Xantusia gracilis

Number of Pages: 2Integrative BiologyGeological Science

Amphibians and Reptiles of United States Department of Defense Installations

The U.S. Department of Defense (DoD) occupies approximately 10.1 million ha of land within the U.S. spanning most ecosystems contained therein. To date, no comprehensive agency-wide inventory of amphibian and reptile species has been compiled. We developed an amphibian and reptile species inventory for 415 DoD installations/sites and evaluated species diversity. The amphibian and reptile species confirmed present on DoD sites represent 66% of the total native species documented in the continental U.S. Snakes are the most widespread group found on DoD lands. Of the military services, Army sites have the greatest number of confirmed species, federally listed, state-listed, and At-risk species. There are 24 federally listed (threatened or endangered), 55 state- listed, and 70 At-risk species confirmed present on DoD sites. Thirty non-native and native transplant amphibian and reptile species/subspecies are also confirmed present on DoD sites. Lastly, we verified that approximately half of the military sites evaluated in this study have at least one venomous snake species confirmed present. Our study results assist directly with ongoing management and conservation of amphibian and reptile species on DoD lands and confirm military lands comprise a significant contribution to biodiversity conservation

Surface-dwelling and Subterranean Invertebrate Fauna Associated with Giant Reed (Arundo donax Poaceae) in Southern California

In the southwestern United States giant reed, Arundo donax, is a nonnative invasive plant that has become widely established in moist places and forms its largest stands along riparian corridors. The most widely reported negative effects include competition with native species, increased rate of transpiration, increased potential for wildfires, and stream channel and bank alteration. However, little is known about the faunal communities associated with this plant and the potential effects on native fauna. In this study, we focused our efforts on determining the faunal composition specifically from rhizome clumps of A. donax from a site located along the Santa Margarita River in San Diego County, California. A total of 2590 individual macro-invertebrates were collected and identified, and represented 64 species from 7 classes. No sensitive species and few vertebrates were found to be in association with A. donax rhizome clumps. Four non-native invertebrate species made up 43% of the total number of captured invertebrates, and 31% of the sampled invertebrates were confirmed as native species. This study demonstrates that A. donax rhizome clumps, and the soils associated with them, provide habitat for several native macro-invertebrate species, but can be dominated by a greater abundance of non-native species

Phylogeography of the Night Lizard, Xantusia henshawi, from Southern California

The granite night lizard, Xantusia henshawi, is a highly specialized crevice dwelling lizard found in the Peninsular Ranges of southern California, United States and northern Baja California, Mexico. Generally, little morphological variation is seen in this species over a variety of habitats throughout its range, from elevations near sea level to approximately 2000 meters, and from Mediterranean habitats near the Pacific coast to arid desert habitat in the Colorado Desert of California. One exception is the variation seen in the subspecies X h. gracilis, which differs from X h. henshawi in morphology, allozymes, ecology, and natural history. In this study, intraspecific variation within Xantusia henshawi was analyzed by constructing a genealogy using mitochondrial DNA (mtDNA) sequence data. A 379 base pair region of mtDNA (cytochrome b) was amplified and sequenced for lizards representing 13 localities across their known range in southern California. •The resulting gene tree was compared to the known geologic history of the area comprising the range of this species. Three (3) haploclades were found in the maximum parsimony (MP) analyses that were separated geographically from one another by two major geologic fault zones. It is believed that the unstable nature of habitat surrounding these faults has led to the unique evolution of the three haploclades. Using the evolutionary species concept, results of this study in combination with those of previous studies warrant the elevation of the subspecies Xantusia henshawi gracilis to full species, Xantusia gracilis. This study has assisted in identifying unknown barriers to gene flow that have contributed to the evolution of these species

Phylogeography and Conservation of the Arroyo Toad (Bufo californicus)

The Arroyo Toad (Bufo cakfomicus) is an endangered species found in rivers of southern California, USA and northern Baja California, Mexico. It has experienced population declines throughout its range, as a result of urbanization, hydrologic alterations, and overall habitat loss. As part of the Recovery Plan for this species, it was determined that more research was needed to assist in management decisions. One of those research needs was to better understand the intraspecific genetic variation within the Arroyo Toad. I conducted a range wide genetic study of the Arroyo Toad to uncover lineages and genetic variation among and between all major watersheds. This information is essential to our understanding of the species by providing data to determine recovery units independent of geographic location, delimit metapopulations, identify closely related populations for the potential augmentation of declining or extinct populations, assess dispersal between watersheds, and quantify genetic diversity throughout its distribution. In the course of this project, I also identified a more precise range of the species in Baja California, Mexico, along with the issues and challenges facing its conservation in the poorly known southern portion of its range

