1. PHYOGENY & THE Tree of life
Campbell and Reece, Chapter 26

2. Phylogeny Systematics
definitions
Phylogeny
Systematics
evolutionary history of a species or group of species
discipline focused on classifying organisms & determining their evolutionary relationships

3. Taxonomy how organisms are classified and named
each step called a taxon (plural: taxa)

4. BINOMIAL NOMENCLATURE
Man’s Genus species: Homo sapiens
used to avoid ambiguity
the Latin scientific name for each individual species
is the Genus species portion of taxonomy

5. 3 DOMAINS DOMAIN ARCHAEA Prokaryotes
many live in Earth’s extreme environments
as molecularly close to eukaryotes as Domain Bacteria
includes multiple kingdoms

6. (notice position of domain Archaea)

7. Domain Archaea
methanogen
thermophile

8. Domain Bacteria Prokaryotic very diverse group
use every major mode of nutrition & metabolism
beneficial: photoautotrophs, alcoholic fermentation, Vit K production
pathologic: strep throat, flesh-eating disease, ulcers, Rheumatic fever

9. Legionella pneumophilia
Domain Bacteria
Gram Positive Bacteria
Streptococcus
(cocci)
Gram Negative Bacteria
Legionella pneumophilia
(rods)

10. Domain Bacteria
Spirochetes
(spirillia)

11. Domain Eukarya Eukaryotic cells more complex, become specialized
able to form multicellular organisms
greatest diversity

12. Domain Eukarya
Plants
Fungi

13. Domain Eukarya
Animal
Protozoa

14. Domain Eukarya
Algae Cells
Algal “bloom”

15. Linnean Classification

16. PHYLOGENETIC TREES
show the evolutionary history of a group of organisms
represented by a branching diagram
each branch point represents the divergence of 2 evolutionary lineages from a common ancestor

17. Phylogenetic Trees
Branch Point

18. sister taxa
basal taxa

19. Phylogenetic Trees patterns of descent common ancestors
What you can learn
What you cannot learn
patterns of descent
common ancestors
does not show phenotypic similarity
cannot tell ages of species based on where branches are in the “tree”
sister taxa did not evolve from each other; they have a common ancestor (that could be extinct)

20. Uses of Phylogenetic Tree
If “close” relatives found they could be source of beneficial alleles that could be transferred to hardier taxa via genetic engineering
2. Using DNA samples are now able to differentiate legal species from illegal species of whale, tuna

21. Phylogenies are inferred from morphological & molecular data
Homology: similarity in characteristics resulting from a shared ancestry

22. Homologous Chromosomes in same species
When chromosomes duplicate in S Phase of Cell Cycle see genes in same loci of each sister chromatid

23. Homologous Chromosomes across Species with Common Ancestor
Genes or certain DNA sequences also homologous if they descended from sequences carried by a common ancestor

24. Organisms that share very similar morphologies or DNA sequences are likely to be more closely related than organisms with vastly different structures
There are examples of organisms that look very different but have very similar DNA sequences because species underwent adaptive radiation.

25. Homology vs. Analogy
Analogy is similarity due to convergent evolution: occurs when similar environmental pressures & natural selection produce similar (analogous) adaptations even though organisms have different ancestors.

26. homoplasies: analogous structures that arose independently (Greek: to mold in same way)
Examples:
bird & bat wing: their common ancestor did not fly

27. The more complex the structure found in 2 species the more likely it is that they have a shared ancestor

28. Molecular Evidence of Evolutionary Relationships
DNA sequence similarities have been documented among prokaryotes & eukaryotes: (comparative genomics)
High degree of sequence similarity noted in some eukaryotic nuclear genes to Archaea & mitochondrial genes are similar to Bacteria

29. Using DNA to map an organism’s evolutionary history
The more recently 2 species have branched from a common ancestor, the more similar their DNA sequences should be
The longer ago 2 species have been on separate evolutionary paths, the more their DNA should have diverged

