Human-specific loss of regulatory DNA and the evolution of human-specific traits

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.     

Evaluating the geographic distribution of plants in Utah from the Atlas of Vascular Plants of Utah

Locations of 73,219 vascular plant vouchers representing 2438 species were digitized from the Atlas of the Vascular Plants of Utah (Albee et al. 1988). Source maps consist of 1:6,000,000-scale shaded relief maps of Utah with points representing collection locations by species. Location points, representing 1 or more specimens, were transposed onto these maps from the approximately 400,000 herbarium records of 3 major universities and federal land management agencies. These source maps were digitized into an ARC/Info TM database in order to reproduce the atlas in digital form. Analysis of all locations revealed a mapping bias of the original authors to avoid placing sample locations on county boundaries and over major river corridors. A comparison between ecoregions and elevation showed that the Colorado Plateau and Wasatch/Uinta Mountains have the highest species diversity, and that areas of low elevation (1000-2000 m) have the highest number of unique species in the state. Further, species richness is related to elevation and to ecoregion boundaries.     

Osteology and myology of the head and neck regions of Callisaurus, Cophosaurus, Holbrookia, and Uma (Reptilia: Iguanidae)

A detailed study of the anterior osteology and myology of Callisaurus, Cophosaurus, Holbrookia, and Uma reveals the phylogenetic relationships among the sand lizards. An SPSS discriminant analysis of osteological characters combined with myological characters indicates that Callisaurus is most primitive, Cophosaurus and Holbrookia are most closely related, and Uma is the most distinct of the sand lizard genera. Because of close relationships between Cophosaurus and Holbrookia, it is postulated that earlessness evolved once, and Cophosaurus is returned to synonymy under Holbrookia.     

Redescription of the Tyee Sucker, Catostomus tsiltcoosensis (Catostomidae)

We resurrect Catostomus tsiltcoosensis, the Tyee sucker of Oregon coastal rivers, from the synonymy of Catostomus macrocheilus and compare it with its congeners. Catostomus tsiltcoosensis is superficially similar to disjunctly distributed Catostomus occidentalis of the Sacramento drainage and Catostomus ardens of the Upper Snake River and Bonneville Basin. However, the gill raker structure, wide frontoparietal fontanelle, location of the ninth cranial foramen, scale radii patterns, and cytochrome b sequences clearly align C. tsiltcoosensis with C. macrocheilus rather than C. occidentalis. Differences in counts of infraorbital pores and dorsal fin rays, in body depth proportions, and in cytochrome b sequences distinguish C. tsiltcoosensis and C. macrocheilus. Within C. tsiltcoosensis, specimens from each of the 4 main drainages (north to south—Siuslaw, Umpqua, Coos, and Coquille) were reciprocally monophyletic based on cytochrome b data but showed no differences in the morphological features examined. Both C. tsiltcoosensis and another Oregon coastal taxon Catostomus rimiculus were paraphyletic based on cytochrome b. Although such discordant mitochondria results can be due to introgression, incomplete lineage sorting, and paralogy, other evidence suggests that introgression and lateral transfer of mitochondria explains the cytochrome b pattern in C. rimiculus. We speculate that lateral transfer might also be responsible for the pattern in C. tsiltcoosensis, except that the Coquille River population appears not to have been included in recent transfers.     

Transiting circumbinary planets Kepler-34 b and Kepler-35 b

Most Sun-like stars in the Galaxy reside in gravitationally bound pairs of stars (binaries). Although long anticipated, the existence of a 'circumbinary planet' orbiting such a pair of normal stars was not definitively established until the discovery of the planet transiting (that is, passing in front of) Kepler-16. Questions remained, however, about the prevalence of circumbinary planets and their range of orbital and physical properties. Here we report two additional transiting circumbinary planets: Kepler-34 (AB)b and Kepler-35 (AB)b, referred to here as Kepler-34 b and Kepler-35 b, respectively. Each is a low-density gas-giant planet on an orbit closely aligned with that of its parent stars. Kepler-34 b orbits two Sun-like stars every 289?days, whereas Kepler-35 b orbits a pair of smaller stars (89% and 81% of the Sun's mass) every 131?days. The planets experience large multi-periodic variations in incident stellar radiation arising from the orbital motion of the stars. The observed rate of circumbinary planets in our sample implies that more than ～1% of close binary stars have giant planets in nearly coplanar orbits, yielding a Galactic population of at least several million.     

Doubling of marine dinitrogen-fixation rates based on direct measurements

Biological dinitrogen fixation provides the largest input of nitrogen to the oceans, therefore exerting important control on the ocean's nitrogen inventory and primary productivity. Nitrogen-isotope data from ocean sediments suggest that the marine-nitrogen inventory has been balanced for the past 3,000?years (ref. 4). Producing a balanced marine-nitrogen budget based on direct measurements has proved difficult, however, with nitrogen loss exceeding the gain from dinitrogen fixation by approximately 200?Tg?N?yr?1 (refs 5, 6). Here we present data from the Atlantic Ocean and show that the most widely used method of measuring oceanic N2-fixation rates underestimates the contribution of N2-fixing microorganisms (diazotrophs) relative to a newly developed method. Using molecular techniques to quantify the abundance of specific clades of diazotrophs in parallel with rates of 15N2 incorporation into particulate organic matter, we suggest that the difference between N2-fixation rates measured with the established method and those measured with the new method can be related to the composition of the diazotrophic community. Our data show that in areas dominated by Trichodesmium, the established method underestimates N2-fixation rates by an average of 62%. We also find that the newly developed method yields N2-fixation rates more than six times higher than those from the established method when unicellular, symbiotic cyanobacteria and γ-proteobacteria dominate the diazotrophic community. On the basis of average areal rates measured over the Atlantic Ocean, we calculated basin-wide N2-fixation rates of 14?±?1?Tg?N?yr?1 and 24?±1?Tg?N?yr?1 for the established and new methods, respectively. If our findings can be extrapolated to other ocean basins, this suggests that the global marine N2-fixation rate derived from direct measurements may increase from 103?±?8?Tg?N?yr?1 to 177?±?8?Tg?N?yr?1, and that the contribution of N2 fixers other than Trichodesmium is much more significant than was previously thought.     

Antibiotics in early life alter the murine colonic microbiome and adiposity

Antibiotics administered in low doses have been widely used as growth promoters in the agricultural industry since the 1950s, yet the mechanisms for this effect are unclear. Because antimicrobial agents of different classes and varying activity are effective across several vertebrate species, we proposed that such subtherapeutic administration alters the population structure of the gut microbiome as well as its metabolic capabilities. We generated a model of adiposity by giving subtherapeutic antibiotic therapy to young mice and evaluated changes in the composition and capabilities of the gut microbiome. Administration of subtherapeutic antibiotic therapy increased adiposity in young mice and increased hormone levels related to metabolism. We observed substantial taxonomic changes in the microbiome, changes in copies of key genes involved in the metabolism of carbohydrates to short-chain fatty acids, increases in colonic short-chain fatty acid levels, and alterations in the regulation of hepatic metabolism of lipids and cholesterol. In this model, we demonstrate the alteration of early-life murine metabolic homeostasis through antibiotic manipulation.