Caribbean hurricanes are getting stronger and more frequent

At last night’s VP debate Mike Pence was asked about climate change. He stated that the National Oceanic and Atmospheric Administration (NOAA) says there are no more hurricanes now than 100 years ago. He’s wrong. And there are. Substantially more.

Coincidentally, Laura Mudge, a graduate student in my lab in the Department of Biology at the University of North Carolina at Chapel Hill, had just presented her work on this topic in her dissertation defense a few hours earlier!

Her results clearly show Caribbean hurricanes are becoming stronger and more frequent. This was predicted decades ago and is due to the increase in heat (which is the fuel of tropical storms) in the ocean (which itself is due 100% to anthropogenic climate change via greenhouse gas emissions). Other studies have reported similar findings.

The finding and graphic came from Laura Mudge’s PhD dissertation “The resilience of coral reef communities to climate-driven disturbances”. Laura will be turning in the dissertation to the graduate school and submitting it for publication to a journal in coming weeks. For now, here’s a synopsis of the methodology from chapter 2 of Laura’s dissertation “Long term trends of tropical storm impacts on caribbean coral reefs”. Laura made the code and data available on her GitHub site here.

The broader purpose of the study was to measure the effects of hurricanes on Caribbean coral reefs and how that’s changed over the last 10-20 years as both hurricanes and reefs have been altered by ocean warming. Laura used the National Oceanic and Atmospheric Administration (NOAA) Atlantic Hurricane Database (HURDAT) and first simply asked: are hurricanes getting stronger and are they more frequent?

Historical storm track data was downloaded directly from the National Oceanic and Atmospheric Administration (NOAA) Atlantic Hurricane Database (HURDAT) using the HURDAT package in R (Trice and Landsea 2019). These historical records contain storm track location (latitudinal and longitudinal coordinates), wind speed (knots), low pressure (millibar), status (landfall, hurricane classification), date and time, with variables recorded every 6-hours. Historical track information from the earliest year (1851) to present was used to analyze overall storm patterns in the Atlantic basin. Linear models were used to investigate changing trends in the frequency and intensity of tropical storms over time in the Atlantic.

Functional programming in R was used to catalog which hurricanes cross which reef sites in the coral reef survey dataset. Code for these procedures was adapted from Elsner and Jagger (2013). For each reef, I searched for all historical storms occurring within a 100km radius of the reef site coordinates. Storms of any strength were retained within a 35km radius of the reef coordinates, storms of category 3-5 on the Saffir-Simpson scale were further retained between 35-60km, and only category 4 and 5 storms retained between 65-100km. These buffers are based on previously published hurricane path impacts to coral reefs (Done, 1992; Treml et al., 1997; Gardner et al., 2005). Each observation in the database is a unique reef-storm intersection. Therefore, reef locations appear multiple times in the database, if more than one storm has hit the reef since 1851, and individual storms appear multiple times if they struck multiple coral reef locations along their path.

Historically (1851-2017), approximately 32% of named storms in the Atlantic basin have hit a coral reef location (1,604 named storms, 521 hit a reef) (Figure 2.2). Between 1970-2017, the time period of coral survey sampling, there were 547 storms total, 152 of which crossed over at least one coral reef site, for a total of 10,058 unique site-storm intersections. Out of 3,144 unique coral reef survey sites, 2,754 sites experienced at least one tropical storm since the beginning of storm records in 1851 (87.6% of reefs impacted, 12.4% of reefs unimpacted). Sites that were not impacted were located in the SW Caribbean, along the coast of Panama, Colombia, and Costa Rica.

Greta Thunberg’s speech to the UN Climate Action Summit

My message is that we’ll be watching you.

This is all wrong. I shouldn’t be up here. I should be back in school, on the other side of the ocean. Yet you all come to us young people for hope. How dare you? You have stolen my dreams, and my childhood, with your empty words. And yet I’m one of the lucky ones.

People are suffering. People are dying. Entire ecosystems are collapsing. We are in the beginning of a mass extinction, and all you can talk about is money, and fairy tales of eternal economic growth. How dare you?

For more than 30 years, the science has been crystal clear. How dare you continue to look away, and come here saying that you’re doing enough, when the politics and solutions needed are still nowhere in sight? You say you hear us and that you understand the urgency. But no matter how sad and angry I am, I do not want to believe that. Because if you really understood the situation and still kept on failing to act, then you would be evil. And that I refuse to believe.

The popular idea of cutting our emissions in half in 10 years only gives us a 50 percent chance of staying below 1.5 degrees [Celsius] and the risk of setting off irreversible chain reactions beyond human control. Fifty percent may be acceptable to you. But those numbers do not include tipping points, most feedback loops, additional warming hidden by toxic air pollution, or the aspects of equity and climate justice. They also rely on my generation sucking hundreds of billions of tons of your CO2 out of the air with technologies that barely exist.

So a 50 percent risk is simply not acceptable to us—we who have to live with the consequences. To have a 67 percent chance of staying below a 1.5 degree global temperature rise—the best odds given by the IPCC [Intergovernmental Panel on Climate Change]—the world had 420 gigatons of CO2 left to emit back on Jan. 1, 2018. Today that figure is already down to less than 350 gigatons.

How dare you pretend that this can be solved with just “business as usual” and some technical solutions? With today’s emissions levels, that remaining CO2 budget will be entirely gone within less than 8½ years.

There will not be any solutions or plans presented in line with these figures here today, because these numbers are too uncomfortable. And you are still not mature enough to tell it like it is.

