The document discusses different concepts of what constitutes a species, including the Biological Species Concept and Phylogenetic Species Concept. The Biological Species Concept defines a species as groups that can interbreed, with reproductive isolation maintained by intrinsic barriers. The Phylogenetic Species Concept defines species as the smallest diagnosable units that form monophyletic groups. Allopatric speciation, where physical isolation allows populations to diverge genetically, is also discussed as a primary mechanism of speciation.

1. “ species” ALWAYS has an “s” at the end !!! SPECIE “ offspring” NEVER has an “s” at the end !!! OFFSPRINGS

2. 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 thus, they were long recognized as different species 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 Historical approach to identifying species

3. 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 Species concepts

4. 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? Definitions for discussing speciation

5. 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 Biological Species Concept (Mayr, 1942)‏

6. 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

7. Problems with the Biological Species Concept: In some living organisms like plants and bacteria, hybridization occurs frequently In many cases, organisms might potentially interbreed if they co-occurred, but since they live in different places they never meet Biological Species Concept (Mayr, 1942)‏

8. Instead of depending on reproductive isolation, this concept revolves around fixed differences between populations Species are the “ minimum diagnosable units ”– meaning, the smallest group that you can reliably describe is a species Another way to say this is to define monophyletic groups Monophyletic groups are taxa (groups of organisms) that contain all the known descendants of a common ancestor - species are the smallest monophyletic groups you can identify; in other words, the smallest population that you don’t have any reason to divide into even smaller populations Phylogenetic Species Concept

9. Monophyletic groups Monophyletic groups are taxa (groups of organisms) that contain all the known descendants of a common ancestor - each blue circle contains a monophyletic group - tips are the smallest monophyletic groups, which are species The tips of the tree branches may each be a different species if they cannot be broken down into even smaller groups common ancestor

10. All birds are a monophyletic group... ... and penguins are a monophyletic group within the birds - all emperor penguins share the same diagnostic features that distinguish them from other penguins, so they are a species Rationale: to be recognized as separate species under the PSC, 2 populations must have been evolutionarily independent long enough for diagnostic traits to have emerged Generally, such groups will also exhibit some degree of reproductive isolation, as a by-product of having been evolving independently for an extended period of time Monophyletic groups

11. Problems with the Phylogenetic Species Concept: What should be considered a “diagnostic difference” ? - this could be anything from a single DNA base change that only exists in one population, to a measurable tendency for begonia flowers to be pinker in one area than in another - there’s some consensus among biologists that multiple fixed differences should be used Also, to apply the PSC to a group of organisms, you need a good phylogeny – a tree showing how they are related by descent Phylogenetic Species Concept

12. Evolution is a change in allele frequencies w/in a population factors limiting gene flow between populations will be critical for allowing two populations to evolve in different directions, and eventually to become two distinct species 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 Gene flow and speciation

13. 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? How do species form?

14. 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 20 th 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 adaptation to different environments Mechanisms of Isolation

15. 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)‏ Allopatric speciation

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

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

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

19. Allopatric speciation via Genetic drift Eventually, differences accumulate by chance at loci controlling mating preference - purple individuals prefer to mate with other purples purple and orange individuals become different in their: - mating song or dance - genital shapes - pheromones - habitat preference results in assortative mating – individuals sort themselves into 2 separate mating pools, only reproducing with similar individuals (Step 3: the populations become reproductively isolated)‏

20. ... but due to assortative mating, the two types do not interbreed have formed sister species that will now evolve separately Allopatric speciation via Genetic drift If the mountain range disappears, the two populations can mix... (Step 4: speciation has occurred)‏

21. The model of allopatric speciation says nothing more is needed for 2 populations to evolve into separate species but geographical isolation + time - this remains the dominant view of how most speciation has taken place over earth’s history - notice: 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 very long time for enough fixed differences to build up to prevent two populations from interbreeding - according to this model, species should only co-exist if they were 1 st isolated from each other for a long time Allopatric speciation via Genetic drift

22. Consider a species found in a desert and a neighboring forest Allopatric speciation #2: Differential selection Hot, dry desert Cool, rainy forest

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

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

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

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

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

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

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

30. 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? Speciation and the Isthmus of Panama Google maps

31. 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 Knowlton & Weight 1998 Alphaeus cylindricus The sister species still closely resembled each other – were they different species ? Sequenced part of a gene and also compared allozyme allele frequencies Finally, did mating crosses to assess reproductive compatibility

