Biogeography Virtual Issue

Photo © An-Yi Cheng

© An-Yi Cheng

To coincide with the International Biogeography Society’s 2017 conference in Tuscon, Arizona, we have compiled a Virtual Issue that shows off new Methods in Ecology and Evolution articles in the field from a diverse array of authors.

To truly understand how species’ distributions vary through space and time, biogeographers often have to make use of analytical techniques from a wide array of disciplines. As such, these papers cover advances in fields such as evolutionary analysis, biodiversity definitions, species distribution modelling, remote sensing and more. They also reflect the growing understanding that biogeography can include experiments and highlight the increasing number of software packages focused towards biogeography.

This Virtual Issue was compiled by Methods in Ecology and Evolution Associate Editors Pedro Peres-Neto and Will Pearse (both of whom are involved in the conference). All of the articles in this Virtual Issue are free for a limited time and we have a little bit more information about each of the papers included here:

Species Distribution Modelling

©Jia-Hong Chen

The Virtual Issue includes two articles that specifically deal with Species Distribution Models or SDMs. In ‘Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models‘ Ovaskainen et al. unify spatial and community-level structures by developing spatially explicit joint SDMs. They utilise spatially structured latent factors to model missing covariates. Brewer et al. propose an alternative parametric form for climate envelopes that appeals to ecological plausibility and can encompass realistic features of species’ presence/climate relationships on several variables simultaneously in their article ‘Plateau: a new method for ecologically plausible climate envelopes for species distribution modelling‘.

Remote Sensing

© Kevin Leempoel, EPFL

In the first of two papers that look into remote sensing, Pettorelli et al. give a brief overview of the role of Satellite Remote Sensing (SRS) in informing frameworks that help coordinate and structure biodiversity monitoring efforts worldwide. Their article ‘How do we want Satellite Remote Sensing to support biodiversity conservation globally?‘ was included in the 5th Anniversary of Methods in Ecology and Evolution Special Feature. You can find out more in their blog post In Defence of Satellite Data. Leempoel et al. provide the second paper on remote sensing. Their article ‘Very high-resolution digital elevation models: are multi-scale derived variables ecologically relevant?‘ explains how using multi-scale digital elevation models variables can provide surrogates for important climatic variables such as humidity, moisture and temperature.

Experiments & Data Collection in Biogeoraphy

© Dale Burzacott 2015

There is specific advice for researchers interested in employing distributed collaborative experiments from Borer et al. in ‘Finding generality in ecology: a model for globally distributed experiments‘. The authors hope to empower others in the scientific community to employ this emerging approach to advance our predictive understanding of global-scale ecological trends and responses. In ‘Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias‘, Ruiz-Gutierrez et al. present a framework for data collection and analysis that is able to efficiently provide reliable inference for occurrence patterns using data from a citizen-science monitoring programme. You can find out more about this in the author’s blog post Being Certain About Uncertainty.

Software Packages

Our Biogeography Virtual issue includes two Applications articles. These are always freely available and – like all of our Applications articles – can be accessed and downloaded without a subscription. The first of these articles comes from Bocedi et al. They introduce RangeShifter – a novel modelling platform which integrates complex population dynamics and dispersal behaviour, includes plastic and evolutionary processes and simulates scenarios on spatially explicit landscapes. Rominger and Merow present the R package meteR in their article ‘meteR: an r package for testing the maximum entropy theory of ecology‘. This package directly calculates all of the maximum entropy theory of ecology’s predictions from a variety of data formats; automatically handles approximations and other technical details; and provides plotting and model comparison functions to explore and interrogate models.

Biodiversity

©Bill Kunin

Towards a unified descriptive theory for spatial ecology: predicting biodiversity patterns across spatial scales‘ by Azaele et al. offers a framework that links and predicts the profile of the species-area relationship and the species-abundance distributions across scales when a limited number of fine-scale scattered samples are available. Chao and Chiu bridge the gap between two popular approached to measuring biodiversity (the variance framework and diversity decomposition) in ‘Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures‘. In the final paper of this section, Pavoine et al.  develop methodologies for analysing species, functional, taxonomic or phylogenetic diversity in a hierarchy of multiple scales using equivalent numbers of species. Their article, ‘‘Equivalent numbers’ for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales‘ also  compares their framework with those other authors have developed.

Biogeography and Policy

As the Editors of this Virtual Issue mention in their introduction, biogeography often has meaningful implications for policy. In ‘How to manipulate landscapes to improve the potential for range expansion‘ Hodgson et al. propose and test two methods that can help to optimise the spatial arrangement of habitat for range expansion. They also discuss this method in their blog post Planning Habitat for Very Long-Distance Connectivity under Climate Change. Our second policy related article – ‘Spatial targeting of infectious disease control: identifying multiple, unknown sources‘ – comes from Verity et al. The authors solve the problem of identifying multiple sources, present a rigorous mathematical and computational method and show why previous Bayesian methods were often outperformed by the empirically developed criminal geographic targeting (CGT) algorithm.

Evolution and Extinction

© Andy Pratt

Boakes et al. focus on methods to estimate extinction in their article ‘Beyond the species–area relationship: improving macroecological extinction estimates‘. They provide guidance on selecting the most appropriate method to infer extinction for a particular sighting record. This is another article with a blog post: ‘When is a Species as Dead as a Dodo?‘. Kitzes and Harte also deal with extinction in ‘Beyond the species–area relationship: improving macroecological extinction estimates‘. The authors propose two methods to predict extinction rates following habitat loss and climate change – the extinction–area relationship and probabilistic species–area relationship. Weir and Lawson’s article ‘Evolutionary rates across gradients’ is also included in this Virtual Issue. In this paper the R package evorag, which tests whether rates of trait evolution vary continuously across such continuous gradients, is introduced.

Climate Change and Invasive Species

© Steve Lindfield

Nadeau and Fuller develop a novel index of climate change (climate overlap) that simultaneously estimates changes in the means, variation and correlation between multiple weather variables in their article ‘Accounting for multiple climate components when estimating climate change exposure and velocity‘. Last, but certainly not least, is ‘Identifying the signal of environmental filtering and competition in invasion patterns – a contest of approaches from community ecology‘ by Gallien et al. In this article developed a mechanistic community assembly model to simulate invasion patterns across a range of communities and tested the performance of four different indices aiming at disentangling environmental filtering vs. competition from these patterns. The lead author, Laure Gallien, won the 2014 Robert May prize for this paper.

To access all of these articles, check out our full Biogeography Virtual Issue. The articles are all freely available for a limited time.

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