Amphibians and Reptiles of United States Department of Defense Installations

The U.S. Department of Defense (DoD) occupies approximately 10.1 million ha of land within the U.S. spanning most ecosystems contained therein. To date, no comprehensive agency-wide inventory of amphibian and reptile species has been compiled. We developed an amphibian and reptile species inventory for 415 DoD installations/sites and evaluated species diversity. The amphibian and reptile species confirmed present on DoD sites represent 66% of the total native species documented in the continental U.S. Snakes are the most widespread group found on DoD lands. Of the military services, Army sites have the greatest number of confirmed species, federally listed, state-listed, and At-risk species. There are 24 federally listed (threatened or endangered), 55 state- listed, and 70 At-risk species confirmed present on DoD sites. Thirty non-native and native transplant amphibian and reptile species/subspecies are also confirmed present on DoD sites. Lastly, we verified that approximately half of the military sites evaluated in this study have at least one venomous snake species confirmed present. Our study results assist directly with ongoing management and conservation of amphibian and reptile species on DoD lands and confirm military lands comprise a significant contribution to biodiversity conservation

Refining genetic boundaries for Agassiz’s desert tortoise (Gopherus agassizii) in the western Sonoran Desert: the influence of the Coachella Valley on gene flow among populations in southern California

Understanding the influence of geographic features on the evolutionary history and population structure of a species can assist wildlife managers in delimiting genetic units (GUs) for conservation and management. Landscape features including mountains, low elevation depressions, and even roads can influence connectivity and gene flow among Agassiz’s desert tortoise (Gopherus agassizii) populations. Substantial changes in the landscape of the American Southwest occurred during the last six million years (including the formation of the Gulf of California and the lower Colorado River), which shaped the distribution and genetic structuring of tortoise populations. The area northwest of the Gulf of California is occupied by the Salton Trough, including the Coachella Valley at its northern end. Much of this area is below sea level and unsuitable as tortoise habitat, thus forming a potential barrier for gene flow. We assessed genetic relationships among three tortoise populations separated by the Coachella Valley. Two adjacent populations were on the east side of the valley in the foothills of the Cottonwood and Orocopia mountains separated by Interstate 10. The third population, Mesa, was located about 87 km away in the foothills of the San Bernardino Mountains at the far northwestern tip of the valley. The Cottonwood and Orocopia localities showed genetic affiliation with the adjacent Colorado Desert GU immediately to the east, and the Mesa population exhibited affiliation with both the Southern Mojave and Colorado Desert GUs, despite having a greater geographic distance (0.5x–1.5x greater) to the Colorado Desert GU. The genetic affiliation with the Colorado Desert GU suggests that the boundary for that GU needs to be substantially extended to the west to include the desert tortoise populations around the Coachella Valley. Their inclusion in the Colorado Desert GU may benefit these often overlooked populations when recovery actions are considered

Multiyear monitoring (2007-2013) of flat-tailed horned lizards (Phrynosoma mcallii)

Monitoring programs for species of conservation concern are notoriously flawed. Notably, many monitoring programs do not establish trigger points or a level of decline in population size that will result in management action. Here we report on the monitoring program for the Flat-tailed Horned Lizard (Phrynosoma mcallii) that has been established across its range throughout the United States by the Flat-tailed Horned Lizard Interagency Coordinating Committee (FTHL ICC). Impor- tantly, we examine whether a trigger point of 30% decline was detected in these populations. Between 2007 and 2013, we detected 955 P. mcallii on 2,714 occupancy surveys and captured 715 individuals on 1,861 demographic surveys. Occupancy surveys have demonstrated that the species occurs through- out the management areas and occupancy estimates range from 0.25–0.89. Demographic surveys have demonstrated that population trends over time are correlated across all management areas; however, they are probably driven by factors at smaller geographic scales. During the study no population decline \u3e 30% was detected after accounting for natural and stochastic fluctuations. Continued mon- itoring is called for to gain a greater understanding of what is driving the trends in populations both range-wide and at the scale of management areas

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (\u3ci\u3eUrocyon littoralis\u3c/i\u3e)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are pre- dicted to be strong on islands and both could drive population divergence and specia- tion. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Chan- nel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mech- anism driving population divergence among island fox populations. In particular, pop- ulations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential