Refugia

General refugia analysis

Deliverable: Leverage existing data for physical climate-change exposure, environmental diversity (e.g., locations with a high diversity of landform types, topographic, soil, and/or local climatic conditions and subsequently a high potential for microrefugia), and climatic velocity to identify locations within Washington that have high refugia potential based on their physical characteristics filter strategies seek to conserve either key sites as determined by natural elements unaffected by climate change, or sites with low climate velocity that are expected to be refugia for climate-displaced species. Compare these physical refugia results with (1) species specific refugia modeling work from previous project and (2) Stralberg et al.’s (2018) tree and bird macrorefugia index to identify the level of agreement between the two efforts.

Data Deliverables

Individual data layers for [physical] refugia showing locations with high to low refugia potential.

Here 33 layers were used to incorporate the General Refugia. The layers represent continuous values, below is the table describing the 33 layers.

Table 1: Description of all the variables

Layer	Description
hli_cool_slopes_pnw	Heat Load Index - Cool Slopes, raw area of cool slopes per HUC in km2.
max_chg_40	Max projected change in stream flow per HUC comparing current and 2040s time periods.
min_cng_40	Min projected change in stream flow per HUC comparing current and 2040s time periods.
index_cng_40	Projected streamflow change index - calculated as the mean percent change in streamflow based on sum of stream segment lengths times flow changes divided by total stream length in a HUC
ergo_valleys_pnw	Theobald Ergo land forms Valley – is proportion of HUC
lc16evc_pnw	Mean forest canopy cover at the HUC12 level
Theobald_HM_270	Theobald Human Footprint
TNC_permeability	Permeability index
TNC_Topoclimate	TNC Topoclimatic diversity
topo7x7x1kmrao_LAEA	Mean topographic complexity, defined as regions with a large variability in elevation and aspect in close proximity, per HUC
prop345.index	Current Wildfire Hazard Index. Area of HUC classified as hazard level 3 (moderate), 4 (high), or 5 (very high) multiplied by 3, 4, , and 5 as weights repectively and divided by the total HUC area.
Davis_MidCent_PctChange	Projected % change in fire suitability for forested areas - mid-century time period
Davis_EndCent_PctChange	Projected % change in fire suitability for forested areas - end-of-century time period
prs.ref	Percent Replacement Severity (prs), raw value reference time period.
prs.55.cng	prs 2055 time period and change metric (2055 – reference)
fri.ref	Fire return interval
fri.55.cng	Fire return interval 2055 change
fri.2055	Fire return interval 2055 raw value
fri.2085	Fire return interval 2085 raw value
prs.2055	Percent Replacement Severity, raw value 2055s
prs.2085	Percent Replacement Severity, raw value 2085s
fri.85.cng	Fire return interval 2085 change
fri.55.perc.cng	Fire return interval 2055 % change
fri.85.perc.cng	Fire return interval 2085 % change
prs.85.cng	Percent Replacement Severity 2085 change
prs.55.perc.cng	Percent Replacement Severity 2055 % change
prs.85.perc.cng	Percent Replacement Severity 2085 % change
cssqkm	total area (Square km) of cool-facing slopes in the HUC
cs.prop	Proportion of huc classified as cool-facing slope
cs.val.prop	proportion of huc classified as cool-facing slope OR valley
medhist	Median Stream Temperature within a HUC. Historical.
med2040	Median Stream Temperature within a HUC. Projected 2040s
med2080	Median Stream Temperature within a HUC. Projected 2080s
change_in_snowpack	Median changes in snowpack as % of Snow Water Equivalent (SWE)
NonForest2Forest_2050	Mean non forest to forest conversion 2050
Resistance_and_Resilience	Median Resistance and Resilience
North_American_Climate_Refugia	North American Climate Refugia probability
drought_refugia_median	Median soil drought probability

Showing the list of the variables with summary statistics, note that areaacres and areasqkm are for information only.

