Stream hierarchy defines riverscape genetics of a North American desert fish

Global climate change is apparent within the Arctic and the south‐western deserts of North America, with record drought in the latter reflected within 640 000 km² of the Colorado River Basin. To discern the manner by which natural and anthropogenic drivers have compressed Basin‐wide fish biodiversity, and to establish a baseline for future climate effects, the Stream Hierarchy Model (SHM) was employed to juxtapose fluvial topography against molecular diversities of 1092 Bluehead Sucker (Catostomus discobolus). MtDNA revealed three geomorphically defined evolutionarily significant units (ESUs): Bonneville Basin, upper Little Colorado River and the remaining Colorado River Basin. Microsatellite analyses (16 loci) reinforced distinctiveness of the Bonneville Basin and upper Little Colorado River, but subdivided the Colorado River Basin into seven management units (MUs). One represents a cline of three admixed gene pools comprising the mainstem and its lower‐gradient tributaries. Six others are not only distinct genetically but also demographically (i.e. migrants/generation <9.7%). Two of these (i.e. Grand Canyon and Canyon de Chelly) are defined by geomorphology, two others (i.e. Fremont‐Muddy and San Raphael rivers) are isolated by sharp declivities as they drop precipitously from the west slope into the mainstem Colorado/Green rivers, another represents an isolated impoundment (i.e. Ringdahl Reservoir), while the last corresponds to a recognized subspecies (i.e. Zuni River, NM). Historical legacies of endemic fishes (ESUs) and their evolutionary potential (MUs) are clearly represented in our data, yet their arbiter will be the unrelenting natural and anthropogenic water depletions that will precipitate yet another conservation conflict within this unique but arid region.     

Ploidy race distributions since the Last Glacial Maximum in the North American desert shrub, Larrea tridentata

• 1 A classic biogeographic pattern is the alignment of diploid, tetraploid and hexaploid races of creosote bush (Larrea tridentata) across the Chihuahuan, Sonoran and Mohave Deserts of western North America. We used statistically robust differences in guard cell size of modern plants and fossil leaves from packrat middens to map current and past distributions of these ploidy races since the Last Glacial Maximum (LGM).
• 2 Glacial/early Holocene (26–10 ¹⁴C kyr bp or thousands of radiocarbon years before present) populations included diploids along the lower Rio Grande of west Texas, 650 km removed from sympatric diploids and tetraploids in the lower Colorado River Basin of south‐eastern California/south‐western Arizona. Diploids migrated slowly from lower Rio Grande refugia with expansion into the northern Chihuahuan Desert sites forestalled until after ~4.0 ¹⁴C kyr bp . Tetraploids expanded from the lower Colorado River Basin into the northern limits of the Sonoran Desert in central Arizona by 6.4 ¹⁴C kyr bp . Hexaploids appeared by 8.5 ¹⁴C kyr bp in the lower Colorado River Basin, reaching their northernmost limits (~37°N) in the Mohave Desert between 5.6 and 3.9 ¹⁴C kyr bp .
• 3 Modern diploid isolates may have resulted from both vicariant and dispersal events. In central Baja California and the lower Colorado River Basin, modern diploids probably originated from relict populations near glacial refugia. Founder events in the middle and late Holocene established diploid outposts on isolated limestone outcrops in areas of central and southern Arizona dominated by tetraploid populations.
• 4 Geographic alignment of the three ploidy races along the modern gradient of increasingly drier and hotter summers is clearly a postglacial phenomenon, but evolution of both higher ploidy races must have happened before the Holocene. The exact timing and mechanism of polyploidy evolution in creosote bush remains a matter of conjecture.

     

Water and community development in the Little Colorado River Basin

Water has historically been a critical limiting factor affecting community development throughout the American West. Within the Little Colorado River Basin of northeastern Arizona, abundant groundwater resources enabled local agricultural communities to overcome the limitations of unstable surfacewater sources. However, industrialization has led to sharp increases in groundwater consumption in the basin and to a decline in groundwater levels and/or quality at several locations. This paper examines the broader historical and regional implications of recent groundwater changes in the basin. Emphasis is placed upon the relationship between local developments and the rapid expansion of metropolitan centers in southern Arizona.     

Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology

We investigated a hybrid zone between two major lineages of fence lizards (Sceloporus cowlesi and Sceloporus tristichus) in the Sceloporus undulatus species complex in eastern Arizona. This zone occurs in an ecotone between Great Basin Grassland and Conifer Woodland habitats. We analysed spatial variation in mtDNA (N=401; 969 bp), chromosomes (N=217), and morphology (N=312; 11 characters) to characterize the hybrid zone and assess species limits. A fine-scale population level phylogenetic analysis refined the boundaries between these species and indicated that four nonsister mtDNA clades (three belonging to S. tristichus and one to S. cowlesi) are sympatric at the centre of the zone. Estimates of cytonuclear disequilibria in the population closest to the centre of the hybrid zone suggest that the S. tristichus clades are randomly mating, but that the S. cowlesi haplotype has a significant nonrandom association with nuclear alleles. Maximum-likelihood cline-fitting analyses suggest that the karyotype, morphology, and dorsal colour pattern clines are all coincident, but the mtDNA cline is skewed significantly to the south. A temporal comparison of cline centres utilizing karyotype data collected in the early 1970s and in 2002 suggests that the cline may have shifted by approximately 1.5 km to the north over a 30-year period. The recent northward expansion of juniper trees into the Little Colorado River Basin resulting from intense cattle overgrazing provides a plausible mechanism for a shifting hybrid zone and the introgression of the mtDNA haplotypes, which appear to be selectively neutral. It is clear that complex interactions are operating simultaneously in this contact zone, including the formation of hybrids between populations within S. tristichus having diagnostic mtDNA, morphology, karyotypes, and dorsal colour patterns, and secondary contact between these and a distantly related yet morphologically cryptic mtDNA lineage (S. cowlesi).     

A quantitative life history of endangered humpback chub that spawn in the Little Colorado River: variation in movement,growth, and survival

While the ecology and evolution of partial migratory systems (defined broadly to include skip spawning) have been well studied, we are only beginning to understand how partial migratory populations are responding to ongoing environmental change. Environmental change can lead to differences in the fitness of residents and migrants, which could eventually lead to changes in the frequency of the strategies in the overall population. Here, we address questions concerning the life history of the endangered Gila cypha (humpback chub) in the regulated Colorado River and the unregulated tributary and primary spawning area, the Little Colorado River. We develop eight multistate models for the population based on three movement hypotheses, in which states are defined in terms of fish size classes and river locations. We fit these models to mark–recapture data collected in 2009–2012. We compare survival and growth estimates between the Colorado River and Little Colorado River and calculate abundances for all size classes. The best model supports the hypotheses that larger adults spawn more frequently than smaller adults, that there are residents in the spawning grounds, and that juveniles move out of the Little Colorado River in large numbers during the monsoon season (July–September). Monthly survival rates for G. cypha in the Colorado River are higher than in the Little Colorado River in all size classes; however, growth is slower. While the hypothetical life histories of life‐long residents in the Little Colorado River and partial migrants spending most of its time in the Colorado River are very different, they lead to roughly similar fitness expectations when we used expected number of spawns as a proxy. However, more research is needed because our study period covers a period of years when conditions in the Colorado River for G. cypha are likely to have been better than has been typical over the last few decades.     

Ecology, Resource Redistribution, and Mormon Settlement in Northeastern Arizona

Successful Mormon colonization of the American West has largely been attributed to the adaptive advantage of cooperative Mormon values. This article shows that successful Mormon colonization of the Little Colorado River Basin had an ultimate ecological basis: the redistribution of surplus resources among settlements situated in dispersed and functionally independent local environments. Two systems of resource redistribution among 19th-century Little Colorado Mormon settlements are examined, showing that ecological considerations explain their differential success as adaptive mechanisms contributing to the success of this local colonization effort. The article concludes by suggesting that general ecology provides a useful theoretical framework for explaining successful Mormon colonization in this region and elsewhere.     

