The evolution towards a post-doctoral research

The first snows of the 2014 also brought the first roundtable of the year. This month Ivan Gomez-Mestre has spoken with the PhD students about his scientific interests and his scientific career.

Ivan started the meeting introducing the field he is dedicated to: evolutionary biology. He explained the most important arguments to understand the great biodiversity that we find both at a micro- and macro-evolutionary scale. He started with a retrospective look, comparing elements of the classical evolutionary theory with the new knowledge that incorporates the extended synthesis, such as environmental induction of gene expression through epigenetic regulation.

Moreover, he presented many examples showing the evolution of phenotypic plasticity as a possible mechanism to understand the great diversity observed in nature, arguing that it cannot be solely explained via gradual accumulation of mutations in protein coding genes. It is not only the genes we have, but also the way they are regulated, that determine the phenotype. The most extreme phenotypes are normally expressed by the most plastic genotypes. The plasticity evolution via genetic accommodation can ultimately lead to new species.

Furthermore, Ivan passed some advice regarding the postdoctoral period. He suggested to find a highly motivated advisor, possibly in his/her tenure track. It is a time to be productive while trying to maintain a coherent and personal line of research. He also spoke about how he formed their current research group after obtaining the Ramón y Cajal contract and how important it was. He thinks that a scientific career is a long-term quest that has to be enjoyed as much as possible along the way.

So, Ivan’s tips for after the thesis were:

–       Enroll in a dynamic group whose advisor is productive and enjoyable.

–       Investigate what you enjoy and that you feel you have more questions to answer.

–       Never stop improving English.

–       DO NOT GIVE UP!! The Spanish science situation will get better!!

 

Link to the group’s website: http://www.gomez-mestre.net/Home.html

By: Pablo Burraco and Rosa Arribas

 

Macroecology at ETH-Zurich

For a couple of months I’ll be in Zurich visiting Levine’s Lab. I came to work with one the post-docs of the group, Jeff Diez, who I met in my first year PhD at University of Michigan. We are currently working on identifying niche shifts of non-native species between the native and the invaded range. You can have a look at a similar study recently published in Science where they found that plant niches are rather conservative between both ranges.  We’re going to build upon their methods using Oxalis pes-caprae  (soursop EN, vinagreta ES, suring AF) as our model species. As it is a ruderal species in both native and invaded range we expect not only to analyze climate shifts but also disturbance and habitat type. So far the analyses are looking great and we already found some niche changes. They aren’t amazingly huge but reflect a trend towards more disturbed sites in the invaded range than in the native one.

Besides my work, I am learning a lot about the projects currently running on the lab. They have very interesting projects about spread of invasive species, competition… Specially they have one on the Calanda mountain near Chur, where using transplanting experiments they try to understand the relative importance of biotic interactions and climate for shaping species’ responses to climate change. I was impressed by the amount of work and resources this project have. Even they had an helicopter to help with the transplanting and during the growing season they are every week up there measuring survival, growth and many more things. I am trying to implement a similar experiment on Sierra Nevada, of course without such amount of resources. Everything will depend on how good I am doing with my PhD, the support of the Ecology Lab from Granada and the required permits. Anyway it seems a really good approach to test how well invaders will perform in future climates. You can have a look at the whole set up of the experiment in this video.

And of course, everything isn’t research while abroad. Zurich is a lively city full of activities, a great lake to hang around and enjoy, gorgeous mountains to hike nearby and really nice people. Of course, prices are really high here. For example I got a very cheap room for Zurich standards in a shared apartment for only 400€ a month! Considering that it isn’t in downtown it’s more than double what we’re paying back home in Sevilla. Anyway there are always cheap ways to enjoy the city such as making barbecues close to the lake or the open air festivals that every weekend some neighborhoods are organizing. Definitely, Zurich is a fancy and expensive city where you never can get bored but at the same time the mountains around and the impressive amount of green areas make you feel in a very comfortable place to enjoy why not, a very well paid post-doc!

PhD seminars – A little bit of “human” science

Due to the closeness of the summer, the round table scheduled for July has been brought forward to this week. This time our invited researcher was Curro Braza, from the department of Ethology and Biodiversity Conservation at the EBD.

