Phylogenetic relationships within the aquatic snail genus Tryonia: implications for biogeography of the North American Southwest

We examined the phylogenetic relationships among 23 species of the North American aquatic snail genus Tryonia (Hydrobiidae), 10 additional representatives of the subfamily Cochliopinae, and two outgroups. Maximum parsimony analysis of a 601-base-pair sequence from the mitochondrial COI gene did not support monophyly of the genus nor its subgenus Paupertryonia. A clade composed of the type species of Tryonia and 16 congeners was strongly supported by the COI data and congruent with recently discovered variation in female genitalic morphology. This "true Tryonia" clade included two large western subclades having a sister-group relationship. The phylogenetic structure of one of these subclades is congruent with vicariant events associated with late Neogene history of the lower Colorado River drainage. The other subclade mirrors development of the modern Rio Grande rift and inception of modern topography in the southwestern Great Basin during the late Neogene. Both subclades are represented in the composite Tryonia fauna of the Amargosa River basin, whose assembly is attributed to the complex geological history of the Death Valley region.     

MITOCHONDRIAL DNA VARIATION AND EVOLUTION OF THE DEATH VALLEY PUPFISHES (CYPRINODON,CYPRINODONTIDAE)

A phylogenetic analysis of mitochondrial DNA (mtDNA) restriction sites was used to examine the geographic history of the Cyprinodon nevadensis complex of pupfishes, a group of four species (seven extant subspp.) in two endorheic (closed) basins of the Death Valley System in California and Nevada (Owens River Valley and Ash Meadows-Death Valley). The mtDNA results suggest that the group contains mtDNAs from two divergent clades. One such clade is represented by the mtDNAs of the Owens Valley pupfish (C. radiosus) and the existing species in the Colorado River (C. macularius), while the other includes the mtDNAs of the Ash Meadows-Death Valley species (C. nevadensis, C. salinus, and C. diabolis) and a species located much farther to the east (C. fontinalis from the Guzman Basin, Chihuahua, Mexico). These results, together with evidence from other studies, suggest two separate invasions of the Death Valley System by pupfishes carrying phylogenetically divergent mtDNAs. The C. nevadensis complex apparently is either an artificial group or else it is monophyletic and its genetic history includes loss of the original mtDNA in either Owens Valley or Ash Meadows-Death Valley following genetic introgression after an invasion by a pupfish carrying a divergent mtDNA.     

Increasing demands on limited water resources: Consequences for two endangered plants in Amargosa Valley, USA

Recent population expansion throughout the Southwest United States has created an unprecedented demand for already limited water resources, which may have severe consequences on the persistence of some species. Two such species are the federally protected Nitrophila mohavensis (Chenopodiaceae) and Grindelia fraxino-pratensis (Asteraceae) found in Amargosa Valley, one valley east of Death Valley, California. Because both species are federally protected, no plant material could be harvested for analysis. We therefore used a chamber system to collect transpired water for isotopic analysis. After a correction for isotopic enrichment during transpiration, δ(18)O values of plant xylem water were significantly different between N. mohavensis and G. fraxino-pratensis throughout the study. Using a multisource mixing model, we found that both N. mohavensis and G. fraxino-pratensis used soil moisture near the soil surface in early spring when surface water was present. However, during the dry summer months, G. fraxino-pratensis tracked soil moisture to deeper depths, whereas N. mohavensis continued to use soil moisture near the soil surface. These results indicate that pumping groundwater and subsequently lowering the water table may directly prevent G. fraxino-pratensis from accessing water, whereas these same conditions may indirectly affect N. mohavensis by reducing surface soil moisture and thus its ability to access water.     

Conservation genomics of desert dwelling California voles (<Emphasis Type="Italic">Microtus californicus</Emphasis>) and implications for management of endangered Amargosa voles (<Emphasis Type="Italic">Microtus californicus scirpensis</Emphasis>)

