This factor comes into play only in the case that all or a portion of the +range within the assessment area may be subject to the effects of a 0.5-1 m or +greater sea level rise and the consequent influence of storm surges and +intrusion of salt water. Most climate model scenarios predict at least a 0.5 m +sea level rise. Because projected sea level rise (0.5-2 m by 2100) is great +compared to historical sea level changes, the negative impact on habitats for +most affected species is expected to be high.
+ +Greatly Increase Vulnerability: >90% of range occurs in area +subject to sea level rise (on low-lying island(s) or in coastal zone).
+ +Increase Vulnerability: 50-90% of range occurs in area subject to sea +level rise (on low-lying island(s) or in coastal zone).
+ +Somewhat Increase Vulnerability: 10-49% of range occurs in area +subject to sea level rise (on low-lying island(s) or in coastal zone).
+ +Neutral: <10% of range occur in area subject to sea level rise (on +low-lying island(s) or in coastal zone). Includes inland areas not subject to +sea level rise. Also, species that occur in an intertidal habitat that is +expected to increase in extent with a rising sea level.
+ +Tools: For information about the sensitivity of the Canadian coast to +potential sea level rise, see CanCoast 2.0.
+ + +This factor assesses the degree to which natural (e.g., topographic, +geographic, ecological) or anthropogenic barriers limit a species' ability to +shift its range in response to climate change. Barriers are defined here as +features or areas that completely or almost completely prevent movement or +dispersal of the species (currently and for the foreseeable future). Species for +which barriers would inhibit distributional shifts with climate change-caused +shifts in climate envelopes likely are more vulnerable to climate change than +are species whose movements are not affected by barriers. Barriers must be +identified for each species (but often are the same for a group of closely +related species). Natural and anthropogenic barriers are defined for many +species and taxonomic groups in NatureServe's Element Occurrence Specifications +(viewable in the Population/Occurrence Delineation section of species accounts +on +Natureserve Explorer), but usually these readily can be determined by +considering a species' basic movement capacity and ecological tolerances.
+ +The distinction between a barrier and unsuitable habitat sometimes may be +unclear; in these cases assume the feature or area is unsuitable habitat +(habitat through which the species can disperse or move but that does not +support reproduction or long-term survival) and score the species here and/or in +factor C1 as appropriate. Note that caves are considered under factor C3: +Restriction to Uncommon Landscape/Geological Features, and not here where the +focus is on barriers that affect the wide array of nonsubterranean species.
+ +Note that no barriers exist for most temperate-zone bird species that simply +fly over or around potential obstructions. Species restricted to habitats that +are believed to persist unchanged in spite of climate change are scored as +Neutral (because in these situations barriers do not contribute to vulnerability +even if climate changes). If a feature or area does not completely or almost +completely prevent dispersal or movement then it is categorized here as +unsuitable or suitable habitat, and the dispersal/movement of individuals across +that feature or area is assessed under factor C1 (Dispersal and Movements). +In most cases, unsuitable habitat is habitat through which propagules or +individuals may move but that does not support reproduction or long-term +survival.
+ +The degree to which a barrier may affect a species' ability to shift its +range in response to climate change depends in part on the distance of the +barrier from the species' current distribution. Barriers that are separated from +a species' range by a long distance of relatively flat topography can +nevertheless affect range shifts because in gentle terrain relatively small +changes in climate can result in large shifts in the location of a particular +climate envelope. If a species changed its range accordingly (to track a +particular climate envelope), it might encounter barriers that were far from its +original range. In contrast, in landscapes in which climatic conditions change +rapidly over small horizontal distances (e.g., mountainous areas, steep slopes, +or other topographically diverse landscapes) a species' distribution would have +to shift a relatively small distance in order to track a particular climate +envelope, so the species is less likely to encounter distant barriers.
+ +To count as a barrier for the purposes of this factor, a feature can be up to +50 km from the species' current range when measured across areas where climate +changes gradually over latitude or longitude (e.g., relatively flat terrain) and +up to 10 km when measured across areas where climate changes abruptly over +latitude or longitude (e.g.mountainous or steep terrain). Use 25 km for species +that occur in intermediate topography, such as moderate hill country. These +distances apply to both terrestrial and aquatic species. These distances are +derived from Loarie et al.(2009, Nature 462:1052).
+ +The following categories and criteria apply to both natural and anthropogenic +barriers, but the two types of barriers are scored separately. Note that it is +illogical for natural and anthropogenic barriers to both cause greatly increased +vulnerability to climate change for a single species (only one or the other can +completely surround a species' range). If both barriers occur, estimate the +relative portions of the circumference of the range blocked by each and then +score accordingly.
+ + +Examples of features that may function as natural barriers for various +species: upland habitat (i.e., absence of aquatic stream, lake, or pond habitat) +is a barrier for fishes (but not for semiaquatic or amphibious species that may +occupy the same body of water); high mountain ranges (especially those that +extend west-east) are a barrier for many lowland plants and nonvolant lowland +animals; warm lowlands are a barrier for some alpine species such as American +pika but not for elk or American pipit; large expanses of water are barriers for +pocket gophers and many other small terrestrial animals (but not for many volant +species, or for plant species that are dispersed by wide-ranging birds, or for +species that readily swim between land areas if the distance is not too great); +a high waterfall is a barrier for fishes (but not for American dippers or garter +snakes that occur along the same stream).
+ +Greatly Increase Vulnerability: Barriers completely OR almost +completely surround the current distribution such that the species' range in the +assessment area is unlikely to be able to shift significantly with climate +change, or the direction of climate change-caused shift in the species' +favorable climate envelope is fairly well understood and barriers prevent a +range shift in that direction. See Neutral for species in habitats not +vulnerable to climate change.
+ +Increase Vulnerability : Barriers border the current distribution such +that climate change-caused distributional shifts in the assessment area are +likely to be greatly but not completely or almost completely impaired.
+ +Somewhat Increase Vulnerability: Barriers border the current +distribution such that climate change-caused distributional shifts in the +assessment area are likely to be significantly but not greatly or completely +impaired.
+ +Neutral: Significant barriers do not exist for this species, OR small +barriers exist in the assessment area but likely would not significantly impair +distributional shifts with climate change, OR substantial barriers exist but are +not likely to contribute significantly to a reduction or loss of the species' +habitat or area of occupancy with projected climate change in the assessment +area.
+ + +Examples of features that may function as anthropogenic barriers: large areas +of intensive urban or agricultural development are barriers for many animals +and plants; waters subject to chronic chemical pollution (e.g., acid mine +drainage) can be a barrier for fishes and other strictly aquatic species; +waters subject to thermal pollution (e.g., from power plants) may be a barrier +for some strictly aquatic species but not for others (note thermal alterations +associated with reservoirs often produce unsuitable habitat rather than impose +a barrier); dams without fish passage facilities and improperly installed +culverts can be barriers for fishes and certain other strictly aquatic species; +tortoise-proof fencing may be barrier for small reptiles and certain other +nonvolant animals (but not for most plants, large mammals, or large snakes).
+ +Greatly Increase Vulnerability: Barriers completely OR almost +completely surround the current distribution such that the species' range in the +assessment area is unlikely to be able to shift significantly with climate +change, or the direction of climate change-caused shift in the species' +favorable climate envelope is fairly well understood and barriers prevent a +range shift in that direction. See Neutral for species in habitats not +vulnerable to climate change.
+ +Increase Vulnerability: Barriers border the current distribution such +that climate change-caused distributional shifts in the assessment area are +likely to be greatly but not completely or almost completely impaired.
+ +Somewhat Increase Vulnerability: Barriers border the current +distribution such that climate change-caused distributional shifts in the +assessment area are likely to be significantly but not greatly or completely +impaired.
+ +Neutral: Significant barriers do not exist for this species, OR small +barriers exist in the assessment area but likely would not significantly impair +distributional shifts with climate change, OR substantial barriers exist but are +not likely to contribute significantly to a reduction or loss of the species' +habitat or area of occupancy with projected climate change in the assessment +area.
+ + +(e.g., plantations for carbon offsets, new seawalls in response to sea level +rise, and renewable energy projects such as wind-farms, solar arrays, or +biofuels production)
+ +Strategies designed to mitigate or adapt to climate change have the potential +to affect very large areas of land, and the species that depend on these areas, +in both positive and negative ways. This factor arguably should be considered in +conservation status assessments, but considering that for most species this +factor has not yet been considered in these assessments, we include it here. +If the land use changes for alternative energy projects have already been +considered in the conservation status assessment for the species, consider not +scoring this factor, especially if the vulnerability assessment results will be +used to revise status ranks.
+ +This factor is NOT intended to +include habitat loss or destruction due to on-going human activities, as these +should already be reflected in existing conservation status ranks. Include only +new activities related directly to climate change mitigation here. There is much +uncertainty about the types of mitigation action that are likely to threaten +habitats and species. Remember that multiple categories can be checked for each +factor to capture uncertainty. As federal and state climate change legislation +is enacted, some of the mitigation directions (and associated threats or +benefits to species) will become clearer.
+ +Increase Vulnerability: The natural history/requirements of the +species are known to be incompatible with mitigation-related land use changes +that are likely to very likely to occur within its current and/or potential +future range. This includes (but is not limited to) the following:
+ +Somewhat Increase Vulnerability: The natural history/requirements of +the species are known to be incompatible with mitigation-related land use +changes that may possibly occur within its current and/or potential future +range, including any of the above (under Increase).
+ +Neutral: The +species is unlikely to be significantly affected by mitigation-related land use +changes that may occur within its current and/or potential future range, +including any of the above; OR it is unlikely that any mitigation-related land +use changes will occur within the species' current and/or potential future +range; OR it may benefit from mitigation-related land use changes.
+ +Tools: For information and maps related to wind energy in Canada, see +Natural Resources Canada Wind Energy and +Environment +and Climate Change Canada's Wind Atlas.
+" + +# split by question numbers or letters + +datB <- data.frame(section = "B", + guide_text = sectionB %>% + str_split_1("(?=Note that these factors relate to +characteristics of the species only. Anthropogenic effects, such as on the +availability of dispersal corridors, should not be considered in this +section.
+ + +This factor pertains to known or predicted dispersal or movement capacities +and characteristics and ability to shift location in the absence of barriers as +conditions change over time as a result of climate change. Species in which +individuals exhibit substantial dispersal, readily move long distances as adults +or juveniles, or exhibit flexible movement patterns should be better able to +track shifting climate envelopes than are species in which dispersal and +movements are more limited or inflexible. This factor pertains specifically to +dispersal through unsuitable habitat, which, in most cases, is habitat through +which propagules or individuals may move but that does not support reproduction +or long-term survival. If all habitat is regarded as suitable (i.e., species can +reproduce and persist in every habitat in which it occurs), then dispersal +ability is assessed for suitable habitat. If appropriate, scoring of species +whose dispersal capacity is not known can be based on characteristics of closely +related species (or species of similar body size in the same major group) with +similar and relevant morphological features.
+ +Barriers, which are here defined as features or areas that completely or +almost completely block dispersal, are treated in factor B2. If a species +requires other species for propagule dispersal, please also complete factor C4d. +The following categorization for plants is loosely based on Vittoz and Engler +(2007 Botanica Helvetica 117:109-124).
+ +A small number of species are confined by barriers to areas that are +smaller than the species' potential dispersal distance (fishes in small +isolated springs or plants that only occur in vernal pools are classic +examples). Most if not all of the fish species that occur in the smallest +such habitat patches could disperse farther than the greatest extent of the +occupied patch if a larger extent of habitat were available to them. For +the purposes of this factor, the dispersal ability of these species is +scored as if the species occurred in a large patch of habitat (longer than +the dispersal distance), based on dispersal or movement patterns or +capabilities of closely related species (or species of similar body size in +the same major group of animals).
+ +Migratory species should be scored according to their ability to shift +their distribution within the assessment area during the period of +occupation or from one year to the next (whichever is larger).
+ +Species in which propagule dispersal is both synchronous among all members +of the population in the assessment area and infrequent (average of several +years between successful reproduction events) should be scored as one +category more vulnerable than the category that would otherwise apply. An +example is the monocarpic giant cane (Arundinaria gigantea), a bamboo +species that reproduces synchronously every 25-50 years and then dies.
