BIOE 440 Conservation Biology
CWP = Mills, Conservation of Wildlife Populations,
RFDS = Wickham & Grolemund, R for Data Science
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Week and
HW due that Friday |
Remote
Lecture & primary papers |
In Class Lecture & CWP Reading |
R Exercise & RFDS Reading |
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Human population growth and resource
use |
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1� Aug 17/19/21 |
Cohen 1995. Population growth and the earth's human carrying capacity. Science 269: 341-346. |
Population growth models CWP CH 1, 11 |
RFDS 1, 2, 3.1-3.6 Tour of R Studio and getting started with R Exercise: Using plots to understand US census projections.
�Data
for census exercise. |
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2 Aug 24/26/28 R census plotting exercise due |
Rojstaczer et al. 2001. Human appropriation of photosynthesis products. Science, 294: 2549-2552. |
Human resource consumption: fossil fuels and TNPP CWP CH 5, 6 (pages 114-125) |
RFDS 3.7 � 3.10, 4 Exercise: Mapping the Human
Footprint Index with ggplot2 using coord_quickmap() |
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Biodiversity: How many species
exist? What are current extinction rates? Are they unusual? |
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3 Aug 31/Sep 2/4 R HFI mapping exercise due |
Pimm et al. 1995. The future of biodiversity. Science 269, 347-350. � |
How many species exist? Describing Patterns of diversity. CWP CH 13 |
RFDS 5, 6, 27 Exercise: Data
wrangling with dplyr to summarize (and plot) differences in group size
between species and habitats |
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4 �Mon off, Sep 9/11 Wrangling group size data exercise �due |
Rosenberg et al. 2019. Decline of the North American avifauna. Science 366: 120-124. (Wed/Fri) |
What are current and historic extinction rates? (Wed/Fri) |
RFDS 7 (On your own) |
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Designing and interpreting
field studies: estimating population density and demographic rates |
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5 Sep 14/16/18 Written summary of Rosenberg et al. methods, results, strengths, weaknesses due |
Who lives and dies? extending ordinary least squares regression to generalized linear models and glm() |
Mean, variance, OLS regression using lm() CWP CH 2 |
RFDS 8, 9 Exercise: Hypothesis
testing for effects on group size using regression models |
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6 Sep 21/23/25 Hypothesis testing exercise �due |
Chandler 2014 Distance sampling analysis in unmarked. CRAN, Vienna, Austria. |
Unbiased estimates of population size: accounting for detection with distance sampling CWP CH 4 |
Hypothesis statement, sampling design and methods to apply distance sampling to test effects on magpie density |
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7 Sep 28/30/Oct 2 Written hypothesis, sampling design & methods for magpie study due |
Rosenblatt et al. 2014. Detecting declines of apex carnivores and evaluating their causes: An example with Zambian lions. Biological Conservation 180, 176-186. |
Unbiased estimates of survival rates: accounting for detection with mark-recapture |
RFDS 10, 11 Magpie data collection Example code: distance sampling for puku in unmarked, as template for magpie analysis |
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8 Oct 5/7/9 Results for analysis of effects on magpie density due |
USFWS 2017. Removing the Greater Yellowstone Ecosystem Population of Grizzly Bears From the Federal List of Endangered and Threatened Wildlife. Federal Register 82:30502-30508 (up to �recovery planning��) |
Age- and stage-structured population growth models: Leslie projection matrix CWP CH 7, 12 |
RFDS 12, 13, 21 Example code: PVA with multiple projection matrices for �Mountain Golden �Heather Exercise: count-based PVA for YGB |
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Genetic issues in
conservation: speciation and the ESA, hybridization, inbreeding |
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9 Oct 12/14/16 YGB PVA exercise due |
US Endangered Species Act (through page 14) USFWS Distinct Population Segment policy from Federal Register |
Speciation and the ESA CWP CH 3 |
RFDS 17,18 Exercise: Piped data processing with high throughput genetic sequencing data |
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10 Oct 19/21/23 Piped genetic data processing exercise due |
Allendorf et al. 2001. The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16: 613-622. |
Hybridization |
RFDS 19 Exercise: Creating functions to avoid repetition
(and error) |
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11 Oct 26/28/30 Coding functions exercise due |
Keller & Waller. 2002. Inbreeding effects in wild populations. Trends Ecol Evol 17: 230-241. Caro & Laurenson 1994. Ecological and genetic factors in conservation: a cautionary tale. Science 263:485-486. |
Inbreeding CWP CH 9 |
RFDS None |
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Connectivity: island biogeography,
isolation by resistance |
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12 Nov 2/4/6 Nov�
3: Vote. |
Simberloff & Wilson 1969. Experimental zoogeography of islands: the colonization of empty islands. Ecology 50, 278-296. |
Island Biogeography CWP CH 10 |
RFDS 21, 27 |
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13 Wed off, Nov 9/13 Paper due |
McRae, B. H. (2006). Isolation by resistance. Evolution 60, 1551-1561. Creel et al. 2019. Carnivores, competition and genetic connectivity in the Anthropocene. Scientific Reports 9, 16339 Mon/Fri |
Isolation by distance and by resistance Mon/Fri |
RFDS 28 (On your own) |
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Graduate student� presentations |
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14 Nov 16/18 |
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RFDS 29 (On your own) |