Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RADtag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.. . .researchers using standard lines of zebrafish that have long been maintained in laboratories are often plagued by severe sex ratio distortions. . .. C. Lawrence, J. P. Ebersole, and R. V. Kesseli (2008) C ONSIDERING the fundamental importance of sex for species propagation, it is surprising that primary sexdetermining mechanisms are not strongly conserved among animal taxa (Bull 1983;Charlesworth 1996;Ming et al. 2011;Bachtrog et al. 2014). Closely related species or even populations of the same species can have different sexdetermining mechanisms (Takehana et al. 2007;Ross et al. 2009;Kobayashi et al. 2013;Heule et al. 2014;Larney et al. 2014). Zebrafish (Danio rerio) is a popular model for studies of vertebrate development, behavior, physiology, evolution, disease, and human health (Mills et al. 2007;Seth et al. 2013;Braasch et al. 2014;Ota and Kawahara 2014;Wilkinson et al. 2014), but researchers struggle with highly variable and distorted sex ratios, and investigations into the genetic nature of zebrafish sex determination are conflicting. To help understand these issues, we conducted a population genomic study of sex determination in multiple zebrafish strains. Zebrafish exhibit...

Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio), neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate), the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA) wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag) markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome.

Caenorhabditis elegans is an androdioecious nematode with both hermaphrodites and males. Although males can potentially play an important role in avoiding inbreeding and facilitating adaptation, their existence is evolutionarily problematic because they do not directly generate offspring in the way that hermaphrodites do. This review explores how genetic, population genomic, and experimental evolution approaches are being used to address the role of males and outcrossing within C. elegans. Although theory suggests that inbreeding depression and male mating ability should be the primary determinants of male frequency, this has yet to be convincingly confirmed experimentally. Genomic analysis of natural populations finds that outcrossing occurs at low, but not negligible levels, and that observed patterns of linkage disequilibrium consistent with strong selfing may instead be generated by natural selection against outcrossed progeny. Recent experimental evolution studies suggest that males can be maintained at fairly high levels if populations are initiated with sufficient genetic variation and/or subjected to strong natural selection via a change in the environment. For example, as reported here, populations adapting to novel laboratory rearing and temperature regimes maintain males at frequencies from 5% to 40%. Laboratory and field results still await full reconciliation, which may be facilitated by identifying the loci underlying among-strain differences in mating system dynamics.

Ecologists are searching for models, frameworks, and principles that provide a bridge between theory and the practice of restoration. Successional management has been proposed as a useful model for managing and restoring invasive-plant-dominated rangeland because it provides a framework in which ecological processes can be manipulated by managers to achieve a desired plant community. Successional management identifies three general causes of succession (site availability [disturbance], species availability [colonization], and species performance) and suggests that managers address the ecological process influencing each general cause in a coordinated fashion to direct plant community dynamics. We tested successional management using various techniques to restore invasive-weed-dominated rangeland. Our hypothesis was that successively modifying the factors influencing the causes of succession in an integrated fashion would favor the establishment and abundance of native grasses over singularly applied treatments. Thus, we anticipated that the majority of responses to multiple treatments would be explained by higher order interactions, especially in the final year of the study (2004). To test this hypothesis, we used a model system within a Festuca campestris/Pseudoroegneria spicata habitat among pothole wetlands dominated by Centaurea maculosa and Potentilla recta, two invasive species. We used three herbicide treatments (none, 2,4-D, and picloram) to influence species performance; two seeding methods (imprinting, i.e., creating a small depression and broadcasting, and no-till drilling) to influence disturbance; three seeding rates (977, 1322, and 1557 seeds/m 2 ) to influence colonization; and two cover crop treatments (with and without Triticum aestivum) to influence soil N and favor native grasses. Treatments were factorially arranged and replicated four times in a randomized complete block design in 2001 and sampled in 2002 and 2004. As predicted, plant response to treatments was dominated by two-and three-way interactions in 2004. The highest seeding rate (colonization) combined with no-till drilling (disturbance) produced the highest native grass density in 2002. These effects persisted into 2004 for P. spicata, but not for F. campestris or F. idahoensis. Combining picloram with no-till drill seeding also produced a high density of P. spicata. Drill seeding at 977 seeds/m 2 favored F. idahoensis density, while no-till drilling at 1322 seeds/m 2 favored its biomass in 2004. F. idahoensis established well after drill seeding with a cover crop and applying 2,4-D. Herbicides reduced native forb density and/or biomass, with early season forbs being more sensitive to picloram and summer forbs being more sensitive to 2,4-D. Herbicides increased exotic grasses' density and biomass but had no effect on native grasses. In most cases, integrating treatments that addressed multiple causes of succession favored a desired plant community. Thus, we accomplished our goal of using successional management to direct plant commu...

Sexual reproduction shuffles genetic variation, potentially enhancing the evolutionary response to environmental change. Many asexual organisms utilize facultative sexual reproduction as a means to escape the trap of low genetic diversity under stress. Self-fertilizing organisms are subject to similar genetic limitations: the consistent loss of genetic diversity within lineages restricts the production of variation through recombination. Selfing organisms may therefore benefit from a similar shift in mating strategy during periods of stress. We determined the effects of environmental stress via starvation and exposure to the stress-resistant dauer stage on mating system dynamics of Caenorhabditis elegans, which reproduces predominantly through self-fertilization but is capable of outcrossing in the presence of males. Starvation elevated male frequencies in a strain-specific manner through differential male survival during dauer exposure and increased outcrossing rates after dauer exposure. In the most responsive strain, the mating system changed from predominantly selfing to almost exclusively outcrossing. Like facultative sex in asexual organisms, facultative outcrossing in C. elegans may periodically facilitate adaptation under stress. Such a shift in reproductive strategy should have a major impact on evolutionary change within these populations and may be a previously unrecognized feature of other highly selfing organisms.

[1] Three-dimensional particle image velocimetry (3D PIV) applied to impact cratering experiments allows the direct measurement of ejecta particle positions and velocities within the ejecta curtain as the crater grows. Laboratory experiments were performed at the NASA Ames Vertical Gun Range with impact velocities near 1 km/s (6.35-mm diameter aluminum spheres) into a medium-grained (0.5 mm) particulate sand target in a vacuum at 90°and 30°from the horizontal. This study examines the first 50% of crater growth, during which the crater has grown to one half its final radius. From the 3D PIV data, the ballistic trajectories of the ejecta particles are extrapolated back to the target surface to determine ejection velocities, angles, and positions. For vertical impacts these ejection parameters remain constant in all directions (azimuths) around the crater center. The 30°impacts exhibit asymmetries with respect to azimuth that persist well into the excavation-stage flow. These asymmetries indicate that a single stationary point source is not adequate to describe the subsurface flow field during an oblique impact. INDEX TERMS:5420 Planetology: Solid Surface Planets: Impact phenomena (includes cratering); 5494 Planetology: Solid Surface Planets: Instruments and techniques; KEYWORDS: Oblique impacts, ejecta flow, particle image velocimetry, Ames Vertical Gun Range, experimental impacts Citation: Anderson, J. L. B., P. H. Schultz, and J. T. Heineck, Asymmetry of ejecta flow during oblique impacts using threedimensional particle image velocimetry,

Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.