United States ent of the interior

FiSH AND WILDLIFE SERVICE South Florida Ecological Services Office 1339 :30m Street Vero Beach, Florida 32960

February 9, 2010

Memorandum

To: Roxa . 11: David Dell

ieid Supervisor, South Florida Ecological Services Office

Subject: Biological opinion addressing effects of issuing a recovery permit (TE206774-0) to Sean Beckmann for research on the Key Largo

This document transmits the Fish and Wildlife Service’s (Service) biological opinion based on our review of the proposed issuance of a section 10(a)(l)(A) recovery permit to conduct surveys and collect genetic material of the endangered Key Largo cotton mouse ( gossypians aflaparicole) (KLCM) Within the hammock habitat on northern Key Largo, Monroe County, Florida. This study will examine if anthropogenic habitat fragmentation has led to a decrease in genetic diversity among isolated southeastern cotton mouse populations. The survey protocol employed in these studies may also incidentally trap the endangered (Neoz‘omafloridana smalli) (KLWR). This document is prepared in accordance with section 7 of the Endangered Species Act of 1973, as amended (Act) (87 Stat. 884; 16 [ISO 1531 et seq.)

This biological opinion is based on published literature, research reports, the permit application and subsequent correspondence, telephone conversations, field investigations, the captive propagation and reintroduction plan for the KLWR (Service 2003), and other sources of information. A complete administrative record of this consultation is on file at the South Florida Ecological Services Office (SFESO) in Vero Beach, Fiorida.

Consultation History

On May 16, 2008, Sean Beckmann of the University of Miami, Florida submitted a recovery permit application to the Service’s Southeast Regional Office. Permit number TE 206774~0 was assigned for the proposed project.

On September 2, 2009, the SFESO received a request from the Southeast Regional Office for formal consultation on the recovery permit mentioned above.

On September 3, 2009, the SFESO contacted the Southeast Regional Office via email to concur that the proposed action was likely to adversely affect the listed species and initiated formal consultation. On September 3, 2009, the Applicant supplied electronic copies of application materials to the SFESO.

BIOLOGICAL OPINION

DESCRIPTION OF PROPOSED ACTION

The proposed research will occur on Key Largo within Crocodile Lake National Wildlife Refuge (CLNWR) and Dagny Johnson Key Largo Hammock Botanical State Park (DJBSP) during October 2009 through August 2010. The proposed research will examine the effects of habitat fragmentation on KLCM genetic diversity. Specifically these studies are designed to help determine if County Road (CR) 905 impedes gene flow between KLCM populations within northern Key Largo. In addition, data from these surveys will also provide data on the status of the KLCM and KLWR within remaining hardwood hammock on northern Key Largo.

KLCM will be captured using live traps (vented Sherman traps with raccoon [Procyon later] proof latches, model number PXLFIS). Traps will be placed in 100 meter (m) X 50 m (328 feet [ft] x 164 ft) grids with two traps set at each 10 m (33 ft) interval resulting in 100 traps. Traps will be baited with a mixture of oats, sunflower seeds, and peanut butter to provide attractive bait for the small . Traps will be set on 4 consecutive nights per trapping session and checked daily no later than 2 hours after sunrise. Traps will remain on-site and baited during the day throughout each trapping event. In the unlikely event that small diurnal mammals, such as the hispid cotton rat (Sigmodon hispidus) enter the traps during daylight hours, then the traps will be closed after checking them in the morning and reopened in the late afternoon.

Trapping data will be recorded daily and shall include the total number of traps set, the total number of traps disturbed (sprung), species captured, and the location of the capture on the trapping array. Data recorded for any small captured will include species, sex, age, weight, and reproductive status. All KLCM and KLWR will be handled as briefly as possible in a humane manner during the time it takes to examine, and identify the species. To avoid stress on captured small mammals, trapping will not be conducted when nighttime temperatures are forecast to be below 600 F. In addition, if temperatures are forecast to be in the mid to low 60’s, cotton balls will be placed in the trap along with the bait to provide insulation against the bare metal of the Sherman trap.

Trap baits can greatly influence the trapping success of small mammals, but can also increase the attractiveness of traps to nontarget mammals, such as raccoons, a species known to cause significant trap disturbance in trapping studies of small mammals. If raccoon disturbance becomes a problem using attracting baits such as peanut butter, then the use of these attractants will be discontinued and plain cats will be used. If raccoon disturbance is continuing at a level that is believed to adversely influence the results of the survey, the Service will be consulted on appropriate action which may include the trapping and removal of raccoons from the study area. Trapping for raccoons will only be conducted in close coordination with the Service. Methods

2 for trapping raccoons and the disposition of any captured will be determined by the Service prior to the initiation of any raccoon trapping activities. If any free-roaming cats (Felis caters) are captured during raccoon trapping, the Service will be notified and the cats will be brought to the local shelter. Any black rats (Ratms rafters) captured during woodrat trapping will be euthanized.

Red imported fire ants (Solenopsis invicta) are capable of inflicting serious injury and death on small mammals while restrained in live traps. To avoid the potential injury or mortality of live-trapped small mammals, fire ant control will be initiated prior to and during the entire study period. Extinguish Professional Fire Ant Bait (Extinguish) will be used to exterminate and deter fire ants in the vicinity of the trapping sites. Extinguish uses an insect growth regulation hormone (Methoprene) to control reproduction and reduce fire ant colonies within 8 to 10 weeks following application. All application of Extinguish will follow label instructions.

Extinguish will be broadcast (consistent with product labeling) over the entire upland trapping area at the rate of 1.2 to 1.7 grams (g) of product per hectare (ha) (0.003 to 0.004 pounds [lbs] of product per acre) using a hand broadcast spreader. Application will begin 2 months prior to the initiation of trapping, and will continue quarterly throughout the study period. In addition to broadcast application, all visible fire ant mounds located throughout the study area and on the adjacent roadsides will be treated with 44.4 to 74 milliliters (3 to 5 tablespoons) of Extinguish placed directly onto the fire ant mound.

KLCM tissue will be collected from tail clippings taken during trapping. The terminal portions of cotton mice tails (1 to 3 millimeters [mm]) (0.04 to 0.1 inches) will be clipped with scissors and cleaned with rubbing alcohol. Before cutting, the mice tails will be numbed in ice cold ethanol. The mice tails will be cleaned with rubbing alcohol before being released to prevent infection. Each tail tip will be stored in a 20 percent dimethyl sulfoxide (6 M NaCl) solution for transport back to the lab. Up to 20 samples will be obtained and analyzed during this study.

The action area is defined as all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action. The Service has determined that the action area for this project to be CLNWR and DJBSP, Key Largo, Florida.

STATUS OF THE SPECIES AND CRITICAL HABITAT RANGEWIDE

The following discussion is summarized from the South Florida Mold-species Recovery Plan (MSRP) (Service 1999), the 5-year status reviews for the KLWR (Service 2008) and KLCM (Service 2009), as well as from recent research publications and monitoring reports. Ongoing research has focused on identifying the cause or causes of recent population declines, and on determining the current distribution and population size for the KLCM and the KLWR.

Key Largo Cotton Mouse

The KLCM was recognized by the Service in a notice of review on July 28, 1980, (45 FR 49961). It was listed as endangered for 240 days on September 21, 1983, through an emergency listing

3 action (48 FR 43 040). The emergency listing was necessary to provide full protection during Service consultation on a loan from the Rural Electrification Administration to the Florida Keys Electric Cooperative. The loan was to upgrade electrical delivery capability, potentially accelerating residential development on north Key Largo. The KLCM was proposed as endangered with critical habitat on February 9, 1984 (49 FR 4951) and was listed as an endangered species on August 31, 1984 (49 FR 34504). The listing cited habitat modification and development pressure as the primary threats to this species. The proposed critical habitat was withdrawn on February 18, 1986 (51 FR 5746).

