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.     

Plant adaptation in the Great Basin and Colorado Plateau

Adaptive features of plants of the Great Basin are reviewed. The combination of cold winters and an arid to semiarid precipitation regime results in the distinguishing features of the vegetation in the Great Basin and Colorado Plateau. The primary effects of these climatic features arise from how they structure the hydrologic regime. Water is the most limiting factor to plant growth, and water is most reliably available in the early spring after winter recharge of soil moisture. This factor determines many characteristics of root morphology, growth phenology of roots and shoots, and photosynthetic physiology. Since winters are typically cold enough to suppress growth, and drought limits growth during the summer, the cool temperatures characteristic of the peak growing season are the second most important climatic factor influencing plant habit and performance. The combination of several distinct stress periods, including low-temperature stress in winter and spring and high-temperature stress combined with drought in summer, appears to have limited plant habit to a greater degree than found in the warm deserts to the south. Nonetheless, cool growing conditions and a more reliable spring growing season result in higher water-use efficiency and productivity in the vegetation of the cold desert than in warm deserts with equivalent total rainfall amounts. Edaphic factors are also important in structuring communities in these regions, and halophytic communities dominate many landscapes. These halophytic communities of the cold desert share more species in common with warm deserts than do the nonsaline communities. The Colorado Plateau differs from the Great Basin in having greater amounts of summer rainfall, in some regions less predictable rainfall, sandier soils, and streams which drain into river systems rather than closed basins and salt playas. One result of these climatic and edaphic differences is a more important summer growing season on the Colorado Plateau and a somewhat greater diversification of plant habit, phenology, and physiology.     

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.     

Mutations in lectin complement pathway genes COLEC11 and MASP1 cause 3MC syndrome

3MC syndrome has been proposed as a unifying term encompassing the overlapping Carnevale, Mingarelli, Malpuech and Michels syndromes. These rare autosomal recessive disorders exhibit a spectrum of developmental features, including characteristic facial dysmorphism, cleft lip and/or palate, craniosynostosis, learning disability and genital, limb and vesicorenal anomalies. Here we studied 11 families with 3MC syndrome and identified two mutated genes, COLEC11 and MASP1, both of which encode proteins in the lectin complement pathway (collectin kidney 1 (CL-K1) and MASP-1 and MASP-3, respectively). CL-K1 is highly expressed in embryonic murine craniofacial cartilage, heart, bronchi, kidney and vertebral bodies. Zebrafish morphants for either gene develop pigmentary defects and severe craniofacial abnormalities. Finally, we show that CL-K1 serves as a guidance cue for neural crest cell migration. Together, these findings demonstrate a role for complement pathway factors in fundamental developmental processes and in the etiology of 3MC syndrome.