Null model analyses of presence–absence matrices need a definition of independence

Tests for species interactions that involve the comparison of a statistic calculated from observed matrix of species presences and absences with the distribution of the same statistic generated from a null model have been used by ecologists for about 30 years. We argue that the validity of these tests requires a specific definition of independence. In particular, we note that an assumption that is often made is that all presence–absence matrices with the same row and column totals are equally likely if there is no interaction. However, we show using a simple model for species presences and absences without any species interactions that, in general, this assumption should be made with caution. Our model incorporates a definition of independence, allowing the computation of probabilities of different patterns in the null matrices. Other definitions of independence are possible; one of them is outlined using a new generalized linear model approach for carrying out tests applicable to different null models with or without the assumption of keeping row and column totals fixed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

RI manager,a microcomputer program for analysis of data from recombinant inbred strains

RI Manager is a microcomputer program for storage and analysis of genetic mapping data from recombinant inbred strains. The program rapidly identifies statistically significant linkage between known loci and a newly described locus, and it facilitates rapid evaluation of alternative map orders for linked loci.     

The generation of diversity in systems of patches and ranked dominance

Aim Mac Nally and Lake proposed a statistic (η) for determining whether the diversity in archipelagos is better generated by several small patches (SS‐dominance) or by a few large patches (SL‐dominance). The η statistic improves the study of the generation of diversity in systems of patches, but the dependence of η on a particular species–area relationship may reduce its effectiveness. In this paper we show that η may be affected by the criterion used to distinguish between large and small patches. We propose alternative measures (ranked m‐dominance indices) for the detection of SS/SL dominance, which separate the effects of each class of patch size on the generation of diversity. Location We use previously published species lists from three archipelagos: lizard species on 25 islands in the Gulf of California; non‐introduced species of reptiles of the Canary Islands (order Squamata); and finch species from 19 islands of the West Indies. We also use one artificial data set. Methods Presence–absence data and the rank order of patch areas are used to define the m‐dominance indices, interpreted as measures of preferential size of patches occupied by m species. A Monte Carlo procedure is implemented for testing the significance of the observed indices. Row and column totals in the simulated presence–absence matrices are kept fixed in order to maintain differences in species richness among sites and differences in occurrence frequencies among species, but the allocation of each occurrence to a specific ranked area is randomized. The analyses are exemplified with the three published data sets taken from the literature, and a hypothetical patch system neither SS‐ nor SL‐dominated. Results The new m‐dominance indices identified correctly the hypothetical patch system, while η was positive, suggesting an incorrect SL‐dominant result. For the lizard data set, the standardized ranked m‐dominance was significantly large for small m, confirming an SL‐dominated system. Islands of varying size in the Canary archipelago hosted restricted reptile species, but matrix sparseness seems to have caused the non‐significant results for the m‐dominance indices in this case. The overall pattern of the West Indies system shows that medium‐large islands are dominant, but most Monte Carlo analyses were not significant, also possibly as a result of matrix sparseness. Main conclusions The m‐dominance indices have the virtue of summarizing composition–area relationships, and including Monte Carlo procedures for testing whether patch size and the type of species distribution (species restricted to m patches, m = 1,…,s) are random or not. When m is as low as 1 or 2, the m‐dominance indices may typify the role of restricted species on the generation of diversity in the system of patches. The procedure developed here can be generalized to include other ordinal properties of patches, such as isolation or habitat heterogeneity.     

lac operator DNA modification in the presence of proteolytic fragments of the repressor protein

Singly end-labeled DNA fragments containing the lactose operator were methylated in the presence of the lactose repressor and homogeneous preparations of its proteolytic fragments. Binding of core protein produced by mild trypsin digestion yielded a methylation perturbation pattern that differed significantly from that elicited by binding to intact repressor, although similarities in the patterns for these related proteins were noted in the central, asymmetric region of the operator. An NH2-terminal peptide (residues 1 to 56) from lac repressor bound operator fragments in a nitrocellulose filter assay, but failed to perturb DNA methylation significantly relative to the pattern in the absence of peptide. Binding of hybrid tetramers of core and intact repressor monomers produced related but unique methylation patterns for the purines on the operator fragment. The general pattern of perturbation observed suggests preferred binding of a single NH2 terminus to the promoter-distal region of the operator and asymmetric interaction of the core region with the operator sequence. Differences in purine methylation patterns produced by the presence of effector complexes of repressor and core protein suggest the possible nature of changes in protein topology that result in the affinity changes accompanying induction.     