Species/critical habitat description

The KLCM is a subspecies of the cotton mouse (Peromyscus gassypinus) that occurs throughout much of south Florida and the southeastern United States. The Key Largo subspecies is larger and more reddish in color than other subspecies of cotton mice from peninsular Florida. The pelage is red dorsally, with dusky brown sides and White underparts, and the tail is bicolored, darker brown on top and whiter underneath. They range in length from 170 t0189 mm (6.7 to 7.4 inches) (Service 1999).

Life history

The KLCM is omnivorous and feeds on a wide variety of fruits, seeds, and invertebrates (Brown 1978b). Over 70 percent of the tropical hardwood hammock trees and shrubs produce fruits and berries that may provide important food items for the KLCM.

The KLCM builds leaf-lined nests in logs, tree hollows, and rock crevices. Occupied holes measure 3 to 9 centimeters (cm) (1.2 to 3.5 inches) in diameter, are often partially covered by leaves or bark, and may be located at the bases of trees and near or in woodrat nests (Goodyear 1985)

The KLCM is capable of breeding year-round and may rear 2 to 3 litters per year, with an average of four young per litter (Brown 1978b). The average life expectancy is approximately 5 months, been there is evidence suggesting that this may be an underestimate (Greene 2008). The reproductive strategies of the KLCM have not been well documented, and it is unknown if there are seasonal fluctuations in reproductive output. Other Florida populations of cotton mice have high reproduction in the fall and early winter (Bigler and Jenkins 1975, Smith and Vrieze 1979) and reproduction may be affected by agonistic behavior by males or decrease in food supply (Smith 1982, Smith et a1. 1984). Cotton mice in the Everglades exhibit highly variable breeding patterns (Smith 1982).

The KLCM can move at least 2 km (1.2 miles) in 1 to 2 days (Service 1999). Males have larger home ranges than females, and home ranges overlap because cotton mice do not defend territories (Service 1999). Population dynamics

Historically, the KLCM occurred throughout the length of Key Largo south nearly to Tavernier (Osgood 1909; Barbour and Humphrey 1982). Their distribution is now patchy, congruous with the loss and fragmentation of hardwood hammock vegetation (Florida Fish and Wildlife Conservation Commission [FWC] 2005; Castleberry et a1. 2008). The present range of the KLCM is constricted to the northern one-third of Key Largo Where large tracts of contiguous tropical hardwood hammock occur, representing about one-half of their original distribution (Barbour and Humphrey 1982). The KLCM was introduced to Lignurnvitae Key in 1970 (Brown and Williams 197 l ), but was apparently unable to successfully establish a population. A trapping survey was conducted on the Key in 2007, and yielded no captures ofKLCM (Greene 2007)

The KLCM uses a variety of tropical hardwood habitats including recently burned, early successional, and mature hammock forests, and glasswort (Salicomia)-bearing coastal strands (sparsely-vegetated saline mud flats) adjacent to these forests (Humphrey 1992). Hammocks provide a shady, humid microclimate with less wind and temperature variation than more exposed habitats.

The KLCM is restricted to the northern portion of Key Largo and relies on the availability of natural cover for refugia and nest sites. Observations of animals released from traps suggest that they seek cover in limestone crevices, within hollow logs, and other cover. These features are relatively abundant in most of the tropical hardwood hammocks on Key Largo and are probably not limiting. Barbour and Humphrey (1982) report that KLCM occurred at lower densities in medium-aged forest than in mature forest, but Goodyear (1985), Frank et a1. (1997), and others, report capturing the KLCM in habitats ranging from mature hammock to recently burned early successional sites and uniform glasswort distribution. These data suggest that KLCM may be habitat generalists within their restricted range.

Status and distribution

The KLCM is restricted to a fraction of its former range. Approximately 880 ha (2,175 acres) of suitable KLCM habitat remains (Humphrey 1988;. Service 1999; FWC 2005) and individuals are found almost exclusively within public lands (CLNWR and DJBSP) (FWC 2005). Prior to development, the Upper Keys contained 4,816 ha (1 1,901 acres) of deciduous or hardwood hammock forests (Strong and Bancroft 1994). Much of the original tropical hardwood hammock on Key Largo was cleared in the past for development or agriculture, and the southern portion of Key Largo is nearly completely developed. Habitat loss and fragmentation have caused the isolation of KLCM populations. The physical separation caused by these activities makes it increasingly difficult to locate a mate and to disperse. Tropical hardwood hammock fragments up to 4 ha (9.9 acres) in size remain on south Key Largo, but may no longer be able to support the KLCM. These hammocks may be too small and isolated to support viable cotton mouse populations (Service 1999). Habitat fragmentation, combined with a decreased range, makes the KLCM more vulnerable to natural catastrophes such as hurricanes or fire, both of which have damaged significant portions of north Key Largo hammocks. Tropicalstorms and hurricanes pose serious threats to the viability of the remaining cotton mice populations. The small size and low elevation of the Keys uplands make it difficult for KLCM to find shelter from damaging winds and storm surge. In 1992, over 240 ha (593 acres) of vegetation in north Key Largo were severely damaged by Hurricane Andrew. Since that time, there is still evidence of habitat disturbance, but signs of KLCM use have been observed in the area.

Measures of trapping success over time have indicated a declining trend in the KLCM population. Long intervals (5 to 10+ years) between monitoring events and the use of various study designs and estimation techniques make KLCM population trends difficult to interpret (Barbour and Humphrey 1982; Humphrey 1988; Frank et a1. 1997; FWC 2005). Density estimates resulting from disparate methods and locations surveyed range from 6.2 KLCM per hectare (15.3 KLCM per acre) (Frank et al. 1997) to 21.2 KLCM per hectare (52.4 KLCM per acre) (Humphrey 1988), and demonstrate no clear population trend. Most recent population estimates (2007) yield approximately 17,000 individuals and an increasing trend from April to December (Castleberry et al. 2008).

Factors other than habitat loss appear to be impacting the cotton mouse. Frank et al. (1997) failed to document the KLCM at the southern end on north Key Largo, an area where only black rats were captured and exotic fire ants were abundant. Animals caught in traps where exotic fire ants were abundant were either dead or badly injured by the ants and trapping was discontinued in these areas following the initial night. This southern section of north Key Largo is generally disturbed; there are three residential subdivisions partly developed and commercial development. Much of the undeveloped area in this vicinity is highly disturbed from past land clearing, unfinished developments, and rock mining. The hammock habitat in this area is bisected by old roads, and several large abandoned buildings associated with the unfinished Port Bougainville development are present. Free-roaming cats are abundant in this area.

Key Largo Woodrat

Species/critical habitat description

The KLWR was first listed as a threatened species under the Endangered Species Conservation Act of 1969, which afforded it protection on Federal lands. The KLWR was recognized as a candidate for listing in a notice of review on July 28, 1980 (45 FR 49961). The KLWR was listed as endangered for 240 days on September 21, 1983, through an emergency listing action (48 FR 43040), to ensure that it was considered during consultation with the Rural Electrification Administration. The KLWR was proposed for listing as an endangered species with critical habitat on February 9, 1984, (49 FR 4951) and was finally listed as endangered on August 31, 1984 (49 FR 34504). The listing cited habitat modification and development pressure as the primary threats to this species. The proposal to designate critical habitat was withdrawn on February 18, 1986 (51 FR 5746). The KLWR is a small mammal endemic to the tropical hardwood hammocks of Key Largo, Monroe County, Florida (Schwartz 1952; Sherman 1955). It is a subspecies of the more widely-distributed eastern woodrat (N. floridana), which occurs throughout the southeastern United States. While eastern woodrats are locally common in north~central Florida, they do not occur in southern peninsular Florida, and the southernmost occurrence reported in peninsular Florida is from DeSoto County (Greer 197 8). The KLWR is geographically separated from the nearest population of eastern woodrats by approximately 241 kilometers (km) (150 miles).

