Historical Context for Molecular Systematics

Darwinian Evolution

1859 - The Origin of Species

The one figure in The Origin of Species is a phylogenetic tree

Darwin's key insights

Living things can be traced back to a common ancestor

Reproductive excess, but roughly stable populations

Variation

Heritability

Mendel was a contemprary, but not understood until turn of century

1900s-1930s - genetics develops as a field

The Modern Synthesis (Neodarwinists) - 1930s and 40s

Reconciliation of genetics and Darwinian evolution

Focused on gene flow in populations

Strong emphasis on importance of selection

Mathematical treatment of evolution

Molecular Biology and the Neutral Theory of Evolution

The Neutral Theory of Evolution

Genetic variation is greater than predicted by neodarwinists

Systematics - the history of evolution

Traditional taxonomy

Subjective

Lots of good work - not to be dismissed lightly

But the method was:

highly dependent upon the individual

difficult to assess and reproduce

not effective with all organisms

Systematics vs. Taxonomy

Systematics - the study of the relationships among organisms

Taxonomy - the naming of groups of organisms

The relationship between systematics and other areas of the biological sciences

Classification as a resource

Consistent and reliable identification

Relationships among...

species and higher taxa

individuals

genes and gene families

The predictive value of classification

Classification as an end unto itself

Studying patterns as a way of understanding the processes that gave rise to them

Loss of biological diversity

Public interest in diversity

Gene families and genome evolution

Modern methods of systematics

Cladistics vs. phenetics

Probabilistic methods

Chemotaxonomy

Molecular systematics

New sources of information

1963 - Sokal & Sneath Principles of Numeric Taxonomy

Used numerical approaches to classify bacteria

1965 - Zuckerkandl and Pauling

Molecules as documents of evolutionary history

Odd terminology:

Semantides carry the information itself

DNA, RNA, proteins; primary, secondary, and tertiary semantides, respectively

Episemantic molecules - synthesized directly by semantides, an indirect source of information

Asemantic molecules - not produced by organism, hence no information

Conceptual advances

Objective methods in systematics

Make hypothesis testing explicit

Simplify reproducing others results

Make analyses (clearly) objective

Record and archivce data in a uniform format

Classification based on phylogeny rather than superficial similarity

This takes into account convergent evolution

The utility of molecular data for inferring evolutionary history

Modeling of sequence evolution

Technical advances

Science tends to emphasize things that have recently become practical to measure

Information technology

Phylogenetic methods

Database search tools

Fast processors

DNA, RNA, and protein sequencing

Huge and growing databases

High throughput methods

The Genomic Revolution

Technological advances have made it practical to determine the DNA sequence of essentially complete genomes.

Functional genomics vs. comparative genomics

The interplay between systematics and genomics

Darwin, C. 1859. The Origin of Species. John Murray, London. Available online from several sources, e.g., from Project Gutenberg. There were multiple editions, with significant changes among the editions. It is easiest to understand Darwin's key observations in the earliest editions.

Delwiche, C. F. 2004. The genomic palimpsest: Genomics in evolution and ecology. Bioscience 54:991-1001.

Zuckerkandl, E., and L. Pauling. 1965. Molecules as Documents of Evolutionary History. Journal of Theoretical Biology 8:357-&.