Curro has focused his carrier on the behavior of mammals in their natural environment. He started his carrier working with ungulates, he then moved to primates and for the last twenty years he has been working with humans. Being humans his study species, apparently, makes him a kind of rara avis at the EBD. Therefore, we wanted him to tell us about his research and the similarities and dissimilarities that the methodology he employs with humans has with the one that we employ with our study species and systems.

Ending up working with humans was for Curro the natural outcome of a carrier focused every time in more intelligent and alimentary efficient species. However, it also implied a qualitative change in the literature he reads, that now embraces areas of Psychology, Physiology, Neurophysiology and Anthropology.

The main objective of his research is to detect social behaviors in children of four-five (sometimes up to 11) years old that could be early signals of certain future risk behaviors (aggression, depression, anxiety) or syndromes (e.g.  autism). The underlying idea is that behaviors that are observed in children irrespectively of their origin, culture, education, etc. might have an adaptative meaning andthere might be mechanisms to minimize their deleterious effects. In that sense, he is currently involved in a study about bulling in schools, a worldwide extended behavior that shows and increasing trend.

To illustrate the similarities and dissimilarities in the methodology he employs, Curro presented us one of his latest papers: “Girls’ and boys’ choices of peer behavioral characteristics at age five” (this and his other publications are listed in http://www.ebd.csic.es/WebSite1/ZEsp/Publicaciones/PublicPersonales.aspx?id=%27000000D6%27). As Curro told us, his work is not that different from ours and we could make some analogies with the Material and Methods section of our studies:

Study species = children of four-five years

Study site = schools’ playgrounds

Selection of study sites = meetings with directors, teachers and parents

Sampling data = films of children interacting, surveys and saliva samplings (for hormone tests)

Response variables = frequency of certain play and behavioral patterns

Independent variables = sex, social status, parental group, levels of certain hormones, etc.

 

Of course, during the round table many curiosities and questions about the results and conclusions of Curro’s investigations arose, but that would need another post…

 

by Ana Montero 

PhD seminars – Tips for scientific writing

This month we hosted a round table discussion led by Carlos Herrera, who chatted with us about how to write scientific papers. We all have the task to communicate our results and the truth is that, even if theory of writing seems easy, the first time we face it, it is not.

Carlos told us that the first thing we need before start writing is a story. It could be something new that we discovered, something that no one did before or something that changes a view or a paradigm. You may describe it, broadcast it and it must be verifiable.

Everything started four centuries ago, in 1665, with the publication “Philosophical Transactions of the Royal Society“. For instance, Leeuwenhoek or Darwin used to publish there. And the aim has always been the same, communicate your story. What has changed is how, where, the style, the trend, etc. all of these things are secondary but also important.

When we have our story, the first thing before starting to write is having a clear idea of what are we going to say. If you don’t, a good advice is to read, read a lot of everything! Even of those papers that are opposite to yours because they will set your brain on fire. It’s common to have good ideas while reading or when we’re doing research, never waste this enlightenment! Write it down wherever you want, a notebook, on the edge of a sheet,… but if you don’t you’ll lose it and never will come back!

A good headache is the introduction – How to give the exact importance to our work? We don’t want to be pretentious and neither underestimate it. However, when starting to write this is difficult to know, so a good thing to take into account is to choose our publication thinking of our public and then decide how to write or ask for advice to our supervisors. Publishing in journals you read will be a sure shot too, as you may like the contents in them.

Another problem is to decide which ideas should be included in the introduction and discussion sections. Carlos advised us that if you hesitate, it must go on the discussion. What’s more, it is useful to do so, because later you can connect introduction and discussion by these points. Remember, in a common paper, an introduction should never have more than three pages. So all that excess could go in the discussion! If you don’t know how to start the discussion, mention those points from the introduction.

Finally, Carlos commented some common errors in PhD students. We usually fail to put things in a logical order (I must admit I did it today) and we don’t connect a chain of structured ideas. We also tend to concentrate only in one hypothesis but we have to strive to be the devil’s advocate! All the alternatives hypothesis we are able to think about might be recorded in the discussion, an ounce of prevention is worth a pound of cure!

PhD seminars – Good oral presentations make you shine

One of our biggest problems is to talk in public, and even if after college and a few seminars we overcome this, there is still a long way to achieve the main goal: to appeal public and make them learn something of your work.