Table 2: Summary statistics of all the layers

	id	mean	median	min	max	range	se
hli_cool_slopes_pnw	1	2688.49	2427.00	9.00	8151.00	8142.00	43.48
max_chg_40	2	-7.18	0.00	-53.87	10.43	64.30	0.31
min_cng_40	3	-30.68	-26.01	-81.67	1.52	83.19	0.56
index_cng_40	4	-20.21	-15.86	-71.29	3.89	75.17	0.42
ergo_valleys_pnw	5	0.13	0.13	0.01	0.74	0.72	0.00
lc16evc_pnw	6	39.05	43.18	0.00	75.52	75.51	0.57
Theobald_HM_270	7	0.18	0.12	0.00	0.89	0.89	0.00
TNC_permeability	8	0.61	0.66	0.01	1.00	0.99	0.01
TNC_Topoclimate	9	0.35	0.36	0.22	0.48	0.27	0.00
topo7x7x1kmrao_LAEA	10	179.33	167.93	6.18	585.55	579.37	3.28
prop345.index	11	0.31	0.19	0.00	0.99	0.99	0.01
Davis_MidCent_PctChange	12	45.15	42.13	0.00	126.42	126.42	0.53
Davis_EndCent_PctChange	13	99.55	95.50	0.00	263.21	263.21	1.38
prs.ref	14	54.84	47.83	10.04	98.00	87.96	0.66
prs.55.cng	15	3.42	2.48	-50.69	52.27	102.97	0.36
fri.ref	16	367.49	368.05	16.39	993.52	977.13	8.08
fri.55.cng	17	-28.88	-7.27	-482.70	365.41	848.10	2.62
fri.2055	18	338.61	356.71	23.30	964.54	941.24	7.19
fri.2085	19	292.44	272.08	24.95	932.41	907.46	6.19
prs.2055	20	58.26	57.70	14.15	97.15	83.00	0.66
prs.2085	21	59.00	60.31	11.05	98.00	86.95	0.63
fri.85.cng	22	-75.05	-40.75	-641.51	823.89	1465.40	4.20
fri.55.perc.cng	23	3.58	-5.29	-87.96	676.95	764.91	1.25
fri.85.perc.cng	24	5.69	-15.81	-90.88	1065.66	1156.54	2.85
prs.85.cng	25	4.16	3.48	-84.89	76.08	160.97	0.63
prs.55.perc.cng	26	10.92	4.22	-57.37	241.12	298.50	0.88
prs.85.perc.cng	27	22.36	6.32	-88.49	492.29	580.77	1.85
cssqkm	28	26.88	24.27	0.09	81.51	81.42	0.43
cs.prop	29	0.30	0.30	0.00	0.74	0.74	0.00
cs.val.prop	30	0.43	0.43	0.03	0.79	0.76	0.00
medhist	31	12.39	12.62	3.75	22.39	18.64	0.08
med2040	32	13.82	14.05	5.26	23.90	18.64	0.08
med2080	33	14.78	15.03	6.25	24.89	18.64	0.08
change_in_snowpack	34	-65.31	-99.00	-100.00	0.00	100.00	1.22
NonForest2Forest_2050	35	0.06	0.01	0.00	0.94	0.94	0.00
Resistance_and_Resilience	36	0.53	0.00	0.00	3.00	3.00	0.03
North_American_Climate_Refugia	37	0.12	0.00	0.00	1.00	1.00	0.01
drought_refugia_median	38	23.19	2.00	0.00	100.00	100.00	0.95

Plot the density distributions of all the layers

Figure 1: Density plot of all the layers in the general refugia

Create the layers for distribution

Sample forest cover layer that twill be exported

[1] "Writing refugia layer.hli_cool_slopes_pnw"
[1] "Writing refugia layer.max_chg_40"
[1] "Writing refugia layer.min_cng_40"
[1] "Writing refugia layer.index_cng_40"
[1] "Writing refugia layer.ergo_valleys_pnw"
[1] "Writing refugia layer.lc16evc_pnw"
[1] "Writing refugia layer.Theobald_HM_270"
[1] "Writing refugia layer.TNC_permeability"
[1] "Writing refugia layer.TNC_Topoclimate"
[1] "Writing refugia layer.topo7x7x1kmrao_LAEA"
[1] "Writing refugia layer.prop345.index"
[1] "Writing refugia layer.Davis_MidCent_PctChange"
[1] "Writing refugia layer.Davis_EndCent_PctChange"
[1] "Writing refugia layer.prs.ref"
[1] "Writing refugia layer.prs.55.cng"
[1] "Writing refugia layer.fri.ref"
[1] "Writing refugia layer.fri.55.cng"
[1] "Writing refugia layer.fri.2055"
[1] "Writing refugia layer.fri.2085"
[1] "Writing refugia layer.prs.2055"
[1] "Writing refugia layer.prs.2085"
[1] "Writing refugia layer.fri.85.cng"
[1] "Writing refugia layer.fri.55.perc.cng"
[1] "Writing refugia layer.fri.85.perc.cng"
[1] "Writing refugia layer.prs.85.cng"
[1] "Writing refugia layer.prs.55.perc.cng"
[1] "Writing refugia layer.prs.85.perc.cng"
[1] "Writing refugia layer.cssqkm"
[1] "Writing refugia layer.cs.prop"
[1] "Writing refugia layer.cs.val.prop"
[1] "Writing refugia layer.medhist"
[1] "Writing refugia layer.med2040"
[1] "Writing refugia layer.med2080"
[1] "Writing refugia layer.change_in_snowpack"
[1] "Writing refugia layer.NonForest2Forest_2050"
[1] "Writing refugia layer.Resistance_and_Resilience"
[1] "Writing refugia layer.North_American_Climate_Refugia"
[1] "Writing refugia layer.drought_refugia_median"

