Landscape genetics Instructor: K. McGarigal Assigned Reading: Manel et al (2003) Objective: Provide an overview of the consequences of landscape pattern to the spatial genetic structure of populations. Highlight the role of landscape structure in gene flow and approaches for examining the relationship between spatial genetic structure and the structure of landscapes. Topics covered: 1. What is landscape genetics? 2. What is gene flow? 3. Why is gene flow important? 4. How much gene flow is enough? 5. Gene flow in heterogeneous landscapes 6. Landscape genetics: statistical approaches and examples Comments: Slides adapted from presentation by Dr. Michael Schwartz, USDA Forest Service Rocky Mountain Research Station, Missoula, Montana. 15.1 1. What is Landscape Genetics Landscape genetics is an approach for understanding of how geographical and environmental features structure genetic variation at both the population and individual levels. Importantly, landscape genetics: a. does not require that discrete populations be identified in advance; b. emphasizes the processes and patterns of gene flow and local adaptation; and c. the analysis involves detection of genetic discontinuities and the correlation of these discontinuities with landscape features. Landscape genetics is an emerging discipline that combines the fields of population genetics and landscape ecology. 15.2 2. What is Gene Flow? Gene flow is the incorporation of genes into the gene pool of one population from other populations. In this regard, it is important to distinguish between the processes of dispersal and migration as defined from a genetics perspective. • Dispersal – the permanent movement away from the site where an organism was born (i.e., its natal site). Note dispersal refers to the movement of an individual away from its natal site; it is not necessarily true that the individuals genes will be incorporated into the new population, since this requires successful reproduction. • Migration – refers to the movement of genes from one population to another accomplished by individuals that move and breed in a population other than their birth site. Migration, as defined here, equals gene flow. Note, migration is defined somewhat differently by biologists, where it generally refers to the periodic (typically seasonal) movement of individuals between geographic locations. 15.3 3. Why is Gene Flow Important? Gene flow is important for many reasons, including the following: • Prevent inbreeding of populations – gene flow reduces the potential for inbreeding, the reduction in fitness due to the random loss of heterozygosity (genetic diversity) associated with small populations, by introducing new genes into a population.. • Prevent depression of population fitness – gene flow functions to increase the heterozygosity of individuals and populations and thereby increase population fitness. • Prevent the suite of demographic problems that arise as a consequence of inbreeding or alone (e.g., allee) – gene flow helps to prevent inbreeding depression, as noted above, and can reduce the potential for the Allee effect in small populations – the rapid loss of fitness (e.g., fecundity) in very small populations. • Decrease extinction risk – by functioning to reduce inbreeding depression and the reduction in fitness due to the loss of heterozygosity, gene flow can serve to decrease the risk of population extinction. 15.4 Example: Greater prairie chicken (Westemeier et al. 1998) In 1933, the greater prairie chicken in Illinois numbered 25,000; in 1962 it was down to 2,000; and in 1993 it was down to just 50 individuals. Moreover, in 1960 there was a 90% hatching success rate, but in 1990 that rate had fallen to 74%. The decrease in fecundity (i.e., fitness) was hypothesized to be due to the loss of genetic diversity associated, which declined 30% between 1960-1990. To reverse the situation, managers introduced birds from Minnesota and Kansas to infuse new genes into the population, and hatching rate success increased to 94%. The population has since recovered from near extinction. 15.5 Example: Scandanavian adder (Maddsen et al. 2001) An Scandanavian adder population crashed between 1983-1993. The population had very low genetic diversity and a large number of stillborn offspring were observed, an indication of low fitness due to inbreeding depression. To counter the population crash, managers introduced 20 males from a larger population for 3 years between 1996-1999. The immediate result was an increase in male recruitment and a decrease in the number of stillborns. Note, the males were returned to their native population after performing their duty. 15.6 As this table illustrates (from Manel et al 2003), there are numerous empirical examples of studies showing genetic rescue effects of induced gene flow to small populations. 