Molecular Phylogenetics _amp; Evolution BI549 Fall 2007 by dffhrtcv3

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									    Molecular Phylogenetics &
            Evolution

             BI549: Fall 2007




    Darwin’s letter to
  Thomas Huxley 1857

• The time will come I
  believe, though I shall not
  live to see it, when we shall
  have fairly true
  genealogical (phylogenetic)
  trees of each great
  kingdom of nature
                                  Haeckel’s pedigree of man




                                                              1
     Aims of the course:
• To introduce the theory and practice of
  phylogenetic inference from molecular
  sequence data
• To introduce some of the most useful
  methods and computer programs




 How to construct a phylogeny


• What kind of data?




                                            2
               Richard Owen




  Owen’s definition of homology
• Homologue: the same organ in different
  animals under every variety of form and
  function (true or essential correspondence)
• Analogy: superficial or misleading similarity
                       Richard Owen 1843




                                                  3
               Charles Darwin




         Darwin and homology
• “The natural system is based upon descent with
  modification .. the characters that naturalists
  consider as showing true affinity (i.e. homologies) are
  those which have been inherited from a common
  parent, and,in so far as all true classification is
  genealogical; that community of descent is the
  common bond that naturalists have been seeking”
     Charles Darwin, Origin of species 1859 p. 413




                                                            4
           Homology is...
• Homology: similarity that is the result of
  inheritance from a common ancestor
• the identification and analysis of
  homologies is central to phylogenetic
  systematics




                                               5
 How to construct a phylogeny


• What kind of data?




 Morphological: e.g., Fossil skulls




                                      6
Family tree for
  primates




                  7
      Molecules as documents of
         evolutionary history
• “We may ask the question where in the now
  living systems the greatest amount of
  information of their past history has survived
  and how it can be extracted”
• “Best fit are the different types of
  macromolecules (sequences) which carry the
  genetic information”




 Applications of Phylogenetic Analysis

  •   Systematics and classification (dates)
  •   Phylogeography and speciation (dates)
  •   Host-parasite co-evolution
  •   Comparative analyses
  •   Molecular evolution
  •   Evolutionary genomics
  •   Biomed, epidemiology and forensics
  •   Ancient DNA




                                                   8
                                                                                                    Cuculus c. canorus
                                                                                        1
                                                                                                    C. c. telephonus
                                                                                            68
                                                                                       4    97
                                                                                                    C. saturatus
                                                                                   16               C. optatus
                                                                                2 100                C. optatus
                                                                                                   C. rochii
                                                                                     14
                                                                                                   C. poliocephalus
                                                                              4 100
                                                                                                 C. solitarius
                                                                        2 68
                                                                                                C. clamosus
                                                                    0
                                                                                         C. fugax
                                                                                       Cercococcyx montanus
                                                              11                            9             Cacomantis merulinus
                                                             100                      4 96                C. variolosus
                                                                               6      77               C. sonneratii
                                                        4             9        80               C. flabelliformis
                                                                      93
                                                                                           C. pallidus
                                                             0                           Scythrops novaehollandiae
                                                  5                                    Urodynamys taitensis
                                                 57                  60                Eudynamys s. scolopacea
                                                                    100                 Eudynamys s. alberti
                                                        4                18                       Chrysococcyx basalis
                                                                        100         25      Ch. l. lucidus
                                                               10                  100       Ch. l. layardi
                                                              100                             Ch. klaas
                                                                        14
                                                                         99       1               Ch. caprius
                                                                                         19            Ch. flavigularis
                                                                                        100            Ch. cupreus
                                                                                                             15    Saurothera longirostris
                                                                                                        11 100      S. merlini
                                                                                                     0 98         S. vieilloti
                                                                                                        0           Coccyzus lansbergi
                                           4
                                          79                                                 31                      C. erythropthalmus
                                                                                            100             11    C. euleri
                                                                                                      100 2




    obligate brood parasites
                                                                                   0                             C. americanus
                                                                                                 82   11
                                                                                                                  C. minor
                                                                                                      99
                                                                            0                                  C. melacoryphus
                                                                                                          Piaya minuta
                                                                                                   Piaya cayana
                                                                      0                            34       Clamator levaillantii
                                                                                           7      100       Cl. jacobinus
                                                                                    6      90
                                                               8
                                                                                                            Cl. glandarius
                                                                            0      94
                                                              90
                                                                                                   Cl. coromandus
                                    2               4
                                                                                                 Phaenicophaeus cumingi
                                                                       13                      P. javanicus
                                                    60
                                                                       98                    P. curvirostris
                                                                                       Ceuthmochares aereus
                                                                                              2          Coua gigas
                                                                                                                                                                   Cuckoo




