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Phylogeny: Determining Evolutionary Relationships of Species Using Molecular Biology

Introduction: For a long time, scientists have relied on structural similarities and differences in order to construct an evolutionary history of life on Earth – a phylogeny, or a “family tree” of life. More recently, however, molecular techniques have been demonstrated to be very powerful in determining relatedness of species. These techniques use DNA sequences, protein structures, and other biochemical comparisons in much the same way that forensic scientists use them to analyze clues from a crime scene. With these tools, scientists can answer such questions as, “Which living animals are most closely related to the Giant Panda?” or “Are birds the descendants of prehistoric dinosaurs like T. rex?” DNA sequences can be used as a kind of “molecular clock” to determine how long ago different groups of organisms diverged from one another. Two species that shared a recent common ancestor have fewer differences in their DNA and protein sequences than between species that share a more distant common ancestor.

  1. Effects of mutations on protein sequences

Transcribe the following DNA template sequences into mRNA, and then translate into amino acids (using the table on page 303 of your textbook). The DNA #2 contains two mutations (in bold).

DNA #1 / C / C / G / T / T / A / G / C / G
mRNA / ____ / ____ / ____ / ____ / ____ / ____ / ____ / ____ / ____
Amino Acid
DNA #2 / C / C / T / T / T / C / G / C / G
mRNA / ____ / ____ / ____ / ____ / ____ / ____ / ____ / ____ / ____
Amino Acid
  1. Are mutations heritable? Why or why not?
  1. Do mutations always change the sequence of amino acids? Cite evidence to support your claim.
  1. Phylogeny from DNA sequence comparisons

Circle nitrogenousbases of chimpanzee and gorilla DNA that differ from the human DNA sequence:

Human DNA / T / C / C / G / T / A / T / T / T / G / G / T / T / G / G / C / T / A / A / T
Chimpanzee DNA / T / C / C / G / G / G / G / A / A / G / G / T / T / G / G / C / T / A / A / T
Gorilla DNA / T / C / C / G / G / G / G / A / A / G / G / T / T / G / G / T / C / C / G / G
  1. How many bases in the chimpanzee sequence were different from the human sequence?
  1. How many bases in the gorilla sequence were different from the human sequence?
  1. Based on this analysis, which organism appears to be more closely related to humans?

  1. Phylogeny from amino acid sequence comparisons

Hemoglobin is a protein complex that allows blood cells to bind to oxygen. Circle the amino acids that differ from the human hemoglobin protein sequence:

Amino Acid # / 87 / 88 / 89 / 90 / 91 / 92 / 93 / 94 / 95 / 96 / 97 / 98 / 99 / 100 / 101
Human / THR / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Chimpanzee / THR / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Gorilla / THR / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Rhesus monkey / GLN / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Horse / THR / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Kangaroo / LYS / LEU / SER / GLU / LEU / HIS / CYS / ASP / LYS / LEU / HIS / VAL / ASP / PRO / GLU
Amino Acid # / 102 / 103 / 104 / 105 / 106 / 107 / 108 / 109 / 110 / 111 / 112 / 113 / 114 / 115 / 116
Human / ASN / PHE / ARG / LEU / LEU / GLY / ASN / VAL / LEU / VAL / CYS / VAL / LEU / ALA / HIS
Chimpanzee / ASN / PHE / ARG / LEU / LEU / GLY / ASN / VAL / LEU / VAL / CYS / VAL / LEU / ALA / HIS
Gorilla / ASN / PHE / LYS / LEU / LEU / GLY / ASN / VAL / LEU / VAL / CYS / VAL / LEU / ALA / HIS
Rhesus monkey / ASN / PHE / LYS / LEU / LEU / GLY / ASN / VAL / LEU / VAL / CYS / VAL / LEU / ALA / HIS
Horse / ASN / PHE / ARG / LEU / LEU / GLY / ASN / VAL / LEU / ALA / LEU / VAL / LEU / ARG / HIS
Kangaroo / ASN / PHE / LYS / LEU / LEU / GLY / ASN / ILE / ILE / VAL / ILE / CYS / LEU / GLU / HIS
  1. On the basis of hemoglobin similarity, which organism appears to be most closely related to humans?
  1. Which organism appears to be least closely related to humans (shares a more distant common ancestor)?

Cytochrome c is a protein (105 amino acids) in the electron transport chain (remember cellular respiration?).

  1. On the basis of cytochrome c, which organism appears to be most closely related to humans?
  1. On the basis of cytochrome c, which two organisms are least closely related to humans?