Controls on vegetation structure in southwestern ponderosa pine forests, 1941 and 2004

Long-term studies can broaden our ecological understanding and are particularly important when examining contingent effects that involve changes to dominance by long-lived species. Such a change occurred during the last century in Southwestern (USA) ponderosa pine (Pinus ponderosa) forests. We used five livestock grazing exclosures established in 1912 to quantify vegetation structure in 1941 and 2004. Our objectives were to (1) assess the effects of historical livestock grazing on overstory structure and age distribution, (2) assess the effects of recent livestock grazing and overstory on understory vegetation, and (3) quantify and explain changes in understory vegetation between 1941 and 2004. In 1941, canopy cover of tree regeneration was significantly higher inside exclosures. In 2004, total tree canopy cover was twice as high, density was three times higher, trees were smaller, and total basal area was 40% higher inside exclosures. Understory species density, herbaceous plant density, and herbaceous cover were negatively correlated with overstory vegetation in both years. Most understory variables did not differ between grazing treatments in 1941 but were lower inside exclosures in 2004. Differences between grazing treatments disappeared once overstory effects were accounted for, indicating that they were due to the differential overstory response to historical livestock grazing practices. Between 1941 and 2004, species density declined by 34%, herbaceous plant density by 37%, shrub cover by 69%, total herbaceous cover by 59%, graminoid cover by 39%, and forb cover by 82%. However, these variables did not differ between grazing treatments or years once overstory effects were accounted for, indicating that the declines were driven by the increased dominance of the overstory during this period. Our results demonstrate that historical livestock grazing practices are an aspect of land-use history that can affect ecosystem development. Grazing history must be considered when extrapolating results from one site to another. In addition, the understory vegetation was more strongly controlled by the ponderosa pine overstory than by recent livestock grazing or by temporal dynamics, indicating that overstory effects must be accounted for when examining understory responses in this ecosystem

Effects of long-term livestock grazing and habitat on understory vegetation

The herbaceous understory stratum contains most of the plant diversity in ponderosa pine (Pinus ponderosa P. & C. Lawson var. scopulorum Engelm.) forests of the American Southwest and provides critical food and habitat for many wildlife species. During the last century, this stratum has been affected by livestock grazing and by increased dominance of overstory trees. We sampled a unique grazing exclosure to examine the relative importance of long-term livestock grazing (grazed or ungrazed) and habitat (park or tree) on the understory community. We sampled 3 plots of 192 contiguous quadrats (each quadrat 0.5 m2) in each of the 4 treatment combinations, for a total of 2304 quadrats. Species-area curves were generated by aggregating quadrats into nonoverlapping areas at grain sizes of 0.5 to 576 m2. The effects of habitat and grazing on species density were evident at very different scales. Species density was higher in park than tree plots at scales ≤32 m2 but did not differ between habitats at larger scales. Species density differed minimally between grazed and ungrazed treatments at small grains, but grazed plots contained more species than ungrazed plots at larger grains. Grazing treatments differed at smaller grains (to 4–8 m2) than did habitats (to 32 m2), with respect to density of native species and graminoids. Grazed plots had more exotic species than ungrazed plots at all grain sizes, though few exotics were present. Twenty-two species were identified as indicator species associated with habitats and/or grazing treatments. Evaluations of plant community response to treatments would be improved by accounting for the grain at which data have been collected and analyzed and by identifying indicator species associated with various treatments. These data would enable more-informed conservation and management decisions

Long-term vegetation studies in the southwest

In this paper, we describe several long-term studies in the ponderosa pine (Pinus ponderosa) forests of the American Southwest, focusing on the unique insights and contributions of these studies. Many of the studies that we discuss were established by staff from the Fort Valley Experiment Station (FVES; http://www.rmrs.nau.edu/fortvalley/)

The hill plots: a rare long-term vegetation study

One legacy of the Fort Valley Experimental Forest is the number and quality of long-term studies associated with it. One such study is the “Hill plots,” which began in 1912 and is still being actively studied. Livestock exclosures were built at five sites to examine vegetation recovery when protected from livestock grazing. Sites span a range of soil types and elevations. Materials associated with the Hill plots include historical data, plant specimens, and photographs. In this paper, we summarize the research that has occurred on the Hill plots, historical personnel who worked on them, threats they have experienced, ecological insights they have provided, and current research directions

Forest structure and tree recruitment changes on a permanent historical Cinder Hills plot over a 130-Year Period

We examined forest structure, tree recruitment, and spatial pattern over a 130-year period on cinder soils in northern Arizona. Data were collected from a 3.24 ha permanent, stem-mapped plot established in 1909. This site is unique in that it represents ponderosa pine (Pinus ponderosa Laws. var. scopulorum Engelm.) growing on black cinder soils, which are of limited extent in the Southwest. Tree diameter, tree density and spatial data reconstructed from 1874 and actual measurements from 1909 and 2004 were compared, and the current stand age-structure of living trees was examined. Unlike most studies of stand dynamics in the Southwest, this site has experienced little change in structure or spatial pattern between 1874 and 2004. This difference is thought to reflect the unique environmental conditions associated with black cinder soils

Detecting Gene-Gene Interactions Using a Permutation-Based Random Forest Method

Identifying gene-gene interactions is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Here, we aimed at developing a permutation-based methodology relying on a machine learning method, random forest (RF), to detect gene-gene interactions. Our approach called permuted random forest (pRF) which identified the top interacting single nucleotide polymorphism (SNP) pairs by estimating how much the power of a random forest classification model is influenced by removing pairwise interactions

Seeding versus natural regeneration: a comparison of vegetation change following thinning and burning in ponderosa pine

The decision whether to seed with native species following restoration treatments should be based on existing vegetation, species present in or absent from the soil seed bank, past management history, microclimate conditions and soils. We installed three permanent monitoring plots in two areas (total 18.6 ha) at Mt. Trumbull, AZ. Trees were thinned and the sites burned in 1996 and 1997. A 5 ha area was seeded with native shrub, grass and forb species; the remaining 13.6 ha were unseeded. Pretreatment species richness ranged from none to five species per plot. We recorded 13 graminoid and eight shrub species in the seeded area, and four graminoid and four shrub species in the unseeded area. The greatest increase in species richness in both seeded and unseeded plots occurred approximately 1.8 years posttreatment. Perennial native species dominated plant cover by 2.8 years, although annual native forbs dominate the soil seed bank. Perennial grasses are nearly absent from the seed bank. The seeded area had the highest diversity, but it also had twice as many nonnative species (14 versus 7 in the unseeded plots). By August 1999, maximum species richness reached 51 species on the seeded plot. Of these species, 80 percent were native. Although seeding increases diversity, it may also have the long-term tradeoff of introducing new genotypes and species, both native and nonnative

Genetic Population Structure Analysis in New Hampshire Reveals Eastern European Ancestry

Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/ Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population

"Growing trees backwards": Description of a stand reconstruction model

We describe an individual-tree model that uses contemporary measurements to "grow trees backward" and reconstruct past tree diameters and stand structure in ponderosa pine dominated stands of the Southwest. Model inputs are contemporary structural measurements of all snags, logs, stumps, and living trees, and radial growth measurements, if available. Key steps include the application of inverse decay functions to estimate snag and log death dates, and the estimation of tree size in the reconstruction year via radial growth data or accrued basal area increment. The model is provided as a function for R, and can be modified for other species and regions