Understanding population genetic structure and levels of genetic variation is critical for the conservation and management of imperiled populations, especially when reintroductions are planned. We used restriction-site associated DNA (RAD) sequencing to study the genetic diversity and evolutionary relationships of the endangered Amargosa vole and other closely related desert-dwelling California voles. Specifically, we sought to determine how Amargosa voles are related to other California voles, how genetic variation is partitioned among subpopulations in wild Amargosa voles, and how much genetic variation is captured within a captive insurance colony of Amargosa voles. Our multilocus nuclear dataset provides strong evidence that Amargosa voles are part of a northern clade of California voles. Amargosa voles have highly reduced genetic variation relative to other California voles, but do exhibit some sub-structure among sampled marshes. Captive Amargosa voles capture approximately half of the total genetic variation present in the wild Amargosa vole populations. We discuss the management implications of our findings in light of reintroductions planned for Amargosa voles. Our study highlights the utility of reduced representation genomic approaches, like RADseq, to resolve relationships among small populations that are difficult to study with traditional markers due to low genetic variation and few individuals left in the wild.     

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.     

Assembly of a micro-hotspot of caenogastropod endemism in the southern Nevada desert,with a description of a new species of Tryonia (Truncatelloidea,Cochliopidae)

Newly obtained and previously published sequences of the cytochrome c oxidase subunit I (COI) gene were analyzed to examine the biogeographic assembly of the caenogastropod fauna (belonging to the families Assimineidae, Cochliopidae, and Hydrobiidae) of an isolated spring along the lower Colorado River in southern Nevada (Blue Point Spring). Based on available COI clock calibrations, the three lineages that comprise this fauna are 2.78–1.42 million years old, which is roughly coeval or slightly younger than the age of Blue Point Spring (inferred from local fossil spring deposits). Two of the lineages—endemic Pyrgulopsis coloradensis and Assiminea aff. infima—are most closely related to snails in the Death Valley area (well to the west) and likely colonized Blue Point Spring by transport on birds. A single haplotype was detected in both of these snails, suggesting that they may have only recently colonized Blue Point Spring. The third lineage—endemic Tryonia infernalis, newly described herein based on morphological and molecular evidence—is most closely related to a geographically proximal species in a lower Colorado River tributary (Tryonia clathrata); the split between these taxa may be the product of vicariance (severance of a prior drainage connection) or a separate jump dispersal event. The considerable genetic diversity in Tryonia infernalis (three haplotypes differing by 0.6% mean sequence divergence) suggests a possibly lengthy history of local differentiation. Our findings also identify Blue Point Spring as a new micro-hotspot of groundwater-dependent biodiversity in Nevada and will assist ongoing efforts to protect and conserve these imperiled ecosystems.     

Characterization of microsatellite loci in chinook salmon (Oncorhynchus tshawytscha) and cross‐species amplification in other salmonids

Previous studies of population genetic structure of fall‐run chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley have either not focused on or have been unable to resolve intertributary differences within the San Joaquin River basin. The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross‐species amplification of 17 microsatellite loci in six species of salmonids. Fourteen of these loci are polymorphic in fall‐run chinook from the San Joaquin River drainage. These results indicate the potential utility of microsatellite markers developed for one species, for both congenerics and species within a closely related genus.     

Systematics of a widely distributed western North American springsnail,Pyrgulopsis?micrococcus (Caenogastropoda,Hydrobiidae), with descriptions?of?three new congeners

We describe three new species of springsnails (genus Pyrgulopsis) from the Amargosa River basin, California and Nevada (P. licina sp. n., P. perforata sp. n., P. sanchezi sp. n.), each of which was previously considered to be part of P. micrococcus. We also restrict P. micrococcus to its type locality area (Oasis Valley) and redefine a regional congener, P. turbatrix, to include populations from the central Death Valley region and San Bernardino Mountains that had been previously identified as P. micrococcus. The five species treated herein form genetically distinct lineages that differ from each other by 4.2–12.6% for mtCOI and 5.2–13.6% for mtNDI (based on previously published and newly obtained data), and are diagnosable by shell and/or penial characters. The new molecular data presented herein confirm sympatry of P. licina and P. sanchezi in Ash Meadows (consistent with morphological evidence) and delineate an additional lineage of P. micrococcus (in the broad sense) that we do not treat taxonomically owing to the paucity of morphological material. Conservation measures are needed to ensure the long term persistence of populations of P. micrococcus and a genetically differentiated lineage of P. sanchezi which live in disturbed habitats on private lands.     