+ +Greatly Increase Vulnerability: Species is characterized by severely +restricted dispersal or movement capability. Species is represented by +sessile organisms that almost never disperse more than 10 meters per +dispersal event.
+ +Increase Vulnerability: Species is characterized by highly restricted +dispersal or movement capability. Species rarely disperses through +unsuitable habitat more than about 10-100 meters per dispersal event; OR +dispersal beyond a very limited distance (or outside a small isolated patch +of suitable habitat) periodically or irregularly occurs but is dependent on +highly fortuitous or rare events; OR species has substantial movement +capability but exhibits a very high degree of site fidelity.
+ +Somewhat Increase Vulnerability: Species is characterized by limited +or moderate but not highly or severely restricted dispersal or movement +capability. A significant percentage (at least approximately 50%) of +propagules or individuals disperse approximately 100-1,000 meters per +dispersal event (rarely farther); OR species has substantial movement +capability but exhibits a moderate to high degree of site fidelity and has +very limited existing or potential habitat within the assessment area; OR +dispersal likely is consistent with one of the following examples.
+ +Neutral: Species is characterized by good to excellent dispersal or +movement capability. Species has propagules or dispersing individuals that +commonly move more than 1 kilometer from natal or source areas; OR species +tends to occupy all or most areas of suitable habitat, or readily or +predictably moves more than 1 kilometer to colonize newly available habitat +(e.g., recently restored areas, areas that become suitable as a result of +fire, insect infestations, or other environmental changes, etc.); OR +dispersal capability likely is consistent with one of the following +examples. Note that species in the Neutral category are not necessarily +'early successional' or 'r-selected' species but also may include +certain 'late successional' or equilibrium ('K-selected') species that +have excellent innate or vector-aided dispersal capability.
+ +Tools: Seed biological trait data for some species can be found at +Royal Botanic +Gardens Kew Data Portal.
+ + +This factor pertains to the breadth of temperature and precipitation +conditions, at both broad and local scales, within which a species is known +to be capable of reproducing, feeding, growing, or otherwise existing. +Species with narrow environmental tolerances/requirements may be more +vulnerable to habitat loss from climate change than are species that thrive +under diverse conditions.
+ + +This factor measures large-scale temperature variation that a +species has experienced in recent historical times (i.e., the past 50 +years), as approximated by mean seasonal temperature variation (difference +between highest mean monthly maximum temperature and lowest mean monthly +minimum temperature) for occupied cells within the assessment area. It is a +proxy for species' temperature tolerance at a broad scale. This factor may +be evaluated by comparing the species range with the Annual Temperature +Variation map (see Figure 5 in the Canadian NatureServe CCVI Guidelines) or calculate using +GIS data downloaded from NatureServe. For +aquatic species, follow the same procedure as for terrestrial species, since +this factor measures broad regional patterns.
+ +Use the annual map for both resident and migratory species. Although +migratory species are not physically present to experience temperature +variations, they nonetheless are affected by these variations through +effects on food supply and habitat availability.
+ +Greatly Increase Vulnerability: Considering the mean seasonal +temperature variation for occupied cells, the species has experienced very small +(< 37° F/20.8° C) temperature variation in the past 50 years. +Includes cave obligates and species occurring in thermally stable groundwater +habitats.
+ +Increase Vulnerability: Considering the mean seasonal temperature +variation for occupied cells, the species has experienced small (37 - 47° +F/20.8 - 26.3° C) temperature variation in the past 50 years. Includes +facultative cave invertebrates.
+ +Somewhat Increase Vulnerability: Considering the mean seasonal +temperature variation for occupied cells, the species has experienced slightly +lower than average (47.1 - 57° F/26.3 - 31.8° C) temperature variation +in the past 50 years.
+ +Neutral: Considering the mean seasonal temperature variation for +occupied cells, the species has experienced average or greater than average +(>57.1° F/43.0° C) temperature variation in the past 50 years.
+ + +Current projections indicate that climate warming will be nearly +pervasive in North America over the next several decades. Species +associated with cool or cold conditions likely will experience a reduction +in habitat extent or quality and may experience declines in distribution or +abundance within a given assessment area. This factor assesses the degree +to which a species is restricted to relatively cool or cold above-ground +terrestrial or aquatic environments that are thought to be vulnerable to +loss or significant reduction as a result of climate change. Species that +depend on these cool/cold environments include (but may not be limited to) +those that occur in the assessment area's highest elevational zones, +northernmost areas, or the coldest waters. The restriction to these +relatively cool environments may be permanent or seasonal.
+ +Species that occur in frost pockets, on north-facing slopes, in shady +ravines, in alpine areas, or similar cool sites are scored here if those +areas represent or are among the coldest environments in the assessment +area; lacking this stipulation, species occurring in such sites may not be +vulnerable to climate change because favorable sites may simply shift in +location without reduction or loss. Species that are associated +specifically with snow or ice are assessed separately in factor C2d. Note +that temperature conditions and hydrological regimes often covary and often +are not neatly separable; these situations should be scored here if +temperature per se appears to be the overriding factor; otherwise they +should be scored under factor C2bii: Physiological Hydrological Niche.
+ +Greatly Increase Vulnerability: Species is completely or almost +completely (> 90% of occurrences or range) restricted to relatively cool or +cold environments that may be lost or reduced in the assessment area as a result +of climate change.
+ +Increase Vulnerability: Species is moderately (50-90% of occurrences +or range) restricted to relatively cool or cold environments that may be lost +or reduced in the assessment area as a result of climate change.
+ +Somewhat Increase Vulnerability: Species is somewhat (10-50% of +occurrences or range) restricted to relatively cool or cold environments that +may be lost or reduced in the assessment area as a result of climate change.
+ +Neutral: Species distribution is not significantly affected by thermal +characteristics of the environment in the assessment area, species occupies +habitats that are thought to be not vulnerable to projected climate change, or +species shows a preference for environments at the warmer end of the spectrum. +
+ + +This factor measures large-scale precipitation variation that a +species has experienced in recent historical times (i.e., the past 50 +years), as approximated by mean annual precipitation variation across +occupied cells within the assessment area. Overlay the species' range on +the mean annual precipitation map (see Figure 6 in the Canadian NatureServe CCVI Guidelines). Subtract the +lowest pixel value from the highest value to assess this factor. Use the +extreme pixel values for this calculation. Use annual data for migratory +species, as this measure reflects the precipitation regime of the ecosystem +as a whole.
+ +Greatly Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced very small +(< 4 inches/100 mm) precipitation variation in the past 50 years.
+ +Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced small (4 - 10 +inches/100 - 254 mm) precipitation variation in the past 50 years.
+ +Somewhat Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced slightly +lower than average (11 - 20 inches/255 - 508 mm) precipitation variation in +the past 50 years.
+ +Neutral: Considering the range of mean annual precipitation across +occupied cells, the species has experienced average or greater than average +>20 inches/508 mm) precipitation variation in the past 50 years.
+ + +This factor pertains to a species' dependence on a narrowly defined +precipitation/hydrologic regime, including strongly seasonal precipitation +patterns and/or specific aquatic/wetland habitats (e.g., certain springs, +vernal pools, seeps, seasonal standing or flowing water) or localized +moisture conditions that may be highly vulnerable to loss or reduction with +climate change. Dependence may be permanent or seasonal, and for migratory +species may include staging areas, migration stops, and wintering areas +outside the assessment area. Aquatic cave obligate species are considered +here according to their hydrological needs and habitat vulnerability. +Species nesting on islands in lakes, reservoirs, and/or wetlands that +prevent predator access can be scored here to the extent that a changed +hydrological regime may influence the availability of these predator-free +breeding sites (for example, birds nesting on islands to avoid predation by +mammals). If a species is dependent on aquatic/wetland habitats that are +actively managed to maintain a particular hydrology, consider whether this +management would be sufficient to ameliorate projected climate change +impacts (and, if so, score as Neutral).
+ +For plant species, the advantage of the C4 photosynthetic pathway for water +use efficiency will likely enable C4 plants to be less vulnerable to +decline under drying conditions than C3 plants (Taylor et al. 2010, New +Phytologist 185:780). The predicted vulnerability of these plants with +respect to this factor has been adjusted accordingly.
+ +For nonmigratory species, 'range' refers to the range within the assessment +area. For migratory species, 'range' encompasses the assessment area and +additional areas (e.g., migration stops, staging areas, wintering areas) +that are used to a significant extent by the populations being assessed. +For example, a migratory bird species for which 95% of the significant +migration stops are in shallow inland/interior wetlands should be assigned +to the Greatly Increase Vulnerability category, even if the species is not +dependent on such habitats within the assessment area.
+ +Note that temperature conditions and hydrological regimes often covary and +often are not neatly separable. These situations should be scored under +factor C2aii (Physiological Thermal Niche) if temperature per se appears to +be the overriding factor; otherwise they should be scored here.
+ +Greatly Increase Vulnerability: Completely or almost completely +(>90% of occurrences or range) dependent on a specific aquatic/wetland +habitat or localized moisture regime that is likely to be highly vulnerable to +loss or reduction with climate change.
+ +Increase Vulnerability: Moderately (50-90% of occurrences or range) +dependent on a strongly seasonal hydrologic regime and/or a specific +aquatic/wetland habitat or localized moisture regime that is likely to be +highly vulnerable to loss or reduction with climate change.
+ +Somewhat Increase Vulnerability: Somewhat (10-50%) dependent on a +strongly seasonal hydrologic regime and/or a specific aquatic/wetland habitat or +localized moisture regime that is highly vulnerable to loss or reduction +with climate change.
+ +Neutral: Species has little or no dependence on a strongly seasonal +hydrologic regime and/or a specific aquatic/wetland habitat or localized +moisture regime that is highly vulnerable to loss or reduction with climate +change; OR hydrological requirements are not likely to be significantly +disrupted in major portion of the range; OR species tolerates a very wide +range of moisture conditions.
+ + +This factor pertains to a species' response to specific disturbance +regimes such as fires, floods, severe winds, pathogen outbreaks, or similar +events. It includes disturbances that impact species directly as well as +those that impact species via abiotic aspects of habitat quality. For +example, changes in flood and fire frequency/intensity may cause changes in +water turbidity, silt levels, and chemistry, thus impacting aquatic species +sensitive to these aspects of water quality. The potential impacts of +altered disturbance regimes on species that require specific river features +created by peak flows should also be considered here; for example, some +fish require floodplain wetlands for larval/juvenile development or high +peak flows to renew suitable spawning habitat. Use care when estimating the +most likely effects of increased fires; in many ecosystems, while a small +increase in fire frequency might be beneficial, a greatly increased fire +frequency could result in complete habitat destruction.
+ +Be sure to also consider species that benefit from a lack of disturbance +and may suffer due to disturbance increases when scoring this factor.
+ +Increase Vulnerability: Strongly affected by specific disturbance +regime, and climate change is likely to change the frequency, severity, or +extent of that disturbance regime in a way that reduces the species' +distribution, abundance, or habitat quality. For example, many +sagebrush-associated species in regions predicted to experience increased fire +frequency/intensity would be scored here due to the anticipated deleterious +effects of increased fire on their habitat.
+ +Somewhat Increase Vulnerability: Moderately affected by specific +disturbance regime, and climate change is likely to change the frequency, +severity, or extent of that disturbance regime in a way that reduces the +species' distribution, abundance, or habitat quality, OR strongly affected +by specific disturbance regime, and climate change is likely to change that +regime in a way that causes minor disruption to the species' distribution, +abundance, or habitat quality. For example, plants in a riverscour +community that are strongly tied to natural erosion and deposition flood +cycles, which may shift position within the channel rather than disappear +as a result of climate change.
+ +Neutral: Little or no response to a specific disturbance regime, OR +climate change is unlikely to change the frequency, severity, or extent of that +disturbance regime in a way that affects the range or abundance of the +species, OR climate change is likely to change the characteristics of the +disturbance regime in a way that increases the species' distribution.
+ +Tools: For information on fire effects, see the USDA Fire Effects +Information System. For a map of modeled future fire regime, see Figure 2 in + +Krawchuck et al. (2009).