That’s why we decided to organise a round table about how to do oral presentations and Jordi Bascompte was our month’s guest. He and his group work on networks of ecological interactions and spatial dimension of population –the architecture- and community dynamics; all within the framework of conservation biology.

But Jordi is not only a good researcher, he is also a good speaker and he proved that during our round table. He prepared a document with tips that I’m going to use -and slightly modify- for this post. And here they are!

I. Some simple rules

1. Be brief. As a rule of thumb, use three quarters of the time allocated (e.g., no more than 45 minutes for a presentation of an hour). Brevity is the mark of distinction of great presentations. Indeed, several sociological studies conclude that we can keep our concentration up to between 4 and 10 minutes, and never more than 20 minutes. Never use more time than allowed.

Everybody hate when someone surpass the scheduled time, so never do so, it’s a deadly sin! If it happens that you have to speak longer than 20 minutes, try to plan your speak in blocks, so when concentration is decaying you change of topic and everybody will listen to you again. You can use those topic-change breaks to answer questions.

2. Think of the presentation as a story. It should have a logical flow that works its way smoothly towards a good ending. Never use it as an enumeration of an independent collection of papers.

The audience will find your speech intriguing. As magic for magic is important the economy of moves, for lectures is the economy of text.

3. Less is more. Do not overload your talk with too much information. Actually, the more information you provide, the less will the audience remember. Never conclude with more than three points. Do not overload visuals: be clear, be simple.

Don’t include all you now and you did, we have to make an effort- a selection exercise. It’s useful to keep information because it could be used during debates.

4. Make the take-home message persistent through the talk and at the end. Use a powerful last slide.

This is what people will remember, we draw it for them. Mainly, we retain what is said at the beginning and at the end. Bear in mind that this message is one sentence, not the conclusions.

5. Use analogies.  They are the most powerful way to deliver complicated ideas.

Use them prudently, too much would end in a very simple, childish concept.

6. A talk has a different format than a paper. Use a different language, e.g., do not write little sections of a paper, but speak about them while highlighting a good visual. Try to avoid writing too much in slides and never read your talk. Walk the audience through a complex figure or equation. Only then make the point.

This is the other speeches’ deadly sin. As a book is different from a based film, your talk must be different from your paper. Too much text indicates lack of experience, knowledge and self-assurance. If the audience have to read, they won’t listen to you. Also try to coordinate what you say with what you show and explain figures before saying the conclusion.

7. Face the audience. Make eye contact, move around the stage, and avoid hiding behind podiums or desks.

Take into account that body language and acting behaviour will mean more than your words. Technologies, such as wireless presenters, help you to control the space. Another tip is to ask for a lapel microphone to avoid fixed microphones.

II. Sources and further information

Jordi gave as a few resources that could help us to improve.

1. TED talks. A great selection of oral presentations given by outstanding speakers. See as many as you can and keep asking yourself: What makes of this a good oral presentation? Two of his own top choices are Steve Job’s speech during a graduation ceremony at Stanford (“How to live before you die”) and Ken Robinson’s talk on “School kills creativity”.

2. Alvarez Marañón, G. (2000). El Arte de Presentar. Gestión 2000, Editorial Planeta. An excellent guide on crafting outstanding talks, from the planning and design to the delivery.

3. Bourne, P.E. (2007). Ten simple rules for making good oral presentations. PLoS Computational Biology, 3: e77.

4. Tufte, E.R. (1990). Envisioning Information. Graphics Press. A beautifully illustrated book on how to plot information in a visually arresting, easily to understand ways. Statistics meets art.

Call for proposals for transnational access to Doñana

AIMS

ExpeER (Distributed Infrastructure for Experimentation in Ecosystem Research), through its coordinated programme of Transnational Access (TA), aims to improve and facilitate access to state-of-the-art research facilities throughout Europe, promoting observational, experimental, analytical, and modelling approaches in ecosystem research.

The deadline for TA applications to be submitted is the 31st July, 2014.
The deadline for TA visits to be completed id the 30th Sep, 2014.

SUPPORT OFFERED

The TA programme offers external users free access to the 31 ExpeER research sites (including DOÑANA) and facilities as detailed in the TA site description sheets including a contribution to users travel and subsistence costs. Users are encouraged to refer to the “infrastructure” part of the ExpeER website for detailed descriptions of each facility, including the modality of access, the offered services and any individual conditions.

