Bi 312 Lecture Guide: Chapter 17 Winter 2010

The Origins of Life and Precambrian Evolution

Introduction

• Major questions:

– What was the first living thing?

– Where did it come from?

– What was the last common ancestor of today’s organisms and when did it live?

– What is the shape of the tree of life?

– How did the last common ancestor’s descendants evolve into modern life forms?

• This discussion is organized around Figure 17.1

What was the last common ancestor of all living things?

• We infer that …

– It was _________________________

• Life has descended from a population of interbreeding cells

– But not a single organism

• Especially if portions of genomes could be readily “swapped”

• Cells convey huge advantages:

– Membranes allow for compartmentalization

– The “linkage” of genotypes and phenotypes

• Figure 17.15

The Phylogeny of All Living Things

• Inference depends on molecular characters

– Prokaryotes lack sufficient structural diversity for morphology-based reconstruction

• The challenge: find a _________________________that can be used to estimate the phylogeny for all of life

– The gene’s product must be essential and subject to strong stabilizing selection because …

• Genetic drift will have obliterated any recognizable similarities in the sequences of distantly related organisms

• Selection on new functions can cause rapid divergence making species “look” less related than they actually are

• One gene that meets these criteria: the small-subunit ribosomal RNA

– It is responsible for translation and therefore it is highly conserved

The Tree of Life – pre 1970

• The five-kingdom model (Whitaker, 1969)

– The first split in the tree (i.e., the earliest) separates what will become prokaryotes

– Eukaryotes on the right

• This view is misleading regarding evolutionary _________________________

• Carl Woese, the chief pioneer in using molecular sequences in estimating the universal phylogeny, produced the first estimate based on small-subunit rRNA (Figure 17.18)

An Examination of Early Cellular Life

• “Rooting” the tree of life has been, and remains, a challenge! Why?

•

• Employ character phylogenetic estimates (e.g., gene phylogenies) to determine outgroup

• Figure 17.19 (understand how a gene phylogenetic inference can “inform” an organismal inference)

Our Understanding of the TOL …

• Relies heavily on molecular data

• Two trends promise to yield many new insights

• First: our knowledge of the Archaea is increasing dramatically

– Understanding their “correct” place on the tree is critically important

• Second: whole-genome sequencing

– From virtually no entire genome sequences to nearly 400 in just 10 years (with many more projects under way)

• Whole-genome sequences, including various genes, are not always congruent (Figure 17.22)

• WHY?

• One explanation is _________________________ (or horizontal) gene transfer

– The fraction of a genome for a single organism acquired through lateral transfer may be quite high

Is There a “Tree” of Life to be “Found”

• Are trees capable of accurately reflecting deep evolutionary history?

• Studies employing different genes to estimate bacterial phylogenies were inconclusive. However,

• Whole-genome approaches that avoided genes known to have been laterally transferred have consistently “recovered” three monophyletic groups (Bacteria, Archaea, Eukarya)

• An important implication of recent studies: the history of life might better be depicted as a set of interconnected roots. Therefore …

– No single species is the ancestor

– A _________________________of interacting species that readily traded their genes

• Figures 17.26

How Did the Last Common Ancestor’s Descendants Evolve into Today’s Organisms?

• How could an ancestral community give rise to the three clades of life?

• Four competing hypotheses:

– The Universal Gene-Exchange Pool Hypothesis

– The Ring of Life Hypothesis

– The Chronocyte Hypothesis

– The Three Viruses, Three Domains Hypothesis

The Universal Gene-Exchange Pool Hypothesis

• Major Points:

• Lateral gene transfer rampant and overshadowed vertical inheritance

• This model is not conducive to ...

– A non-Darwinian mechanism of communal evolution

– Proteins gradually became more interdependent so that the modularity (i.e., independent functioning) of genomes became more integrated and stable

– Organismal self-replication became more prominent, this is the point at which populations have reached the Darwinian threshold and began to evolve via natural selection

• Three stable lineages emerged independently (i.e., crossed the Darwinian threshold

• Criticisms/Problems:

– What is the mechanism responsible for non-Darwinian communal evolution?

• Figure 17.30

The Ring of Life Hypothesis (Figure 17.32)

• Major Points:

• Based on analyses of amino acids:

– Eukaryotic genes involved in the storage and use of genetic information tend to be more similar to archaean genes

– Eukaryotic genes involved in certain metabolic processes tend to be more similar to bacterial genes

• The first _________________________arose when a bacterium fused with an archaean

• The resulting lineage retained informational genes from the archaean and metabolic genes from the bacterium

• Criticisms/Problems:

– Eukaryotic metabolic genes should be somewhat closely related to mitochondrial genes – they’re not! However,

• The initial union of a bacterium and an archaean might long predate the acquisition of the mitochondrion

– Perhaps more importantly, bacteria and archaea lack a cytoskeleton necessary for phagocytosis!

The Chronocyte Hypothesis (Figure 17.33)

• Major Points:

• The TOL includes a lineage that will become the Bacteria and the Archaea derived from the lineage that will become the Eukarya (the Chronocytes)

• The chronocyte lineage evolved a cytoskeleton & phagocytosis

• A chronocyte ate an archaean that resisted digestion and became an endosymbiont which eventually became a nucleus

• The nucleus preserved the information-processing genes from its archaeal ancestor but incorporated cytoskeletal genes from its host

• Chronocytes led to the Eukarya which later acquired mitochondria and chloroplasts in a similar fashion

• Evidence includes Eukaryotic genes NOT found in either Bacteria or Archaeans

– These genes were inherited from _________________________ancestors

• Criticisms/Problems:

– No living chronocytes (has a cytoskeleton but lacks organelles)

The Three Viruses, Three Domains Hypothesis

• Major Points:

• Viruses infecting RNA-based cells first evolved DNA as a defensive counter-measure

• DNA was then transferred to cellular life when DNA-based viruses became endosymbionts

• The three domains first diverged while still carrying their genetic information in RNA

– Each ancestor was converted to DNA by a separate virus

• This explains why the “machinery” used by bacteria for DNA replication appears to be unrelated to the machinery used by archaeans and eukaryotes and that these three lineages outcompeted and eliminated all other lineages of RNA-based cells

• Criticisms/Problems:

– No known cellular organisms with RNA genomes

– Must test this hypothesis using only inferred gene phylogeny estimates

• Figure 17.34