Tag Archives: Traits

Phylogenies, Trait Evolution and Fancy Glasses

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Post provided by Daniel S. Caetano

Phylogenetic trees represent the evolutionary relationships among different lineages. These trees give us two crucial pieces of information:

  1. the relationships between lineages (which we can tell from the pattern of the branches (i.e., topology))
  2. the point when lineages separated from a common ancestor (which we can tell from the length of the branches, when estimated from genetic sequences and fossils).
Phylogeny of insects inferred from genetic sequences showing the time of divergence between ants and bees.

Phylogeny of insects inferred from genetic sequences showing the time of divergence between ants and bees.

As systematic biologists, we are interested in the evolutionary history of life. We use phylogenetic trees to uncover the past, understand the present, and predict the future of biodiversity on the planet. Among the tools for this thrilling job are the comparative methods, a broad set of statistical tools built to help us understand and interpret the tree of life.

Here’s a Tree, Now Tell Me Something

The comparative methods we use to study the evolution of traits are mainly based on the idea that since species share a common evolutionary history, the traits observed on these lineages will share this same history. In the light of phylogenetics, we can always make a good bet about how a species will look if we know how closely related it is to another species or group. Comparative models aim to quantify the likelihood of our bet being right and use the same principle to estimate how fast evolutionary changes accumulate over time. Continue reading →

Inverse Modelling and IPMs: Estimating Processes from Incomplete Information

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Post provided by Edgar J. González

In demography, a set of processes (survival, growth, fecundity, etc.) interacts to produce observable patterns (population size, structure, growth rate, etc.) that change over time. With traditional approaches you follow the individuals of a population over some timespan and track all of these processes.

Demographic patterns and processes (Click to expand)

Demographic patterns and processes (Click to expand)

However, depending on the organism, some processes may be very hard to quantify (e.g. mortality or recruitment in animals or plants with long lifespans). You may have observed the patterns for the organism that you’re studying and, even better, measured some, but not all, of the processes. The question is: can we use this limited information to estimate the processes we couldn’t measure? Continue reading →

Key Technologies Used to Build the plant Package (and Maybe Soon Some Other Big Simulation Models in R)

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Post provided by RICH FITZJOHN and DANIEL FALSTER

Our paper in Methods in Ecology and Evolution describes a new software package, plant. plant is an individual-based simulation model that simulates the growth of individual trees, stands of competing plants, or entire metacommunities under a disturbance regime, using common physiological rules and trait-based functional trade-offs to capture differences among species.

Non-Linear Processes and Thousands of Plants

Since the development of gap models in the 1970s (e.g. Botkin 1972), researchers have been using computer simulations to investigate how elements of plant biology interact with competition and disturbance regimes to influence vegetation demography, structure and diversity. Simulating the competitive interactions among many thousands of plants, however, is no easy task.

Despite widespread recognition of the importance of key non-linear processes — such as size-structured competition, disturbance, and trait-based trade-offs — for vegetation dynamics, relatively few researchers have been brave (or daft) enough to try and incorporate such processes into their models. The situation is most extreme in theoretical ecology, where much contemporary theory (e.g. coexistence theory, neutral theory) is still built around completely unstructured populations.

Features of plant

Key processes modelled within the plant package.

Key processes modelled within the plant package.

The plant package attempts to change that by providing an extensible, open source framework for studying trait-, size- and patch-structured dynamics. One thing that makes the plant model significant is the focus on traits. plant is one of several attempts seeking to integrate current understanding about trait based trade-offs into a model of individual plant function (see also Moorcroft et al 2001, Sakschewski et al 2015).

A second feature that makes the plant software significant, is it that is perhaps the first example where a computationally intensive model has been packaged up in a way that enables widespread usage, makes the model more usable and doesn’t  sacrifice speed.

In this post we will describe the key technologies used to build the plant software. Continue reading →

Methods Beyond the Population

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Post Provided by SEAN MCMAHON and JESSICA METCALF

“Demography Beyond the Population” is a unique Special Feature being published across the journals of the British Ecological Society.  The effort evolved from a symposium of the same name hosted in Sheffield, UK last March. Both the meeting and the Special Feature were designed to challenge ecologists from a range of fields whose research focuses on populations.

The participants were charged with sharing how they are pushing the work they do beyond the stage where the population is the focus into research where the population is just the beginning and the focus spans scales, systems and tools. This encompasses a broad suite of biological research, including range modelling, disease impacts on communities, biogeochemistry, evolutionary theory, and conservation biology. The meeting was a great success, and this Special Feature should be equally valuable to the broad readership of the BES journals.

Methods in Ecology and Evolution has a special place in the Special Feature, hosting four papers. These papers not only introduce new efforts in population biology, they provide the methods that other scientists can use to implement them. With the tools provided by these four papers, researchers will be able to advance forest modelling, evolutionary theory, climate change biology and statistical inference of hidden population parameters.  Seriously good stuff! Continue reading →

Traits, community ecology and demented accountants

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McGill et al. (2006) argued that community ecology had lost its way. Shipley (2010) accused community ecologists of acting like a bunch of demented accountants. Strong words – so what’s the issue exactly?  And what can we do about it?

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Doing some end-of-financial-year field work? © Dannymanic

Their beef was that when studying groups of species and their environmental association, ecologists often were not thinking enough about the reasons for variation across species. (In this post we’ll focus on variation in abundance or in environmental response of abundance across species. We’re interpreting “abundance” loosely – counts, biomass, 1-0, whatever.)  While alternative methods are more readily available nowadays, “accountancy” is still common.

Continue reading →