You are failing us. But the young people are starting to understand your betrayal. The eyes of all future generations are upon you. And if you choose to fail us, I say: We will never forgive you. We will not let you get away with this. Right here, right now is where we draw the line. The world is waking up. And change is coming, whether you like it or not

A case for evidence-based reef conservation

Like forests formed by trees, tropical coral reefs are built up by corals over thousands of years via the slow accumulation of their skeletons. Corals – related to jellyfishes and sea anemones – provide shelter to countless other species, including the fishes we travel to see and love to eat.

But corals and coral reefs are in trouble. We’ve lost at least two thirds of the world’s reef-building corals over the last few decades, mainly due to ocean warming. About 90% of the additional heat being trapped on earth by greenhouse gases goes into the ocean. This causes reefs to warm, leading to disease outbreaks and coral bleaching.

An ineffective solution

The most common response by policy makers and reef managers to coral decline is to ban fishing. The idea is that fishing indirectly exacerbates ocean warming by enabling seaweeds that suffocate corals. More generally, the approach is based on the assumption that threats to species and ecosystems are cumulative: by minimizing as many as possible, we can make ecosystems “resilient” to climate change and other threats that cannot be addressed locally.

Unfortunately, there is now an overwhelming body of evidence that this approach, called “managed resilience” by conservation scientists, doesn’t work. At least for coral reefs. This is the key finding of our new study published in the Annual Review of Marine Science.

We performed a meta-analysis: a systematic review of 18 case studies that field-tested the effectiveness of the managed resilience approach. None found that it was effective. Protecting reefs inside Marine Protected Areas (MPAs) did not reduce how much coral was killed by extreme temperatures related to global warming or how quickly threatened coral populations recovered.

The 18 individual studies compared the impact of large-scale disturbances (mass bleaching events, major storms, and disease outbreaks) inside MPAs to unprotected reefs. Many also measured the rate of coral population recovery after disturbances. Overall, the meta-analysis included data from 66 protected reefs and 89 unprotected reefs from 15 countries around the world. No form of local protection, include large-scale fishing bans on some of the world’s most isolated reefs, had any effect on how much coral was killed off by climate change. Fisheries restrictions, while clearly beneficial for over-harvested species, don’t help reef-building corals cope with human-caused climate change.

We currently devote much of our conservation budget towards a solution we know isn’t effective. Billionaires like Michael Bloomberg have been giving NGOs millions to expand managed resilience. The United States government’s new plan to save reefs is based on it. So is Australia’s plan for managing the Great Barrier Reef. (Notably neither plan prioritizes greenhouse gas emissions or climate change.)

Why do we embrace ineffective “managed resilience”?

There are probably many reasons for the widespread acceptance of managed resilience in reef conservation. Most obviously, it blames and puts the burden of change on other people. Instead of not flying, driving, eating meat, etc., scientists and managers in the US, Australia, Canada, and Europe (nearly all Caucasian) can implement policies that demand sacrifice of people they’ll never meet: mainly poor, non-white fisherman and their families. Such neocolonialist thinking in reef management almost feels like a form of white supremacy.

Managed resilience also fits the universal storytelling frame of the villain and the hero. In this case, the villain is seaweed that purportedly overgrows hapless corals, and the heroes are fishes that eat it, protecting corals, and making reefs resilient to disturbances. Yet the reality is that seaweed blooms are usually a result of coral mortality and a general symptom of reef degradation, rather than the cause of it.

Managed resilience can also be highly lucrative. Foundations, federal agencies, and especially billionaires love resilience thinking: tackling a global problem without any lifestyle changes! The funds pour in to the labs and NGOs willing to go down this path. One group was recently awarded 444 million dollars by the Australian government to save the Great Barrier Reef (as long as saving it doesn’t mean reducing coal exports or addressing climate change). Such awards typically sidestep peer review and other scientific norms designed to ensure accountability, effectiveness, and scientific rigor.

Finally, attempting to manage the impacts of global warming on reefs via local conservation efforts is widely seen as doing something – anything to help slow the loss.

A sea of ineffective solutions

Whether its straw and sunscreen bans or expensive contraptions designed to scoop up garbage, marine conservation is now dominated by displacement activities: ineffective actions that make us feel like we’re doing something to protect the biodiversity of the oceans. Rather than tackling the big problems like carbon emissions head on, we devise pseudo solutions that require only minor inconvenience instead of fundamental societal change (e.g., curbside recycling instead of reduced consumption and getting by without straws instead of switching to renewable energy sources).

Managed reef resilience fits firmly within the sea of displacement activities now favored by many NGOs and conservation scientists. We’re told these “gateway” activities will eventually lead to more meaningful change. Yet in the meantime, they are taking up much of the funding and media coverage that could be directed towards proven solutions.

A more effective way forward

Many outcome-based fields (e.g., public policy and health care) have adopted a more stringent evidence-based approach to solving problems. The idea is that resource allocation should be based on a stringent evidence standard (primarily on quantitative systematic reviews) rather than dogma and anecdote. Advocates of managed reef resilience often argue that due to the severity of the threat and the shortness of remaining time, we need to just “try anything” regardless of the science. But I’ve been hearing this for over twenty years and it’s gotten us nowhere: there is literally no reef on earth where the coral framework has been locally protected from climate change. Even the world’s most isolated, diverse, and well-managed reefs have succumbed.

A recent survey of international bleaching experts found that an overwhelming majority believe managed resilience works. Clearly, our greatest outreach challenge isn’t convincing the public that reefs are in trouble – its convincing reef scientists, NGOs, and the federal agencies tasked with saving reefs. We need to abandon the false promise of managed resilience and get to work on halting the real driver of reef decline: greenhouse gas emissions. And to achieve that we know exactly what to do.

