1. Chapter 25: Phylogeny and Systematics

2. phylogeny – evolutionary history of a species or group of species

3. systematics – analytical approach to understanding the diversity and relationships of present and past organisms

4. Phylogenies based on common ancestors using fossil, morphological and molecular evidence

5. the fossil record – based mostly on the sequence in which fossils have accumulate in sedimentary rock strata (layers)

6. Sedimentary rock forms when silt builds up on bottom of waterway
Sedimentary rock forms when silt builds up on bottom of waterway. More deposited on top, compress older sediments into rock.

7. morphological and molecular homologies
organisms with similar morphology or similar DNA closely related

8. analogy is not homology; analogy is a similarity due to convergent evolution (organisms adapting to similar environment/niche but no common ancestor)
distinguishing analogy from homology critical to constructing phylogenies

9. homoplasies – analogous structures that have evolved independently
Marsupial mole
(Australia)
No recent common ancestor
eutherian mole
(North America)

10. molecular homologies
compare nucleic acids of two species; if very similar, organisms closely related
a hard to tell how long ago they shared a common ancestor; must also look at fossil record
mathematical tools can distinguish between distant homologies from coincidental matches

11. Systematics connects classification with evolutionary history

12. taxonomy – ordered division of organisms into categories

13. bionomial nomenclature – scientific name
binomial – 2- part scientific name developed by Linnaeus “Linnean system”
genus – first part of name
specific epithet – second part of name

14. Homo sapiens = humans, means “wise man”

15. Heirarchical classification
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

16. mnemonic to help you remember:
“Dreadful King Phillip Came Over From Great Spain”

17. Linking classification with phylogeny

18. phylogenetic trees – branching diagrams that depict hypotheses about evolutionary relationships.

19. uses groups nested within more inclusive groups
constructed from series of dichotomies
(2-way branch points)
each branch point represents a divergence of two species from a common ancestor

20. cladogram – shows patterns of shared characteristics

21. clade – group of species that includes an ancestral species and all of its descendants

22. cladistics – analysis of how species grouped into clades
clades can be nested inside larger clades
– ex. cat family within a larger clade that includes dog family

23. monophyletic group – ancestral species and all of its descendants

24. paraphyletic group– when we lack information about some members of the clade

25. polyphyletic group– several species that lack a common ancestor (need more work to uncover species that tie them together into a monophyletic clade)

26. Shared Characteristics – types of homologous similarities
Chordate characteristics

27. Shared primitive character – shared beyond the taxon.

28. Shared derived character – evolutionary novelty unique to that clade.
Ex. hair only found in mammals

29. Why morphology alone does not show evolutionary relationship:
Closely related organisms not always similar in appearance (rapid environmental change leads to rapid evolution; also, small changes in genes can lead to large morphological differences)
Organisms that appear similar not always closely related (convergent evolution)
Just because 2 groups share primitive characters does not mean they are closely related

30. outgroups – species or group of species closely related to the ingroup

31. less closely related than members of the ingroup
have a shared primitive character that predates both ingroup and outgroup members

32. phylogenetic trees – show estimated time since divergence
chronology of a phylogenetic tree is relative; not absolute

33. phylograms – length of a branch reflects number of changes in a DNA sequence

34. ultrametric trees – length of branch reflects amounts of time

35. maximum parsimony “Occam’s Razor” – first investigate the simplest explanation that is consistent with the facts
Aim is to find the shortest tree that has the smallest number of changes
The top tree has the most parsimony

36. maximum likelihood – given certain rules of how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

37. Often the most parsimonious tree is also the most likely

38. phylogenic trees are hypotheses of how the organisms are related to each other
Best hypothesis is one that fits all the available data
May be modified when new evidence introduced
Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious

39. Organisms’ genomes document their evolutionary history
importance of studying rRNA and mitochondrial DNA (mtDNA)

40. rRNA changes very slowly; used to study divergences that happened a very long time ago

41. mtDNA changes very rapidly; used to study divergences that happened recently
– useful for studying relationships between groups of humans

42. ex. how Native Americans descend from Asian population that crossed the Bering Land Bridge 13,000 years ago

44. Gene duplication one of most important types of mutation in evolution because it increases # of genes in genome.
can lead to further evolutionary changes

45. gene families – groups of related genes in an organism’s genome
result of repeated duplications
have a common ancestor

47. orthologous genes – homologous genes passed in a straight line from one generation to the next.
can diverge only after speciation
can be found in separate gene pools due to speciation

48. paralogous genes – result of gene duplication
paralogous genes – result of gene duplication. Found in more than one copy of the same genome
can diverge in the same gene pool

51. Genome evolution
Orthologous genes are widespread and can extend over huge evolutionary distances
99% of genes in humans and mice are orthologous; 50% of genes in humans and yeast are orthologous
– demonstrates that all living organisms share many biochemical and developmental pathways

53. Molecular clocks – way of measuring absolute time of evolutionary change
based on some genes seem to evolve at a constant rate
# of nucleotide substitutions in orthologous genes is proportional to time elapsed since the species branched from common ancestor

56. neutral theory – for genes that change regularly enough to use as a molecular clock, these changes are probably a result of genetic drift and are mostly neutral (neither adaptive nor detrimental)

57. conclusion: much evolutionary change has no effect on fitness; therefore, not influenced by selection.
most new mutations are harmful and therefore removed quickly

58. The universal tree of life
Genetic code universal to all forms of life so all life must share a common ancestor

59. Researchers trying to link all organisms in a “tree of life”
use rRNA genes for this; as they evolve most slowly

60. The Tree of Life has three domains: bacteria, archae and eukarya

61. The early history of these domains is not yet clear
due to horizontal gene transfer, substantial interchanges of genes between organisms of different domains
horizontal gene transfer due to transposable elements and fusion of different organisms (first eukaryote fusion of ancient bacteria with ancient archae)