©2000 Timothy G. Standish Genesis 1: 24, 25 24And God said, Let the earth bring forth the living...

©2000 Timothy G. Standish

Genesis 1: 24, 2524 And God said, Let the earth bring

forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so.

25 And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.


Timothy G. Standish, Ph. D.

Evolution and Evolution and GeneticsGenetics


Historical ScienceHistorical Science“…Darwin introduced historicity into science.

Evolutionary biology, in contrast with physics and chemistry, is a historical science -- the evolutionist attempts to explain events and processes that have already taken place. Laws and experiments are inappropriate techniques for the explication of such events and processes. Instead one constructs a historical narrative, consisting of a tentative reconstruction of the particular scenario that led to the events one is trying to explain."

Ernst Mayr 2000 July issue of Scientific American.


Family TreesFamily TreesFrom the late Renaissance, noble families in

Europe had their pedigrees drawn in the form of trees - geneaological trees. By a giant leap of scientific imagination and analogy, these family trees became the prototype for a new theory of humanity's place in the Universe: "I believe this simile largely speaks the truth," wrote Charles Darwin in The Origin of Species (1859), imagining evolution as a tree branching through time.

Hestmark, Geir. 2000. Temptations of the tree. Nature 408:911.


Imposing Nature on a TreeImposing Nature on a TreeIn 1776, the German-Russian naturalist Peter Simon

Pallas proposed in his Elenchus Zoophytorum a systematic arrangement of all organisms in the image of a tree; and in 1861 Heinrich Bronn presented such a tree based on fossil evidence. But it was Ernst Haeckel, in his monumental Generelle Morphologie (1866), who drew the first tree of the common descent of all life on Earth. Haeckel also coined the term 'phylogeny' from the Greek words for tribe or race and origin, and presented phylogenetic trees for all major groups of organisms.



They Look So RealThey Look So RealPhylogenetic trees are common in today's scientific journals,

but there it is seldom realized how speculative they are because they look so real. This rhetorical power was significant in the popularization and triumph of evolutionary theory. Yet phylogenies are only sketches of historical hypotheses, constructed from imperfect historical evidence: fossils; morphological and anatomical similarity; biogeographic patterns; and, recently, comparison of different molecular sequences. Some phylogenetic trees are certainly more probable than others, but the inherently imperfect nature of the evidence seems to guarantee that we will never be able to reconstruct, except perhaps by accident, the true phylogeny of life on Earth.



What is a Species?What is a Species?Six major concepts:1 A - Morphospecies - If it looks different, it is a different species

1 B - Cohesion - Defined by an integrated complex of genes and set of adaptations

2 A - Biological - Reproductively isolated groups of organisms

2 B - Recognition - If two organisms don’t recognize one another as potential mates, they are different species

3 Ecological - If they do not occupy the same niche, they are not the same species

4 Evolutionary - If they share the same common ancestor and niche, they are related and may be the same species


EvolutionEvolutionMicroevolution - Changes in allele

frequency over time (Population genetics)Macroevolution - Accumulation of

changes in a population until it becomes a new species

Macroevolution requires the production of new “information”; microevolution deals with how that information in the form of alleles behaves in populations


How Species EvolveHow Species Evolve Anagenesis - (an = without, genesis = beginning) Over

time the environment in which a species lives changes and the species continually adapts to the new environment. Thus the species changes over time and eventually becomes a new species

Cladogenesis - (clad = branch, genesis = beginning) As new niches become available, members of existing species move into and exploit them. As these individuals adapt to their new environment, they become distinctly new species


How Species EvolveHow Species Evolve

CladogenesisAnagenesis Morphology

Time

Morphology

Time


Where Speciation OccursWhere Speciation OccursAllopatric Speciation - Speciation that does

not occur in the same place. First two populations are separated, then they change and become different species.

Sympatric Speciation - Speciation in the same place. Species arise within the same population due to something other than a physical reproductive barrier.


Reproductive BarriersReproductive Barriers If a species is to be produced, some sort of

reproductive barrier needs to come into play between two populations of the same species

Reproductive barriers fall into two classes: Prezygotic - Those that occur before a zygote is

produced Post zygotic - Those that prevent the offspring of

two species (mule) from reproducing


Physical Reproductive BarriersPhysical Reproductive Barriers If a population is separated into two populations by

a physical barrier the Hardy-Weinburg assumption of random mating will be violated

If different selective pressures are brought to bear on the separate populations, they will develop different allelic frequencies

Evolutionary theory extrapolates from here to say that they will form new species and, if they drift enough, new genera and so on

This requires the production of new alleles that improve the fitness of individuals in the population, as mere changes in allele frequencies do not make new species


Phylogeny Based on Phylogeny Based on Homologous Structures/FossilsHomologous Structures/Fossils

Spontaneous Generation of Life

Last Universal Common Ancestor (LUCA)

Hypothetical common ancestors

Archaea Fungi Plantae AnimaliaBacteria


Phylogeny Based on Phylogeny Based on Homologous Genes/ProteinsHomologous Genes/Proteins

Last Universal Common Ancestor (LUCA) a eukaryote?