Bruno et al. 2019 ARMS review: Supplemental info on MPA enforcement

One question I’ve gotten recently after presenting the results of the primary meta-analysis in this paper is whether the MPAs (most of which are fully protected marine reserves) were effective in protecting fish populations. Are they well-designed, well-enforced, etc. and are there more fishes, particularly herbivorous fishes, inside them than in neighboring unprotected sites?

It’s a fair question and one we talked about extensively at several stages of the study. That an MPA was proven effective in terms of fish conservation was not a criteria for inclusion in the study. But I was aware that nearly all the component studies were based on MPAs that did indeed have greater fish biomass. And also that some were clearly ineffective, whether due to size, age, isolation or any of the NEOLI features of Edgar et al. 2014.

The primary finding was that protection did not affect the resistance or recovery of the coral community (in terms of total live cover) in response to large scale disturbances, i.e., storms, bleaching and disease.

This meta-analysis was based on 18 studies that included 66 MPAs and 89 unprotected control sites:

For each study, are the protected sites believed or shown to be effective in protecting fishes, particularly herbivorous fishes?

Bégin et al., 2016 Yes

The cover of all benthic biotic components has changed significantly over the decade, including a decline in coral and increase in macroalgae. Protection status was not a significant predictor of either current benthic composition or changes in composition.

A series of small no-take MPAs, known as the Soufriere Marine Management Area (SMMA), was created in 1995 on the west coast of the island. These MPAs have had a high level of compliance [28, 29], and within six years of estab- lishment, total biomass of fishes had quadrupled inside the reserves and tripled outside the reserves, with the greatest increase observed for herbivores [30]. Greater biomass of herbivorous fish inside the SMMA compared to adjacent sites was observed again in early 2014 (R. Steneck, personal communication). However, the initial benefits of the SMMA did not extend to coral, which decreased in cover by 35–46% over this 6-year period, owing to disease (in 1997), bleaching (in 1998), hurricane damage (in 1999), as well as chronic sedimentation stress from the Soufriere River [31–34].

28. Burke L, Greenhalgh S, Prager D, Cooper E. Coastal Capital—Economic Valuation of Coral Reefs in Tobago and St. Lucia. World Resources Institute, 2008.

29. Roberts CM, Bohnsack JA, Gell F, Hawkins JP, Goodridge R. Effects of marine reserves on adjacent fisheries. Science. 2001; 294(5548):1920–3. PMID: 11729316

30. Hawkins JP, Roberts CM, Dytham C, Schelten C, Nugues MM. Effects of habitat characteristics and sedimentation on performance of marine reserves in St. Lucia. Biological Conservation. 2006; 127 (4):487–99. PMID: ISI:000234960900012.

Bood, 2006 No via Cox et al. 2017:

Coelho and Manfrino, 2007 YES via Dromard et al 2011

Darling et al., 2010 Yes

Seven sites were located on intensively fished reefs (Diani, two sites; Kanamai, two sites; Ras Iwatine, one site; Vipingo, two sites) and five sites were located on reefs inside unfished, no-take marine re- serves (Malindi Marine National Park, two sites; Mombasa Marine National Park, two sites; Watamu Marine National Park, one site); fished and unfished sites are interspersed along the coast (for map, see McClanahan & Obura 1995). Fishing prohibition is enforced in all Marine National Parks while artisanal fishers intensively exploit the nonpark reef sites (McClanahan et al. 2008).

McClanahan, T.R., Obura D. (1995) Status of Kenyan coral reefs. Coast Manage 23, 57–76.
McClanahan, T.R., Hicks C.C., Darling E.S. (2008) Malthusian overfishing and efforts to overcome it on Kenyan coral reefs. Ecol Appl 18, 1516–1529.

Graham et al., 2008 and 2015: Yes, eg via Graham et al 2007

Halpern et al., 2013 No
Harris et al., 2014 Yes
Huntington et al., 2011 No
Jones et al., 2004 Somewhat…
Manfrino et al., 2013 Yes via Dromard et al 2011:

McClanahan, 2008 Yes
Mcclanahan et al., 2001 Yes
Miller et al., 2009 No (based on personal comm. and no evidence to the contrary that I can find)
Mumby and Harborne, 2010 Yes
Muthiga, 2009 Yes:

Russ, 2015 Yes

Toth et al., 2014 Yes via Kramer and Heck, 2007

So in summary, most the MPAs in the study are effective in protecting fishes: 12 of the 18 studies included such MPAs. I don’t see it as a design flaw that some are not. First, that’s just the reality. In fact; it’s the norm. Second, had there been an effect of protection on coral resilience, it would have been useful to try to assess why, e.g., due to the enforcement.

