Lecture 2

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  • FINISHED WITH THIS SLIDE, LECTURE 3 2007

  • HIV: A retrovirus (virus particle carries RNA, not DNA) that causes AIDS in humans



  • As we know, HIV has a very high mutation rate, allowing it to quickly thwart the defenses of the immune system and drugs.



  • env gene encodes surface glycoprotein of virus



  • Seems very likely to be involved in very early stages of infection of a cell

  • Sequenced regions of the env gene from six children who were infected with HIV during pregnancy

  • Sequences were determined at four different time points from ~12 viral clones each time

  • Initially, all viruses within a child were similar. Over time, however, the viral sequences changed

  • Ganeshan et al. illustrated these changes using a phylogenetic tree, which places sequences that are similar to one another close together

  • (Branch distance between two sequences on the tree is related to the number of sequence differences between them.)



  • D, E, F appeared to have a stronger immune response.



  • How might we explain the faster rate of evolution in D, E, F?

  • Selection

  • Higher mutation rate



  • How can we tease these apart?



  • FINISHED HERE, LECTURE 3 2008

  • Sequenced regions of the env gene from six children who were infected with HIV during pregnancy

  • Sequences were determined at four different time points from ~12 viral clones each time

  • Initially, all viruses within a child were similar. Over time, however, the viral sequences changed

  • Ganeshan et al. illustrated these changes using a phylogenetic tree, which places sequences that are similar to one another close together

  • (Branch distance between two sequences on the tree is related to the number of sequence differences between them.)



  • D, E, F appeared to have a stronger immune response.



  • How might we explain the faster rate of evolution in D, E, F?

  • Selection

  • Higher mutation rate
  • Lecture 2

    1. 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. 2. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) 2 http://www.thebody.com/nmai/cycle.html
    3. 3. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) env 2 http://www.thebody.com/nmai/cycle.html
    4. 4. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
    5. 5. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
    6. 6. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
    7. 7. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 3
    8. 8. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4
    9. 9. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 4
    10. 10. Evolution in Natural Populations Human Immunodeficiency Virus (HIV) – Ganeshan et al. 1997 4@?71+2=03+/9?A9=0=?=02@9:B++C< % $&$$$($ $ 5-=+/2>/+*21?=02@ $&$$$!$ & ) ' ( $&$$$'$ !quot;#$! #quot;#$quot; %quot;#$quot; !quot;#$quot; #quot;#$# %quot;#$# )*+,-.+/*0,-1/12-3/456)/7280+9:;1< 5
    11. 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. 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. 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. 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. 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. 16. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
    17. 17. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
    18. 18. Evolution in Natural Populations Blackcap migration – Berthold et al. 1992 www.dicktruedesign.com/PRINTS/prints.fin&feather.htm 7
    19. 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. 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. 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. 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. 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. 24. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996 10
    25. 25. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    26. 26. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    27. 27. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    28. 28. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    29. 29. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    30. 30. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    31. 31. Evolution in Natural Populations Dispersal in island plant populations – Cody & Overton 1996
    32. 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. 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. 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. 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. 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

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