Earlham College

The Large sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) general survey is a spectroscopic survey that will eventually cover approximately half of the celestial sphere and collect 10 million spectra of stars, galaxies and QSOs. Objects in both the pilot survey and the first year regular survey are included in the LAMOST DR1. The pilot survey started in October 2011 and ended in June 2012, and the data have been released to the public as the LAMOST Pilot Data Release in August 2012. The regular survey started in September 2012, and completed its first year of operation in June 2013. The LAMOST DR1 includes a total of 1202 plates containing 2 955 336 spectra, of which 1 790 879 spectra have observed signal-to-noise ratio (SNR)>= 1 0. All data with SNR >= 2 are formally released as LAMOST DR1 under the LAMOST data policy. This data release contains a total of 2 204 696 spectra, of which 1 944 329 are stellar spectra, 12 082 are galaxy spectra and 5017 are quasars. The DR1 not only includes spectra, but also three stellar catalogs with measured parameters: late A, FGK-type stars with high quality spectra (1 061 918 entries), A-type stars (100 073 entries), and M-type stars (121 522 entries). This paper introduces the survey design, the observational and instrumental limitations, data reduction and analysis, and some caveats. A description of the FITS structure of spectral files and parameter catalogs is also provided.

Abstract The grand challenges of contemporary fundamental physics—dark matter, dark energy, vacuum energy, inflation and early universe cosmology, singularities and the hierarchy problem—all involve gravity as a key component. And of all gravitational phenomena, black holes stand out in their elegant simplicity, while harbouring some of the most remarkable predictions of General Relativity: event horizons, singularities and ergoregions. The hitherto invisible landscape of the gravitational Universe is being unveiled before our eyes: the historical direct detection of gravitational waves by the LIGO-Virgo collaboration marks the dawn of a new era of scientific exploration. Gravitational-wave astronomy will allow us to test models of black hole formation, growth and evolution, as well as models of gravitational-wave generation and propagation. It will provide evidence for event horizons and ergoregions, test the theory of General Relativity itself, and may reveal the existence of new fundamental fields. The synthesis of these results has the potential to radically reshape our understanding of the cosmos and of the laws of Nature. The purpose of this work is to present a concise, yet comprehensive overview of the state of the art in the relevant fields of research, summarize important open problems, and lay out a roadmap for future progress. This write-up is an initiative taken within the framework of the European Action on ‘Black holes, Gravitational waves and Fundamental Physics’.

Knowledge of atmospheric mercury speciation is critical to understanding its fate once released from point sources. The water-soluble compounds of Hg that exist in flue gases (termed reactive gaseous mercury, RGM) are subject to far greater local removal rates than is elemental Hg vapor, but few ambient air data exist. We developed a method using refluxing mist chambers to quantify the airborne concentrations of RGM in more than 250 ∼1-h samples under ambient conditions and summarize here the results of several RGM sampling campaigns in Tennessee and Indiana from 1992 to 1995. Measured levels of RGM were generally on the order of 50−200 pg/m3, representing about 3% of total gaseous mercury (TGM) and generally exceeding regional particulate Hg concentra tions. RGM exhibits significant correlations (p < 0.05) with temperature, solar radiation, O3, SO2, and TGM, suggesting seasonal trends similar to those of other regional air pollutants. The concentrations of RGM show reproducible diel trends, peaking during midday and decreasing sharply at night. A sharp spike in RGM was measured during a local plume impaction event in Tennessee. Concentration gradients over vegetation suggested a strong ground-level sink for RGM, and RGM concentrations decreased sharply during rain events, as expected for a water-soluble gas. The levels of RGM measured here support the hypothesis that Hg dry and wet deposition may be strongly influenced by the behavior of RGM and that elevated ecosystem exposure may be possible near major point sources of RGM compounds.

There are currently ca. 317 recognized species of turtles and tortoises in the world. Of those that have been assessed on the IUCN Red List, 63% are considered threatened, and 10% are critically endangered, with ca. 42% of all known turtle species threatened. Without directed strategic conservation planning, a significant portion of turtle diversity could be lost over the next century. Toward that conservation effort, we compiled museum and literature occurrence records for all of the world's tortoises and freshwater turtle species to determine their distributions and identify priority regions for conservation. We constructed projected range maps for each species by selecting geographic information system–defined hydrologic unit compartments (HUCs) with verified locality points, and then added HUCs that connected known point localities in the same watershed or physiographic region and that had similar habitats and elevations as the verified HUCs. We analyzed a total of 305 turtle species and assigned each to 1 of 7 geographic regions of the world. Patterns of global turtle species distributions were determined and regional areas of turtle species richness identified. In only 2 areas of the world did as many as 18 or 19 species occur together in individual HUCs. We then compared species distributions with existing global conservation strategies (GCSs) and established biodiversity priority areas. Presence of a species in a GCS was defined as ≥ 5% its range. Of the 34 biodiversity hotspots, 28 collectively contain the projected ranges of 192 turtle species, with 74 endemic; the 5 high-biodiversity wilderness areas contain 72 species, with 17 endemic; and 16 other wilderness areas contain 52 species, with 1 endemic. However, 116 turtle species have either < 50% of their ranges in existing GCSs (57 species) or do not occur in them at all (59 species, 19.3%), thus potentially leaving many tortoises and freshwater turtles without any regional GCS. For each of these 116 species we identify a priority Ecoregion for further conservation consideration, and we identify 3 new global Turtle Priority Areas for conservation based on aggregated Ecoregions. These are the Southeastern United States, Lower Gangetic Plain, and Coastal Australia Turtle Priority Areas.

Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant (Linepithema humile), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis. Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium, which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

We present a review and analysis of the conservation status and International Union for Conservation of Nature (IUCN) threat categories of all 360 currently recognized species of extant and recently extinct turtles and tortoises (Order Testudines). Our analysis is based on the 2018 IUCN Red List status of 251 listed species, augmented by provisional Red List assessments by the IUCN Tortoise and Freshwater Turtle Specialist Group (TFTSG) of 109 currently unlisted species of tortoises and freshwater turtles, as well as re-assessments of several outdated IUCN Red List assessments. Of all recognized species of turtles and tortoises, this combined analysis indicates that 20.0% are Critically Endangered (CR), 35.3% are Critically Endangered or Endangered (CR+EN), and 51.9% are Threatened (CR+EN+Vulnerable). Adjusting for the potential threat levels of Data Deficient (DD) species indicates that 56.3% of all data-sufficient species are Threatened. We calculated percentages of imperiled species and modified Average Threat Levels (ATL; ranging from Least Concern = 1 to Extinct = 8) for various taxonomic and geographic groupings. Proportionally more species in the subfamily Geoemydinae (Asian members of the family Geoemydidae) are imperiled (74.2% CR+EN, 79.0% Threatened, 3.89 ATL) compared to other taxonomic groupings, but the families Podocnemididae, Testudinidae, and Trionychidae and the superfamily Chelonioidea (marine turtles of the families Cheloniidae and Dermochelyidae) also have high percentages of imperiled species and ATLs (42.9-50.0% CR+EN, 73.8-100.0% Threatened, 3.44-4.06 ATL). The subfamily Rhinoclemmydinae (Neotropical turtles of the family Geoemydidae) and the families Kinosternidae and Pelomedusidae have the lowest percentages of imperiled species and ATLs (0%-7.4% CR+EN, 7.4%-13.3% Threatened, 1.65-1.87 ATL). Turtles from Asia have the highest percentages of imperiled species (75.0% CR+EN, 83.0% Threatened, 3.98 ATL), significantly higher than predicted based on the regional species richness, due to much higher levels of exploitation in that geographic region. The family Testudinidae has the highest ATL (4.06) of all Testudines due to the extinction of several species of giant tortoises from Indian and Pacific Ocean islands since 1500 CE. The family Testudinidae also has an ATL higher than all other larger polytypic families (≥ 5 species) of Reptilia or Amphibia. The order Testudines is, on average, more imperiled than all other larger orders (≥ 20 species) of Reptilia, Amphibia, Mammalia, or Aves, but has percentages of CR+EN and Threatened species and an ATL (2.96) similar to those of Primates and Caudata (salamanders).

A complete description of the serological response following exposure of humans to complex pathogens is lacking and approaches suitable for accomplishing this are limited. Here we report, using malaria as a model, a method which elucidates the profile of antibodies that develop after natural or experimental infection or after vaccination with attenuated organisms, and which identifies immunoreactive antigens of interest for vaccine development or other applications. Expression vectors encoding 250 Plasmodium falciparum (Pf) proteins were generated by PCR/recombination cloning; the proteins were individually expressed with >90% efficiency in Escherichia coli cell-free in vitro transcription and translation reactions, and printed directly without purification onto microarray slides. The protein microarrays were probed with human sera from one of four groups which differed in immune status: sterile immunity or no immunity against experimental challenge following vaccination with radiation-attenuated Pf sporozoites, partial immunity acquired by natural exposure, and no previous exposure to Pf. Overall, 72 highly reactive Pf antigens were identified. Proteomic features associated with immunoreactivity were identified. Importantly, antibody profiles were distinct for each donor group. Information obtained from such analyses will facilitate identifying antigens for vaccine development, dissecting the molecular basis of immunity, monitoring the outcome of whole-organism vaccine trials, and identifying immune correlates of protection.