Successful care and propagation of the endangered amargosa vole (Microtus californicus scirpensis) in captivity

The Amargosa vole (Microtus californicus scirpensis) is a highlyendangered rodent endemic to a small stretch of the California portion of the Amargosa River basin in Inyo County's Mojave Desert. Although the Amargosa vole has survived in this naturally fragmented ecosystem for thousands of years, recent habitat degradation due to land development, water drainage, and marsh exploitation has further isolated the species and reduced its available habitat. As part of a conservation effort to preserve the species, a captive breeding population was established in 2014 to serve as an insurance colony and as a source of individuals to release into the wild as restored habitat becomes available. As this is the only captive colony for this species, there is little published information about appropriate care and husbandry for the Amargosa vole. Here we provide information about behavior, diet, reproduction, drug sensitivities, and diseases that affect successful captive care. We also provide recommendations for housing and disease management to preserve natural behaviors and defenses in captive‐born animals.     

Following the rivers: historical reconstruction of California voles Microtus californicus (Rodentia: Cricetidae) in the deserts of eastern California

The California vole, Microtus californicus, restricted to habitat patches where water is available nearly year‐round, is a remnant of the mesic history of the southern Great Basin and Mojave deserts of eastern California. The history of voles in this region is a model for species‐edge population dynamics through periods of climatic change. We sampled voles from the eastern deserts of California and examined variation in the mitochondrial cytb gene, three nuclear intron regions, and across 12 nuclear microsatellite markers. Samples are allocated to two mitochondrial clades: one associated with southern California and the other with central and northern California. The limited mtDNA structure largely recovers the geographical distribution, replicated by both nuclear introns and microsatellites. The most remote population, Microtus californicus scirpensis at Tecopa near Death Valley, was the most distinct. This population shares microsatellite alleles with both mtDNA clades, and both its northern clade nuclear introns and southern clade mtDNA sequences support a hybrid origin for this endangered population. The overall patterns support two major invasions into the desert through an ancient system of riparian corridors along streams and lake margins during the latter part of the Pleistocene followed by local in situ divergence subsequent to late Pleistocene and Holocene drying events. Changes in current water resource use could easily remove California voles from parts of the desert landscape.     

Factors influencing species diversity in saline waters of Death Valley,USA

Salinity is a major factor influencing the distributions and abundances of aquatic macroinvertebrates of saline waters in Death Valley, California, USA. A general pattern of declining numbers of species with increasing salinity is seen in Death Valley waters. Some species are restricted to low salinities, others are found only in highly saline pools, and still others are widely distributed over a broad range of salinities.Salinity alone cannot explain distributions seen in the field. Distributions and abundances of species such as the caddisfly Limnephilus assimilis Banks are broader than would be predicted on the basis of laboratory studies of salinity and temperature. I present evidence that for such species, biotic factors such as reduced predation at high salinities may compensate for increased physiological stress.     

Exogenous vasotocin alters aggression during agonistic exchanges in male Amargosa River pupfish (Cyprinodon nevadensis amargosae)

Pupfishes in the Death Valley region have rapidly differentiated in social behaviors since their isolation in a series of desert streams, springs, and marshes less than 20,000 years ago. These habitats can show dramatic fluctuations in ecological conditions, and pupfish must cope with the changes by plastic physiological and behavioral responses. Recently, we showed differences among some Death Valley populations in brain expression of arginine vasotocin (AVT). As AVT regulates both hydromineral balance and social behaviors in other taxa, these population differences may indicate adaptive changes in osmoregulatory and/or behavioral processes. To test whether AVT is relevant for behavioral shifts in these fish, here we examined how manipulations to the AVT system affect agonistic and reproductive behaviors in Amargosa River pupfish (Cyprinodon nevadensis amargosae). We administered exogenous AVT (0.1, 1, and 10 microg/g body weight) and an AVP V1 receptor antagonist (Manning compound, 2.5 microg/g body weight) intraperitoneally to males in mixed-sex groups in the laboratory. We found that AVT reduced the initiation of aggressive social interactions with other pupfish but had no effect on courtship. The effects of AVT were confirmed in males in the wild where AVT (1 microg/g body weight) reduced the aggressive initiation of social interactions and decreased aggressive responses to the behavior of other males. Combined, these results show that AVT can modulate agonistic behaviors in male pupfish and support the idea that variation in AVT activity may underlie differences in aggression among Death Valley populations.     

