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Lower Colorado River Multi-Species Conservation Program Balancing Resource Use and Conservation

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Colorado River Cotton Rat

      (Sigmodon arizonae plenus)

First Colorado River Cotton Rat Found in Southern Nevada since 1961, March 2012 - Photo by Nick Rice SWNAColorado River Cotton RatColorado River Cotton Rat
  • DESCRIPTION
  • DISTRIBUTION
  • HABITAT
  • CONSERVATION
  • MULTIMEDIA

General Description

Cotton rats are members of the genus Sigmodon. Species within this genus are described as rodents that are thick bodied, with a medium-length tail slightly shorter than its head and body. Their ears barely project above their fur, and their tail is sparsely haired. There are two subspecies of cotton rats along the Lower Colorado River (LCR); the Colorado River cotton rat (Sigmodon arizonae plenus) and the Yuma hispid cotton rat (Sigmodon hispidus eremicus). The two subspecies are indistinguishable using only external characteristics but can be identified using skull measurements. They are also distinguishable using molecular techniques such as DNA sequencing. It is unknown whether the two subspecies ranges overlap along the LCR.

Legal Status

The Colorado River cotton rat is a species of special concern in the state of California.

Taxonomy

The Colorado River cotton rat is a subspecies of the Arizona cotton rat (Sigmodon arizonae).  Previously, the Arizona cotton rat was considered to be a subspecies of the hispid cotton rat (Sigmodon hispidus). In 1970, DNA evidence determined the Arizona cotton rat as a distinct subspecies.

Reproduction

No specific information exists on the breeding habits for the Colorado River cotton rat but it is assumed to be similar to other species of Sigmodon. Cotton rats are known to breed throughout the year in the southern portion of their range, and the young of Colorado River cotton rats have been collected during almost every month of the year. Cotton rats are known to construct nests of woven grass either in burrows or on the ground. They do not migrate and are active both day and night. An Arizona cotton rat was bred in the laboratory with a hispid cotton rat and produced only infertile young. This would suggest that hybridization is rare, if it occurs at all.

Diet

The Colorado River cotton rat is known to feed primarily on grasses. Other species are much more general, eating crops, some insects, eggs, and carrion. Colorado River cotton rats may vary their diet with some of these items as well.

Threats

Backwater habitat along the lower Colorado River has been altered by channelization, agricultural use, and storage of water, invasion by saltcedar, and decreased flow regimes due to dam construction. These alterations all may have contributed to a decline in the population of cotton rats along the lower Colorado River.

Population density is regulated by disease and avian predators; mammal predation is considered to be incidental. The principal competitors for resources for hispid cotton rats include other rodents.

More Information

Additional information on this species, as well as source documentation, can be found in the species accounts located at this link (PDF). The Conceptual Ecological Model (CEM) can be found here (PDF). Technical Reports on this species can be found here.

Updated December 8, 2017

The Arizona cotton rat has a current distribution that includes southeastern California, Arizona, and western Mexico and historically extended up to extreme southern Nevada. The exact current and historical distributional range of the Colorado River cotton rat is not well known. In Nevada, the earliest records of cotton rats in the state were in 1934 and 1961, where individual cotton rats were captured in a marsh in the extreme southern portion of the state, which subsequently dried up. Further capture efforts were unsuccessful and the species had been considered extirpated in Nevada, but in 2012 cotton rat surveys were conducted at the Big Bend Conservation Area, just south of Laughlin in Nevada and two cotton rats were captured. Further south, records of the Colorado River cotton rat are more common. Individuals have been documented in Arizona from Havasu NWR south to Cibola NWR. In California, the species has been reported in three locations: 1) Needles, California, 2) near Parker, Arizona, and 3) 15 miles southwest of Ehrenburg, Arizona. The California Department of Fish and Game has recorded the species in Imperial, Riverside, and San Bernardino counties, from Palo Verde to Needles.

Trapping for a variety of small mammal species at three sites along the Colorado River were conducted in 1998, and at each site several Colorado River cotton rats were captured. The survey sites included a site recently re-vegetated on the Cibola NWR Unit #1, No-Name Lake near Parker, Arizona, and at one site on the Bill Williams River National Wildlife Refuge. All sites were located on the eastern (Arizona) side of the river. Studies suggest that, within its area of occurrence, the presence of the Colorado River cotton rat is isolated and spotty, rather than continuous. The southern extent of the range of this species is still unknown.