+ + +This factor pertains to a species' dependence on habitats associated +with ice (e.g., sea ice, glaciers) or snow (e.g., long-lasting snow beds, +avalanche chutes) throughout the year or seasonally during an essential +period of the life cycle. For aquatic species, the importance of snowpack +for maintaining downstream water temperatures should be considered here. +'Range' refers to the range within the assessment area.
+ +Greatly Increase Vulnerability: Highly dependent (>80% of +subpopulations or range) on ice- or snow-associated habitats; or found almost +exclusively on or near ice or snow during at least one stage of the life cycle. +For example, polar bear (Ursus maritimus) is strongly dependent on sea ice +throughout its range.
+ +Increase Vulnerability: Moderately dependent (50-80% of subpopulations +or range) on ice- or snow-associated habitats; or often found most abundantly +on or near ice or snow but also regularly occurs away from such areas. For +example, Kittlitz's murrelet (Brachyramphus brevirostris) feeding habitat +is moderately to strongly associated with tidewater glaciers.
+ +Somewhat Increase Vulnerability: Somewhat (10-49% of subpopulations or +range) dependent on ice- or snow-associated habitats, or may respond +positively to snow or ice but is not dependent on it. For example, certain +alpine plants are often associated with long-lasting snowbeds but also +commonly occur away from such areas; certain small mammals experience +increased survival and may develop relatively large populations under +winter snow cover but do not depend on snow cover. Species that benefit +from a minimum thickness of ice or snowpack for winter insulation should +also be scored here.
+ +Neutral: Little dependence on ice- or snow-associated habitats (may be +highly dependent in up to 10% of the range).
+ + +This factor pertains to a species' need for a particular +soil/substrate, geology, water chemistry, or specific physical or landscape +feature (e.g., caves, cliffs, active sand dunes, islands) for reproduction, +feeding, growth, shelter, or other aspects of the life cycle. It focuses on +the commonness of suitable conditions for the species on the landscape, as +indicated by the commonness of the features themselves combined with the +degree of the species' restriction to them. Climate envelopes may shift +away from the locations of fixed (within at least a 50 year timeframe) +landscape or geological features or their derivatives, making species tied +to these uncommon features potentially more vulnerable to habitat loss from +climate change than are species that thrive under diverse conditions.
+ +This factor does NOT include habitat preferences based on temperature, +hydrology, or disturbance regime, as these are covered elsewhere in the +Index. For example, species dependent on springs or ephemeral pools should +not be scored as more vulnerable for this factor solely on that basis +(addressed under factor C2bii: Physiological Hydrological Niche). However, +restriction to aquatic features with regionally uncommon water chemistry +should be considered here. This factor also does NOT include habitat +features such as stream riffles or basking rocks. Finally, this factor does +NOT include biotic habitat components; for example, species that require +features such as tree snags or a particular type/condition of plant +community (e.g., old growth forest) should not be scored as more vulnerable +for this factor.
+ +If the idea of specificity to soil/substrate, geology, or specific physical +or landscape features is not relevant to the species (e.g., many birds and +mammals), choose Neutral.
+ +Increase Vulnerability: Highly dependent upon (i.e., more or less +endemic to, or > 85% of occurrences found on) a particular highly uncommon +landscape or geological feature or derivative (e.g., soil, water chemistry).
+ +Somewhat Increase Vulnerability: Moderately dependent upon a +particular uncommon landscape or geological feature or derivative, i.e., (1) an +indicator of but not an endemic to (65-85% of occurrences found on) the +types of features described under Increase, OR (2) more or less restricted +to a landscape or geological feature or derivative that is not highly +uncommon within the species' range, but is not one of the dominant types.
+ +Neutral: Having a clear preference for (> 85% of occurrences found +on) a particular landscape or geological feature or derivative, but the +feature/derivative is among the dominant types within the species' range; +OR somewhat flexible in dependence upon geological features or derivatives +(i.e., found on a subset of the dominant substrate/water chemistry types +within its range); OR highly generalized relative to dependence upon +geological features or derivatives; species is described as a generalist +and/or occurrences have been documented on widely varied substrates or +water chemistries.
+ + +The primary impact of climate change on many species may occur via +effects on synchrony with other species on which they depend (Parmesan +2006, ARES 37:637), rather than through direct physiological stress.
+ + +This factor pertains to a species' dependence on uncommon/restricted +habitats that are generated or maintained by other species. Species that +are dependent on a small number of other species likely are more vulnerable +to climate change than are species that have more flexibility or that do +not have specialized habitat requirements.
+ +Habitat refers to any habitat (e.g., for reproduction, feeding, +hibernation, seedling establishment) necessary for completion of the life +cycle, including those used only on a seasonal basis. This includes +specific (often structural) features within a more generalized habitat type +(e.g., burrows created by other species in a grassland habitat; +woodpecker-created cavities in a forest habitat). These habitats must be +required for completion of the life cycle (e.g., reproduction, feeding, +hibernation, seedling establishment, etc.) and may include habitats used +only on a seasonal basis. For plants, species-specific relationships +involved in creating specific habitat conditions necessary for seedling +establishment should be considered here; nutritional relationships +necessary for seedling establishment (e.g., parasitic or obligately +myco-heterotrophic plants) should be considered under C4g. The relationship +between freshwater mussels and their larval hosts should be scored only +under factor C4d (Dependence on other species for propagule dispersal).
+ +This factor is concerned specifically with habitats generated or maintained +by particular species and does NOT include ecological dependencies based +primarily on disturbance regime, geological features, or diet, as these are +covered elsewhere in the Index. Required habitats involving +temperature/hydrological conditions that are generated by a small number of +particular species are included in this factor, but +temperature/hydrology-related habitats that are not primarily species +dependent are considered under C2aii and C2bii (thermal and hydrological +niches); if in doubt, score under C2aii or C2bii.
+ +Increase Vulnerability: Required habitat is generated primarily by one +species.
+ +Somewhat Increase Vulnerability: Required habitat is generated by only +a few species.
+ +Neutral: Required habitat is generated by more than a few species; or +species does not require any uncommon/restricted habitats; or habitat +requirements do not involve species-specific processes.
+ + +This factor pertains to the diversity of food types consumed by +animal species. Dietary specialists are more likely to be negatively +affected by climate change than are species that readily switch among +different food types.
+ +Note that the relationship between freshwater mussels and their larval +hosts should be scored only under factor C5d (Dependence on other species +for propagule dispersal).
+ +Increase Vulnerability: Completely or almost completely (>90%) +dependent on one species during any part of the year; equivalent +alternatives to this single-species food resource are not readily +available.
+ +Somewhat Increase Vulnerability: 'Completely or almost completely +(>90%) dependent during any part of the year on (1) a few species from a +restricted taxonomic group or (2) a narrow guild the members of which are +thought to respond similarly to climate change.
+ +Neutral: 'Diet flexible; during any season species readily switches +among multiple food resources according to availability; not strongly dependent +on one or a few species; omnivorous, with diet including numerous species +of both plants and animals.
+ + +Quantitative thresholds loosely follow data in Waser et al. (1996, +Ecology 77:1043). If appropriate, scoring of species whose pollinators is +not known can be based on characteristics of closely related species that +have similar and relevant morphological floral features that may have +similar pollination syndromes (Willmer 2011, Pollination and Floral +Ecology, Princeton Press).
+ +In some cases, sympatric, sequentially flowering species may enhance +reproductive success for each other through maintenance of pollinator +populations. Species that are documented to benefit from such interactions +with one or only a few sympatric species should be scored one category +higher (Hegland et al. 2009, Ecology Letters 12:184).
+ +Increase Vulnerability: Completely or almost completely dependent on +one species for pollination (> 90% of effective pollination accomplished by +1 species) or, if no observations exist, morphology suggests very significant +limitation of potential pollinators (e.g., very long corolla tube).
+ +Somewhat Increase Vulnerability: Completely or almost completely +dependent on 2-4 species for pollination (> 90% of effective pollination +accomplished by 2-4 species) or, if no observations exist, morphology +suggests conformation to a specific 'pollination syndrome' (e.g., +van der Pijl, 1961).
+ +Neutral: Pollination apparently flexible; five or more species make +significant contributions to pollination or, if no observations exist, +morphology does not suggest pollinator limitation or pollination syndrome. +Score wind-pollinated species as Neutral.
+ +Tools: The Inouye Pollinator Reference Database is a source for +literature references to pollination. A table describing traits of pollinator +syndromes can be found at USDA Pollinator Syndromes.
+ +Can be applied to plants or animals. Examples: Different species of +freshwater mussels can be dispersed by one to many fish species; fruit +dispersal by animals.
+ +Increase Vulnerability: Completely or almost completely (roughly > +90%) dependent on a single species for propagule dispersal.For example, +whitebark pine would fit here because Clark's nutcracker is the primary +dispersal agent.
+ +Somewhat Increase Vulnerability: Completely or almost completely +(roughly > 90%) dependent on a small number of species for propagule +dispersal. For example, a freshwater mussel for which only a few species of fish +can disperse larvae.
+ +Neutral: Disperses on its own (most animals, wind-dispersed plants) OR +propagules can be dispersed by more than a few species (many plants).
+ + +This factor refers to pathogens and natural enemies (e.g., +predators, parasitoids, or herbivores) that can increase or become more +pathogenic due to climate change, or vectors of disease when they expand +their distributions due to changes in climate and therefore become more +harmful or influence a greater portion of the distribution of the species +being evaluated. Examples include the chytrid fungal pathogen that can +become more harmful to frogs because of climate change (Pounds et al. 2006 +Nature 439:161) or sudden oak death in California caused by a pathogen that +is invasive under favorable climate conditions (Meentenmeyer et al. 2011 +Ecosphere 2:1).
+ +Increase Vulnerability: Species is negatively affected to a high +degree by a pathogen or natural enemy that is likely to increase in +distribution, abundance, or impact as a result of climate change. Example: The +cold-sensitive non-native hemlock woolly adelgid commonly causes a high +level of mortality in eastern hemlock, and the distribution/abundance/impact of +the adelgid may increase in areas where winter temperatures become milder.
+ +Somewhat Increase Vulnerability: Species is negatively affected to a +moderate degree by a pathogen or natural enemy that is likely to increase +in distribution, abundance, or impact as a result of climate change.
+ +Neutral: There is no indication that the species is currently or in +the foreseeable future likely to be significantly affected by a pathogen or +natural enemy that is likely to increase in distribution, abundance, or +impact as a result of climate change; OR the negative impact of pathogens +or natural enemies is likely to decrease with climate change. Example: A +warmer/drier climate may reduce the negative impact of certain fungal +pathogens that depend/thrive on relatively cold/moist conditions.
+ + +Species may suffer when competitors are favored by both changing +climates and the effects these climates have on disturbance regimes +(Abatzoglou and Kolden 2011 Rangeland Ecology & Management 64:471, +Dukes et al. 2011 Ecological Applications 21:1887, Pintó-Marijuan and +Munné-Bosch 2013, Grossman and Rice 2014 Ecology Letters 17:710). However, +in some cases climate change will decrease the spread of particular +invasive species (Bradley et al. 2010 Trends in Ecology & Evolution +25:310). To score this factor, some indication is needed that a potential +competitor is favored by projected future climates.
+ +Increase Vulnerability: Strongly affected by a native or non-native +competing species that is likely to be favored by climate change.
+ +Somewhat Increase Vulnerability: Moderately affected to a moderate +degree by a native or non-native competing species that is likely to be favored +by climate change.
+ +Neutral: Little or no response to a native or non-native species that +is likely to shift its distribution or abundance due to climate change OR +climate change is likely to decrease or have no effect on the spread or +abundance of a native or non-native species that negatively impacts the +species.
+ + +Can be applied to plants or animals. Here an interspecific +interaction can include mutualism, parasitism, or commensalism. Refers to +interactions unrelated to habitat, seedling establishment, diet, +pollination, or propagule dispersal. For example, an acacia bush requiring +an ant colony for protection against herbivores.
+ +Increase Vulnerability: Requires an interaction with a single other +species for persistence.
