Evidence of spatial genetic structure in a California bunchgrass population

We investigated the scale of genetic variation of purple needlegrass (Nassella pulchra), a species commonly used in California for grassland restoration. Common garden and field data revealed evidence of genetic differentiation between two intermixed microhabitats characterized by differences in soil depth and community composition. We assessed the genetic variation within a single population using randomly amplified polymorphic DNA (RAPD) data collected from clusters of five individuals in 40 locations. We found no evidence for genetic structure at the whole population level. At smaller spatial scales, however, we found strong evidence that genetic subdivision of the population occurs at the level of the maternal neighborhood. We suggest that the interaction between widespread pollen dispersal and restricted seed dispersal may be the primary factor generating these results; panmictic pollen dispersal will make detection of genetic patterning difficult at larger spatial scales while limited seed dispersal will generate local genetic structure. As a result, the detection of population genetic structure will depend on the spatial scale of analysis. Local selection gradients related to topography and soil depth are also likely to play a role in structuring local genetic variation. Since N. pulchra is widely used in California in grassland and woodland habitat restoration, we suggest that, as a general rule, care should be exercised in transferring germplasm for the purposes of conservation when little is known about the within-population genetic subdivision of a plant species. Received: 23 December 1996 / Accepted: 20 May 1997     

Population structure of loggerhead shrikes in the California Channel Islands

The loggerhead shrike (Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity.     

Demographic structure of California chaparral in the long-term absence of fire

Abstract. Demographic structure of 12 chaparral sites unburned for 56 to 120 years was investigated. All sites were dominated by vigorous shrub populations and, although there was colonization by seedlings of woodland tree species in several stands, successional replacement of chaparral was not imminent. Although successional changes in community composition were evident, there was no indication of a decline in species diversity. Non-sprouting species of Ceanothus suffered the greatest mortality at most, but not all, sites. Sprouting shrubs, such as Quercus and Heteromeles had very little mortality, even in stands more than a century old. All postfire resprouting species had multiple stems of different ages indicating these shrubs were capable of continuously regenerating their canopy from basal sprouts. Ceanothus populations were highly clumped and there was a significant correlation across all sites between variance/mean ratio and percentage mortality. As Ceanothus populations thinned, they became less clumped. In mixed chaparral stands, Quercus and Heteromeles were significantly taller than associated Ceanothus shrubs and overtopped the Ceanothus; at two sites, the density of live Quercus per plot was correlated with the density of dead Ceanothus. Thus, mortality of Ceanothus stems is likely related to both intra and interspecific interations. Seedling recruitment was observed for most shrub species that regenerate after fire by resprouting; seedling and sapling densities ranging from 1000–36 500 ha^-1 were recorded for Quercus dumosa, Rhamnus crocea, Prunus ilicifolia, Heteromeles arbutifolia and Cercocarpus betuloides. For all but the last species, seedlings and saplings were most abundant beneath the canopy cover and not in gaps. Across all sites, recruitment was significantly correlated with depth and bio-mass of the litter layer. Cercocarpus betuloides was present in several stands, but seedling establishment was found only in one very open, disturbed stand. Regardless of stand age, taxa such as Adenostoma, Arctostaphylos and Ceanothus, which recruit seedlings after fire, had no significant seedling production.     

Population genetic structure of a California endemic branchiopod,Branchinecta sandiegonensis

Branchinecta sandiegonensis (Crustacea: Anostraca) is a narrow range endemic fairy shrimp discontinuously distributed in ephemeral pools on coastal mesas in San Diego County, USA. Ten populations across the range of the species were subjected to allozyme analysis for eleven loci. The species exhibits low variability (P₉₅ =9.1–45.5) and one third of the loci tested did not conform to Hardy-Weinberg equilibrium expectations. The species also exhibited a high degree of genetic differentiation between populations. F _ST values (fixation index) for most pairs of populations were above 0.25 (0.036–0.889).Low genetic variability and high genetic structure may result from low gene flow and founder effects due to habitat fragmentation and the lack of potential vectors for cyst dispersal. The unpredictable rainfall of the region also creates potential for variable population sizes which could affect structure and variability. This revised version was published online in August 2006 with corrections to the Cover Date.     

