1. Species and Speciation
Chapter 15

2. What is a species?
The “species” is a fundamental concept in biology – paradoxically, there is no definition of species that is universally applicable
Freeman and Herron suggest that “most biologists agree … [that a species] is the smallest evolutionarily independent unit” (p. 584)
Evolutionary independence occurs when gene flow between populations ceases (or becomes very low); and when drift, mutation, and selection operate on populations separately
The “essence of speciation is lack of gene flow,” and speciation involves at least two stages:
Genetic isolation
Differentiation

3. Species concepts Biological species concept
Phylogenetic species concept
Morphological species concept
Ecological species concept

4. Biological species concept: (Ernst Mayr 1942)
A biological species is a group of interbreeding (or potentially interbreeding) individuals, that is reproductively isolated from other groups of interbreeding individuals
A species is a gene pool that is not exchanging genes other gene pools
Reproductive isolation means that individuals of different species will not mate and produce offspring, or offspring will be sterile

5. Biological species concept – 2
The BSC is the “textbook” standard definition of species
It is applicable to sexually reproducing organisms
It can be difficult to apply in practice because we generally do not know if populations that have separate ranges can interbreed, unless we do the experiment
Doesn’t apply to asexual organisms
Can’t be applied to fossils
How to apply to many plant and some animal species that hybridize freely?

6. Phylogenetic species concept = genealogical species concept
A species is the smallest monophyletic group
Suppose we sample 5 individuals from each of two populations, A and B, and construct a tree – based perhaps on genetic information

7. Phylogenetic species concept – 2
If our tree looks like this, then populations A and B represent different species: A1 A2 A3 A4 A5 B1 B2 B3 B4 B5

8. Phylogenetic species concept – 3
If our tree looks like this, then populations A and B are NOT different species: A1 A2 A3 A4 A5 B1 B2 B3 B4 B5

9. Phylogenetic species concept – 4
What happens if our tree looks like this? A1 B4 A3 A4 B2 B1 A5 B3 A2 B5

10. Phylogenetic species concept – 5
The logic of the phylogenetic species concept is that traits can only distinguish populations on a phylogeny if the populations have been isolated in terms of gene flow and have diverged genetically and/or morphologically
To be considered separate phylogenetic species, populations must have been separated long enough to have evolved unique derived diagnostic characters
Unlike the BSC, the PSC can be applied to asexual organisms
Like the BSC, the PSC may be difficult to apply in practice because it requires a lot of information to construct good trees that will identify monophyletic groups

11. BSC and PSC overlap
A “good” biological species is a monophyletic group of individuals – individuals of the same species are more closely related to one another than they are to individuals of other species
Therefore, the BSC and PSC may agree on species designations some of the time
However, the PSC could greatly increase the number of species because separate populations of a biological species might be monophyletic but still able to interbreed – if individuals from population A can interbreed with individuals from population B, we have one biological species but two phylogenetic species

12. BSC and PSC overlap – 2
If individuals from population A can interbreed with individuals from population B, then we have one biological species but two phylogenetic species A1 A2 A3 A4 A5 B1 B2 B3 B4 B5

13. Morphological Species Concept – 1
A species is a group of phenotypically similar individuals
This is, in fact, how most species are actually defined in the absence of detailed information about reproductive compatibility and/or phylogenetic relationship
Only species concept applicable to fossils

14. Morphological Species Concept – 2
Disadvantages
Not “evolutionary” (genetic or phylogenetic)
Arbitrary and idiosyncratic: two people may disagree about where to draw species boundaries, or statistical phenetic methods may disagree about how to create groups of morphologically similar individuals
Cryptic species cannot be distinguished

15. Ecological Species Concept
A species is a group of phenetically similar organisms that occupy a given ecological niche (or set of niches)
Species integrity is maintained not so much by reproductive isolation, but by selection to adapt each species to its niche
Hybridization is not a problem if hybrids are less fit than parental species or have very restricted ranges
Works for asexual species
Problem:
Hard to define niches independently of the species that occupy them

16. Applying Species Concepts The marine copepod, Eurytemora affinis
Small estuarine copepod (1 – 2 mm), world -wide distribution, important part of zooplankton and marine food chains.
Lee (2000) sequenced 2 genes in individuals from 38 populations and performed matings between individuals from different populations in the laboratory

17. Eurytemora affinis http://life.bio.sunysb.edu/marinebio/pl_23.jpg

18. A phylogeny of E. affinis populations (Lee 2000) (Fig. 15.3 b)
This phylogeny supports “at least 8” phylogenetic species
Breeding tests indicate that individuals from two different phylogenetic species are reproductively isolated

19. How many species of elephants? (Roca et al. 2001) (Fig. 15.4 b)
This phylogeny supports two African elephant species
195 elephants from 21 African populations
4 genes sequenced

