PWS 551 Quantitative Ecology.txt

  1. What is quantitative ecology and what lead to the quantitative trend in ecology?
    • The application of mathematical and statistical tools to address questions in ecology
    • The trend reflects the demand to interpret larger and more complex data sets
    • Also in response to criticism from other scientific disciplines for ecologists to use more quantitative approaches
  2. What are the 5 steps in ecological research?
    • Make observations
    • Formulate objectives/hypotheses
    • Collect and analyze data
    • Draw conclusions
    • Evaluate hypotheses
  3. What are Krebs’ rules for ecological methodology?
    • 1. Not everything that can be measured should be measured
    • 2. Find a problem and state your objectives clearly
    • 3. Collect data that will satisfy your objectives and a statistician
    • 4. Some ecological questions are impossible to answer at the present time
    • 5. Decide on # of significant figures for continuous data prior to starting
    • 6. Never report an estimate without measure of possible error
    • 7. Be skeptical about the results of significance tests 
    • 8. Never confuse statistical with biological significance
    • 9. Code all your data and enter it on a computer in some readable format
    • 10. Garbage in, garbage out
  4. Why are preliminary and pilot studies important?
    • Address simple questions of technique
    • Determine sample sizes needed for a particular level of precision
  5. What are the different scales of measurement in ecology?
    • Nominal - attributes like sex or species
    • Ranking - ranks attributes in relation to one another, but not a numerical value 
    • Interval/ratio - all characteristics of ranking, but know distance between classes; data may be discrete or continuous
  6. Compare and contrast accuracy and precision.
    • Accuracy - measure of bias
    • Precision - measure of spread
  7. Why is statistical inference difficult in ecology?
    • Usually can not sample in random manner
    • Hidden variables confound our interpretations
    • Statistics can only deal with random error, not detecting biased data
  8. Compare and contrast absolute abundance with relative abundance
    • Absolute abundance - exact count of species 
    • Relative abundance - measure of dominance relative to co-ocurring species
  9. What are the common measures of abundance used in ecological studies?
    • Frequency - % of sampling points or quadrats with species
    • Density - # of individuals per unit area
    • Biomass - dominance (cover), production, number
  10. What are the different ways that we measure abundance in animal populations?
    • Mark-recapture
    • Removal/resight
    • Distance
  11. What is the Peterson estimate?
    • Simplest mark-recapture method to estimate population size
    • Mark individuals once, release them, and then recapture to check for marks
    • Tends to overestimate; bias is large for small populations
  12. What are the assumptions of the Peterson estimate?
    • Closed population
    • Equal catchability
    • Marking doesn't alter catchability
    • Marks aren't lost between sampling
    • All marks are reported upon discovery in second sample
  13. What is the Seber modification of the Peterson estimate and why is it used?
    Reduces the over-estimation bias of the Peterson estimate
  14. What is the Schnabel method, when is it used?
    • Extension of the Peterson mark-recapture estimate for population size
    • Used for closed populations and multiple samples
  15. What are the assumptions of the Schnabel method?
    • Closed population
    • Equal catchability
    • Marking doesn't alter catchability
    • Marks aren't lost between sampling
    • All marks are reported upon discovery in second sample
  16. What is the Jolley-Seber method?
    • Mark-recapture method for open populations
    • Estimate of population size
  17. When and how is the Jolly-Seber method accomplished?
    • 3 or more mark-recapture samples
    • Individuals are marked to be specific for that sampling time
    • Samples are usually point samples of short duration separated by a long duration from the next sample