Population structure and adaptation of a bacterial pathogen in California grapevines

Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.     

Genetic structure of mountain lion (Puma concolor) populations in California

Analysis of 12 microsatellite loci from431 mountain lions (Puma concolor)revealed distinct genetic subdivision that wasassociated with geographic barriers andisolation by distance in California. Levels ofgenetic variation differed among geographicregions, and mountain lions that inhabitedcoastal areas exhibited less heterozygositythan those sampled inland. The San FranciscoBay and Sacramento-San Joaquin River Delta, theCentral Valley, and the Los Angeles Basinappeared to be substantial barriers to geneflow, and allele frequencies of populationsseparated by those features differedsubstantially. A partial barrier to gene flowappeared to exist along the crest of the SierraNevada. Estimated gene flow was high amongmountain lions inhabiting the Modoc Plateau,the western Sierra Nevada, and northern sectionof the eastern Sierra Nevada. SouthernCalifornia mountain lion populations mayfunction as a metapopulation; however, humandevelopments threaten to eliminate habitat andmovement corridors. While north-south geneflow along the western Sierra Nevada wasestimated to be very high, projected loss andfragmentation of foothill habitat may reducegene flow and subdivide populations. Preservation of existing movement corridorsamong regions could prevent population declinesand loss of genetic variation. This studyshows that mountain lion management andconservation efforts should be individualizedaccording to region and incorporatelandscape-level considerations to protecthabitat connectivity.     

Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of California

The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small F_ST values (?0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep‐water channel from the coastal sites, however, was significantly divergent (large F_ST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size.     

Population structure of California coyotes corresponds to habitat-specific breaks and illuminates species history

Little is known about the relationship between animal movements and the emergent structure of populations, especially for species occupying large continuous distributions. Some such mammals disperse disproportionately into habitat similar to their natal habitat, a behavioural bias that might be expected to lead to habitat-conforming genetic structure. We hypothesized that coyotes (Canis latrans) would exhibit such natal-biased dispersal, and used 13 microsatellite loci to test, correspondingly, whether genetic structure conformed to major habitat breaks. First, we used a model-based approach to assign coyote genotypes to distinct genetic clusters irrespective of geographical location. Visualization on a geographical information system revealed a strong concordance between the locations of cluster assignments and habitat bioregions, not explainable in terms of physical dispersal barriers or intervening low-quality habitat. Next, we used a multiple Mantel test, which controlled for effects of geographical distance (itself, marginally significant; P = 0.06), to statistically determine that genetic distance was indeed higher between than within bioregions (P < 0.001). Whereas previously published examples of landscape effects on gene flow have typically been explainable in terms of species-wide habitat affinities or dispersal barriers, our finding that genetic subdivisions were associated with unobstructed boundaries between contiguous habitats suggests a role for intraspecific variability in habitat affinities as a factor underlying genetic structure. In addition, our data combined with previously published data suggest a pattern of genetic isolation-by-distance throughout western North America, consistent with independent evidence that the western half of the coyote range predates European settlement.     

