Tag Archives: genetics

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

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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 →

International Marine Connectivity Conference: Pre-Booking Now Open

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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 →

Issue 6.11

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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 6.8

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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 6.7

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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 →

Latest issue and other articles

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A dragonfly

Cover image for issue 3.4 © Dennis Paulson.

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 on hormone assay, phylogenetic comparative analysis, stable isotopes (featuring our cover article), plant physiology and finally, statistical methods.

About the cover

Stable-isotope ratios measured in migrating animals have proven to be of great value in understanding migration. For example, when a dragonfly emerges from the water, the isotope signature in that water body is fixed in its wing tissues, which thus provide information about its geographic origin. In A dragonfly (δ2H) isoscape for North America: a new tool for determining natal origins of migratory aquatic emergent insects,  Keith Hobson, David Soto, Dennis Paulson, Leonard Wassenaar and John Matthews compared the isotope value from dragonfly wings of known origin with spatially explicit isoscapes based on water isotopes in precipitation. The relationship was strong, confirming the value of the method to study dragonfly migration.

One of the species used in the analysis was Pachydiplax longipennis. This individual was photographed at Red Slough Wildlife Management Area, Oklahoma. Photo © Dennis Paulson.

Early View articles

Also, these recently accepted articles have appeared on Early View:

Rapid determination of comparative drought tolerance traits: using an osmometer to predict turgor loss point by Megan K. Bartlett, Christine Scoffoni, Rico Ardy, Ya Zhang, Shanwen Sun, Kunfang Cao and Lawren Sack

Free application: taxonstand: An r package for species names standardisation in vegetation databases by Luis Cayuela, Íñigo Granzow-de la Cerda, Fabio S. Albuquerque and Duncan J. Golicher

Projecting species’ range expansion dynamics: sources of systematic biases when scaling up patterns and processes by Greta Bocedi, Guy Pe’er, Risto K. Heikkinen, Yiannis Matsinos and Justin M. J. Travis

Review: Temporal dynamics and network analysis by Benjamin Blonder, Tina W. Wey, Anna Dornhaus, Richard James and Andrew Sih

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Issue 3.2

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Aerial photograph of a forest

Cover image for issue 3.2
© Getzin & Wiegand – Biodiversity Exploratories

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 vehicle (UAV) at 250 meter above ground. In this photograph one can clearly recognize individual tree crowns and even smallest gaps. UAVs are increasingly used for ecological surveys because they provide extremely fine resolutions and thus allow the identification of previously undetected object details. Furthermore, UAVs can be considered as very cost-effective tools for the acquisition of data that can be used also very flexibly.

In Assessing biodiversity in forests using very high-resolution images and unmanned aerial vehicles Getzin, Wiegand and Schöning tested the hypothesis that gap-structural information on aerial images can be principally used for the ecological assessment of understorey plant diversity in forests. The authors demonstrate that spatially implicit information on gap shape metrics is indeed sufficient to reveal strong dependency between gap patterns as a filter for incoming light and plant biodiversity. The study highlights that understorey biodiversity can be actively controlled by the spatial quality, and not just quantity, of tree removal. Thus, even under the same quota of tree harvesting, the promotion of complex and irregularly shaped gaps may be beneficial to foster biodiversity in forests.

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