Chapter 25Phylogeny and Systematics

PhylogenyPhylogeny

• The evolutionary The evolutionary history of a species history of a species or a group of or a group of species over species over geologic timegeologic time

Descent with modification:Evolutionary tree of elephant family, based on fossil evidence)

Phylogeny is the evolutionary history of a species or group of related species. A.  Fossil record and geologic time            1.  Sedimentary rocks are the richest source of fossils.                        a.  The fossil record refers to the order in which fossils appear within layers of rock that mark the passing of geologic time.                         b.  Organic substances in dead organisms typically decay rapidly.  Parts that are rich in minerals (e.g., teeth, bones) may become fossils.

            2.  Paleontologists use many methods to date fossils.

a.  Relative dating                                    i.  Fossils near the surface are relatively recent, while those that are deeper are relatively older.                                     ii.  Geologists have established a geologic time scale that reflects a consistent sequence of historical periods. 

Those periods are grouped into four eras:  Precambrian, Paleozoic, Mesozoic, and Cenozoic.

b.  Absolute dating – age is given in years, instead of relative terms (before/after, early/late).                                   i.  Radiometric dating is the measurement of radioactive isotopes found in fossils and rocks, to determine age. 

The half-life of an isotope is the number of years it takes for 50% of the original sample to decay. 

3.  The fossil record is substantial, but does not provide a complete evolutionary history.                       a.  The fossil record usually tells us about abundant, widespread organisms with hard shells or skeletons. 4.  Phylogeny has a biogeographic basis in continental drift.                        a.  Moving continents isolate populations, allowing for evolution to occur. b.  250 million years ago all continents were connected as Pangaea. c.  Pangaea “broke” apart about 180 million years ago. 

Crustal plate boundaries

San Andreas fault

                        b.  Permian extinction                                    i.  90% of marine species went extinct.                                     ii.  Pangaea formed and some species began competing with each other for the first time.                                     iii.  Mass extinction was caused by volcanic eruptions and climate changes.                                                c.  Cretaceous extinction                                    i.  Dinosaurs went extinct.                                     ii.  An asteroid (or comet) hit the earth and created a cloud of debris that blocked out sunlight for months.  Temperatures dropped and plants died.

65 Million years ago the curtain came down on the Age of Dinosaurs when a cataclysmic event led to mass extinctions. This interval of abrupt change in Earth's history, called the K/T Boundary, closed the Cretaceous (K) Period and opened the Tertiary (T) Period.

This 40 centimeter slice of seafloor supports the hypothesis that an asteroid collision devastated terrestrial and marine environments. It also shows a record of flourishing marine life before the event, followed by mass extinction and then evolution of new species and slow recovery of surviving life forms after the event.

Foraminifera are single-celled organisms that have inhabited the oceans for more than 500 million years. Both living and fossil foraminifera come in a variety of shapes and sizes and occur in many different marine environments.

Their abundance, wide distribution, and sensitivity to environmental variations make them good indicators of past climate change.

1997 Core – Tiny Creatures Tell a Big Story

Tektites--glassy material condensed from the hot vapor cloud produced by the impact--rained down and accumulated in a distinctive layer within the core (SEM image).

Post-impact foraminifera from the Tertiary Period.Only tiny, less ornate foraminifera survived; a few new species evolved.

Pre-impact foraminifera from the Cretaceous Period. Large, ornate foraminifera flourished.

B.  Systematics:  Connecting classification to phylogeny            Systematics: the study of biological diversity in an evolutionary context, including taxonomy and phylogenetics. 1.  Taxonomy uses a hierarchical classification system

a.  Review the Linnaean (binomial) system of classification:  genus and species. b.  Review hierarchical classfication:  Kingdom, Phylum, Class, Order, Family, Genus, Species                                    - A named taxonomic unit at any level is called a taxon. 

                        c.  Phylogenetic trees are used to place different taxonomic schemes together, and to show connection between classification and phylogeny.   

2.  Modern phylogenetic systematics are based on cladistic analysis

a.  A phylogenetic diagram (tree) is also called a cladogram.   b.  Each branch in the tree is called a clade.  c.  Monophyletic pertains to a taxon that is derived from a single ancestral species. only legitimate cladogram type! d.  Polyphyletic pertains to a taxon whose members were derived from two or more ancestors not common to all members. e.  Paraphyletic pertains to a taxon that excludes some members that share a common ancestor with members included in the taxon.

            3.  Constructing cladograms                        a.  Identify homologies shared characteristics derived from one ancestor.