The KLWR is a medium~sized with grey-brown fur on its back, shading into cinnamon coloration on the sides, and cream or white on the underside. The forefeet are white to the wrist, and the hindfeet are primarily white to the ankles. The woodrat has large round ears, large protuberant eyes, and a hairy tail. The head-and~body length ranges from 120 to 230 mm (4.7 to 9.1 inches), with a total length (including the tail) of 250 to 420 mm (9.8 t016.5 inches). On average, males weigh approximately 258 g (0.57 lbs), and females weigh 210 g (0.46 lbs) (Hersh 1981)

Life history

The KLWR is a resident of tropical hardwood hammocks on Key Largo, which is the climax vegetation of upland areas in the Keys. Hammocks provide a shady, humid microclirnate with less wind and temperature variation than more exposed habitats. The soils are poorly developed, typically consisting of shallow humus and litter overlaying the limestone substrate. The hammocks on the Keys are dominated by an overstory 9 to 12 m (29.5 to 39.4 feet) in height and composed of a variety of tropical species of trees, shrubs, and vines that occur throughout the West Indies. Common overstory species include gumbo limbo (Bursera simumba), pigeon plum (Cocoloba diversifolia), poisonwood (Metopium toxzfemm), and wild tamarind (Lysoloma latisiliquum). Understory vegetation is similarly composed of a variety of tropical shrubs.

Vegetative composition and structure influence density and distribution of woodrats by affecting their ability to find food resources, nest materials, and secure cover. KLWRs have been reported to reach their highest densities in the oldest, most mature tropical hardwood hammocks (Hersh 1981;, Barbour and Humphrey 1982). However, survey results from the 1990’s suggest that rock piles (including junk, building materials, tree-trimming refuse, and coral rock from agricultural and road-building operations) provide sites preferred by woodrats for their burrows and stick piles (Humphrey 1992). Humphrey (1992) indicates that density of small marmnals or signs of activity are often very high where trash is piled adjacent to roads, in utility rights~of~way and in forest tracts in which surface rock has been piled or windrowed by heavy machinery. Additionally, Humphrey (1992) suggests that, if not developed, a forest with a variety of seral ages can be suitable to KLWRs. Results of the most recent trapping efforts (2003 to 2005) have resulted in woodrat captures in all hammock age classes (Winchester 2007).

Crucial components of KLWR habitat include materials for building stick nests and ample cover (Rainey 1956). More recently, however, KLWRs have been found to occupy areas without obvious stick nests, instead using rock crevices, solution holes, abandoned cars, refuse, or rock piles for the basis of their nests (Goodyear 1985; Service 1999). Over 150 supplemental nest

7 structures (constructed of rock, wood, and recycled materials) have been placed Within CLNWR, with approximately 33 percent of these in use (Potts 2008).

KLWRs are nocturnal that feed primarily upon a variety of leaves, buds, seeds, and fruits (Brown 1978a). A variety of tropical fruits that occur in the hammocks is probably the dietary staple. KLWRs probably also consume a variety of invertebrates. As do other woodrat species, KLWRS cache food, such as seeds, for long periods of time.

Both male and female KLWRs are reported to reach sexual maturity at an age of approximately 5 months (Hersh 1981). The average gestation period for the KLWR is 38 days (Alligood et a1. 2008), which is similar to the 30 to 37 day gestation reported for the eastern woodrat (Timm et a1. 2000). KLWRS can breed year-round, though peaks in productivity appear to occur in the winter, and they may produce two broods annually (Brown 1978a). Captures of pregnant and nursing females suggest a peak in reproductive activity during the summer (Hersh 1981). The litter size in KLWRS ranges from one to four young, with two being the most common. After birth, young probably remain with females for several months, but probably leave the natal territory within 3 to 4 months. The life expectancy for the KLWR remains unknown, but is probably similar to that for the eastern woodrat, With an average life expectancy of approximately 1 year, and a maximum of approximately 3 years (Pitch and Rainey 1956, Goertz 1970).

KLWRs are generally territorial, and both males and females maintain home ranges (Hersh 1981). Overlapping ranges occur more frequently among females than among males, who appear to have low tolerance for one another (McCleery 2003). Home range size is approximately 0.24 ha (0.59 acres) (Hersh 1978), which is similar to that for the eastern woodrat. Nest sites may be focal points of territories. Dispersal patterns and timing remain largely unknown.

Population dynamics

Efforts to monitor the status of the KLWR population began in the 19703 and have continued intermittently (Frank et a1. 1997). Past studies and monitoring efforts indicate that the KLWR population has experienced a substantial decline sometime in the late 1980s and early 19905 (Frank et a1. 1997).

Key Largo woodrat densities on north Key Largo have been variously estimated at 12 animals per ha (3 per acre) (Brown 1978a), 2.2 per ha (5.4 per acre) (Barbour and Humphrey 1982), 2.5 per ha (6.2 per acre) (Hersh 1981), and 7.6 per ha (18.8 per acre) (Humphrey 1988). The large differences in the density estimates of Barbour and Humphrey (1982) and Humphrey (1988) apparently result from differences in sampling techniques. The methods used by Humphrey (1988) are statistically based and may provide the most reliable estimate of population densities. Overall, Key Largo woodrat populations occurred in low densities (Barbour and Humphrey 1982). Both male and female densities follow a similar pattern of gradual increase in late summer to early fall (Hersh 1981). Populations adjacent to housing complexes usually have much lower densities (3.1 per ha [7.7 per acre]), than areas removed from development (12.2 per ha [302 acre]).

Goodyear (1985), Frank et al. (1997), Keith and Gaines (2002), and McCleery (2003) all conducted trapping along transects or grids that were widely distributed throughout hammock vegetation on north Key Largo. Goodyear (1985) reported that KLWRs were present on 30 of the 45 transects (67 percent) where they trapped. Frank et al. (1997) reported KLWR presence on 14 of the 41 transects (34 percent) where they trapped. Keith and Gaines (2002) reported the presence of KLWRs on 21 of 35 transects sampled from 1997 to .1999. McCleery (2003) placed traps in 60 randomly-placed trapping grids on north Key Largo in 2002 and trapped KLWRs on only 10 (17 percent) of them. Since intensive trapping of KLWRs began in 1976 (Hersh 1981), trap success has declined. In 1976, the average number of trap nights required to capture one KLWR was only 15, compared with 250 in 2001 (McCleery 2003).

Barbour and Humphrey (1982) conducted a status survey in 1979 and estimated that there were 3,666 KLWR stick nests and 645 individual KLWRs over an area of 90 ha (222 acres). The largest decline appears to have occurred between 1986 and 1995, when no KLWR monitoring was conducted, and the population appears to have continued this decline since 1995. The estimated population size from March to September 2002 was 106 individuals, while estimates from four surveys done from October 2002 to April 2003 only yielded estimates of 26 to 46 individuals (McCleery 2003), however, this estimate appears to be low. In 2005, a combined trapping effort by Service biologist B. Muiznieks and graduate student C. Winchester (University of Georgia) yielded 88 individual woodrats captured in 2005 (Winchester 2007). The population may have declined to the point where extinction is likely (Frank et al. 1997), and even if limiting factors are ameliorated, it will be many generations before the population size rebounds.