Ocean warming caused most Caribbean coral loss: a review of the evidence


Coral cover on Caribbean reefs has declined precipitously over the last few decades, e.g.; Gardner et al. 2003 (Science PDF here):Screen Shot 2013-09-14 at 8.35.07 AM

and Schutte et al. 2010 (MEPS PDF here):Screen Shot 2013-09-13 at 10.02.04 PM

Also see Hughes 1994Cote et al. 2005, and Jackson et al 2014. There is substantial evidence that human-caused ocean warming is the primary cause of this loss of reef-building corals on most Caribbean reefs:


In support of the Biscayne Bay marine reserve

The ongoing battle over the planned marine reserve in Biscayne Bay has scientists and citizens scratching our heads. The impassioned opposition to the proposed protection of a tiny sliver of our shared resource is stunningly out of proportion to what the National Park Service (NPS) has proposed. Moreover, the arguments made by opponents have not been based on science and are mostly illogical. For example, citing a scientific paper I co-authored, Representative Ros-Lehtinen correctly pointed out in an op-ed that a marine reserve in Biscayne Bay National Park wouldn’t protect Florida’s remaining corals from global warming. However, this is analogous to arguing brushing your teeth is unnecessary because it doesn’t prevent cancer. Protecting corals from climate change isn’t the purpose of a marine reserve, although reserves provide countless other benefits. If Rep. Ros-Lehtinen wants to protect corals from climate change, her party and her CORAL bill should support the move to renewable energy, one of the few actions that could in fact protect and restore corals and the reefs they build.


Response to Avigdor Abelson

The graphics below are to supplement our response to the criticisms of Avigdor Abelson about our recent paper in Scientific Reports.

Possible Conceptual Figure OK-2


Back to Belize

I arrived in Belize yesterday with three former lab members (Abel Valdivia from CBD, Courtney Cox from the Smithsonian, and Jenny Hughes, a recent graduate from UNC). Although field ecology is really fun (if pretty challenging) we are actually here to work. In 2008 my lab took over a reef monitoring program Melanie McField set up in the mid 1990s to track the state (AKA “health”) of reefs along the Meso-American reef in Belize (we also work in Mexico and Honduras). Most years, we come down in May after classes are over to survey 16-19 sites from the north, just below the Mexican border, all the way down to the far-offsore cays near Honduras.


Are isolated central Pacific reefs really “healthier”?

In a new paper – that got a lot of media coverage – Smith et al 2016 quantified benthic reef composition “across 56 islands spanning five archipelagos in the central Pacific”.

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I think it’s an admirable project and an interesting data set, and there is a lot to like about the paper. However, some of the main interpretations, particularly in the press coverage, are off the mark.


Top 10 take-home lessons from Dayton 1971


10) Natural communities are enormously complex, often governed by networks of positive and negative indirect interactions. (complexity, indirect effects)

9) Multiple factors and processes interact to influence community assembly, including competition, predation, facilitation, recruitment, disturbance, physiological stress, patch dynamics, and succession. (multifactoralism)

8) The relative importance of various factors is highly context dependent. (AKA it depends…)

7) Recruitment limitation is important! (supply side ecology)

6) Disturbance can prevent competitive exclusion, maintaining diversity.

5) You don’t need R, Github or even a computer to do transformative science.

4) Pattern quantification and experimentation go hand in hand. One without the other doesn’t get you nearly as far as combining them does.

3) Natural history (local knowledge of a system and its inhabitants) is crucial to interpreting empirical results.

2) Experimental ecology is a very powerful tool.

1) Paul Dayton is badass.

Dayton_diving copyThe image above is of Paul, about to dive beneath the ice in McMurdo Sound, Antarctica, I believe in the early 1970s.  The link to Dayton 1971 at the ESA website is here.   


That wild caught shrimp you just ate? It might be from a skanky, destructive farm

Like lots of people, you probably love shrimp. Love to eat them that is. And hopefully you know, shrimp farming is highly destructive. To make a shrimp farm, you first clear out all the mangroves, destroying a critical coastal ecosystem.  Mangrove loss results in greater storm and tsunami impacts, greatly reduced fisheries production (mangrove roots, below the water, act as fish nurseries), and also reduced carbon sequestration. BIG BUMMER.  So you do the right thing and only buy wild caught shrimp. Moreover, you want to supper local fisherman, like the families that have been shrimping in our vast estuaries here in North Carolina for decades. But how do you know what you buy isn’t actually coming from a polluted, destructive shrimp farm in Thailand? You don’t.

You are at the mercy of the vendor.  Yet many seafood vendors don’t know where their product comes from or they are just dishonest about it. A NC food processor (why do we even have “food processors”?) was just busted for mislabeling shrimp:

Federal prosecutors say a Dunn-based seafood processor and distributor used a bit of bait-and-switch when falsely labeling almost 25,000 pounds of farm-raised imported shrimp headed for Louisiana. source

Beyond this, wild caught shrimp is generally highly environmentally destructive too. Usually, shrimp are caught by dragging huge nets across the bottom. This destroys habitat too (like seagrass beds) and also kills countless other critters that get scooped up and die as bycatch. More on that later…

Steller’s sea cow – candidate for de-extinction?

Today in Evolunch, we discussed de-extinction.  One species we evaluated for post-extinction-reintroduction via the magic of genetics is the Steller’s sea cow, extinct in the wild since 1768 (less than 30 years after it was “discovered”) .

Below is an excerpt from The Unnatural History of the Sea by Callum Roberts that describes the discovery and subsequent loss of Steller’s Sea Cow on Bering island in the mid-18th century. Roberts begins with the trials of an expedition led by Captain Vitus Bering and his men, stranded on Bering Island in the frigid north Pacific in 1741/1742. The descriptions of the now extinct Steller’s Sea Cow by German naturalist Georg Steller is particularly poignant.

