10th Anniversary Volume 8: Phylogenetic tree visualization with multivariate data

Post provided by Guangchuang Yu and Tommy Tsan-Yuk Lam

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 8, we have selected ‘ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data‘ by Yu et al. (2016).

In this post, the authors share their inspiration behind the ggtree package for R and present new resources of ggtree and a series of other related packages.

The team publishing the ggtree paper is working in the field of emerging infectious diseases. Particularly the corresponding author Tommy Lam (TL) has been advocating the integration of different biological and epidemiological information in the studies of fast-evolving viral pathogens. The lead author Guangchuang Yu (GY) joined The University of Hong Kong to pursue his doctorate degree under the supervision of TL and Yi Guan (co-author in the paper), as he was very curious about the application of genomics and phylogenetics in the study of emerging infectious diseases.

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10th Anniversary Volume 3: paleotree: A Retrospective

Post provided by David bapst

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature on the Methods.blog. For Volume 3, we have selected ‘paleotree: an R package for paleontological and phylogenetic analyses of evolution‘ by David W. Bapst (2012). In this post, David discusses the background to the Application he wrote as a graduate student, and how the field has changed since.

I was a fourth year graduate student when I first had the idea to make an R package. Quite a few people thought it was a bit silly, or a bit of a time-waste, but I thought it was the right thing to do at the time, and I think it has proven to be the right decision in hindsight.

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O Problema com os ‘Fósseis Vivos’: Uma Perspectiva Filogenética Molecular

Blog escrito por: gustavo burin

This post is also available in English

Fóssil de caranguejo-ferradura (Museu de História Natural de Berlin)

Há alguns dias, me deparei com um interessante vídeo sobre os chamados “fósseis vivos”. O vídeo focou mais nos problemas de usá-los como argumentos contra a teoria da evolução, e aproveitei a oportunidade para falar mais sobre essas linhagens longevas.

Fóssil vivo‘ é um termo usado para descrever linhagens que acredita-se terem se originado há muito tempo e que mantêm características que se assemelham a seus parentes fósseis. Alguns exemplos bem conhecidos dessas linhagens são os Tuatara da Nova Zelândia (Sphenodon punctatus) e as árvores Gingkos (Gingko biloba).

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The Problem with ‘Living Fossils’: A Molecular Phylogenetic Perspective

post provided by: gustavo burin

Este post também pode ser lido em Português

Fossil of a Horseshoe crab (Museum of Natural History Berlin)

A couple of days ago I came across a nice video (in Portuguese only, sorry) about so-called “living fossils”. The video focused on the problems of using them as arguments against evolution. But I’d like to take the opportunity to talk more about these long-lived lineages.

Living fossil’ is a term used to describe lineages that are thought to have been around for a very long time and retain characteristics that resemble of their fossil relatives. A couple of well-known examples of these lineages are the Tuatara of New Zealand (Sphenodon punctatus) and the Gingko tree (Gingko biloba).

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Using Molecular Power to Reconstruct Hyperdiverse Food Webs

Post provided by JORDAN CASEY

Coral Reefs: The Ocean’s Most Extravagant Buffet

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

There are an estimated 830,000 species on coral reefs worldwide. At some stage in their lives, nearly all of these species are consumed as prey items. In this super diverse buffet of fishes, corals, crabs, worms, and other critters, the number of possible interactions between predators and prey is nearly inexhaustible.

The extreme diversity of coral reefs has fascinated naturalists for centuries. Pinpointing predator-prey dynamics is essential to fully understand coral reef ecosystem dynamics, and visual analysis of gut contents has been a staple technique of coral reef ecologists. While the joy of spending copious hours looking through a microscope at half-digested marine mush is undeniable, this type of visual inspection has limitations. Even so, visual gut content analysis (along with stable isotope analysis and behavioural observations) has showcased a highly complex dietary network.

