How many & what kinds of loci change?
    Observed genetic differences between species may accumulate
       Before: intraspecific polymorphism
       During: what happens during cladogenesis?
       After: subsequent anagenesis

Speciation is difficult to study:
       Speciation is a lengthy process (10 ⁶s of generations)
       Cannot be observed directly from beginning to end
       Therefore: we study successive stages in existing organisms

Protein changes can provide basis of new species
       Ex.: Mammals do not digest plant material directly:
              Bacteria break down cellulose, lysozyme breaks down bacteria.
             Ruminant Artiodactyls (cows & deer) have efficient lysozyme,
                     most other creatures don't
             Leaf-eating macaques (Macaca, Cercopithecidae)
                  have evolved an artiodactyl-like lysozyme, in parallel with cows (Stewart, 1984)
                  New mutations permit effective exploitation of new feeding niche

       Protein electrophoresis can measure genetic differentiation at many protein loci

       Genetic Identity (I) = prob. that two alleles drawn from separate individuals are identical
       Genetic Distance (D) = -ln (I)   1 - I  (if D is small)
                                               ~ average number of mutations / locus
 

Genetic differentiation in Drosophila

Stage	D	I	% Loci Fixed	Organismal Differences
Populations	0.03	0.97	1%	Geographic polymorphism
Subspecies	0.23	0.80	5%	Polytypic races
Sibling Species	0.58	0.56	>30%	Reproductively isolated,  morphologically identical
Species	>1.0	0.35	>62%	Morphologically distinct

       Ayala suggests the following patterns:
              Critical changes for habitat & ethological shifts occur in first 5%
              Many loci become fixed during isolation (next 25%)
              Remaining differences accumulate after speciation

Speciation in Primates
       King and Wilson (1975) compared proteins of chimps & humans
          Pan and Homo show D = 0.62 :
              Genetic differences are similar to those between sibling species of Drosophila
                [one major chromosome rearrangement]
                but morphological, cultural differences place them in separate families
            Genetic & organismal evolution are "uncoupled"
                    morphological differences can't be predicted from genetic differences

       Li et al. (1987) compared DNA sequence differences among Great Apes
 

# substitutions / 100 base pairs = % sequence difference

Species	Family	Ho	Pa	Go	Po	Rh	Common Name
Homo	Hominidae	-					Humans
Pan	Pongidae	1.45	-				Chimps
Gorilla	Pongidae	1.51	1.57	-			Gorillas
Pongo	Pongidae	2.98	2.94	3.04	-		Orang-utans
Rhesus	Cercopithecidae	7.51	7.55	7.39	7.10	-	Old-World monkeys

       Humans, chimps, & gorillas are all about equally different (ca. 1.5%)
           Orangs are about twice as different from any of these (ca. 3.0%)
               Old-World Monkeys are more than twice as different again (ca. 7.4%)

       Genetic differences are proportional to time of separation,
         not to morphological differentiation
         Homework: calculate UPGMA tree for these data

Speciation in freshwater fishes (Avise 1987)

       Minnows (Cyprinidae) vs. sunfish (Centrarchidae) [Perciformes]
              minnows are speciose (many species / taxon)
              sunfish are species depauperate (few species / taxon)
              both families are of equivalent geological age

       If speciation is always accompanied by a large "genetic revolution"
         then a typical pair of minnow species ought on average to be more different
                     than a typical pair of sunfish species

       Data: average pairwise D between species is identical between families
            no"genetic revolution" at speciation

Studies of protein & DNA variation may not tell us much about speciation

       Species differences typically do not result from modification of structural proteins
            difference bx chimp & human is not "chimp stuff" vs "human stuff"

       Speciation may result from changes in gene regulation
              When & where are protein loci turned on & off?
                     recall 5' promoter & enhancer sequences
              How much product is produced?

    See material on Origin of Evolutionary Novelty for some alternatives