This dataset tracks annual diversity score from 1991 to 2023 for Lower Lake High School vs. California and Konocti Unified School District

California was the state with the highest resident population in the United States in 2024, with 39.43 million people. Wyoming had the lowest population with about 590,000 residents. Living the American Dream Ever since the opening of the West in the United States, California has represented the American Dream for both Americans and immigrants to the U.S. The warm weather, appeal of Hollywood and Silicon Valley, as well as cities that stick in the imagination such as San Francisco and Los Angeles, help to encourage people to move to California. Californian demographics California is an extremely diverse state, as no one ethnicity is in the majority. Additionally, it has the highest percentage of foreign-born residents in the United States. By 2040, the population of California is expected to increase by almost 10 million residents, which goes to show that its appeal, both in reality and the imagination, is going nowhere fast.

High severity fire may promote or reduce plant understory diversity in forests. However, few empirical studies test long-standing theoretical predictions that productivity may help to explain observed variation in post-fire plant diversity. Support for the influence of productivity on disturbance-diversity relationships is found predominantly in experimental grasslands, while tests over large areas with natural disturbance and productivity gradients are few and have yielded inconsistent results. Here, we measured the response of post-fire understory plant diversity to natural gradients of fire severity and productivity in a large-scale observational study in California’s subalpine forests. We found that plant species richness increased with increasing fire severity and that this trend was stronger at high productivity. We used plant traits to investigate whether release from competition might contribute to increasing diversity and found that short-lived and far-dispersing species benefited more from high severity fire than their long-lived and near-dispersing counterparts. For far-dispersing species only, the benefit from high severity fire was stronger in high productivity plots where unburned species richness was lowest. Our results support theoretical connections between fire severity, productivity and plant communities that are key to predicting the consequences of increasing fire severity and frequency on diversity in the coming decades.

Methods Fire and plot selection

Over the course of three summers (July – September, 2017 – 2019), we sampled 248 plots across 13 fires in subalpine forest (see Appendix S1: Table S1 for fire information). We identified fires that contained each of six fire severity classes (unburned, low, low-moderate, moderate, high-moderate, and high) corresponding to fire-caused basal area mortality (0%, 0-25%, 25-50%, 50-75%, 75-90%, and 90-100% respectively) using the remotely sensed relativized differenced normalized burn ratio (RdNBR; Miller and Thode 2007). Relativized fire severity measures such as RdNBR report relative change such that areas of both sparser and denser vegetation can experience the full fire severity spectrum. This helps to decouple the correlation between fire severity and productivity that can arise with absolute measures of biomass change or mortality (Pausas and Bradstock 2007). We sampled all 10 subalpine fires in the study region that contained six fire severity classes and were within two days hike of a trailhead as well as 3 smaller fires with fewer severity classes. Time since fire at the time of sampling ranged relatively evenly from 2-17 years.

We used a stratified random sampling design, placing 405 square meter circular plots at the crosshairs of a 200x200 meter grid in upland areas with no recorded history of previous fire or logging. We stratified plots across preliminary fire severity classes (from RdNBR) as well as aspect (see Appendix S1: Supplemental Methods & Figure S1) and estimated final plot-level fire severity based on fire-caused basal area mortality as described above as well as relative fuel consumption (see Appendix S1: Table S2 for fire severity class descriptions). We subsequently censused all vascular plant species in the plot by systematically searching the plot area. Species richness was low in our study area (median 10), making it easy to locate all species.