{r} # #| message: false # #| warning: false # #| echo: false # # # Load shapefile # wwf_shp <- st_read("./data/GIS/Combined/allhucsforestcover.shp", stringsAsFactors = F) # # # Rasterize biome field and write to disk # # sfvect <- terra::vect("./data/GIS/Combined/allhucsforestcover.shp") # r <- terra::rast(sfvect, ncols=750, nrows=750) # fp <- terra::rasterize(sfvect,r) # terra::writeRaster(fp, "./data/GIS/Combined/allhucsforestcover.tiff",overwrite=TRUE) # #

Analysis of the relative distribution of refugia potential based on different input data layers (i.e., which types of locations have high value for different data inputs, are they highly correlated? How do they differ? Which are duplicates versus complementary?)

Here we utilized individual layers, and overlaid to find HUCs find out the common ones

Figure 2: Correlation plot of all the layers in the general refugia

Alternative way to visualize the correlation

Figure 3: Stripped correlation plot of all the layers in the general refugia

Integrated refugia data layer(s) showing locations with high priority across multiple refugia metrics and approaches.

Three refugia maps -Aquatic, Sage and Forest with predefined list of layers

Aquatic Refugia Map -

Aquatic or Amphibia Includes the salamanders, frogs, toads, and caecilians.

Here we use the below layers

1. Historic median stream temperatures (medhist)

2. Median stream temperatures 2040s (med2040)

3. Median stream temperatures 2080s (med2080)

4. Cool Slopes Proportion (cs.prop)

5. Stream flow loss (index_cng_40)

6. Forest canopy (lc16evc_pnw)

Show the distribution of 7 variables

Figure 4: Density distribution of Aquatic input layers

Show the quartiles

Figure 5: Density distribution of Aquatic input layers with top 15%

Plot the Aquatic refugia map - criteria median stream temperature below 10 degrees Celsius, proportion of cool slopes at HUC level more than 40%, flow loss less than 30%, forest canopy more than 40%, and drought refugia less than 30%.

Figure 6: Aquatic refugia map

Sage Refugia Map -

Sage Includes the Sage Grouse …

Here we use the below layers

1. TNC Permeability (TNC_permeability)

2. Current Fire WHP (prop345_in)

3. NonForest-2-Forest Conversion 2055 (NonForest2Forest_2050)

4. Resistance and Resilience (Resistance_and_Resilience)

5. Drought refugia (drought_refugia_median)

Show the distribution of 6 variables

Figure 7: Density distribution of Sage input layers

Show the quartiles

Figure 8: Density distribution of Sage input layers with top 15%

Plot the Sage refugia map - TNC Permeability of 0.8 or higher, and Current Wildfire Hazard Index of 0.2 or lower

Figure 9: Sage refugia map

Forest Refugia Map -

Forest Includes the Fisher, White headed wood-pecker …

Here we use the below layers

1. Mean forest cover per HUC (%) (lc16evc_pnw)
2. TNC Permeability (TNC_permeability)
3. Current Fire WHP (prop345_in)
4. Proportion of HUC classified as cool slopes (cs.prop)
5. Drought refugia (drought_refugia_median)
6. Change in snowpack % SWE
7. North American Climate Refugia (North_American_Climate_Refugia)

Show the distribution of 6 variables

Figure 10: Density distribution of Forest input layers

Show the quartiles

Figure 11: Density distribution of Forest input layers with top 15%

Plot the Forest refugia map - TNC Permeability of 0.8 or higher, Current Wildfire Hazard Index of 0.8 or higher, proportion of cool slopes at HUC level more than 40%, forest canopy more than 40% and drought probability less than 40%.

