Spatial models of metapopulations and benthic communities in patchy environments

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2000The distribution of organisms in space has important consequences for the function and structure of ecological systems. Such distributions are often referred to as patchy, and a patch-based approach to modeling ecosystem dynamics has become a major research focus. These models have been used to explore a wide range of questions concerning population, metapopulation, community, and landscape ecology, in both terrestrial and aquatic systems. In this dissertation I develop and analyze a series of spatial models to study the dynamics of metapopulations and marine benthic communities in patchy environments. All the models have the form of a discrete-time Markov chain, and assume that the landscape is composed of discrete patches, each of which is in one of a number of possible states. The state of a patch is determined by the presence of an individual of a given species, a local population, or a group of species, depending on the spatial scale of the model. The research is organized into two main parts as follows. In the first part, I present an analysis of the effects of habitat destruction on metapopulation persistence. Theoretical studies have already shown that a metapopulation goes extinct when the fraction of suitable patches in the landscape falls below a critical threshold (the so called extinction threshold). This result has become a paradigm in conservation biology and several models have been developed to calculate extinction thresholds for endangered species. These models, however, generally do not take into account the spatial arrangement of habitat destruction, or the actual size of the landscape. To investigate how the spatial structure of habitat destruction affects persistence, I compare the behavior of two models: a spatially implicit patch-occupancy model (which recreates the extinction patterns found in other models) and a spatially explicit cellular automaton (CA) model. In the CA, I use fractal arrangements of suitable and unsuitable patches to simulate habitat destruction and show that the extinction threshold depends on the fractal dimension of the landscape. To investigate how habitat destruction affects persistence in finite landscapes , I develop and analyze a chain-binomial metapopulation (CBM) model. This model predicts the expected extinction time of a metapopulation as a function of the number of patches in the landscape and the number of those patches that are suitable for the population. The CBM model shows that the expected time to extinction decreases greater than exponentially as suitable patches are destroyed. I also describe a statistical method for estimating parameters for the CBM model in order to evaluate metapopulation viability in real landscapes. In the second part, I develop and analyze a series of Markov chain models for a rocky subtidal community in the Gulf of Maine. Data for the model comes from ten permanent quadrats (located on Ammen Rock Pinnacle at 30 meters depth) monitored over an 8-year period (1986-1994). I first parameterize a linear (homogenous) Markov chain model from the data set and analyze it using an array of novel techniques, including a compression algorithm to classify species into functional groups, a set of measures from stochastic process theory to characterize successional patterns, sensitivity analyses to predict how changes in various ecological processes effect community composition, and a method for simulating species removal to identify keystone species. I then explore the effects of time and space on successional patterns using log-linear analysis, and show that transition probabilities vary significantly across small spatial scales and over yearly time intervals. I examine the implications of these findings for predicting equilibrium species abundances and for characterizing the transient dynamics of the community. Finally, I develop a nonlinear Markov chain for the rocky subtidal community. The model is parameterized using maximum likelihood methods to estimate density-dependent transition probabilities. I analyze the best fitting models to study the effects of nonlinear species interactions on community dynamics, and to identify multiple stable states in the subtidal system.This work was supported by the Office of Naval Research and the National Science Foundation through the following grants to Hal Caswell: ONR-URIP Grant NOOOl492- J-1527, NSF Grants DEB-9119420, DEB-95-27400, OCE-981267 and OCE-9302238

