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Conceptual Restoration Plan Update: Phase I


A review of the Service’s Information for Planning and Consulting (IPaC) database, the Biota Information System of New Mexico (BISON-M), and the New Mexico Rare Plants website identified a federally and state-listed species for Socorro County (Service 2019a; BISON-M 2019; NMRPTC 1999). Federally and state-listed threatened and endangered species with the potential to occur in the Project Area also were identified. Federally listed species with the potential to occur, and that have been documented to occur, in the Project Area are addressed in detail following the table.

Southwestern Willow Flycatcher

The flycatcher was listed as endangered in February 1995 (60 FR 10694, February 27, 1995). Critical habitat was finalized in 2013 (78 FR 343, February 4, 2013), and the Project Area is wholly contained within the MRG Management Unit within the Rio Grande Recovery Unit. The flycatcher is an obligate riparian species and nests in thickets associated with rivers, streams, and wetlands where dense growth of willow, Russian olive, saltcedar, or other plants are present (Finch and Stoleson 2000).

Presence in the Project Area

Reclamation personnel have conducted presence/absence surveys and nest monitoring for the flycatcher during the May–July survey season within the Rio Grande Basin since 1995. Presence/absence surveys based on established survey protocols are conducted to determine the distribution and abundance of the endangered flycatcher during the relatively brief breeding season when it becomes a seasonal resident of the southwestern United States. Because of the detailed survey data available, flycatcher presence and the presence of suitable habitat will be addressed reach by reach.

Reach 1

Most sites within Reach 1 are bounded by an extensive levee system on each side. The majority of habitat in this reach consists of a mix of cottonwood (Populus deltoides) gallery, with sparse saltcedar, Russian olive, and/or coyote willow understory. Suitable flycatcher habitat is patchy and consists primarily of developing stands of willows and Russian olive on lower terraces and recently established river bars. While the overall flycatcher population has been slowly growing north of the reach since pairing was first documented in 2005, only one mating pair was documented during 2017 and 2018 surveys in a cottonwood-Russian olive/coyote willow vegetation community adjacent to the Rio Grande.

Reach 2

The river channel within Reach 2 is contained by levees on both the east and west sides but is extremely active within the floodplain due to the high sediment loads brought in by the Rio Salado. Habitat ranges from highly suitable flycatcher habitat composed of coyote willow and Russian olive along the banks of the river to overstory cottonwood gallery and sparse, decadent saltcedar. On lower terraces and river bars, moderate overbank flooding occurs during high-flow events. Based on 2016 habitat mapping/modeling, 895 acres of suitable or moderately suitable habitat are located within this reach. Either coyote willow, Russian olive, or young cottonwood was the dominant vegetation feature in occupied habitat during 2017 and 2018 surveys. No mating pairs were documented within vegetation communities with a significant saltcedar component.

Reach 3

Habitat within Reach 3 is dominated by dry, decadent exotic vegetation in the form of saltcedar and Russian olive with an occasional cottonwood overstory. Quality flycatcher habitat within this reach is very limited—only 516 acres were mapped in 2016—and composed of small patches of native vegetation along the river channel. Very little overbank flooding occurs due to the degraded nature of the river channel. Sporadic high river flows during the past several years combined with the formation of river bars and lower terraces have resulted in reestablishment of riparian vegetation, both native and exotic, along these bars and terraces, but they have not resulted in increased utilization from the flycatcher. No territorial flycatchers were documented in this reach between 2010 and 2018. Due to the limited habitat within this reach, it is unlikely that a substantial number of flycatcher territories will become established here in the near future without restoration treatment or changes in hydrologic conditions.

Reach 4

Habitat within Reach 4 varies widely from decadent, dense saltcedar to large, mature cottonwood galleries to dense patches of coyote willow and Russian olive. High aggradation and sediment plugs cause major portions of the active floodplain to be inundated during high flows. Although ephemeral in nature, sediment plug formation enhances flycatcher habitat value within the reach when it occurs. Flooding of existing habitat increased suitability for breeding flycatchers between 2008 and 2010. Subsequently, multiple years of extreme drought eliminated overbank flooding and drew down the water table. Much of the native component of the occupied habitat in this reach was either severely stressed or died between 2010 and 2013. Recently, however, native vegetation has begun to recover in certain areas and, in 2017, high river flows and the sediment plug covered the floodplain with as much as 10 feet of water. A total of 873 acres of suitable flycatcher habitat was mapped within this reach in 2016, but channel realignment activities at BDANWR will likely dramatically shift the hydrologic and vegetation conditions of this reach as well as the reaches downstream of it. Although small in number, resident flycatcher mating pairs have consistently used this reach since 2002.

Reach 5

Much of the habitat in Reach 5 was burned by the Tiffany Fire, which began on June 26, 2017. Prior to the fire, vegetation in this reach consisted primarily of various age classes of saltcedar with occasional patches of Russian olive and native willows and cottonwoods, particularly near the river. A large, dry marsh also exists at the foot of Black Mesa, upstream from the railroad trestle. Portions of this reach receive overbank flooding during high river flows, and a sediment plug in the southern end of this reach in both 2005 and 2008 forced river water through habitat in the southern end.

Reach 6

More flycatcher territories occur within Reach 6 than in all the other reaches in the Project Area combined. Habitat in this reach consists of some of the best native flycatcher habitat within the subspecies’ range. Vast expanses of native Goodding’s willow and coyote willow habitat formed in the conservation pool of Elephant Butte Reservoir as the reservoir receded during the late 1990s and early 2000s. This habitat, located primarily on the west side of the floodplain, is irrigated by the low-flow conveyance channel (LFCC) outfall, which filters through the interspersed patches of willow, saltcedar, and cattail (Typha sp.) marsh. River channel degradation through the reach in 2005 lowered the water table in this reach, which negatively impacted suitable flycatcher habitat.

Habitat Needs and Habitat Restoration Potential

Flycatcher nests are frequently associated with an overstory of scattered cottonwood. Throughout the flycatcher’s range, these riparian habitats are now reduced, widely separated, and occur in small and/or linear patches. Flycatchers nest in thickets of trees and shrubs approximately 623 feet in height or taller, with a densely vegetated understory approximately 12 feet or more in height. Surface water or saturated soil is usually present beneath or adjacent to occupied thickets (Muiznieks et al. 1994). Habitats not selected for nesting include narrow (less than 30 feet wide) riparian strips, small willow patches, and stands with low stem density (Service 2002). Areas not used for nesting may still be used during migration (Yong and Finch 1997). The two greatest ongoing threats to flycatchers in the MRG are the decline in the quality of critical nesting habitat related to the current prolonged drought conditions and reduced annual water supply, currently thought to be due to climate change, and to the invasion of Tamarisk Leaf Beetle (TLB), which causes loss of important nesting substrate and opens the nesting canopy habitat to produce nest failure. In some areas, nest predation by the brown-headed cowbird (Molothrus ater) can be a third threat.

Rio Grande Silvery Minnow

The silvery minnow was listed by the Service as endangered in 1994 because of widespread decline of the species’ range (59 FR 36988, July 20, 1994). The listing also cited the presence of mainstream dams; growth of agriculture and cities in the Rio Grande Valley; overutilization for commercial, recreational, scientific, or educational purposes; disease or predation, particularly during periods of low or no flow; inadequacy of existing regulatory mechanisms, including the lack of recognition that instream flows are a beneficial use of state waters; and dewatering of a large percentage of its habitat, including dewatering downstream from San Acacia, as threats to the continued survival of the species. The silvery minnow prefers habitats of moderate depth with low velocities over sand and silt substrates. Designated critical habitat for the silvery minnow extends from Cochiti Dam to the full pool at RM 62 (68 FR 8088, February 19, 2003), including the entire Project Area. The recovery plan was updated in 2010 (Service 2010) and no species status assessments have been published.

Presence in the Project Area

Population data on silvery minnow and the associated ichthyofaunal community in the entire Middle Rio Grande have been gathered since 1987. These population monitoring surveys provide an assessment of recruitment over short time periods, a basis for comparing the changes in recruitment success over the years, and timely information about the status of the species during periods of reduced abundance and could be used to assess seasonal survivorship (Dudley et al. 2018). Platania (1993) conducted the first studies (1987–1992) to determine spatial and temporal changes in the Middle Rio Grande ichthyofaunal community and to provide resolution of species-specific habitat use patterns. Sampling efforts during 1989 and 1990 revealed that silvery minnow population numbers had declined markedly since 1987 (Platania 1993), supporting the need for listing under the ESA.