“FAST TRACK” APPLICATION PROCESS AND UPDATES TO REVIEW PROCESS       

ExpeER offers “Fast Track” transnational access applications to researchers interested in *visiting one or more TA sites for a brief

period (max. 5 days)*. “Fast Track” applications aim to facilitate researchers wishing to perform basic activities (e.g. short sampling

campaigns, measurements, run a small experiment, access data archives, etc). In contrast to the regular application procedure (i.e. short

pre-application detailed full application), only a brief application (max. 1 page). Application procedures can be found here.

PhD Seminars – The importance of “WHAT?”

April’s roundtable was chaired by Eloy Revilla, scientific researcher at the Conservation Biology Department. He chatted with us about his own scientific career and how it evolved from his thesis times, struggling to know “life and miracles” of the Eurasian badger in Doñana, to the “modeling world” in which he is more immersed now.

This apparently big step is just a question of focus, his piece of advice was not to concentrate just on our study system but to go beyond and find the common characteristics that this system has with something more global. We sometimes are too worried about proving the singularity of our system trying to differentiate from the rest to enhance its value, forgetting that it could be even more valuable if we could transgress with our findings to something more general. (Look at your thesis data again… maybe you are able to find a common methodology for sampling in a determined biome, or design a model to predict probability of presence of your study species which has not been used before!)

The important thing is the researching question and not the system itself.

He encouraged us to not being afraid of apparently arid tools as programming languages, which can help us to do exactly what we want and not only “canned functions” wrapped in fancy programs that we often don’t know what are exactly doing. Programming is a versatile tool useful in many fields, and the maximum abstraction with which we’ll be able to answer nearly any ecological (and not) question. However, if Math are not your piece of cake, don’t despair, Wilson have other suggestions for you ;).

The important thing is the “WHAT?” and not the “HOW?”. If you don’t lose your objectives, many ways of solving your problem will come out (maybe in the form of lines and lines of code in strange languages that you thought were just for those computer geeks at the Informatics faculty).

Barriers or corridors? The overlooked role of unpaved roads in endozoochorous seed dispersal

After almost three years of fieldwork in the Doñana National Park, the results of our research are coming out.

We are assessing the effects of widespread human structures (specifically trails and firebreaks) on plant-animal interactions and how this third-order interaction affect plant communities and landscape structure. These human-made linear structures represent weaker landscape alterations than paved roads and highways, having probably subtle and unknown ecological effects. Therefore, we termed them “Soft Linear Developments” (SLD).

We found that, as a kind of avenue, SLD can promote the movement of some mammals such as rabbits and foxes, which positively select SLD verges for defecation. Interestingly, these mammals are usual fruit consumers, and often disperse countless viable seeds within their faeces, acting as natural gardeners. In the picture, a rabbit letrine placed in a SLD verge. On the left side, two small saplings of one typical rabbit-dispersed shrub in the area (Juniperus phoenicea subsp. turbinata) are growing.

Through such seed dispersal service, these animals can contribute to the creation and the expansion of plant populations along SLD verges and probably also along their surroundings. Thus, SLD verges can act as seed and plant corridors, helping to connect isolated plant populations.

As long as the community includes seed dispersers that positively select SLD for defecation, these structures can be used as management tools to promote reforestation of humanized landscapes, as well as to identify invasion pathways of mammal-dispersed alien plants. Prior to SLD construction or removal, we suggest to careful consider their potential advantages and disadvantages. Given their important ecological role in plant restoration, we suggest cautious management of seed dispersing wildlife (for example the red fox, in the picture, is severely hunted worldwide, despite they provide an important service for plant populations) and SLD verges (avoiding the use of herbicides and destructive mechanical methods).

These intriguing results have been recently published in the Journal of Applied Ecology, and are already available in “Early view”. You can see the abstract and get a pdf copy in the following link: http://onlinelibrary.wiley.com/doi/10.1111/1365-2664.12080/abstract

If you do not have access to the journal, please do not hesitate to ask me for a copy (suarezesteban.a@gmail.com).

In addition, you can find a great summary of our paper in the volume 496 (401) of Nature, in the “Research highlights” section. We hope to keep increasing our knowledge about the effects of human activities on terrestrial ecosystems, in order to improve their management and conservation, which is undoubtedly needed.