Comparative taxonomic structure of the floras of two Mediterranean-climate regions: Iberia and California

Two major events were invoked to understand recent biodiversity patterns in Mediterranean floras: northern hemisphere glaciations and historical human impacts. These two events were considered in this work, where we investigated general patterns in plant species richness and rarity attributes in two different Mediterranean regions: California and Iberia. Our goal was to assess whether comparisons of this sort provided evidence of different extinctions rates, making an effort to decouple anthropogenic from ice age‐related effects in both regions. We employed a taxonomically revised database for eight Mediterranean floras containing information on species richness for 298 families and rarity attributes for 11,834 taxa. We used summary statistics (Gini coefficient) and randomly generated models to test for general patterns of the distribution of diversity within and among taxonomic groups. We then used this general pattern among Mediterranean floras to provide a context in which to evaluate our two focal areas. Results indicated that floras of California and Iberia share the closest taxonomic structure among Mediterranean regions. Differences emerged in rarity attributes and the taxonomic identities of rarity rich groups. These findings were interpreted in the light of Pleistocene changes. In addition, a closer focus on rarity attributes allowed us to pinpoint some segments of these floras where anthropogenic activities may drive variation from general patterns, specifically for rare species in ecologically sensitive habitats.     

Population genetic diversity and structure of two rare vernal pool grasses in central California

Vernal pool ecosystems are declining throughout California, with only 10% of historic habitat remaining. This has endangered many specialist endemic plant species, leaving extant populations fragmented, isolated, and threatened or endangered. Recovery plans for the increasing number of endangered vernal pool species require information on their genetic and ecological status to guide conservation and restoration efforts. Federally threatened Neostapfia colusana (Colusa grass) and federally endangered Tuctoria greenei (Greene’s tuctoria) are two endemic vernal pool grasses of high conservation concern in central California. Remaining populations are highly fragmented due to range-wide habitat destruction. Using five polymorphic microsatellite markers for each species, we performed genetic surveys of 240 individuals from eight vernal pools for N. colusana, and 317 individuals from 13 vernal pools for T. greenei. We detected high within-population genetic diversity for both species, with average allelic diversities of 24 alleles/locus (mean Hobs = 0.68, mean Hexp = 0.71) for N. colusana, and 19 alleles/locus (mean Hobs = 0.77, and mean Hexp = 0.79) for T. greenei. Bayesian clustering and AMOVA indicated two genetically distinct population groups for N. colusana (Fst = 0.268, P < 0.0001), and three for T. greenei (Fst = 0.11, P < 0.0001). We found very slight temporal genetic structure at one N. colusana (Fst = 0.013, P < 0.05) and two T. greenei (Fst = 0.015, Fst = 0.018, P < 0.05) pools. These estimates of population genetic diversity and structure are critical measures for both species that will help inform recovery management actions.     

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ_ST values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ_ST (0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ_ST = 0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.     

Sediment microbial community structure and mercury methylation in mercury-polluted Clear Lake, California

Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of Desulfobacter and Desulfovibrio groups of sulfate-reducing bacteria suggests that Desulfobacter-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.     

Effects of variable precipitation on the structure and diversity of a California salt marsh community

Abstract. We measured the effects of annual variation in climate and experimentally augmented rainfall on patterns of distribution and above-ground productivity in annual plant communities at Carpinteria Salt Marsh in central California. In the driest year, Hutchinsia procumbens was codominant throughout much of the upper marsh; however, Hutchinsia was very rare or not present in the wetter years. Conversely, Juncus bufonius was common in the wettest year and absent in the driest year. Elevational distributions of other annual species also differed among years with different total precipitation. In 1989–1990, an exceptionally dry season, supplemental water decreased soil salinity, increased above-ground productivity of annuals, and caused significant changes in spatial patterns and relative density. In the lowest zone, Hutchinsia occurred only in watered plots and supplemental water increased the density of Spergularia marina. At intermediate elevations Lasthenia glabrata occurred only in watered plots and supplemental water increased the density of Spergularia, Hutchinsia, and Parapholis incurva. At upper elevations, Juncus occurred only in watered plots, and Lasthenia was the only species that increased significantly in density with watering. Unlike natural shifts in species abundance, no species declined significantly in cover in any zone in the watered treatment. Although climatic variation has complex affects on annual plant communities, our experiments isolated important affects of total annual rainfall on the structure of annual plant communities that were similar to those that occurred with natural variation in rainfall. We conclude that variation in total annual precipitation promotes dynamic community composition and spatial distributions among years, and thus increases overall species diversity in the salt marsh.     

