Changes in kit fox–coyote–prey relationships in the Great Basin Desert, Utah

Variation in kit fox ( Vulpes macrotis ) population parameters can be influenced by vegetative cover and the distribution and abundance of other predator and prey species. Dramatic changes to Great Basin Desert habitats, which can potentially impact mammalian species, have occurred in some areas in Utah. We examined kit fox demographics and prey populations from 1999 to 2001 on Dugway Proving Ground (DPG), a U.S. Army facility in Utah, and compared some parameters to historical levels (1956–1958, 1966–1969). Adult survival rates were fairly consistent between 1999 and 2000 and between 1999 and 2001; however, survival was greater in 2001 than in 2000. Reproductive rates ranged from 1.0 to 3.8 pups per female in 1999–2000 and were similar to historical numbers (1.0–4.2 pups per female). We found a decrease in pre-whelping kit fox density from the 1960s (0.12 foxes ? km –2 ) to 1999–2001 (0.04 foxes ? km –2 ); however, densities were similar between the current study and the 1950s (0.08 foxes ? km –2 ). Using 9 years of data, we found density dependence between reproductive rates of the current year and annual fox density from the previous year. Using 7 years of data, we found a slight correlation between kit fox annual density and a 1-year lag in leporid abundance, even though leporid abundance was lower during the present study than it was historically. Compared to historical levels, current small mammal abundance and species composition has changed in several habitats. Kit fox breeding density and annual density were inversely correlated with coyote ( Canis latrans ) density. Changes to the landscape at DPG, especially due to invasion of cheatgrass ( Bromus tectorum ) and addition of artificial water sources, have caused a change in available kit fox habitat and prey species, and have increased the abundance of coyotes, the kit fox's major competitor.     

Breeding biology and flower visitors of the rare White River penstemon, Penstemon scariosus var. albifluvis (Scrophulariaceae)

We studied the breeding system and flower visitors of White River penstemon, a rare endemic from the Uintah Basin of eastern Utah and western Colorado. Bagging treatments and hand-pollination treatments showed that Penstemon scariosus var. albifluvis has a mixed mating system: while some seeds and fruits are produced through selfpollination (both autogamy and geitonogamy), significantly more are produced when flowers are cross-pollinated. The primary flower visitors, and likely pollinators, were several species of native twig- and ground-nesting bees in the families Apidae, Halictidae, and Megachilidae. We found no differences in fruit or seed production between open-pollinated controls and hand-outcrossed flowers, suggesting that pollinator visits were sufficient to maximize female reproductive success. Management plans to conserve White River penstemon must recognize that full reproductive success of this rare plant taxon relies on a suite of pollinating bees, and that the species richness and abundances of bee visitors should be maintained.     

Human trampling effects on regeneration and age structures of Pinus edulis and Juniperus monosperma

We examined effects of human foot traffic on age structures and densities of seedlings and saplings of Pinus edulis (Colorado pinyon) and Junisperus monosperma (one-seed juniper) in a heavily used urban park, Garden of the Gods, Colorado. Age structures show no stand-destroying disturbances, but they do contain small peaks 85-95 yr ago (minimum age), which have been interpreted as responses to heavy grazing. For Pinus edulis reverse J-shaped age structures indicate a strongly reproducing population, while flat age structures of J. monosperma show low present reproduction. Young trees showed strong preferences for establishing under existing trees and shrubs and not among herbs or on bare soil. Pinus edulis seedling density was reduced by 73% in heavily trampled areas compared to lightly trampled areas. However, there were no differences in density when only the area protected by rocks, shrubs, or trees was considered. This indicates that direct effects such as physical damage and soil erosion kill young trees, and indirect effects, such as lower seed production, do not cause the lower densities in heavily trampled areas. Pinus edulis saplings and J. monosperma seedlings and saplings showed no differences in density across trampling intensities. In heavily trampled areas of Garden of the Gods Park, recent increases in use have apparently reduced Pinus edulis seedling establishment enough that long-term regeneration is threatened. Managers of all pinyon-juniper woodlands must recognize that in areas strongly impacted by foot traffic, and also presumably by similar disturbances such as vehicle traffic, sufficient regeneration likely does not occur to replace trees. The areal extent of severely disturbed areas should be limited, and managers should seek to avoid further degradation of less damaged areas.     

Plants of Navajo National Monument

The floristic composition of Navajo National Monument is presented. The flora of the monument consists of 293 species of vascular plants, representing 177 genera and 66 families. The species are scattered throughout 12 plant communities found within the monument. The flora is dominated by forbs (60 percent), followed by shrubs (16 percent), grasses (12 percent) and trees (5 percent). Betatakin canyon exhibits the greatest floristic richness with 223 species being represented and 123 species found only in that area. This is due primarily to two factors: (1) the greater variety of habitats available in the area, and (2) the much longer time the area has been protected from grazing and other manmade disturbance.     

Some aspects of succession in the spruce-fir forest zone of northern Utah

A site in the Rocky Mountain subalpine forest zone with which a series of hypotheses concerning ecosystem succession was tested is characterized. Succession from herb-dominated meadows to climax forests of Engelmann spruce and subalpine fir can follow at least four identified pathways. After fire, spruce and fir may reinvade a site directly, follow invasion by aspen, or follow invasion by lodgepole pine, the pathway depending on a combination of physical and biotic factors. In other cases, succession begins with long-established meadows which do not owe their existence to fire. In this latter pathway, aspen invades meadows by suckering and changes the environment near the soil surface so as to facilitate establishment of the climax tree species. The biota and soils of four characteristic seral stages (meadow, aspen, fir, spruce-fir) in this latter pathway are described.     

Bayesian inference of ancient human demography from individual genome sequences

Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San population of southern Africa diverged from other human populations approximately 108-157 thousand years ago, that Eurasians diverged from an ancestral African population 38-64 thousand years ago, and that the effective population size of the ancestors of all modern humans was ～9,000.     

Length of western tent caterpillar egg masses and diameter of their associated stems

Stems bearing egg masses of the western tent caterpillar ( Malacosoma californicum ), collected in Arizona and northern New Mexico during 1977–1980, had mean diameters between 2.9 and 4 mm. Mean lengths of the egg masses were consistently between 11 and 14 mm.     

Genome-wide association study of leaf architecture in the maize nested association mapping population

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.     

Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis

Thoracic aortic aneurysms and dissections are a main feature of connective tissue disorders, such as Marfan syndrome and Loeys-Dietz syndrome. We delineated a new syndrome presenting with aneurysms, dissections and tortuosity throughout the arterial tree in association with mild craniofacial features and skeletal and cutaneous anomalies. In contrast with other aneurysm syndromes, most of these affected individuals presented with early-onset osteoarthritis. We mapped the genetic locus to chromosome 15q22.2-24.2 and show that the disease is caused by mutations in SMAD3. This gene encodes a member of the TGF-β pathway that is essential for TGF-β signal transmission. SMAD3 mutations lead to increased aortic expression of several key players in the TGF-β pathway, including SMAD3. Molecular diagnosis will allow early and reliable identification of cases and relatives at risk for major cardiovascular complications. Our findings endorse the TGF-β pathway as the primary pharmacological target for the development of new treatments for aortic aneurysms and osteoarthritis.     

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.