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25,26 (phylogeny and the tree of life (phylogenies inferred (phenotypic…

- - - - the relationships are depicted by branch points, representing divergence of evolutionary lineages
      - taxa B and C are sister taxa representing an immediate common ancestor
        
        rooted, a branch point within the tree farthest to the left which represent common ancestor to all taxa on the tree
        
        basal taxon, a lineage diverging earlier in the history of a group taxon G, originated near the common ancestor
        
        taxa D-F are a polytomy, a point where more then two descendants groups emerge
  - - - a systematic called cladistics, the common ancestry mainly used to classify organisms
        
        clades are where species are placed, including all ancestral and descendant species. clades are within larger clades ex: cat group Felidae represents a clade within a larger clade Carnivora it also inlcudes the dog group canidae
        
        monophyletic,includes ancestral species and all the descendants
        
        paraphyletic, includes ancestral species and some descendants
        
        polyphyletic, includes distantly related but not common ancestor
    - - shared derived character, a novelty unique to a clade ex: hair in mammals but not in their common ancestor
        
        so using derived characters can be used to infer evolutionary relationships, to do this there has to be an out-group a group diverged before the lineage that we are studying the in-group
    - - parsimony, the simplest explanation, the fewest evolutionary events another name called Occams razor
      - likelihood, tree that most likely produced a given set of DNA data, based on certain probability rules about how DNA sequences change over time
  - - - using molecular systematics also helps to uncover relationships between groups with little morphological similarities
      - different genes evolve at different rates, so molecular trees represent short or long period of time depending on the genes used
    - - gene duplication increases the # of genes in the genome which can give more opportunities for evolutionary change
      - now molecular techniques can trace phylogenies of gene duplication, these phylogenies account for repeated duplications resulted in gene families,a group of related genes within an organisms genome
      - orthologous genes(one copy) homology that resulted in speciation events and are found in genes between different species ex:humans & dogs
        
        these genes diverge after speciation, after genes are found in separate gene pools
      - paralogous genes, homology resulting in gene duplication thus (multiple copies) of these genes diverged from one another within a species
        
        paralogous genes are able to diverge within the species b/c they are present in more then one copy of the genome
    - - in orthologous genes the # of nucleotide substitutions is proportional to time elapsed since genes branched from a common ancestor
      - in paralogous genes the # of substitutions is proportional to time since the ancestral gene was duplicated
      - differences in clock speed
        
        mutations are selectively neutral meaning they are neither beneficial or detrimental (rate of evolution is neutral then it should be like a regular clock)
        
        difference in clock rate for different genes are a function to how important a gene is
      - potential problems with clocks
        
        many irregularities are likely to be the result of natural selection in which certain DNA changes are favored over other
    - - in prokaryotes, transformation (uptake of free DNA), conjugation (plasmid-mediated transfer),& transduction (phage mediated transfer)
      - in eukaryotes, endosymbiosis, bacteria present in nucleus, nuclear genes from bacteria and archea
      - phlyogenetic trees are based on genes being passed vertically, but b/c of horizontal gene transfer can help explain why trees built using different genes can give inconsistent results
- - - - 1) abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases
      - 2) joining of the small molecules into macro-molecules, such as proteins and nucleic acids
      - 3) these molecules packaged into protocells, membranes that maintain internal chemistry that is different from their surroundings
      - 4) origin self-replicating molecules making inheritance possible
    - - the record in incomplete chronicle, meaning that some organisms did not die in the right time be to preserved as fossils
        
        fossil records favor animals that existed for a long time, ones that were abundant and widespread, animals w/th hard shells, skeletons and parts that facilitated their fossilization
        
        the fossil record has limitations, if animals were squishy and if they were rare
      - fossils in rock strata lets us know the sequence in which they were laid down but not their age
        
        we can determine fossil age by radiometric dating, which is the decay of radioactive isotopes
        
        so the parent isotope decay into the daughter isotope at a characteristic rate, called a half life time required for 50% of parent isotope to decay
        
        fossils have isotopes of elements that accumulate when they are alive, carbon-12 and carbon-14
        
        a dead organism carbon stops accumulating, carbon-12 does not change but carbon-14 slowly changes into nitrogen-14.
        
        the ratio of these two carbons can determine fossils age but only fossils that are 75,000 yrs old nothing older than that b/c they have to little carbon-14
  - - - 3 eons, Hadean, Archean, Proterozoic lasted 4 billion years. Phanerozoic lasted half billion years. its divided into 3 eras Mesozoic, Cenozoic, & Paleozoic
        
        the eras represent distant ages in of earth life & history
        
        4 eras, Precambrian (Hadean, Archean, Proterozoic) 4.5 billion-541 million yrs ago. Paleozoic 541 -252 million yrs ago. Mesozoic 252-66 million yrs ago (age of reptiles). Cenozoic 66 million-present (rise of mammals)
        
        these eras are separated by catastrophic events (extinction)
    - - endosymbiont theory, mitochondria and plastids were small prokaryotes that lived in other larger cells
      - endosymbiont a cell lives within another cell called the host cell
      - some endosymbiosis began as prey & parasites had developed into a mutual beneficial relationship
  - - - slight genetic differences can produce major morphological differences between species
      - ex: chimpanzees and humans (mutations slowed the growth of the jaw)
      - an organisms shape depends on the growth rates of different body parts during development
      - heterochrony can alter timing of reproductive development relative to development of nonproductive organs
        
        a term called paedomorphosis, when reproductive organs develop faster than other organs so the organism retains juvenile features
        
        ex: salamander has aquatic larvae that undergo metamorphosis to become adults
    - - homeotic genes, are genes that determine where features on the body will go (a pair of wings and legs will go on a bird)
        
        something called a Hox genes provide the information in the embryo, it prompts the cells into appropriate structures for a particular location
        
        changes in Hox genes and how they are expressed can have an impact on morphology
    - - ex: changing in the UBX gene have been identified as a turn off in leg development
    - - ex: threespine stickleback fish. some live where there are predators and have the spines, whereas other live in a lake with no predators and thus they have reduced spines