NOTE: Analogous structures may look similar to one another, but are not derived from a common ancestor. These are in contrast to homologous structures. Fig. 25.10 is an example of an analogous structure in two distantly related plants.

When two organisms have analogous structures, this is an example of convergent evolution Independent development of similarity between species due to similar selection pressures.

b.  When constructing a cladogram, the greater the number of homologous parts between two organisms, the more closely related they are.

c.  The classification scheme must reflect these similarities.

These similarities can be either:

-Shared primitive characters, I.e. homologous characters that are shared by more than one taxon, e.g. backbone is shared by mammals and reptiles.

-Shared derived characters, I.e. an evolutionary novelty that is unique for a particular clade. The more derived characters that a species has, the more evolutionarily unique it is.

Example of how to construct a cladogram:

1. Select your species for which you want to make a cladogram. These are called the ingroup. They have shared primitive and derived characters.

2. Select an outgroup a species that is closely related to the species under study, the outgroup has a shared primitive character that is common to all species.

3. Construct a character table and tabulate the data. The more shared characters, the more closely related are the species.

4. Construct a cladogram based on the number of shared characters. For example:

Figure 25.11 (p. 497) – Constructing a cladogram.

The outgroup here, the lancelet has a notochord, the shared primitive character. The ingroup is five vertebrates.

4.  Phylogeny can be inferred also from molecular data                        a.  DNA and RNA sequences of nucleic acids can be compared to determine phylogeny. Example to follow.

Note that each change in a nucleic acid = one evolutionary event! The more events, the more distantly related are the species. Fewer events means that a species is more closely related.

5.  The principle of parsimony helps systematists reconstruct phylogenya.  Phylogenies can be extremely complicated. b.  The principle of parsimony states that a theory about nature should be the simplest explanation that is consistent with facts.                                    - “Keep it simple.”                                    - Sometimes called “Occam’s Razor.” c.  A phylogenetic tree is a hypothesis.  There may be many possible trees, but the simplest one is probably the most accurate.

Parsimony and the analogy-versus-homology pitfall.

Isolation of full length Cp-sHSP gene

HSE TATA Transit PeptideA. stononifera

S. alterniflora

C.album NY

C.album MS

A. americana

F. wislizenii

A.retroflexus

HSE

HSE

HSE

HSE

HSE

HSE

TATA

TATA

TATA

TATA

TATA

TATA

+1

+1

+1

+1

+1

+1

+1

100bp

100bp

390bp

436bp

?bp

390bp

421bp

Transit Peptide

Transit Peptide

Transit Peptide

Transit Peptide

Transit Peptide

Transit Peptide

con II

Met-rich

Met-rich

Met-rich

Met-rich

Met-rich

Met-rich

Met-rich

con II

con II

con II

con II

con II

con II

con I

con I

con I

con I

con I

con I

con I

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- - - - - - M A A A N A P F A L V S R L S S P A A R L P I R A W R A A S P A P L G A G - - - - - - - - R A R P L T T A S A S Q D N R D N - S V D V Q V S Q N G G G - - N QA . s t o l e n i f e r a 2 ( 1 )

- - - - - - M A A A N A P F A L V S R L S S P A T R L P A R A W R A A R P A P V A A G - - - - - - - - R T R P L T T A S A S Q E N R D N - S V D V Q V S Q N G G - - - N QA . s t o l e n i f e r a 3 ( 1 )

- - - - - - - - - - M A L A R L A L R N L Q Q K L S P S L M G Q S C E R G L V G N R H N - - - - - - P M K L N R F M A T S A G E Q E D K M N T E V S V S E K K - - - - S PA . t h a l i a n a ( 1 )

- - - - M A S S T A K S G F H T F M E A L T G A G R E P V T A V S C R P P C Y G F R R - - - - - - - L A V V S S S Q Q E N A S E N S D R S L T Q L P R Q D G G S R - - S PF . h y g r o m e t r i c a ( 1 )

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- - - - - - M A A A T A P F A L V S R L S - Q A A R L P I R A W R A A R P A P L W T G - - - - - - - - R T R P L S V A S A A Q E D R D N - S V D V Q V S Q A R N A G - N QH . v u l g a r e ( 1 )

- - - M A Y T S L T S S P L V S N V S V G G T S K I N N N K - - V S A P C S V F V P - - - - - - S M R R P T T R L V A R A T G D N K D T - S V D V H H S S A Q G G - N N QL . e s c u l e n t u m ( 1 )

- - - - - L T C S A A S P L S N V V N V S A A S S R S N N R - - V T A P C S V F F P - - - S A C N V K R P A S R L V A Q A T G D N K D T - S V D V H V S S G Q G G N N N QN . s y l v e s t r i s ( 1 )