Eastern woodrats appear to be more limited by availability of shelter than by food, and the same may also be true for KLWRs. The destruction of hammock trees can directly affect the KLWR’S ability to build its large stick nests which provide a place for shelter, nesting, feeding, and breeding. The availability of stick nest material and ground cover may be essential for KLWR survival. Loss of hammock trees also results in the loss of arboreal habitat used by this species. Sufficient available habitat is also necessary for the development of social interactions and systems of organization (Kinsey 1977). Where shelter is sparse and stick nests are limited, territorial and competitive behaviors are exhibited more frequently. These behaviors result in a breakdown of social organization and aggressive behaviors that may result in death or casting out of subordinate animals (Kinsey 1977 ; McClure 1981). The majority of currently known KLWR nests occur within rock/rubble piles or old debris piles (116., boats, refrigerators, discarded concrete) and to a lesser degree in stick nests or nests with obvious stick piling (Winchester, 2006)

Although woodrats are omnivorous, habitat destruction or degradation directly affects food resources and the ability of woodrats to forage. Without adequate nutrition, reproductive behaviors may be impaired. Under normal conditions, some small mammal mothers expend lactation energy equally between male and female offspring, but when food resources are limited, the mothers tend to a greater bias for nursing female young over males (McClure 1981).

9 When KLWR mothers are faced with limited food resources, they may respond similarly by either favoring female offspring, or reducing the fitness of large litters. Either way, a reduction in fitness in the young may be a maternal response to adverse environmental conditions (Sikes 1995).

Physical separation caused by habitat loss and fragmentation leads to increased difficulty locating a mate and can isolate populations. Any lack of recruitment ofjuveniles into the population will result in a decline of the population. Small, isolated populations are subject to inbreeding depression, which can cause populations to decline over time. An increase in urbanization also results in an increase in the need for roads that separate and fragment habitats. The KLWR requires a minimum habitat size for daily activities, and habitat destruction can directly reduce home range size and disrupt movement and dispersal patterns. The hammocks on north Key Largo are bisected by a high-speed road (CR 905), which disrupts the integrity of the hammocks and causes road mortality of dispersing woodrats.

The apparent decline in the woodrat population has been dramatic, and there is no evidence that the population is recovering. During the period of greatest decline, there was almost no loss of tropical hardwood hammock habitat on upper Key Largo. To date, the cause or causes of the decline remain poorly understood.

Status and distribution

While population trends are difficult to interpret from the various study designs and estimation techniques (Barbour and Humphrey 1982; Humphrey 1988; McCleery 2003; Potts et al. 2007), surveys in the last 20 to 25 years suggest a declining population, currently at very low densities (FWC 2005; McCleery et al. 2006; Winchester 2007). There is no appropriate estimate of population size to more precisely assess the severity of the decline. Population modeling yielded a high risk of extinction for KLWR within the next 10 years (McCleery et a1. 2005; McCleery et al. 2006).

The distribution of KLWRs within the hammocks ofNorth Key Largo appears to have changed over time. Goodyear (1985), Frank et al. (1997), and McCleery (2003) all conducted trapping along transects or grids that were widely distributed throughout hammock vegetation on North Key Largo. Goodyear (1985) reported that KLWRs were present on 30 of the 45 transects where she trapped (66 percent). Frank et al. (1997) reported KLWR presence on 14 of the 41 transects where they trapped (32 percent). McCleery (2003) trapped at 60 randomly-placed plots on North Key Largo, and found KLWRs on 10 (17 percent). Winchester (2007) captured KLWRs on 7 of 40 randomly placed grids (18 percent). These data suggest a consistent reduction in the distribution of KLWRs on North Key Largo. Recently however, Greene (2007) trapped KLWRS at 17 of 34 random grids (50 percent). At present, it is unclear whether the most recent field data indicate a true increase in abundance or a change in detection probabilities.

The largest decline appears to have occurred between 1986 and 1995, when no KLWR monitoring was conducted. The population appears to have continued this decline since 1995. Comparisons of population size estimated by Humphrey (1988) and more recent population

10 estimates suggest that the population may have declined by 97 percent or more since 1986 (Service 2003). This magnitude of decline has not been recorded in other woodrat species without substantial changes in habitat characteristics that result in inhospitable conditions or outbreak of a lethal disease. There is no evidence that either of these events have occurred on Key Largo.

Historically, the KLWR occurred throughout the length of Key Largo south nearly to Tavemier (116., Rock Harbor; Schwartz 1952). Their distribution is now patchy, congruous with the loss and fragmentation of hardwood hammock vegetation (McCleery 2003; FWC 2005). The present range of the KLWR includes the northern one-third of Key Largo where large tracts of contiguous tropical hardwood hammock occur, representing about one-half of their original distribution (Barbour and Humphrey 1982; Humphrey 1992).

Residential and commercial development is considered the cause of extirpation of KLWR south of the intersection of US 1 and CR 905 (Brown 1978; Hersh 1981). Approximately 880 ha (2,175 acres) of suitable KLWR habitat remains (Humphrey 1988; Service 1999; McCleery 2003; Service 2003; FWC 2005), and individuals are found almost exclusively within public lands (CLNWR and DJBSP) (FWC 2005). A few private tracts adjacent to public lands contain suitable habitat and are vulnerable to urbanization.

Much of the original tropical hardwood hammock on Key Largo was cleared in the past for development or agriculture, and the southern portion of Key Largo is nearly completely developed. These unnatural, patchy incidences of disturbance have resulted in a mosaic of various patch ages that together represent habitat of inferior quality to KLWRs. The only remaining large contiguous tract of tropical hardwood hammock vegetation occurs on the northern half of Key Largo. Approximately 880 ha (2,175 acres) of the remaining 1,011 ha (2,498 acres) of tropical hardwood hammock are protected within the boundaries of CLNWR and DJBSP (Service 2003). Much of the remaining (unprotected) 131 ha (324 acres) consists of private lands cleared several decades ago and abandoned. Successful regrowth of the hammock, and consequently the suitability of the habitat to KLWRs, varies among these sites.

CLNWR and DJBSP were acquired in 1980 and 1982, respectively. Since initial acquisition, both sites have been managed to maintain and restore the native tropical hardwood hammock vegetation on which the KLWR depends, and have continued acquisition of remaining hammock habitat on north Key Largo. Many tracts on these sites were cleared for development or agriculture earlier this century, but hammock vegetation has returned to many of these previously cleared sites. The remaining forest is now composed of a variety of successional stages of tropical hardwood hammock vegetation, reflecting the time since and extent of disturbance.

Theories regarding the habitat preference of KLWR appear to conflict. Once believed to reach highest densities in mature hardwood hammocks (Brown 1978; Hersh 1981; Barbour and Humphrey 1982; Service 1999), KLWRs are now known to use a variety of successional habitat conditions (Goodyear 1985), possibly preferring young hardwood hammock (McCleery 2003). As these habitat types differ mainly in species composition, their physiognomies (in, life form, architecture of canopy layers) being comparable, the conflicting assessments of preferred habitat

11 may be a result of differing uses of habitat nomenclature. Furthermore, hammock age classes are confounded with disturbance and the presence of artificial structures, making habitat preference associations with trapping data problematic (Winchester 2007).

A captive KLWR breeding population was established in April 2002 when a juvenile male and a juvenile female were brought to Lowry Park Zoo, in Tampa, Florida. Since the inception of captive propagation program, a total of 15 wild~caught KLWRs have been brought into captivity for the purpose of captive propagation, and 14 KLWRs were born in captivity. Several deaths of captive KLWRs have occurred, and at the end of 2005, 21 individuals (9 wild~caught and l2 captive born) remained in captivity. All captive births to date occurred during 2003 and 2004 at Lowry Park Zoo. In 2005, captive propagation efforts expanded when the captive population at Lowry Park Zoo was split, and ll KLWRs were transferred to Disney's Animal Kingdom, in Orlando, Florida, to found a second captive population. Successful reproduction in captivity appears to be the primary factor limiting the captive population. During 2005, there were no KLWR births in captivity, despite well over 100 captive breeding attempts. Efforts to successfully breed KLWRs in captivity are the current focus of the captive propagation program.

Current threats

Research and monitoring of the KLWR and KLCM has revealed more information about threats to these Species since the time Multi-Species Recovery Plan (Service 1999) and 5-year status reports (Service 2008; Service 2009) were prepared. The following discussion is intended to give an up-to~date analysis.

