phylogenetics

Change (your seed size) fast and multiply

Our latest paper examining the role of life history traits in explaining the vast unevenness of species diversity across the flowering plant Tree of Life has just appeared online at PLoS Biology.  The paper was led by Javi Igea and emerged from a very successful BBSRC DTP rotation project by Eleanor Miller, in collaboration with Alex Papadopulos.

Using the largest available phylogenetic tree of plants coupled with an unparalleled trait dataset, we analysed how seed size and its rate of change across the phylogeny were correlated with the rate of species formation.  Seed size is crucial to plant evolution because it confers adaptation to different environment conditions and influences many other aspects of life history, including dispersal, resistance to stress, and colonisation potential.  We subsequently found that faster rates of seed size change were associated with faster rates of speciation, probably by fostering the appearance of reproductive barriers between lineages.  We also found that smaller-seeded species speciated faster than larger-seeded ones.  These results underscore the importance of morphological traits, and particularly their rate of evolution, in promoting species divergence across one of the largest radiations of organisms on the planet.

Although it has taken a bit longer than we would have liked – no thanks to some poor timing with #BAMMgate – the paper brings together an impressive toolbox of complementary macro-evolutionary analyses to deliver a compelling explanation for one of nature’s enduring mysteries.  Well done all!

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Rewinding the Tape of Life

Journal of Ecology Blog

If evolution happened anew, what would the present-day plant world look like?  That is, would the randomized processes that govern evolutionary change tell a different story? And particularly for plants which are sessile organisms, is the starting point of ‘who gets there first’ the most important of all?

Priority effects – the order and timing of species arrival into local communities – can affect ecological community structure and functioning, with profound effects for species persistence and ecological interactions (Chase et al., 2000; van de Voorde et al., 2011). As such, the arrival of different species at different times can dramatically alter the evolutionary tapestry of any given system on ecological time frames, but also in evolutionary time. In particular, the diversification of early arriving species can pre-empt available niche space to prevent the establishment, dominance or diversification of species that arrive later on down the road.

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Explaining the origins of species diversity

The July 2015 issue of New Phytologist has come out and its a doozy!  The entire issue features work on evolutionary plant radiations, drawing together a range of papers that summarize the current state of knowledge about “where, when, why, and how” plant radiations happened.  An editorial by Colin Hughes, Reto Nyffeler Peter Linder outlines the content of what will surely be a landmark issue for years to come!

Many, if not all, of these papers were presented at a symposium organized in Zurich that we attended with our New Zealand collaborators Professors Bill and Daphne Lee in June 2014:

We're somewhere in the crowd

We’re somewhere in the crowd …

For me, this was possibly one of the most intellectually stimulating meetings that I’ve ever attended.  Talks drew major figures in plant ecology, evolution, and systematics and really pushed the boundaries out on ‘diversification’ research.  The field itself is still arguably quite new, with many of the key questions synthesized in a 2008 paper by Peter Linder.  In fact, we have a PhD studentship available to follow-up some of these questions and build on what we talked about at the meeting.

You might have noticed that we even have a contribution in the New Phytologist Special Issue.  Our paper tests the mechanisms by which plant evolutionary radiations emerge and influence ecological dynamics.  We apply more of our expertise in structural equation modelling to focus on 16 species-rich genera in the alpine zone of New Zealand.

Diversity in New Zealand’s alpine.  Celmisia, Chionochloa, Dracophyllum, and Veronica all appear in this photo.

One of the most exciting aspects of our paper is that we’ve tried to reconstruct the niche space that each genus has occupied over the last 20 million years.  This is fairly ambitious and has involved tasks like reconstructing sea surface temperatures through the Cenozoic from isotopic measurements of foraminifera deposited in marine sediment cores, and then using these to estimate past land temperatures.  We’ve also had to consider that the alpine zone has grown immensely over time with uplift of the Southern Alps.  To do so, we collated radiometric dates of rocks and tried to infer their rate of uplift since the Miocene.

Overall, our results suggest that genera that colonized New Zealand earlier encountered more ‘vacant’ environmental space, which promoted species diversification and further occupancy of the environment.  Genera that occupied more environmental space were subsequently more dominant in present-day vegetation plots.  The key message is that time not only explains why diversity arises, but how this diversity influences ecological dynamics.  The Special Issue has many other fabulous papers, so do check it out!

Why do zebras have stripes?

 

The function of zebra stripes by Tim Caro et al. just published in Nature Communications is a neat paper that I came across this afternoon and felt like sharing.  It does a good job demonstrating the power and simplicity of comparative analyses.

 

Essentially, why zebras have stripes has been an elusive riddle for over a century.  Caro et al. set out to solve this once and for all.  They tested whether striping has arisen due to camouflage, as an anti-predator disruption, for heat management, or to benefit social interactions.  But it is their fifth hypotheses – avoidance of biting tsetse flies – that seems to gain the most support.  This came from predicting striping on different parts of the zebra’s body simply by fitting phylogenetic generalized least-squares models with different covariates.  It goes a long way to show how a well-founded set of hypotheses around the function of traits and morphological characters can be inferred from modelling observational data.  Although there is no substitute for a good experiment, like placing model horses in fly-infested fields, experiments that test multiple co-occurring mechanisms are challenging!

Harnessing the Tree of Life for conservation

I spent Monday in London at The Royal Society for a discussion meeting on Phylogeny, extinction risks and conservation.  As someone who is increasingly using comparative phylogenetic tools to ask how evolutionary history might influence conservation decisions, I took away at least three points (several more rattling in my mind at present):

(1) Measures of phylogenetic diversity are increasingly being used to inform conservation decisions (or at least that was the perception I got).

Perhaps the most notable way this is being done is through the EDGE (evolutionarily distinct globally endangered) programme.  EDGE classifies species based on the product of their IUCN Red List category and their evolutionary distinctiveness (ED).  ED is itself calculated by dividing the lengths of each branch in a phylogenetic tree by the number of species that subtend that branch.  These values are then summed for all the branches from which a species is descended.

(2) Risk of extinction is fairly clustered within evolutionary lineages – and this can lead to rather large losses in phylogenetic diversity (PD).  Losing PD may reduce ecosystem function and limit the range of biodiversity features that can respond to future change – if in fact there is an association between PD and function – though this is debatable.

This of course also assumes that closely-related species are more likely to go extinct because they share similar traits that make them more vulnerable to threats.  Large mammals are an excellent example of such a group.  But this might not be true for plants, particularly in areas with rapid diversification where species most classified as threatened are the recently-evolved ones that cluster within short branches at the tips of phylogenies.

(3)  Systematists are developing great new tools for assembling dated phylogenetic trees.

We heard about two specific resources.  The first was TimeTree, which is essentially a curated database collating all published estimates of divergence times among organisms.  By visiting the website, you can instantly search for a divergence time between any two species and find all published estimates, allowing you to not only get a date but also a statistical distribution for that estimate.  Unfortunately this means that its only as good as the primary literature and the curators’ ability to keep up with it.  I tried it quickly for two of our NZ alpine species (Ourisia macrocarpa and Veronica odora) but was told that “No molecular data available for this query”, which was surprising considering they do exist.

The second resource we heard about was the Open Tree of Life.  As the name says, it’s essentially trying to assemble a giant “tree of life” that will be continuously updated by the scientific community.  This is a really nice complement to TimeTree because rather than focusing on branch lengths, it’s just concerned with synthesizing tree topologies.  You can begin to explore the tree here.