M A C K T L T C S A A S P L - - V V N G V T A S S R S N N R - - V A A P F S V F F P - - - S T C N V K R P A S R L V V E A T G D N K D T - S V D V H V S S G Q G G N N N QN . t a b a c u m ( 1 )

- - - - - - - - - M A A P F A L V S R V S - P A A R L P I R A A W R S E P T V G L P S S - - - - - - G R A R Q L A V A S A A Q E N R D N T A V D V H V N Q D G G - - - N QO . s a t i v a ( 1 )

M A C K T L T C S A S P L V S - - N G V V S A T S R T N N K K T T T A P F S V C F P Y - - S K C S V R K P A S R L V A Q A T G D N K D T - S V D V H V S N N N Q G G N N QP . h y b r i d a ( 1 )

- - - - - - - - M A Q S V S L S T I A S P I L S Q K P G S S V K S T P P C M A S F P L R R Q L P R L G L R N V R A Q A G G D G D N K D N - S V E V H R V N K D - - - - D QP . s a t i v u m ( 1 )

- - - - - - M A A A N A P F A L V S R L S - P A A R L P I R A W R A A R P A P L S T G G - - - - - - - R T R P L S V A S A A Q E N R D N - S V D V Q V S Q A Q N A G - N QT . a e s t i v u m ( 1 )

- - - - - - - - M A A A P F A I A G R L S - P V A R L P V R A W R P A H G F A S S G R - - - - - - - - - A R S L A V A S A A Q E N R D N - S V D V Q V S Q N G G N - - R QZ . m a y s ( 1 )

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -C . a l b u m N Y ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -F . w i s l i z e n i i ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -S . a l t e r n i f lo r a ( 1 )

A A P L A R R A R A A D N R D S V D V V S N QC o n s e n s u s ( 1 )8 6 1 7 51 0 0 1 1 0 1 2 0 1 3 0 1 4 0 1 5 0 1 6 0( 8 6 )Q G N A V Q R R P R - R A G F D V A P - - - - - - - F G L V D P M S P M R T M R Q M L D T M D R L F D D - A V G F P T T R R S - P A A A S E A P R M P W D I V E D D K E V K M R F DA . s t o l e n i f e r a 1 ( 6 9 )

Q G N A V Q R R P R - R T G F D V A P - - - - - - - F G L V D P M S P M R T M R Q M L D T M D R L F D D - A V G F P T T R R S - P A A A S E A P R M P W D I V E D D K E V K M R F DA . s t o l e n i f e r a 2 ( 6 9 )

Q G N A V Q R R P R - R A G F D I S P - - - - - - - F G L V D P M S P M R T M R Q M L D T M D R L F D D - T V G F P T T R R S - P A T A S E V P R M P W D I M E D D K E V K M R F DA . s t o l e n i f e r a 3 ( 6 8 )

R Q N F P R R R G R K S L W R N T D D H G Y F T P T L N E F F P P T I G N T L I Q A T E N M N R I F D N - - F N - - - - - - - - - - - - V N P F Q L M G Q V K E Q D D C Y K L R Y EA . t h a l i a n a ( 6 6 )

G P R R P M G L R R G D T R R D L T S S - - - - - L F D I W D P F I G D R S L K Q M L N T V D R L F A D P F F G S P P S - - - - - - A T A L D L R T P W D V K E D A D A Y K L R F DF . h y g r o m e t r i c a ( 7 3 )

G - T A V E K K P R - R T A M D I S P - - - - - - - F G I L D P W S P M R S M R Q I L D T M D R V F E D - T M T F P G R N - - - - - I G G G E I R A P W D I K D E E H E I R M R F DG . m a x ( 2 0 )

Q G N A V Q R R P R - R A G F D I S P - - - - - - - F G L V D P M S P M R T M K Q M S D T M D R L F D D - A V G F P T A R R S P A A A A G E M P R M P W D I M E D D K E V K M R F DH . v u l g a r e ( 6 9 )

G - T A V E R R P T - R M A L D V S P - - - - - - - F G V L D P M S P M R T M R Q M I D T M D R L F E D - T M T F P G R N R A - - - S G T G E I R T P W D I H D D E N E I K M R F DL . e s c u l e n t u m ( 7 3 )

G S T S V Q R R P R - K M A L D V S T - - - - - - - F G L L D P M S P M R T M R Q M M D T M D R L F E D - T M T F P G S N R - - - - A S T G E I R A P W D I K D D E N E I K M R F DN . s y l v e s t r i s ( 7 5 )