  18. What are the assumptions of the Jolley-Seber method?
    • Equal catchability
    • Equal survivability for marked individuals
    • Individuals do not lose their marks and marks are not missed in sampling
    • Sampling time is negligible in relation to the time between samples
  19. What affects precision in the Jolly-Seber method?
    • Capture probability
    • # of sampling intervals
    • Survival rates
  20. What removal/resight methods are used for exploited populations?
    • Change-in-ratio 
    • Eberhardt's removal
    • Catch-Effort
  21. What are the Change-in-ratio methods?
    • Estimate of abundance/density from the change in sex ratio during a hunting season
    • Assumptions:
    • Composed of males/females and adults or young
    • A differential change in the numbers of the two types of organisms occurs during the observation period
  22. What is Eberhardt’s removal method and when is it used?
    • If a population size index can be made before and after removal of a known # of individuals, we can use the indices to estimate absolute density
    • Easier use of removal data
    • Effective when >40% of the population is seen and >20% is removed
  23. What are catch-effort methods and when are they used?
    • Estimate population size by the decline in catch-per-unit effort over time
    • Highly restricted because it only works well if a large fraction of population is removed so that there is a decline in the catch-per-unit-effort
  24. What is the Leslie estimate and what is the theory behind the method?
    • Catch-per-unit-effort is directly proportional to the existing population size
    • Because the population must be declining time to time by an amount equal to the catch, a regression plot (accumulated catch vs. catch-per-unit-effort) should be a straight line
    • Doesn't assume equal effort
  25. What is the Moran-Zippen method?
    • Two sample method of removal
    • Assumes equal removal effort for both samples
  26. What are resight methods and how do we estimate density in animal populations?
    • Methods used to "resight" radio-collared/tagged individuals
    • Maximum likelihood estimation for density
  27. What is the boundary strip method?
    • Used to estimate density
    • Adds a "boundary strip" around the trapping area which is half the movement radius of the animals under study
  28. What is the nested grids method and is it biased?
    • If a large area is sampled you can break the data up into a series of nested grids to estimate density
    • Large positive bias
  29. What is a trapping web and why use this method?
    • Used to estimate density
    • Type of removal method, because each individual is counted only the first time and recaptures are ignored
    • Trap density is lower as you move away from center
    • Assumes every animal in the center is caught
    • Individuals are not attracted to web from outside area
  30. What is a quadrat and when is it used for sampling?
    A measured area, of any shape and size, that is used as a sample area in a survey of plants or of sessile/sedentary animals.
  31. What are the requirements for using quadrats?
    • Area (or volume) counted is known
    • Organisms are immobile during counting
  32. What are quadrat size effects?
    • Small quadrats require larger sample sizes for a specified level of adequacy than larger quadrats
    • Small quadrats are more expensive than large based on number of objects sampled per unit time
    • Coefficient of variation values are largest for small quadrats and sparse populations on average
  33. What are quadrat shape effects?
    • Rectangle quadrats are more accurate for aggregated populations because they typically include portions of aggregated and unoccupied patches in a single sample
    • Circles are poor because they generally land completely within or outside of a patch
    • Each quadrat shape tends to over estimate density parameters
  34. What is an isodiametric quadrat?
    • Quadrat has the same diameter (e.g., circle, square)
