1. Historical approach to identifying species
In past centuries, species were defined by apparent similarities
to other known species– i.e., by morphological comparisons
Similar organisms were grouped together, and the most similar
kinds of organisms that could somehow be differentiated were
classified as different species of the same genus
Lions and tigers live in different places, they look and act
differently, and if they mate, their offspring are sterile
But for many organisms, it is not so clear whether populations
can be grouped together as one species or divided into two
different species, each needing its own scientific name

2. Species concepts
What do biologists mean when they refer to a “species” ?
At least 22 different definitions have been proposed to explain
what a “species” is
- in different kinds of organisms, different criteria are useful
for defining what constitutes a species
We will discuss 2 major concepts of what constitutes a species:
(1) the Biological Species concept
(2) the Phylogenetic Species concept

3. Definitions for discussing speciation
Gene flow = movement of alleles between 2 populations
Migration movement of individuals between 2 populations
or Dispersal
Reproductive isolation = two groups of organisms that do not
produce offspring, either because:
- they do not mate
- they mate, but produce hybrid offspring that are infertile
Big question: what can cause one population to split into 2 new
populations that do not reproduce with each other?

4. Biological Species Concept (Mayr, 1942)
Defined a species as a group of actually or potentially
inter-breeding individuals
The boundaries between species are defined by intrinsic barriers
to gene flow that have a genetic basis
- “intrinsic barrier” means something innate (built into the
organism) that limits gene flow, not something external like
a river or mountain range
- although a river may form the boundary between two species,
it cannot explain why those species aren’t able to reproduce
- reproductive isolation must be due to genetic differences
between the two groups

5. These barriers to gene flow may be expressed thru effects on:
(1) key features of the mating system (mate choice, sperm-egg
recognition, timing of gamete release)
(2) ecological characteristics like habitat preference, that affect
the probability of mating
- pre-zygotic isolation: prevents hybridization before the
zygote forms (sperm never meets egg)
(3) developmental pathways, producing infertility in hybrid
offspring
- post-zygotic isolating mechanisms act after the zygote
forms, resulting in dead or infertile hybrid offspring

6. Biological Species Concept (Mayr, 1942)
Slight problem with the Biological Species Concept: some hybridization among related species occurs in most groups!
 How much is “too much”..?
In many cases, organisms might potentially interbreed if they co-
occurred, but since they live in different places they never meet
- hard to assess reproductive isolation for non-overlapping
populations
However, BSC is still the “gold standard” for describing two
populations as separate species: it recognizes that something
has to stop gene flow for groups to become different over time

7. Gene flow and speciation
Evolution is a change in allele frequencies w/in a population
In one sense, a “species” = a boundary to the spread of alleles
- a species could be defined as a unique set of alleles,
not all shared with any other species
Different species are evolutionary independent, follow distinct
trajectories (we also call these lineages)

8. How do species form? Step 1 – gene flow is reduced or interrupted
Step 2 – populations diverge
(especially important: mating preference traits change)
Step 3 – reproductive isolation arises
Step 4 – speciation ultimately results
What can initially interrupt gene flow between 2 populations?

9. Mechanisms of Isolation
Studies of biogeography revealed that the edges of a species’
range are often defined by a geographical boundary
- species distributions can be determined by geological features
This led to the prevailing opinion for most of the 20th century that
speciation requires a long period of geographic isolation
This is termed allopatric speciation – the requirement of
physical isolation as the first step in the speciation process
In the allopatric model, speciation results from differences in
mating preference that arise from 2 possible sources:
1) genetic drift
2) disruptive natural selection

10. Allopatric speciation
Gene flow can be interrupted by physical barriers preventing
migration between two populations
(A) vicariance – chance interruption of migration by changes in geography
- a new river, glacier, or mountain range forms
- an isthmus or land bridge arises, cutting off two
previously connected bodies of water
(B) colonization of a new, unoccupied habitat by founders
- islands
- postglacial lakes (Canada), volcanic crater lakes (Africa)

11. Allopatric speciation #1: Genetic drift
Initially, there is migration between 2 nearby populations of a
forest-dwelling animal with two alleles controlling color
because of gene flow, the allele frequencies will be the same
in the two populations

12. Allopatric speciation via Genetic drift
Over time, a barrier to migration arises between populations:
mountain range
The allele frequencies in each population will start to change
due to genetic drift
(Step 1: gene flow has been interrupted)