15.7 4. How Much Gene Flow is Enough? So, if gene flow is important, at the very least to reduce the potential for inbreeding depression in small populations, how much is enough? While this is not an easy question to answer, the general rule of thumb that has been put forth is that one migrant per generation is necessary to prevent the adversities of inbreeding depression, while also allowing for divergence in allele frequencies among subpopulations. Mills and Allendorf (1996) authors argue that one migrant per generation is an appropriate minimum, but that the “rule” should be broadened to include a maximum of 10 migrants per generation. Vucetich and Waite (2000) question whether that rule of thumb is sufficient for fluctuation populations, and demonstrate that most populations fluctuate enough to require >10 migrants per generation and many may even require >20 per generation. 15.8 Example: Brassica campestris (Newman and Tallmon 2001) In this inbreeding experiment involving the mustard Brassica campestris, five of six fitness related components were negatively effected by inbreeding. The researchers experimentally introduced migrant treatments of 0, 1, and 2.5. The results were dramatic. The 1 migrant treatment and 2.5 migrant treatment produced higher fitness components than the 0 migrant treatment, and there was no difference between 1 and 2.5 migrant treatments, suggesting that in this case the 1 migrant per generation rule may be enough to prevent inbreeding depression. 15.9 Example: Peromyscus maniculatus (Schwartz and Mills 2005) In this study involving Peromyscus maniculatus, the researchers compared survival rates in a relatively isolated control population against two different treatments: a migrant treatment in which individuals from another distant source population were introduced to the local population, and an inbreeding treatment in which a population was experimentally inbreed. The migrant treatment resulted in a dramatic increase in survival. Surprisingly, the inbreeding treatment also resulted in an increase in survival, which the authors attribute to a number of factors. 15.10 5. Gene Flow in Heterogeneous Landscapes The question we are most interested in is whether landscape patterns, in particular those created by human land uses, influence gene flow and to what extent. Consider the following series of slides and try to answer the question, is gene flow occurring? 15.11 15.12 15.13 In order to answer the question, is gene flow occurring, we need to sidetrack and do a quick genetics primer for those that either haven’t had genetics or had it too long ago. Collection of genetic samples The first thing we need to do is collect genetic samples. There are many ways to do this. Optimal samples (i.e., containing the most DNA) include tissue and blood, but the collection of these samples requires invasive sampling. Sub-optimal samples include hair, scat, urine, skins/museum specimens, feathers and guano, and these can generally be obtained using non-invasive methods. 15.14 Types of DNA 1. Mitochondrial DNA (mtDNA) – is contained (obviously) in the mitochondria of cells and there are thousands of copies per cell (at least 20 times more DNA than in cell nucleus). Mitochondrial DNA is maternally inherited, so it is passed down directly from mother to offspring, and is highly conserved; i.e., it is very stable and does not change much over generations. Thus, the DNA in your mitochondria and very much the same as those that were carried by your great, great, great, great, etc. grandmother. 2. Nuclear DNA – is contained (obviously) in the nucleus of cells and there are two copies per cell. Nuclear DNA is inherited from both parents, one copy from each parent. There are highly variable regions called microsatellites that are very useful for distinguishing individuals and for differentiating very recent population divergences. 15.15 Species ID using mtDNA mtDNA is especially useful for distinguishing among species, which is often the first thing that must be done after collecting non-invasive samples in order to be sure of the species. There are two common approaches for this purpose: 1. Restriction digests (RFLP) – in which known genes are extracted using restriction enzymes and the size of the alleles are used to distinguish among species. 2. DNA sequence analysis – in which the exact nucleotide sequence for a section of DNA is determined and differences in the sequence are used to distinguish among species. 15.16 Restriction Digests Step 1. The first step is to separate the DNA from other cellular material. Note, at this stage all of the DNA, both nuclear and mitochondrial, is mixed together. Step 2. The next step is to add a primer pair (2 short pieces of DNA, approximately 20 base pairs in length), which latch on to either side of an area of interest (typically a 100-800 bp length of DNA). Step 3. The next step is to make many copies of the genetic fragment using Polymerase chain reaction (PCR). Step 4. Finally, the last step is to separate the fragments by size using gel electrophoresus. Essentially, this entails putting the genetic material on a gel and passing an electrical current across it. The DNA fragments migrate across the gel according to their size; large fragments only move a short distance, while small fragments move farther across the gel.