Issue 11.4: Population Dynamics, Machine Learning, Morphometrics and More

The April issue of Methods is now online!

The latest issue of Methods in Ecology and Evolution is now online! This month’s issue is a little shorter than our last few. But, as they say, good things come in small packages!

Senior Editor Lee Hsiang Liow has selected six Featured Articles this month. You can find out about all of them below. We’ve also got five Applications articles and a Practical Tools article in the April issue that we’re going to cover. Those six papers are freely available to everyone – no subscription required!

On top of all that, the April issue includes articles on camera traps, land cover classification, presence-absence sampling and more.

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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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Issue 11.3: Tracking, Slicing, Classifying, Modelling and More

The March issue of Methods is now online!

The latest issue of Methods in Ecology and Evolution is now online! This month’s issue is a little shorter than our last few. But, as they say, good things come in small packages!

Executive Editor Aaron Ellison has selected six Featured Articles this month. You can find out about all of them below. We’ve also got five Applications articles in the March issue that we’re going to cover.

On top of all that, the March issue includes articles on 3D modelling, estimating plant density and more.

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Ultraconserved Elements are Widely Shared across the Tree of Life

Post provided by SILAS BOSSERT

Large-scale phylogenies are increasingly fueled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Large-scale phylogenies are increasingly fuelled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Sequencing ultraconserved DNA for phylogenetic research is a hot topic in evolution right now. As the name implies, Ultraconserved Elements (UCEs) are regions of the genome that are nearly identical among distantly related organisms. They can provide useful information for difficult phylogenetic questions. The list of advantages is long – among others, UCEs are:

A key reason for the method’s success is the developers’ commitment to full transparency, active tutoring, and willingness to help next-gen sequencing newbies like me to get started. Help is just a github-issue post away.

It took little to convince me that I wanted to use UCEs to reconstruct the phylogeny of one of my favourite groups of bees. I eventually met that objective but it won’t be part of this post. This blog post is about the journey to get there—the background story to the article ‘On the universality of target‐enrichment baits for phylogenomic research’. Continue reading

The Dark and Bright Sides of Phylogenetics and Comparative Methods

Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.

Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it! 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

2018 Robert May Prize Winner: Laura Russo

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2018 winner is Laura Russo, for her article ‘Quantitative evolutionary patterns in bipartite networks: Vicariance, phylogenetic tracking or diffuse co‐evolution?‘.

Plant-pollinator interactions are often considered to be the textbook example of co-evolution. But specialised interactions between plants and pollinators are the exception, not the rule. Plants tend to be visited by many different putative pollinator species, and pollinating insects tend to visit many plant hosts. This means that diffuse co-evolution is a much more likely driver of speciation in these communities. So, the standard phylogenetic methods for evaluating co-evolution aren’t applicable in most plant-pollinator interactions. Also, many plant-pollinator communities involve insect species for which we do not yet have fully resolved phylogenies. 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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Issue 10.4: Bayesian Models, Isoscapes, Camera Traps and More

The April issue of Methods is now online!

This month we’re thinking about hierarchical Bayesian models and Approximate Bayesian Computation, improving ecological niche models, and learning how to make our own Environmental Microcontroller Units (more on that below). We’ve got articles on Phylogenetics, Space (not outer space), Camera Traps and much more. Plus, there are six papers that are completely free to everybody, no subscription required!

Find out a little more about the new issue of Methods in Ecology and Evolution (including details about the bobcat on this month’s cover) below. Continue reading