The except starts here:

By the dawn of the eighteenth century, two hundred years of European exploration had sketched out much of the world’s coastline. But the north pacific, stretching from eastern Russia and Japan to North America, and the Southern Ocean, the name given to the waters  around  Antarctica, remained unknown and thereby enticing to adventures of the day…

As the winter set in, the land disappeared under deep snow. But food remained plentiful in the form of  sea mammals. The naive sea otters could still be approached and clubbed with ease. The otters, wrote Steller,

at all seasons of the year, more, however, during the winter than in the summer, leave the sea in order to sleep, rest, and play all sorts of games with each other…it is a beautiful and pleasing animal, cunning and amusing in its habits, and at the same time ingratiating and amorous. Seen when they are running, the gloss of their hair surpasses the blackest velvet.


Academic-NGO partnerships to optimize and utilize conservation science


Problems: (1) Many academic scientists in conservation biology are isolated from end-users of their work, including policy makers, stakeholders, and conservation NGOs (CNGOs). (2) CNGOs rely on science and scientists, however, a science staff is very expensive to maintain.

Assumptions: (1) Science is valuable and useful to CNGOs. (2) Some academic scientists want to produce conservation-relevant science.

Solution: Link academic scientists with CNGOs via two-way exchanges. These could include short (weeks to months) and long term (years to semi-permanent) placements. For example, CNGOs staff could be based in an academic research group and collaborate on applied research with academic scientists and their students. Academic scientists could work at or collaborate more directly with local CNGOs offices in their area or spend longer periods of time based at CNGO offices or field sites (whole semesters via sabbatical or even years by taking a leave of absence). Joint retreats could facilitate collaborations and linked projects.

Benefits for the NGO include: greatly reduced cost to achieve scientific output1, far greater connectivity with world-class science, staff training, career advancement opportunities, and a conduit for future staff and student interns. NGO’s would also gain access to students (advised, mentored, and managed by academic scientists) that can work on CNGO research projects.

Benefits to academic scientists and institutions include: far greater involvement with conservation, a better sense of what is needed, and inclusion in the conservation community. Academic scientists will also gain a greater understanding of how to communicate science outputs and to achieve real world conservation outcomes.


1Many of the costs associated within maintaining a science group could be absorbed by the academic institution, including office/lab space, IT support (as well as wireless, software, etc.), PI salary and some staff salaries, journal access, proximity to colleagues in many disciplines, and countless other resources available on a college campus.

New tools for science collaboration

The problem with science is email. You all know what I mean.

Nearly everything we do is done via email. On the one hand, email is faster than snail mail and enables me to effortlessly share large amounts of information via attachments, links, etc.  Email – even more than Word, r, and Excel – is the nexus of professional life not just in science, but in business, the arts, politics, everything.

However, one giant, crippling problem with email is the massive volume we all receive (dozens to hundreds of non-SPAM messages a day). Email efficiency (wasn’t that a benefit?) makes it too easy for people to ask for assistance or to generally bug, distract, and grouch at you. I have been steadily moving away from email, feeling less and less guilty about simply not responding. (I use texting with my students and primary collaborators and sometimes google chat. I only check and deal with email a few times a week and never, ever answer my office phone or check my office phone inbox.)

Email is also a pretty lame collaboration tool. We all use email to communicate with partners on our science projects and papers. We email ideas, draft manuscripts and proposals, data, r code, images, ppt presentations, and complain about NSF and journal reviewers.  It works for all this and more, but there are several problems.  It is really hard to keep the correspondence for a project together, especially since many collaborations last years and can encompass hundreds or thousands of emails.  It is hard to track, archive, and find all that correspondence (too many threads, deleted messages, lame university email storage, etc.).  I also don’t like how the project communications are stored separately from other project files (data, code, manuscripts, etc.), which nowadays usually reside in drop box, git hub or similar.

Last week, I was driving home from the field with my collaborator Dr. Laura Moore and she was making pretty much the same points. For our NSF funded project “The role of ecomorphodynamic feedbacks in barrier island response to climate change”, we have three PIs, two post docs, several grad students, undergrad interns, etc. and we all keep losing communication threads in email, have no way to share and view data, images, plans, ideas, calendars, etc.  There has got to be a new tool that would enable all this: simply, affordably, and in one place without any email!

Turns out, there are many of them. Dozens at least. I’ve explored about a ten and read several posts about various next gen communications and project management apps and below I’ve summarized what I’ve learned so far about a few of the options. Doing this has helped me refine what exactly I was looking for.  I’ll be testing these over the coming months and will update this periodically.

These tools are not meant to replace a shared document, like a Word file in drop box or a google doc or ether pad. They are fine for collecting notes, ideas, links, for collaboratively writing a paper, etc. But they are poor communications tools and are not a good way to share other project files or manage a team or broader collaboration.

Screen Shot 2014-06-30 at 8.53.01 AM

There many apps designed for project managers in the business world such as Asana. This is what my asana looks like:

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These online tools seem focused on tracking fairly discrete jobs and managing teams. To me they seem designed to assign tasks, track work products, deadlines, and other things that business folk do. This could be transferable to science, especially in hierarchical labs, however, many of my collaborations are with pers and my grad students and assigning tasks isn’t really how we do things. But on the other hand, teams of scientists are terrible at clarifying who is doing what, setting and sticking to deadlines, and generally making and communicating about work plans. So maybe this kind of tool could increase productivity.

What caught my eye initially about asana was the tagline “teamwork without email” – the point of my quest. And I really like the To Do list capacity. This could be useful for tracking what your students and collaborators are doing.

The next class of collaboration platforms are somewhat simpler tools like flow dock (built by vikings!), slack (the much-buzzed-about new kid on the block) and basecamp. They (and many similar tools) are designed for email-free communications, project / team organization and integration, and file sharing. Check out this cool example of how basecamp was used to manage the development of retail headquarters for Keen.

