It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Nature just released “Statistics for Biologists”, a free  on-line collection of articles offering practical statistical guidance and information we all should be familiar with.

Here is a link to an awesome podcast interview with eminent professor Hall Caswell, conducted by Roberto Salguero-Gómez, an associate editor of the Journal of Ecology.

Museums of natural history are suffering severe reductions in their budgets all over the World, becoming just a threatened as some of the species they preserve. See a special article, written by Christopher Kemp, on this subject here.

– Vinicius Bastazini

The value of returning apex predators to historic habitat in order to restore biodiversity has been a hot topic in the past few years. Researchers in Australia propose allowing dingos to recolonize Sturt National Park as an ecological experiment testing this theory. Title dingo photo by Henry Whitehead via Wikimedia Commons

Sexual size dimorphism as a promoter of diversification, and associated with reduced extinction rates by Stephen De Lisle et al in ProcB. PS: Larger ladies are a bigger contributor

Also, my favorite title of the week, from the most recent American Naturalist: The mothematics of female pheromone signalling: Strategies for aging virgins

-Emily Grason

Two interesting articles in a recent issue of Ecology Letters by Fitzpatrick and colleagues: using genomics data and community models to predict how environmental change will impact adaptive genetic diversity, and the maintenance of phenotypic differentiation despite high gene flow.

-Kylla Benes

February 20, 2015

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Jon recently posted a great introduction to machine learning in his blog. If you are interested in learning more about these techniques you should definitely check it out! And also, take a look at this older publication: “Machine Learning Methods Without Tears: A Primer for Ecologists”.

Scott L. Nuismer and Luke J. Harmon evaluated the factors affecting the explanatory power of phylogenetic information on species interaction in their recently published paper “Predicting rates of interspecific interaction from phylogenetic trees”. Their findings suggest that mutualistic networks exhibit less phylogenetic signal in rates of interactions than competitive ones and that if interactions  depend on a mechanism of phenotype differences, phylogenetic information has little predictive power for trait evolution and interaction rates.

Tim Coulson, 
senior editor of the Journal of Animal Ecology, shares his experience of working with theoreticians and empiricists in a very awesome post titled “Modelers to the left of me, field biologists to the right; here I am, stuck in the middle with you”.

Here is another great post, which was also recently posted in the Journal of Animal Ecology blog on model complexity.

At last, yesterday we celebrated the International Darwin Day,  a date intended to “inspire people to reflect and act on the principles of intellectual bravery, perpetual curiosity, scientific thinking, and hunger for truth as embodied in Charles Darwin”. So Happy late Darwin Day!

– Vinicius Bastazini

February 13, 2015

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Science just released its annual list with the top 10 scientific achievements of  the year.

A new study led by Anthony R. Rafferty, shows that online supplementary material may acts as a “citation black role”, as these citations are invisible to search engines. The authors estimated that about 6% of all citations are only included in online supplementary material and therefore, are not considered in citation counts.

Andrew E. Noble and William F. Fagan propose a new framework to combine effects of selection, drift, speciation and dispersal on community dynamics, in their new paper “A niche remedy for the dynamical problems of neutral theory“.

Marco A. R. Mello and colleagues explored the ecological features of keystone species in seed dispersal networks across the Neotropics, in their paper ”Keystone species in seed dispersal networks are mainly determined by dietary specialization“. They evaluated the role of different  species traits, such as dietary specialization, body size and geographic range, and found that dietary specialization seems to be the main feature that makes a species a keystone.

At last, here is a plea for basic science: “Fundamental ecology is fundamental”

– Vinicius Bastazini

Millions of citizen scientists contribute time and money to biodiversity research, but are their data reaching a scientific audience? You can find out in the most recent issue of Biological Conservation. (And congrats to co-author and fellow blogger Hillary!)

– Kylla Benes

Better kick the habit now, in this month’s Climatic Chance issue researchers claim that climate change will adversely affect the global supply of coffee beans. The authors of “A bitter cup: climate change profile of global production of Arabica and Robusta coffee” utilized modeling to determine that the number of sites suitable for the growth of coffee beans could be cut in half by 2050.

Check out these wonderful close-ups from this year’s BioScapes competition!

– Nate Johnson

December 19, 2014

A reintroduced wolf in Yellowstone (source: http://en.wikipedia.org/wiki/History_of_wolves_in_Yellowstone)

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Emily just wrote a really cool piece on the importance of social media as a source of biodiversity data. So here is a paper that might help you to analyze this sort of “opportunistic”, unplanned, data in conjunction with data obtained from standard surveys, using hierarchical models.

Marti Anderson and colleagues propose a new method for assessing sample-size adequacy for multivariate data, when using dissimilarity-based analyses, in their new paper “Measures of precision for dissimilarity-based multivariate analysis of ecological communities”.

Marcos C. Vieira and Mário Almeida-Neto developed a new stochastic model for simulating complex extinction cascades, in their paper “A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance”. Their results show that traditional topological models are likely to misestimate co-extinctions and that highly connected mutualistic networks are more likely to undergo extinction cascades.