Evidence for concerted movement of nuclear and mitochondrial clines in a lizard hybrid zone

Moving hybrid zones provide compelling examples of evolution in action, yet long‐term studies that test the assumptions of hybrid zone stability are rare. Using replicated transect samples collected over a 10‐year interval from 2002 to 2012, we find evidence for concerted movement of genetic clines in a plateau fence lizard hybrid zone (Sceloporus tristichus) in Arizona. Cline‐fitting analyses of SNP and mtDNA data both provide evidence that the hybrid zone shifted northward by approximately 2 km during the 10‐year interval. For each sampling period, the mtDNA cline centre is displaced from the SNP cline centre and maintaining an introgression distance of approximately 3 km. The northward expansion of juniper trees into the Little Colorado River Basin in the early 1900s provides a plausible mechanism for hybrid zone formation and movement, and a broadscale quantification of recent land cover change provides support for increased woody species encroachment at the southern end of the hybrid zone. However, population processes can also contribute to hybrid zone movement, and the current stability of the ecotone habitats in the centre of the hybrid zone suggests that movement could decelerate in the future.     

Phylogenetic relationships of assimineid gastropods of the Death Valley–lower Colorado River region: relicts of a late Neogene marine incursion?

Aim A small fauna of amphibious snails (genus Assiminea Fleming, 1828) living in association with highly mineralized springs in the Death Valley–lower Colorado River region (DVLCR) is thought to be a relict of the Bouse Embayment, a putative late Miocene–early Pliocene transgression of the ancestral Gulf of California along the lower Colorado River valley. We analysed the phylogenetic relationships of this fauna using mtDNA sequence data (1171 bp) to determine whether, as would be consistent with this hypothesis, it forms a substantially divergent unit sister to marine coastal congeners. Location South‐western Great Basin and lower Colorado River region, USA. Methods Two genes [mitochondrial cytochrome c oxidase subunit I (COI) and the mitochondrial 16S ribosomal RNA gene] were sequenced for 10 populations of DVLCR assimineas (Assiminea infima Berry, 1947 ; Assiminea sp.). We also sequenced an undescribed population from a spring in the Colorado River delta; western North American Pacific Coastal Assiminea californica (Tryon, 1865); the three other congeners that live on the continent; and three Old World assimineids (outgroups). Phylogenies based on the combined data set were obtained using Bayesian methods, and divergence times were estimated using a COI molecular clock for related gastropods. Results Composite haplotypes of the DVLCR assimineas, together with that observed in the Colorado River delta population, formed a weakly supported clade that was sister to a clade composed of populations of North American Pacific and Atlantic coastal species. The genetic distance between members of these two clades was 3.46 ± 0.47% for COI and 1.69 ± 0.38% for 16S. The former clade was composed of five subunits that differed from each other by 1.29–2.84% (COI) and 0.52–1.98% (16S) sequence divergence. Main conclusions Application of the COI clock suggests that progenitors of the DVLCR fauna diverged from coastal ancestors 2.13–1.89 Ma (late Pliocene), several million years after the Bouse Embayment would have been terminated by the establishment of the lower (freshwater) Colorado River. This finding, together with shallow genetic structuring of several DVLCR lineages that are widely distributed across the topographically complex regional landscape, suggests that the Assiminea fauna of this inland area was more likely to have been founded by coastal colonists transported on water birds than through a direct connection with the sea.     