Contribution of non-native species to soft-sediment marine community structure of San Francisco Bay,California

While non-native species (NIS) are important components in many coastal bays and estuaries, quantitative measures that characterize their effects on community structure at bay-wide scales are rare. In this study, we measure species composition and abundance for soft-sediments to assess the contribution of NIS to multiple dimensions of community structure, focusing on one of the most highly invaded bays in the world, San Francisco Bay. Benthic macrofauna was sampled in the high salinity, muddy shallow subtidal (2 m depth) across 10 sites, using replicate 0.1 m² Van Veen grabs. Invertebrates retained on a 1 mm sieve were identified, counted, and used to estimate the overall contribution of NIS to (a) abundance (b) species richness, and (c) community similarity. Soft-sediment communities were dominated numerically by NIS, which accounted for 76 % of all organisms detected and had a mean bay-wide abundance that was three and half-fold higher than native biota. Overall, NIS contributed to 36 % of observed taxa and 24–29 % of total estimated regional diversity. Native species accounted for 21 % of total abundance and 45 % of total species richness. Compared to native species, NIS occurred more frequently among samples and also explained more of the variation in community structure among sites. NIS dominate several key attributes of the soft-sediment infaunal community in San Francisco Bay. Percent contribution of NIS to species richness was at least two-fold higher than reported from two decades ago. Unique to this bay, these measures establish a quantitative baseline on the state of invasions and provide an important model for evaluating the extent of NIS in estuaries. Application of this approach across estuaries, with repeated measures over time, is critically needed to advance scientific understanding of invasions and also evaluation of efficacy and gaps in management to reduce new invasions.     

Little evidence for climate effects on local-scale structure and dynamics of California kelp forest communities

Climatic variables such as temperature and precipitation play an important role in controlling local and regional scale differences in population dynamics and species distributions, and large-scale climatic events such as El Niño southern oscillation (ENSO) have been shown to affect population dynamics of key species in many ecosystems, particularly in kelp forests. Few studies have been able to evaluate the consequences of climate variables on the structure and dynamics of biological communities, in large part because the lack of data at appropriate spatial and temporal scales has made it difficult to adequately address local-scale responses of species and communities to such events over relevant time scales. Here, we combined an unprecedented dataset of kelp forest species' abundances from the Channel Islands, California with data for several local, regional, and global scale climatic variables to evaluate the temporal and spatial scale at which one can detect community-wide effects of climate variables, in particular ENSO events. We found large and significant local-scale differences in community structure, but these differences were not related to differences in climatic variables. Moreover, giant kelp abundance, which has been shown to be highly sensitive to water temperature and storm disturbance, was a poor predictor of community differences, and all communities tended to decline in abundance over the 20-year sampling period, suggesting a press perturbation to the system such as PDO cycles or sustained fishing pressure. Although ENSO events can have dramatic impacts on the abundance and distribution of giant kelp itself across the range of the species, such events appear to have little effect on local-scale kelp forest community structure or dynamics.     

Contemporary genetic structure of Xantus's Hummingbird (Basilinna xantusii) in the Baja California peninsula