Remotely sensed environmental variables

We used NDVI, a remotely sensed measure of photosynthetic activity, to represent plot-level productivity. NDVI has strong theoretical and empirical links to Gross Primary Productivity (GPP; Glenn et al. 2008), and robust correlations have been found between NDVI and tree radial growth measurements in other energy-limited systems like boreal forest (Beck et al. 2011). NDVI derived from 30x30m Landsat imagery is commonly used to represent productivity in montane forest (Burkle et al. 2015) and a recent study in Sierra Nevada subalpine forest found that it declined with mortality in whitebark pine stands and that inter-annual variability in NDVI tracked snow accumulation throughout a 30 year study period (Potter and Dolanc 2016). Using Google Earth Engine, we removed snow and cloud pixels from Landsat V imagery and calculated the average of maximum annual NDVI for the years 1995 through 2000 (Pettorelli et al. 2005, Gorelick et al. 2017). This six-year time period predates sampled fires, represents both wet and dry years in the study region, and its average correlates well with total aboveground tree biomass calculated for 37 unburned plots (Appendix S1: Fig. S1). We calculated Heat Load Index, a single metric accounting for slope, aspect, and some elements of slope position and shadow (essentially total plot-level solar radiation), using the R package spatialEco (McCune and Keon, 2002).

Plant trait data

We compiled available information on plant life history and dispersal syndrome for species in our dataset using the University of California Jepson Herbarium (http://ucjeps.berkeley.edu), the USDA Forest Service Fire Effects Information System (feis-crs.org), JSTOR Global Plants (https://plants.jstor.org/), and our own familiarity with the species. We characterized species life history as either annual/biennial, short-lived perennial (non-woody perennial without rhizomes, stolons, bulbs or root storage organs) or long-lived perennial (woody perennials and/or perennials with rhizomes, stolons, bulbs, or other storage organs), and species dispersal syndrome as either far-dispersing (vertebrate or wind dispersal syndrome) or near-dispersing (unassisted dispersal syndrome) (Supplement S1: Table S3). Species dispersal syndrome was classified as vertebrate-dispersing if the reproductive structures were fleshy or adhesive, wind-dispersing if the reproductive structure included a pappus, and unassisted if the reproductive structure had none of the previously described characteristics.

Despite a large number of ecological studies that document diversity loss resulting from anthropogenic disturbance, surprisingly few consider how disturbance affects temporal patterns of diversity that result from seasonal turnover of species. Temporal dynamics can play an important role in the structure and function of biological assemblages. Here, we investigate the temporal diversity patterns of bee faunas in Southern California coastal sage scrub ecosystems that have been extensively fragmented by urbanization. Using a two-year dataset of 235 bee species (n = 12,036 specimens), we compared 1-ha plots in scrub fragments and scrub reserves with respect to three components of temporal diversity: overall plot-level diversity pooled over time (temporal gamma diversity), diversity at discrete points in time (temporal alpha diversity), and seasonal turnover in assemblage composition (temporal beta diversity). Compared to reserves, fragments harbored bee assemblages with lower species richness and assemblage evenness both when summed across temporal samples (i.e., lower temporal gamma diversity) and at single points in time (i.e., lower temporal alpha diversity). Bee assemblages in fragments also exhibited reduced seasonal turnover (i.e., lower temporal beta diversity). While fragments and reserves did not differ in overall bee abundance, bee abundance in fragments peaked later in the season compared to that in reserves. Our results argue for an increased awareness of temporal diversity patterns, as information about the distinct components of temporal diversity is essential both for characterizing the assemblage dynamics of seasonal organisms and for identifying potential impacts of anthropogenic disturbance on ecosystem function through its effects on assemblage dynamics.

This dataset tracks annual diversity score from 2001 to 2008 for Valley Center Elementary Lower vs. California and Valley Center-Pauma Unified School District

The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89–1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.

Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.

Methods See: Mendelsohn B, Bedrosian B, Love Stowell SM, Gagne RB, LaCava MEF, Godwin BL, Hull JM, and Ernest HB. (2020) Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America. Conservation Genetics.

Aim: Fire can strongly influence ecosystem function, and human activities are disrupting fire activity at the global scale. Ecological theory and a growing body of literature suggest that a mixed severity fire regime promotes biodiversity in western North America. Some researchers advocate the use of pyrodiversity (i.e., heterogeneity in aspects of the fire regime such as time since fire or severity) as a conservation index to be maximized. Others caution against this approach arguing that the index oversimplifies fire-biodiversity interactions across trophic, spatial, and temporal scales. We evaluated the effects of several landscape-scale pyrodiversity indices, and their severity and time-since-fire components, on species richness of forest carnivores.

