Abbreviated inner primaries: a sex-linked dimorphism in the Acorn Woodpecker

ABSTRACT.   In at least 15 species of woodpeckers, the inner primaries of nestlings are reduced in size. This trait is polymorphic in Acorn Woodpeckers ( Melanerpes formicivorus ) at Hastings Reservation in central coastal California, where most nestlings (90.1%) had reduced first and second primaries, 9.8% had only a reduced first primary, and 0.1% had no reduced primaries. More males (11.1%) had large second primaries than did females (5.3%), and females with this trait were less likely to survive their first year of life. Smaller inner primaries may provide a temporary energetic savings for nestlings that facilitate faster growth, but, if so, why this trait is not more common among other cavity-nesting species remains unknown. This trait appears to be more ecologically interesting than previously suspected and warrants study in other species and populations of woodpeckers.     

CLONING: a microcomputer program for cloning simulations

A comprehensive computational tool is presented that performs cloning simulations using IBM PC/XT/AT or compatible microcomputers. The CLONING program contains a specific data base for restriction sites, gene markers, fragment sources and reference comments. It draws complete linear or circular maps either on the screen or employing conventional dot-matrix printers. The design of new recombinant molecules is a totally interactive process.     

Acorn removal and dispersal by the dung beetle Thorectes lusitanicus: ecological implications

Abstract.  1. Plant–animal interactions, and in particular the processes of seed predation and dispersal, are crucial for tree regeneration and forest dynamics. A novel and striking case of interaction between a dung beetle ( Thorectes lusitanicus ) and two Quercus species ( Q. suber and Q. canariensis ) in forests of southern Spain is presented here.
2. During the autumn, T. lusitanicus beetles (endemic to the southern Iberian Peninsula) bury and feed on single-seeded fruits (acorns) of Quercus , with important ecological implications.
3. Field experiments found differences in the removal rate of acorns by T. lusitanicus , depending on the type of microsite within the forest, the species of oak, the exclosure of large herbivores, and the forest site.
4. Acorn consumption by T. lusitanicus was studied under laboratory conditions, confirming for the first time that this dung beetle is a legitimate seed predator.
5. In addition, some buried acorns can be abandoned partially predated or even intact, and emerge as seedlings; thus, T. lusitanicus also has a potential role as secondary seed disperser.     

MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families

Background

Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins and development of physiological features in present day organisms. Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses.

Methodology

Our focus was to increase the number of bootstrap replications that can be performed on large protein datasets using the maximum parsimony, distance matrix, and maximum likelihood methods. We have modified the PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time. This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets.

Conclusions

Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. Of the three protein methods tested, the maximum likelihood method scales the best, followed by the distance method, and then the maximum parsimony method. However, the maximum likelihood method requires significant memory resources, which limits its application to more moderately sized protein datasets.     

Acorn production prediction models for five common oak species of the eastern United States

Acorn production varies considerably among oak (Quercus) species, individual trees, years, and locations, which directly affects oak regeneration and populations of wildlife species that depend on acorns for food. Hard mast indices provide a relative ranking and basis for comparison of within- and between-year acorn crop size at a broad scale, but do not provide an estimate of actual acorn yield—the number of acorns that can potentially be produced on a given land area unit based on the species, number, and diameter at breast height (dbh) of oak trees present. We used 10 years of acorn production data from 475 oak trees to develop predictive models of potential average annual hard mast production by five common eastern oak species, based on tree diameter and estimated crown area. We found a weak (R² = 0.08–0.28) relationship between tree dbh and acorn production per unit crown area for most species. The relationship between tree dbh and acorn production per tree was stronger (R² = 0.33–0.57). However, this is because larger-dbh trees generally have larger crowns, not because they have a greater capacity to produce more acorns per unit crown area. Acorn production is highly variable among individual trees. We estimated that dbh of at least 60 dominant or codominant oak trees per species should be randomly sampled to obtain an adequate representation of the range of dbhs (≥12.7 cm dbh) in a given forest area, and achieve precise estimates when using these equations to predict potential acorn production. Our predictive models provide a tool for estimating potential acorn production that land managers and forest planners can apply to oak inventory data to tailor estimates of potential average annual acorn production to different forest management scenarios and multiple spatial scales. © 2011 The Wildlife Society.     

Marfan Database (third edition): new mutations and new routines for the software.

The Marfan database is a software that contains routines for the analysis of mutations identified in the FBN1 gene that encodes fibrillin-1. Mutations in this gene are associated not only with Marfan syndrome but also with a spectrum of overlapping disorders. The third version of the Marfan database contains 137 entries. The software has been modified to accommodate four new routines and is now accessible on the World Wide Web at http://www.umd.necker.fr     

MicroclimOz – A microclimate data set for Australia,with example applications

Many problems in pure and applied ecology require the quantification of above‐ and below‐ground microclimates. Here I describe a data set of hourly microclimates for the Australian continent, simulated from the years 1990 to 2017 across a grid of 1893 locations approx. 60 km apart. The data were generated with the NicheMapR microclimate model, driven by 0.05° gridded daily meteorological forcing data (air temperature, wind speed, humidity, cloud cover, rainfall), 0.025° elevation and 0.008° soil texture data. The above‐ground microclimate variables include horizontal plane solar radiation, solar zenith angle, sky temperature (from which down‐welling longwave radiation can be computed), air temperature, relative humidity and wind speed at 1 and 120 cm height, and snow depth. The below‐ground variables include soil temperature, pore humidity, soil moisture and soil water potential for 0, 2.5, 5, 10, 15, 20, 30, 50, 100 and 200 cm below‐ground. The computations are for four shade levels (0%, 50%, 70% and 90%). The data set can be used for a wide variety of applications, including the computation of heat and water budgets of organisms, the potential for vegetation growth, and the computation of stress and growth indices. The use of daily forcing data also allows assessments of the consequences of extreme events including heat waves. Example applications are provided for computing plant growth potential, grasshopper egg development, lizard body temperature and mammalian energy and water requirements.     

SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry

A software package suitable for personal computers and designedto handle simulation and fitting problems related to the studyof biomolecules under pre-steady and steady state conditionsis presented, and its overall architecture as well as the implementedalgorithms illustrated. The peculiar features of the packageare: (i) integrated capability of simulating dynamic modelsand fitting to them experimental data; (ii) handling of stiffproblems; (iii) free use of algebraic as well as differentialequations; (iv) objective comparison of models of differentcomplexity. The above features are discussed through a numberof examples taken from the direct experience of the authorsin enzyme kinetics and ligand binding. Received on May 23, 1989; accepted on August 21, 1989     

Optimal annual routines: behaviour in the context of physiology and ecology

Organisms in a seasonal environment often schedule activities in a regular way over the year. If we assume that such annual routines have been shaped by natural selection then life-history theory should provide a basis for explaining them. We argue that many life-history trade-offs are mediated by underlying physiological variables that act on various time scales. The dynamics of these variables often preclude considering one period of the year in isolation. In order to capture the essence of annual routines, and many life-history traits, a detailed model of changes in physiological state over the annual cycle is required. We outline a modelling approach based on suitable physiological and ecological state variables that can capture this underlying biology, and describe how models based on this approach can be used to generate a range of insights and predictions.     

A microcomputer program for the identification of tRNA genes

A microcomputer program which locates tRNA genes within longDNA sequences is described. The search is performed either byidentifying tRNA-like secondary structures or by locating eukaryoticRNA polymerase III promoter consensus sequences. The programis also useful in finding inverted repeats allowing the formationof stem-loop secondary structures in tRNA. The program has beendeveloped in BASIC and 6502 Assembler and runs on the AppleII plus and He microcomputers. The execution is quite fast;all the operations are carried out in 1–90 s, dependingon the required task and on the sequence length. Received on March 1, 1985; accepted on April 25, 1985     

A microcomputer system for the measurement of finger forces

In the analysis of hand functions, the production and control of forces exerted during voluntary contraction of the finger muscles plays an important role; unfortunately such an analysis is rarely seen in routine clinical examinations of neurological patients. A microcomputer controlled system for the measurement and analysis of finger forces is described. The system consists of a modified Z80 based microcomputer, a commercially available high precision force transducer, a specially designed force signal amplifier and a suite of menu-driven user interactive programs. A variety of tasks is implemented by means of the computer programs. In addition to the measurement of maximum hand grip force, the system is able to record forces continuously as a function of time. Task characteristics and the type of feedback presented to the subject are under user control; they can be varied to meet clinical or experimental requirements. Examples of programs and clinical applications are presented and discussed.     

ANTHEPROT: a package for protein sequence analysis using a microcomputer

A simple microcomputer package is described to make the theoreticalanalysis of protein sequences. Several methods designed to comparetwo sequences, to model proteolytic reactions and to predictthe secondary structure, the hydro-phobic/hydrophilic regionsand the potential antigenic sites of proteins have been includedin an Apple II microcomputer software. The package comprises21 programs as well as the secondary structure database of Kabschand Sander (1983). Received on November 24, 1987; accepted on March 8, 1988     

Acorn cake during the Holocene: experimental reconstruction of its preparation in the western Pyrenees,Iberia

In many agricultural and hunter-gatherer communities, edible wild plants are still a relevant food source, although their use has been, in many cases, undervalued. In this sense, acorns have been known as a foodstuff in written sources since antiquity, as well as from scientific analyses in archaeobotany and ethnobotany. We have tried to reconstruct the chaîne opératoire in the preparation of acorn cake, with experiments using materials similar to those potentially used in the western Pyrenees in the past. Furthermore, we have considered some ethnographic data which are available for this area. The results show that the treatment of pre-selected acorns by raw-roasting and leaching is feasible and we emphasise their nutritional value. The results of the experiments improved considerably with the use of pottery and optimal storage conditions. In addition, several by-products useful for other daily tasks were generated which may have been used as well in the past.     

BP: A microcomputer program for use in a hypertension clinic

This paper presents details of a computer program, BP, designed for use with an outpatient clinic. The program is implemented on a PET4000, microcomputer and is intended principally for a hypertension follow-up clinic, although it could be easily adapted for other clinics. It allows for initial patient data entry, the entry of data acquired at subsequent visits, the alteration of data, list of all data or a pre-determined subset, and a data sort and tabulation facility. The program is intended to be run by staff who have little experience with computers.     

UDP-glucuronosyltransferase: fluorometric determination and microcomputer method for bisubstrate kinetics analysis

A method for analysing UDP-glucuronosyltransferase activity in rainbow trout hepatic microsomes is described, using 1-naphthol as a substrate and fluorometric determination of glucuronide. Kinetic constants are computed with a classical plot in a weighted regression. The computer uses the least-squares method for each value of a variable which is set and incremented. To get confidence intervals, the computer generates random values around experimental data (in a confidence interval they determine), and then computes again. With each simulation, a weighted regression with classical secondary plots gives simulated kinetic parameters. From each population of simulated values, an interval containing a given percentage of the population is determined.