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Lines of evidence

1. Direct observation of change in natural populations
2. Direct observation of change under artificial
   selection
3. Homologous traits
4. Homologies tend to be nested
5. The fossil record



                           1
Evolution in Natural Populations
      Human Immunodeficiency Virus (HIV)




                      2                   http://www.thebody.com/nmai/cycle.html
Evolution in Natural Populations
      Human Immunodeficiency Virus (HIV)




               env
                      2                   http://www.thebody.com/nmai/cycle.html
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




3
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




3
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




3
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




3
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




4
Evolution in Natural Populations
    Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997




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Evolution in Natural Populations
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       5
Evolution in Natural Populations
                                      Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997
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Evolution in Natural Populations
                                      Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997
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Evolution in Natural Populations
                                      Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997
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       5
Evolution in Natural Populations
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Evolution in Natural Populations
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       6
Evolution in Natural Populations
     Blackcap migration – Berthold et al. 1992




                                         www.dicktruedesign.com/PRINTS/prints.fin&feather.htm




                         7
Evolution in Natural Populations
     Blackcap migration – Berthold et al. 1992




                                         www.dicktruedesign.com/PRINTS/prints.fin&feather.htm




                         7
Evolution in Natural Populations
     Blackcap migration – Berthold et al. 1992




                                         www.dicktruedesign.com/PRINTS/prints.fin&feather.htm




                         7
Evolution in Natural Populations
             Blackcap migration – Berthold et al. 1992

Is there evidence for a genetic basis to the migration shift?




  British parents:                               German young:
  WNW (279°)                                      SW (227°)



                                 8
Evolution in Natural Populations
             Blackcap migration – Berthold et al. 1992

Is there evidence for a genetic basis to the migration shift?




  British parents:       British offspring:      German young:
  WNW (279°)              WNW (273°)              SW (227°)



                                 8
Evolution in Natural Populations
                    Blackcap migration – Berthold et al. 1992

                          British parents:
                          WNW (279°)



                          British offspring:
                           WNW (273°)



                          German young:
                           SW (227°)

Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species.
Nature 360: 668-670.                             9
Evolution in Natural Populations
                    Blackcap migration – Berthold et al. 1992

                          British parents:
                          WNW (279°)



                          British offspring:
                           WNW (273°)



                          German young:
                           SW (227°)

Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species.
Nature 360: 668-670.                             9
Evolution in Natural Populations
                    Blackcap migration – Berthold et al. 1992

                          British parents:
                          WNW (279°)



                          British offspring:
                           WNW (273°)



                          German young:
                           SW (227°)

Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species.
Nature 360: 668-670.                             9
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996




                                                              10
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
Dispersal in island plant populations – Cody & Overton 1996
Evolution in Natural Populations
 Dispersal in island plant populations – Cody & Overton 1996
Hypochaeris radicata




                 www.missouriplants.com/Yellowalt/Hypochaeris_radicata_page.html


Lactuca muralis




  biology.burke.washington.edu/herbarium/imagecollection.php?Genus=Mycelis&Species=muralis
                                                                                             12
Evolution in Natural Populations
 Dispersal in island plant populations – Cody & Overton 1996
Hypochaeris radicata




                 www.missouriplants.com/Yellowalt/Hypochaeris_radicata_page.html


Lactuca muralis




                                                                                                  www.bartleby.com/61/imagepages/A4achene.html
  biology.burke.washington.edu/herbarium/imagecollection.php?Genus=Mycelis&Species=muralis
                                                                                             12
Evolution in Natural Populations
                     Dispersal in island plant populations – Cody & Overton 1996
                Hypochaeris radicata
Dispersal ability (VP/VA)
     (Mean ± SD)




                            Main- Island
                            land (Old)




 Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant
 populations. J. of Ecology 84:53-61.
                                                 11
                                                 13
Evolution in Natural Populations
                     Dispersal in island plant populations – Cody & Overton 1996
                Hypochaeris radicata
                                                                         Lactuca muralis
Dispersal ability (VP/VA)




                                             Dispersal ability (VP/VA)
     (Mean ± SD)




                                                  (Mean ± SD)

                                                                                Mainland 1–4   5–7   8–9   10+
                            Main- Island
                                                                                           Age (years)
                            land (Old)




 Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant
 populations. J. of Ecology 84:53-61.
                                                                         11
                                                                         13
Evolution in Natural Populations
                     Dispersal in island plant populations – Cody & Overton 1996
                Hypochaeris radicata
                                                                         Lactuca muralis
Dispersal ability (VP/VA)




                                             Dispersal ability (VP/VA)
     (Mean ± SD)




                                                  (Mean ± SD)

                                                                                Mainland 1–4   5–7   8–9   10+
                            Main- Island
                                                                                           Age (years)
                            land (Old)




 Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant
 populations. J. of Ecology 84:53-61.
                                                                         11
                                                                         13