Work conducted in 1990 found this species occurring north of the Palo Verde Mountains, along the LCR, and the Yuma hispid cotton rat occurring south of the mountains. It was concluded that a good estimate of species relativity was location because the two species occupy different geographical areas. There is no conclusive data indicating that the two species do not overlap along the LCR and there is evidence indicating that they may be expanding their ranges into agricultural areas. In some areas of eastern Arizona this species is does occupy areas with the Yuma hispid cotton rat.  However, these areas are limited.

 

Little information has been collected on Colorado River cotton rat life history and habitat requirements, although there is an assumption that they are similar to other subspecies of the Arizona cotton rat and the closely related hispid cotton rat. Originally, this species was considered to be associated strongly with marsh vegetation, but further research has found the species to inhabit a greater variety of habitats. The species is known to use riparian thickets with moderate to dense grass cover, but may also use drier grassy areas. It has also been found in areas associated with common reed.

In capture studies conducted in 1998, cotton rats were most readily captured in grass/cattail communities. In restoration sites, this species was not captured until an herbaceous understory had developed. As such, it was concluded that the development of an understory may be the most important element in providing quality habitat for many species of small mammals, including the Colorado River cotton rat. In presence/absence studies conducted by the Bureau of Reclamation at the Cibola NWR Unit #1 restoration site on the Cibola National Wildlife Refuge, cotton rats were captured in areas with a dense understory of Johnson grass. Habitat studies have shown that Colorado River cotton rats have a preference for grassy areas with some shrubs or trees.

 

LCR MSCP Conservation Measures

The Habitat Conservation Plan provides conservation measures specific to each species. Listed below are the species specific conservation measures for the Colorado River cotton rat. Click on the arrows to expand the table.

CRCR1—Conduct research to better define Colorado River cotton rat habitat requirements

Conduct research, if needed, to better define the elements of Colorado River cotton rat habitat and provide information necessary to design and manage created habitat.

CRCR2—Create 125 acres of Colorado River cotton rat habitat

Of the 512 acres of marsh to be created to create Yuma clapper rail habitat (Section 5.7.1 in the HCP), or the 5, 940 acres of cottonwood-willow and 1,320 acres of honey mesquite III to be created as habitat for covered species, at least 125 acres will be designed to also provide Colorado River cotton rat habitat in Reaches 3 and 4 near occupied habitat (Figure 5-2 in the HCP). Additional habitat may be provided by marsh vegetation that establishes along margins of the 360 acres created backwaters (Section 5.4.3.4 in the HCP).

MRM2—Monitor and adaptively manage created covered and evaluation species habitats

Created species habitats will be managed to maintain their functions as species habitat over the term of the LCR MSCP. Created habitat will be monitored and adaptively managed over time to determine the types and frequency of management activities that may be required to maintain created cottonwood-willow, honey mesquite, marsh, and backwater land cover as habitat for covered species. This conservation measure applies to those species for which comparable measures are not subsumed under species-specific conservation measures (Section 5.7 in the HCP). They are not applicable to species for which habitat would not be created under the LCR MSCP Conservation Plan, such as the desert tortoise, relict leopard frog, humpback chub, and threecorner milkvetch.

MRM5—Monitor selenium levels in created backwater and marsh land cover types, and study the effect of selenium released as a result of dredging activities

Conduct monitoring of selenium levels in sediment, water, and/or biota present in LCR MSCP created backwater and marsh land cover types. If monitoring results indicate that management of the LCR MSCP conservation areas increases levels of selenium in created backwaters and marshes or in covered species that use them, the LCR MSCP will undertake research to develop feasible methods to manage the conservation areas in a manner that will eliminate or compensate for the effects of increased selenium levels. If feasible management methods are identified, they will be implemented. This conservation measure will include monitoring the effects of dredging and dredge spoil disposal associated with creating and maintaining backwaters and marshes. If monitoring results indicate that current or future dredging and dredge spoil disposal methods increase selenium levels, the LCR MSCP will only implement methods that will have the least effect on selenium levels. A study will also be conducted to look at the effects of potential releases of selenium from dredging in general.

CMM1—Reduce risk of loss of created habitat to wildfire

Management of LCR MSCP conservation areas will include contributing to and integrating with local, state, and Federal agency fire management plans. Conservation areas will be designed to contain wildfire and facilitate rapid response to suppress fires (e.g., fire management plans will be an element of each conservation area management plan).

CMM2—Replace created habitat affected by wildfire

In the event of created-habitat degradation or loss as a result of wildfire, land management and habitat creation measures to support the reestablishment of native vegetation will be identified and implemented.