Annual population monitoring from the Angostura Diversion Dam in Sandoval County to below the San Marcial railroad bridge in Socorro County has consistently found that occurrence and density of silvery minnows is highest in the furthest downstream reaches of the Rio Grande (Dudley et al. 2018), which is in the Project Area. Pronounced changes in the occurrence and density of silvery minnow since at least the early 2000s appear to be closely related to the duration, magnitude, and timing of river flows during spring and summer (e.g., spring spawning and sustained summer flows) (Dudley et al. 2018). Because of limitations of the survey methodology and much that is still not understood about the biology of the silvery minnow, it is difficult to identify with any certainty trends in population since 2004 in the Project Area. As of 2018, Reclamation surveys have confirmed the persistence of the silvery minnow in the Rio Grande within the Project Area (Dudley et al. 2018).

Habitat Needs and Habitat Restoration Potential

Silvery minnow are pelagic spawners, producing numerous semi-buoyant, non-adhesive eggs. Most spawning typically has been observed in the spring, from late April through June, accompanying the period of snowmelt runoff (Reclamation 2012). Spawning also has been observed during some runoff events following summer monsoons. Both juvenile and adult silvery minnow primarily use mesohabitats with moderate depths (15–40 centimeters), low water velocities (4–9 centimeters per second), and silt/sand substrates. Successful recruitment appears to be linked with sustained elevated spring flows (1–2 months) that allow for longer term inundation of nursery habitat, necessary for growth through early larval stages (Dudley et al. 2017). During winter months, these silvery minnows become less active and seek habitats with cover such as debris piles and other areas with low water velocities. During spring sampling, large concentrations of reproductively mature silvery minnow are often collected on inundated lateral overbank habitats (Hatch and Gonzales 2008). Surveys of inundated overbank habitats often have captured large numbers of gravid females and ripe male silvery minnows (Gonzales and Hatch 2009).

Analysis of potential habitat at two locations in the Project Area using a FLO 2D model across a range of flows indicates that the area around Bosque del Apache contains the highest quality feeding and rearing habitat and highest quality spawning and egg/larval retention habitat compared to model locations in the Albuquerque and Isleta reaches (Tetra Tech 2014). Farther downstream at San Marcial, however, there is relatively little highest quality feeding and rearing or highest quality spawning and egg/larval retention habitats and, as flows increase, they drop off precipitously because of the lack of channel complexity (Tetra Tech 2014).

Yellow-Billed Cuckoo

The western distinct population segment of Yellow-Billed Cuckoo was listed by the Service as threatened in 2014 (79 FR 59992, October 3, 2014) and critical habitat was proposed at that time. Since then, the public comment period on proposed critical habitat has been reopened twice (Service 2014b; 85 FR 11458, February 27, 2020). There is no designated critical habitat at this time. The cuckoo is an obligate riparian species occurring in scattered locations in the western United States during the breeding season. Threats to the cuckoo include a decrease in habitat availability and suitability from loss and degradation of riparian habitat and habitat regeneration. Major factors contributing to habitat loss are the disruption of hydrological processes necessary to maintain a healthy riparian system, including fluctuating reservoir levels, poorly managed grazing, development activities, extractive uses, expansion of nonnative vegetation, and uncontrolled wildfire.

Presence in the Project Area

Reclamation personnel have conducted presence/absence surveys for the cuckoo during the June–August survey season within the Rio Grande Basin since 2006 from Isleta Pueblo south to Elephant Butte Reservoir. Presence/absence surveys based on established survey protocols are conducted to determine the distribution and abundance of the threatened cuckoo during the breeding season, when they are present in the southwestern United States.

Cuckoo detections and territories have consistently been documented in each of the six reaches identified in the Project area with much higher numbers at the furthest downstream end of the reach (Dillon et al. 2019). The area identified in the Reclamation surveys as the San Marcial Reach extends from RM 68.5 to RM 31.5 and represents the furthest downstream end of Reach 5 and all of Reach 6 for this Project. The San Marcial Reach has maintained a fairly large and consistent population of cuckoos since 2009, ranging from 49 to 70 territories annually (Dillon et al. 2019). The Escondida Reach (RMs 104–84) and BDANWR Reach (RMs 84–74) jointly correspond with the Project Area’s Reach 4, and these reaches also have consistently high numbers of detections and territories, although not nearly as high as San Marcial (Dillon et al. 2019).

