The Vortex program is an interactive simulation model; it asks you a list of questions and uses your data to determine the probability that your population will survive a specified number of generations. Most Vortex questions are described below, with a brief explanation of what the model is looking for from you. If you make a mistake you can use the up-arrow key to go back and change an entry, or use the F10 key in version 8.* to cancel the program and start again.
Note: before you run Vortex you should read the contents of the Vortex.doc file. It might help.
Do you want to enter values from the keyboard? (K,F or D)
Simply hit the Enter key (or K enter) if you wish to enter data manually. You will have to do it this way the first time at least. Alternatively, you may answer F and use the values in an existing input file (e.g., VORTEX.IN). The most useful one is D, for using defaults from a file! That way if you saved a previous set of inputs, then you can pull those up and edit them!
Output file name (or S for screen)
Type in a name for your output file, something like RHINO1.OUT, or BEAR1.OUT for your term project... The results will be saved in this file, you should be warned that it will append to this file with each run, unless you specify a different name each time - RHINO2.OUT, etc. You probably want to hang on to these output files in order to print them... Also you can edit them with a Text editor and add a comment at the top (e.g. this is my first run of the Bear term paper, and does not include inbreeding).
Do you want data files produced for graphing?
Type the letter Y the first time you run the program as its kind of helpful to visualize what's happening as the program runs. However, if you are running on an old computer, then graphing can slow things down, you can type N to make it run faster.
Detailed data on population structure each year and iteration?
Type N to start.
How many times do you want the simulation repeated?
Since the simulation has random elements built into it, it should be repeated many times in order to generate meaningful averages for the population variables. The terminology for this can be confusing, but these are repetitions or trials or iterations (NOT runs or simulations!). However, when you first start putting in values for term paper, you might set this number low, like 2-3 times, just so you can make sure things work without waiting, but once you have selected appropriate values, you should iterate the simulation at least 100 times to get meaningful results. You might even want to consider 500 or 1000 times.
How many years do you want the simulation to run?
Using the population and environmental data which you will enter, the program will track the population on a yearly basis. Typical values used in Population Viability Assessments (PVAs) range from 50-200 years. To begin, use 10 years so the model will run faster. For your term paper use 100 years once you have the program running correctly. Or if you feel strongly you can use 200 years or 50 years, but then be sure to note that in your paper and say why you thought you should use that longer (or shorter!) time period. You are making decisions about the fate of this species - think about it.
At what time interval do you want extinction reports?
The program will "check" the status of the population at increments (of years) and notify you when a population goes extinct. This is a decision for you to make, but every five years is probably an appropriate increment.
Extinction defined as: 0=only one sex; or min population size
For this you generally want 0. You may consider something else if you know your species is like flamingos or cockroaches where they won't breed unless there are many of them. But remember that the Allee effect (below) also takes this into account somewhat.
How many populations do you want to model?
Generally you will want to just enter 1. This assumes you are working with an isolated population with no gene flow. It gets rather complicated when you consider migration between populations (a metapopulation).
Do you want to incorporate inbreeding depression?
Inbreeding depression can be defined as the reduction in fitness resulting from breeding with closely related individuals. In small, interbreeding populations, inbreeding is very common. Read the homework assignment carefully to determine if you should use inbreeding. For your term paper you should not incorporate inbreeding depression on the initial/base simulation, but you should run at least one simulation that includes some form of inbreeding (see term paper assignment).
How many lethal equivalents per diploid genome in the population?
This number is very difficult to find for a given species. Unless you have this information for your species leave the default value (3.14)
What percent of genetic load is due to lethal alleles?
Unless you have this information for your species use the default value (50.0). If you do not understand what a lethal equivalent is, press F1 (this will show you what the question is asking for).
Do you want EV (reproduction) to be concordant with EV (survival)?
EV is the variation in the probabilities of reproduction and survival that occur because of environmental variation, e.g., the variation in reproduction caused by year-to-year changes in weather, food availability, parasites, etc. Enter Yes if you feel that good years for reproduction are also good years for survival, and vice versa, for your critter.
How many types of catastrophes do you want to model?
For the homework #1 start with only 1. For your term project you should spend some time thinking about this. What sorts of factors effecting your population might be modeled as catastrophes? They should be major events that occur once in a while, not minor factors that occur regularly.
Monogamous (M), Polygynous (P), or Hermaphroditic (H) breeding system?
Responding with M tells Vortex that there must be one breeding male for every breeding female in your population. Thus the number of males may be a limiting factor restricting breeding. Responding P indicates that one male is sufficient to breed all of the females in your population. Responding with H (may apply to fish and plants) indicates that all individuals are both male and female and therefore mating can occur among among any two individuals (If this option applies, press F1 for more information).