    • These have fewer problems with parallax and moving around
  35. What is simple random sampling?
    A subset chosen entirely by chance from the entire population
  36. What is meant by stratified random sampling?
    • The population is divided into non-overlapping subpopulations 
    • Once these strata are chosen, you sample each stratum separately
  37. What are the benefits of stratification?
    Means and confidence intervals can be estimated for each subpopulation
  38. Can strata be given different weights?
    Stratum weights can be assigned if subpopulations are unequal
  39. What is meant by systematic sampling?
    To regularly or systematically place samples
  40. When and why is systematic sampling used?
    • Simplicity of application
    • Sample evenly across whole population or habitat
  41. What is the statistical problem with using a systematic sample and how common is the problem in ecological systems?
    • Systematic sampling is not random and may incorporate periodic variation
    • Periodic variation rarely seems to occur in ecological systems
  42. In our lab exercise which method of sample placement best estimated density?
    Stratified > regular > random
  43. How do we determine the appropriate size and shape of quadrat to use?
    • Wiegert's method
    • Hendricks' method
    • Nmin method
    • Nested quadrats method
    • Want normal distribution and high precision
  44. What criteria should be met in determining adequate quadrat size and shape?
    • No species should occur (or be equally abundant) in all quadrats
    • All important species should be in the sample at least occasionally
    • Observe all parts of the quadrat with minimum personal movement
    • Time for specified reliability should be minimized
  45. What is Wiegert’s method?
    • Determines quadrat size and shape
    • Easy and fast
    • Select quadrat size and shape that minimizes cost and variance (time = money)
  46. What is Hendricks’ method?
    • Determines quadrat size and shape
    • More accurate, strict assumptions, but slower
    • Variance decreases with larger quadrat size
    • Time to read a quadrat is proportional to size (2m2 is twice as costly as 1m2)
  47. What is the Nmin method?
    Determines adequacy and efficiency of sampling
  48. What is the nested quadrats method?
    • Determines quadrat size and shape
    • Used to define a species-area curve for plant communities
  49. What are quadrat size and shape effects?
    • Rectangular quadrats are the best in heterogeneous habitats
    • Circular quadrats work well with permanently marked points in sequential sampling (not in grasslands)
    • Size and shape effects are not about biased abundance estimates as much as they are about efficiency
    • Do pilot studies to determine optimal size and shape for your particular study (statistically, ecologically, and logistically)
  50. Take home message on quadrat size and shape
    • No single quadrat size or shape can be universally used
    • Do a pilot study to gather means, variances, and costs
  51. When can you ignore recommendations about size and shape of quadrats?
    • If you want to compare your data with older data gathered with a specific quadrat
    • If sampling several habitats, species, across seasons
  52. How do we determine where to place quadrats?
    There is no evidence that random placement of sample units gives better results than stratified or regular placement
  53. How do we determine sampling strategy?
    • Clearly specify the statistical population
    • Decide your sampling units and your experimental units
    • Select a sample and adopt a variety of sampling plans as necessary
  54. What is sampling design?
    Method of placement and # of samples must be decided before sampling
  55. What is meant by adaptive sampling?
    Take advantage of spatial pattern in the population to obtain more precise measures of abundance
  56. What is an adaptive cluster sample?
    Begins with normal random sampling but when an organism of interest is detected, additional quadrats in the vicinity of the original quadrat are added to the sample
  57. What is meant by multi-stage sampling?
    Used to describe any design where there are > 2 levels of sample selection
  58. What is cover?
    % of area (ground) covered by vegetation or other material
  59. What are the four basic types of cover obtained in ecological sampling?
    • Basal cover
    • Canopy cover
    • Foliar cover
    • Ground cover
  60. Why do we measure cover?
    • Cover is an indicator of ecological processes
    • Cover also serves as a management indicator for monitoring
  61. How does cover measure dominance?
    Cover is an ecological indicator of which species are dominating the site
  62. What are the common methods for assessing cover?
    • Simple quadrats (1m2 square)
    • Line intercept
    • Point quadrats
    • Loop methods
    • Ocular estimate method
  63. What is the line-intercept method?
    Assessment of the distance (and sometimes width) along a line that is intercepted by a plant species or type
  64. What are point methods (to assess cover)?
    Examination of many points on a site to estimate the proportion of "hits" of a species
  65. What are ocular methods (to assess cover)?
    Uses concept that even if it is not possible to accurately estimate precise cover for a given quadrat, it may be easy to estimate broad cover classes
  66. From our lab exercise of estimating plant cover what are factors to consider prior to sampling?
    • Time efficiency
    • Vegetation type
    • How to calculate variance and SD
    • Sample consistency
  67. In our lab of estimating plant cover which method best estimated cover?
    Ocular > 1-point > line-intercept > true mean > 10-point
  68. What is the difference between correlation and regression?
    • Correlation - variables simply vary together  
    • Regression - variables vary together but there is evidence of a causal relationship
  69. What is a contingency table?
    Display format used to analyze the relationship between two or more categorical variables
  70. What is a chi-square analysis?
    • Used to determine if there is a difference between expected and observed frequencies in one or more categories
    • Non-parametric
  71. What is the chi-square formula?
    Image Upload 1
  72. How do you calculate expected frequencies for a chi-square analysis of a contingency table?
    Image Upload 2
  73. What are the types of t-tests?
    • Equal variance (parametric)
    • Unequal variance (non-parametric)