G S T S V D R R P R - K M S L D V S P - - - - - - - F G L L D P M S P M R T M R Q M M D T M D R L L E D - T M T F P G R N R S - - - S A V G E I R A P W D I K D D E N E I K M R F DN . t a b a c u m ( 7 8 )

Q G N A V Q R R P R - R S S A F G R H L - - - - - P F G L V D P M S P M R T M R Q M L D T M D R M F D D V A L G F P A T P R R - - S L A T G E V R M P W D V M E D D K E V R M R F DO . s a t i v a ( 6 7 )

G - S A V E R R P R - R M A L D V S P - - - - - - - F G L L D P M S P M R T M R Q M M D T M D R L F E D - T M T F P G S R N - - - - R G T G E I R A P W D I K D D E N E I K M R F DP . h y b r i d a ( 8 1 )

G - T A V E R K P R - R S S I D I S P - - - - - - - F G L L D P W S P M R S M R Q M L D T M D R I F E D - A I T I P G R N - - - - - I G G G E I R V P W E I K D E E H E I R M R F DP . s a t i v u m ( 7 3 )

Q G N A V Q R R P R - R A G F D I S P - - - - - - - F G L V D P M S P M R T M R Q M L D T M D R L F D D - A V G F P T A R R S - P A A A S E T P R M P W D I M E D E K E V K M R F DT . a e s t i v u m ( 7 0 )

Q G N A V Q R R P R R A T A L D I S P S - - - - - P F G L V D P M S P M R T M R Q M L D T M D R L F D D - A V G F P M G T R R - S P A T T G D V R L P W D I V E D E K E V K M R I DZ . m a y s ( 6 5 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M R Q M M D T M D R M F E D - A M T F P G S S R S - - - - T A G E I R A P W D I M E D E K E V K M R F DA . a m e r i c a n a ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M R Q M L D T M D R L F E D - T M T V P T R - - - - - - - - M G E M R A P W D I M E D E N E Y K M R F DC . a l b u m M S ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M R Q M M D T M D R L F E D - T M T V P T R - - - - - - - - M G E M Q A P W D I M V G R E R V Q V G S TC . a l b u m N Y ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M R Q M L D S M D R L F E D - A M T M P G - - - - - - - - G M A E M R A P W D I V E D D N E V K M R F DF . w i s l i z e n i i ( 1 )

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - M R Q M I D T M D R L F D D - - - - - - - - - - - - - T M G C P P A R C G C R G T S R A T R K I C W L DS . a l t e r n i f lo r a ( 1 )

A V R R P R R A D I S P F G L V D P M S P M R T M R Q M L D T M D R L F E D M T F P R A G E I R P W D I M E D E E V K M R F DC o n s e n s u s ( 8 6 )1 7 6 2 6 51 9 0 2 0 0 2 1 0 2 2 0 2 3 0 2 4 0 2 5 0( 1 7 6 )M P G L S R D E V K V M V E D D T L V I R G E H K K E V S E G Q G D G A E G Q G D G W W K E R S V S S Y D M R L A L P D E C D K S Q V R A E L K N G V L L V S V P K T E - - T E R KA . s t o l e n i f e r a 1 ( 1 4 9 )

M P G L S R D E V K V M V E D D T L V I R G E H K K E V S E G Q G D G A E G Q G D G W W K E R S V S S Y D M R L A L P D E C D K S Q V R A E L K N G V L L V S V P K T E - - T E R KA . s t o l e n i f e r a 2 ( 1 4 9 )

M P G L S R D E V K V M V E D D T L V I R G E H K K E A G E G Q G D G A E G Q G D G W W K E R S V S S Y D M R L T L P D E C D K S Q V R A E L K N G V L L V T V P K T E - - T E R KA . s t o l e n i f e r a 3 ( 1 4 8 )

V P G L T K E D V K I T V N D G I L T I K G D H K A E E E K G S P - - - - - E E D E Y W S S K S Y G Y Y N T S L S L P D D A K V E D I K A E L K N G V L N L V I P R T E K - P K K NA . t h a l i a n a ( 1 4 2 )

M P G L S K E E V K V S V E D G D L V I R G E H N A E D Q K E D S - - - - - - - - - - W S S R S Y G S Y N T R M A L P E D A L F E D I K A E L K N G V L Y V V V P K S K K D A Q K KF . h y g r o m e t r i c a ( 1 5 2 )