These three examples, asana, and their competitors all integrate surprisingly easily with many related and supporting tools. Integration with drop box and google drive makes file sharing a breeze.

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There is social media integration, as well as github, other code sharing tools, and project and team management tools like working on (basically, you use it to notify your team and boss about what you are working on in a simple, twitter-like manner) and Breeze (essentially a drag-n-drop To Do list for individuals or groups.)

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One of the many cool features of slack is the way it handles code sharing via different built in formats, that enable you to add a longer, formatted “post” and code snipers in addition to the traditional simple message:

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The key to normal people actually using these tools is simplicity. (Remember Google Wave?) Developers seems to have finally figured this out. Nearly every tool I looked at had very clean, modern designs and font, simple interface and great support via pop ups, videos, etc. You don’t need to read the instruction manual for any of these, although some seem simpler and more intuitive than others.

Another of my favorites (so far) is HipChat, which seems more focused on simple communications than flowdock and slack. Hipchat, like Campfire and others is an “instant messaging service” (see comparisons and reviews here and here). You can share files with HipChat and it also has powerful integration with GitHub, etc. And Laura will love this: you can set up notification of new messages via email, SMS, bouncy icon, sound alert, etc.

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The basic plan is free and you can upgrade for $2 per month per user (to get video chat, etc).

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Unlike some of the other options, HipChat can be downloaded onto your computer (a desktop client) or used online. I think I prefer online programs these days.


I’ve invited a few of my students and collaborators to try a few of these out with me this summer. If you want to join in, let me know, by email:) Ironic, I know. But this is what email should be for. Necessary but infrequent communication. External, rather than internal communication. In the 1980s you wouldn’t have mailed a letter to your coworker down the hall. And you shouldn’t send them an email in 2014.

So more on this soon. And let us all know (via the comments section) if you have other suggestions or views of these tools.

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Living Shorelines

dfsa Jared Brumbaugh of the eastern NC NPR affiliate did a great piece and interview with Rachel Gittman (a 5th year PhD student in my lab) about her work on salt marsh conservation and living shorelines. Protecting shorelines with natural, vegetative barriers is not only better for the ecosystem, it’s a more effective means of slowing shoreline erosion.  We speak to a local researcher about her work with “living shorelines.”

A new way of keeping water at bay is taking hold not only in eastern North Carolina but up and down the East Coast and local research is helping spread the word on living shorelines.  In high wave action areas, manmade bulkheads make the most sense, but for low to medium wave areas, such as rivers, estuaries, and soundside properties, living shorelines can be more cost effective and better for the environment. Bulkheads are a common sight along waterways in eastern North Carolina.  The wood or concrete structures protect the shoreline from erosion and keep water from encroaching on homes and businesses. But bulkheads can have negative impacts to the ecosystem.  A more environmentally beneficial way of stabilization is living shorelines, whereby stone, gravel or oyster shell filled bags are placed one on top of the other creating a sill. Read the rest and listen to the interview here.

Threatened staghorn coral invades Fort Lauderdale!

Last week I was visiting FIU and talking with Lionfish guru Zack Judd when the topic of the Acropora range shift came up.  He and Laura Bhatti wanted to take me to do something fun on my last day in Miami.  So we decided on snorkeling off the beach on the world famous Fort Lauderdale strip to see one of the local coral reefs.  Seriously.  I was skeptical. First, because this is what the shoreline looks like:


Close up of a typical coastal habitat: 2007573-Elbo_Room_Fort_Lauderdale


I had heard from my buddy Bill Precht that Acropora cervicornis (AKA staghorn coral) is moving northward along the Florida reef track in response to global warming. Precht and Aronson have a great paper in FEE (2004) “Climate flickers and range shifts of reef corals” that outlines all of this.


Though now rare throughout their Caribbean range (mainly due to white band disease), staghorn corals appear to be moving northward into Palm Beach County:


But still, I didn’t think these new populations would be, literally, right off the strip, in pretty shallow water (3-5 m depth). And I didn’t imagine how massive they would be. They were huge and the thickets were fairly thick, even though hurricane Sandy recently rolled over them. Check out these photos Zack took:




I know of other persisting or new staghorn thickets elsewhere in Caribbean (Bill and I documented one such example in Jamaica in 2003) but nothing quite this large. This is really good news. And it is in agreement with my growing sense that climate change is going to be more about change (range shifts, altered composition, new players, etc.) than outright destruction and extinction. We will have some of that, but the science to date suggests that species are changing their distribution and phenological timing in response to warming much more than they are simply dying out and going extinct.  They aren’t giving up quite yet.

The case study also emphasizes the over-dispersion of many marine species and the huge role of abiotic factors, like temperature, in limiting distributions. (I think in general, we are way to concerned about connectivity in the ocean – there seems to be plenty of that.)

Listen, Acropora cervicornis and palmata for thousands of years were two of the dominant reef-building corals  in the Caribbean. Their populations were decimated regionally in the 1980s and their loss radically changed countless aspects of coral reef communities. Their expansion into South Florida does not mitigate that regional loss. It also does not mean future threats won’t wipe them out. And they can’t keep moving forever; there is no shallow water hard bottom habitat to settle on too far north of Florida and other environmental factors, like water sediment and nutrient load, would probably prevent colonization anyway. Range shifts will not save all species. Many, like Australia seaweeds will range shift into oblivion (e.g., the southern ocean). But I think it is still pretty cool to see species like this continue to bounce back. It gives me hope. And I think it should be teaching us some broader lessons.

One is that local impacts and local human population density in general has very little to do with the loss of corals. Look at the shoreline these corals are colonizing! There is nowhere in the Caribbean with such high urbanization and yet here they come. The presence of people per se is not driving coral loss or limiting recovery.

Interview with Abel Valdivia about lionfish and biotic resistance

I LOVE this interview PeerJ just posted (and excerpted below) with Bruno lab PhD student Abel Valdivia about our new paper on lionfish and biotic resistance.  

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PJ: What were your motivations for undertaking this research?

AV: The invasion of lionfish into the Caribbean basin over the past ten years provides a unique possibility to study marine species invasion at a large geographical scale. Species invasion is one of the major threats the oceans face today, and can be closely related to issues such as fishing and climate change. With rising temperatures due to global warming, several marine species are shifting their geographical range; occupying new environments; establishing new ecological interactions with established residents, and therefore changing the community structure and composition of the invaded systems. Marine invasions due to human introductions or ocean warming are important to understand at a large spatial scale since it will be a very common phenomenon in the near future.

Lionfish have spread to every shallow and deep habitat of the Western Atlantic and the Caribbean, including coral reefs environments, seagrass meadows, mangrove root systems, estuarine habitats, and even depths over 90 meters. Lionfish have even been reported in the colder waters near Boston, Massachusetts. We are still investigating the negative impacts of this invader on all of these already disturbed ecosystems, but one thing is clear – their voracious appetite threatens small fish and juveniles of depleted fish populations including commercially and ecologically important species such as groupers, snappers, and herbivores.  The failure of the Caribbean region to constrain invasion success may be partially associated with the lack of native predatory capacity due to overfishing, or simply to weak biotic resistance by native predators and competitors to a novel predator.

PJ: How would you say your study is controversial?

AV: Over the past few years some studies have hinted that native groupers could potentially prey on invasive lionfish and therefore act as natural bio-control of the invader. There is one study that reported lionfish in the stomachs of at least two species of large groupers. However, it was not clear if the lionfishes were already dead when the groupers ate them. Another study found a negative relationship between the biomass of native Nassau grouper and lionfish at a relative small spatial scale in the Exuma Cays Land and Sea Park in the Bahamas. In fact, we were excited to test the generality of this negative relationship in a paper published last year. Unfortunately, we did not find any evidence that grouper or any other predators (including sharks) or competitors (same size native predators) were negatively related to lionfish and concluded that other physical environmental variables and culling were the main drivers of lionfish distribution and abundance.

Our current study expands on those findings by adding new factors that are known to affect fish abundance (e.g., fishing and reef structural complexity). We also tested whether lack of native predatory capacity was an issue across the Caribbean. While some reefs actually had a low abundance of native predators due to overfishing, other well-protected reefs with high abundances of sharks, groupers and snappers exhibited a high abundance of lionfish. Therefore, the lack of predatory capacity does not limit the control of the invader. In general there is actually little to no evidence that abundant native predators can constrain the distribution and abundance of invasive predators. For example, the expansion and proliferation of the invasive Burmese python in the Florida Everglades was never constrained by the abundant native American alligator.

Read the rest here

Coral reef resilience: a biogeographic perspective

GBR_corals-590x400Coral reefs are affected by a large range of disturbances including disease, bleaching, storms, and Acanthaster planci, also known as crown of thorn starfish (COTS) outbreaks.  There appears to be a lot of variation of how much coral cover is affected by physical and biological disturbances and in how quickly coral communities recover from it.  Those two ecological processes, resistance to and recovery from disturbance, make up “resilience” (although in some corners of coral reef science, the recovery component is emphasized and nearly synonymous with resilience).  Resistance and recovery (and the disturbance regime they are linked to) control ecological “stability” or the degree to which population or community state varies with time.

People have been quantifying coral community resilience in the field for many decades. Stoddart (1974) studied the effects of hurricane hattie on the near-pristine reefs of Belize in 1961 (when it was still part of the British Empire and called “British Honduras”) and Endean and Stablum (1973) documented the effects of the first of many COTS outbreaks on the Great Barrier Reef.

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And of course Joe Connell studied the waxing and waning of shallow water coral cover (and species richness) in response to disturbance on Heron Island, GBR for decades (and probably still is).  Connell (1997) was also the first person I know of to synthesize this literature, although exhaustive, he employed pre-meta-analysis “vote counting” and his effort wasn’t exactly quantitatively sophisticated:

Screen Shot 2014-03-28 at 7.02.28 PMGraham et al. 2011 sort of picked up where Connell left off with a meta-analysis of the recovery of coral communities around the world.  Surprisingly, they found that disturbance type, e.g., “physical” vs. “biological” disturbances, and other reef characteristics including connectivity had little effect on recovery rate.  Region did seem to affect recovery, with it being fastest in the western Pacific, i.e., the most diverse place:Screen Shot 2014-03-28 at 10.32.01 PM Human population density and management status also appeared to effect recovery rates, but not in ways that you would have expected! 

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Reefs with lower post-disturbance coral cover tended to recover more quickly:

Screen Shot 2014-03-28 at 10.40.48 PM I recently taught an undergraduate seminar class in which for a class project, we expanded on the Graham et al study and asked: Is coral species richness related to resistance to and recovery from disturbances?

More diverse communities are thought to be more stable—the diversity–stability hypothesis—due to increased resistance to and recovery from disturbances. For example, high diversity can make the presence of resilient or fast growing species and key facilitations among species more likely. How natural, geographic biodiversity patterns and changes in biodiversity due to human activities mediate community-level disturbance dynamics is largely unknown, especially in diverse systems. For example, few studies have explored the role of diversity in tropical marine communities, especially at large scales.

We contacted Dr. Nick Graham, he shared his database with us (thanks Nick!)(which you can download here). We synthesized the results of 41 field studies conducted on 82 reefs, documenting changes in coral cover due to disturbance, across a global gradient of coral richness. The students added the resistance / coral loss data (the original study just looked at recovery) and we used Veron’s coral richness maps to estimate local richness (at the sites of the disturbance studies). 

Our results (Zhang et al. 2014) indicate that coral reefs in more species-rich regions were marginally less resistant to disturbance and did not recover more quickly.  

Screen Shot 2014-03-28 at 6.40.00 PMCoral community resistance was also highly dependent on pre-disturbance coral cover, probably due in part to the sensitivity of fast-growing and often dominant plating acroporid corals to disturbance. Our results suggest that coral communities in biodiverse regions, such as the western Pacific, may not be more resistant and resilient to natural and anthropogenic disturbances. Further analyses controlling for disturbance intensity and other drivers of coral loss and recovery could improve our understanding of the influence of diversity on community stability in coral reef ecosystems. Read more here at PeerJ: Zhang et al. 2014.

Literature Cited

Connell, J.H. (1997). Disturbance and recovery of coral assemblages. Coral Reefs, 16, S101–S113.

Endean, R. & Stablum, W. (1973). The apparent extent of recovery of reefs of Australia’s Great Barrier Reef devastated by the crown-of-thorns starfish. Atoll Research Bulletin, 168, 1–41.

Stoddart, D.R., 1974. Post-hurricane changes on the British Honduras reefs: resurvey of 1972. In: Proceedings of the Second International Coral Reef Symposium, vol. 2, pp. 473–483

Recent and future impacts of ocean warming on marine biodiversity

I am a (relatively junior) member of an NCEAS/NSF funded international working group that is assessing how climate change is affecting ocean ecosystems.  Today, we published our third major paper (in Nature; Burrows et al. 2014), that predicts how ocean warming will affect global patterns of Biodiversity. Read a nice non-technical summary here and a nice summary by the editor:

To survive in a changing climate, a species may need to move in order to stay in an area with a constant average temperature. Such mobility would depend on an ability to keep pace with a moving climate — and on the absence of physical barriers to migration. These authors use the velocity of climate change to construct a global map of how ecological climate niches have shifted in recent decades and go on to predict changes in species distribution to the end of this century. The map indicates areas that will act as climate sources and sinks, and geographical barriers likely to impede species migration. The data show that geographical connections and physical barriers — mostly coasts — have profound effects on the expected ability of organisms to track their preferred climate. This work underlines the importance of migration corridors linking warmer and cooler areas as a means of maintaining biodiversity.

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Our first major paper came out in Science in 2012 (Burrows et al. 2012) in which we described the “velocity” of warming of the planet at relatively fine grains.

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Our second paper “Global imprint of climate change on marine life” – and really the primary output of our working group – was published last year in Nature Climate Change. Read my summary here at Skeptical Science and less technical summaries here and here.

We synthesized all available studies of the consistency of marine ecological observations with expectations under climate change. This yielded ametadatabase of 1,735 marine biological responses for which either regional or global climate change was considered as a driver. Included were instances of marine taxa responding as expected, in a manner inconsistent with expectations, and taxa demonstrating no response. From this database, 81–83% of all observations for distribution, phenology, community composition, abundance, demography and calcification across taxa and ocean basins were consistent with the expected impacts of climate change. Of the species responding to climate change, rates of distribution shifts were, on average, consistent with those required to track ocean surface temperature changes. Conversely, we did not find a relationship between regional shifts in spring phenology and the seasonality of temperature. Rates of observed shifts in species’ distributions and phenology are comparable to, or greater, than those for terrestrial systems.

Working group leader Mike Burrows and I (with Chris Harley) also summarized the output of our team and other literature in a new book chapter (Bruno et al. 2014) which I serialized here.

Top 5 Things I Learned at The Benthic Ecology Meeting 2014

Justin Baumann has a very nice piece on his first experience at the Benthic Ecology Meeting here.

I was really impressed by his insight and the general maturity of his post. I am on Justin’s committee but I haven’t interacted with him enough to get this clear a sense of what he is doing and thinking.  Like so many newish grad students, Justin is really into blogging and science outreach.  I worry sometimes about students putting time into outreach, but one clear benefit is that it enables them to communicate ideas and opinions with their mentors and community.  So go check out his piece and some of his other posts at his website or the superb grad-student-run Under-The-C-Blog.

1) Benthic Ecology Meeting is incredibly student friendly!

According to the official conference booklet, 67% of all oral and poster presentations were given by students. As a conference attendee, I would say that it was safe to assume that students outnumbered faculty by at least 2:1, if not more. There were students everywhere. I’ve never been to so many student talks. This conference is not ASLO Ocean Sciences, it’s smaller, more personal, and less overwhelming. It offers students (both undergraduate and graduate) a great platform for being introduced to a conference and for giving a presentation to a large group of peers without feeling extremely overwhelmed. As someone who gave their first major research presentation in front of a room of the most well known faculty in my field (International Coral Reef Symposium), I would say that coming to Benthics first would have been dramatically better. Plus, since most of the attendees are students, it is a great way to meet colleagues in the field and discuss ideas without being overly intimidated. If you are a marine science student and you have never presented at a conference or want to work on your presentation skills, I suggest that you give Benthics a try!

Read the rest here