Location: Northern California, United States

Methods: We gathered data on fire history and mammal occurrence from camera trap surveys at 1,451 sites across Northern California public and private forestlands during 2009–2018. We used this data to model the effects of fire severity diversity, and its components (i.e., low, moderate, and high severity wildfires), on carnivore richness at short (10 years) and longer (25 years) timeframes. We repeated the modeling using a measure of time-since-fire diversity and its components (<10 yrs, 10–20 yrs, 20–30 ys, 30–40 yrs, 40–100 yrs.). We used Bayesian multispecies occupancy modeling to correct for imperfect measurement of species richness.

Results: We found that carnivore richness was highest at locations with intermediate fire severity diversity (0.46, 90%CI: 0.40–0.52) calculated using Simpson’s Measure of Evenness (range: 0–1) for the 10-yr timeframe, and the results were almost identical yet less precise for the longer timeframe. When we separated fire severity diversity into its components, we found that carnivore richness was highest at locations where 17% (90%CI: 4–20) of the landscape had experienced low severity burns over the past decade. In contrast, we found no association between time-since-fire diversity and carnivore richness, however, an intermediate amount of one of the components (e.g, the total amount of fire in the past 10 years) was positively associated with carnivore richness. Our results are consistent with a mixed severity fire regime wherein there is a greater extent of low severity than high severity fire.

Main Conclusions: Overall our results suggest that carnivores would benefit from landscapes managed for greater, but not maximal, fire severity diversity. Our results also suggest that prescribed, low severity burns may provide ecological services to wildlife not otherwise provided by silviculture in a managed forest landscape.

Methods For 2009 through 2018 we conducted wildlife surveys using camera traps at a total of 1,451 sites across the study area. Our annual survey season began in early August and continued through late November or early December. The duration of surveys was 2–5 weeks, and both camera traps within a hexagon were always surveyed concurrently. We reviewed photos from camera surveys to identify all mammal detections to species. We created a detection history for each site that indicated whether (“1”) or not (“0”) a species was observed for each 24-hour survey day up to 30 days. Average survey duration was 18.7 days.

We used the Monitoring Trends in Burn Severity (MTBS) spatial database of fire severity of all wildfires >500 ha in the USA since 1984. To measure fire severity diversity, we computed Simpson’s Measure of Evenness (SME) of the four burn category proportions from MTBS (none, low, moderate, high) at both the 10-year and 25-year timeframes. We repeated a similar analytical process for calculating covariates pertaining to time since fire, although the data available allowed us to inspect a longer timeframe than we used for fire severity.

Data were processed in R and are available in a .Rdata file.

See the accompanying manuscript for a full description of methodology.

This data sets corresponds to a publication in Methods in Ecology and Evolution titled: Plant biodiversity assessment through soil eDNA reflects temporal and local diversity