Disease: Raccoon roundworrn (Baylz’sascaris procyom‘s), while a concern for other woodrat subspecies, has not been reported in south Florida (Forrester 1992). Surveillance for the raccoon roundworm was initiated on Key Largo in 2002, and there is no evidence that this parasite is present within the range of the KLWR (McCleery et a1. 2005). As this roundworrn is a common parasite of raccoons throughout much of North America and usually results in death in woodrat species (Logiudice 2001), the severity of this threat is high, while the scope remains low.

There are a wide variety of other diseases and parasites that might infect the KLWR and KLCM, but we lack evidence of the presence of such diseases or parasites. Additional parasite and disease surveillance effort is necessary to evaluate this potential threat.

Predation: The KLWR and KLCM have a number of natural predators: raptors, corn snakes (Elaphe guttato), diamondback rattlesnakes (Crotalus adamanteus), Florida black racers (Colaber constrictor priapus), Keys rat snakes (Elaphe obsolete deckerti), owls, and possibly raccoons (Procyon later). Nonnative predators include free-roaming cats, fire ants, and may include young Burmese pythons (Python molums bivz‘tattus).

Fire ants have been identified as a threat to small mammals (Killion and Grant 1993), ground- nesting birds (Allen et al. 1995), and other species. Newborn or hatching animals are susceptible to being killed by fire ants, as well as any confined animal (Vinson 1997). Fire ants would not

12 normally pose a threat to adults that are capable of escaping. There have been two instances where the ants have been found scavenging on KLCM carcasses within a trap (despite the use of Sevin dust). However, necropsies of these individuals discovered serious illnesses (116., pulmonary congestion, parasites) and determined the fire ant attacks as post mortem (Thomas 2002)

Precuroarning cats almost certainly would pursue and kill KLWRs if the opportunity arose (Churcher and Lawton 1987; Hawkins et al. 1999; Castillo 2001). Cats have been observed within the tropical hardwood habitats where the KLWR occurs (Muiznieks 2006). Clarke and Pacin (2002) report that between 1995 and 1999 a managed cat colony consisting 500 to l000 individuals has been maintained at the Ocean Reef Club on the north end of Key Largo. This location is immediately adjacent to tropical hardwood hammock habitats that at one time supported the KLWR.

Studies of food habits of feral cats have shown that mice often compose a large proportion of the diet (Churcher and Lawton 1989). The free-roaming cats on North Key Largo undoubtedly impact cotton mouse populations. The direct and indirect impacts of cats on the cotton mouse population are difficult to quantify. However, researchers have shown that 34 percent of residences on Key Largo own cats (FWC 2003). The FWC (2003) indicates that 60 percent of the cats on Key Largo are maintained occasionally or entirely outdoors and that these cats will stalk prey in cotton mice suitable habitat. Not only will the cats prey on the cotton mice but they also may cause behavioral changes. Studies suggest that prey behavioral changes in response to predation risk can result in significant effects on prey-body growth rate and reproductive output. The nonlethal impacts of predation risk are most likely determined by a complex mix of predator abundance, prey food supply, habitat structure and the relative distribution of these in space (Arthur et al. 2004).

Seven nonnative Burmese pythons have been captured in Key Largo since April 2007, and predation of KLWRS by Burmese pythons was documented in 2007 (Snow 2008). An eradication program for this nonnative predator is in place, but largely relies on reports from the public. Inna-agency partnerships have developed to assess ecological risks, encourage responsible pet ownership, organize exotic pet amnesty days and media campaigns, and form a rapid response team. To specifically protect the KLWR and KLCM, the Service has funded a USGS project that includes a multifaceted effort to detect and control Burmese pythons on Key Largo using visual surveys and several types of experimental traps to capture pythons.

Competitors: Dumping of trash increases the size ofblack rat populations, and rodent control agents used for black rats also kill KLCM and KLWR. Black rats may compete against KLCM and KLWR, but their effect these species is not known (Service 1999). The presence of competitors, particularly nonnative species, is a significant influence on habitat suitability. Black rats are believed to be the primary cause of extinctions of two other cotton mouse subspecies (Service 1999), and have been shown to cause KLCM to reduce their home range size (Sasso and Gaines 2002). In the past, black rats were captured at equal or greater numbers as KLWRs on hammock study sites (Hersh 1981), and thought to be a serious competitor, but

13 subsequent trapping sessions have yielded very few captures of brown rats (Rattas norvegz'cus) (Barbour and Humphrey 1982; Goodyear 1985).

Gambian giant pouch rats (Cricetomys gambianus), were unintentionally released in Marathon, Florida in 1999. Possible sightings on Key Largo have not been confirmed with trapping (Engeman et al. 2006), but due to their large size, high fecundity, and similar habitat requirements, their impact on KLCM and the KLWR could be extensive. An eradication program initiated in Marathon appears to have been successful, though the pouch rats could emigrate by several means (Engeman et al. 2006). Furthermore, the hurricanes of 2005 may have assisted in their dispersal to nearby islands. The severity of this threat is high, while the scope remains moderate. 7

Hurricanes: Hurricanes influence vegetational succession in the Florida Keys. Undisturbed hammocks are presumably more resistant to storms than hammocks that have been fragmented or have had surrounding mangrove and transitional vegetation removed. Damage to habitat from past hurricanes has included windshear, significant canopy loss, uprooting of large trees, understory damage, and significant soil disturbance. Extensive damage represents habitat loss to KLWR and KLCM, but some disturbance serves to open habitat and allow for greater plant diversity. The severity and scope of this threat are variable and stochastic.

Sea level rise: The longwterm record at Key West (approximately 161 km [100 miles] southwest of Key Largo) shows that sea level rose approximately 8.76 inches (22.4 cm) over the last 100 years (NCAA 2008). Projections from current modeling (IPCC 2007; Rahmstorf 2007; TNC 2009) suggest SLR ranging from 18 cm (7 in) to 140 cm (55.1 in) by the year 2100. However, the specific effects across the landscape will be affected by complex interactions between geomorphology, tides, and fluctuations in energy and matter. Human developments will also likely be significant factors influencing whether natural communities can move and persist (IPCC 2008). It is not known whether KLWR and KLCM habitat are already impacted by SLR. However, SLR has been shown to affect conversions of upland communities with low soil and moisture salinities to communities comprised of more salt tolerant plant species and higher soil and groundwater salinities (Ross et al. 1994). Therefore SLR, even under the more modest predictions, will likely result in a substantial loss of suitable KLWR and KLCM habitat through inundation or vegetative species composition changes on northern Key Largo.

ENVIRONMENTAL BASELINE

The environmental baseline includes the effects of past and ongoing human and natural factors leading to current status of the species and their habitats.

Climate Change

According to the Intergovernmental Panel on Climate Change Report (IPCC 2007), warming of the earth’s climate is unequivocal, as is now evident from observations of increases in average global air and ocean temperatures, widespread melting of snow and ice, and rising sea level. The IPCC Report (2007) describes changes in natural ecosystems with potential widespread effects

14 on many organisms, including marine mammals, reptiles, and migratory birds. The potential for rapid climate change poses a significant challenge for fish and wildlife conservation. Species abundance and distribution are dynamic, relative to a variety of factors, including climate. As climate changes, the abundance and distribution of fish and wildlife will also change. Highly specialized or endemic species are likely to be most susceptible to the stresses of changing climate. Based on these findings and other similar studies, the Department of the Interior requires agencies under its direction to consider potential climate change effects as part of their long-range planning activities (Service 2008).