+ +Somewhat Increase Vulnerability: Requires an interaction with a one +member of a small group of taxonomically related species for persistence. Could +also include cases where specificity is not known for certain, but is +suspected. Many Orchidaceae will be in this category because of their +requirement for a specific fungal partner for germination (Tupac Otero and +Flanagan 2006, TREE 21: 64-65).
+ +Neutral: Does not require an interspecific interaction or, if it does, +many potential candidates for partners are available.
+ + +Species with less standing genetic variation will be less able to +adapt because the appearance of beneficial mutations is not expected to +keep pace with the rate of 21st century climate change. Throughout this +question, 'genetic variation' may refer neutral marker variation, +quantitative genetic variation, or both. To answer the question, genetic +variation should have been assessed over a substantial proportion of a +species' range.
+ +Because measures of genetic variability vary across taxonomic groups, there +cannot be specific threshold numbers to distinguish among the categories. +The assessor should interpret genetic variation in a species relative to +that measured in related species to determine if it is low, high, or in +between.
+ +Increase Vulnerability: Genetic variation reported as 'very low' +compared to findings using similar techniques on related taxa, i.e., lack of +genetic variation has been identified as a conservation issue for the species. +
+ +Somewhat Increase Vulnerability: Genetic variation reported as 'low' +compared to findings using similar techniques on related taxa.
+ +Neutral: Genetic variation reported as 'average' or 'high' compared to +findings using similar techniques on related taxa.
+ + +In the absence of rangewide genetic variation information (C5a), +this factor can be used to infer whether reductions in species-level +genetic variation that would potentially impede its adaptation to climate +change may have occurred. Only species that suffered population reductions +and then subsequently rebounded qualify for the Somewhat Increase or +Increase Vulnerability categories.
+ +Increase Vulnerability: Evidence that total population was reduced to +≤ 250 mature individuals, to one occurrence, and/or that occupied area was +reduced by >70% at some point in the past 500 years.
+ +Somewhat Increase Vulnerability: Evidence that total population was +reduced to 251-1000 mature individuals, to less than 10 occurrences, and/or that +occupied area was reduced by 30-70% at some point in the past 500 years.
+ +Neutral: No evidence that total population was reduced to ≤ 1000 +mature individuals and/or that occupied area was reduced by > 30% at some +point in the past 500 years.
+ + +In plants, genetic variation is strongly linked to reproductive +mode. Therefore, in the absence of measured genetic variation and knowledge +of recent genetic bottlenecks, a plant's reproductive system may serve as a +proxy for a species' genetic variation or capacity to adapt to novel +climatic conditions. For example, species that can outcross may be better +able to adapt to novel environments (Morran et al. 2009, Morran et al. +2011). Species with mixed mating systems, which make up 42% of the world's +flora, appear to favor selfing as a buffering mechanism to climate change +(Jones et al. 2013).
+ +Increase Vulnerability: Genetic variation of the species is assumed to +be 'very low' in the assessment area because the species is restricted to +asexual reproduction (vegetatively or apomicticly). These species are +expected to be negatively impacted because rapid climate change can +strongly impact genetic variation, ultimately reducing fitness (Jump and +Penuelas 2005).
+ +Somewhat Increase Vulnerability: Genetic variation assumed to be 'low' +in the assessment area due to known disruptions or barriers to gene flow among +subpopulations, range disjunctions, or documented outbreeding depression +(Franks et al. 2014). Reproductive system may be either mixed or obligate +outcrossing.
+ +Neutral: Genetic variation is assumed to be 'average' in the +assessment area based on reproductive system. Includes species that have either +mixed mating systems or are obligate outcrossers AND there are no known major +disruptions to gene flow.
+ + +Recent research suggests that some phylogenetic groups are declining +due to lack of response to changing annual temperature dynamics (e.g., +earlier onset of spring, longer growing season), including European bird +species that have not advanced their migration times (Moller et al. 2008), +and some temperate zone plants that are not moving their flowering times +(Willis et al. 2008) to correspond to earlier spring onset. This may be +assessed using either published multi-species studies such as those cited +above or large databases such as that of the U.S. National Phenology +Network.
+ +Increase Vulnerability: Seasonal temperature or precipitation dynamics +within the species' range show detectable change, but phenological +variables measured for the species show no detectable change.
+ +Somewhat Increase Vulnerability: Seasonal temperature or precipitation +dynamics within the species' range show detectable change, and phenological +variables measured for the species show some detectable change, but the +change is significantly less than that of other species in similar habitats +or taxonomic groups.
+ +Neutral: Seasonal temperature or precipitation dynamics within the +species' range show detectable change, and phenological variables measured for +the species show detectable change which is average compared to other species +in similar habitats or taxonomic groups; OR seasonal dynamics within the +species' range show no detectable change.
+ +Tools: Some phenological information can be gleaned from papers listed +in the Inouye +Pollinator Reference Database
+" + +# split by question numbers or letters + +datC <- data.frame(section = "C", + guide_text = sectionC %>% + str_split_1("(?=This factor pertains to the degree to which a species is known to +have responded to recent climate change based on published accounts in the +peer-reviewed literature. Time frame for the reduction or increase is 10 +years or three generations, whichever is longer. Some examples include +population declines due to phenology mismatches between species and +critical food or pollinator resources, e.g., great tits (Parus major) or +pied flycatchers (Ficedula hypoleuca) with winter moth (Operophtera +brumata) caterpillars, or honey-buzzards (Pernis apivorus) with wasps.
+ +Note that not all responses to climate change necessarily indicate +vulnerability. Species that respond to climate change by shifting (but not +contracting) their range, for example, show adaptability to climate change +and should be scored as Neutral for this factor. Similarly, species that +respond by changing their phenology (without a related decline in +population) should also be scored as Neutral.
+ +Greatly Increase Vulnerability: Distribution or abundance undergoing +major reduction (>70% over 10 years or three generations) believed to be +associated with climate change.
+ +Increase Vulnerability: Distribution or abundance undergoing moderate +reduction (30-70% over 10 years or three generations) believed to be +associated with climate change.
+ +Somewhat Increase Vulnerability: Distribution or abundance undergoing +small but measureable (10-30% over 10 years or three generations) believed to be +associated with climate change.
+ +Neutral: Distribution and abundance not known to be decreasing with +climate change. Includes species undergoing range shifts without loss of +distributional area or species undergoing changes in phenology but no net +loss in range size or population size. Includes species in which climate +change is documented to be causing an increase in range size or abundance.
+ + +This factor can include both distribution models and population +models. Models should be developed based on reasonably accurate locality +data (error < 5km) using algorithms that are supported by peer-reviewed +literature. Areas of obvious overprediction should be removed from current +and predicted future distributions. Projections should be based on 'middle +of the road' climate scenarios for the year 2050. Range size should be +based on 'extent of occurrence' sensu IUCN Red List. Population models +should be based on known processes as described in peer-reviewed +literature. Examples include (a) phenological changes that are likely to +result in a mismatch with critical dietary, pollination, or habitat +resources (Visser and Both 2005) or (b) documented narrow temperature +tolerances and thermal safely levels, particularly in insects (Deutsch et +al. 2008, Calosi et al. 2008).
+ +If necessary, check multiple boxes to reflect variation in model output.
+ +Greatly Increase Vulnerability: Predicted future range disappears +entirely from the assessment area OR predicted future abundance declines to zero +as a result of climate change processes.
+ +Increase Vulnerability: Predicted future range represents 50-99% +decrease relative to current range within the assessment area OR predicted +future abundance represents 50-99% decrease associated with climate change +processes.
+ +Somewhat Increase Vulnerability: Predicted future range represents a +20-50% decrease relative to current range within the assessment area OR +predicted future abundance represents 20-50% decrease associated with climate +change processes.
+ +Neutral: Predicted future range represents an increase, no change, or +a decrease of less than a 20% relative to current range within the assessment +area OR predicted future abundance increases, remains stable, or decreases +< 20% as a result of climate change processes.
+ + +Distribution models of current and projected future ranges should +meet standards described in the notes for D2. Overlap is calculated as the +percent of the current range represented by an intersection of the +predicted future and current ranges. If the range disappears or declines +> 70% within the assessment area, such that factor D2 is coded as +Greatly Increase Vulnerability, this factor should be skipped to avoid +double-counting model results.
+ +Greatly Increase Vulnerability: There is no overlap between the +current and predicted future range within the assessment area.
+ +Increase Vulnerability: Predicted future range overlaps the current +range by 30% or less within the assessment area.
+ +Somewhat Increase Vulnerability: Predicted future range overlaps the +current range by 30-60% within the assessment area.
+ +Neutral: Predicted future range overlaps the current range by > 60% +within the assessment area.
+ + +'Protected area' refers to existing parks, refuges, wilderness +areas, and other designated conservation areas that are relatively +invulnerable to outright habitat destruction from human activities and that +are likely to provide suitable conditions for the existence of viable +populations of the species. Models of current and projected future ranges +should meet standards described in the notes for D2. Modeled future +distribution may refer to a single season (e.g., breeding season +distribution or winter distribution) for migratory species. This factor +considers ranges and protected areas within the assessment area only.
+ +Increase Vulnerability: < 5% of the modeled future distribution +within the assessment area is encompassed by one or more protected areas.
+ +Somewhat Increase Vulnerability: 5-30% of the modeled future +distribution within the assessment area is encompassed by one or more protected +areas.
+ +Neutral: >30% of the modeled future distribution within the +assessment area is encompassed by one or more protected areas.
" + +datD <- data.frame(section = "D", + guide_text = sectionD %>% + str_split_1("(?=+ The Index treats exposure to climate change as a modifier of sensitivity and + adaptive capacity. If the climate in a given assessment area will not change + much, none of the sensitivity/adaptive capacity factors will weigh heavily, + and a species is likely to score at the Less Vulnerable end of the range. + A large change in temperature or moisture availability will amplify the effect + of any related sensitivity/adaptive capacity factor, and will contribute + to a score reflecting higher vulnerability to climate change. In most cases, + changes in temperature and moisture availability will combine to modify + sensitivity and adaptive capacity factors. However, for factors such as + sensitivity to temperature change (factor 2a) or precipitation/moisture + regime (2b), only the specified climate driver will have a modifying effect. +
" + +exposure <- data.frame(section = "exposure", guide_text = exposure) + +# Combine #===================================================================== +# Combine and save as csv to be edited for improved html readability +guide_dat <- bind_rows(datB, datC, datD, exposure) + +if(file.exists("data-raw/guideline_lu_tbl.csv")){ + message("The guideline look up table already exists and may contian edits") + prompt <- readline("Are you sure you want to replace it? (y/n) ") + if(prompt == "y"){ + write.csv(guide_dat, "data-raw/guideline_lu_tbl.csv", row.names = FALSE) + } +} + +# Need to run lookup_tbls.R to add it to internal package data diff --git a/data-raw/guideline_lu_tbl.csv b/data-raw/guideline_lu_tbl.csv new file mode 100644 index 0000000..e66f5d7 --- /dev/null +++ b/data-raw/guideline_lu_tbl.csv @@ -0,0 +1,1235 @@ +"section","question","sub_question","guide_text","sub2_question" +"B",NA,NA," + + +This factor comes into play only in the case that all or a portion of the +range within the assessment area may be subject to the effects of a 0.5-1 m or +greater sea level rise and the consequent influence of storm surges and +intrusion of salt water. Most climate model scenarios predict at least a 0.5 m +sea level rise. Because projected sea level rise (0.5-2 m by 2100) is great +compared to historical sea level changes, the negative impact on habitats for +most affected species is expected to be high.
+ +Greatly Increase Vulnerability: >90% of range occurs in area +subject to sea level rise (on low-lying island(s) or in coastal zone).
+ +Increase Vulnerability: 50-90% of range occurs in area subject to sea +level rise (on low-lying island(s) or in coastal zone).
+ +Somewhat Increase Vulnerability: 10-49% of range occurs in area +subject to sea level rise (on low-lying island(s) or in coastal zone).
+ +Neutral: <10% of range occur in area subject to sea level rise (on +low-lying island(s) or in coastal zone). Includes inland areas not subject to +sea level rise. Also, species that occur in an intertidal habitat that is +expected to increase in extent with a rising sea level.