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Lecture 2

  • 1. Lines of evidence 1. Direct observation of change in natural populations 2. Direct observation of change under artificial selection 3. Homologous traits 4. Homologies tend to be nested 5. The fossil record 1
  • 2. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) 2 http://www.thebody.com/nmai/cycle.html
  • 3. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) env 2 http://www.thebody.com/nmai/cycle.html
  • 4. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
  • 5. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
  • 6. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
  • 7. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
  • 8. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4
  • 9. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 4
  • 10. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
  • 11. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 56585 56557 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
  • 12. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 56585 56557 quot; ! 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
  • 13. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 56585 56557 quot; 5 5 ! 1 1 ! quot; 4 #$%&'()*%+,-+.//&0- 4@?71+2=03+/9?A9=0=?=02@9:B++C< 1(,2()*.3,(3&0- % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
  • 14. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 56585 56557 < < < < < < ; ; ; ; ; ; = > D E F G !quot;?,-+@%?A&BA$..,(B ;+&2+@%?A&BA$..,(B 4@?71+2=03+/9?A9=0=?=02@9:B++C< ;+&2+@%$C&+C,(B !quot;?,-+@%$C&+C,(B % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
  • 15. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 56585 56557 < < ;< < < ;< ; ; ; ; = > D E F G !quot;?,-+@%?A&BA$..,(B ;+&2+@%?A&BA$..,(B ;+&2+@%$C&+C,(B !quot;?,-+@%$C&+C,(B 565:7 !quot;#$%&'%()*+$&#,-$%.)/.#,#)#,&( 565:5 0()*+$&#,-$.12$$34 56597 56595 56587 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 56585 5-=+/2>/+*21?=02@ $&$$$!$ 56557 & D D ; ; ) ' ( $&$$$'$ <=> EFG !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# !quot;?,-+@%?A&BA$..,(B ;+&2+@%?A&BA$..,(B )*+,-.+/*0,-1/12-3/456)/7280+9:;1< ;+&2+@%$C&+C,(B !quot;?,-+@%$C&+C,(B 6
  • 16. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
  • 17. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
  • 18. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
  • 19. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 Is there evidence for a genetic basis to the migration shift? British parents: German young: WNW (279°) SW (227°) 8
  • 20. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 Is there evidence for a genetic basis to the migration shift? British parents: British offspring: German young: WNW (279°) WNW (273°) SW (227°) 8
  • 21. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 British parents: WNW (279°) British offspring: WNW (273°) German young: SW (227°) Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species. Nature 360: 668-670. 9
  • 22. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 British parents: WNW (279°) British offspring: WNW (273°) German young: SW (227°) Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species. Nature 360: 668-670. 9
  • 23. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 British parents: WNW (279°) British offspring: WNW (273°) German young: SW (227°) Source: Berthold et al. 1992. Rapid microevolution of migratory behaviour in a wild bird species. Nature 360: 668-670. 9
  • 24. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 10
  • 25. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 26. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 27. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 28. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 29. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 30. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 31. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
  • 32. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 Hypochaeris radicata www.missouriplants.com/Yellowalt/Hypochaeris_radicata_page.html Lactuca muralis biology.burke.washington.edu/herbarium/imagecollection.php?Genus=Mycelis&Species=muralis 12
  • 33. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 Hypochaeris radicata www.missouriplants.com/Yellowalt/Hypochaeris_radicata_page.html Lactuca muralis www.bartleby.com/61/imagepages/A4achene.html biology.burke.washington.edu/herbarium/imagecollection.php?Genus=Mycelis&Species=muralis 12
  • 34. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 Hypochaeris radicata Dispersal ability (VP/VA) (Mean ± SD) Main- Island land (Old) Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant populations. J. of Ecology 84:53-61. 11 13
  • 35. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 Hypochaeris radicata Lactuca muralis Dispersal ability (VP/VA) Dispersal ability (VP/VA) (Mean ± SD) (Mean ± SD) Mainland 1–4 5–7 8–9 10+ Main- Island Age (years) land (Old) Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant populations. J. of Ecology 84:53-61. 11 13
  • 36. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 Hypochaeris radicata Lactuca muralis Dispersal ability (VP/VA) Dispersal ability (VP/VA) (Mean ± SD) (Mean ± SD) Mainland 1–4 5–7 8–9 10+ Main- Island Age (years) land (Old) Source: Cody and Overton. 1996. Short-term evolution of reduced dispersal in island plant populations. J. of Ecology 84:53-61. 11 13

Notes de l'éditeur

  1. FINISHED WITH THIS SLIDE, LECTURE 3 2007
  2. HIV: A retrovirus (virus particle carries RNA, not DNA) that causes AIDS in humans
  3. As we know, HIV has a very high mutation rate, allowing it to quickly thwart the defenses of the immune system and drugs.
  4. env gene encodes surface glycoprotein of virus
  5. Seems very likely to be involved in very early stages of infection of a cell
  6. Sequenced regions of the env gene from six children who were infected with HIV during pregnancy
  7. Sequences were determined at four different time points from ~12 viral clones each time
  8. Initially, all viruses within a child were similar. Over time, however, the viral sequences changed
  9. Ganeshan et al. illustrated these changes using a phylogenetic tree, which places sequences that are similar to one another close together
  10. (Branch distance between two sequences on the tree is related to the number of sequence differences between them.)
  11. D, E, F appeared to have a stronger immune response.
  12. How might we explain the faster rate of evolution in D, E, F?
  13. Selection
  14. Higher mutation rate
  15. How can we tease these apart?
  16. FINISHED HERE, LECTURE 3 2008
  17. Sequenced regions of the env gene from six children who were infected with HIV during pregnancy
  18. Sequences were determined at four different time points from ~12 viral clones each time
  19. Initially, all viruses within a child were similar. Over time, however, the viral sequences changed
  20. Ganeshan et al. illustrated these changes using a phylogenetic tree, which places sequences that are similar to one another close together
  21. (Branch distance between two sequences on the tree is related to the number of sequence differences between them.)
  22. D, E, F appeared to have a stronger immune response.
  23. How might we explain the faster rate of evolution in D, E, F?
  24. Selection
  25. Higher mutation rate