Clan Lethals and Inter-Year Allelism in Death Valley DROSOPHILA PSEUDOOBSCURA

A chromosome 2 lethal allelism rate of about 3% was found in the 1974 population of D. pseudoobscura in Death Valley, California. This rate was significantly higher than allelism rates in other Southern California populations. The Death Valley population was sampled again in 1975 and 1977, with allelism rates of 1% and 0.5%, respectively. In 1974, several lethals were in high frequencies (about 1%), a pattern that reappeared in 1975 and 1977. However, none of the lethals in high frequency one year were in high frequency another year; the particular lethal alleles present in this ephemeral population appear to be due to their random presence in the flies which refound the population every winter. The results for the Death Valley population are compared with a Japanese population of D. melanogaster in which lethals in high frequency one year are also in high frequency in succeeding years and with earlier work on chromosome 3 of D. pseudoobscura, which showed a lower lethal frequency and higher allelism rate.     

Rapid phenotypic change in a native bird population following conversion of the Colorado Desert to agriculture

Humans are modifying our planet's ecosystems with increasing frequency and intensity. Exploring population responses to anthropogenic modifications of natural habitat provides insights into how species persist in the Anthropocene. Here, we leverage natural history collections to document rapid phenotypic change within a native bird population following ~80 yr of agriculture in the Colorado Desert of southeastern California. By comparing spectrophotometric measurements of horned lark Eremophila alpestris specimens collected in the Imperial Valley from 1918 to 1934 to those collected from 1984 to 2014, we found that more recent birds have darker backs, napes, and crowns. This dorsal darkening may have resulted from a shift in selective pressures for camouflage induced by land use: previously, the lark population nested on light‐colored desert flats, whereas contemporary larks occupy darker soil associated with agricultural fields. Adaptation and/or introgression may have contributed to this instance of rapid phenotypic change following the rise of agriculture in the Imperial Valley.     

Introduced Schistosomiasis: Evaluation as a Public Health Hazard

Schistosomiasis was found in many agricultural workers from Yemen who are residing in the San Joaquin Valley, and a study was done to evaluate the public health hazard of this imported disease. If the necessary intermediate hosts are present, a local focus of infection could be established.Numerous Biomphalaria obstructa snails collected in the vicinity of the Avenue 82 irrigation canal near Oasis, Riverside County, showed no evidence of natural schistosome infection. Laboratory-reared offspring of these snails were exposed to miracidia of Schistosoma mansoni originating from Yemen immigrants and to miracidia from a standard laboratory strain of Puerto Rican origin obtained from the National Institutes of Health. All exposures of California B. obstructa were made with a laboratory stock of highly susceptible B. glabrata snails also obtained from NIH as controls. Although miracidia penetrated California snails no evidence of infection was detected whereas the B. glabrata controls showed normal, mature infections with numerous cercariae.There appears little likelihood that B. obstructa can serve as intermediate host for schistosomiasis.     

Evaluation of potential impacts of perchlorate in the Colorado River on the Salton Sea,California

Ammonium perchlorate, a component of rocket fuel, entered Lake Mead through drainage and shallow groundwater in the Las Vegas Valley, Nevada, and is now found in the lower Colorado River from Lake Mead to the international boundary with Mexico. Perchlorate is a threat to human health through reduction of thyroid hormone production. Perchlorate has been found in water throughout the lower Colorado system and in crops in the California’s Imperial Valley, as well as in several other states, but it has not previously been included in investigations of the Salton Sea. Because perchlorate behaves conservatively in the Colorado River, it was postulated that it could be accumulating at high levels along with other salts in the Salton Sea. Results show that perchlorate is not accumulating in the Sea, although it is present in tributaries to the Sea at levels similar to those found in the Colorado River. Bacterial reduction of perchlorate is the most likely explanation for the observed results. The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged. Guest editor: S. H. Hurlbert The Salton Sea Centennial Symposium. Proceedings of a Symposium Celebrating a Century of Symbiosis Among Agriculture, Wildlife and People, 1905–2005, held in San Diego, California, USA, March 2005     

Population genetic history of the dreissenid mussel invasions: expansion patterns across North America

