Evaluating the ability of microsatellite DNA markers and otolith microchemistry to distinguish spatially separated populations and identify recruitment sites of common carp (Cyprinus carpio) in interconnected lake systems of the North American Midwest

University of Minnesota M.S. thesis. October 2017. Major: Conservation Biology. Advisor: Peter Sorensen. 1 computer file (PDF); v, 211 pages.The common carp (Cyprinus carpio) is an invasive fish whose populations have grown to ecologically damaging levels in the North American Midwest and many areas throughout the world. Recent research has shown that abundance of this species in areas of the North American Midwest is driven by its propensity to use shallow basins as productive nursery habitats. The ability of managers to discriminate which shallow basins are producing carp across a large sub-watershed of interconnected lakes has the potential to increase the efficacy of management practices which are aimed at the disruption of successful recruitment (i.e. surviving to join adult population). This study assessed whether carp nurseries could be distinguished based on differences in 12 microsatellite DNA markers in carp across the twin cities metropolitan area (n=1023) and the concentrations of 11 trace elements measured in carp otoliths collected in the Six-Mile Creek sub-watershed, Minnesota, USA (n=157). I found that genetic assessment could separate carp populations at a regional scale, but not between individual putative nurseries. Microchemical otolith analysis revealed that it is feasible to classify carp to their capture locations, discriminate between nursery and non-nursery habitat types, and distinguish juvenile carp from individual nursery sites. Elemental signatures of otoliths were obtained from laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Ratios of aluminum (Al), barium (Ba), copper (Cu), iron (Fe), potassium (K), lithium (Li), magnesium (Mg), sodium (Na), phosphorus (P), and strontium (Sr) to calcium (Ca) in otolith edges differed significantly among carp from all eight capture sites in a 70 km2 watershed. Ratios of Ba, Fe, Li, manganese (Mn), and P to Ca differed significantly among juvenile carp from three nursery basins. Ratios of Al, Ba, Cu, Fe, Li, K, Na, P, and Sr to Ca were significantly different between nursery and non-nursery habitat types. Quadratic discriminant analysis (QDA) could accurately classify otoliths to collection site (total accuracy 54%). QDA had increased accuracy when restricted to juvenile carp (76%) and classifying carp to nursery and non-nursery habitat types (87%) in contrast to individual sites. Further evaluation of differences between elemental signatures of the core and edge region (i.e. recent and natal signatures) and water samples from multiple years suggests that elemental parameters in otoliths and water are changing across time preventing identification of past recruitment sources. Identification of past natal origins of carp in these systems using otolith microchemistry will require obtaining continuous signatures across larger spatial and temporal scales

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Analysis of potential systematics

We analyze the density field of galaxies observed by the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS) included in the SDSS Data Release Nine (DR9). DR9 includes spectroscopic redshifts for over 400,000 galaxies spread over a footprint of 3,275 deg^2. We identify, characterize, and mitigate the impact of sources of systematic uncertainty on large-scale clustering measurements, both for angular moments of the redshift-space correlation function and the spherically averaged power spectrum, P(k), in order to ensure that robust cosmological constraints will be obtained from these data. A correlation between the projected density of stars and the higher redshift (0.43 < z < 0.7) galaxy sample (the `CMASS' sample) due to imaging systematics imparts a systematic error that is larger than the statistical error of the clustering measurements at scales s > 120h^-1Mpc or k < 0.01hMpc^-1. We find that these errors can be ameliorated by weighting galaxies based on their surface brightness and the local stellar density. We use mock galaxy catalogs that simulate the CMASS selection function to determine that randomly selecting galaxy redshifts in order to simulate the radial selection function of a random sample imparts the least systematic error on correlation function measurements and that this systematic error is negligible for the spherically averaged correlation function. The methods we recommend for the calculation of clustering measurements using the CMASS sample are adopted in companion papers that locate the position of the baryon acoustic oscillation feature (Anderson et al. 2012), constrain cosmological models using the full shape of the correlation function (Sanchez et al. 2012), and measure the rate of structure growth (Reid et al. 2012). (abridged)Comment: Matches version accepted by MNRAS. Clarifications and references have been added. See companion papers that share the "The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey:" titl

Methods for Rapidly Processing Angular Masks of Next-Generation Galaxy Surveys

As galaxy surveys become larger and more complex, keeping track of the completeness, magnitude limit, and other survey parameters as a function of direction on the sky becomes an increasingly challenging computational task. For example, typical angular masks of the Sloan Digital Sky Survey contain about N=300,000 distinct spherical polygons. Managing masks with such large numbers of polygons becomes intractably slow, particularly for tasks that run in time O(N^2) with a naive algorithm, such as finding which polygons overlap each other. Here we present a "divide-and-conquer" solution to this challenge: we first split the angular mask into predefined regions called "pixels," such that each polygon is in only one pixel, and then perform further computations, such as checking for overlap, on the polygons within each pixel separately. This reduces O(N^2) tasks to O(N), and also reduces the important task of determining in which polygon(s) a point on the sky lies from O(N) to O(1), resulting in significant computational speedup. Additionally, we present a method to efficiently convert any angular mask to and from the popular HEALPix format. This method can be generically applied to convert to and from any desired spherical pixelization. We have implemented these techniques in a new version of the mangle software package, which is freely available at http://space.mit.edu/home/tegmark/mangle/, along with complete documentation and example applications. These new methods should prove quite useful to the astronomical community, and since mangle is a generic tool for managing angular masks on a sphere, it has the potential to benefit terrestrial mapmaking applications as well.Comment: New version 2.1 of the mangle software now available at http://space.mit.edu/home/tegmark/mangle/ - includes galaxy survey masks and galaxy lists for the latest SDSS data release and the 2dFGRS final data release as well as extensive documentation and examples. 14 pages, 9 figures, matches version accepted by MNRA

