biological diversity: a molecular re-analysis

Biological Diversity: a molecular re-analysis

• Phylogenetic refresher• History of kingdom conceptions• Molecular re-analysis of organism

grouping

Jason Price, PhDScience LibrarianJason.price@cuc.claremont.edu

Main sources: http://tinyurl.com/jameswbrown

http://tinyurl.com/normpace

The fundamental question in evolutionary biology

• Why are some biological traits the same and others different among a group of organisms?

• e.g. Why are most plants green? vs Why is there such variation in flower color?

• e.g. Why are prokaryotes all single-celled while eukaryotes vary so much in body size?

• These types of questions, asked at every level of organization are fundamental to scientific questions about why things are the way they are.

One aspect of the answer: phylogeny

• Why are some biological traits the same and others different among a given group of organisms?

• Phylogeny: Phylon = race/class –geny = born The history of the descent of a group of

organisms [from their common ancestor]• We construct these groups (and their histories)

based on estimates of similarity between organisms

Morphology alone

Bill Sellers: http://homepage.mac.com/wis/Personal/lectures/human-evol/2.html

http://thelifewire.com Chapter 25; interactive quizzes #2

2 types of similarity Homology: (agreement) similar traits from a shared ancestor

e.g. Forelimb skeletal anatomy of birds and bats

Homoplasy: (-plasia molding) similar traits not from shared ancestryConvergent evolution: e.g. Wings in birds and batsEvolutionary ‘reversals’ e.g.

Why does tree accuracy matter?

• To predict the properties of organisms based on their relatives

• To prevent inaccurate comparisons– E.g. euglena for study of photosynthesis in plants– Between not-so-distantly-related outgroups

• C. elegans & D. melanogaster

What has this got to do with Bio43?

• You’ll study other types of “morphology” far richer than external characters….

• Biochemistry• Cell Biology• DNA -> Protein• Genetics• Anatomy & Physiology

History of kingdom conceptions…

http://www.mbio.ncsu.edu/MB451/lecture/evolutionaryConcepts/lecture.html James W. Brown

1. Ladder of life

2. Darwin: species originate by divergence

3.

Tim

e (a

nd S

uper

iorit

y?)

Eukaryotes from prokaryotes

Purves, Orians, Heller 1995

Enter on the Scene: Molecular phylogenyPace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html

* By comparing macromolecular sequences, we can calculate evolutionary distances between organisms

Organism A is 70% identical to organism B,Fractional identity is 0.70,30% different.

* You can't compare sequences unless they are homologous - of common ancestry. Homologous sequences are not necessarily identical and identical sequences are not necessarily homologous

HOMOPLASY

Which molecules should be used?Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html

Need to: a) Be homologous and occur in all organisms consideredb) Have enough nucleotides or amino acids to be statistically robustc) Changes have to exist across the evolutionary distance—i.e. not be

randomized

• originated with protein sequences, since 1980s easier to isolate and sequence genes

• most common choice - ribosomal RNAs• Effect protein synthesis• Present in all organisms (& major organelles)• Large enough for reasonable statistics

d) No lateral transfer – genes have to be related by decent rather than jumping

How is a tree made from sequence data?Pace 1999 http://plantbio.berkeley.edu/~volkman/courses/microbial_diversity.html

1. Align sequences in pairs & count the number of changes2. Correct for multiple back mutations at any given site3. Computer fit overall tree to best fit pair wise dist.

Close to 3000 sequences available as of 1999

And they immediately began to indicated that major tree re-arrangement was necessary

Brooker et al 2011

Pace Science 2 May 1997:Vol. 276. no. 5313, pp. 734 - 740

What are the differences?

Key differences in the diagramsMorphological Phylogeny Molecular Phylogeny

Subjective & Qualitative Objective & quantitative

Branch length is meaningless Branch length indicates evolutionary dist.

Higher (superior) & lower (inferior) positions are suggestive of hierarchy

No (less?) hierarchy is suggested

Fungi, plnts & animals 3/5 of total diversity Multicellular Eukarya just tip of 1 branch

Eukaryotes evolve from prokaryotes Eukaryotes as ancient as and separate from prokaryotes

Prokaryotes 1/5 or 2/6 of Tree Prokaryotes fill 2/3 of tree (2 of 3 domains)

No comparison between kingdoms All organisms can be compared

Includes mitochondria & chloroplasts(support endosymbiont theory of origin)

Published by AAAS

S. L. Baldauf et al., Science 290, 972 -977 (2000)

kingdom-level phylogeny of eukaryotes, based on combined protein sequences

Drilling (back) down one level…Focus on the Eukaryotes

Published by AAAS

S. L. Baldauf et al., Science 290, 972 -977 (2000)

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Your textbook (Brooker 2011)

* So, in conclusion, molecular phylogeny is leading to drastic changes in our understanding of evolutionary history between and among “kingdoms”

*Understanding all of the underlying mechanisms you will learn about in Bio43 informs our understanding of the relatedness, sameness and differentness which is the stuff of organismal biology (Bio 44)

*Where will your textbook need major revision?

Main sources: http://tinyurl.com/jameswbrown http://tinyurl.com/normpace

Doolittle 2000Scientific American282(2):90-95

The next great revolution?

Fmi: http://www.talkingsquid.net/archives/663