At what age do females normally begin breeding?
Enter the age (in years). Get this information from the literature. Enter the average age at which females give birth to (not conceive!) their first offspring.
At what age do males normally begin breeding?
Enter the age (in years). Apply the same criterion as for #12, above.
What is the maximum breeding age?
Enter the age (in years) after which animals cease to breed; note that this is the reproductive lifespan, not life expectancy. This information should be taken from the literature.
What is the sex ratio (percent males) at birth?
Enter the percent (0 - 100) of a given litter that is typically male. Usually, it is 50%, but may vary with the species.
What is the maximum number of young per year?
Can be obtained from the literature. If your species reproduces more than once in a year, enter the maximum number of offspring born during one year. If it reproduces once every two years, then you have two ways to deal with that problem. If two young are produced every two years then you might just assume that one young is produced every year. Or if three young are produced every two years, then you might have to do some fancy stuff. See suggestions.
Is reproduction density dependent?
Although the reproductive rate of your population may change with changing population density you should enter No for your homework assignment. For your term paper you may need to read the help screens or Vortex manual on this topic if you think it will have a significant effect on your species. It certainly may be the case for you species.
At this point, you will be asked to: "Please enter population label(s) (names) and optional state variables. Names cannot contain spaces. Up to two state variables (B and C) can be specified. State variables should follow population name, separated by spaces."
Use a descriptive name for your population(s) (e.g. rhino), or accept the default value(s). You can ignore specifying any state variables.
What % adult females breed each year?
Obtain this information from the literature for your species or for a closely related species.
What is the SD (standard deviation) in % breeding annually?
Environmental fluctuation can often have adverse effects on reproduction rates; for example, a reduction in the food supply might prevent females from achieving parturition because of energy limitations. In the question above, you stated the percent of females that produce litters each year. Now you will have to give the standard deviation (SD) of the percent of females breeding. This fluctuation is the magnitude of the impact of EV on reproduction. You can do this in three ways (see lecture notes). First, if year to year data on fecundity is available, you can use a spreadsheet program such as Excel to calculate the SD. Second, you can estimate the SD from the absolute range based on "N" years / data points as follows: For N ~ 10, assume range defines +/- 1.5 SD. For N ~ 25, assume range defines +/- 2SD For N ~ 50, assume range defines +/- 2.25 SD For N ~ 100, assume range defines +/- 2.5 SD For N ~ 200, assume range defines +/- 2.75 SD For N ~ 300, assume range defines +/- 3 SD. Alternatively, if the 95% CI is given, you can divide this range by 4 to come up with the SD. Finally, if no information is available on the variability, you will have to "guesstimate" the SD. Specifically, choose one of the three classifications below, and multiply the % of females that produce litters in a normal year by the appropriate fudge factor (0.05, 0.25 or 0.5). Enter the product as the Standard Deviation due to Environmental Variation. Highly susceptible to EV: SD = 0.5 x (% reproductive females). Slightly tolerant of EV: SD = 0.25 x (% reproductive females). Highly tolerant of EV: SD = 0.05 x (% reproductive females)
Of females that breed, what % produce: xx offspring?
You will be asked a series of questions regarding the reproductive rates of adult females in your population. Enter the percentages in whole numbers (i.e. 15, 50). Note that the percentages must add up to 100. These data may be difficult to find. A good place to look is in a life table or demographic study for your species or a related species. Otherwise, be creative!
What is the percent mortality of females in each age class? What is the percent mortality of males in each age class?
You will be asked to supply the % of individuals in each age group (up to adult) which die in an average year. For example, in a population of green-striped wallabies, infant mortality is typically quite high, say 30% (for the age class 0-1) and decreases sharply to 5% for the sub-adult age classes. At sexual maturity (age > 5), male mortality increases to 10% (due to old age and fighting over mates) while female mortality remains at 5%.
What is the Standard Deviation in the above mortality due to Environmental Variation?
You will be asked this question for each age/sex class. You may use the categories (highly susceptible, slightly tolerant, and highly tolerant) outlined in question #19. Think of the possible environmental effects on the mortality of each cohort (age/sex class). For example, extremely cold winters may have severe implications for juvenile wallabies not directly protected by their mothers (as are infants) and that haven't yet developed their insulating layer of fat (like the adults). Thus, the juvenile cohort would have a higher SD in mortality due to EV than either the infants or the adults.
Probability and Severity of Type I Catastrophe:
Having identified an environmental catastrophe that has some probability of affecting your population (e.g., a disease), enter the percentage (whole number) chance that the catastrophe will occur in an average year. You will next be asked to gauge the severity of the catastrophe with respect to both reproduction and mortality. The scale ranges from 0 to 1 (note: 0 = total loss of reproduction or total mortality, 1 = no effect). You may think of the value you enter as the fraction surviving the catastrophe.