Figure 12: Forest refugia map

Filtered refugia data by land cover/land use/land ownership – which locations have high refugia potential and high landscape integrity/good habitat potential otherwise?

• We will produce for e.g., % of refugia found in public, [private lands]
• % Of refugia that are in public or private lands

TODO - Add information on whhere the layers came from - Add total area

First using 25% threshold (atleast 25% of the HUC is protected)

At 25%, given the criteria above for the refugia’s, there are 363 HUCs that are in protected (public, state or conservancy) in WA. 8 HUCs that are in Aquatic refugia are protected, 0 HUCs that are in Sage refugia are protected, and 32 HUCs that are in Forest refugia are protected. Total HUCs that are protected are 11% of identified refugiaHUCs.

Using 50% threshold (atleast 50% of the HUC is protected)

At 50%, given the criteria above for the refugia’s, there are 271 HUCs that are in protected (public, state or conservancy) in WA. 8 HUCs that are in Aquatic refugia are protected, 0 HUCs that are in Sage refugia are protected, and 30 HUCs that are in Forest refugia are protected. Total HUCs that are protected are 14% of total protected HUCs.

Using 75% threshold (atleast 75% of the HUC is protected)

At 75%, given the criteria above for the refugia’s, there are 674 HUCs that are in protected (public, state or conservancy) in WA. 11 HUCs that are in Aquatic refugia are protected, 17 HUCs that are in Sage refugia are protected, and 6 HUCs that are in Forest refugia are protected. Total HUCs that are protected are 5% of the total protected HUCs.

Locations having high landscape integrity

Done by calculating average Theobald value per huc and generating a bar chart comparing refugia hucs to non-refugia hucs based on average Theoboald value. Do this for all three general refugia types. (will probably need to use only forest, sage, and aquatic hucs in the comparisons– if possible).

Figure 13: WA Landscape Integrity

Analysis of the number and types of species that could be potentially served by different refugia locations by overlaying locations with high refugia potential over current range distributions of priority species and habitats (either PHS or SGCN).

We will take the generalized layers of refugia and overlay habit maps of species given by WDFW Use the 100+ species , and map it to one of the three At the HUC level - # of species Species - How many HUCs (all three refugia) for a Species , make a table.

A total of 83 species are there

Number of HUCs that overlaps each type of Refugia and Species potential ranges

Table 3: Number of HUCs that overlaps each type of Refugia and Species potential ranges

Refugia	nohucs
Aquatic	161
Forest	825
Sage	326

Number of Species served by each Refugia

Table 4: Number of species served by each refugia

Refugia	NoOfSpecies
Aquatic	31
Forest	55
Sage	52

Number of HUCs for species that overlaps with obtained refugias (Aquatic, Sage and Forest)