+ +Tools: For information about the sensitivity of the Canadian coast to +potential sea level rise, see CanCoast 2.0.
+ + +",NA +"B","2",NA,"This factor assesses the degree to which natural (e.g., topographic, +geographic, ecological) or anthropogenic barriers limit a species' ability to +shift its range in response to climate change. Barriers are defined here as +features or areas that completely or almost completely prevent movement or +dispersal of the species (currently and for the foreseeable future). Species for +which barriers would inhibit distributional shifts with climate change-caused +shifts in climate envelopes likely are more vulnerable to climate change than +are species whose movements are not affected by barriers. Barriers must be +identified for each species (but often are the same for a group of closely +related species). Natural and anthropogenic barriers are defined for many +species and taxonomic groups in NatureServe's Element Occurrence Specifications +(viewable in the Population/Occurrence Delineation section of species accounts +on +Natureserve Explorer), but usually these readily can be determined by +considering a species' basic movement capacity and ecological tolerances.
+ +The distinction between a barrier and unsuitable habitat sometimes may be +unclear; in these cases assume the feature or area is unsuitable habitat +(habitat through which the species can disperse or move but that does not +support reproduction or long-term survival) and score the species here and/or in +factor C1 as appropriate. Note that caves are considered under factor C3: +Restriction to Uncommon Landscape/Geological Features, and not here where the +focus is on barriers that affect the wide array of nonsubterranean species.
+ +Note that no barriers exist for most temperate-zone bird species that simply +fly over or around potential obstructions. Species restricted to habitats that +are believed to persist unchanged in spite of climate change are scored as +Neutral (because in these situations barriers do not contribute to vulnerability +even if climate changes). If a feature or area does not completely or almost +completely prevent dispersal or movement then it is categorized here as +unsuitable or suitable habitat, and the dispersal/movement of individuals across +that feature or area is assessed under factor C1 (Dispersal and Movements). +In most cases, unsuitable habitat is habitat through which propagules or +individuals may move but that does not support reproduction or long-term +survival.
+ +The degree to which a barrier may affect a species' ability to shift its +range in response to climate change depends in part on the distance of the +barrier from the species' current distribution. Barriers that are separated from +a species' range by a long distance of relatively flat topography can +nevertheless affect range shifts because in gentle terrain relatively small +changes in climate can result in large shifts in the location of a particular +climate envelope. If a species changed its range accordingly (to track a +particular climate envelope), it might encounter barriers that were far from its +original range. In contrast, in landscapes in which climatic conditions change +rapidly over small horizontal distances (e.g., mountainous areas, steep slopes, +or other topographically diverse landscapes) a species' distribution would have +to shift a relatively small distance in order to track a particular climate +envelope, so the species is less likely to encounter distant barriers.
+ +To count as a barrier for the purposes of this factor, a feature can be up to +50 km from the species' current range when measured across areas where climate +changes gradually over latitude or longitude (e.g., relatively flat terrain) and +up to 10 km when measured across areas where climate changes abruptly over +latitude or longitude (e.g.mountainous or steep terrain). Use 25 km for species +that occur in intermediate topography, such as moderate hill country. These +distances apply to both terrestrial and aquatic species. These distances are +derived from Loarie et al.(2009, Nature 462:1052).
+ +The following categories and criteria apply to both natural and anthropogenic +barriers, but the two types of barriers are scored separately. Note that it is +illogical for natural and anthropogenic barriers to both cause greatly increased +vulnerability to climate change for a single species (only one or the other can +completely surround a species' range). If both barriers occur, estimate the +relative portions of the circumference of the range blocked by each and then +score accordingly.
+ + +",NA +"B","2","a","Examples of features that may function as natural barriers for various +species: upland habitat (i.e., absence of aquatic stream, lake, or pond habitat) +is a barrier for fishes (but not for semiaquatic or amphibious species that may +occupy the same body of water); high mountain ranges (especially those that +extend west-east) are a barrier for many lowland plants and nonvolant lowland +animals; warm lowlands are a barrier for some alpine species such as American +pika but not for elk or American pipit; large expanses of water are barriers for +pocket gophers and many other small terrestrial animals (but not for many volant +species, or for plant species that are dispersed by wide-ranging birds, or for +species that readily swim between land areas if the distance is not too great); +a high waterfall is a barrier for fishes (but not for American dippers or garter +snakes that occur along the same stream).
+ +Greatly Increase Vulnerability: Barriers completely OR almost +completely surround the current distribution such that the species' range in the +assessment area is unlikely to be able to shift significantly with climate +change, or the direction of climate change-caused shift in the species' +favorable climate envelope is fairly well understood and barriers prevent a +range shift in that direction. See Neutral for species in habitats not +vulnerable to climate change.
+ +Increase Vulnerability : Barriers border the current distribution such +that climate change-caused distributional shifts in the assessment area are +likely to be greatly but not completely or almost completely impaired.
+ +Somewhat Increase Vulnerability: Barriers border the current +distribution such that climate change-caused distributional shifts in the +assessment area are likely to be significantly but not greatly or completely +impaired.
+ +Neutral: Significant barriers do not exist for this species, OR small +barriers exist in the assessment area but likely would not significantly impair +distributional shifts with climate change, OR substantial barriers exist but are +not likely to contribute significantly to a reduction or loss of the species' +habitat or area of occupancy with projected climate change in the assessment +area.
+ + +",NA +"B","2","b","Examples of features that may function as anthropogenic barriers: large areas +of intensive urban or agricultural development are barriers for many animals +and plants; waters subject to chronic chemical pollution (e.g., acid mine +drainage) can be a barrier for fishes and other strictly aquatic species; +waters subject to thermal pollution (e.g., from power plants) may be a barrier +for some strictly aquatic species but not for others (note thermal alterations +associated with reservoirs often produce unsuitable habitat rather than impose +a barrier); dams without fish passage facilities and improperly installed +culverts can be barriers for fishes and certain other strictly aquatic species; +tortoise-proof fencing may be barrier for small reptiles and certain other +nonvolant animals (but not for most plants, large mammals, or large snakes).
+ +Greatly Increase Vulnerability: Barriers completely OR almost +completely surround the current distribution such that the species' range in the +assessment area is unlikely to be able to shift significantly with climate +change, or the direction of climate change-caused shift in the species' +favorable climate envelope is fairly well understood and barriers prevent a +range shift in that direction. See Neutral for species in habitats not +vulnerable to climate change.
+ +Increase Vulnerability: Barriers border the current distribution such +that climate change-caused distributional shifts in the assessment area are +likely to be greatly but not completely or almost completely impaired.
+ +Somewhat Increase Vulnerability: Barriers border the current +distribution such that climate change-caused distributional shifts in the +assessment area are likely to be significantly but not greatly or completely +impaired.
+ +Neutral: Significant barriers do not exist for this species, OR small +barriers exist in the assessment area but likely would not significantly impair +distributional shifts with climate change, OR substantial barriers exist but are +not likely to contribute significantly to a reduction or loss of the species' +habitat or area of occupancy with projected climate change in the assessment +area.
+ + +",NA +"B","3",NA,"(e.g., plantations for carbon offsets, new seawalls in response to sea level +rise, and renewable energy projects such as wind-farms, solar arrays, or +biofuels production)
+ +Strategies designed to mitigate or adapt to climate change have the potential +to affect very large areas of land, and the species that depend on these areas, +in both positive and negative ways. This factor arguably should be considered in +conservation status assessments, but considering that for most species this +factor has not yet been considered in these assessments, we include it here. +If the land use changes for alternative energy projects have already been +considered in the conservation status assessment for the species, consider not +scoring this factor, especially if the vulnerability assessment results will be +used to revise status ranks.
+ +This factor is NOT intended to +include habitat loss or destruction due to on-going human activities, as these +should already be reflected in existing conservation status ranks. Include only +new activities related directly to climate change mitigation here. There is much +uncertainty about the types of mitigation action that are likely to threaten +habitats and species. Remember that multiple categories can be checked for each +factor to capture uncertainty. As federal and state climate change legislation +is enacted, some of the mitigation directions (and associated threats or +benefits to species) will become clearer.
+ +Increase Vulnerability: The natural history/requirements of the +species are known to be incompatible with mitigation-related land use changes +that are likely to very likely to occur within its current and/or potential +future range. This includes (but is not limited to) the following:
+ +Somewhat Increase Vulnerability: The natural history/requirements of +the species are known to be incompatible with mitigation-related land use +changes that may possibly occur within its current and/or potential future +range, including any of the above (under Increase).
+ +Neutral: The +species is unlikely to be significantly affected by mitigation-related land use +changes that may occur within its current and/or potential future range, +including any of the above; OR it is unlikely that any mitigation-related land +use changes will occur within the species' current and/or potential future +range; OR it may benefit from mitigation-related land use changes.
+ +Tools: For information and maps related to wind energy in Canada, see +Natural Resources Canada Wind Energy and +Environment +and Climate Change Canada's Wind Atlas.
+",NA +"C",NA,NA," + + +Note that these factors relate to +characteristics of the species only. Anthropogenic effects, such as on the +availability of dispersal corridors, should not be considered in this +section.
+ + +",NA +"C","1",NA,"This factor pertains to known or predicted dispersal or movement capacities +and characteristics and ability to shift location in the absence of barriers as +conditions change over time as a result of climate change. Species in which +individuals exhibit substantial dispersal, readily move long distances as adults +or juveniles, or exhibit flexible movement patterns should be better able to +track shifting climate envelopes than are species in which dispersal and +movements are more limited or inflexible. This factor pertains specifically to +dispersal through unsuitable habitat, which, in most cases, is habitat through +which propagules or individuals may move but that does not support reproduction +or long-term survival. If all habitat is regarded as suitable (i.e., species can +reproduce and persist in every habitat in which it occurs), then dispersal +ability is assessed for suitable habitat. If appropriate, scoring of species +whose dispersal capacity is not known can be based on characteristics of closely +related species (or species of similar body size in the same major group) with +similar and relevant morphological features.
+ +Barriers, which are here defined as features or areas that completely or +almost completely block dispersal, are treated in factor B2. If a species +requires other species for propagule dispersal, please also complete factor C4d. +The following categorization for plants is loosely based on Vittoz and Engler +(2007 Botanica Helvetica 117:109-124).
+ +A small number of species are confined by barriers to areas that are +smaller than the species' potential dispersal distance (fishes in small +isolated springs or plants that only occur in vernal pools are classic +examples). Most if not all of the fish species that occur in the smallest +such habitat patches could disperse farther than the greatest extent of the +occupied patch if a larger extent of habitat were available to them. For +the purposes of this factor, the dispersal ability of these species is +scored as if the species occurred in a large patch of habitat (longer than +the dispersal distance), based on dispersal or movement patterns or +capabilities of closely related species (or species of similar body size in +the same major group of animals).
+ +Migratory species should be scored according to their ability to shift +their distribution within the assessment area during the period of +occupation or from one year to the next (whichever is larger).
+ +Species in which propagule dispersal is both synchronous among all members +of the population in the assessment area and infrequent (average of several +years between successful reproduction events) should be scored as one +category more vulnerable than the category that would otherwise apply. An +example is the monocarpic giant cane (Arundinaria gigantea), a bamboo +species that reproduces synchronously every 25-50 years and then dies.
+ +Greatly Increase Vulnerability: Species is characterized by severely +restricted dispersal or movement capability. Species is represented by +sessile organisms that almost never disperse more than 10 meters per +dispersal event.
+ +Increase Vulnerability: Species is characterized by highly restricted +dispersal or movement capability. Species rarely disperses through +unsuitable habitat more than about 10-100 meters per dispersal event; OR +dispersal beyond a very limited distance (or outside a small isolated patch +of suitable habitat) periodically or irregularly occurs but is dependent on +highly fortuitous or rare events; OR species has substantial movement +capability but exhibits a very high degree of site fidelity.
+ +Somewhat Increase Vulnerability: Species is characterized by limited +or moderate but not highly or severely restricted dispersal or movement +capability. A significant percentage (at least approximately 50%) of +propagules or individuals disperse approximately 100-1,000 meters per +dispersal event (rarely farther); OR species has substantial movement +capability but exhibits a moderate to high degree of site fidelity and has +very limited existing or potential habitat within the assessment area; OR +dispersal likely is consistent with one of the following examples.