To digest this extreme complexity and surmount the hurdle of dietary unknowns, researchers frequently lump fishes into broad trophic categories, such as ‘mobile herbivores’. Broad generalisations are pragmatic and may be help us detect broad ecological trends, but they oversimplify species’ actual dietary preferences. As coral reefs are changing due to anthropogenic disturbances, it’s critical to thoroughly examine how well trophic groupings capture dietary linkages among reef organisms. Continue reading

Early Spring: Predicting Budburst with Genetics

Below is a press release about the Methods in Ecology and Evolution article ‘On the importance of accounting for intraspecific genomic relatedness in multi‐species studies‘ taken from the Université de Montréal.

Bud of American beech (Fagus grandifolia). ©Tim Savas

Researchers from Canada and the USA found that tree and shrub genetics can be used to produce more accurate predictions of when leaves will burst bud in the spring. Their study was published in Methods in Ecology and Evolution.

Although climate sceptics might find it hard to believe with this year’s endless snow and freezing temperatures, climate change is making warm, sunny early springs increasingly common. And that affects when trees start to leaf out. But how much?

Simon Joly, biology professor at Université de Montréal and Elizabeth Wolkovich, an ecology professor at University of British Columbia, showed that a plant’s genetics can be used to produce more accurate predictions of when its leaves will burst bud in spring. Continue reading

Introducing fishtree and fishtreeoflife.org

This post was originally published on Jonathan Chang’s blog.

In our recent publication (Rabosky et al. 2018) we assembled a huge phylogeny of ray-finned fishes: the most comprehensive to date! While all of our data are accessible via Dryad, we felt like we could go the extra mile to make it easy to repurpose and reuse our work. I’m pleased to report that this effort has resulted in two resources for the community: the Fish Tree of Life website, and the fishtree R package. The package is available on CRAN now, and you can install it with:

install.packages("fishtree")

The source is on GitHub in the repository jonchang/fishtree. The manuscript describing these resources has been published in Methods in Ecology and Evolution (Chang et al. 2019).

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The babette R Package: How to Sooth the Phylogenetic BEAST2

Post provided by Richel Bilderbeek

 What is babette?

‘babette‘ is an R package that works with the popular phylogenetic tool BEAST2. BEAST2 uses one or more alignments and a model setup to create a Bayesian posterior of jointly estimated model parameters and phylogenies.

babette lets you call BEAST2 from an R script. This makes it easier to explore models and/or alignments than using the graphical user interface programs that BEAST2 provides. It will also help you to improve the reproducibility of your work with BEAST2.

babette Tutorial Videos

If you’re new to phylogentic analyses, the video ‘babette demo‘ demonstrates the package. It has all of the information that you need to be able to start using the package

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Phylogenies, Trait Evolution and Fancy Glasses

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

RPANDA: A Time Machine for Evolutionary Biologists

Post provided by HÉLÈNE MORLON

Yesterday saw the start of this year’s annual Evolution meeting and to celebrate Hélène Morlon has written a blog post discussing the amazingly versatile RPANDA package that she is developing with her research group. A description of RPANDA was published in the journal earlier this year and, like all our Applications papers, is freely available to read in full.

If you are attending Evolution, as well as attending the fabulous talks mentioned by Hélène below, do stop by booth 125 to see our BES colleague Simon Hoggart. Simon is the Assistant Editor of Journal of Animal Ecology and would be happy to answer your questions about any of our journals or any of the other work we do here at the BES.

RPANDA: a time machine for evolutionary biologists

Imagine “Doc”, Marty’s friend in Back to the Future, trying to travel back millions of years in an attempt to understand the history of life. Instead of building a time machine from a DeLorean sports car powered by plutonium, he could dig fossils, or more likely, he would use molecular phylogenies.

Molecular phylogenies are family trees of species that can be built from data collected today: the genes (molecules) of present-day species (Fig 1). They are often thought of as trees, in reference to Darwin’s tree of life. The leaves represent the present: species that can be found on Earth today. The branches represent the past: ancestral species, which from time to time split, giving rise to two independent species. The structure of the tree tells us which species descend from which ancestors, and when their divergence happened.

birds_phylog

Fig 1: The phylogenetic tree of all birds (adapted from Jetz et al. 2012). Each bird order is represented by a single bird silloutter and a specific colour (the most abundant order of Passeriformes, for example is represented in dark orange). Each terminal leaf represents a present-day bird species, while internal branches represent the evolutionary relationships among these species.

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