In August 2018, a single soil eDNA sample was collected from the centre of each permanent plot (1m2) in the Solhomfjell Forest Reserve stablished by the Sommerfeltia program. The soil eDNA samples were stored in individual plastic bags for transportation to the lab and stored at -20 °C prior to freeze-drying under vacuum. Each soil eDNA sample was separately homogenized with ceramic beads and one gram was used for eDNA extraction. The latter was done in five rounds of two steps: (1) CTAB/chloroform pre-treatment to increase the separation of the organic phase and (2) aqueous phase and using the E.Z.N.A. soil DNA kit following the manufacturer’s protocol (Omega Bio-tek, Norcross, Georgia, USA). The chloroplast marker trnL (UAA) intron P6 loop was chosen as its short sequence can yield amplification of old DNA material degraded in eDNA samples. This marker was amplified for each sample with the g and h primers by PCR, using three technical replicates (Taberlet et al. 2007; 5'-GGGCAATCCTGAGCCAA-3', 5'-CCATTGAGTCTCTGCACCTATC-3'). Forward and reverse primers were tagged with a unique 12 bp oligonucleotide on the 5’ end (Fadrosh et al. 2014). Unique combinations of tagged primers were set up in panels for each PCR reaction for a total of 309 samples (100 samples with 3 PCR replicates each, 5 extractions blanks and 4 PCR negatives). The PCR negatives had no DNA template and were placed on the 96th well position in each panel. Composition of PCR reactions, final volumes and number of cycles can be found in Supporting Information Data S1. The PCR products were run on a 2% agarose gel, and the amplicon concentrations were measured via band intensity using ImageLab software (Bio-Rad, California, USA). The lowest concentration (μM) available for all PCR products and its relative volume was identified and the relative concentrations of the PCR products were adjusted to this same concentration. Amplicons were pooled in one library using a Biomek 4000 automated liquid handler (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The library was cleaned using AMPure XP reagent beads (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The length for all amplicons in the library was determined using a Fragment Analyzer (Agilent Technologies, Santa Clara, California, USA). The library was sequenced on an Illumina MiSeq platform with 150 bp paired-end reads (Illumina Inc., San Diego, California, USA).

Sequence data was analyzed and curated using OBITools 2 (Boyer et al. 2016) following the wolf tutorial with adaptations for demultiplexing dual indexes from QIIME2 (Caporaso et al. 2010). Sequences were retained with both indexes for dereplication for further analysis. Similar sequences were clustered with obiclean (Boyer et al. 2016) only when the read count of the less abundant sequence was below 5% of the most abundant sequence. To reduce multiple identifications of the same sequence, taxonomic assignment of dereplicated and denoised sequences was done by matching to three reference sequences databases containing: (i) only taxa registered in the local Solholmfjell reference library; (ii) the complete arctic boreal database for vascular plants and bryophytes (Sønstebø et al.2010; Willerslev et al. 2014; Soininen et al. 2015); and (iii) taxa available in the EMBL database (downloaded on 7/02/2020) filtered to sequences with trnL (UUA) intron g-h primers using ecoPCR tool from OBITools (Boyer et al. 2016). Resulting identifications from the three databases were merged by sequence and duplicates were eliminated giving priority to reference databases (i), (ii), and (iii) in that order. To minimize erroneous taxonomic assignments, only taxa with a 100% match to a reference sequence were retained. We observed that below this threshold, sequences remained without a taxonomic rank assigned. Further, assigned taxa names were changed to the lowest taxonomic rank possible with trnL (UUA) intron and thus are identical to those registered in vegetation surveys. When different sequences were identified with identical taxa names, a unique entry was retained and the read counts within plots and replicates were summed. Read counts were averaged across all samples and negative controls (extraction + PCR).

All analyses are plot-based, and coded using R v 1.4.17 (R Core Team, 2019) and with packages listed in the code. Separate analyses are made for vascular plants and bryophytes, and/or for spruce and pine data subsets, or combinations thereof, when relevant.

Rice (Oryza sativa) is the second leading cereal crop in the world and is one of the most important field crops in the US, valued at approximately $2.5 billion. Kernel smut (Tilletia horrida Tak.), once considered as a minor disease, is now an emerging economically important disease in the US. In this study, we used multi-locus sequence analysis to investigate the genetic diversity of 63 isolates of T. horrida collected from various rice-growing areas across in the US. Three different phylogeny analyses (maximum likelihood, neighbor-joining, and minimum evolution) were conducted based on the gene sequence sets, consisting of all four genes concatenated together, two rRNA regions concatenated together, and only ITS region sequences. The results of multi-gene analyses revealed the presence of four clades in the US populations, with 59% of the isolates clustering together. The populations collected from Mississippi and Louisiana were found to be the most diverse, whereas the populations from Arkansas and California were the least diverse. Similarly, ITS region-based analysis revealed that there were three clades in the T. horrida populations, with a majority (76%) of the isolates clustering together along with the 22 Tilletia spp. from eight different countries (Australia, China, India, Korea, Pakistan, Taiwan, The US, and Vietnam) that were grouped together. Two of the three clades in the ITS region-based phylogeny consisted of the isolates reported from multiple countries, suggesting potential multiple entries of T. horrida into the US. This is the first multi-locus analysis of T. horrida populations. The results will help develop effective management strategies, especially breeding for resistant cultivars, for the control of kernel smut in rice.