Neutrino masses from clustering of red and blue galaxies: a test of astrophysical uncertainties

Combining measurements of the galaxy power spectrum and the cosmic microwave background (CMB) is a powerful means of constraining the summed mass of neutrino species sum(m_nu), but is subject to systematic uncertainties due to non-linear structure formation, redshift-space distortions and galaxy bias. We empirically test the robustness of neutrino mass results to these effects by separately analyzing power spectra of red and blue galaxies from the Sloan Digital Sky Survey (SDSS-II) Data Release 7 (DR7), combined with the CMB five-year Wilkinson Microwave Anisotropy Probe (WMAP5) data. We consider fitting for a range of maximum wavenumber k using twelve different galaxy bias models. For example, using a new model based on perturbation theory and including redshift space distortions (Saito et al. 2009), the all-galaxy power spectrum combined with WMAP5 for a wavenumber range of k<0.2 Mpc/h yields 95% CL sum(m_nu)<0.46 eV. The red and blue galaxy power spectra give 0.41 and 0.63 eV respectively for this model. Using mock catalogues, we find the expected difference in these limits assuming a true neutrino mass of zero is 0.10 + or - 0.14 eV. Thus the difference of 0.22 eV between upper limits on neutrino mass for red and blue galaxies is approximately 1 sigma from the expected value. We find similar results for the other models and k ranges tested. This indicates good agreement for current data but hints at possible issues for next-generation surveys. Being able to perform such systematic tests is advantageous, and future surveys would benefit by including broad galaxy populations and luminosities that enable such a decomposition.Comment: 15 pages, 6 figures, matches version published in MNRA

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measuring structure growth using passive galaxies

We explore the benefits of using a passively evolving population of galaxies to measure the evolution of the rate of structure growth between z=0.25 and z=0.65 by combining data from the SDSS-I/II and SDSS-III surveys. The large-scale linear bias of a population of dynamically passive galaxies, which we select from both surveys, is easily modeled. Knowing the bias evolution breaks degeneracies inherent to other methodologies, and decreases the uncertainty in measurements of the rate of structure growth and the normalization of the galaxy power-spectrum by up to a factor of two. If we translate our measurements into a constraint on sigma_8(z=0) assuming a concordance cosmological model and General Relativity (GR), we find that using a bias model improves our uncertainty by a factor of nearly 1.5. Our results are consistent with a flat Lambda Cold Dark Matter model and with GR.Comment: Accepted for publication in MNRAS (clarifications added, results and conclusions unchanged

Understanding the faint red galaxy population using large-scale clustering measurements from SDSS DR7

We use data from the SDSS to investigate the evolution of the large-scale galaxy bias as a function of luminosity for red galaxies. We carefully consider correlation functions of galaxies selected from both photometric and spectroscopic data, and cross-correlations between them, to obtain multiple measurements of the large-scale bias. We find, for our most robust analyses, a strong increase in bias with luminosity for the most luminous galaxies, an intermediate regime where bias does not evolve strongly over a range of two magnitudes in galaxy luminosity, and no evidence for an upturn in bias for fainter red galaxies. Previous work has found an increase in bias to low luminosities that has been widely interpreted as being caused by a strong preference for red dwarf galaxies to be satellites in the most massive halos. We can recover such an upturn in bias to faint luminosities if we push our measurements to small scales, and include galaxy clustering measurements along the line-of-sight, where we expect non-linear effects to be the strongest. The results that we expect to be most robust suggest that the low luminosity population of red galaxies is not dominated by satellite galaxies occupying the most massive haloes.Comment: Matches version accepted by MNRA

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of synbiotics

In May 2019, the International Scientific Association for Probiotics and Prebiotics (ISAPP) convened a panel of nutritionists, physiologists and microbiologists to review the definition and scope of synbiotics. The panel updated the definition of a synbiotic to “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host”. The panel concluded that defining synbiotics as simply a mixture of probiotics and prebiotics could suppress the innovation of synbiotics that are designed to function cooperatively. Requiring that each component must meet the evidence and dose requirements for probiotics and prebiotics individually could also present an obstacle. Rather, the panel clarified that a complementary synbiotic, which has not been designed so that its component parts function cooperatively, must be composed of a probiotic plus a prebiotic, whereas a synergistic synbiotic does not need to be so. A synergistic synbiotic is a synbiotic for which the substrate is designed to be selectively utilized by the co-administered microorganisms. This Consensus Statement further explores the levels of evidence (existing and required), safety, effects upon targets and implications for stakeholders of the synbiotic concept