+ +Neutral: Species is characterized by good to excellent dispersal or +movement capability. Species has propagules or dispersing individuals that +commonly move more than 1 kilometer from natal or source areas; OR species +tends to occupy all or most areas of suitable habitat, or readily or +predictably moves more than 1 kilometer to colonize newly available habitat +(e.g., recently restored areas, areas that become suitable as a result of +fire, insect infestations, or other environmental changes, etc.); OR +dispersal capability likely is consistent with one of the following +examples. Note that species in the Neutral category are not necessarily +'early successional' or 'r-selected' species but also may include +certain 'late successional' or equilibrium ('K-selected') species that +have excellent innate or vector-aided dispersal capability.
+ +Tools: Seed biological trait data for some species can be found at +Royal Botanic +Gardens Kew Data Portal.
+ + +",NA +"C","2",NA,"This factor pertains to the breadth of temperature and precipitation +conditions, at both broad and local scales, within which a species is known +to be capable of reproducing, feeding, growing, or otherwise existing. +Species with narrow environmental tolerances/requirements may be more +vulnerable to habitat loss from climate change than are species that thrive +under diverse conditions.
+ + +",NA +"C","2","a","This factor measures large-scale temperature variation that a +species has experienced in recent historical times (i.e., the past 50 +years), as approximated by mean seasonal temperature variation (difference +between highest mean monthly maximum temperature and lowest mean monthly +minimum temperature) for occupied cells within the assessment area. It is a +proxy for species' temperature tolerance at a broad scale. This factor may +be evaluated by comparing the species range with the Annual Temperature +Variation map (see Figure 5 in the Canadian NatureServe CCVI Guidelines) or calculate using +GIS data downloaded from NatureServe. For +aquatic species, follow the same procedure as for terrestrial species, since +this factor measures broad regional patterns.
+ +Use the annual map for both resident and migratory species. Although +migratory species are not physically present to experience temperature +variations, they nonetheless are affected by these variations through +effects on food supply and habitat availability.
+ +Greatly Increase Vulnerability: Considering the mean seasonal +temperature variation for occupied cells, the species has experienced very small +(< 37° F/20.8° C) temperature variation in the past 50 years. +Includes cave obligates and species occurring in thermally stable groundwater +habitats.
+ +Increase Vulnerability: Considering the mean seasonal temperature +variation for occupied cells, the species has experienced small (37 - 47° +F/20.8 - 26.3° C) temperature variation in the past 50 years. Includes +facultative cave invertebrates.
+ +Somewhat Increase Vulnerability: Considering the mean seasonal +temperature variation for occupied cells, the species has experienced slightly +lower than average (47.1 - 57° F/26.3 - 31.8° C) temperature variation +in the past 50 years.
+ +Neutral: Considering the mean seasonal temperature variation for +occupied cells, the species has experienced average or greater than average +(>57.1° F/43.0° C) temperature variation in the past 50 years.
+ + +","i" +"C","2","a","Current projections indicate that climate warming will be nearly +pervasive in North America over the next several decades. Species +associated with cool or cold conditions likely will experience a reduction +in habitat extent or quality and may experience declines in distribution or +abundance within a given assessment area. This factor assesses the degree +to which a species is restricted to relatively cool or cold above-ground +terrestrial or aquatic environments that are thought to be vulnerable to +loss or significant reduction as a result of climate change. Species that +depend on these cool/cold environments include (but may not be limited to) +those that occur in the assessment area's highest elevational zones, +northernmost areas, or the coldest waters. The restriction to these +relatively cool environments may be permanent or seasonal.
+ +Species that occur in frost pockets, on north-facing slopes, in shady +ravines, in alpine areas, or similar cool sites are scored here if those +areas represent or are among the coldest environments in the assessment +area; lacking this stipulation, species occurring in such sites may not be +vulnerable to climate change because favorable sites may simply shift in +location without reduction or loss. Species that are associated +specifically with snow or ice are assessed separately in factor C2d. Note +that temperature conditions and hydrological regimes often covary and often +are not neatly separable; these situations should be scored here if +temperature per se appears to be the overriding factor; otherwise they +should be scored under factor C2bii: Physiological Hydrological Niche.
+ +Greatly Increase Vulnerability: Species is completely or almost +completely (> 90% of occurrences or range) restricted to relatively cool or +cold environments that may be lost or reduced in the assessment area as a result +of climate change.
+ +Increase Vulnerability: Species is moderately (50-90% of occurrences +or range) restricted to relatively cool or cold environments that may be lost +or reduced in the assessment area as a result of climate change.
+ +Somewhat Increase Vulnerability: Species is somewhat (10-50% of +occurrences or range) restricted to relatively cool or cold environments that +may be lost or reduced in the assessment area as a result of climate change.
+ +Neutral: Species distribution is not significantly affected by thermal +characteristics of the environment in the assessment area, species occupies +habitats that are thought to be not vulnerable to projected climate change, or +species shows a preference for environments at the warmer end of the spectrum. +
+ + +","ii" +"C","2","b","This factor measures large-scale precipitation variation that a +species has experienced in recent historical times (i.e., the past 50 +years), as approximated by mean annual precipitation variation across +occupied cells within the assessment area. Overlay the species' range on +the mean annual precipitation map (see Figure 6 in the Canadian NatureServe CCVI Guidelines). Subtract the +lowest pixel value from the highest value to assess this factor. Use the +extreme pixel values for this calculation. Use annual data for migratory +species, as this measure reflects the precipitation regime of the ecosystem +as a whole.
+ +Greatly Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced very small +(< 4 inches/100 mm) precipitation variation in the past 50 years.
+ +Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced small (4 - 10 +inches/100 - 254 mm) precipitation variation in the past 50 years.
+ +Somewhat Increase Vulnerability: Considering the range of mean annual +precipitation across occupied cells, the species has experienced slightly +lower than average (11 - 20 inches/255 - 508 mm) precipitation variation in +the past 50 years.
+ +Neutral: Considering the range of mean annual precipitation across +occupied cells, the species has experienced average or greater than average +>20 inches/508 mm) precipitation variation in the past 50 years.
+ + +","i" +"C","2","b","This factor pertains to a species' dependence on a narrowly defined +precipitation/hydrologic regime, including strongly seasonal precipitation +patterns and/or specific aquatic/wetland habitats (e.g., certain springs, +vernal pools, seeps, seasonal standing or flowing water) or localized +moisture conditions that may be highly vulnerable to loss or reduction with +climate change. Dependence may be permanent or seasonal, and for migratory +species may include staging areas, migration stops, and wintering areas +outside the assessment area. Aquatic cave obligate species are considered +here according to their hydrological needs and habitat vulnerability. +Species nesting on islands in lakes, reservoirs, and/or wetlands that +prevent predator access can be scored here to the extent that a changed +hydrological regime may influence the availability of these predator-free +breeding sites (for example, birds nesting on islands to avoid predation by +mammals). If a species is dependent on aquatic/wetland habitats that are +actively managed to maintain a particular hydrology, consider whether this +management would be sufficient to ameliorate projected climate change +impacts (and, if so, score as Neutral).
+ +For plant species, the advantage of the C4 photosynthetic pathway for water +use efficiency will likely enable C4 plants to be less vulnerable to +decline under drying conditions than C3 plants (Taylor et al. 2010, New +Phytologist 185:780). The predicted vulnerability of these plants with +respect to this factor has been adjusted accordingly.
+ +For nonmigratory species, 'range' refers to the range within the assessment +area. For migratory species, 'range' encompasses the assessment area and +additional areas (e.g., migration stops, staging areas, wintering areas) +that are used to a significant extent by the populations being assessed. +For example, a migratory bird species for which 95% of the significant +migration stops are in shallow inland/interior wetlands should be assigned +to the Greatly Increase Vulnerability category, even if the species is not +dependent on such habitats within the assessment area.
+ +Note that temperature conditions and hydrological regimes often covary and +often are not neatly separable. These situations should be scored under +factor C2aii (Physiological Thermal Niche) if temperature per se appears to +be the overriding factor; otherwise they should be scored here.
+ +Greatly Increase Vulnerability: Completely or almost completely +(>90% of occurrences or range) dependent on a specific aquatic/wetland +habitat or localized moisture regime that is likely to be highly vulnerable to +loss or reduction with climate change.
+ +Increase Vulnerability: Moderately (50-90% of occurrences or range) +dependent on a strongly seasonal hydrologic regime and/or a specific +aquatic/wetland habitat or localized moisture regime that is likely to be +highly vulnerable to loss or reduction with climate change.
+ +Somewhat Increase Vulnerability: Somewhat (10-50%) dependent on a +strongly seasonal hydrologic regime and/or a specific aquatic/wetland habitat or +localized moisture regime that is highly vulnerable to loss or reduction +with climate change.
+ +Neutral: Species has little or no dependence on a strongly seasonal +hydrologic regime and/or a specific aquatic/wetland habitat or localized +moisture regime that is highly vulnerable to loss or reduction with climate +change; OR hydrological requirements are not likely to be significantly +disrupted in major portion of the range; OR species tolerates a very wide +range of moisture conditions.
+ + +","ii" +"C","2","c","This factor pertains to a species' response to specific disturbance +regimes such as fires, floods, severe winds, pathogen outbreaks, or similar +events. It includes disturbances that impact species directly as well as +those that impact species via abiotic aspects of habitat quality. For +example, changes in flood and fire frequency/intensity may cause changes in +water turbidity, silt levels, and chemistry, thus impacting aquatic species +sensitive to these aspects of water quality. The potential impacts of +altered disturbance regimes on species that require specific river features +created by peak flows should also be considered here; for example, some +fish require floodplain wetlands for larval/juvenile development or high +peak flows to renew suitable spawning habitat. Use care when estimating the +most likely effects of increased fires; in many ecosystems, while a small +increase in fire frequency might be beneficial, a greatly increased fire +frequency could result in complete habitat destruction.
+ +Be sure to also consider species that benefit from a lack of disturbance +and may suffer due to disturbance increases when scoring this factor.
+ +Increase Vulnerability: Strongly affected by specific disturbance +regime, and climate change is likely to change the frequency, severity, or +extent of that disturbance regime in a way that reduces the species' +distribution, abundance, or habitat quality. For example, many +sagebrush-associated species in regions predicted to experience increased fire +frequency/intensity would be scored here due to the anticipated deleterious +effects of increased fire on their habitat.
+ +Somewhat Increase Vulnerability: Moderately affected by specific +disturbance regime, and climate change is likely to change the frequency, +severity, or extent of that disturbance regime in a way that reduces the +species' distribution, abundance, or habitat quality, OR strongly affected +by specific disturbance regime, and climate change is likely to change that +regime in a way that causes minor disruption to the species' distribution, +abundance, or habitat quality. For example, plants in a riverscour +community that are strongly tied to natural erosion and deposition flood +cycles, which may shift position within the channel rather than disappear +as a result of climate change.
+ +Neutral: Little or no response to a specific disturbance regime, OR +climate change is unlikely to change the frequency, severity, or extent of that +disturbance regime in a way that affects the range or abundance of the +species, OR climate change is likely to change the characteristics of the +disturbance regime in a way that increases the species' distribution.
+ +Tools: For information on fire effects, see the USDA Fire Effects +Information System. For a map of modeled future fire regime, see Figure 2 in + +Krawchuck et al. (2009).
+ + +",NA +"C","2","d","This factor pertains to a species' dependence on habitats associated +with ice (e.g., sea ice, glaciers) or snow (e.g., long-lasting snow beds, +avalanche chutes) throughout the year or seasonally during an essential +period of the life cycle. For aquatic species, the importance of snowpack +for maintaining downstream water temperatures should be considered here. +'Range' refers to the range within the assessment area.
+ +Greatly Increase Vulnerability: Highly dependent (>80% of +subpopulations or range) on ice- or snow-associated habitats; or found almost +exclusively on or near ice or snow during at least one stage of the life cycle. +For example, polar bear (Ursus maritimus) is strongly dependent on sea ice +throughout its range.