Climate change at the global level drives alterations in weather at the regional level, although weather is also strongly affected by season and local effects (e.g., elevation, topography, latitude, proximity to the ocean). Average temperature is predicted to rise from 2 to 5 0C (36 to 41013) for North America by the end of this century (IPCC 2007). Other processes to be affected by this projected warming include rainfall (amount, seasonal timing, and distribution), storms (frequency and intensity), and sea level rise. However, the exact magnitude, direction, and distribution of these changes at the regional level are not well understood or easy to predict. Seasonal change and local geography make prediction of the effects of climate change at any location variable. Climatic changes in south Florida could amplify current land management challenges involving habitat fragmentation, urbanization, invasive species, disease, parasites, and water management (Pearlstine 2008).

Air Temperature

Current models predict changes in mean global temperature in the range of 15.6 to 13.3 0C (4 to 80F) by 2100. How this manifests at the regional and local scale is uncertain. A change ofjust a couple degrees can have profound effects, particularly at temperature extremes. For example, in Florida, winter frost, a 2-degree transition from 33oF to 310F, greatly affects vegetation. While predicted changes in average annual temperature appear small, local and seasonal temperature variation may be greater. It is also important to consider that an increase in the temperature of the global atmosphere may manifest as an increase or a decrease in local means and extremes. We do not currently know either the direction or anticipated size of temperature change in Florida, but the following possibilities at the local level should be considered:

Changes (likely small) in mean annual temperature. Greater extremes of temperature in summer (average highs) and Winter (average lows). More prolonged and seasonally extended frosts. Shifts in the distribution of temperature regimes (ag, isotherms and growing zones). Changes in the seasonal onset of temperature changes (e.g., earlier spring). Changes in the duration of temperature regimes (e.g., longer and warmer summers). NQ‘SAF‘WS‘Q?‘ Changes in both air and water (lake, river, ocean) temperature. Most organisms have preferred ranges of temperature and lethal temperature limits they cannot survive. Many organisms require temperature signals or suitable temperature regimes to successfully complete life cycle activities such as nesting and winter dormancy. Some are sensitive to for sex determination sea organisms temperature incubation, (e.g. , turtles,

15 alligators), or seed germination. The oxygen content of water (affecting fish) and the water content of vegetation (affecting fire combustion) are temperature-dependent. Some noxious or undesirable organisms may proliferate under different temperature regimes (e. g, blue green algae in lakes and exotic species). Changes in temperature will likely affect fish and wildlife resources in many ways depending on the direction, amount, timing, and duration of the changes.

Rainfall

Ecosystems in Florida are sensitive to variation in rainfall. Well-drained soils, rapid runoff, and high plant transpiration quickly redistribute water available to organisms. Despite a high average rainfall, much of Florida experiences seasonal drought that profoundly affects fish and wildlife resources. Florida’s rain depends on both global and regional climate factors (rag, jet stream, storms and and local weather sea El Nifio, frontal progression, hurricanes) (9.g. , thunderstorms, breezes, lake effects and local circulation) that are likely affected by climate change. The following possibilities at the local level should be considered:

in annual rainfall or Changes average (e.g. , higher lower). Changed seasonal distribution of rainfall (ag, when rain falls). Changed regional distribution of rainfall (rag, where rain falls). :‘rWP‘JT‘ Changed intensity (e.g., more severe storm rain, or dispersed “misty” rain).

Rainfall changes are affected by temperature. The affects of changes in rainfall will likely be mediated through responses by vegetation and the changed availability of surface water (eg, lakes, ponds, rivers, swamps, and wet prairies) on which many organisms depend. In the longer term, changes in deposition or recharge to surficial and deep aquifers may affect spring flow. Florida has an unusually large area of wetland habitats supporting wildlife. lf climate change reduces rainfall, then desertification of much of Florida is possible and it may come to resemble “desert islands” such as much of the Bahamas that occur at the same latitude. Rainfall changes may have the most profound effects on Florida’s fish and wildlife resources.

.Strnms

Another predicted effect of climate change is to increase the frequency and intensity of severe storms, particularly tropical cyclones (hurricanes). Higher sea temperatures and high atmosphere conditions generate energy and conditions suitable for storms. There is some controversy about whether this effect is already discernible against the background of natural variation and cycles of hurricane occurrence.

Hurricanes are generally considered detrimental to human interests and may directly cause wildlife mortality. However, their effect in natural systems is generally transient; plants and animals tend to rapidly recover. Hurricanes do have significant secondary effects, reshaping coastal habitat structure (barrier islands, beaches, salt/fieshwater intrusion to marshes, and estuaries), replenishing water bodies and aquifers and renewing plant succession, which are not completely negative for wildlife. Hurricane effects will interact with rainfall and sea level changes, possibly exacerbating coastal flooding. Hurricanes also redistribute organisms,

l6 particularly plants, by spreading seeds and other propagules. The following possibilities at the local level should be considered:

Changes in storm intensity and frequency. Nina Changes in the possibility of more concentrated storm tracks leading to more frequent storm landfall. 3. Interaction of surge and sea level for more severe coastal and adjacent inland effects. 4. Distribution of invasive species.

Sea Level Rise

All current predictions suggest sea level will rise due to melting of continental and glacial ice and thermal expansion of the oceans. Florida, with its extensive coastline and low topography is highly vulnerable to SLR. The magnitude of the predicted rise is currently unknown and estimates vary from a few inches to yards. Modeled predictions using median consensus sea level rise estimates indicate that significant portions of Florida’s coastline will be inundated and a major redistribution of coastal habitats is likely. However, to put this in context, Florida’s coast currently experiences sea level fluctuations of 0.6 to 1.8 m (2 to 6 feet) twice daily as tides and is exposed to storm surges of 3 to 4.9 m (10 to 16 feet) in occasional hurricanes. Sea level changes will be superimposed on these normal, larger fluctuations. While these changes will likely be disastrous to human structures and activities, the effect on Wildlife and its habitat may be less damaging. In essence, coastal habitats Will migrate inland and Florida’s flat coastal topography, a result of previous sea level changes, will mitigate the effect. Current coastal forests, dunes and beaches will migrate inland and be displaced by marsh, while current marsh will become sea grass, barrier islands will become sandbars and new barrier islands arise. The primary effect for wildlife will be redistribution, and possibly increase in some habitats at the expense of others.

More profound changes in the coastal and marine environment may be driven by the temperature and rainfall effects that may promote the distribution of mangroves and coral reefs into the expanded coastal zone. The main hazard to Wildlife from SLR will arise from efforts to protect human structures from these changes by dikes, seawalls, dredging, beach nourishment and similar engineering responses. Changes in temperature regimes in the ocean may cause shifts in distribution of marine species, and profound but entirely unpredictable effects may be generated if climate changes causes large scale change in ocean circulation such as the Florida Current. The following possibilities at the local level should be considered:

1. but effects on vulnerable coastal beach Transient damaging species (a.g. , nesting shorebirds, and sea turtles). 2. Redistribution of coastal habitats with disruptions of productivity. DJ Sedimentation effects during the transition. with other climate effects and storm to 4. Interactive synergy (6.g. , temperature, frequency) generate unanticipated second order effects. 5. Disruption of coastal migration patterns, particularly “passive” migrations of larvae driven by local water movement effects.

17 6. Secondary effects of protection of human structures. 7. Migration zones and corridors available to allow changes in distribution.

To summarize, effects of climate change on wildlife in Florida are likely to be widespread and profound, and occur over a variety of dimensions and variables. As these effects cannot be prevented or delayed under current circumstances, a practical response will be to identify key areas and key species and habitats that are vulnerable to irreversible change and develop policy and planning to mitigate effects on these vulnerable entities.

Global warming will be a particular challenge for endangered, threatened, and other “at risk” species. It is difficult to estimate, with any degree of precision, which species will be affected by climate change or exactly how they will be affected. However, as it relates to nesting sea turtles, if predictions about global warming are realized, increased storms and rising sea levels could damage or destroy nests and nesting habitat, and temperature changes could skew sex ratios. In regard to piping plovers, increased storms and rising sea levels could damage, destroy, or otherwise alter foraging and roosting habitat. Consequently, the Service will use Strategic Habitat Conservation planning, an adaptive sciencewdriven process that begins with explicit trust resource population objectives, as the framework for adjusting our management strategies in response to climate change (Service 2006).