Effects of livestock exclusion on density,survival and biomass of the perennial sagebrush grass Hymenachne pernambucense (Poaceae) from a temperate fluvial wetland

In Argentina, the intensification of soybean production has displaced a substantial proportion of cattle ranching to fluvial wetlands such as those in the Delta of the Paraná River. Cattle grazing affects structure and dynamics of native forage plants but there is little information on this impact in populations from fluvial wetlands. This study addresses the effect of cattle ranching on density, survival, mean life-span and aerial biomass of Hymenachne pernambucense (Poaceae), an important forage species in the region. The study was carried out monthly for one year in permanents plots subject to continuous grazing and plots excluded from grazing in the Middle Delta of the Paraná River. In plots excluded from grazing, tillers showed significantly higher population density and survival, and a two-fold increase in mean life-span, while continuous grazing decreased survival of cohorts. The largest contribution to tiller density in ungrazed and grazed populations was made by spring and summer cohorts, respectively. Total and green biomass were significantly higher in the ungrazed population, with highest differences in late spring-early summer. Cattle grazing affected the relationship between tiller density and green biomass suggesting that cattle prefer sprouts because they are more palatable and nutritious than older tissue.     

Landscape associations of the sand fly, Lutzomyia (Heleocyrtomyia) apache (Diptera: Psychodidae), in the southwestern United States: a geographic information system analysis.

Landscape associations of the sand fly, Lutzomyia apache, Young and Perkins, in the southwestern U.S. were investigated by light/suction trap sampling and the development of a GIS-generated distribution map. In the mid-Rio Grande River valley, N.M., female and male L. apache were captured in updraft light/suction traps set in desert shrubland, irrigation levee, and bosque vegetation communities. Small numbers of flies were captured, but the presence of males and females in spatially separate and diverse plant communities at two locations suggest that L. apache are dispersed among available vegetation types. These data, along with 22 previously published collection site records, were used with a suite of physiographic features to characterize the biogeographic conditions suitable for L. apache. Suitable conditions encompass three life zones: the Rocky Mountain steppe province, the Colorado semi-plateau province, and the American semi-desert province, all within the dry domain region of the western U.S. The potential range of L. apache was then estimated based on elevation, mean and max - min temperature, precipitation, wet days, and relative humidity. The estimated range includes large contiguous areas in north-central Colorado, east-central New Mexico and west Texas, the lower mid-Rio Grande River valley, and southern Arizona, along with smaller, patchy, areas in northern Arizona, California, Nevada, Utah, and central Idaho. The spatial relationship between the estimated distribution of L. apache and the location of livestock exposed to vesicular stomatitis virus at the onset of recent outbreaks is presented.     

Changing environmental gradients over forty years alter ecomorphological variation in Guadalupe Bass Micropterus treculii throughout a river basin

Understanding the degree of intraspecific variation within and among populations is a key aspect of predicting the capacity of a species to respond to anthropogenic disturbances. However, intraspecific variation is usually assessed at either limited temporal, but broad spatial scales or vice versa, which can make assessing changes in response to long‐term disturbances challenging. We evaluated the relationship between the longitudinal gradient of changing flow regimes and land use/land cover patterns since 1980 and morphological variation of Guadalupe Bass Micropterus treculii throughout the Colorado River Basin of central Texas. The Colorado River Basin in Texas has experienced major alterations to the hydrologic regime due to changing land‐ and water‐use patterns. Historical collections of Guadalupe Bass prior to rapid human‐induced change present the unique opportunity to study the response of populations to varying environmental conditions through space and time. Morphological differentiation of Guadalupe Bass associated with temporal changes in flow regimes and land use/land cover patterns suggests that they are exhibiting intraspecific trait variability, with contemporary individuals showing increased body depth, in response to environmental alteration through time (specifically related to an increase in herbaceous land cover, maximum flows, and the number of low pulses and high pulses). Additionally, individuals from tributaries with increased hydrologic alteration associated with urbanization or agricultural withdrawals tended to have a greater distance between the anal and caudal fin. These results reveal trait variation that may help to buffer populations under conditions of increased urbanization and sprawl, human population growth, and climate risk, all of which impose novel selective pressures, especially on endemic species like Guadalupe Bass. Our results contribute an understanding of the adaptability and capacity of an endemic population to respond to expected future changes based on demographic or climatic projection.     

