chapter 25 - phlogenetic trees Flashcards
name and describe the function of the parts of the phylogenic tree
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
what is a polytomy?
- a node on the tree with 3 descendants
- means the best possible tree format isn’t determined
distinguish homology from homoplasy
both indicate similar traits, but homology is due to shared ancestry, homoplasy is not
homoplasy
when traits are similar for reasons other than common ancestry.
convergent evolution is a common cause of homoplasy
difference between convergent and divergent evolution
convergent: NS favours solutions to similar ways of life, making similar traits
divergent: traits inherited from a common ancestor
explain why bird and bat wings are not homologous. describe how this example defines homology.
2 populations developed wings independently - therefore not homologous, even if bones are homologous.
shows that homology is directly tied to convergent/divergent evolution
what 4 strategies do researchers use to estimate phylogenies?
4 GENERAL STRATEGIES
- PHENETIC (distance)
- *CLADISTIC (maximum parsimony)
- MAXIMUM LIKLIHOOD
- BAYESIAN
explain the cladistic (maximum parsimony) approach to estimating phylogenies
- 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
explain the whippo hypothesis
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
explain DNA barcoding
high throughput coding based on a variable gene to classify species
- inventory biodiversity
- automate and expedite species identification
cryptic species
- 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
background rate of extinction
rate of extinction when mass extinction isn’t happeneing
difference between mass and background extinctions
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
name 5 mass extinctions (oldest to newest)
Ordovician
Devonian
Permian
Triassic
Cretaceous
(and the 6th: now!)
what killed the dinosaurs? evidence? what survived?
impact hypothesis: meteor struck earth, killed 60-80% of species
evidence: crater, concentration of mineral deposits, fossils
differential survival: mammals, crocodilians, amphibians, turtles
differential survival
some lineages better able to withstand environmental changes
6th mass extinction: name types
- 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)
cichlid fish case study
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
atavism
ancestral characteristic that is lost but then re-emerges during evolution
how do cichlid fish show adaptive radiation
- 2 jaws created a biological innovation that opened up new ecological niches
- allowed fish to greatly diversify
life’s timeline
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
what is a metazoan? traits
animals!
- eukaryotic + multicellular
- different tissues types in one organism
- have a gut
- heterotrophic (ingest other organisms)
- sexually reproduce, usually
what caused Cambrian explosion?
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
hox genes as a cause of Cambrian explosion
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.
hox genes
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
how does genetically based morphological diversification occur in animals?
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
evolutionary development via ‘switches’
promoters
- switch genes on/off
eg distal-less in snakes
evolutionary development via ‘gradients’
- 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)