Habitat Needs and Habitat Restoration Potential

The cuckoo nests almost exclusively in low-to-moderate elevation riparian woodlands with native, broadleaf trees and shrubs that are at least 50 acres in size and at least 325 feet (100 meters) in width (79 FR 59992, October 3, 2014). Mature cottonwood forest with well-developed willow understory appears to be an important characteristic of habitat for the cuckoo (Buffington et al. 1997; Gaines and Laymon 1984). While willows appear to be a preferred nest tree, the species will also nest in dense saltcedar stands. In addition, as the proportion of saltcedar increases, the suitability of the habitat for cuckoos decreases, and sites with a monoculture of saltcedar are unsuitable for breeding cuckoos (Service 2014b). Fire is also a threat to cuckoo breeding habitat (78 FR 61621, December 2, 2013). Because of the loss of habitat, cuckoos now breed in small, isolated populations. These populations are increasingly at risk for further declines as a result of increased predation rates, lack of abundance of prey, migratory obstacles (e.g., weather events, collision with structures, and so forth), conversion of habitat from native to exotic vegetation, defoliation of saltcedar caused by TLBs, increased fire risk, and climate change (Thompson 1961; Wilcove et al. 1986). Riparian habitat restoration activities in the Project Area would be conducive to enhancing and maintaining habitat for the cuckoo.

New Mexico Meadow Jumping Mouse

The New Mexico meadow jumping mouse (mouse) was listed as endangered by the Service in 2014 (79 FR 33119, June 10, 2014), and there is designated critical habitat within BDANWR, which is within the Project Area (81 FR 14263, March 16, 2016). The mouse is a small, nocturnal, solitary mammal and an obligate riparian subspecies. The Service found a significant reduction in occupied localities likely due to cumulative habitat loss and fragmentation across the range for this mouse. Because the species occurs only in areas that are water-saturated, populations have a high potential for extirpation when habitat dries due to groundwater and surface water depletion, draining of wetlands, or drought.  The habitat within this area is believed to be occupied by the subspecies within the middle Rio Grande having the capability to support breeding and reproduction. While this is close to the north end of the Project Area, there is no critical habitat designated within the Project Area (81 FR 14263, March 16, 2016).


Presence in the Project Area

The most recent data for the mouse in the Project Area was  conducted by Frey and Kopp (2014). They completed a preliminary assessment of mouse habitat down to RM 38 using GIS-based vegetation mapping and field evaluations of irrigation drains and the LFCC. The study area included riparian areas along the Rio Grande from U.S. Highway 60 to Elephant Butte Dam. The evaluation was based on interpretation of 2007 aerial photography and 2008 field verifications (Ahlers et al. 2010). Mapping did identify potentially suitable habitat (herbaceous and regenerating willow) but, because of the coarseness of the available data, it was a conservative effort and overestimated the amount of habitat. No potentially suitable habitat was identified on the LFCC. The only known occupied habitat is within Bosque del Apache, where the mouse has been documented annually through 2017 (Lehnen et al. 2018).

Habitat Needs and Habitat Restoration Potential

The mouse hibernates for about 8 or 9 months of the year and is active for only 3 or 4 months during the summer. Within this short timeframe, it must breed, birth, and raise young and store up sufficient fat reserves to survive the next year’s hibernation period. As a result, if resources are not available in a single season, populations can be greatly impacted. In addition, the mouse lives only 3 years or less and has one small litter annually, with seven or fewer young. Because of this low fecundity (reproductive potential), the subspecies has limited capacity for high population growth rates (79 FR 33119, June 10, 2014). As a result, the mouse has exceptionally specialized habitat requirements to support these life history needs and maintain adequate population sizes. The subspecies chiefly uses patches or narrow strips of riparian vegetation composed of well-developed, tall (averaging at least 24 inches), dense riparian herbaceous vegetation (plants with no woody tissue) primarily composed of sedges—plants in the Cyperaceae family that superficially resemble grasses but usually have triangular stems—and forbs—broad-leafed herbaceous plants. This suitable habitat is found only when wetland vegetation achieves full growth potential associated with saturated soils along the edge of open, perennial flowing water. This vegetation is an important resource need for the mouse because it provides vital food sources (insects and seeds) as well as the structural material for building day nests that are used for shelter from predators. In addition, individual mice also need intact upland areas—up gradient and beyond the floodplain of rivers and streams—adjacent to riparian wetland areas to build nests or use burrows to give birth to young in the summer and to hibernate over the winter (79 FR 33119, June 10, 2014).