We are in debt with many people that, in one or another way, helped us to collect, process and present the data. We want to especially thank Gemma Calvo and the staff of Doñana Biological Reserve and Doñana Biological Station for they support.

Alberto Suárez-Esteban

https://sites.google.com/site/asuarezesteban/home

Landscape context modulates alien plant invasion in Mediterranean forest edges

A highly invaded forest patch

We have recently published a paper on Biological Invasions which is my first PhD chapter! In this study we tried to understand the influence of landscape and local characteristics on biological invasions by exploring the level of plant invasion and alien species traits in forest edges in the highly urbanized landscape of the Vallès county (Catalonia, Northeast Spain). Overall we found landscape characteristics the most important determinant of the level of invasion in the forest edge and interior and the type of exotic species we can encounter. This finding suggests that invasion at these sites is a dynamic process primarily related to the propagule pressure from the surrounding landscape. High human-alteration of the landscape contributes to further expansion of alien plant species from forest edges into the interior. The global trend towards forest fragmentation, which increases the length of the interfaces between urban and forest areas, will exacerbate plant invasions by gardening species (Martin et al. 2009).

A bit of methods:

Sampling protocol (Nuria Gassó)

The CREAF team (Nuria Gassó and Joan Pino) identified all plant species in 73 paired plots in the edge and 50 m towards the interior of the forest. For each plot they also collected information about the local chracteristics: habitat and edge type and disturbance regime. We maybe missed information about light availability using the density of trees or LAI but edge type was valid proxy. Once in the office we calculated the landscape variables (% land-cover type and road distance) using GIS.  Then I explored the association between alien species richness and similarity in species composition between edge and interior plots with landscape and local variables, using generalized linear models and variance partitioning techniques. I found this last technique very useful because it can separate the importance of several group of variables, landscape and local variables in our case. I took the idea from a paper of Martina Carrete and customized the R function varpart from the VEGAN package. Definitely messing up R codes is the way to learn this powerful tool!

Management conclusions:

A priori it is very useful to identify which exotic species could become successful invaders. In fact, the analysis of plant traits related to invasiveness has been one of the main focuses in invasion biology (Hayes and Barry 2007) and the basis for invasion risk analyses. However, identifying general patterns is complicated as many plant traits associated with invasion are dependent on the habitat type and the stage of invasion. Our results indicate that these risk analyses should also include characteristics of the landscape matrix of the recipient region because successful or more abundant alien plant traits are likely to be different depending on the surrounding landscape (Vilà and Ibáñez 2011). For example species of Mediterranean origin and introduced for agriculture were associated with higher agriculture use in the landscape (very obvious but not tested yet).

Once on the field, management of plant invasion must also consider the landscape adjacent to natural areas in order to reduce the propagule pressure from human-derived land-uses. Possible landscape management measures could include changes in gardening practices or constant monitoring of plant invasion in urban-forest interfaces.

Carolina Soto Navarro

Hi everybody!

I´m Carolina Soto and I’ve just finished my PhD at Conservation Biology Department. Along with my supervisor Dr. Francisco Palomares Fernández we have explored how habitat selection patterns are influenced by differences in species’ ecological traits and by inter-specific interactions using as a model of study a carnivore guild in the Mediterranean protected area DoñanaNational Park.

We have explored the ecological structure of the carnivore community using methods aiming at analyze niche segregation between species and we have analyzed how species in upper positions at the guild affect negatively the habitat selection patterns of species with lower competitive advantages, displacing them potentially to suboptimal habitats called “refuges of predation”.

In parallel we have analyzed the incidence of domestic species such as the domestic dog in the protected area. The presence of domestic species in natural areas is an increasing world-wide conservation concern. These species represents a conservation problem due to competition, predation and/or disease transmission to native species and there is a huge demand for more knowledge about and experience with this type of situation in order to help prevent or diminish their impacts on native fauna. Additionally we have carried out the first study about the conservation status of the European wildcat in the Doñana area, a species which exhibit a surprisingly low abundance in the area probably due to the historic negative interaction with the Iberian lynx as a main explicative factor.

This four-year period has been really enriching. I feel lucky to work in a research institute of international renown where moreover I have met really great people! I encourage all present and future PhD students to work hard on their projects because it’s really worth!

If you want to know more about me and my scientific research please visit my personal site at:

https://sites.google.com/site/carolinasotonavarrophd/