30. Different genes evolve at different rates
Nuclear DNA
Mitochondrial DNA
changes slowly
useful for investigating relationships between taxa that diverged hundreds of millions of yrs ago
evolves rapidly
useful to investigate more recent evolutionary events

31. Eukaryotic genes consist of numerous coding regions (exons) that are separated by noncoding regions (introns)
both transcribed into pre-mRNA and then intron sequences are removed

32. in humans 90% of the exons are homologous to exons found in Drosophila & Caenorhabditis (nematode worms

33. Puffer Fish is vertebrate with smallest known genome (1/7th human genome) & yet has all exons present in humans
in chromosomes: “homologous” means sequences are so similar that they are not likely due to chance so are considered the result of common ancestry

34. Duplication in human genome
both of genes & chromosome segments

35. Based on these duplications & new combinations of exons it seems that
the vertebrate evolution has required very few new proteins
evolutionary change involves making new genes by rearranging functional domains into novel combinations (called “exon shuffling”)

36. Exon Shuffling
Important source of genetic variation (in addition to mutations & crossing over)
still investigating mechanism

37. Homologous Genes
60% of human genes that encode proteins are homologous to genes from other organisms
high degree of conservation of both genes & exons among widely diverse organisms from all 3 Domains is strong evidence for their common ancestry

39. Nonfunctional Sequences
another bit of strong evidence for relatedness among diverse organisms is the similarity in DNA sequences that have no apparent function.
one category of these are pseudogenes

40. Pseudogenes 2 kinds:
1. arises from DNA replication  mutations  STOP codons in one of duplicates; other no mutation
2. Processed Pseudogenes:
arise during transcription or translation: lack a promoter sequence so cannot be transcribed

41. To date, 2909 pseudogenes in human genome

42. Other functionless DNA
LINEs
SINEs
Long Interspersed Nucleotide Element
Families: 1,2,3
Are retrotransposons
Short Interspersed Nucleotide Element
Also 3 families in humans
Specific LINEs & SINEs found only in cloven-hooved mammals & whales

43. Retroviruses RNA virus
Infects cell and turns its single strand  double strand which inserts into host genome

44. RetrovirusRetrotransposon
Retrovirus inserts self into host genome but somewhere along the way genes for capsids lost
If LINEs in different species are homologous it is considered to be strong evidence that these 2 species share a common ancestor where that particular LINE first became established

46. Review: Phylogeny can be inferred from –the fossil record,
–morphological homologies
–molecular homologies

47. Shared characters are used to construct phylogenetic trees
Phylogenetic trees are used to depict hypotheses about the evolutionary history of a species
Shared characters are used to construct phylogenetic trees
Shared ancestral characters group organisms into clades
Shared derived characters distinguish clades & form branching points in the tree of life

48. Shared Characteristics are used to Construct Phylogenetic Trees
Cladistics: an approach to systematics in which organisms are placed into groups based primarily on common descent
Clades:groups organisms are placed in:
1 clade will include ancestor & all its descendants
3 types:

49. 1. Monophyletic Group equivalent to a clade
ancestral species & all its descendants

50. 2. Paraphyletic Group
consists of an ancestral species & some of its descendants

51. 3. Polyphyletic Group
Some members of this group will have different ancestors

52. Name That Group:

53. Shared Derived Character Shared Ancestral Character
character that originated in an ancestor of the taxon
an evolutionary novelty unique to a clade.

54. Shared Ancestral Character Shared Derived Character

55. How to Build a Cladogram
dograms/Open-This-File.swf

56. Making a Phylogenetic Tree
SHOULD BE POSSIBLE TO DETERMINE THE CLADE ANY SHARED DERIVED CHARACTER 1ST APPEARED
Construct a CHARACTER TABLE:
1 axis has list of organisms, 1 has characters

57. CHARACTER TABLE FROG IGUANA DUCK-BILLED PLATYPUS KANGAROO BEAVER
AMNION
HAIR, MAMMARY GLANDS
GESTATION
LONG GESTATION