  74. What are ANOVAs?
    • Analysis of variance that compares two or more means
    • Parametric
  75. What are plotless sampling procedures and when are they used?
    • Another way of estimating abundance and density
    • An alternative to mark/recapture and quadrats
    • They are useful for plants and animals that do not move much or can be located before they move
  76. How do plotless sampling techniques work?
    • Based on the reciprocal relationship between density and nearness of individuals to one another
    • Only necessary to know the distance between regularly spaced individuals to calculate density
  77. What is line transect sampling?
    • Method of estimating density
    • An observer travels along a randomly positioned line, recording the distances and angles from the line to each organism detected
  78. What are the assumptions of line transect sampling?
    • Animals directly on the transect line will never be missed
    • Animals do not move before being detected and are never counted twice
    • Distances and angles are measured exactly
    • Sightings of individual animals are independent events
  79. What is the detection function of line-transect sampling?
    Detectability will fall off with distance from the center line of the transect
  80. What are the estimators for density using line transect sampling?
    D = n/2La

    • D = density of animals/unit area
    • n = # animals seen on transect
    • L = total length of transect
    • a = half the effective strip width (a constant)
  81. What are the two basic approaches to distance methods?
    • Select random organism and measure distance to nearest neighbor
    • Select random point and measure the distance from the point to the nearest neighbor
  82. If an area has moderate to high density of sessile organisms and they are randomly dispersed, are distance methods or quadrats better?
    Quadrats - less biased and do not overestimate density
  83. If an area has low density of sessile organisms and they are randomly dispersed, are distance methods or quadrats better?
    Distance methods - less costly in terms of money and time
  84. What is random pairs?
    • Both this and quarter method determine the average distance between organisms
    • Measures distance between the object nearest to the sampling point and a second object that lies outside an exclusion angle of 180 degrees
  85. What is nearest neighbor?
    • Distance from an organism to the one closest to it
    • Sometimes incorporates multiple neighbors
  86. What is the point-quarter method?
    • Plotless distance method to estimate density
    • Quick, easy, and objective
    • A series of random points is selected, often along a transect, with the constraint that points should not be so close that the same individual is measured at two successive points
    • The area around each random point is divided into four quadrants and the distance to the nearest tree is measured in each quadrant
    • Thus four point-to-organism distances are generated at each random point to the first-, second-, third-, and fourth-nearest neighbors
    • Overestimates density
  87. What is the Bitterlich method?
    • Plotless distance method to estimate density
    • For tree basal area is very accurate and quick
    • Use sighting scope
    • Turn 360 degrees and only count objects that are greater than the cross-bar
    • Issues with parallax especially in grasslands
  88. What is the Byth and Riply procedure and why is it used?
    • Useful for large areas
    • Set out 2n sampling points in study area 
    • Select half of the 2n points at random and measure distance to nearest organism
    • Around other half of points set out plots that include about 5 individuals each
    • Select n of these at random
    • Measure distance from selected organism to its nearest neighbor
  89. What is the T-Square method?
    • Most robust estimator of density
    • Measure distance from random points to nearest organism and then to its nearest neighbor
    • Only used in randomly distributed populations
  90. Compare all distance methods
    • All distance methods are sensitive to spatial pattern (biased in clumped populations)
    • Estimators based on point to organism are better in clumped
    • Estimators based on organism to nearest neighbor are not so good in clumped
  91. What are the three spatial patterns in nature and what gives rise to these patterns?
    • Aggregated - some constraint on the population, environmental heterogeneity, gregarious behavior, reproductive behaviors
    • Random - environmental homogeneity or non-selective behavioral patterns
    • Uniform - negative interactions and competition
  92. What are the two statistical distributions and their spatial patterns? 
    • Poisson - random pattern
    • Negative binomial - aggregated
  93. What is a community?
    Associations of populations of many species that occupy the same geographical area
  94. What are the historic community concepts?
    • Organismic (holistic)