Key Largo Cotton Mouse and Key Largo Woorat

Status of the Species/Critical Habitat Within the Action Area

The entire known ranges for the KLCM and KLWR occur within the action area. Information presented in the preceding section establishes the Environmental Baseline for the KLCM and KLWR. The information from that section is incorporated here by reference.

No critical habitat has been designated for the KLCM and KLWR.

Factors Affecting the Species Habitat Within the Action Area

Long-term habitat impacts from developmentwrelated disturbance in the 19603 and 1970s have resulted in degraded habitat conditions on Key Largo. Much of the original tropical hardwood hammock on Key Largo was cleared in the past for development or agriculture, and the southern portion of Key Largo is nearly completely developed. In addition, the hammocks on northern Key Largo are bisected by a high-speed road (CR 905), which disrupts the integrity of the hammocks and causes road mortality of dispersing cotton mice.

Habitat fragmentation, combined with a decreased range, makes the KLCM and KLWR more vulnerable to genetic isolation and natural catastrophes such as hurricanes or fire, both of which have damaged significant portions of north Key Largo hammocks. Hurricanes influence vegetational succession in the Florida Keys. Undisturbed hammocks are presumably more resistant to storms than hammocks that have been fragmented or have had surrounding mangrove and transitional vegetation removed. In August 1992, Hurricane Andrew hit Elliott Key, a few

18 miles north of Key Largo. The northern one-third of Key Largo suffered the most extensive damage, with about 240 to 280 ha (593 to 692 acres) affected. The area of greatest impact, comprising about 80 ha (198 acres), suffered 70 percent canopy loss. -

The majority of remaining high quality hammock habitat on north Key Largo has been protected through acquisition and management by the Service and State of Florida. CLNWR was acquired in 1980, and DJBSP was acquired in 1982. Approximately 880 ha (2,175 acres) of the remaining 1,011 ha (2,498 acres) of tropical hardwood hammock are protected within the boundaries of these two sites, and acquisitions continue. Many tracts on these two sites were cleared for development or agriculture in the early 1900’s, but hammock vegetation has returned in many areas. The remaining forest is now composed of a variety of successional stages of tropical hardwood hammock vegetation, reflecting the time since disturbance. As a result of these efforts and current land use regulations in place by Monroe County, the threat of occupied habitat loss from development on northern Key Largo is low.

EFFECTS OF THE ACTION

This section includes an analysis of the direct and indirect effects of the proposed action on the species and/or critical habitat and its interrelated and interdependent activities. All activities authorized by the Service under section lO(a)(l)(A) of the Act must meet permit issuance criteria at 50 CFR 17.22 and 17.32. All activities considered must be justified in relation to enhancement of survival and recovery, effects to the wildlife species, peer review, and qualifications of permittees. By definition, authorized activities should benefit species recover with minimal adverse effects by qualified pennittees. -

Factors to be Considered

The work that will be conducted under the proposed research will examine if anthropogenic habitat fragmentation has led to a decrease in genetic diversity among isolated southeastern cotton mouse populations. In addition, data from these surveys will help to determine the status of the KLCM within remaining hardwood hammocks on northern Key Largo. While conducting KLCM surveys, KLWRs are likely to be incidentally trapped.

Analysis for Effects of the Action

Beneficial Effects - The proposed research will examine the effects of habitat fragmentation on KLCM genetic diversity. Specifically these studies may help measure the extent to which CR 905 impedes gene flow between KLCM populations within northern Key Largo. In addition, data from these surveys will help to determine the status of the KLCM within remaining hardwood hammock on northern Key Largo. The expected benefit of the proposed research is that it will ultimately aid. in the recovery of the KLCM.

Adverse Effects - Handling of the KLCM and KLWR may result in incidental injury or death of individuals. While this type of effect is uncommon with proper training or experience in handling of , the potential for such injuries or deaths remains.

19 Species’ Response to the Proposed Action

Although the Applicant does not anticipate any injury or mortality of KLCM or KLWR, the capture and handling of these species may result in injury or mortality of some individuals. Once confined within traps, the rodents may be subject to depredation by predators, such as raccoons or fire ants. All live traps will have a mechanism to prevent raccoons from opening traps that contain rodents to minimize the potential for this type of mortality. The Sherman live traps have locking doors to prevent raccoon predation. Fire ants have been known to attack and kill rodents confined within the traps (Muiznieks 2005). Use of an approved pesticide, Extinguish, around traps in areas where fire ants are known to occur will reduce the potential of captured rodents being killed or injured by fire ants.

The capture, handling, and monitoring of the KLCM is needed to help determine if anthrogenic - habitat fragmentation has led to a decrease in genetic diversity among isolated southeastern cotton mouse populations.

CUMULATIVE EFFECTS

Cumulative effects include the effects of future State, local, or private actions that are reasonably certain to occur in the action area considered in this biological opinion. Future Federal actions that are unrelated to the proposed action are not considered in this section because they require separate consultation pursuant to section 7 of the Act.

Because nearly the entire remaining potential habitat for the KLCM and KLWR occurs within publicly-owned land, actions resulting in cumulative effects are unlikely. Management activities within hammock habitat in CLNWR and DJB SP are entirely conservation-oriented. The Service is not aware of any State, local, or private activities that are reasonably certain to occur within the action area that would adversely affect the KLCM or the KLWR.

SUMMARY OF EFFECTS

Although short-term, adverse effects to the KLCM and KLWR may occur from trapping, and handling, which may result in injury or death; this research will lead to an increased understanding of the status these endangered species within the action area. The net effect of the research is beneficial.

CONCLUSION

Although both the KLCM and KLWR are endangered, the potential for their recovery is great if threats can be identified and then eliminated or minimized. Information concerning present levels of genetic diversity and variation in these species on northern Key Largo is limited. Measuring the extent to which habitat fragmentation impedes gene flow between KLCM and KLWR populations will greatly aid in the recovery of these species. The proposed studies are designed to help gather this important data for the KLCM.

20 After reviewing the current status of the KLCM and the KLWR, the environmental baseline for the action area, the effects of the proposed action, and the cumulative effects, it is the Service’s biological opinion that the issuance of a recovery permit, as proposed, is not likely to jeopardize the continued existence of the KLCM or the KLWR. No critical habitat has been designated for these species; therefore, none will be affected.

INCIDENTAL TAKE STATEMENT

Section 9 of the Act and Federal regulation pursuant to section 4(d) of the Act prohibit the take of endangered and threatened species, respectively, without a special exemption. Take is defined as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to engage in any such conduct.- Harm is further defined by the Service to include significant habitat modification or degradation that results in death or injury to listed species by significantly impairing essential behavioral patterns such as breeding, feeding, or sheltering. Harass is defined by the Service as intentional or negligent actions that create the likelihood of injury to listed species to such an extent as to significantly disrupt normal behavior patterns, which include, but are not limited to, breeding, feeding, or sheltering. Incidental take is defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise lawful activity. Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to and not intended as part of the agency action is not considered to be prohibited taking under the Act provided that such taking is in compliance with the terms and conditions of this incidental take statement.

The measures described below are nondiscretionary, and must be undertaken by the Service so that they become binding conditions of any grant or permit issued, as appropriate, for the exemption in action 7(o)(2) to apply. The Service has a continuing duty to regulate the activity covered by this incidental take statement. If the Service (1) fails to assume and implement the terms and conditions or (2) fails to require the applicant to adhere to the terms and conditions of the incidental take statement through enforceable terms that are added to the permit or grant document, the protective coverage of section 7(o)(2) may lapse. To monitor the impact of incidental take, the Service and researchers must report the progress of the action and its impact on the species as specified in the incidental take statement.