This study tests population genetic patterns across the Eurasian dreissenid mussel invasions of North America—encompassing the zebra mussel Dreissena polymorpha (1986 detection) and the quagga mussel D. rostriformis bugensis (detected in 1990, which now has largely displaced the former in the Great Lakes). We evaluate their source-spread relationships and invasion genetics using 9–11 nuclear microsatellite loci for 583 zebra mussels (21 sites) and 269 quagga mussels (12 sites) from Eurasian and North American range locations, with the latter including the Great Lakes, Mississippi River basin, Atlantic coastal waterways, Colorado River system, and California reservoirs. Additionally, mtDNA cytochrome b gene sequences are used to verify species identity. Our results indicate that North American zebra mussels originate from multiple non-native northern European populations, whereas North American quagga mussels trace to native estuaries in the Southern Bug and Dnieper Rivers. Invasive populations of both species show considerable genetic diversity and structure (zebra F _ST = 0.006–0.263, quagga F _ST = 0.008–0.267), without founder effects. Most newer zebra mussel populations have appreciable genetic diversity, whereas quagga mussel populations from the Colorado River and California show some founder effects. The population genetic composition of both species changed over time at given sites; with some adding alleles from adjacent populations, some losing them, and all retaining closest similarity to their original composition. Zebra mussels from Kansas and California appear genetically similar and assign to a possible origin from the St. Lawrence River, whereas quagga mussels from Nevada and California assign to a possible origin from Lake Ontario. These assignments suggest that overland colonization pathways via recreational boats do not necessarily reflect the most proximate connections. In conclusion, our microsatellite results comprise a valuable baseline for resolving present and future dreissenid mussel invasion pathways.     

Molecular phylogeny of Tornier's cat snake (Crotaphopeltis tornieri), endemic to East African mountain forests: biogeography, vicariance events and problematic species boundaries

Five isolated populations of the East African snake species Crotaphopeltis tornieri were investigated using mitochondrial sequence data from the genes cytochrome B and NADH2. The congeneric species Crotaphopeltis hotamboeia and three species of the closely related genera Dipsadoboa were used as outgroups. The results were analysed using unweighted parsimony and the reconstructed phylogeny revealed four well-defined evolutionarily significant units. Very high levels of genetic diversity was observed. The highest levels of divergence was observed between specimens from Mount Rungwe and the remaining populations. A similar pattern but with much lower divergence levels has been observed for the bird species Andropadus masukuensis . Together they indicate that Mt Rungwe is an important area for future conservation efforts. In the analysis of the combined data set C. tornieri appear as non-monophyletic with C. hotamboeia being the sister group to all C. tornieri populations except those on Mt Rungwe. The validity of C. tornieri and C. hotamboeia as species was thereby questioned by the data. However, the support for this is very weak and no nomenclatural consequences are suggested at present.     

Genetic divergence, population structure and historical demography of rare springsnails (Pyrgulopsis) in the lower Colorado River basin

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.     

Two distinct phylogenetic clades of infectious hematopoietic necrosis virus overlap within the Columbia River basin

Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus, causes a highly lethal disease of salmonid fish in North America. To evaluate the genetic diversity of IHNV from throughout the Columbia River basin, excluding the Hagerman Valley, Idaho, the sequences of a 303 nt region of the glycoprotein gene (mid-G) of 120 virus isolates were determined. Sequence comparisons revealed 30 different sequence types, with a maximum nucleotide diversity of 7.3% (22 mismatches) and an intrapopulational nucleotide diversity of 0.018. This indicates that the genetic diversity of IHNV within the Columbia River basin is 3-fold higher than in Alaska, but 2-fold lower than in the Hagerman Valley, Idaho. Phylogenetic analyses separated the Columbia River basin IHNV isolates into 2 major clades, designated U and M. The 2 clades geographically overlapped within the lower Columbia River basin and in the lower Snake River and tributaries, while the upper Columbia River basin had only U clade and the upper Snake River basin had only M clade virus types. These results suggest that there are co-circulating lineages of IHNV present within specific areas of the Columbia River basin. The epidemiological significance of these findings provided insight into viral traffic patterns exhibited by IHNV in the Columbia River basin, with specific relevance to how the Columbia River basin IHNV types were related to those in the Hagerman Valley. These analyses indicate that there have likely been 2 historical events in which Hagerman Valley IHNV types were introduced and became established in the lower Columbia River basin. However, the data also clearly indicates that the Hagerman Valley is not a continuous source of waterborne virus infecting salmonid stocks downstream.