Unformatted text preview: Population Genetics
Lecture 2, Fall 2007 Reading assignment: Chapter 14 Dr. Charles Maynard 216 Marshall Hall x-6560 [email protected] Last lecture we covered Hardy-Weinberg equilibrium: ( p2 + 2pq + q2) Calculating gene and genotype frequencies from a gel Calculating genetic `distances' among populations This lecture we will cover
Effective population size & things that influence it ! Population structure & things that influence it ! Geography and Population Genetics
! Mendelian Population ! ! ! ! (or Panmictic population, Panmictic unit, or neighborhood, or deme, or local population) A population within which there is an equal probability of mating occurring among any of the individuals Expected to have a population structure close to Hardy-Weinberg equilibrium. (p2+2pq+q2) A species will usually be composed of dozens to hundreds of Mendelian populations Population size: A lot more complex than just counting
Physiological sterility ! Unequal numbers of males and females ! Unequal production of gametes ! Major changes in population size over generations ! Flowering synchronization (in plants) ! Dominance hierarchies (in animals)
! Idealized Population
! No migration ! Generations don't overlap ! Population size is constant over generations ! Equal number of males and females ! All individuals are fertile and "eligible" ! There is no selection ! Matings are completely at random ! The mutation rate is zero ! The mean number of offspring per adult is 1 with a variance of 1 Idealized Population
! No migration ! Generations don't overlap ! Population size is constant over generations ! Equal number of males and females ! All individuals are fertile and "eligible" ! There is no selection ! Matings are completely at random ! The mutation rate is zero ! The mean number of offspring per adult is 1 with a variance of 1 How do you deal with the deviations from this "ideal population"?
! Define something called the "Effective Population Size" (Ne) Ne
! The effective population size is the size of an ideal population which acts the same (genetically) as the real population in question To estimate the effective population size (Ne) for a species that fluctuates widely between generations you calculate the harmonic mean 1 -----Ne = 1 1 1 1 ----- + ----- + ----- + ----N1 N2 N3 Nt t Given: A population recovering from a crash. The first generation has 10 individuals, the second 100, the third 1000. N1 = 10, N2 = 100, N3 = 1000 The mean population size is: (10+100+1000)/3 = 370 The effective population size is:
1 -----Ne = 1 1 1 ----- + ----- + ----10 100 1000 3 1 ------ = Ne
If: .1 + .01 + .001 3
.037 = .037 1 ------ = Ne Then: Ne = 1 -----.037 = 27 Summary
The mean population size is 370 ! The Effective population size is 27 ! LESS THAN 1/10th of the mean!
! ! OK, what about populations that have unbalanced gender ratios? Given: Unequal sex ratios (5 males and 35 females) 1 -----Ne
For: = 1 1 ----- + ----4Nf 4Nm Nf = 35 and Nm = 5 1 ------ = Ne If: 1 1 ----- + ----4(35) 4(5) Then: = .007143 + .05 1 ------ = .057143 Ne Ne 1 = -----.057143 = 17.5 Some examples of skewed populations
Females 20 30 35 39 10,000 20 10 5 1 1 Males N(actual) 40 40 40 40 10,001 40 30 17.5 3.9 4.0 Ne Some examples of skewed populations
Females 20 30 35 39 10,000 20 10 5 1 1 Males N(actual) 40 40 40 40 10,001 40 30 17.5 3.9 Ne 4.0 !!! Take-home lesson:
Effective population sizes are virtually always smaller than a census count ! For many populations, Ne may be 1/10th of the census count! ! Think about the implications for rare and endangered species
! Populations differ not only in size, but in "structure"
Definition: Population structure -- Differences in allele frequency among populations Remember our gels?