20. Mechanisms of genetic isolation
Geographic (physical) isolation – allopatric speciation
Isolation based on differential resource use without geographic isolation – sympatric speciation
Isolation by selection and limited gene flow in continuously distributed populations – parapatric speciation
Isolation based on changes in chromosome number or chromosomal rearrangements – chromosomal speciation

21. Allopatric speciation (Ernst Mayr 1942, 1963)
Two or more populations of a species become geographically isolated from one another (either by dispersal or vicariance)
Separated populations will evolve independently of one another provided there is no (or very little) gene flow between them
In a “pure” allopatric model, speciation is an “accidental” by-product of separate evolutionary trajectories that eventually result in genetic (reproductive) incompatibility between individuals from different populations

22. Isolation by dispersal and vicariance (Fig. 15.5)

23. Geographic isolation by dispersal: Hawaiian drosophilids
Over 500 endemic species in 2 genera
Occupy a wide variety of ecological niches
Many species have ranges restricted to single islands
One of the most famous adaptive radiations
“Founder hypothesis” – one gravid female (or a few individuals) disperse to another island and start a new isolated population
Predictions:
Closely related species should tend to be on neighboring islands
At least some phylogenetic branching sequences should correspond to the sequence in which islands were formed

24. Evidence for speciation by dispersal and colonization events – Hawaiian Drosophila (DeSalle and Giddings 1986) (Fig. 15.7) Based on mtDNA

25. Geographic isolation by vicariance Snapping shrimp and the Isthmus of Panama (Knowlton et al. 1993)
Before the formation of the Panamanian land bridge about 3 million years ago, the Pacific Ocean and Carribean Sea were connected. The formation of the land bridge was a vicariant event that divided populations of marine organisms
Seven species pairs identified on the basis of morphology – one member of each pair in the Carribean and the other member in the Pacific. This is what would be expected if there were seven species originally, and each was subsequently split by the formation of the land bridge.
Data on mtDNA sequences confirms this hypothesis

26. mtDNA phylogeny of 7 morphological species pairs of snapping shrimp (Knowlton et al. 1993)(Fig b) (P = Pacific Ocean; C = Carribean Sea; numbers designate morphospecies)
Alpheus armillatus

27. Mechanisms of divergence
Given that populations become geographically isolated, what then causes them to diverge genetically?
Founder effect speciation – maybe, if number of founders is very small and new population stays small for a long time
Genetic drift – likely to require a long time unless populations are very small
Natural selection, sexual selection, mutation operating differently in isolated populations

28. Sympatric Speciation Genetic isolation without geographic isolation
A single population becomes subdivided by alternative habitat preferences or alternative resource use
Sympatric speciation commonly invoked for herbivorous insects – alternative host plants give rise to host races that ultimately become separate species

29. Apple and hawthorn maggot flies (Rhagoletis pomonella) – 1
Fly is native to northeastern and north-central US
Native host plant is hawthorn (Crategus)
Flies first recorded as a pest of apples in the mid 1800’s
Female flies lay eggs on the fruit, larvae hatch and burrow into the fruit: after about a month the fruit falls to the ground, the larvae leave and pupate in the soil, and emerge as adults the following summer

30. Rhagoletis pomonella (Photo: Guy Bush) (http://www. ento. psu

31. Apple and hawthorn maggot flies (Rhagoletis pomonella) – 2
Are flies that parasitize apple fruits and hawthorn fruits distinct populations?
host race hypothesis
implies selection for exploiting different hosts
Or, do flies that parasitize apple fruits and hawthorn fruits interbreed freely and are they a single population?
this hypothesis seems more likely because the two host trees occur together (sympatrically) throughout their ranges, and flies are known to travel distances of more than a mile

32. Apple and hawthorn maggot flies (Rhagoletis pomonella) – 3
Flies that parasitize apple and hawthorn fruits are distinct host races
genetically differentiated
show preference for their own fruit type in choice tests
Field observations indicate that only 6% of matings take place between apple and hawthorn flies
This is still a fair amount of gene flow
it would prevent genetic divergence of host races unless selection was acting differently on the two hosts
Natural selection for divergence appears to be based on different times of fruit ripening
apple fruits ripen 3 – 4 wks before hawthorn
natural selection for apple flies to complete development well before hawthorn flies

33. Allele frequency changes caused by differences in temperature experienced by hawthorn maggot flies (Feder et al. 1997) (Fig )

34. How common is sympatric speciation?
Historically, a controversial idea
Simple population models suggest that genetic isolation in sympatry is likely to be difficult
However, host race formation is much more likely to occur if individuals tend to mate and lay eggs on the same kind of fruit that they grew up on – assortative mating reduces gene flow
There is more and more evidence that sympatric speciation may be relatively common – most examples involve herbivorous insects