We present an extensive study of a novel class of de novo designed tetrahedral M(4)L(6) (M = Ni, Zn) cage receptors, wherein internal decoration of the cage cavities with urea anion-binding groups, via functionalization of the organic components L, led to selective encapsulation of tetrahedral oxoanions EO(4)(n-) (E = S, Se, Cr, Mo, W, n = 2; E = P, n = 3) from aqueous solutions, based on shape, size, and charge recognition. External functionalization with tBu groups led to enhanced solubility of the cages in aqueous methanol solutions, thereby allowing for their thorough characterization by multinuclear ((1)H, (13)C, (77)Se) and diffusion NMR spectroscopies. Additional experimental characterization by electrospray ionization mass spectrometry, UV-vis spectroscopy, and single-crystal X-ray diffraction, as well as theoretical calculations, led to a detailed understanding of the cage structures, self-assembly, and anion encapsulation. We found that the cage self-assembly is templated by EO(4)(n-) oxoanions (n ≥ 2), and upon removal of the templating anion the tetrahedral M(4)L(6) cages rearrange into different coordination assemblies. The exchange selectivity among EO(4)(n-) oxoanions has been investigated with (77)Se NMR spectroscopy using (77)SeO(4)(2-) as an anionic probe, which found the following selectivity trend: PO(4)(3-) ≫ CrO(4)(2-) > SO(4)(2-) > SeO(4)(2-) > MoO(4)(2-) > WO(4)(2-). In addition to the complementarity and flexibility of the cage receptor, a combination of factors have been found to contribute to the observed anion selectivity, including the anions' charge, size, hydration, basicity, and hydrogen-bond acceptor abilities.

This study identifies how the amidoximate anion, AO, interacts with the uranyl cation, UO(2)(2+). Density functional theory calculations have been used to evaluate possible binding motifs in a series of [UO(2)(AO)(x)(OH(2))(y)](2-x) (x = 1-3) complexes. These motifs include monodentate binding to either the oxygen or the nitrogen atom of the oxime group, bidentate chelation involving the oxime oxygen atom and the amide nitrogen atom, and η(2) binding with the N-O bond. The theoretical results establish the η(2) motif to be the most stable form. This prediction is confirmed by single-crystal X-ray diffraction of UO(2)(2+) complexes with acetamidoxime and benzamidoxime anions.

The first part of this article gives a brief overview of the four levels of the Chomsky hierarchy, with a special emphasis on context-free and regular languages. It then recapitulates the arguments why neither regular nor context-free grammar is sufficiently expressive to capture all phenomena in the natural language syntax. In the second part, two refinements of the Chomsky hierarchy are reviewed, which are both relevant to the extant research in cognitive science: the mildly context-sensitive languages (which are located between context-free and context-sensitive languages), and the sub-regular hierarchy (which distinguishes several levels of complexity within the class of regular languages).

Biological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plant Ambrosia artemisiifolia. We explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for nonadaptive population differentiation using 11 598 single nucleotide polymorphisms. We revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines. Our data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.

Abstract Evidence that global warming has altered the phenology of the biosphere, possibly contributing to increased plant production in the northern hemisphere, has come from a diversity of observations at scales ranging from the view of the back yard to satellite images of the earth. These observations, coupled with an understanding of the effects of temperature on plant phenology, suggest that future changes in the atmosphere and climate could alter plant phenology with unknown or unpredictable consequences. We assessed the effects of simulated climatic warming and atmospheric CO 2 enrichment on the spring and autumn phenology of maple trees ( Acer rubrum and A. saccharum ) growing for four years in open‐top field chambers. CO 2 enrichment (+300 ppm) had no consistent effects on the timing of budbreak and leaf unfolding in the spring or leaf abscission in the autumn. Warming (+4°C) usually had predictable effects: in two of the three years of assessment, budbreak occurred earlier in warm chambers than in ambient temperature chambers, and leaf abscission always occurred later. The lengthening of the growing season could contribute to increased productivity, although effects of temperature on other physiological processes can concurrently have negative effects on productivity. In 1995, budbreak was unexpectedly delayed in the warmer chambers, apparently the result of advanced budbreak leading to injury from a late‐spring frost. Likewise, there was increased risk associated with longer leaf retention in the autumn: in 1994, leaves in the warm chambers were killed by freezing temperatures before they had senesced. These observations support the premise that global warming could increase the length of the growing season. Phenological responses should, therefore, be part of any assessment of the possible consequences of global change, but our results also suggest that those responses may not always have positive effects on production.