Historically, these wetland habitats would have been in large patches to allow for movements of 650–2,300 feet to disperse to other habitat patches within stream segments. Connectivity between patches of suitable habitat is necessary to facilitate daily and seasonal movements, as well as dispersal to increase the likelihood of long-term viability of jumping mouse populations (Service 2014d). In the MRG valley, the mouse is known to use both natural wetlands and riparian habitats associated with irrigation channels (Morrison 1988, cited in Service 2016b; Frey and Wright 2012). The Service estimates that resilient populations of mice need connected areas of suitable habitat in the range of at least about 68–181 acres along 6–15 miles of flowing streams, ditches, or canals. The suitable habitat patches must be no more than about 650 feet apart, because the mouse has limited movement and dispersal capacity for natural recolonization (Service 2014d, 2016b).

The mouse was originally listed as endangered due to the present or threatened destruction, modification, or curtailment of its habitat or range; the inadequacy of existing regulatory mechanisms; and the natural and manmade factors affecting its continued existence (79 FR 33119, June 10, 2014).

In addition, the isolated state of existing populations makes natural recolonization of impacted areas highly unlikely or impossible in most areas (79 FR 33119, June 10, 2014).  The primary causes of current and future habitat losses include grazing pressure (which removes the needed vegetation) and water management and use (which causes vegetation loss from mowing and drying of soils), lack of water due to drought (exacerbated by climate change), and wildfires (also exacerbated by climate change). Additional causes of habitat loss are likely to occur from scouring floods, loss of beaver, highway reconstruction, residential and commercial development, coal bed methane development, and unregulated recreation. Nearly all current populations of the species are isolated and widely separated, and all of the 29 populations located since 2005 have patches of suitable habitat that are too small to support resilient populations.

Pecos Sunflower

The Pecos sunflower was listed as threatened in 1999 and, at the time, was known only from 25 sites in New Mexico (none of which were in Socorro County) and Texas (64 FR 56582, October 20, 1999). It is an annual member of the sunflower family, a wetland species that requires saturated saline soils of desert wetlands, and usually associated with desert springs, or “cienegas,” or the wetlands created from modifying desert springs at 3,300–6,600 feet of elevation (NMRPTC 1999). Threats to the species include wetlands drying from groundwater depletions, alteration of wetlands, competition from nonnative plant species, excessive livestock grazing, and highway maintenance (NMRPTC 1999; 64 FR 56582, October 20, 1999). The Service published a recovery plan in 2005 (Service 2005), and critical habitat was designated in 2008 (73 FR 17761, April 1, 2008). There have been no published species status assessments of the Pecos sunflower

Presence in Project Area

There are two populations of Pecos sunflower known to exist in the Project Area. One population is at La Joya State Wildlife Management Area near the confluence of the Rio Grande and the Rio Puerco; it was not known to be occupied at the time the Pecos sunflower was listed but was discovered in 2004. It is one of the largest populations of sunflower in NM (between 100,000 and 1,000,000 plants) and is currently threatened by encroachment of nonnative vegetation (73 FR 17761, April 1, 2008). The area has been excluded from critical habitat designation because there is currently a Pecos Sunflower Habitat Management Plan in place (73 FR 17761, April 1, 2008). The second population is located on private property in Socorro County and is the result of collaborative restoration efforts dating from approximately 2006–2012 and funded largely by a grant from the Service’s Management of Exotics for Recovery of Endangered Species habitat restoration program.

Habitat Needs and Habitat Restoration Potential

The Pecos sunflower grows in permanently saturated soils, areas most commonly associated with cienegas, but also may include stream and lake margins (64 FR 56582, October 20, 1999). These soils are typically saline or alkaline because the waters are high in dissolved solids and associated plant species include saltgrass, alkali sacaton, and other indicators of those soils (Service 2005). Like all sunflowers, the species requires open areas that are not shaded by taller vegetation. In the Rio Grande, the largest threat to the sunflower is encroachment of nonnative vegetation, especially saltcedar. High densities of saltcedar can dry out shallow groundwater and create an overstory canopy that reduces light to the understory (Service 2005). Riparian habitat restoration activities in the Project Area would be conducive to creating conditions required by the Pecos sunflower, and there is an opportunity to support additional populations.


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