A new study published by Robert B. Wielgus and Kaylie A. Peebles shows that lethal wolf control in not an effective measure to protect livestock; on the contrary, it may actually lead to an increase in the number of dead livestock! Using data collected for more than two decades in the USA, they show that the number of livestock depredated the following year increased with the number of wolves killed the  year before, and that the odds of livestock depredations increases with increased wolf control (4% for sheep and 5–6% for cattle).

James T. Stroud and Kenneth J. Feeley show how academia can minimize greenhouse gas emissions by optimizing conference locations, in a paper recently published in Ecography (you can also see a review of this paper on the Ecography blog here).

At last, here is a nice theoretical physicist’s view on biology.  – Vinicius Bastazini

Welcome to the dark side… of diversity. If you haven’t heard of Partels ‘dark diversity’, the basic idea is to look at the species that could be in a community (based on their habitat preferences), but aren’t. Seems like a neat idea, especially, say, when thinking about ecologcal processes that exclude species (e.g. dispersal limitation, predation, competition,… um…actually just about any process except facilitation). Check out the groups’ most recent paper out this week in Ecography that looks at what’s missing (a lot!) and why (traits?) from over 1000 European grassland plots. -Jes Coyle

December 5, 2014

The famous evolutionary tree, drawn by Darwin in one of his notebooks in 1837

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

This week we celebrated the155th anniversary of Darwin’s masterpiece the “Origin of species” (published on November 24, 1859).  The “Origin” is undoubtedly one of the most important books of all times, it revolutionized science, philosophy and our understanding of the World. To celebrate this special date, the Cambridge Digital Library released online more than 16,000 pages of the original manuscripts written by Darwin, in high resolution (see it  here). By the end of the project, more than 30,000 pages will be available online for free. You can also download this material at the Darwin Manuscripts Project and at the Darwin Correspondence Project.

Do you want a Nobel Prize? Here is an easy way to get one!  James D. Watson, one of the co-discoverers of the structure of DNA, is selling his Nobel Medal. Watson plans to donate  part of the money to his “philanthropic legacy of supporting scientific research, academic institutions and other charitable causes.” See it here.

The latest issue of Nature has a couple of interesting pieces on the peer review system, here and here. One of the papers shows scams where some authors were caught reviewing their own work. – Vinicius Bastazini

Rub Dunn lists 45 things that he’s learned about science since he was a student. My favorites:

33-There are tens of thousands of great ideas in books and papers that no one has ever followed up on. If you are lucky, you will have six of you own great ideas. The odds favor reading old books and papers to improve your chances of working on something novel. If you no longer have old books and old papers in your library, try to read just outside your area of research. Maybe it’ll help you if you do know something about the C cycle after all.

 

45-The more interesting your ideas, the harder it will become to find anyone to tell whether they are brilliant or mad.

The Marine Science institute at UC Santa Barbara is recruiting a post-doc to focus on biodiversity estimation across multiple data sources

A very cool new paper by Michael G. Just et al in Ecosphere shows that humans act as important biogeographical filters for global disease distributions. -Fletcher Halliday

November 28, 2014

Mount Huangshan Scenic Area, one of the reserves in the IUCN “Green List”

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Last week, the International Union for the Conservation of Nature (IUCN) announced the first “Green List of Protected Areas”. The idea behind this list is to recognize protected areas  all over the World that are successfully meeting their goals. Insofar, the IUCN has evaluated parks in eight countries (Australia, China, Colombia, France, Italy, Kenya, South Korea and Spain) and the list contains 24 reserves.

Khan Academy has a nice tutorial, with videos and texts, on biodiversity and ecosystem services and functioning.

Denis Valle et al. propose a new multivariate model-based approach to analyse and decompose species diversity, in a new paper in Ecology Letters. – Vinicius Bastazini. 

Bird Life International released a report this past week defining over 300 globally threatened regions that are ecologically significant for the conservation of biodiversity. Check out the full report here.

Ever seen the shrimp on a treadmill video? Well, read what the lead researcher behind that internet sensation plans on doing with his contraption.

In stark contrast to the recent chills that afflicted most of the U.S. these past couple of weeks, this summer brought about the warmest global mean sea surface temperatures on record. Mostly influenced by the surprisingly warm North Pacific, these temperatures have been associated with coral bleaching, weakened trade winds, and shifted hurricane tracks. – Nate Johnson

I want to second Nate’s suggestion of reading about the bad-faith abuse and distortion of legitimate science to advance political agendas. It’s not biodiversity per se, but critical to the survival of all scientific disciplines.

Second, those of us on the west coast of the US have been blasted with news items this week about how the virus causing Sea Star Wasting Disease has apparently been identified. You can read about it in the PNAS paper by Hewson et al. that is in early edition. If you want even more exciting news about this story, I also wrote a piece on my own blog about it, with the caveat, based on a talk I saw at a conference this weekend, that the story might ultimately be more complicated than a single virus. But lets be clear, people: it certainly doesn’t have anything to do with radiation from the Fukushima-Daiichi plants. – Emily Grason

A few notables all from Oikos this week. A discussion of neutral stochasticity in ecological communities by M. Vellend and others. A two long-term studies of biodiversity-ecosystem function; one exploring effects of interspecific diversity on below-ground biomass in plant communities and another on intraspecific diversity effects on herbivory in birch tree stands. – Kylla Benes

November 21, 2014

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

Nature  just published two pieces that will certainly interest  all conservation biologists out there. The first paper is an evaluation of the performance and potential of protected areas, and the second one  is a “to-do list” for protected areas.