                                                                                         1 70            C. serriana
                                                                                  10     52           C. cursor




                                                                                                                                               Cuckoo Phylogeny
                                                                          3      98
                                                                                                 C. reynaudii
                                                               18       68
                                                                                           C. ruficeps
                                                                                                                                                                  Phylogeny




                                                   7          100        13                     C. caerulea
                                                  95                     99                 C. cristata
                                                                                Carpococcyx renauldi
                               8          3                                              9             Centropus senegalensis
                               59                                                  0 93                   C. superciliosus
                                                               77                        1             C. toulou
                                                             100                         54              C. grillii
                                                                                            C. sinensis
                                                                            20                   Geococcyx californianus
                                                                  7        100                   G. velox
                                                        6        94       25                 Neomorphus rufipennis
                                                        97               100                     N. geoffroyi
                                               3                                    Morococcyx erythropygus
                                               61                              43                       Dromococcyx pavoninus
                                                            26                100                    D. phasianellus
                                      3                    100                              Tapera naevia
                                                                            46             Crotophaga ani
                                                               11          100              Cr. sulcirostris
                                                 29           100                      Cr. major
                                                100                                    Guira guira
                                                    19                                  Treron sieboldii
                                        8
                                                                                                                       (doves)
                                                    99                                Columba leucocephala
                                2                                                  Opisthocomus hoazin               (Hoatzin)
                                       16                             Musophaga violacea
                                                                                                          (tauracos)
                                       99                          Crinifer piscator
                                                         31                                Neophema elegans              (parrots)
                                             2          100                                     Nandayus nenday
                                                           45                                   Urocolius macrourus
                                    4                     100                                  Colius striatus             (mousebirds)
                                                                23                                      Vidua chalybeata
                                                7              100                                          Lanius senator (songbirds)
                               4               52                                             Smithornis sharpei
                                                                      13                                        Rhea americana
                                                      4               99                                    Struthio camelus       (ratites)
                                       6
                                                                                              Aythya americana (duck)
                                                                              Gallus gallus (chicken)




9
                                                                                                                                                                                                                          Cuculus c. canorus
                                                                                                                                                                                                              1
                                                                                                                                                                                                                          C. c. telephonus
                                                                                                                                                                                                                  68
                                                                                                                                                                                                             4    97
                                                                                                                                                                                                                          C. saturatus
                                                                                                                                                                                                         16               C. optatus
                                                                                                                                                                                                      2 100                C. optatus
                                                                                                                                                                                                                         C. rochii
                                                                                                                                                                                                          14
                                                                                                                                                                                                                         C. poliocephalus
                                                                                                                                                                                                    4 100




     •
     •
     •
     •
     •
     •
     •
     •
                                                                                                                                                                                                                       C. solitarius
                                                                                                                                                                                              2 68
                                                                                                                                                                                                                      C. clamosus
                                                                                                                                                                                          0
                                                                                                                                                                                                               C. fugax
                                                                                                                                                                                                             Cercococcyx montanus
                                                                                                                                                                                    11                            9             Cacomantis merulinus
                                                                                                                                                                                   100                      4 96                C. variolosus
                                                                                                                                                                                                     6      77               C. sonneratii
                                                                                                                                                                              4             9        80               C. flabelliformis
                                                                                                                                                                                            93
                                                                                                                                                                                                                 C. pallidus
                                                                                                                                                                                   0                           Scythrops novaehollandiae
                                                                                                                                                                        5                                    Urodynamys taitensis
                                                                                                                                                                       57                  60                Eudynamys s. scolopacea
                                                                                                                                                                                          100                 Eudynamys s. alberti
                                                                                                                                                                              4                18                       Chrysococcyx basalis
                                                                                                                                                                                              100         25      Ch. l. lucidus
                                                                                                                                                                                     10                 100        Ch. l. layardi
                                                                                                                                                                                    100                             Ch. klaas
                                                                                                                                                                                              14
                                                                                                                                                                                               99       1               Ch. caprius
                                                                                                                                                                                                               19            Ch. flavigularis
                                                                                                                                                                                                              100            Ch. cupreus
                                                                                                                                                                                                                                   15    Saurothera longirostris
                                                                                                                                                                                                                              11 100      S. merlini
                                                                                                                                                                                                                           0 98         S. vieilloti




     Ancient DNA
                                                                                                                                                                                                                              0           Coccyzus lansbergi
                                                                                                                                                                 4
                                                                                                                                                                79                                                 31                      C. erythropthalmus
                                                                                                                                                                                                                  100             11    C. euleri
                                                                                                                                                                                                                            100 2
                                                                                                                                                                                                        0                              C. americanus
                                                                                                                                                                                                                       82   11
                                                                                                                                                                                                                                        C. minor
                                                                                                                                                                                                                            99
                                                                                                                                                                                                  0                                  C. melacoryphus
                                                                                                                                                                                                                                Piaya minuta
                                                                                                                                                                                                                         Piaya cayana
                                                                                                                                                                                                                                                                            New World




