on today.

C. Closely related species are similar at the genetic, developmental, and structural levels.

D. Populations living today are related (genetically) to populations that lived in the past, but they are not identical.

E. Both C and D apply.

E

What will happen to the size and shape of beaks in medium ground finches, in the future?

A. They will continue to get deeper and wider.

B. They will continue to get deeper, but they should eventually begin to get narrower as well.

C. It depends on changes in the environment.

D. They may fluctuate in size and shape, but they will remain roughly constant over the long term.

C (not enough information in question for other options) 

Which of the following could be used as evidence of descent from a common ancestor?

A. Species of tortoise living in close proximity are more similar than tortoise species living far apart.

B. Genes for limb formation have almost identical sequences in salamanders and chimpanzees.

C. Antibiotics can cure the same diseases in rabbits and humans.

D. All of the above could be used as evidence.

D 

Analogy vs. Homology

• Analogy

  • same function

  • different structure

• Homology

  • common ancestor

  • similar structure

  • can have different functions

Which of the following is a true statement?

A. An individual with an adaptation is said to have evolved.

B. An individual who is naturally selected has more offspring than an unselected individual.

C. An individual that needs an adaptation to survive is more likely to evolve it.

D. Over time organisms will become increasingly complex as evolution makes them more adapted.

B:  

• A: individual do note evolve 

• B: survival and reproduction correlated --> unselected = dead 

• C: correct state survive and others that don't do not 

  • Next generation has more of survived trait being expressed 

• D: microbes and bacteria body plan for single celled organisms hasn't changed for thousands of years 

What are the predictions based on evolution?

• • If life originated on Earth in the distant past and then evolved, we should see evidence in the fossil record

• If evolution occurred within lineages, and those lineages sometimes split then we should see change in species or morphology through the fossil record

• If creatures share a common ancestry, then we should see transitional forms • We should see evidence of retrodictions and vestigial characters

• We should be able to see evidence of natural selection

Why is this not a snake?

• Shares more lizard features than snaks

  • • moveable eyelids

  • immobile jaw

  • ear openings

  • autonomy – can shed tail

  • shed skin in patches

What is an amniotic egg?

• a self-contained, air-breathing egg that provides a protective, moist environment for a developing embryo on land

• found in vertebrates

What kind of structure do we use for classification?

Binomial hierarchical naming system: ex (homo sapein = human being) 

What are common names?

• convey meaning in casual

• monkey, finch, lilac

What is the issue with common names?

• confusing: some do not accurately reflect type of organism

What kind of names do we use instead?

use Latin scientific names

what does the hierarchy group organisms?

increasingly inclusive categories

How are the Latin names given to organisms?

• Genus name + species name

  • similar enough to be in the same genus, but different enough to be their own species

What is the order of hierarchical classification

• • Related Species are grouped into Genera 

• Genera group into Families 

• Families group into Orders

• Orders group into Classes

• Classes into Phyla

• Phyla into Kingdoms 

• and Kingdoms into Domains

What is a genus (plural: genera)?

closely related species

What is a family?

closely related genre —> grouped to more inclusive branch

What is order?

closely related families 

What is domain?

• three largest limbs of entire tree

• Eukarya, Bacteria, Archaea

What is a node?

where an ancestor diverges into two species or more

What is sister taxa?

• closest relative

• two branches from the same node

• most related taxa on tree

• PT is a set of sister groups —> adding species means finding sister group

What is a taxa (singular: taxon)

a set of organisms

What is a polytomy?

• Common ancestor of two diverging species that is still unkown

What happens to evolutionary relationships when nodes are rotated?

Nothing changes

• order does not impact the relationship

What are phylogenetic trees?

• Evolutionary history of a group of organisms can be represented in a grouping diagram

What is phylogeny?

History of descent with branchiing

What differentiates a cladogram and phylogenetic tree? 

• A phylogenetic tree shows branch order and branch lengths

  • captures order and timing of splits

• Cladogram: branching diagram with no implication of time

What are PTs build from?

analysis of morphological features and molecular attributes

What is systematics?

The science of organizing the history of organismal evolution; use phylogenies

What must characters be to be used in classification?

1. Independent traits cannot have environmental phenotypic variation

2. Independent traits must be independent

Why should independent traits not have environmental phenotypic variation for building PT?

• Need to focus on traits that is expressed mainly through genetic component 

  • Couldn't create species based on human height because based on environment 

What is pleiotropy? 

• Expression of multiple unrelated traits by a single gene

• single gene influencing multiple traits 

Why should pleiotropy be avoided in PTs?

• if gene correlated with multiple traits —> can’t fully distinguish if trait comes common ancestor or other cause

What are frizzles chicken feathers considered?

derived within chickens —> differs from ancestral feather structure

What do phylogenies also represent?

hypotheses that can change as we obtain new data or apply new methods of constructing the phylogeny

When can people be confident about evolutionary relationships?

Only when multiple lines of evidence and multiple methods of analysis converge on the same tree

What are phylogenies often combined with to find timeline of evolution?

fossil record

What can fossil record + phylogenies show us?

• give us a glimpse of the temporal patterns of diversification

• Ex: bone found between two volcanic events and place it there 

What can phylogenies combined with biogeographic data show?

allow us to infer dispersal and vicariance

What is Vicariance?

a lineage splits due to geological events, e.g., the breakup of continents, new island formations the uplifting of a new mountain range

What does the Raffelsia flower show?