+ +Increase Vulnerability: Moderately dependent (50-80% of subpopulations +or range) on ice- or snow-associated habitats; or often found most abundantly +on or near ice or snow but also regularly occurs away from such areas. For +example, Kittlitz's murrelet (Brachyramphus brevirostris) feeding habitat +is moderately to strongly associated with tidewater glaciers.
+ +Somewhat Increase Vulnerability: Somewhat (10-49% of subpopulations or +range) dependent on ice- or snow-associated habitats, or may respond +positively to snow or ice but is not dependent on it. For example, certain +alpine plants are often associated with long-lasting snowbeds but also +commonly occur away from such areas; certain small mammals experience +increased survival and may develop relatively large populations under +winter snow cover but do not depend on snow cover. Species that benefit +from a minimum thickness of ice or snowpack for winter insulation should +also be scored here.
+ +Neutral: Little dependence on ice- or snow-associated habitats (may be +highly dependent in up to 10% of the range).
+ + +",NA +"C","3",NA,"This factor pertains to a species' need for a particular +soil/substrate, geology, water chemistry, or specific physical or landscape +feature (e.g., caves, cliffs, active sand dunes, islands) for reproduction, +feeding, growth, shelter, or other aspects of the life cycle. It focuses on +the commonness of suitable conditions for the species on the landscape, as +indicated by the commonness of the features themselves combined with the +degree of the species' restriction to them. Climate envelopes may shift +away from the locations of fixed (within at least a 50 year timeframe) +landscape or geological features or their derivatives, making species tied +to these uncommon features potentially more vulnerable to habitat loss from +climate change than are species that thrive under diverse conditions.
+ +This factor does NOT include habitat preferences based on temperature, +hydrology, or disturbance regime, as these are covered elsewhere in the +Index. For example, species dependent on springs or ephemeral pools should +not be scored as more vulnerable for this factor solely on that basis +(addressed under factor C2bii: Physiological Hydrological Niche). However, +restriction to aquatic features with regionally uncommon water chemistry +should be considered here. This factor also does NOT include habitat +features such as stream riffles or basking rocks. Finally, this factor does +NOT include biotic habitat components; for example, species that require +features such as tree snags or a particular type/condition of plant +community (e.g., old growth forest) should not be scored as more vulnerable +for this factor.
+ +If the idea of specificity to soil/substrate, geology, or specific physical +or landscape features is not relevant to the species (e.g., many birds and +mammals), choose Neutral.
+ +Increase Vulnerability: Highly dependent upon (i.e., more or less +endemic to, or > 85% of occurrences found on) a particular highly uncommon +landscape or geological feature or derivative (e.g., soil, water chemistry).
+ +Somewhat Increase Vulnerability: Moderately dependent upon a +particular uncommon landscape or geological feature or derivative, i.e., (1) an +indicator of but not an endemic to (65-85% of occurrences found on) the +types of features described under Increase, OR (2) more or less restricted +to a landscape or geological feature or derivative that is not highly +uncommon within the species' range, but is not one of the dominant types.
+ +Neutral: Having a clear preference for (> 85% of occurrences found +on) a particular landscape or geological feature or derivative, but the +feature/derivative is among the dominant types within the species' range; +OR somewhat flexible in dependence upon geological features or derivatives +(i.e., found on a subset of the dominant substrate/water chemistry types +within its range); OR highly generalized relative to dependence upon +geological features or derivatives; species is described as a generalist +and/or occurrences have been documented on widely varied substrates or +water chemistries.
+ + +",NA +"C","4",NA,"The primary impact of climate change on many species may occur via +effects on synchrony with other species on which they depend (Parmesan +2006, ARES 37:637), rather than through direct physiological stress.
+ + +",NA +"C","4","a","This factor pertains to a species' dependence on uncommon/restricted +habitats that are generated or maintained by other species. Species that +are dependent on a small number of other species likely are more vulnerable +to climate change than are species that have more flexibility or that do +not have specialized habitat requirements.
+ +Habitat refers to any habitat (e.g., for reproduction, feeding, +hibernation, seedling establishment) necessary for completion of the life +cycle, including those used only on a seasonal basis. This includes +specific (often structural) features within a more generalized habitat type +(e.g., burrows created by other species in a grassland habitat; +woodpecker-created cavities in a forest habitat). These habitats must be +required for completion of the life cycle (e.g., reproduction, feeding, +hibernation, seedling establishment, etc.) and may include habitats used +only on a seasonal basis. For plants, species-specific relationships +involved in creating specific habitat conditions necessary for seedling +establishment should be considered here; nutritional relationships +necessary for seedling establishment (e.g., parasitic or obligately +myco-heterotrophic plants) should be considered under C4g. The relationship +between freshwater mussels and their larval hosts should be scored only +under factor C4d (Dependence on other species for propagule dispersal).
+ +This factor is concerned specifically with habitats generated or maintained +by particular species and does NOT include ecological dependencies based +primarily on disturbance regime, geological features, or diet, as these are +covered elsewhere in the Index. Required habitats involving +temperature/hydrological conditions that are generated by a small number of +particular species are included in this factor, but +temperature/hydrology-related habitats that are not primarily species +dependent are considered under C2aii and C2bii (thermal and hydrological +niches); if in doubt, score under C2aii or C2bii.
+ +Increase Vulnerability: Required habitat is generated primarily by one +species.
+ +Somewhat Increase Vulnerability: Required habitat is generated by only +a few species.
+ +Neutral: Required habitat is generated by more than a few species; or +species does not require any uncommon/restricted habitats; or habitat +requirements do not involve species-specific processes.
+ + +",NA +"C","4","b","This factor pertains to the diversity of food types consumed by +animal species. Dietary specialists are more likely to be negatively +affected by climate change than are species that readily switch among +different food types.
+ +Note that the relationship between freshwater mussels and their larval +hosts should be scored only under factor C5d (Dependence on other species +for propagule dispersal).
+ +Increase Vulnerability: Completely or almost completely (>90%) +dependent on one species during any part of the year; equivalent +alternatives to this single-species food resource are not readily +available.
+ +Somewhat Increase Vulnerability: 'Completely or almost completely +(>90%) dependent during any part of the year on (1) a few species from a +restricted taxonomic group or (2) a narrow guild the members of which are +thought to respond similarly to climate change.
+ +Neutral: 'Diet flexible; during any season species readily switches +among multiple food resources according to availability; not strongly dependent +on one or a few species; omnivorous, with diet including numerous species +of both plants and animals.
+ + +",NA +"C","4","c","Quantitative thresholds loosely follow data in Waser et al. (1996, +Ecology 77:1043). If appropriate, scoring of species whose pollinators is +not known can be based on characteristics of closely related species that +have similar and relevant morphological floral features that may have +similar pollination syndromes (Willmer 2011, Pollination and Floral +Ecology, Princeton Press).
+ +In some cases, sympatric, sequentially flowering species may enhance +reproductive success for each other through maintenance of pollinator +populations. Species that are documented to benefit from such interactions +with one or only a few sympatric species should be scored one category +higher (Hegland et al. 2009, Ecology Letters 12:184).
+ +Increase Vulnerability: Completely or almost completely dependent on +one species for pollination (> 90% of effective pollination accomplished by +1 species) or, if no observations exist, morphology suggests very significant +limitation of potential pollinators (e.g., very long corolla tube).
+ +Somewhat Increase Vulnerability: Completely or almost completely +dependent on 2-4 species for pollination (> 90% of effective pollination +accomplished by 2-4 species) or, if no observations exist, morphology +suggests conformation to a specific 'pollination syndrome' (e.g., +van der Pijl, 1961).
+ +Neutral: Pollination apparently flexible; five or more species make +significant contributions to pollination or, if no observations exist, +morphology does not suggest pollinator limitation or pollination syndrome. +Score wind-pollinated species as Neutral.
+ +Tools: The Inouye Pollinator Reference Database is a source for +literature references to pollination. A table describing traits of pollinator +syndromes can be found at USDA Pollinator Syndromes.
+ +",NA +"C","4","d","Can be applied to plants or animals. Examples: Different species of +freshwater mussels can be dispersed by one to many fish species; fruit +dispersal by animals.
+ +Increase Vulnerability: Completely or almost completely (roughly > +90%) dependent on a single species for propagule dispersal.For example, +whitebark pine would fit here because Clark's nutcracker is the primary +dispersal agent.
+ +Somewhat Increase Vulnerability: Completely or almost completely +(roughly > 90%) dependent on a small number of species for propagule +dispersal. For example, a freshwater mussel for which only a few species of fish +can disperse larvae.
+ +Neutral: Disperses on its own (most animals, wind-dispersed plants) OR +propagules can be dispersed by more than a few species (many plants).
+ + +",NA +"C","4","e","This factor refers to pathogens and natural enemies (e.g., +predators, parasitoids, or herbivores) that can increase or become more +pathogenic due to climate change, or vectors of disease when they expand +their distributions due to changes in climate and therefore become more +harmful or influence a greater portion of the distribution of the species +being evaluated. Examples include the chytrid fungal pathogen that can +become more harmful to frogs because of climate change (Pounds et al. 2006 +Nature 439:161) or sudden oak death in California caused by a pathogen that +is invasive under favorable climate conditions (Meentenmeyer et al. 2011 +Ecosphere 2:1).
+ +Increase Vulnerability: Species is negatively affected to a high +degree by a pathogen or natural enemy that is likely to increase in +distribution, abundance, or impact as a result of climate change. Example: The +cold-sensitive non-native hemlock woolly adelgid commonly causes a high +level of mortality in eastern hemlock, and the distribution/abundance/impact of +the adelgid may increase in areas where winter temperatures become milder.
+ +Somewhat Increase Vulnerability: Species is negatively affected to a +moderate degree by a pathogen or natural enemy that is likely to increase +in distribution, abundance, or impact as a result of climate change.
+ +Neutral: There is no indication that the species is currently or in +the foreseeable future likely to be significantly affected by a pathogen or +natural enemy that is likely to increase in distribution, abundance, or +impact as a result of climate change; OR the negative impact of pathogens +or natural enemies is likely to decrease with climate change. Example: A +warmer/drier climate may reduce the negative impact of certain fungal +pathogens that depend/thrive on relatively cold/moist conditions.
+ + +",NA +"C","4","f","Species may suffer when competitors are favored by both changing +climates and the effects these climates have on disturbance regimes +(Abatzoglou and Kolden 2011 Rangeland Ecology & Management 64:471, +Dukes et al. 2011 Ecological Applications 21:1887, Pintó-Marijuan and +Munné-Bosch 2013, Grossman and Rice 2014 Ecology Letters 17:710). However, +in some cases climate change will decrease the spread of particular +invasive species (Bradley et al. 2010 Trends in Ecology & Evolution +25:310). To score this factor, some indication is needed that a potential +competitor is favored by projected future climates.
+ +Increase Vulnerability: Strongly affected by a native or non-native +competing species that is likely to be favored by climate change.
+ +Somewhat Increase Vulnerability: Moderately affected to a moderate +degree by a native or non-native competing species that is likely to be favored +by climate change.
+ +Neutral: Little or no response to a native or non-native species that +is likely to shift its distribution or abundance due to climate change OR +climate change is likely to decrease or have no effect on the spread or +abundance of a native or non-native species that negatively impacts the +species.
+ + +",NA +"C","4","g","Can be applied to plants or animals. Here an interspecific +interaction can include mutualism, parasitism, or commensalism. Refers to +interactions unrelated to habitat, seedling establishment, diet, +pollination, or propagule dispersal. For example, an acacia bush requiring +an ant colony for protection against herbivores.
+ +Increase Vulnerability: Requires an interaction with a single other +species for persistence.
+ +Somewhat Increase Vulnerability: Requires an interaction with a one +member of a small group of taxonomically related species for persistence. Could +also include cases where specificity is not known for certain, but is +suspected. Many Orchidaceae will be in this category because of their +requirement for a specific fungal partner for germination (Tupac Otero and +Flanagan 2006, TREE 21: 64-65).
+ +Neutral: Does not require an interspecific interaction or, if it does, +many potential candidates for partners are available.