                                                                                                                                                                                            0                            34       Clamator levaillantii
                                                                                                                                                                                                                 7      100       Cl. jacobinus
                                                                                                                                                                                                          6      90
                                                                                                                                                                                     8
                                                                                                                                                                                                                                  Cl. glandarius
                                                                                                                                                                                                  0




     Molecular evolution
                                                                                                                                                                                                         94              Cl. coromandus
                                                                                                                                                                                    90
                                                                                                                                                          2               4
                                                                                                                                                                                                                       Phaenicophaeus cumingi
                                                                                                                                                                                             13                      P. javanicus
                                                                                                                                                                          60
                                                                                                                                                                                             98                    P. curvirostris




     Comparative analyses
                                                                                                                                                                                                             Ceuthmochares aereus




     Evolutionary genomics
                                                                                                                                                                                                                    2          Coua gigas
                                                                                                                                                                                                               1 70           C. serriana
                                                                                                                                                                                                       10      52           C. cursor
                                                                                                                                                                                                                                                                                        Cuckoo Phylogeny




                                                                                                                                                                                                3      98
                                                                                                                                                                                                                       C. reynaudii
                                                                                                                                                                                     18       68
                                                                                                                                                                                                                 C. ruficeps
                                                                                                                                                                         7          100        13                     C. caerulea




     Host-parasite co-evolution
                                                                                                                                                                        95                     99                 C. cristata
                                                                                                                                                                                                      Carpococcyx renauldi
                                                                                                                                                      8         3                                              9             Centropus senegalensis
                                                                                                                                                     59                                                  0 93                   C. superciliosus
                                                                                                                                                                                     77                        1             C. toulou
                                                                                                                                                                                   100                         54              C. grillii
                                                                                                                                                                                                                  C. sinensis
                                                                                                                                                                                                  20                   Geococcyx californianus
                                                                                                                                                                                       7         100                   G. velox
                                                                                                                                                                              6        94       25                 Neomorphus rufipennis
                                                                                                                                                                              97               100                     N. geoffroyi
                                                                                                                                                                     3                                   Morococcyx erythropygus
                                                                                                                                                                     61                             43                        Dromococcyx pavoninus
                                                                                                                                                                                  26                100                    D. phasianellus
                                                                                                                                                            3                    100                             Tapera naevia
                                                                                                                                                                                                  46             Crotophaga ani




     Biomed, epidemiology and forensics
                                                                                                                                                                                     11          100              Cr. sulcirostris
                                                                                                                                                                       29
                                                                                                                                                                                                                                                                New World




                                                                                                                                                                                    100                      Cr. major
                                                                                                                                                                      100                                    Guira guira




     Systematics and classification (dates)
                                                                                                                                                                          19                                  Treron sieboldii
                                                                                                                                                              8
                                                                                                                                                                                                                                             (doves)




     Phylogeography and speciation (dates)
                                                                                                                                                                          99                                Columba leucocephala
                                                                                                                                                      2                                                  Opisthocomus hoazin               (Hoatzin)
                                                                                                                                                             16                             Musophaga violacea
                                                                                                                                                                                                                                (tauracos)
                                                                                                                                                             99                         Crinifer piscator
                                                                                                                                                                               31                                Neophema elegans              (parrots)
                                                                                                                                                                   2          100                                     Nandayus nenday
                                                                                                                                                                                 45                                   Urocolius macrourus
                                                                                                                                                          4                     100                                  Colius striatus             (mousebirds)
                                                                                                                                                                                      23                                      Vidua chalybeata
                                              Applications of Phylogenetic Analysis
                                                                                                                                                                      7              100                                          Lanius senator (songbirds)
                                                                                                                                                     4               52                                             Smithornis sharpei
                                                                                                                                                                                            13                                        Rhea americana
                                                                                                                                                                            4               99                                    Struthio camelus       (ratites)
                                                                                                                                                             6
                                                                                                                                                                                                                    Aythya americana (duck)
                                                                                                                                                                                                    Gallus gallus (chicken)
                                                                                      Sorenson & Payne 2005 in Bird Families of the World: Cuckoos




10
                                                                                             1             1
              Cooktown

          1                                                                                  3            1 2
                                                                                3                                   2