M P G L A K E D V K V S V E D D M L V I K G G H K S E Q E H G G - - - - - - - - D D S W S S R T Y S S Y D T R L K L P D N C E K D K V K A E L K N G V L Y I T I P K T K - - V E R KG . m a x ( 9 5 )

M P G L S R E E V K V M V E D D A L V I R G E H K K E A G E G Q G E A A - G G G D G W W K E R S V S S Y D M R L A L P D E C D K S Q V R A E L K N G V L L V S V P K R E - - T E R KH . v u l g a r e ( 1 5 0 )

M P G L S K E D V K V S V E N D M L V I K G E H K - K E E D G R - - - - - - - - D K H S W G R N Y S S Y D T R L S L P D N V V K D K I K A E L K N G V L F I S I P K T E - - V E K KL . e s c u l e n t u m ( 1 5 0 )

M P G L S K E D V K V S V E N D V L V I K G E H K - K E E S G - - - - - - - - - D D N S W G R N Y S S Y D T R L S L P D N V E K - - - - - - - - - - - - - - - - - - - - - - - - - -N . s y l v e s t r i s ( 1 5 2 )

M P G L S K D E V K V S V E D D L L V I K G E Y K - K E E T G - - - - - - - - - D D N S W G R N Y S S Y D T R L S L P D N V E K D K I K A E L K N G V L F I S I P K T K - - V E K KN . t a b a c u m ( 1 5 6 )

M P G L S R E E V K V M V E D D A L V I R G E H K K E E G E G A E - - - - G S G D G W W K E R S V S S Y D M R L A L P D E C D K S K V R A E L K N G V L L V T V P K T E - - V E R KO . s a t i v a ( 1 4 9 )

M P G L S K E E V K V S V E D D V L V I K G E H K - K E E S G - - - - - - - - - K D D S W G R N Y S S Y D T R L S L P D N V D K D K V K A E L K N G V L L I S I P K T K - - V E K KP . h y b r i d a ( 1 5 7 )

M P G V S K E D V K V S V E D D V L V I K S D H R - - E E N G G - - - - - - - - E D C W S R K S Y S C Y D T R L K L P D N C E K E K V K A E L K D G V L Y I T I P K T K - - I E R TP . s a t i v u m ( 1 4 8 )

M P G L S R E E V R V M V E D D A L V I R G E H K K E A G E G Q G - - - - E G G D G W W K E R S V S S Y D M R L A L P D E C D K S Q V R A E L K N G V L L V S V P K R E - - T E R KT . a e s t i v u m ( 1 5 0 )

M P G L A R D E V K V M V E D D T L V I R G E H K K E E G A E G G S G - - G D G D G W W K Q R S V S S Y D M R L A L P D E C D K S K V R A E L K N G V L L V T V P K T E - - V E R KZ . m a y s ( 1 4 8 )

M P G M S K E E V K V S V E D N V L V I K G E H K A E E G E G E E - - - - G K D E S W W R G K S S S N Y D M R L M L P D N C E K D K V R A E L K N G V L L - - - - - - - - - - - - -A . a m e r i c a n a ( 4 8 )

M P G L D K G D V K V S V E D N M L V I K G E R K - K E E G G - - - - - - - - - D D A W S K R S Y S S Y D T R L Q L P D N C E M D K I K A E F K N G V L L - - - - - - - - - - - - -C . a l b u m M S ( 4 4 )

C R G S T R G M S R C R S R I T C L S S K E S A R R K K E V T M H G - - - - - - - - - - V K E V I A H M I L G F N C L I I V S W I R L R P S S R T E C F Y - - - - - - - - - - - - -C . a l b u m N Y ( 4 4 )

M P G L S K E D V K V M V E D D M L V I R G E T K - K E E G G - - - - - - - - - D D A W K R R S Y S S Y D T R L Q L P D D C E M D K I K A E L K N G V L L - - - - - - - - - - - - -F . w i s l i z e n i i ( 4 4 )

M P G L E R D E V K V M V E D D T L V I R G E P K K E K G A E A S G - - - - - - D G W W K E S S V S A Y H M R L A L P E A C D K S K V R A E L K N G V L L - - - - - - - - - - - - -S . a l t e r n i f lo r a ( 4 0 )

M P G L S K E E V K V S V E D D M L V I K G E H K E E E G D W W K R S Y S S Y D T R L A L P D E C D K D K V R A E L K N G V L L V S V P K T E R KC o n s e n s u s ( 1 7 6 )

Alignment of the derived amino acid sequence

Phylogenetic comparisons of Cp-sHspBased on full length genes

Phylogenetic comparisons of Cp-sHspBased on conserved region