Posts Tagged ‘phylogenetics’

A recipe for collaboration

A recipe for collaboration

By EcoEvo@TCD | News, Research

Recently, along with Adam Kane, Kevin Healy, Graeme Ruxton and Andrew Jackson, we published a review on scavenging behaviour in vertebrates through time in Ecography. This paper was my first review paper as well as my first paper written from afar, without ever actually meeting in a room with the co-authors for working on the project. Difficulty: * Preparation time: 5 month to submission Serves: 5 people (but any manageable number of people who you like working with will do) Ingredients: An exciting topic: For this recipe you will need an exciting topic. In this case, prior [&hellip

Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association

Ecology & Science in Ireland: the inaugural meeting of the Irish Ecological Association

By EcoEvo@TCD | Research

In the years to come, 140 ecologists working in Ireland will look back with fond memories of being part of the inaugural meeting of the Irish Ecological Association (24th-26th November). We will remember hard-hitting plenaries, compelling oral presentations, data-rich posters, influential workshops and the formation of the IEA’s first committee. The lively social events might be harder for some of us to remember… There could not have been a more fitting way to open the conference than the plenary seminar from Professor Ian Montgomery (QUB) on Thursday night. Within the hour, he managed to given an incredibly [&hellip

The Skeleton in the Closet

The Skeleton in the Closet

By EcoEvo@TCD | News, Research

After a few ups and downs, everything you always wanted to know about the effect of missing data on recovering topology using a Total Evidence approach is now available online (Open Access)! This paper also treats many different questions that people might be interested in (Bayesian vs. ML; how to compare tree topologies; comparing entire distributions, not only their means and variance; and many more!) but I’ll leave it to you to discover it… Back on track, more than one an a half CPU centuries of calculation ago, Natalie and myself wanted to build a Total Evidence tip-dated [&hellip

Do you speak Yamnaya?

Do you speak Yamnaya?

By EcoEvo@TCD | Research

I bet you do! One nice non-biological thing you can do with phylogenetics (unlike beers) is study the evolution of languages. If you aren’t familiar with evolutionary linguistics, it’s basically the same principles that we use to study the descent with modification of organisms but applied to words. Even though words do not evolve in a biological way, we can still apply similar phylogenetic principles by just adjusting the evolutionary models. OK but let’s go back to my assumption (that you do speak Yamnaya). Since you are reading this blog post that I’m trying to write in [&hellip

The more the better?

The more the better?

By EcoEvo@TCD | Reviews

These days I’m writing up the discussion of my sensitivity analysis paper on missing data using the Total Evidence method (more about it here and here). One evident opening for proposing future improvement on my analysis is the obvious “let’s-do-it-again-with-more-data” one… But a recent Science paper by Jarvis et al made me reconsider that. Is more the always better? Jarvis and his numerous colleagues just published one of the biggest bird phylogenies that contrasts with the previous reference one (by Jetz et al in Nature). In Jetz’s paper, the authors were interested in the relations among modern [&hellip

A Rose by Any Other Name

A Rose by Any Other Name

By EcoEvo@TCD | Perspectives

Carl Linnaeus has a lot to answer for. As a young medical student he became obsessed with botany, then a necessity as most medicines were derived from plants. At the time the naming of plants was a rather haphazard affair, some names were given to multiple plants, others could be many words long. It all made for great confusion and difficulty disseminating information. In an attempt to manage the situation, in 1735 he published the first edition of his masterpiece of classification, the Systema Naturae. Most people remember this book as being the first time that plants [&hellip

Hopsolete Trees

Hopsolete Trees

By EcoEvo@TCD | Perspectives

One of the most unusual benefits of being in Ireland from a Southern French PhD student’s perspective is not so much the rain and the pronounced taste for culinary oddities (some weird, some excellent) but the awesome trend towards a new age of craft beers (and I’m not mentioning the pillar of Irish pub culture). Looking at the increasing beer richness available in any decent pub/off-licence, I was inspired to combine two of my passions: beer-related stuff and phylogeny-related stuff. Despite an honourable attempt by J.L. Brown, I would like to discuss the three reasons why it’s [&hellip

School of Natural Sciences Postgraduate Symposium 2014: Part2/4

School of Natural Sciences Postgraduate Symposium 2014: Part2/4

By EcoEvo@TCD | Research, Seminars

On the 20th and 21st of February we had our annual School of Natural Sciences Postgraduate Symposium. Over the course of two days many of our PhD students presented their work to the School. We also had two interesting plenary talks from Dr Sophie Arnaud-Haond (Ifremer) and Dr Lesley Morrell (University of Hull). Unfortunately our third speaker, Dr Fiona Jordan (University of Bristol) had to cancel due to illness. For those of you who are interested in exactly what we work on here at EcoEvo@TCD, here are the abstracts from the PhD student presentations. Check out the TCD website for more details! Aoife Delaney: Eco-hydrology of [&hellip

A brave new world of monkeying around with trees

A brave new world of monkeying around with trees

By EcoEvo@TCD | Perspectives, Research

I’ve spent the last few days writing an introduction for my first PhD paper on the practical issues of adding fossils to molecular phylogenies (full recipe here). This is my starting point: most people working in macroevolution agree that we should integrate fossils into modern phylogenetic trees. Of the many possible methods that are available, Ronquist’s total evidence method looks to be the most promising (however, some nice other ones also exist). Recently Schrago et al. published a nice attempt to use this method on the Plathyrrini (New-World monkeys to you and me): As a reminder, the [&hellip

The Placental mammal saga; special summer double episode

The Placental mammal saga; special summer double episode

By EcoEvo@TCD | Reviews

As I wrote in a previous post last winter, O’Leary et al. added their oar into the Placental Mammal origins debate. For anyone who missed that episode, they argued, with the backing of masses of morphological data, that placental mammal orders appeared right after the extinction of non-avian dinosaurs (also known as the explosive model). This was in opposition to two other views based on DNA data which argue that placentals appeared way before (long-fuse model) or slightly before (short-fuse model) the Mexican dinosaurs had to deal with some meteorite… Again, have a look at this previous [&hellip