Last week, Nature published a list with the 100 most cited papers of all times in the Thomson Reuters database.  There is no “pure” ecology or evolution papers in the list,  except for papers that propose new methods (or softwares)  for building phylogenetic trees. Among these methodological papers, the article written by N. Saitou  & M. Nei, on the neighbor-joining method, is the most cited one (occupying the 20th position in the rank, with 30,176).

A large group of scientists, led by Bernhard Misof, just published a paper trying to resolve the phylogeny of insects. Using phylogenomic analysis of protein-coding genes combined with fossil analysis, the authors estimated date the origin of insects to the Early Ordovician (~479 Ma). They also estimated  that the origin of flight in this group took place the Early Devonian (~406 Ma). – Vinicius Bastazini.

An article was published last week in PLOS ONE on the reintroduction of giant tortoises in the Galapagos that presents a great example of the differences between population recovery and ecosystem function restoration. While we’re on the topic of reptiles, a paper in Science details phenotypic divergence between two closely related lizard species within only about 20 generations, presenting an intriguing case where evolution, influenced by strong selective pressures, can be seen observed on such a short time scale.

A study presented at a recent meeting of the American Society of Tropical Medicine and Hygiene claims that deforestation in Malaysia may be to blame for an increase in malaria cases. Researchers suggest that the increased contact between humans and local macaque populations, caused by habitat loss via deforestation, has led to more people in the area being infected with malaria. On a more positive note, Palau has decided to use crowdfunding as part of their plan to turn their waters into a no-take marine reserve.

Finally, the great minds over at Deep Sea News have put out a series of posts detailing the amazing diversity of marine species, from the torpedo ray to carnivorous sponges. Check them out here. – Nate Johnson

November 6, 2014

It’s Friday and that means that it’s time for our Friday link dump, where we highlight some recent papers (and other stuff) that we found interesting but didn’t have the time to write an entire post about. If you think there’s something we missed, or have something to say, please share in the comments section!

It feels like ESA Sacramento just ended, but plans for next year’s conference are already coming together. And here’s an opportunity for YOU from the desks of Heather Leslie and Paul Armsworth:

We’re pulling together a proposal for an Organized Poster Session at next year’s centennial ESA meeting in Baltimore. The session will focus on “Ecological science that can make a difference in the real world.” Our goal is to provide a venue for students engaged in conservation science and applied ecology to showcase their work.

 

If you think you fit the bill, send an email to Heather Leslie with the title ‘ESAConSci’ by 10 PM, Sunday, September 21.  

As part of the session proposal, due September 25, we need to include names of provisional poster presenters. The primary author should be a grad student, ideally in the first or second year.  Note that the one presentation rule will apply.  

If we are successful with this proposal, we will do our best to recruit a team of leading conservation practitioners to visit and review the posters and provide feedback, perhaps in a panel format later in the meeting. We also are exploring awarding a prize for ‘best poster.’

 

Interested students should send HL an email with the following information: 

1. A likely title for the poster (not definitive), 

2. A few sentences describing the topic  

3. A list of all likely authors and affiliations

4. A statement identifying the educational stage of the primary, student author (undergraduate / first year grad student, etc).

5. One criterion by which ESA will evaluate this proposal is whether it offers ‘range of perspectives… and a diverse mix of speakers.’ Any details you can provide that relate to this theme would be great.  

 

We hope to see you in Baltimore in 2015,  

Heather Leslie & Paul Armsworth 

(Brown Univ and Univ of Tennessee, respectively)

-Fletcher Halliday

Early warnings of regime shifts: evaluation of spatial indicators from a whole-ecosystem experiment – Benno Simmons

Here is a compilation of photos and drawings of some vertebrates extinct in the past 100 years. This compilation is based on the data provided by the Sixth Extinction, a website dedicate to provide information about the current biodiversity crisis.

Charles Fisher and Pankaj Mehta show that ecological communities transit between selection-dominated regimes and drift dominated regimes, in their new paper “The transition between the niche and neutral regimes in ecology”.

An interesting article by Rachel Nuwer scientific misbehavior: Scientific Misconduct Should Be a Crime.

At last, videos of the talks delivered during “The Frontiers in Phylogenetics 4th Annual Symposium“ are available online in three parts:

• Opening (Mike Braun, John Kress, Guillermo Orti), Lacey Knowles, Kevin Kocot, Ingo Ebersberger;
• Ingo Ebersberger (cont.), Derick Zwickl, Dave Swofford;
• Dave Swofford (cont.), Luay Nakleh, Bastien Boussau, round table discussion.

– Vinicius Bastazini.

September 19, 2014