    • Individualistic
    • Intermediate
  95. Who are Clements and Gleason?
    Proposed the open community view and individualistic view
  96. What is meant by ecotone?
    • Transition area between two biomes
    • It is where two communities meet and integrate
  97. What is meant by open vs. closed communities?
    • Closed have obvious ecotones between species distribution
    • Open is overlapping
  98. What is meant by interspecific associations and how do we test for this?
    • Associations between two different species
    • Test using a Chi-square
  99. How are communities classified?
    • Delineation of communities can be difficult unless the transition between adjacent communities is abrupt
    • —Often arbitrary
    • Require statistical approaches such as ordination and cluster analysis
  100. How do we determine where one community ends and another begins?
    • Ordination
    • Cluster analysis
  101. What are measurements of community similarity?
    • Binary coefficients
    • Distance coefficients
    • Correlation coefficients
  102. What are binary coefficients?
    • Used for presence/absence data
    • Jaccard index
    • Ochiai index
    • Sorensens’ similarity index
    • Dice index
    • Baroni-Urbani and Buser coefficient
  103. What are distance coefficients?
    • Measures of dissimilarity rather than similarity
    • When a distance coefficient = 0, communities are identical
    • Require some measure of species abundance in the community
    • Euclidean distance, Bray-Curtis measure, Canberra metric
  104. What do binary coefficients of similarity deal with?
    Simplest similarity measure that deals with presence/absence data
  105. How many binary coefficients of similarity are available in the literature?
    > 20 binary similarity measures
  106. What is the Jaccard index?
    • Binary coefficient of similarity in presence/absence data
    • Deficiency - no significance test
  107. What is the Ochiai index?
    Binary coefficient of similarity in presence/absence data
  108. What is the Sorenson’s index?
    • Binary coefficient of similarity in presence/absence data
    • Weights species composition matches between 2 samples more heavily than mismatches
    • Deficiency - no significance test
  109. What is the simple matching coefficient?
    • Simplest binary coefficient of similarity in presence/absence data
    • Makes use of negative matches as well as positive matches
  110. What is the Baroni-Urbani and Buser coefficient?
    • More complex binary coefficient of similarity
    • Makes use of negative matches
  111. How do binary coefficients of similarity compare?
    In general, the Sorenson’s coefficient yields the highest similarity whereas the Jaccard’s coefficient results in the lowest similarity
  112. What is the Bray-Curtis measure?
    • Measure of community dissimilarity
    • Weighs abundant species more heavily than rare species
  113. Compare Bray-Curtis and Canberra metric
    • Both are particularly poor in diverse communities with large sample sizes
    • Both are best used in situations with low species diversity and small sample size
  114. What are the two types of correlation coefficients and when is each used?
    • Pearsons product moment - used for parametric data
    • Spearman’s rank - used for non-parametric data
  115. What is percentage similarity?
    Percent similarity between two communities
  116. What is Ruzicka’s index?
    • Image Upload 3
    • Similarity index— for quantitative data
    • Relatively unbiased
    • —Easy to compute
  117. What is Morisita’s index?
    • Similarity index for counts of individuals (not for other abundance estimates based on biomass, productivity, or cover)
    • Also a dispersion coefficient
  118. What is the simplified Morisita’s index?
    Similarity index for proportional data (biomass, cover, or productivity)
  119. What is Horn’s index?
    • Similarity index
    • Least sensitive to sample size and gives the best representation of similarity
    • Can be calculated from raw data (numbers) or from relative abundances (proportions or percentages)
  120. Describe the multivariate technique called cluster analysis?
    Graphical way of portraying results from a large matrix of interspecific association (or similarity) indices
  121. What is simple linkage clustering?
    • Also called nearest neighbor method
    • Simple to compute
    • One inaccurate sample may compromise the entire process
    • Tends to produce long, strung out clusters
  122. What is complete linkage clustering?
    • Farthest neighbor clustering method
    • Opposite of single linkage
    • Tends to produce compact clusters
  123. What is average linkage clustering?
    Consists of the Weighted Pair Group Method of Averaging and the Unweighted Pair Group Method of Averaging (UPGMA)
  124. Compare and contrast the weighted and unweighted pair-group methods of averaging (UPGMA)
    • Weighted average procedure is more conservative than the unweighted method because it weighs the new addition to the cluster just as heavily as everything else
    • Whereas the UPGMA assigns equal weights to each individual component within clusters
Card Set
PWS 551 Quantitative Ecology.txt