Table 5: Number of HUCs for species that overlaps with obtained refugias

index	Common_Name	Scientific_Name	Aquatic	Sage	Forest
1	Spotted sandpiper	Actitis macularia	0	1	10
2	Clark's grebe	Aechmophorus clarkii	0	3	0
3	Western grebe	Aechmophorus occidentalis	0	5	0
4	Sagebrush Sparrow	Amphispiza nevadensis	0	6	1
5	Tiger salamander	Ambystoma tigrinum	0	9	1
6	Western toad	Anaxyrus boreas	9	7	47
7	Woodhouse's toad	Anaxyrus woodhousii	0	4	0
8	Golden eagle	Aquila chrysaetos	4	10	28
9	Rocky Mountain Tailed Frog	Ascaphus montanus	0	1	1
10	Burrowing owl	Athene cunicularia	0	11	1
11	Cascade red fox	Vulpes vulpes cascadensis	4	0	3
12	Side-blotched lizard	Uta stansburiana	0	4	0
13	Washington ground squirrel	Urocitellus washingtoni	0	5	0
14	Townsend's Ground Squirrel - nancyae	Urocitellus townsendii nancyae	0	2	0
15	Grizzly bear	Ursus arctos	6	0	16
16	Columbian Sharp-tailed Grouse	Tympanuchus phasianellus	0	7	0
17	Brush prairie pocket gopher-Northern	Thomomys talpoides douglasii	0	0	0
18	Mazama (Western) pocket gopher	Thomomys mazama	0	0	6
19	American Badger	Taxidea taxus	0	13	4
20	Northern Spotted Owl	Strix occidentalis	9	1	46
21	Great gray owl	Strix nebulosa	1	3	6
22	Valley silverspot	Speyeria zerene bremnerii	1	0	16
23	Pygmy nuthatch	Sitta pygmaea	3	9	4
24	Western bluebird	Sialia mexicana	3	0	20
25	Slender-billed white-breasted nuthatch	Sitta carolinensis aculeata	0	0	0
26	Western gray squirrel	Sciurus griseus	2	2	3
27	Sagebrush lizard	Sceloporus graciosus	0	10	2
28	Olympic torrent salamander	Rhyacotriton olympicus	0	0	19
29	Columbia torrent salamander	Rhyacotriton kezeri	0	0	0
30	Cascade torrent salamander	Rhyacotriton cascadae	2	0	5
31	Woodland caribou	Rangifer tarandus	0	0	0
32	Oregon spotted frog	Rana pretiosa	0	0	9
33	Northern leopard frog	Rana pipiens	0	1	0
34	Columbia spotted frog	Rana luteiventris	6	9	6
35	Purple martin	Progne subis	0	0	10
36	Mardon skipper	Polites mardon	0	0	0
37	Oregon vesper sparrow	Pooecetes gramineus affinis	0	0	4
38	Red-necked grebe	Podiceps grisegena	0	6	0
39	Van dyke's salamander	Plethodon vandykei	3	0	20
40	Larch mountain salamander	Plethodon larselli	3	0	6
41	Dunn's salamander	Plethodon dunni	0	0	0
42	White-headed woodpecker	Picoides albolarvatus	3	5	4
43	Pygmy Short-horned Lizard	Phrynosoma douglasii	0	10	1
44	American white pelican	Pelecanus erythrorhynchos	0	8	0
45	Western screech-owl	Otus kennicottii	8	0	42
46	Flammulated owl	Otus flammeolus	3	5	4
47	Sage thrasher	Oreoscoptes montanus	0	9	2
48	Columbian white-tailed deer	Odocoileus virginianus leucurus	0	0	0
49	American Pika	Ochotona princeps	9	2	27
50	Shaw Island Townsend's vole	Microtus townsendii pugeti	0	0	0
51	Kincaid meadow vole	Microtus pennsylvanicus kincaidi	0	6	0
52	Lewis' woodpecker	Melanerpes lewis	0	6	3
53	Striped whipsnake	Masticophis taeniatus	0	3	0
54	Fisher	Martes pennanti	9	2	46
55	Olympic marmot	Marmota olympus	0	0	18
56	Lynx	Lynx canadensis	5	4	11
57	White-tailed jackrabbit	Lepus townsendii	0	13	2
58	Black-tailed jackrabbit	Lepus californicus	0	12	2
59	Silver-haired bat	Lasionycteris noctivagans	9	13	47
60	Loggerhead shrike	Lanius ludovicianus	0	8	0
61	Hoary bat	Lasiurus cinereus	9	13	47
62	Desert Nightsnake	Hypsiglena chlorophaea	0	10	2
63	Bald eagle	Haliaeetus leucocephalus	4	12	42
64	Wolverine	Gulo gulo	9	4	22
65	Common loon	Gavia immer	3	0	13
66	Peregrine falcon	Falco peregrinus	9	12	47
67	Spotted bat	Euderma maculatum	1	5	1
68	Streaked horned lark	Eremophila alpestris strigata	0	0	0
69	Ring-necked Snake	Diadophis punctatus	0	1	0
70	Cope's giant salamander	Dicamptodon copei	2	0	18
71	Townsend's Big-eared Bat	Corynorhinus townsendii	9	13	47
72	Sharp-tailed Snake	Contia tenuis	0	1	1
73	Yellow-billed cuckoo	Coccyzus americanus	0	2	2
74	Greater Sage-grouse	Centrocercus urophasianus	0	4	0
75	Gray wolf	Canis lupus	4	4	7
76	Ferruginous hawk	Buteo regalis	0	9	1
77	Marbled murrelet	Brachyramphus marmoratus	9	0	43
78	Pygmy rabbit	Brachylagus idahoensis	0	1	0