Extensions to Kiritani and Nakasuji’s method for analysing insect stage-frequency data

Summary There is evidence that the simple method ofKiritani andNakasuji (1967) for the analysis of insect stage-frequency data produces estimates of stage-specific survival rates that compare well with the estimates from more complicated methods (Manly, 1975). However the method as originally proposed byKiritani andNakasuji cannot always be applied because it assumes that the insect population involved was sampled at regular intervals of time. Furthermore, parameters such as the durations of stages are not estimated. In this note modifications to the basic method are suggested with the idea of overcoming these limitations.     

Histones Stimulate Polyribonucleotide-Directed Polydeoxyribonucleotide Synthesis by Murine Leukemia Virus

The rate of homoribopolymer-directed DNA synthesis by detergent-disrupted Moloney murine leukemia virus can be stimulated or inhibited by histone, depending on the ratio of histone to template. Of the fractions which can be separated from the whole histone, f1 causes both the greatest stimulation and the greatest inhibition. The effect of histone f1 is qualitatively similar whether the template is polyadenylate (poly A), polycytidylate, or polyuridylate, but the stimulation is greatest with poly A. The pattern of stimulation and inhibition differs, however, for a different polymerase; the DNA polymerase of Micrococcus luteus is inhibited by histone concentrations which stimulate the viral enzyme and stimulated by concentrations which inhibit the viral enzyme. For the viral enzyme, the optimum histone concentration is unaffected by changes in the virus or primer concentration; but it varies in proportion to the template concentration, suggesting that histone acts by combining stoichiometrically with the template. These data raise the possibility that a histone-like protein may participate in the synthesis of the provirus of RNA tumor viruses.     

Sex differences in Adélie penguin foraging strategies

Consistent sex differences in foraging trip duration, feeding locality and diet of breeding Adélie penguins (Pygoscelis adeliae) were demonstrated at two widely separated locations over several breeding seasons. Differences in foraging behaviour were most pronounced during the guard stage of chick rearing. Female penguins made on average longer foraging trips than males, ranged greater distances more frequently and consumed larger quantities of krill. In contrast, males made shorter journeys to closer foraging grounds during the guard period and fed more extensively on fish throughout chick rearing. Mean guard stage foraging trip durations over four seasons at Béchervaise Island, Eastern Antarctica and over two seasons at Edmonson Point, Ross Sea ranged between 31 and 73 h for females and 25 and 36 h for males. Ninety percent of males tracked from Béchervaise Island by satellite during the first 3 weeks post-hatch foraged within 20 km of the colony, while the majority (60%) of females travelled to the edge of the continental shelf (80–120 km from the colony) to feed during this period. Received: 10 December 1997 / Accepted: 10 April 1998     

The warming trend at Helgoland Roads,North Sea: phytoplankton response

We combine the temperature and phytoplankton data from one of the longest aquatic data sets in history, the Helgoland Roads (North Sea, 54°11.3N, 7°54.0E) timeseries to evaluate the effects of climate change on the base of marine food webs. The data shows that, despite an obvious warming of 1.1°C since 1962, the mean diatom day of the algal spring bloom is delayed and shifted to the end of the first quarter of the year. This is apparently related to a warming of the autumn (October–December) temperatures. It is the first indication of a warming related shift in phytoplankton succession, the consequences of which would range from lifecycle/food resource mismatches to regime shifts in the North Sea system.