AMOUNT OR EXTENT OF TAKE

Incidental take is expected to occur from trapping and handling KLCM and KLWR. The Service anticipates that the trapping and handling may result in the injury or death of one individual KLCM and the injury of one individual KLWR over the duration of the permit.

EFFECT OF THE TAKE

In the accompanying biological opinion, the Service determined that this level of anticipated take is not likely to result in jeopardy to these species.

21 REASONABLE AND PRUDENT MEASURES

The Service believes the applicant has incorporated all reasonable and prudent measures necessary and appropriate to minimize impacts of incidental take of the KLCM and KLWR. The applicant and designated agents acting on behalf of the applicant must provide resumes or summary of qualifications demonstrating their ability to safely conduct trapping and handling of the KLCM and KLWR. To monitor the effect and extent of take, the applicant must provide a written report on the results of the research activities. The applicant will innnediately cease all activities if an individual KLCM or KLWR is injured or killed.

TERMS AND CONDITIONS

In order to be exempt from the prohibitions of section 9 of the Act, the Service must comply with the following terms and conditions, which implement the reasonable and prudent measures, described above and outline required reporting/monitoring requirements. These terms and conditions are non-discretionary.

1. The Service shall require the applicant and designated agents acting on behalf of the applicant to furnish resumes or summary of qualifications demonstrating their ability to safely conduct trapping and handling. Only those individuals who can demonstrate that they hold all necessary permits and have sufficient experience to trap and handle the KLWR and KLCM with a minimum of risk to the rodents, and those individuals that are capable of recognizing indications of injury or ill health in the rodents will be permitted.

2. The reporting and monitoring requirements outlined in the section 10(a)(1)(A) permit will also satisfy the reporting/monitoring requirements required pursuant to section 7 of the Act and its implementing regulations. -

3. Permit issuance will be conditioned to require the permittee and designated agents acting on behalf of the permittee to immediately cease all activities if an individual KLWR or KLCM

is injured or killed and to report any such injury or death to the Service (Field Supervisor, . South Florida Ecological Services Office; 1339 20a"l Street; Vero Beach, FL 32960; 772-562-3909; AND Permit Coordinator; 1875 Century Boulevard, Suite 200; Atlanta, Georgia 30345-3301; 404-679-4176).

4. Upon locating a dead, injured, or sick threatened or endangered species, initial notification must be made to the nearest Service Law Enforcement Office (9549 Koger Boulevard, Suite 111; St. Petersburg, Florida 33702; 727-570-5398). Secondary notification should be made to the Florida Fish and Wildlife Conservation Commission; South Region; 3900 Drane Field Road; Lakeland, Florida, 33811-1299; 1-800-282-8002. Care should be taken in handling sick or injured specimens to ensure effective treatment and care or in the handling of dead specimens to preserve biological material in the best possible state for later analysis as to the cause of death. In conjunction with the care of sick or injured specimens or preservation of biological materials from a dead animal, the finder has the responsibility to carry out instructions provided by Law Enforcement to ensure that evidence intrinsic to the

22 specimen is not unnecessarily disturbed. Permitted activities that appear to be resulting in excessive injury or death will be immediately suspended until more protective measures or an alternative resolution can be initiated.

CONSERVATION RECOMMENDATIONS

Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the purposes of the Act by carrying out conservation programs for the benefit of endangered and threatened species. Conservation recommendations are discretionary agency activities to further minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to help implement recovery plans, or to develop information. The Service should continue to implement the MSRP (Service 1999).

REINITIATION NOTICE

This concludes formal consultation on this action as outlined in the request. As required by 50 CFR 402.16, reinitiation of formal consultation is required if:

1. The amount or extent of incidental take is exceeded.

2. New information reveals effects of the action that may affect listed species or critical habitat in a manner or to an extent not considered in this opinion.

3. The action is subsequently modified in a manner that causes an effect to the listed species or critical habitat not considered in this opinion.

4. A new species is listed or critical habitat designated that may be affected by the action.

In instances where the amount or extent of incidental take is exceeded, any operations causing such take most cease pending reinitiation.

If you have any questions, please contact Mark Salvato at 772-562-3909, extension 340.

cc: electronic copy only FWC, West Palm Beach, Florida (Ricardo Zambrano) Service, Big Pine Key, Florida (Anne Morkill) Service, Key Largo, Florida (Steve Klett)

23 LITERATURE CITED

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Alligood, C. A., C. J. Wheaten, H. M. Forde, KN. Smith, A. J. Daneault, R. C. Carlson, and A. Savage. 2008. Pup Development and Maternal Behavior in Captive Key Largo Woodrats (Neoz‘omanoridaaa smalli ). Zoo Biology 27(5): 394405.

Arthur, A.D., R.P. Pooh and CR. Dickman. 2004. Habitat structure mediates the non-lethal effects of predation on enclosed populations of house mice. Journal of Animal Ecology 73:867~877.

Barbour, DB. and SR. Humphrey. 1982. Status and habitat of the Key Largo woodrat and cotton mouse (Neoz‘omoflorz’dana smallz‘ and Peromyscas gossypinas allapaz‘icola). Journal of Mammalogy 63(1):144-148.

Bigler, W.J. and J.H. Jenkins. 1975. Population characteristics of Peromyscus gossypinus and Sigmodon hispidus in tropical hammocks of south Florida. Journal of Mammalogy 56(3):633-644.

Brown, L.N. 1978a. Key Largo woodrat. Pages 11~12 in J.N. Layne, editor. Rare and endangered biota of Florida. Mammals. University Press; Gainesville, Florida.

Brown, L.N. 1978b. Key Largo cotton mouse. Pages 1041 in J .N. Layne, editor. Rare and endangered biota of Florida. Mammals. University Press; Gainesville, Florida.

Brown, L.N. and EL. Williams. 1971. The Key Largo woodrat (Neotoma floridana smalli) and cotton mouse (Peromyscus gossypinus allapaz‘icola) on Lignum Vitae Key, Florida. Florida Naturalist 44: 95-96.

Castillo, DC. 2001. Population estimates and behavioral analysis of managed cat (Felis cams) colonies located in Miami-Dade County, Florida, Parks. M.S. thesis. Florida International University; Miami, Florida.

Castleberry, S., M. Mengak, and D. Greene. 2008. Progress report on Key Largo cotton mouse research. Unpublished report. University of Georgia, Athens (July 2008).

Churcher, PB. and J.H. Lawton. 1987. Predation by domestic cats in an English Village. Journal of Zoology, London 212:439-455.

Charcher, PB. and J .H. Lawton. 1989. Beware of well-fed felines. Natural History 7:40-46.

Clarke, AL. and T. Pacin. 2002. Domestic cat “colonies” in natural areas: a growing exotic species threat. Natural Areas Journal 22(2): 1 54-159.

24 Engeman, R., J.W. Woolard, N.D. Perry, G. Witner, S. Hardin, L. Brashears, H. Smith, 13. Mniznieks, and B. Constantin. 2006. Rapid assessment for a new invasive species threat: the case of the Gambian giant poached rat in Florida. Wildlife Research 33:439-448.

Florida Fish and-Wildlife Conservation Commission (FWC). 2003. - Impacts of feral and free- ranging domestic cats on wildlife in Florida. FFWCC. Tallahassee, Florida.

Florida Fish and Wildlife Conservation Commission (FWC). 2005. Long term monitoring plan for the Key Largo woodrat and cotton mouse. Report to US. Fish and Wildlife Service, Vero Beach, Florida.

Fitch, HS. and D.G. Rainey. 1956. Ecological observations of the woodrat, Neotomafloridana. University of Kansas publications, Museum ofNatural History 83499-633.

Forrester, DJ. 1992. Parasites and diseases of wild mammals in Florida. University of Florida Press, Gainesville, Florida. -

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