Degradation and accumulation of inhibitory substances fromJuniperus osteosperma (Torr.) Little

Two or more compounds present in leaves ofJuniperus osteosperma (Torr.) Little are active growth inhibitors. One of these, a blue fluorescent spot, is degraded fairly rapidly, but the other accumulates in the humus and in certain heavy clay soils. This persistent compound may slowly release monomers during degradation. Station's central headquarters is maintained at Fort Collins, in cooperation with Colorado State University. Research reported here was conducted while Dr. Jameson was at project headquarters at Flagstaff in cooperation with Northern Arizona University; he is now Associate Professor of Range Science at Colorado State University.     

Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone

We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n = 103), G. morafkai in Arizona (n = 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co‐occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.     

THE ROLE OF INTROGRESSIVE HYBRIDIZATION IN THE EVOLUTION OF THE GILA ROBUSTA COMPLEX (TELEOSTEI: CYPRINIDAE)

Abstract The extent and impact of introgressive hybridization was examined in the Gila robusta complex of cyprinid fishes using mitochondrial DNA (mtDNA) sequence variation. Lower Colorado River basin populations of G. robusta, G. elegans, and G. cypha exhibited distinct mtDNAs, with only limited introgression of G. elegans into G. cypha. The impact of hybridization was significant in upper Colorado River basin populations; most upper basin fishes sampled exhibited only G. cypha mtDNA haplotypes, with some individuals exhibiting mtDNA from G. elegans. The complete absence of G. robusta mtDNA, even in populations of morphologically pure G. robusta, indicates extensive introgression that predates human influence. Analysis of the geographic distribution of variation identified two distinctive G. elegans lineages; however, the small number of individuals and localities sampled precluded a comprehensive analysis. Analysis of haplotype and population networks for G. cypha mtDNAs from 15 localities revealed low divergence among haplotypes; however, significant frequency differences among populations within and among drainages were found, largely attributable to samples in the Little Colorado River region. This structure was not associated with G. cypha and G. robusta, as morphotypes from the same location are more similar than conspecific forms in other locations. This indicates that morphological and mtDNA variation are affected by different evolutionary forces in Colorado River Gila and illustrates how both hybridization and local adaptation can play important roles in evolution.     

Life cycle consumptive water use for oil shale development and implications for water supply in the Colorado River Basin

Purpose

Oil shale is an unconventional petroleum source that can be produced domestically in the USA. Oil shale resources are primarily located in Utah, Wyoming, and Colorado, within the Colorado River Basin. In this paper, we analyze the life cycle consumptive water use for oil shale production and its impacts on water resources of the Colorado River Basin.

Methods

The study is focused on life cycle consumptive water use for oil shale development. Consumptive water use is defined as “water that is evaporated, transpired, incorporated into products, or otherwise removed from the immediate water environment.” The analysis includes direct consumptive water requirements to extract, process, and refine shale oil, as well as indirect consumptive water use for generating the electricity associated with the extraction and processing. From the results, strategies for water supply certainty are discussed, and strategies for implementation are suggested. In addition, refining the shale oil outside of the oil shale region (removing the need for local water), using dry cooling systems for electricity generation, and building desalination plants in California (to replace water) are evaluated.

Results and discussion

Life cycle consumptive water use for oil shale is significant and could impact water availability for consumers in the lower Colorado River Basin. At a level of oil production of 2 million barrels per day, the life cycle consumptive water use would be significant: between 140 and 305 billion gallons (0.4 and 0.9 million acre-ft.) of water per year if surface mining and retorting is done, or between 150 and 340 billion gallons (0.5 and 1 million acre-ft.) of water per year if the Shell in situ process is used. Strategies could be implemented to provide water supply certainty including refining the shale oil outside of the region (removing some need for local water), using dry cooling systems for electricity generation, and building desalination plants in California (to replace water).

Conclusions

Water supply in the Colorado River Basin could be a primary constraint to the development of oil shale. At a level of oil production of 2 million barrels per day, the life cycle consumptive water use would be significant. Energy companies or governments may want to invest in water management and supply strategies that would eliminate the uncertainty associated with the water availability in the Colorado River Basin for oil shale development.     