              2                                                                                            4            4
3
                                                                                                           4
          4             BMC                        3
                                                   4   5                                                            6
                                               4             5                                            5 7
                           Cairns                                               7            7             9                5
                                               1    1      1                                      10
                   5                                                                              11
                                6              2             6
                                                    2 3                                      11                     8
                                                     4
                   7        8
                                                                                                                    8

                                                                    1       1           1         1
                       9                                       10

                   10                      9        8 9
                                                    10
                                                                                    4                 2
                                                                                                               2                Schneider et al.
                                                                                                                2
                                               8
                                                                        4           4
                                                                                                                                1998 Mol. Ecol.
                                                   9 10 11                          4             3             3
                        11                         12 13
                                                                                                                6
                                                    11
    100
                           12                                           9                                       6


                                                                        9               8         5             5


                                    13                                  9               11                      5

                                                                                        11
     0        km                         Townsville




    Applications of Phylogenetic Analysis

     •        Systematics and classification (dates)
     •        Phylogeography and speciation (dates)
     •        Host-parasite co-evolution
     •        Comparative analyses
     •        Molecular evolution
     •        Evolutionary genomics
     •        Biomed, epidemiology and forensics
     •        Ancient DNA




                                                                                                                                                   11
       pocket gophers           chewing lice




                                         Page & Hafner 1996




Applications of Phylogenetic Analysis

•   Systematics and classification (dates)
•   Phylogeography and speciation (dates)
•   Host-parasite co-evolution
•   Comparative analyses
•   Molecular evolution
•   Evolutionary genomics
•   Biomed, epidemiology and forensics
•   Ancient DNA




                                                              12
Dendrobatid Frogs




                                      From K. Summers and M. E. Clough, 2001, PNAS




correlation of independent contrasts for toxicity and
conspicuousness




                                      From K. Summers and M. E. Clough, 2001, PNAS




                                                                                     13
Applications of Phylogenetic Analysis

•   Systematics and classification (dates)
•   Phylogeography and speciation (dates)
•   Host-parasite co-evolution
•   Comparative analyses
•   Molecular evolution
•   Evolutionary genomics
•   Biomed, epidemiology and forensics
•   Ancient DNA




          Gene duplication
• duplication followed by divergence and
  acquisition of new function
• duplication followed by concerted
  evolution through gene conversion
• duplication followed by loss of function
    –pseudogenes




                                             14
(from Piontkivska & Hughes, 2003, JME)



Phylogeny of α subunits
of voltage-gated calcium
channels

 example of gene
 duplication
 followed by
 independent
 evolution and
 divergence




   Applications of Phylogenetic Analysis

    •   Systematics and classification (dates)
    •   Phylogeography and speciation (dates)
    •   Host-parasite co-evolution
    •   Comparative analyses
    •   Molecular evolution
    •   Evolutionary genomics
    •   Biomed, epidemiology and forensics
    •   Ancient DNA




                                                 15
          Archetypal Vertebrate Hox
                   Cluster
 3’                                                                              5’

      1    2   3   4   5       6       7      8      9     10          11 12 13 Evx


Spatial colinearity


 Rostral                                                                  Caudal

Temporal colinearity
             Early   Intermediate                        Late




                                     HOX                               ParaHOX
                           1 2 3 4 5 6 7 8 9 10 11 12 13 Evx     Gsx Xlox      Cdx


      Deuterostomia


                                                                 Ind           caudal


      Ecdysozoa



                                                                       Xlox



      Lophotrochozoa


                                                                anthox2       anthox4
      Cnidaria




                                                                                        16
Applications of Phylogenetic Analysis

•   Systematics and classification (dates)
•   Phylogeography and speciation (dates)
•   Host-parasite co-evolution
•   Comparative analyses
•   Molecular evolution
•   Evolutionary genomics
•   Biomed, epidemiology and forensics
•   Ancient DNA




                                  Ou et al. 1992 Science




                                                           17
Applications of Phylogenetic Analysis

•   Systematics and classification (dates)
•   Phylogeography and speciation (dates)
•   Host-parasite co-evolution
•   Comparative analyses
•   Molecular evolution
•   Evolutionary genomics
•   Biomed, epidemiology and forensics
•   Ancient DNA




                                  Sorenson et al. 1999 PRSB




                                                              18
   Preview: Tree-building methods

 • Parsimony (Cladistic)
 • Neighbor-joining, minimum evolution
   (Phenetic)
 • Maximum Likelihood
 • Bayesian Inference




• Systematics - testing phylogenetic
  hypotheses (hypotheses of genealogical
  relationship)
• Taxonomy/Classification - delineating
  species, translating phylogenetic
  hypotheses into a system of names
• Phylogenetics - the methods for
  constructing phylogenetic trees and
  using trees to test hypotheses




                                           19

								
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