Abstract Behavioral field studies were conducted to determine if bumble bees ( Bombus terrestris L.) can use pollen odor to assess pollen availability in flowers of Rosa rugosa (Rosaceae), a nectarless species with a distinctive pollen odor. Pollen volatiles were added singly and in mixtures to newly opened flowers from which anthers were removed and were offered to free‐flying bumble bees in an array that included intact flowers as controls. The addition of 2‐tridecanone and geranyl acetate reduced landing responses, but the addition of tetradecyl acetate and especially eugenol significantly increased landing frequency as well as the display of vibratile pollen‐collecting behavior, suggesting that they are key chemicals in a bee’s assessment of pollen availability in individual flowers. Bee responses to flowers in which androecia were exchanged between first‐day flowers (with pollen reward) and second‐day flowers (without pollen reward) provide evidence that bee discrimination between flowers is based mainly on stimuli from the anthers. Overall, the findings show that bumble bees foraging on R. rugosa use primarily pollen odor in concert with visual stimuli from the androecium and secondarily petals odors and colors in selecting rewarding flowers. Controlled pollination and bagging studies indicate that R. rugosa requires cross‐pollination by insects, pointing to the selective advantage that pollen odor provides by increases plant fitness through the enhanced foraging efficiency of bumble bee pollinators.

A nursery population of M. sodalis was discovered in Indiana and studied for 2 years. The nursery roost was located under the loose bark of a dead tree. Sometimes the bats temporarily moved to bark crevices of a living shagbark hickory tree. Weather strongly affected roost microclimate. The nursery tree was unshaded and received maximal solar warmth during clear, mild or hot weather, whereas temperature at the shaded alternate tree was more stable during spring and autumn cold. The nursery population consisted of adult females and young, and few males were netted in local foraging areas. Each female bore a single young and these incurred eight percent mortality between birth and weaning. Social behaviors included “checking,” mothers carrying young to an apparently warmer portion of the roost tree, and apparent mother-young foraging flights as the young became volant. Unusually cool weather in summer 1974 slowed the growth of young; this delayed recruitment of flying young more than 2 weeks and the completion of migration by 3 weeks. The delay exposed some bats to freezing weather at the nursery and may have affected mortality, autumn mating, or fat storage for winter. No problems were evident during the favorable summer of 1975. Foraging habitat included the foliage of riparian and floodplain trees, and the 50 bats used a 0.82 kilometer (km) linear strip of creek. Similar habitat was used by two other populations in Ohio. Before young were volant, adults fed only about riparian trees; when young began to fly, feeding extended to solitary trees and forest edge on the floodplain. This reduced foraging density from 17 to 11 bats per hectare (ha). Suitable foraging habitat occurs over much of the eastern United States, and use of local trees for nurseries makes a large summer distribution possible. Humans also value floodplain habitat, and a land use conflict exists between the two species.

The bilayer bending modulus (Kc) is one of the most important physical constants characterizing lipid membranes, but precisely measuring it is a challenge, both experimentally and computationally. Experimental measurements on chemically identical bilayers often differ depending upon the techniques employed, and robust simulation results have previously been limited to coarse-grained models (at varying levels of resolution). This Communication demonstrates the extraction of Kc from fully atomistic molecular dynamics simulations for three different single-component lipid bilayers (DPPC, DOPC, and DOPE). The results agree quantitatively with experiments that measure thermal shape fluctuations in giant unilamellar vesicles. Lipid tilt, twist, and compression moduli are also reported.

The painted turtle, Chrysemys picta, is currently recognized as a continentally distributed polytypic species, ranging across North America from southern Canada to extreme northern Mexico. We analyzed variation in the rapidly evolving mitochondrial control region (CR) in 241 turtles from 117 localities across this range to examine whether the painted turtle represents a continentally distributed species based on molecular analysis. We found strong support for the novel hypothesis that C. p. dorsalis is the sister group to all remaining Chrysemys, with the remaining Chrysemys falling into a single, extremely wide-ranging and genetically undifferentiated species. Given our goal of an evolutionarily accurate taxonomy, we propose that two evolutionary lineages be recognized as species within Chrysemys: C. dorsalis (Agassiz 1857) in the southern Mississippi drainage region, and C. picta (Schneider 1783) from the rest of the range of the genus. Neither molecular nor recent morphological analyses argue for the hybrid origin of C. p. marginata as previously proposed. Within C. picta, we find evidence of at least two independent range expansions into previously glaciated regions of North America, one into New England and the other into the upper Midwest. We further find evidence of a massive extinction/recolonization event across the Great Plains/Rocky Mountain region encompassing over half the continental United States. The timing and extent of this colonization is consistent with a recently proposed regional aridification as the Laurentide ice sheets receded approximately 14,000 years ago, and we tentatively propose this paleoclimatological event as a major factor shaping genetic variation in Chrysemys.