58. Important step in cladistics is the comparison of the
Ingroup: the taxa whose phylogeny is being investigated
Outgroup: the taxon that diverged before the lineage leading to the members of the ingroup
Use to identify the derived characters that define the branch points in the phylogeny of the ingroup

59. PHYLOGENETIC TREES
WHEN CONSTRUCTING A PHYLOGENETIC TREE, SCIENTISTS USE PARSIMONY, LOOKING FOR THE SIMPLEST EXPLANATION FOR OBSERVED PHENOMENA

60. SYSTEMATISTS USE MANY KINDS OF EVIDENCE, BUT EVEN THE BEST TREE REPRESENTS ONLY THE MOST LIKELY HYPOTHESIS

61. Shared characters are used to construct phylogenetic trees
The phylogenetic tree of reptiles shows that crocodiians are the closest living relatives of birds

62. Crocodiles & Birds share:
4-chambered heart
“singing” to defend territories
parental care of eggs within nests

63. Phylogenetic Trees with Proportional Branch Lengths
branch lengths are proportional to the amount of genetic change in each lineage
So the longer the line the more genetic changes have occurred

64. Principle of Maximum Parsimony
1st investigate the simplest explanation that is consistent with the facts
aka “Occum’s Razor”
for phylogenies based on DNA: the most parsimonious tree requires the fewest base changes

65. Principle of Maximum Likelihood
given certain probability rules about how DNA sequences change over time, a tree can be made that reflects the most likely sequence of evolutionary events

66. currently using computer programs to search for trees that are parsimonious & have a high probability

68. Phylogenetic Trees as Hypotheses
Scientists can make & test predictions based on the assumption that a phylogeny (the hypothesis) can be supported or not.
Prediction: features shared by 2 groups of closely related organisms are also present in their common ancestor & all of its descendants

69. An organism’s evolutionary history is documented in its genome: 2 Types of Homologous Genes
Orthologous Genes
Paralogous Genes
Exact copies found in different species
Origin: common ancestor
Homology result of gene duplication: multiple copies of a gene in same species all came from same gene

71. Genome Evolution
By investigating entire genomes of different species see 2 patterns:
Lineages that diverged long ago can share orthologous genes
# of genes a given species has does not seem to increase thru duplication at same rate as increase in phenotype changes

72. Molecular Clocks
is a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes & other regions of genomes appear to evolve at constant rates.
is based on assumption that the # of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor (known as divergence time)

73. Molecular Clocks
calibration of a molecular clock is done by graphing the # of genetic differences against the dates of evolutionary branch points that are known from fossil record

74. finding the average rates of genetic change from such graphs can be used to estimate dates of events that cannot be discerned from fossil record

75. genes that appear to follow molecular clock are really only acting in statistically average rate of change
of course parts of the genome appear to have evolved in irregular bursts
some genes seem to have different rates of change in different organisms
some genes evolve a million times faster than others

76. Neutral Theory
states much of the evolutionary change in genes & proteins has no effect on fitness & therefore is not influenced by natural selection
many new genes are harmful so are quickly removed
differences in the clock rate for different genes are a function of how important a gene is

77. Problems with Molecular Clocks
Natural selection favors some DNA changes
Many scientists remain skeptical about:
the “Neutral Theory”,
about using the molecular clock beyond time span documented by fossil record (about 550 million years)

78. Dating the Origin of HIV with a Molecular Clock
HIV is descended from viruses that infected chimps & other primates but did not cause same AIDS-like illness
When did this happen?

79. HIV Strains multiple strains have infected humans
multiple strains implies multiple origins
most widespread strain in HIV-M
using molecular clock best guess is HIV-M strain 1st spread to humans in the 1930’s

80. Is the tree of Life Really a Ring of Life?
there has been substantial movements of genes between organisms in the 3 domains
mechanism: horizontal gene transfer: plasmids, viral infection, maybe even fusion of organisms

81. Ring of Life
some scientists think horizontal gene transfer so common that early history of life should be represented as a ring with 3 domains emerging from the ring