13. Allopatric speciation via Genetic drift
Different alleles may eventually fix in the 2 populations
mountain range
The populations will slowly diverge as different alleles become
fixed at many loci throughout the genome
(Step 2: populations differentiate)

14. Allopatric speciation via Genetic drift
Eventually, differences accumulate by chance at loci controlling
mating preference
- purple individuals prefer to mate with other purples
results in assortative mating – individuals sort themselves into separate mating pools, only reproduce with similar individuals
(Step 3: the populations become reproductively isolated)

15. Allopatric speciation via Genetic drift
If the mountain range disappears, the two populations can mix...
... but due to assortative mating, the two types do not interbreed
(Step 4: speciation has occurred)

16. Mayr’s model of allopatric speciation says nothing is needed
for two populations to evolve into separate species except
geographical isolation + time
- this remains the dominant view of how most speciation
has taken place over Earth’s history
- note: there is no requirement for natural selection to
play a role in species formation (Darwin who?)
Because drift is a random process, it may take a long time
for enough fixed differences to build up to prevent two
populations from interbreeding
- according to this model, species should only co-exist today
if they were previously isolated for a long time

17. Allopatric speciation #2: Differential selection
Consider a species found in a desert and a neighboring forest
Cool,
rainy
forest
Hot, dry
desert
Mayr also recognized that if populations were isolated in
different environments, then selection could quickly fix the
changes that ultimately result in speciation

18. Allopatric speciation via Differential selection
Selection will favor different alleles in the desert and forest
Cool,
rainy
forest
Hot, dry
desert
Natural selection will favor
forest-adapted individuals
Natural selection will favor
desert-adapted individuals

19. Allopatric speciation via Differential selection
After selection, the two populations will be genetically different
Cool,
rainy
forest
Hot, dry
desert
forest-adapted individuals
have survived here
desert-adapted individuals
have survived here

20. Allopatric speciation via Differential selection
But, migration will keep mixing alleles between the populations
Cool,
rainy
forest
Hot, dry
desert

21. Allopatric speciation via Differential selection
But, migration will keep mixing alleles between the populations
Cool,
rainy
forest
Hot, dry
desert
Natural selection won’t produce desert-adapted and
forest-adapted populations when gene flow is high

22. Allopatric speciation via Differential selection
Now: a barrier to gene flow arises between the 2 habitats
mountains
Cool,
rainy
forest
Hot, dry
desert

23. Allopatric speciation via Differential selection
Now: a barrier to gene flow arises between the 2 habitats
mountains
Cool,
rainy
forest
Hot, dry
desert
Natural selection will favor
forest-adapted individuals
Natural selection will favor
desert-adapted individuals

24. Allopatric speciation via Differential selection
Each population evolves into a distinct, well-adapted species
mountains
Cool,
rainy
forest
Hot, dry
desert
Forest-adapted population
Desert-adapted population
Species #1
Species #2

25. Speciation and the Isthmus of Panama
Caribbean and Pacific oceans were linked until the Isthmus
of Panama formed ~3 million years ago
Prevented any more
gene flow between
marine organisms
on each side of the
new land barrier
Did this result in the
evolution of new
sister species pairs
separated by the
Isthmus?
Google
maps

26. Speciation and the Isthmus of Panama
Knowlton et al. studied pairs of snapping shrimps that were
morphologically similar, where one member of the pair was
found on the Caribbean side and the other on the Pacific side
The sister species still closely
resembled each other –
were they different species?
Sequenced part of a gene
and also compared allozyme
allele frequencies
Alphaeus cylindricus
Finally, did mating crosses to assess reproductive compatibility
Knowlton & Weight 1998

27. (1) based on DNA sequences, the members of 15 pairs were always
each other’s closest relatives
= Pacific member of pair
= Caribbean member
(2) members of most pairs snapped
at each other instead of mating
 pre-zygotic isolation: mating rituals
changed so much, sister species
don’t look / smell / act right 
get treated like an enemy, not a
potential mate
P = pacific species
C = Caribbean species
Knowlton & Weigt 1998

28. Speciation and the Isthmus of Panama
(3) when a male of one species was held with a female of
its sister species [from the other side of Panama] for a month,
no offspring were produced except for one single pair
This is post-zygotic reproductive isolation –
even if you put sperm + egg together, dad’s alleles and
mom’s alleles are too different to work together to build a
zygote (= baby)
Thus, 3 million years is enough time for complete
reproductive isolation to occur