AMM1—To the extent practicable, avoid and minimize impacts of implementing the LCR MSCP on existing covered species habitats

To the extent practicable, establishment and management of LCR MSCP–created habitats will avoid removal of existing cottonwood-willow stands, honey mesquite bosques, marsh, and backwaters to avoid and minimize impacts on habitat they provide for covered species. Temporary disturbance of covered species habitats, however, may be associated with habitat creation and subsequent maintenance activities (e.g., controlled burning in marshes and removal of trees to maintain succession objectives). LCR MSCP conservation measures that could result in such temporary disturbances will, to the extent practicable, be designed and implemented to avoid or minimize the potential for disturbance. In addition to implementing AMM3 and AMM4 below, these measures could include conducting preconstruction surveys to determine if covered species are present and, if present, implementing habitat establishment and management activities during periods when the species would be least sensitive to those activities; or redesigning the activities to avoid the need to disturb sensitive habitat use areas; staging construction activities away from sensitive habitat use areas; and implementing BMPs to control erosion when implementing ground disturbing activities.

AMM2—Avoid impacts of flow-related covered activities on covered species habitats at Topock Marsh

Impacts on groundwater levels that support covered species habitat at Topock Marsh will be avoided by maintaining water deliveries for maintenance of water levels and existing conditions. At times, flow-related activities could lower river elevations to levels that could disrupt diversion of water from the river to the marsh.  Improvements to intake structures that allow water to continue to be diverted or other measures to maintain the water surface elevation will avoid effects on groundwater elevation. Avoidance of effects could be accomplished with the purchase, installation, and operation of two electric pumps sized to the current inflow at the Topock Marsh diversion inlet. The pumps would most likely need to be operated during summer to make up for the lower flow periods.

Implementation of this conservation measure would maintain existing habitat at Topock Marsh for the Yuma clapper rail, southwestern willow flycatcher, Colorado River cotton rat, western least bittern, California black rail, yellow-billed cuckoo, gilded flicker, vermilion flycatcher, Arizona Bell's vireo, and Sonoran yellow warbler. The extent of covered species habitat impacts that will be avoided by maintaining water deliveries to Topock Marsh are presented in Table 4-2 in the HCP. Maintaining water deliveries to Topock Marsh will also maintain razorback sucker and bonytail habitat associated with disconnected backwaters managed for these species.
AMM5—Avoid impacts of operation, maintenance, and replacement of hydroelectric generation and transmission facilities on covered species in the LCR MSCP planning area

To the extent practicable, before implementing activities associated with OM&R of hydroelectric generation and transmission facilities, measures will be identified and implemented that are necessary to avoid take of covered species where such activities could otherwise result in take. These measures could include conducting surveys to determine if covered species are present and, if so, deferring the implementation of activities to avoid disturbance during the breeding season; redesigning the activities to avoid the need to disturb covered species habitat use areas; staging of equipment outside of covered species habitats; delineating the limits of vegetation control activities to ensure that only the vegetation that needs to be removed to maintain infrastructure is removed; stockpiling and disposing of removed vegetation in a manner that minimizes the risk of fire; and implementing BMPs to control erosion when implementing ground disturbing activities.

AMM6—Avoid or minimize impacts on covered species habitats during dredging, bank stabilization activities and other river management activities

To the extent practicable, before initiating activities involved with river maintenance projects, measures will be identified and implemented that avoid or minimize take of covered species where such activities could otherwise result in take. Such measures could include alternative methods to achieve project goals, timing of activities, pre-activity surveys, and minimizing the area of effect, including offsite direct and indirect effects (e.g., avoiding or minimizing the need to place dredge spoil and discharge lines in covered species habitats; placing dredge spoils in a manner that will not affect covered species habitats).

Research and Monitoring Activities

LCR MSCP conduct a variety of research and monitoring activities along the LCR encompassing both MSCP and non-MSCP species. For a complete list of all activities, please see the Research and Monitoring Activities web page.

This gallery includes photos of this species. If you require larger photos, please contact our webmaster Michelle Reilly at mreilly@usbr.gov.

Colorado River cotton rat, captured in 2007 at Cibola National Wildlife Refuge, near Blythe, CA - Photo by Reclamation Colorado River cotton rat captured in 2006 at the Beal Restoration Site, within Havasu National Wildlife Refuge, near Needles, CA - Photo by Reclamation Colorado River cotton rat captured in 2009 at Pintail Slough, within Havasu National Wildlife Refuge, near Needles, CA - Photo by Reclamation These two were captured together in 2009 on a low terrace next to the Colorado River and the Palo Verde Ecological Reserve near Blythe, CA - Photo by Reclamation Colorado River cotton rat backing out of a trap in 2009 next to the Colorado River and the Palo Verde Ecological Reserve near Blythe, CA - Photo by Reclamation First Colorado River Cotton Rat found in Southern Nevada since 1961, March 2012 - Photo by Nick Rice SWNA