Hypothetical common ancestors

Spontaneous Generation of Life

Archaea Fungi Plantae AnimaliaBacteria


Problems With HomologyProblems With Homology Before Darwin, Richard Owen (1840s) defined

homology as structures derived from a common “archetype”

Darwin redefined homologous structures as those derived from a common ancestor

He then turned around and said that homology is evidence of common ancestry

But this is circular reasoning Common ancestry Homology


Problems Using Molecular DataProblems Using Molecular Data Molecular data run into the same problems as any

other data that assumes homology Molecular information frequently exhibits

dramatically different expression in different organisms. For example genes with similar sequences control production of limbs in:– Echinoderms- Tube feet– Polychaete worms- Setae– Vertebrates- legs and feet– Insects- jointed legs

Homologous structures can be produced by different genes


Prezygotic BarriersPrezygotic Barriers Habitat isolation - If they live in different places, they can’t mate Behavioral isolation - If species recognition is behavior based,

organisms with different behaviors will not mate (i.e., eastern and western meadowlarks are identical in almost all things except song)

Temporal isolation - If they breed at different times, they will not breed with each other

Mechanical isolation - Need any more be said? Gametic isolation - Gametes have complex recognition

mechanisms so that gametes from one species will rarely fuse with those of another species


Postzygotic BarriersPostzygotic Barriers Inviable Hybrids - Hybrids may develop from a zygote

formed from the sperm of one species and the egg of another, but they are weak inferior creatures and may not even survive until birth

Infertile Hybrids - Hybrids may be hardy creatures, but they are incapable of reproduction, frequenctly due to difficulties in producing gametes due to strange chromosome combinations resulting from meiosis

Hybrid Breakdown - At first hybrids are fairly successful, but over the course of several generations problems develop


Hybrid breakdown

Barriers To Hybrid FormationBarriers To Hybrid FormationHabitat isolation

Behavioral isolationTemporal isolation

Mechanical isolation

Gametic isolation

Infertile hybridsInviable hybrids

++

Happy Hybrid

PrezygoticBarriers

PostzygoticBarriers


Sympatric Speciation:Sympatric Speciation:AutopolyploidyAutopolyploidy

Somatic nondisjunction

Diploid plant2n = 4

Tetraploid cells develop into flowers

Tetraploid flowers make diploid gametes

Self fertilization results in tetraploid offspring which cannot interbreed with the original diploid species


2n=10 hybrid(fertile)

Mitotic nondisjunction produces diploid cells capable of producing

fertile gametes

Sympatric Speciation:Sympatric Speciation:Allopolyploidy - Scenario 1Allopolyploidy - Scenario 1

Plant species A2n = 4

Plant species B2n = 6

1n=3 gamete

1n=2 gamete

1n=5 hybrid(infertile)

Gametes combine to make a hybrid


Sympatric Speciation:Sympatric Speciation:Allopolyploidy - Scenario 2Allopolyploidy - Scenario 2

Plant species A2n = 4

Plant species B2n = 6

Unreduced 2n gamete

Normal gamete

1n=3 gamete

Gametes combine to make a hybrid 1n=7 hybrid

(infertile)

Meiotic nondisjunction produces unreduced

gamete

Unreduced gamete

2n=10 hybrid(fertile)


Tempo Of EvolutionTempo Of Evolution

Morphology

Time

Punctuated Equilibrium

Morphology

Time

Gradualism


Eldredge on Punctuated EquilibriaEldredge on Punctuated Equilibria"At the core of punctuated equilibria lies an empirical observation: once evolved,

species tend to remain remarkably stable, recognizable entities for millions of years. The observation is by no means new, nearly every paleontologist who reviewed Darwin's Origin of Species pointed to his evasion of this salient feature of the fossil record. But stasis was conveniently dropped as a feature of life's history to be reckoned with in evolutionary biology. And stasis had continued to be ignored until Gould and I showed that such stability is a real aspect of life's history which must be confronted - and that, in fact, it posed no fundamental threat to the basic notion of evolution itself. For that was Darwin's problem: to establish the plausibility of the very idea of evolution, Darwin felt that he had to undermine the older (and ultimately biblically based) doctrine of species fixity. Stasis, to Darwin, was an ugly inconvenience."

Eldredge N., "Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria", Simon & Schuster: New York NY, 1985, p 188-189


The Rate of EvolutionThe Rate of Evolution Sometimes evolution has occurred at an amazingly rapid

rate: Drosophila pseudo-obscura, a native species, has declined

since 1978 when the European species Drosophila subobscura was introduced into Chile

In Europe D. subobscura exhibits an increase in wing size as one goes from south to north

A south to north wing size gradient went unobserved when D. subobscura was studied around 1989, but a decade later a difference in wing size distribution mimicking that seen in European flies was evident.

Thus this wing size difference must have evolved in a decade or less, but no new species and no new alleles have been shown to arise in the American population


The Rate of EvolutionThe Rate of Evolution Galapagos finches are also known to have evolved

very rapidly in nature After a drought in 1978, a dramatic shift in beak

size was observed in a local population of finches However, it is worth noting that when conditions

returned back to normal, the finches’ beaks also reverted back

Thus, selection did produce a morphological change in the finches which appeared to be heritable, but no new species of finch were produced and at the end of it all, the same kinds of finches that were previously there were still present


When the Data SpeaksWhen the Data Speaks“For example, researchers have calculated that

‘mitochondrial Eve’--the woman whose mtDNA was ancestral to that in all living people--lived 100,000 to 200,000 years ago in Africa. Using the new clock, she would be a mere 6,000 years old.

No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?”

Gibbons, A. 1998. Calibrating the mitochondrial clock. Science 279:28-29



Rooted In Eubacteria?Rooted In Eubacteria?“...this rooting [in the eubacteria] was rapidly

accepted and advertised in the community of evolutionary biologists and beyond, being now systematically used to draw universal trees in review papers, and even textbooks.” (p 511)

“We have shown in this paper that the rooting of the tree of life in the eubacterial branch has been based on unreliable phylogenies.” (p 521)

Philippe Herve' and Patrick Forterre. 1999. "The Rooting of the Universal Tree of Life Is Not Reliable," Journal of Molecular Evolution 49:509-523.

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