Stephen A. Harris

Bio: Stephen A. Harris is an academic researcher from University of Oxford. The author has contributed to research in topics: Population & Vulpes. The author has an hindex of 48, co-authored 173 publications receiving 7542 citations. Previous affiliations of Stephen A. Harris include Derriford Hospital & University of St Andrews.

Analysis of multilocus fingerprinting data sets containing missing data

Abstract: Missing data are commonly encountered using multilocus, fragment-based (dominant) fingerprinting methods, such as random amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP). Data sets containing missing data have been analysed by eliminating those bands or samples with missing data, assigning values to missing data or ignoring the problem. Here, we present a method that uses random assignments of band presence-absence to the missing data, implemented by the computer program [smallcapital famd] (available from http://homepage.univie.ac.at/philipp.maria.schlueter/famd.html), for analyses based on pairwise similarity and Shannon's index. When missing values group in a data set, sample or band elimination is likely to be the most appropriate action. However, when missing values are scattered across the data set, minimum, maximum and average similarity coefficients are a simple means of visualizing the effects of missing data on tree structure. Our approach indicates the range of values that a data set containing missing data points might generate, and forces the investigator to consider the effects of missing values on data interpretation.

Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission

Abstract: Summary Harris, S. A. & Ingram, R.: Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission. - Taxon 40: 393-412. 1991. - ISSN 0040-0262. The widespread application of chloroplast DNA (cpDNA) to plant biosystematics is usually based on a number of assumptions. The assumption of low levels of intraspecific cpDNA variation is reviewed and the conclusion reached that far from being rare, intraspecific cpDNA variation is relatively common. The evidence for the assumption of predominantly maternal plastid transmission is also reviewed. In both of the cases some of the possible effects on phylogenetic reconstruction are considered.

A quantitative analysis of the abundance and demography of European hares Lepus europaeus in relation to habitat type, intensity of agriculture and climate.

Abstract: 1. European hares Lepus europaeus have declined throughout Europe since the 1960s. Possible reasons for this include agricultural intensification and changes in climate and predator numbers, but no clear consensus has been reached as to the relative importance of each of these. We aimed to identify factors associated with high and low hare numbers throughout Europe, to determine which could have caused population declines. 2. Results of 77 research papers from 12 European countries were summarized. Relationships between hare density and demographics and habitat, climate, hunting and predator variables were examined and quantified where possible. Temporal changes in factors identified as being associated with high or low numbers of hares were then examined to see if they could explain population declines. 3. Data from pastural habitats were limited, but densities of hares were low. Arable habitats had higher densities than mixed areas in spring, unless farming was intensive in which case densities were similar. In autumn the two habitats had similar densities. Field size, temperature, precipitation and hunting had no effect on density throughout Europe. Fecundity was affected by climate. 4. Arable land, various crops, fallow habitat and temperature were positively associated, and monoculture, precipitation and predators negatively associated with hare abundance. The relationship of field size, pasture and woodland with abundance depended on spatial scale. 5. Habitat changes caused by agricultural intensification are the ultimate cause of hare population declines. Effects of changes in climate or predator numbers are magnified by the loss of high-quality year-round forage and cover. Further research is required on how habitat changes affect fecundity and survival, and to identify which parameters have the greatest impact on population numbers. Farmland management policies that target the re-establishment of some of the habitat diversity lost within fields, farms and landscapes will help to reverse the decline of the European hare.

The Theory of Island Biogeography

Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Modern Applied Statistics With S

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Climate Change 2007: Impacts, Adaptation and Vulnerability.

Abstract: Impatti, adattamento e vulnerabilita Le cause e le responsabilita dei cambiamenti climatici sono state trattate sul numero di ottobre della rivista Cda. Approfondiamo l’argomento presentando il documento: “Cambiamenti climatici 2007: impatti, adattamento e vulnerabilita” votato ad aprile 2007 dal secondo gruppo di lavoro del Comitato Intergovernativo sui Cambiamenti Climatici (Intergovernmental Panel on Climate Change). Si tratta del secondo di tre documenti che compongono il quarto rapporto sui cambiamenti climatici.

The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0-55 cal kBP)

Abstract: Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.