Allele 1 2 3 4
. Pop#1 0.0 .15 .15 .25 .15 .30 Pop #2 .10 .10 .35 0.0 .30 .15 Pop#3 0.0 0.0 .15 .30 .55 0.0 5 6 How might the populations have gotten that way? Forces that change population structure
!Selection !Migration !Drift !Mutation Forces that change population structure (weighted)
!Selection !Migration ! Drift
! Mutation Forces that change population structure (weighted) Maybe even: !Selection !Migration
! Mutation Mutation
The base rate of mutation is extremely low (10-4 to 10-9) ! Most mutations are "silent" -absolutely no effect on the gene within which they occur (3rd base redundancy, occur in an intron or leader sequence)
! Mutation (continued)
! Many of the rest are "very quiet" mutation to a codon for an amino acid with similar properties. mutation away from the active site of an enzyme. Mutation (continued)
! Most are recessive (In a diploid organism, the
wild type allele makes enough gene product for the organism to function normally) ! Probably the overwhelming majority of the visible mutations are deleterious (or lethal) ! Yet mutation is the fundamental source of all of the other sources of genetic variation! Mutation, Net Effect:
! ! Long run- absolutely essential Short run - absolutely trivial ?!? Selection
Differential survival or reproduction based on the phenotype of an individual (Darwinian fitness) ! Original concept lead to the idea that for each species:
! 1. there is an single ideal phenotype and 2. all alternatives are "throwbacks", "mutants" or worse Problems with this view of "fitness"
1. Predicts that at most loci there will be only a single allele disproven ! 2. Predicts that homozygotes carrying this allele will be more "fit" than heterozygotes virtually never the case ! 3. Lead to some appalling social injustices
! Eugenics movement
Originated in Great Britain in late 1800s ! Wanted to improve the human species through breeding ! Very popular in the US in the 20s-30s ! Was considered "mainstream science" ! Driven underground by the Nazi atrocities of WWII ! Re-emerging in the propaganda of the neoNazi and white supremacists
! With a few rare exceptions, all organisms:
Have moderate to large numbers of alleles at many loci ! The "fitness" of any given allele changes in different environments ! Are much more likely to exhibit hybrid vigor in wide crosses and inbreeding depression in close matings than the reverse
! Selection comes in three flavors: Directional selection Diversifying selection (also called "disruptive selection") Stabilizing selection Number of individuals or or Fur color in a starting population (light to dark ) Directional selection favors an extreme phenotype. Disruptive selection favors 2 different phenotypes. Stabilizing selection favors an intermediate phenotype. Migration
In animals, migration takes place primarily through physical movement of adult animals ! Large animals with broad ranges (i.e.: wolves, bears, migratory birds) usually have little population structure
! Migration (continued)
Small or sedentary animals (mice, prairie dogs, scale insects) tend to have structured populations ! Pack, herd, troop or other "groupie" animals tend to have highly structured or even strongly inbred populations
! Migration (continued)
Migration in plants is through dispersal of pollen & seeds ! Light seeded species and wind pollinated species tend to have little population structure ! Heavy-seeded insect-pollinated species, especially if they occur in clumps, tend to have highly structured populations
Random changes in gene frequency due to sampling effects ! Is a small-population phenomenon ! Usually causes random loss of rare alleles ! Can be strong enough to counteract selection
! Drift comes in three "flavors"
Pure drift ! Pure founder effect ! Pure bottleneck
! Drift (continued)
Pure drift- an island population where habitat constraints maintain a small but fairly stable population size for many generations ! Pure founder effect - a small population crosses some barrier into a large patch of suitable habitat where it rapidly expands to fill the new habitat
! Drift (continued)
! Pure bottleneck - glaciation reduces a oncewidespread species to a tiny remnant which then expands back to its original range after the glacier retreats Drift (continued)
! Neutral evolution
New mutations are continuously occurring in a population. Selection removes most of the strongly deleterious mutations and random drift finishes off most of the rest. However, a small number become fixed in the population each generation. Over long periods of evolutionary time, these neutral mutations will cause isolated populations to "drift apart" If the process goes on long enough the populations will form new species. Populations and Geography
! Barriers to gene flow Simple distance mountains, deserts, large lakes or oceans ! Genetic barriers polyploidy chromosome translocations & inversions Take selection & drift together and . . . Resulting patterns
! Clines and ecotypes Cline An environmental gradient (temperature, rainfall, soil pH . . .) and a corresponding phenotypic gradient in a population of plants or animals. ! Where clines have been evaluated by provenance tests, clines are often found to have a genetic basis. ! Translation: Where you have gradual changes in the environment, you will see gradual changes in gene frequency. ! Example: balsam fir on Mt. Washington
! Example: balsam fir on Mt. Washington Ecotype A sub-population of a species that occurs in a particular well-defined environment, usually showing better adaptation to that environment than the species as a whole. ! Example: white spruce limestone ecotype
! When do you get an ecotype?
Abrupt change in the environment ! Intense selection pressure ! Strong barriers to gene flow
! When do you get a cline?
Gradual change in the environment ! Weak barriers to gene flow ! Suitable habitat all along the gradient
! The Population Genetics of Range Maps Douglas-fir range map Where would you expect to see clines? Where would you expect to see ecotypes? Where would you expect to see the most genetically variable populations? The least genetically variable? Clinal or Ecotypic variation? Clinal or Ecotypic variation? Acer rubrum Abies concola Clinal or Ecotypic variation? Red Pine: The genetic anomaly
Large natural range Lots of natural barriers to gene flow Mixture of large & small populations Considerable variation in environments You should expect lots of population structure, mostly clinal. But you don't! The species is nearly monomorphic How do you think it got that way? Real-World Applications
! Conservation of Rare & Endangered Species Uniqueness v.s. inbreeding depression
" Recent isolation of formerly continuous pop. = add diversity and stir: field mice or prairie dogs. " Near-species distinction = try very hard to maintain separations: elephants, Florida panther " Florida panther ? . . . " Well, let's discus it next time. ...
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- Fall '07
- Population Genetics, population size, effective population size