chapter 25 - phlogenetic trees

Question 1

name and describe the function of the parts of the phylogenic tree

Answer 1

ROOT: ancestral node

BRANCHES/EDGES: ancestral lineages

INTERNAL NODES: represent ancestors of the descendant taxa

TERMINAL NODES: current variation of species/gene/population)

TAXA: present genes, populations, species

Question 2

what is a polytomy?

Answer 2

• a node on the tree with 3 descendants
• means the best possible tree format isn’t determined

Question 3

distinguish homology from homoplasy

Answer 3

both indicate similar traits, but homology is due to shared ancestry, homoplasy is not

Question 4

homoplasy

Answer 4

when traits are similar for reasons other than common ancestry.

convergent evolution is a common cause of homoplasy

Question 5

difference between convergent and divergent evolution

Answer 5

convergent: NS favours solutions to similar ways of life, making similar traits

divergent: traits inherited from a common ancestor

Question 6

explain why bird and bat wings are not homologous. describe how this example defines homology.

Answer 6

2 populations developed wings independently - therefore not homologous, even if bones are homologous.

shows that homology is directly tied to convergent/divergent evolution

Question 7

what 4 strategies do researchers use to estimate phylogenies?

Answer 7

4 GENERAL STRATEGIES

• PHENETIC (distance)
• *CLADISTIC (maximum parsimony)
• MAXIMUM LIKLIHOOD
• BAYESIAN

Question 8

explain the cladistic (maximum parsimony) approach to estimating phylogenies

Answer 8

• focus on SYNAPOMORPHIES (shared derived characteristics)
• synapomorphy is a novel trait that a clade has that others don’t

maximum parsimony assumes that the best pattern is the one that has the least amount of change
- tree will reflect the fewest amount of evolutionary changes

Question 9

explain the whippo hypothesis

Answer 9

GENETIC HOMOLOGY
- whales thought to be their own clade outside artiodactyls
- SINEs genes found in whales and hippos, not in other artiodactyls
- SINEs genes therefore SYNAPOMORPHIES and support hypothesis that whales and hippos are closely related
- homoplasy in SINEs very rare compared to morphology

PARSIMONY
- new phylogeny less parsimonious to the last with respect to astragalus evolution, but more overall with respect to all new data found

MORPHOLOGY
- transitional forms

Question 10

explain DNA barcoding

Answer 10

high throughput coding based on a variable gene to classify species

• inventory biodiversity
• automate and expedite species identification

Question 11

cryptic species

Answer 11

• unknown species
• difficult to distinguish species based on morphology
• animals/plants not easy to identify sometimes
• most diverse parts of the world are the least known

Question 12

background rate of extinction

Answer 12

rate of extinction when mass extinction isn’t happeneing

Question 13

difference between mass and background extinctions

Answer 13

background:
- happen when normal environmental change, disease or competition reduce some populations to 0

mass:
- happen bc of extraordinary, sudden and temporary changes in environment. causes extinction randomly with respect to individual’s normal fitness

Question 14

name 5 mass extinctions (oldest to newest)

Answer 14

Ordovician
Devonian
Permian
Triassic
Cretaceous
(and the 6th: now!)

Question 15

what killed the dinosaurs? evidence? what survived?

Answer 15

impact hypothesis: meteor struck earth, killed 60-80% of species

evidence: crater, concentration of mineral deposits, fossils

differential survival: mammals, crocodilians, amphibians, turtles

Question 16

differential survival

Answer 16

some lineages better able to withstand environmental changes

Question 17

6th mass extinction: name types

Answer 17

• ancient (marsupial extinction with first humans is AU)
• historical (dodo bird)
• mass (cichlid fish)
• island fauna (brown snake introduction)
• once abundant fauna (passenger pigeon)
• disease related
• biological phenomena (bison migration patters)

Question 18

cichlid fish case study

Answer 18

largest mass extinction of contemporary vertebrates

• nile perch introduced to lake Victoria to increase food for locals
• fast maturity, lots of offspring, wide diet

consequences (environmental, economic)
- algae blooms because cichlids ate algae
- consequent decrease in O2 forces fish to top of lake
- nile perch overfished, therefore smaller, causing fishing businesses to close

Question 19

atavism

Answer 19

ancestral characteristic that is lost but then re-emerges during evolution

Question 20

how do cichlid fish show adaptive radiation

Answer 20

• 2 jaws created a biological innovation that opened up new ecological niches
• allowed fish to greatly diversify

Question 21

life’s timeline

Answer 21

measured in eons

precambrian supereon
- earth cools, water, origins of life, eukaryotes, bilateral animals

cambrian explosion
- rapid diversification of metazoans (animals)
- documented by fossils

phanerozoic era

Question 22

what is a metazoan? traits

Answer 22

animals!

• eukaryotic + multicellular
• different tissues types in one organism
• have a gut
• heterotrophic (ingest other organisms)
• sexually reproduce, usually

Question 23

what caused Cambrian explosion?

Answer 23

1) environmental change
- increased O2
- increase thickness of ozone layer
- flooding of continental shelves
- increased Ca2+ in oceans

2) ecological engineers
- animals that change environment and open up ecological niches, allowing diversification

3) developmental/morphological adaptations
- possible role of developmental genes (hox genes)
- **not a necessary catalyst for animal diversification bc some animals don’t have many hox genes

Question 24

hox genes as a cause of Cambrian explosion

Answer 24

developmental adaptations: “new genes, new bodies”
- genome duplication in ancestors duplicated # of hox genes
- caused developmental/morphological adaptations = increased diversity
- not a necessary catalyst for animal diversification because some species with great diversity did not undergo hox GENOME duplication.

Question 25

hox genes

Answer 25

GENERAL FUNCTION
- determine what each section of the body is, NOT what structures form there
- occur in groups along 1 or a set of chromosomes
- generally in same order on chromosome
- encode proteins to bind to DNA, driving/suppressing expression of other genes (TRANSCRIPTION FACTORS)

DNA
- contains DNA sequence called a HOMEOBOX
- homebox encodes DNA binding domain
- not all genes with homebox domain are hox genes, all hox genes have homebox domain

HISTORICAL
ancient metazoans have hox genes, just in different organization and pattern of expression

Question 26

how does genetically based morphological diversification occur in animals?

Answer 26

1) change in hox gene number
2) broad changes of hox gene expression
3) subtle changes within hox domains (on/off)
4) changes in regulation or function of downstream genes (promoters)

transcription factors act as
- switches
- gradients
that rigger biological cascades in a continuous fashion

Question 27

evolutionary development via ‘switches’

Answer 27

promoters
- switch genes on/off
eg distal-less in snakes

Question 28

evolutionary development via ‘gradients’

Answer 28

• gradients of gene expression develop into segment specific patterns
• cdetermine where genes will be expressed along the body
  (eg genes for head expressed more at head, less at tail)