Markov chain analysis of succession in a rocky subtidal community

Author Posting. © University of Chicago Press, 2004. This article is posted here by permission of University of Chicago Press for personal use, not for redistribution. The definitive version was published in American Naturalist 164 (2004): E46-E61.We present a Markov chain model of succession in a rocky subtidal community based on a long-term (1986–1994) study of subtidal invertebrates (14 species) at Ammen Rock Pinnacle in the Gulf of Maine. The model describes successional processes (disturbance, colonization, species persistence, and replacement), the equilibrium (stationary) community, and the rate of convergence. We described successional dynamics by species turnover rates, recurrence times, and the entropy of the transition matrix. We used perturbation analysis to quantify the response of diversity to successional rates and species removals. The equilibrium community was dominated by an encrusting sponge (Hymedesmia) and a bryozoan (Crisia eburnea). The equilibrium structure explained 98% of the variance in observed species frequencies. Dominant species have low probabilities of disturbance and high rates of colonization and persistence. On average, species turn over every 3.4 years. Recurrence times varied among species (7–268 years); rare species had the longest recurrence times. The community converged to equilibrium quickly (9.5 years), as measured by Dobrushin’s coefficient of ergodicity. The largest changes in evenness would result from removal of the dominant sponge Hymedesmia. Subdominant species appear to increase evenness by slowing the dominance of Hymedesmia. Comparison of the subtidal community with intertidal and coral reef communities revealed that disturbance rates are an order of magnitude higher in coral reef than in rocky intertidal and subtidal communities. Colonization rates and turnover times, however, are lowest and longest in coral reefs, highest and shortest in intertidal communities, and intermediate in subtidal communities.This research was supported by National Science Foundation grants DEB-9527400, OCE-981267, OCE-9302238, and OCE-0083976 and by the National Oceanic and Atmospheric Administration’s National Undersea Research Program, University of Connecticut—Avery Point

Reproducibility of measurements of oestrogen-receptor concentration in breast cancer.

The reproducibility of measurements of oestrogen-receptor activity has been examined in multiple specimens from a rabbit uterus, a rat mammary tumour and human breast tumours. The relationship between receptor concentration and tumour histology has also been investigated in 11 large primary tumours. In the animal tissues, receptor measurements were relatively reproducible (coefficient of variance: wet wt. basis 16-17%, protein basis 16-21%) but in human breast tumours receptor activity varied considerably (c.v.: wet wt. basis, 22-125%; protein basis, 28-72%). In addition to these variations in receptor activity within tumours, there was a difference between tumours, as demonstrated by an analysis of variance (P less than 0.01). In the 11 primary breast cancers selected for study, the level of receptor activity was related to menopausal status and the tumour content of the specimen. We conclude that the receptor activity detected varies within a tumour and depends upon the tumour content of the biopsy specimen. Predictions based on precise quantitation of receptor concentrations may therefore necessitate replicate tumour sampling and correction for the fraction of non-tumour tissue in each sample

Site-selective adsorption of naphthalene-tetracarboxylic-dianhydride on Ag(110): First-principles calculations

The mechanism of adsorption of the 1,4,5,8-naphthalene-tetracarboxylic-dianhydride (NTCDA) molecule on the Ag(110) surface is elucidated on the basis of extensive density functional theory calculations. This molecule, together with its perylene counterpart, PTCDA, are archetype organic semiconductors investigated experimentally over the past 20 years. We find that the bonding of the molecule to the substrate is highly site-selective, being determined by electron transfer to the LUMO of the molecule and local electrostatic attraction between negatively charged carboxyl oxygens and positively charged silver atoms in [1-10] atomic rows. The adsorption energy in the most stable site is 0.9eV. A similar mechanism is expected to govern the adsorption of PTCDA on Ag(110) as well.Comment: 8 pages, 4 figures, high-quality figures available upon reques

Inelastic x-ray scattering investigations of lattice dynamics in SmFeAsO1−x_{1-x}Fy_y superconductors

We report measurements of the phonon density of states as measured with inelastic x-ray scattering in SmFeAsO$_{1-x}$F$_y$ powders. An unexpected strong renormalization of phonon branches around 23 meV is observed as fluorine is substituted for oxygen. Phonon dispersion measurements on SmFeAsO$_{1-x}$F$_y$ single crystals allow us to identify the 21 meV A$_{1g}$ in-phase (Sm,As) and the 26 meV B$_{1g}$ (Fe,O) modes to be responsible for this renormalization, and may reveal unusual electron-phonon coupling through the spin channel in iron-based superconductors.Comment: 4 pages, 3 figures, submitted for SNS2010 conference proceeding