32. P = pacific species C = Caribbean species Knowlton & Weigt 1998 P = Pacific member of pair C = Caribbean member (1) based on DNA sequences, the members of each pair were indeed each other’s closest relatives - they were evolutionary offspring of a common ancestor however, some pairs were much older than others, suggesting they had been isolated long before the Isthmus finally closed

33. Speciation and the Isthmus of Panama (2) the less-related pairs of shrimp showed less interest in mating snapped at each other instead of mating! black = mated white = attacked This is pre-zygotic isolation – their mating rituals changed relatedness  relatedness (allozymes)‏

34. 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 –

35. The idea that species could form in the absence of prolonged isolation has been hotly debated for decades Sympatric speciation occurs when two populations become reproductively isolated “within cruising range” of each other For this to occur, assortative mating has to arise despite gene flow, and without relying on genetic drift How might this happen? Sympatric speciation: divergence without isolation?

36. Disruptive selection and assortative mating Thoday and Gibson (1962) - started with 4 wild flies that had different # of bristles on their bodies - their offspring had a normal distribution of bristle #’s

37. Disruptive selection and assortative mating Thoday and Gibson (1962) - started with 4 wild flies that had different # of bristles on their bodies - every generation, took the 8 flies with the most bristles, and the 8 with the least bristles - let them interbreed to form the next generation - after only 12 generations, there were no intermediate flies : all offspring had either lots of bristles (white), or very few bristles (black)‏

38. Disruptive selection and assortative mating What occurred? - disruptive selection : individuals with high or low bristle # survived to reproduce; average number = no reproduction (you were selected against)‏ - over time, no hybrid offspring were produced (no flies with intermediate # of bristles)‏ - assortative mating resulted from selection against hybrids: hairy flies only mated with other hairy flies, and hairless with hairless

39. Controversy! .. no one could reproduce the results of Thoday and Gibson -- including themselves (got lucky the 1st time?)‏ It was argued that normally, selection and recombination have opposing effects -- - selection : builds up disequilibrium between trait (bristle #) and mating preference for that trait - recombination : removes disequilibrium between a trait and mating preference for that trait In a sexual population, recombination will prevent disruptive selection from promoting assortative mating and speciation Disruptive selection and assortative mating

40. Disruptive selection and assortative mating hairy prefer selection favors linkage disequilibrium hairy between these 2 traits, since that will mates prevent hybrids from forming hairy prefer recombination removes disequilibrium hairy between these 2 traits, as crossing over events will keep on separating them hairless prefer hairless

41. Rice (1987) and others demonstrated that you could get around this problem if the trait under selection caused assortative mating as a by-product (basically, coincidentally)‏ -i.e., when assortative mating was a correlated character , instead of a separate trait controlled by other genes Example: habitat choice - if individuals mate only in their preferred habitat, then traits controlling habitat choice indirectly control mating preference - recombination can’t tear down this association, since it’s not due to linkage of alleles controlling two different traits Disruptive selection on habitat choice

42. The best examples of sympatric speciation are cases of host- switching in specialized arthropods such as insects (herbivores or parasites)‏ Following the introduction of a new host plant by agriculture, some individuals of an insect species will switch onto the new host Adults are most likely to encounter what other adults….? Disruptive selection on habitat choice

43. The best-studied example is the apple maggot fly, Rhagoletis pomonella This species originally used the hawthorn tree as its host plant Following the introduction of apples into the U.S. around 1850, some individuals switched from hawthorns onto apples In only 150 years, hawthorn and apple races became highly genetically differentiated - but, gene flow still occurs at ~ 6% a year, due to adults that are not perfectly loyal to their original host tree Case study: the apple maggot fly

44. Despite persistent gene flow, the two host races are genetically differentiated and appear destined to speciate Natural selection maintains 94% reproductive isolation, mainly resulting from different fruiting times of the two trees - apples mature 3 weeks earlier than hawthorn fruit - adults of the apple race hatch earlier to take advantage of new apples, and thus do not overlap with most hawthorn flies This represents a case of incipient speciation; it’s happening as we watch Case study: the apple maggot fly

45. Steps in sympatric speciation Result (1) mate on preferred host promotes assortative mating, so decreases gene flow (2) host-specific adaptations selects against hybrids, so build up over time reinforces assortative mating (3) other adaptations arise complete the speciation that increase pre-zygotic process isolation, like host fidelity and other mating traits Sequence for speciation by host shift