• dispersal event in Malay archipelago —> new species in tropical rainforest

What can phylogeny also be combined with?

behaviour, ecology or morphology data

What does phylogeny + behavior, ecology or morphology data show us?

• understand the origin and loss of traits and predict traits of unstudied species

• Ex: Angler fish 

  • Sexual dimorphism --> hard to find mates so male attaches to female  

  • Female can mate whenever she wats, feeds him, or can kick him off 

  • different kinds of male attachment styles can be traced back to common ancestors

What are facultative parasites?

• Angler fish

  • dependent on female for food

What are obligates (Angler fish)?

male will die if it separates from female

What are the styles of male sexual dimorphism in Angler fish?

• White: free living 

• Yellow: males attach temporally 

• Green: Facultative parasites

• Obligate: will die if he separates 

What applications does phylogenies have?

• Enhances our understanding of evolution

• Control agriculture pests and diseases

• Identify endangered species, manage wildlife

• Select plants and animals for research

How can P control agriculture disease?

• Disease that impacts broccoli will impact cauliflower (same species)

• Create plant communities that are better at capturing water based on how they are related

  • More related they are the more likely they are able to compete

  • The most different; able to split resources more well

What are homologous traits?

• similar origin

• Result from common ancestry

• Are a product of divergent evolution

• Fundamental to systematics

• Similar structure and embryonic formation

What are analogous traits?

• similar function

• Do not reflect common ancestry

• Not used in systematics

• Are the outcomes of convergent evolution

How are analogous traits used in systematics?

• they are not used

  • traits from convergent evolution show no relation to each other through common ancestors 

What is convergent evolution?

When two or more different organisms independently evolve the ability to do the same thing

What can convergent evolution be a result of?

• adaptive radiations that occur in Allopatry

• ex: Placental mammals vs. Australia marsupials

  • evolved to occupy similar niches but evolved independently

What is allopatry/allopatric?

• Describes populations that are geographically separated from each other.

What is homoplasy?

Any similarity in traits that is not due to shared ancestry

What kind of trait are homoplasis?

• analogous traits

• traits resulting from parallelism

• Evolutionary reversal

• similar structure —> no common ancestor

What is parallelism?

similar traits evolve independently in different species, not because they are closely related but because they have a similar starting genetic or molecular basis, leading to the same phenotype

What can cause homoplasies?

• Same conditions resulting in repeated evolution of same structure independently  

  • Ex: Eye in human and octopus: similar in structure --> evolved independent of each other 

• simple as gene changes

complex and involve reorganization of multiple systems to converge on a solution

What is evolutionary reversal?

• A character reverts from a derived state back to the ancestral state.

• Ex: Gastrotheca guentheri regained teeth in the lower jaw after lost in frogs for 200 million years

  • ancestor of frog had teeth —> lost it —> one species regained it 

What is a homologous trait for most insects?

four wings

Why do flies have two wings?

Hind wings replaced by halteres instead

What are the hind wings in flies used for?

gyroscopic mechanisms

What is a gyroscope?

detect deviation of an object from desired orientation

What insect also has hindwings?

• twisted wing parasites

• also used for gyroscopy

What kind of trait/evolution is this example?

• homoplasy

• convergent evolution

  • similar function, different origin

In what two ways can traits appear?

ancestral or derived based on context (point of reference in phylogeny)

What is an ancestral trait?

A trait that was present in the ancestor of a group/clade

What is a derived trait?

A trait that differs from close ancestral trait

What are derived traits a subset of?

• subset of ancestral traits common to a group of interest

• Ex: bird feathers are ancestral in birds, but are derived when considering all living vertebrates.

What is synapomorphy?

• Derived traits that are shared among a group of descendants and are viewed as evidence of the common ancestry of the group

• Ex: the vertebral column is a synapomorphy of all vertebrates when considering all animals

What is milk production considered?

synapomorphy of all mammals when considering for vertebrates

• Ex: Monotreme: milk production keeps together even if one develops eggs 

how are derived characters determined?

by comparing with fossils and embryos/larval stage which preserve information about ancestral states and developmental origins

When do derived characters appear?

• later in development (novel traits to particular groups of organisms)

What do derived characters need to be compared to?

outgroup

What is an outgroup?

a lineage that falls outside the group being studied but is closely related to that group

What is a monophyletic group?

includes a common ancestor and all of its descendants.

Shows the entire evolutionary path a group has taken since

its origin.

• blue

• one cut to separate from PT

What is a clade?

a monophyletic group

What is a paraphyletic group?

includes a common ancestor and some, but not all, of its descendants

• green

• two cuts to separate from PT

What is a polyphyletic group?

does not include the common ancestor.

• members share trait that evolved independently by convergent evolution

• red

• Ex": Flying tetrapods includes bats and birds: cut out individual species and leaving ancestor out 

Which group is the only accurate reflection of evolutionary relationships?

• monophyletic group

• Shows the entire evolutionary path a group has taken since its origin.

Summary

What is the relation between bat and bird wings?

• wings of bats and birds are analogous because they evolved independently for flight

• forelimbs of mammals are homologous because they share a common skeletal structure inherited from a common ancestor

What is the order of taxonomic groups?

• Domain —> kingdom —> phylum —> class —> order —> family —> genus —> species

• Doctor King Phillip came over for good soup