Tag: genetics

Methods papers, Online extras, Practical Tools

The Arborist Throw-line Launcher

Collecting leaves or seeds from tall trees is a difficult task that many plant physiologists, ecologists, geneticists and forest managers encounter repeatedly. In a series of videos on the Methods in Ecology and Evolution YouTube channel, Kara N. Youngentob, Christina Zdenek and Eva van Gorsel demonstrate how to use the arborist throw-line launcher, which significantly simplifies this task. This new way of collecting seeds and leaves from tall trees is explained in their Applications article ‘A simple and effective method to collect leaves and seeds from tall trees‘. As this is an Applications paper, it is freely available to everyone.

Basic Techniques for the Arborist Throw-line Launcher

The first of the three videos is a basic overview of the method. In this tutorial, the authors teach you how to find the ideal branch, how to use the throw-line launcher and go through some important safety information. Continue reading “The Arborist Throw-line Launcher”

Unknown's avatarIndia Stephenson2 Comments
Methods papers, Statistical methods

My Entropy ‘Pearl’: Using Turing’s Insight to Find an Optimal Estimator for Shannon Entropy

Post provided by Anne Chao (National Tsing Hua University, Taiwan)

Shannon Entropy

Not quite as precious as my entropy pearl
Not quite as precious as my entropy pearl ©Amboo Who

Ludwig Boltzmann (1844-1906) introduced the modern formula for entropy in statistical mechanics in 1870s. Since its generalization by Claude E. Shannon in his pioneering 1948 paper A Mathematical Theory of Communication, this entropy became known as ‘Shannon entropy’.

Shannon entropy and its exponential have been extensively used to characterize uncertainty, diversity and information-related quantities in ecology, genetics, information theory, computer science and many other fields. Its mathematical expression is given in the figure below.

In the 1950s Shannon entropy was adopted by ecologists as a diversity measure. It’s interpreted as a measure of the uncertainty in the species identity of an individual randomly selected from a community. A higher degree of uncertainty means greater diversity in the community.

Unlike species richness which gives equal weight to all species, or the Gini-Simpson index that gives more weight to individuals of abundant species, Shannon entropy and its exponential (“the effective number of common species” or diversity of order one) are the only standard frequency-sensitive complexity measures that weigh species in proportion to their population abundances. To put it simply: it treats all individuals equally. This is the most natural weighing for many applications. Continue reading “My Entropy ‘Pearl’: Using Turing’s Insight to Find an Optimal Estimator for Shannon Entropy”

Unknown's avatarIndia Stephenson2 Comments
Methods papers

How Did We Get Here From There? A Brief History of Evolving Integral Projection Models

Post provided by MARK REES and Steve Ellner

The Early Days: Illyrian Thistle and IBMs

Illyrian Thistle
Illyrian Thistle

Back in 1997 MR was awarded a travel grant from CSIRO to visit Andy Sheppard in Canberra. CSIRO had been collecting detailed long-term demographic data on several plant species and Andy was keen to develop data-driven models for management.

Andy decided Illyrian thistle (Onopordum Illyricum) would be a good place to start, as this was the most complicated in terms of its demography. The field study provided information on size, age and seed production. The initial goal was to quantify the impact of seed feeders on plant abundance, but after a few weeks of data analysis it became apparent that the annual seed production per quadrat was huge (in the 1000s) but there were always ~20 or so recruits. This meant that effects of seed feeders (if any) occurred outside the range of the data, which wasn’t ideal for quantitative prediction.

So the project developed in a different direction. Onopordum is a monocarpic perennial (it lives for several years then flowers and dies) and Tom de Jong and Peter Klinkhamer had recently developed models to predict at what size or age monocarps should flower, so it seemed reasonable to see if this would work. Continue reading “How Did We Get Here From There? A Brief History of Evolving Integral Projection Models”

Unknown's avatarIndia Stephenson1 Comment
Meetings

International Marine Connectivity Conference: Pre-Booking Now Open

Background of the iMarCo

iMarCoiMarCo is a new initiative aimed at creating an international network for promoting collaborative projects among European scientists interested in the study of marine connectivity. The network covers a broad spectrum of marine science disciplines including physical oceanography, microchemistry, genetics and evolutionary ecology, behaviour, tagging, fisheries and aquaculture.

The strategic objective of iMarCo is to organise and create synergies among the European scientific community sharing an interest in the understanding of the spatial dynamics of marine populations. Continue reading “International Marine Connectivity Conference: Pre-Booking Now Open”

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Journal updates

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

– mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

– Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading “Issue 6.11”

Unknown's avatarIndia StephensonLeave a comment
Journal updates, Methods papers

Issue 6.8

Issue 6.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

– LEA: This R package enables users to run ecological association studies from the R command line. It can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets. The package derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results.

– PIPITS: An open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.

Giovanni Strona and Joseph Veech provide this month’s Open Access article. Many studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners, as a method of measuring the structure of ecological networks. In ‘A new measure of ecological network structure based on node overlap and segregation‘ the authors introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species’ tendency against sharing interacting partners).

In addition to this, our August issue features articles on Estimating Diversity, Ecological Communities and Networks, Genetic Distances and Immunology. Continue reading “Issue 6.8”

Unknown's avatarIndia StephensonLeave a comment
Journal updates, Methods papers

Issue 6.7

Issue 6.7 is now online!

The July issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

– fuzzySim: Binary similarity indices are widely used in ecology. This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, producing more realistic similarity assessments. fuzzySim is an open source software package which is also available for R.

– Actave.net: A freely accessible, web-based analysis tool for complex activity data, actave.net provides cloud-based and automatic computation of daily aggregates of various activity parameters based on recorded immersion data. It provides maps and graphs for data exploration, download of processed data for modelling and statistical analysis, and tools for sharing results with other users.

Anna Sturrock et al. provide this month’s Open Access article. In ‘Quantifying physiological influences on otolith microchemistry‘ the authors test relationships between otolith chemistry and environmental and physiological variables. The influence of physiological factors on otolith composition was particularly evident in Sr/Ca ratios, the most widely used elemental marker in applied otolith microchemistry studies. This paper was reported on in the media recently. You can read more about it here.

Our July issue also features articles on Monitoring, Remote Sensing, Conservation, Genetics and three papers on Statistics. Continue reading “Issue 6.7”

Unknown's avatarIndia StephensonLeave a comment
Journal updates

Latest issue and other articles

Issue 3.4 Our latest issue covers an impressive array of subjects: from metabarcoding (with associated presentation), to population genetics and population monitoring (with video explaining a microphone array system). Modelling and monitoring dispersal also features heavily with four articles, one of which is accompanied by a video for a novel telemetry system to track wild animals. Articles also include topics such as transient dynamics, a review … Continue reading Latest issue and other articles

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Journal updates

Issue 3.2

About the issue With topics ranging from phylogenetic analysis to statistics and distribution modelling, conservation, citizen science, surveys, genetic and demographic models to avian biology, our issue 3.2 should be of interest to most ecologists and evolutionary biologists. The issue also contains 5 free applications. About the cover This very high-resolution image of a beech-dominated forest in central Germany was taken by an unmanned aerial … Continue reading Issue 3.2

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