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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In Praise of Small Conferences

Post provided by NATALIE COOPER

Conferences come in many shapes and sizes, from mega-conferences like the Ecological Society of America (ESA) or Evolution with up to 5000 attendees, to small BES Special Interest Group (SIG) meetings with fewer than 100 attendees. There are pros and cons to both kinds of conference, but I’d like to take this opportunity to focus on small meetings*. Here are five reasons why I think they’re great, and why they’re particularly good for Early Career Researchers.

1. Networking is Much Easier

At a big conference networking can be really hard. Not only do you have to find the people you want to talk to, but you also have to compete with all the other people who want to talk to them! This is even worse if you’re also nervous about approaching them.

Networking more generally (i.e. without specific targets in mind), or just finding people to hang out with, can also be harder. Large meetings tend to cause groups to close ranks**. The sheer numbers of people around can make it really intimidating (there are some tips for networking at bigger meetings here). 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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Phylogenetic Tip Rates: How Well Can We Estimate Diversification?

Post provided by Pascal Title and Dan Rabosky

Analyzing diversification rate heterogeneity across phylogenies allows us to explore all manner of questions, including why Australia has such an incredible diversity of lizards and snakes.

Analyzing diversification rate heterogeneity across phylogenies allows us to explore all manner of questions, including why Australia has such an incredible diversity of lizards and snakes.

Within the tree of life there are differences in speciation and extinction rates over time and across lineages. Biologists have long been interested in how speciation rates change as a function of ecological opportunity or whether key innovations lead to increases in the rate of speciation. Exploring this rate variation and examining how clades differ in terms of their diversification dynamics can help us to understand why species diversity varies so dramatically in time and space. Learning more about the relationship between traits and diversification rates is especially important because it has the potential to reveal the causes of pervasive variation in species richness among clades and across geographic regions.

Several different classes of methods are available for studying the effects of species traits on lineage diversification rates. These include state-dependent diversification models (e.g., BiSSE, QuaSSE, HiSSE) and several non-model-based approaches. In our article – ‘Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?’ – we assessed the accuracy of a number of model-free metrics (the DR statistic, node density metric, inverse of terminal branch lengths) and model-based approaches (Bayesian Analysis of Macroevolutionary Mixtures, BAMM) to determine how they perform under a variety of different types of rate heterogeneity. The “tip rates” using these approaches have become widely used for a few reasons, including ease of computation and how easy it is to pair them with other types of data. Continue reading

The BES Macroecology (& Macroevolution) SIG: Who We Are, What We Do and What to Look Out for at #BES2018

Post provided by Natalie Cooper

Defining macroecology should be easy; it’s just ecology at large spatial scales, right? In reality though, it’s a little more complex than that. No-one agrees on exactly how large the spatial scale should be, and many studies that could be macroecology may also be defined as biogeography, landscape ecology, community ecology etc. Working at large spatial scales can also mean working at large temporal scales, often in deep-time. So there’s a lot of overlap with studies of macroevolution both on living and extinct species too.

This breadth of definitions means the BES Macroecology Special Interest Group (or BES Macro as we usually call it) has members with interests across ecology, evolution and palaeontology. Probably the most common statement at any of our events is “I’m not a macroecologist but…”. So, if you’re interested in broad-scale ecology and evolution, in a living or palaeo context, the SIG is for you, even if you don’t identify as a macroecologist! Continue reading

BES Macroecology 2018: Macroecology and Data

Post provided by Faith Jones

© Matthew Leonard

© Matthew Leonard

The annual BES Macroecology Special Interest Group conference took place on the 10th and 11th of July. This year the meeting was in St Andrews, Scotland. Over 100 delegates came together in this old University town to discuss the latest research and concepts in macroecology and macroevolution.

Remote Sensing, Funky Koalas and a Science Ceilidh

The conference opened with a plenary by Journal of Applied Ecology Senior Editor Nathalie Pettorelli from ZSL. She talked about how remote sensing can be used in ecological and conservation studies. In the other plenary talks, we heard from:

  • Methods in Ecology and Evolution Senior Editor Bob O’Hara from NTNU on, among other things, how useful occupancy models are when “occupancy” is such a broad term
  • Anne Magurran from the University of St Andrews discussing turnover and biodiversity change
  • Brian McGill from the University of Maine talking about the data-driven approach to the “biodiversity orthodoxy” and challenging the conventional wisdom about macroecological change

We also hosted a student plenary speaker, Alex Skeels, who gave a lively talk about diversification and geographical modelling using some pretty funky disco koalas. In addition to these talks, there were 60 short 5 minutes talks and 20 posters. Continue reading

At Last, a Paleobiologist is a Senior Editor for Methods in Ecology and Evolution!

Post provided by Lee Hsiang Liow

An Asian, female Senior Editor under 45? Progressive! I have loved Methods in Ecology and Evolution since it appeared in 2010 and am thrilled to have been selected to join Rob, Bob and Jana to help with the journal’s continued development.

OK, so you want to know who the new Senior Editor on the MEE block is.  I’m just another scientist, I guess. On the outside, we look different but on the inside, we’re all the same. (OK, perhaps we are a little different, even on the inside, but that makes life and research interesting, right?)

Here’s my academic life history: I did my Bachelors thesis on the systematics/phylogenetics of an obscure group of marine pulmonate slugs with one of the greatest Icelandic biologists I know, Jon Sigurdsson, at the National University of Singapore. I followed this up with an almost-half-year stint at the Museum of Natural Science in Berlin as a “nobody”, digitizing data. Then I won the academic lottery and headed up to Uppsala to do my masters in conservation biology on tropical pollinator diversity, (un)supervised by two amazing supervisors that never met each other, the late Navjot Sodhi (National University of Singapore) and Thomas Elmqvist, now at Stockholm University. Continue reading

Decoupling Functional and Phylogenetic Dissimilarity between Organisms

Francesco de Bello describes the main elements of the method he has recently published in Methods in Ecology and Evolution. The method aims at decoupling and combining functional trait and phylogenetic dissimilarities between organisms. This allows for a more effective combination of non-overlapping information between phylogeny and functional traits. Decoupling trait and phylogenetic information can also uncover otherwise hidden signals underlying species coexistence and turnover, by revealing the importance of functional differentiation between phylogenetically related species.

In the video Francesco visually represents what the authors think their tool is doing with the data so you can see its potential. This method can provide an avenue for connecting macro-evolutionary and local factors affecting coexistence and for understanding how complex species differences affect multiple ecosystem functions.

This video is based on the article ‘Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly‘ by de Bello et al.