+ + +",NA +"C","5",NA,"Species with less standing genetic variation will be less able to +adapt because the appearance of beneficial mutations is not expected to +keep pace with the rate of 21st century climate change. Throughout this +question, 'genetic variation' may refer neutral marker variation, +quantitative genetic variation, or both. To answer the question, genetic +variation should have been assessed over a substantial proportion of a +species' range.
+ +Because measures of genetic variability vary across taxonomic groups, there +cannot be specific threshold numbers to distinguish among the categories. +The assessor should interpret genetic variation in a species relative to +that measured in related species to determine if it is low, high, or in +between.
+ +Increase Vulnerability: Genetic variation reported as 'very low' +compared to findings using similar techniques on related taxa, i.e., lack of +genetic variation has been identified as a conservation issue for the species. +
+ +Somewhat Increase Vulnerability: Genetic variation reported as 'low' +compared to findings using similar techniques on related taxa.
+ +Neutral: Genetic variation reported as 'average' or 'high' compared to +findings using similar techniques on related taxa.
+ + +",NA +"C","5","b","In the absence of rangewide genetic variation information (C5a), +this factor can be used to infer whether reductions in species-level +genetic variation that would potentially impede its adaptation to climate +change may have occurred. Only species that suffered population reductions +and then subsequently rebounded qualify for the Somewhat Increase or +Increase Vulnerability categories.
+ +Increase Vulnerability: Evidence that total population was reduced to +≤ 250 mature individuals, to one occurrence, and/or that occupied area was +reduced by >70% at some point in the past 500 years.
+ +Somewhat Increase Vulnerability: Evidence that total population was +reduced to 251-1000 mature individuals, to less than 10 occurrences, and/or that +occupied area was reduced by 30-70% at some point in the past 500 years.
+ +Neutral: No evidence that total population was reduced to ≤ 1000 +mature individuals and/or that occupied area was reduced by > 30% at some +point in the past 500 years.
+ + +",NA +"C","5","c","In plants, genetic variation is strongly linked to reproductive +mode. Therefore, in the absence of measured genetic variation and knowledge +of recent genetic bottlenecks, a plant's reproductive system may serve as a +proxy for a species' genetic variation or capacity to adapt to novel +climatic conditions. For example, species that can outcross may be better +able to adapt to novel environments (Morran et al. 2009, Morran et al. +2011). Species with mixed mating systems, which make up 42% of the world's +flora, appear to favor selfing as a buffering mechanism to climate change +(Jones et al. 2013).
+ +Increase Vulnerability: Genetic variation of the species is assumed to +be 'very low' in the assessment area because the species is restricted to +asexual reproduction (vegetatively or apomicticly). These species are +expected to be negatively impacted because rapid climate change can +strongly impact genetic variation, ultimately reducing fitness (Jump and +Penuelas 2005).
+ +Somewhat Increase Vulnerability: Genetic variation assumed to be 'low' +in the assessment area due to known disruptions or barriers to gene flow among +subpopulations, range disjunctions, or documented outbreeding depression +(Franks et al. 2014). Reproductive system may be either mixed or obligate +outcrossing.
+ +Neutral: Genetic variation is assumed to be 'average' in the +assessment area based on reproductive system. Includes species that have either +mixed mating systems or are obligate outcrossers AND there are no known major +disruptions to gene flow.
+ + +",NA +"C","6",NA,"Recent research suggests that some phylogenetic groups are declining +due to lack of response to changing annual temperature dynamics (e.g., +earlier onset of spring, longer growing season), including European bird +species that have not advanced their migration times (Moller et al. 2008), +and some temperate zone plants that are not moving their flowering times +(Willis et al. 2008) to correspond to earlier spring onset. This may be +assessed using either published multi-species studies such as those cited +above or large databases such as that of the U.S. National Phenology +Network.
+ +Increase Vulnerability: Seasonal temperature or precipitation dynamics +within the species' range show detectable change, but phenological +variables measured for the species show no detectable change.
+ +Somewhat Increase Vulnerability: Seasonal temperature or precipitation +dynamics within the species' range show detectable change, and phenological +variables measured for the species show some detectable change, but the +change is significantly less than that of other species in similar habitats +or taxonomic groups.
+ +Neutral: Seasonal temperature or precipitation dynamics within the +species' range show detectable change, and phenological variables measured for +the species show detectable change which is average compared to other species +in similar habitats or taxonomic groups; OR seasonal dynamics within the +species' range show no detectable change.
+ +Tools: Some phenological information can be gleaned from papers listed +in the Inouye +Pollinator Reference Database
+",NA +"D",NA,NA," + + +This factor pertains to the degree to which a species is known to +have responded to recent climate change based on published accounts in the +peer-reviewed literature. Time frame for the reduction or increase is 10 +years or three generations, whichever is longer. Some examples include +population declines due to phenology mismatches between species and +critical food or pollinator resources, e.g., great tits (Parus major) or +pied flycatchers (Ficedula hypoleuca) with winter moth (Operophtera +brumata) caterpillars, or honey-buzzards (Pernis apivorus) with wasps.
+ +Note that not all responses to climate change necessarily indicate +vulnerability. Species that respond to climate change by shifting (but not +contracting) their range, for example, show adaptability to climate change +and should be scored as Neutral for this factor. Similarly, species that +respond by changing their phenology (without a related decline in +population) should also be scored as Neutral.
+ +Greatly Increase Vulnerability: Distribution or abundance undergoing +major reduction (>70% over 10 years or three generations) believed to be +associated with climate change.
+ +Increase Vulnerability: Distribution or abundance undergoing moderate +reduction (30-70% over 10 years or three generations) believed to be +associated with climate change.
+ +Somewhat Increase Vulnerability: Distribution or abundance undergoing +small but measureable (10-30% over 10 years or three generations) believed to be +associated with climate change.
+ +Neutral: Distribution and abundance not known to be decreasing with +climate change. Includes species undergoing range shifts without loss of +distributional area or species undergoing changes in phenology but no net +loss in range size or population size. Includes species in which climate +change is documented to be causing an increase in range size or abundance.
+ + +",NA +"D","2",NA,"This factor can include both distribution models and population +models. Models should be developed based on reasonably accurate locality +data (error < 5km) using algorithms that are supported by peer-reviewed +literature. Areas of obvious overprediction should be removed from current +and predicted future distributions. Projections should be based on 'middle +of the road' climate scenarios for the year 2050. Range size should be +based on 'extent of occurrence' sensu IUCN Red List. Population models +should be based on known processes as described in peer-reviewed +literature. Examples include (a) phenological changes that are likely to +result in a mismatch with critical dietary, pollination, or habitat +resources (Visser and Both 2005) or (b) documented narrow temperature +tolerances and thermal safely levels, particularly in insects (Deutsch et +al. 2008, Calosi et al. 2008).
+ +If necessary, check multiple boxes to reflect variation in model output.
+ +Greatly Increase Vulnerability: Predicted future range disappears +entirely from the assessment area OR predicted future abundance declines to zero +as a result of climate change processes.
+ +Increase Vulnerability: Predicted future range represents 50-99% +decrease relative to current range within the assessment area OR predicted +future abundance represents 50-99% decrease associated with climate change +processes.
+ +Somewhat Increase Vulnerability: Predicted future range represents a +20-50% decrease relative to current range within the assessment area OR +predicted future abundance represents 20-50% decrease associated with climate +change processes.
+ +Neutral: Predicted future range represents an increase, no change, or +a decrease of less than a 20% relative to current range within the assessment +area OR predicted future abundance increases, remains stable, or decreases +< 20% as a result of climate change processes.
+ + +",NA +"D","3",NA,"Distribution models of current and projected future ranges should +meet standards described in the notes for D2. Overlap is calculated as the +percent of the current range represented by an intersection of the +predicted future and current ranges. If the range disappears or declines +> 70% within the assessment area, such that factor D2 is coded as +Greatly Increase Vulnerability, this factor should be skipped to avoid +double-counting model results.
+ +Greatly Increase Vulnerability: There is no overlap between the +current and predicted future range within the assessment area.
+ +Increase Vulnerability: Predicted future range overlaps the current +range by 30% or less within the assessment area.
+ +Somewhat Increase Vulnerability: Predicted future range overlaps the +current range by 30-60% within the assessment area.
+ +Neutral: Predicted future range overlaps the current range by > 60% +within the assessment area.
+ + +",NA +"D","4",NA,"'Protected area' refers to existing parks, refuges, wilderness +areas, and other designated conservation areas that are relatively +invulnerable to outright habitat destruction from human activities and that +are likely to provide suitable conditions for the existence of viable +populations of the species. Models of current and projected future ranges +should meet standards described in the notes for D2. Modeled future +distribution may refer to a single season (e.g., breeding season +distribution or winter distribution) for migratory species. This factor +considers ranges and protected areas within the assessment area only.
+ +Increase Vulnerability: < 5% of the modeled future distribution +within the assessment area is encompassed by one or more protected areas.
+ +Somewhat Increase Vulnerability: 5-30% of the modeled future +distribution within the assessment area is encompassed by one or more protected +areas.
+ +Neutral: >30% of the modeled future distribution within the +assessment area is encompassed by one or more protected areas.
",NA +"exposure",NA,NA,"+ The Index treats exposure to climate change as a modifier of sensitivity and + adaptive capacity. If the climate in a given assessment area will not change + much, none of the sensitivity/adaptive capacity factors will weigh heavily, + and a species is likely to score at the Less Vulnerable end of the range. + A large change in temperature or moisture availability will amplify the effect + of any related sensitivity/adaptive capacity factor, and will contribute + to a score reflecting higher vulnerability to climate change. In most cases, + changes in temperature and moisture availability will combine to modify + sensitivity and adaptive capacity factors. However, for factors such as + sensitivity to temperature change (factor 2a) or precipitation/moisture + regime (2b), only the specified climate driver will have a modifying effect. +
",NA diff --git a/data-raw/lookup_tbls.R b/data-raw/lookup_tbls.R index 75e9007..adb53cd 100644 --- a/data-raw/lookup_tbls.R +++ b/data-raw/lookup_tbls.R @@ -22,7 +22,7 @@ usethis::use_data(comb_index_tbl, overwrite = TRUE) # made a csv with the codes and questions but need to tidy it up -lu_tbl <- read.csv("../CCVI_analysis/data/Code_Q_lookup.csv") +lu_tbl <- read.csv("data-raw/Code_Q_lookup.csv") vulnq_code_lu_tbl <- mutate_all(lu_tbl, stringr::str_trim) %>% mutate(Question = stringr::str_remove(Question, "^..?\\)\\s") %>% @@ -41,5 +41,10 @@ ui_build_table <- ui_build_table %>% usethis::use_data(ui_build_table, overwrite = TRUE) +# table of guidelines (created in guideline_lu_tbl but edited in csv) +# Only needed internally +guideline_lu_tbl <- read.csv("data-raw/guideline_lu_tbl.csv") + # need to include all object for internal because they are saved together. -usethis::use_data(vulnq_code_lu_tbl, comb_index_tbl, ui_build_table, overwrite = TRUE, internal = TRUE) +usethis::use_data(vulnq_code_lu_tbl, comb_index_tbl, ui_build_table, guideline_lu_tbl, + overwrite = TRUE, internal = TRUE) diff --git a/data/comb_index_tbl.rda b/data/comb_index_tbl.rda index 58f1b35..b882db8 100644 Binary files a/data/comb_index_tbl.rda and b/data/comb_index_tbl.rda differ diff --git a/data/guideline_lu_tbl.rda b/data/guideline_lu_tbl.rda new file mode 100644 index 0000000..85ad676 Binary files /dev/null and b/data/guideline_lu_tbl.rda differ diff --git a/data/ui_build_table.rda b/data/ui_build_table.rda index 3213dd3..d6922ab 100644 Binary files a/data/ui_build_table.rda and b/data/ui_build_table.rda differ diff --git a/data/vulnq_code_lu_tbl.rda b/data/vulnq_code_lu_tbl.rda index 2d1d746..cee64b9 100644 Binary files a/data/vulnq_code_lu_tbl.rda and b/data/vulnq_code_lu_tbl.rda differ