For example, there is a 5% chance in a given year that a pack of dingos will wander into the wallaby's territory searching for food. Such a predation event would have a relatively large effect on mortality, but a relatively small effect upon reproduction (e.g., 0.25 for mortality and 0.8 for reproduction).
Are all adult males in the breeding pool?
Do all the adult males in the population have a chance to mate (probability of mating>0)? Answer Y or N. If you answer no, then select question (a) and supply the % of adult males that successfully breed. For your term paper you might have to think about this and draw it out of your research.
Start at stable age distribution and population size?
Generally the answer to this is Yes. Give the size of your population for year 1 of the simulation. Pick a distinct breeding population of individuals for your animal, not the entire species. In other words, look for how many are in a particular park, or area, and use that number. If you know the number of individuals in your population, AND you know their ages or ages classes, then you would answer No to this and specify the numbers of each age.
What is the population carrying capacity?
How many individuals can the environment support before adverse effects of overcrowding are felt? Note: the model will not allow your population to grow to a number greater than K. Vary carrying capacity keeping other factors constant and observe the results. (See term paper assignment and suggestions below.)
What is the Standard Deviation in K (carrying capacity) due to environmental variation?
For the homework, set SD = 0. For your term project, why might this not be zero? What information do you have on this for your species (note you will have to draw it out of the research - you will not find it listed as SD of K!).
Is there a trend projected in the carrying capacity? (Y/N)
For the homework, choose N. This will hold carrying capacity constant throughout your simulation. If you have reason to believe that the habitat for your population will continue to shrink over time, you can model this later (choose Y). When choosing Y you will have to enter the number of years over which K will change and the direction and rate of change.
Harvest the population? (Y/N)
For the homework we will not need to harvest our populations. Enter No. For your term paper, how might you use this parameter?
Supplement the population? (Y/N)
For the homework, we will not need to supplement the population. Enter No. For your term paper, might this term be appropriate?
After Vortex completes the simulation, it does not show you your results on the screen! It saves your results to an output to a file called VORTEX.OUT. You can view or print these results by using EDIT (i.e. you could type EDIT VORTEX.OUT from the DOS prompt) or using NOTEPAD under Windows. You may want to rename this file to remind yourself what you were doing, e.g., PANDA2.OUT. You can do this by using File Manager in Windows or typing RENAME VORTEX.OUT PANDA2.OUT from DOS). If you do not rename the file and VORTEX.OUT already exists on your disk, your new output will be appended to the previous output. This can be confusing! If you allow it to keep appending, then you should edit the VORTEX.OUT after each run and put a note in there for yourself so you know where your CURRENT results start and end. If you keep appending results then the file may become extremely large and it will become difficult to differentiate among various runs.
Vortex automatically saves the data you entered to a file called VORTEX.IN (or you can choose some other name). This file is a sequential list of the Vortex questions and your answers. You can use the EDIT text editor or any other editor of ASCII files to alter your answers in the input file, and then rerun your revised data file in Vortex. Enter the appropriate input file name for question #1, above. By doing this you avoid typing in all the values each time you run the program. (But beware that if you change some Y/N questions, then the program will ask you some questions dependent upon your answer. If you edit your input file but this the program stops working, then you may need to enter values from the keyboard again).
Each time you enter new values into the program using the keyboard, the previous version of the vortex.in file will be overwritten, so rename the file first if you want to save the original values from the file.
The simulation will generate several values of interest to you, the manager of the population. You should think carefully about what these results mean. In your term paper you should discuss these results, not just list the values. In other words what if you ran 100 simulations for a 10 year period and your results indicated that 0% went extinct, but the heterozygosity (one of the measures of genetic variation) dropped by 50%. What would you expect would happen if you re-ran your simulation for 100 years? What is the meaning of this sort of result in terms of management? Compare your results between different runs. How did the survival time change, how did the genetics change?
1. The fate of each population. i.e., the number of populations that survived the specified time.
2. Summary statistics on the probability of population extinction over specified time intervals, e.g., every 5 or 10 years.
3. The mean time to extinction of those populations that went extinct.
4. The levels of genetic variation remaining in surviving populations.
5. The intrinsic rate of natural increase (r). This value represents the exponential rate of increase realized by the population parameters you specified.
6. The finite rate of increase (lambda), represents the number of individuals that will be present next year for each individual present this year.
7. The net reproductive rate (R0). An R0=1 means that the population is replacing itself exactly. An R0<1 means that the population is declining (excluding immigration, emigration). An R0>1 means that the population is increasing.
**Note: the values given for r, lambda, and R0 are based upon the founder population, not for the surviving population.