This dataset tracks annual diversity score from 1999 to 2023 for Juliette Low School Of The Arts vs. California and Magnolia Elementary School District

The Pacific harbor seal (Phoca vitulina richardii) occurs in the Mexican Pacific region at the southernmost edge of the subspecies’ distribution, along 700 km of coastline and on nine islands west of the Baja California peninsula. Its abundance corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which make it vulnerable to stochastic processes; thus, reproductive and genetic isolation of the Mexican Pacific colonies is expected. This study aimed to genetically characterize the harbor seal in the Mexican Pacific to inform conservation efforts. We estimated the levels of genetic diversity for five colonies, using a 572-base pair mitochondrial DNA control region fragment and nine microsatellite loci. We examined the population genetic structure and its phylogeographic patterns. We found 15 variable sites that defined 18 mitochondrial DNA haplotypes. Results show one of the lowest levels of diversity re..., , , This README file was generated on 2024-01-17 by Alicia AbadÃa-Cardoso.

GENERAL INFORMATION

1. Title of Dataset: The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution

2. Author Information A. Principal Investigator Contact Information Name: Yolanda Schramm
   Institution: Universidad Autónoma de Baja California Address: Ensenada, Baja California, Mexico Email:

3. Date of data collection (single date, range, approximate date): 2014-2016

4. Geographic location of data collection: Baja California, Mexico (Todos Santos Island, Punta Banda Estuary, San Jerónimo Island, Natividad Island, and San Roque Island)

5. Information about funding sources that supported the collection of the data: National Science and Technology Council (Fondo SEP-CONACyT call CB-2012-01, project 179451)

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC...

aSize is defined as total length (TL), and size range the difference between the largest and smallest individual from n individuals sampled.bMean expected Hardy-Weinberg heterozygosity.cRarefied allelic richness.dHeterozygosity estimates obtained from McCraney et al. (2010).Habitat size, location, demographic parameters and genetic diversity measures (across nine microsatellite loci) of 17 tidewater goby populations in northern California.

Land-use change frequently reduces local species diversity. Species losses will often result in loss of trait diversity, with likely consequences for community functioning. However, the converse need not be generally true: management approaches that succeed in retaining species richness could nevertheless fail to maintain trait diversity. We evaluated this possibility using bee communities in a California agroecosystem. We examined among-site patterns in bee species diversity and functional-trait diversity in a landscape composed of a mosaic of semi-natural habitat, organic farms, and conventional farms. We sampled bees from all three habitat types, and compiled a database of life-history (“functional”) traits for each species. Although species richness was higher on organic farms than conventional farms, functional diversity was lower in both farm types than in natural habitat. Nesting location (below-ground vs. above-ground) was the primary trait contributing to differences in functional diversity between farms and natural habitat, reflecting observed differences in availability of nesting substrates among habitat types. Other traits, including phenology and sociality, were also associated with species’ occurrences or dominance in particular site types. These patterns suggest that management practices common to all farms act as environmental filters that cause similarly low functional diversity in their bee communities. Synthesis and applications. Although our results support the value of organic farming in maintaining abundant and species-rich bee communities, components of bee functional diversity are not well supported in farmed landscapes, regardless of farming practice. Maintenance of natural habitat, and/or the addition of natural-habitat elements to farms, is therefore important for the retention of functionally diverse bee assemblages in agroecosystems.