Genetic structure and phylogeographic patterns of natural populations are of great importance in assessing the conservation status of species. These population properties can be estimated using molecular markers of either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) to understand the historical, ecological and dispersal patterns that influence genetic exchange within and between populations. Basilinna xantusii is a sexually dimorphic hummingbird endemic to the Baja California Peninsula (BCP). It comprises three ancestral mitochondrial lineages linked to vicariant events, late Pleistocene climate changes and the geographical distribution of oases. This study aimed to determine and understand the current population genetic structure of this hummingbird. The genotypes of 16 microsatellite loci from 100 individuals collected across the geographical range of this species were compared with mtDNA sequences previously published. Cluster analyses identified five populations, two with almost no genetic admixture in the northern part of the BCP and three others with varying levels of admixed ancestry across the BCP. In San José de Magdalena, at the northernmost end of the range of Xantus's Hummingbird, 40% of individuals collected belong to one genetic cluster and the remaining 60% to another, both genetic clusters showing very little admixed ancestry. We hypothesize that, despite being in sympatry, these individuals do not interbreed, unlike the other populations where individuals showed ancestry coefficients of the other genetic groups. The philopatric behaviour of males and the long-range dispersal capacity of females probably determine the observed genetic differentiation pattern. The mito-nuclear discordance detected could be due to the molecular markers used and to female-biased dispersal. Gene flow is asymmetric in this species, being greater from north to south than vice versa, which is probably related to differences in the seasonality of precipitation across the BCP and to urbanization of the oases.     

Spatial structure and dynamics of breeding bird populations at a distribution margin,southern California

Aim Local‐scale processes at species distribution margins can affect larger‐scale distribution dynamics, but are rarely studied. The objective of this research was to elucidate the nature of distribution limits by studying the comparative structure, dynamics and environmental associations of breeding bird populations at their distribution margin. We hypothesized that climate is principally responsible for setting distribution limits, whereas biotic habitat features are more strongly associated with distribution patterns within the range. Location Southern California, USA. Methods During 2005–2007 we studied the distribution patterns of breeding birds in three study areas, each spanning a low‐elevation (200–1800 m) desert scrub‐to‐chaparral gradient. We used logistic regression with hierarchical partitioning to assess the independent effects of environmental variables (e.g. climate versus habitat) on distributions. We tested for shifts in the relative importance of these environmental variables in determining distribution limits versus within‐range patterns, and we also compared higher‐ and lower‐elevation groups of species. Results Distribution patterns were highly variable among species, but were remarkably static over the three study areas and 3‐year study period. Across species, habitat floristic variables performed relatively well at explaining distribution patterns. For higher‐elevation species (chaparral birds), climate was relatively important in setting their lower distribution limits, and there was a shift to a greater importance of biotic habitat (mainly habitat structural variables) for determining within‐range patterns. Relationships were more mixed for lower‐elevation species (desert scrub birds), but with respect to distribution limits, biotic habitat variables tended to be more important relative to climate than we observed for chaparral birds. Main conclusions Along this warm, arid elevational gradient, higher‐elevation chaparral birds are more limited by climate at their lower margin than are lower‐elevation desert birds at their upper margin, suggesting that climate plays a strong role (relative to other values) in excluding non‐desert birds from desert. However, given the strong differences among species, predictive distribution models will need to be individually tailored, and for most species biotic habitat variables were of greater importance than climate in determining limits. This research highlights the usefulness of studying environmental relationships at distribution margins and the importance of considering biotic relationships in forecasting distribution shifts under changing climates.     

Abundance, age structure, and voltinism of light brown apple moth populations in California

The light brown apple moth, Epiphyas postvittana (Walker), is native to Australia and first was detected in California in 2006. In this study, we regularly sampled populations on Leptospermum laevigatum (Gaertn.) F.Muell. at two sites in San Francisco and on Arctostaphylos densiflora M.S. Baker at two sites in Santa Cruz over a 2-yr period to monitor the abundance, age structure, and voltinism of this potential pest in relation to degree-days. Our results showed that larval abundance declined at two sites, cycled with peaks in midsummer at one site, and remained steady at one site. Generations overlapped at all four sites with the full range of larval instars being present for most of the year, although populations during the winter were predominantly mid to late instars. Accumulated degree-days predict an average of 3.27 and 4.58 generations per year in San Francisco and Santa Cruz, respectively, which matched our observed peaks of late-instar larvae in the field remarkably well. This new information on light brown apple moth phenology in coastal California will be invaluable for the development of effective monitoring and management strategies for this new invader in the studied region.