INFLUENCE OF VARIOUS EXPOSURE PERIODS ON THE BIOMASS AND CHLOROPHYLL A OF CLADOPHORA GLOMERATA (CHLOROPHYTA)1

The biomass of Cladophora glomerata (L.) Kütz. was estimated at selected sites in the Colorado River between Glen Canyon Dam, Arizona, and River Kilometer 354. C. glomerata biomass was significantly higher at sites above Lees Ferry (25 km downstream from the Dam) than sites below the Ferry. Biomass and chlorophyll a were significantly reduced when C. glomerata was subjected to one-time exposures to the atmosphere for 12 daylight h in more. Repeated 12/12 h and 24/24 h (exposure/submergence) cycles over a two-week period also showed a significant reduction in biomass. The adaptations of C. glomerata to “stranding” during regulated flows are discussed.     

Parasitic infection of Filaroides osleri, Capillaria aerophila and Spirocera lupi in coyotes from the Southwestern United States

A total of 181 coyotes (Canis latrans) was examined for helminth parasites Filaroides osleri, Capillari aerophila, and Spirocerca lupi. Coyote carcasses were obtained from Kansas, western Oklahoma-northern Texas, Colorado, New Mexico, Arizona and southern California. Cysts of F. osleri were present in the trachea or bronchial division in 39 (22%) coyotes. C. aerophila were present in only 7 (4%) coyotes. S. lupi lesions were present in the aorta of 59 (33%) coyotes. Esophageal infections of S. lupi were found in only 4 of 142 (3%) coyotes. F. osleri, C. aerophila and S. lupi infections were more prevalent in western Oklahoma-northern Texas, low in southern Arizona-California, and absent in northern Arizona.     

Intraspecific Phylogeography of Red Squirrels (Tamiasciurus hudsonicus) in the Central Rocky Mountain Region of North America

We used variation in a portion of the mitochondrial DNA control region to examine phylogeography of Tamiasciurus hudsonicus, a boreal-adapted small mammal in the central Rocky Mountain region. AMOVA revealed that 65.66% of genetic diversity was attributable to variation within populations, 16.93% to variation among populations on different mountain ranges, and 17.41% to variation among populations within mountain ranges. Nested clade analysis revealed two major clades that likely diverged in allopatry during the Pleistocene: a southern clade from southern Colorado and a northern clade comprising northern Colorado, Wyoming, eastern Utah, and eastern Idaho. Historically restricted gene flow as a result of geographic barriers was indicated between populations on opposite sides of the Green River and Wyoming Basin and among populations in eastern Wyoming. In some instances genetic structure indicated isolation by distance.     

Trophic interactions and benthic animal community structure in the Colorado River, Arizona, U.S.A.

1. Cladophora glomerata is the dominant filamentous green alga in the tailwaters of the Colorado River, U.S.A., below Glen Canyon Dam, but becomes co-dominant with filamentous cyanobacteria, Oscillatoria spp., below the confluence of the Paria River (26km below the dam) where suspended sediments are elevated. 2. Benthic algal assemblages played an important role in the distribution of the amphipod, Gammarus lacustris, in the dam-controlled Colorado River through Grand Canyon National Park, Arizona. Cladophara and G. lacustris showed a weak positive relationship at ten cobble-riffle habitats in the Colorado River from Lees Ferry (25km below the dam) to Diamond Creek (362km downstream), while no relationship was found between Oscillatoria and G. lacustris. 3. The relationship between algal substrata and G. lacustris was tested by a series of in situ habitat choice experiments. G. lacustris showed a significant preference for Cladophora (with epiphytes) over Oscillatoria spp., detritus and gravel in treatment pans at Lees Ferry. 4. Epiphytic diatoms (i.e. food) were the overriding determinant of subtratum choice by G. lacustris in laboratory experiments. Gammarus chose the Cladophora/epiphytic diatom community over sonicated Cladophora with few diatoms. The amphipods also chose string soaked in diatom extract over string without diatom extract. 5. Importance of mutualistic interactions in aquatic benthic community structure is discussed.