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target-capture method was used to detect genome-wide polymorphisms in a panel of 174 flowering time-related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas

Temporal trends (1977-2007) and ethnic inequity in child mortality in rural villages of southern Guinea Bissau

Background Guinea Bissau is one of the poorest countries in the world, with one of the highest under-5 mortality rate. Despite its importance for policy planning, data on child mortality are often not available or of poor quality in low-income countries like Guinea Bissau. Our aim in this study was to use the baseline survey to estimate child mortality in rural villages in southern Guinea Bissau for a 30 years period prior to a planned cluster randomised intervention. We aimed to investigate temporal trends with emphasis on historical events and the effect of ethnicity, polygyny and distance to the health centre on child mortality. Methods A baseline survey was conducted prior to a planned cluster randomised intervention to estimate child mortality in 241 rural villages in southern Guinea Bissau between 1977 and 2007. Crude child mortality rates were estimated by Kaplan-Meier method from birth history of 7854 women. Cox regression models were used to investigate the effects of birth periods with emphasis on historical events, ethnicity, polygyny and distance to the health centre on child mortality. Results High levels of child mortality were found at all ages under five with a significant reduction in child mortality over the time periods of birth except for 1997-2001. That period comprises the 1998/99 civil war interval, when child mortality was 1.5% higher than in the previous period. Children of Balanta ethnic group had higher hazard of dying under five years of age than children from other groups until 2001. Between 2002 and 2007, Fula children showed the highest mortality. Increasing walking distance to the nearest health centre increased the hazard, though not substantially, and polygyny had a negligible and statistically not significant effect on the hazard. Conclusion Child mortality is strongly associated with ethnicity and it should be considered in health policy planning. Child mortality, though considerably decreased during the past 30 years, remains high in rural Guinea Bissau. Temporal trends also suggest that civil wars have detrimental effects on child mortality. Trial Registration Current Controlled Trials ISRCTN5243333

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role

Sinusoidal magnetic structure in a three-dimensional antiferromagnetic Co2(OH)AsO4: Incommensurate-commensurate magnetic phase transition

Co2 OH AsO4 has been prepared by hydrothermal synthesis and characterized from x-ray and neutron powder diffraction. The structure consists of a three-dimensional framework in which Co 1 O5-trigonal bipyramid dimers and Co 2 O6-octahedra chains are simultaneously present. The magnetic structure has been determined by neutron D2B and D1B powder-diffraction data. Below 22 K, the Co2 OH AsO4 phase shows an incommensurate antiferromagnetic structure along the b direction. The propagation vector 0, ,0 is temperature dependent with a value of =0.430 at the lowest temperature 1.8 K . Magnetization measurements of Co2 OH AsO4 show a complex magnetic behavior with the presence of three different signals. Between 6 and 21 K, a strong dependence of the magnetic field is observed with a shift of the inflexion point associated to the three-dimensional antiferromagnetic ordered from 18 K at 1 kOe to 20.1 K at 90 kOe. The small splitting observed in the zero-field-cooled-field-cooled curves at low temperatures is characteristic of ferromagnetic interactions but saturation is not reached even up to 90 kOe. Heat-capacity measurements show an unusual dependence on the magnetic field for antiferromagnetic transitions with a jump at the Neél temperature quite small 2 J/Kmol . The magnetic contribution exhibits a -type anomaly associated to the three-dimensional antiferromagnetic ordering. Surprisingly, the anomaly grows with the magnetic field and becomes better defined. Neutron powder diffraction in different fields shows a magnetic phase transition. The incommensurate magnetic structure evolves at low temperatures toward a collinear AF phase for fields higher than 35 kOe