Opening up open access

At a conference a few years ago I spoke with a friend who said “when I talk to people who say “I’m going to publish 5 papers this year, even though I haven’t submitted any” and it’s July I smile inside. It takes so long to publish papers there is no way they will be able to publish 5 by December”. It’s true, it takes forever to publish (after the writing and submitting part, which for me takes awhile too).

But some scientist, even Nobel Prize laureates, are publishing things online before even submitting it for review in an “official” publication. Not only does this cut out the journals who are arguably making a ton of profit off our free labor (see here and here), but it gets your work out to the scientific community faster.

Read about it over at the New York Times! 

from asapbio.org/yourekascience.org

from asapbio.org/yourekascience.org

Happy Anniversary Planet Earth! Episode 6: Ice Worlds

Both poles of our planet are covered in ice. They are the largest and most demanding wildernesses of all.

Sigh. We’ve made it to the Ice Worlds episode – the one where the changes of the last ten years are most obvious.

Our understanding of climate change has increased greatly in ten years, although many (especially in the US) remain in doubt. The episode begins and ends in the Arctic, where polar bears are the keystone predator and our adopted mascot for efforts to stop climate change. Maybe you’ve seen the super depressing pictures of starving polar bears. Or the pictures of them swimming in open water. Unfortunately, these aren’t the only animals threatened in these habitats – in fact, basically all animals are negatively impacted by climate change.

Long term studies show Adelie penguin and Chinstrap penguin populations are declining. Antarctic sea ice provide fungus for krill to eat, which the penguins survive on. Emperor penguins fare no better, and their populations are expected to decline massively over the next 50 years or so. Humpback whales also feed on krill in the Antarctic and may be starving as the krill populations decline.  Several birds breed in the Antarctic. Climate change affects these birds in many ways – there may be more nesting habitat for these birds, like Snow Petrels, but the birds also seem to be breeding later in the year as sea ice cover timing changes.

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Time for your close up, Ms. Krill.

The sun’s influence diminishes and the ocean starts to freeze. the greatest seasonal change on our planet is underway…

Antarctica is losing ice. This topic has been discussed extensively (see various links here) and is of obvious importance. Unbelievable amounts of ice are doing (nearly) unbelievable things. Weather systems are becoming more dangerous and more costly. What is being done? The White House has enacted some plans for combating climate change and in 2015, the United Nations Climate Change Conference in Paris led to the “Paris Agreement”, outlining a global reduction of climate change (specifically, a limit of global warming and greenhouse gas emissions). These steps are necessary and it’s encouraging that the Paris Agreement has global support. I guess it remains to be seen whether these efforts are enough.

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Ice. It’s pretty. I hope it’s not an endangered species.

Unlike Antarctica, the Arctic is a vast frozen sea surrounded by land.

The same threats and stories are occurring in the Arctic as the Antarctic. Arctic Musk oxen are declining and their range contracting due to climate change as well (and this may have been occurring for the last 10000 years – covered previously at NiB!)

Bad news is everywhere you look when it comes to the Ice Worlds. I’ve watched this episode several times now and it depresses me more each time. Time to focus on getting mad (and proactive) instead of get sad though: here are some tips from the USA Environmental Protection Agency  on how to start combating climate change on a local scale.

The episode ends with more shots of polar bears. I really hope 10 years from now we’re reporting population growth and decreased greenhouse gas emissions, instead of the easier to imagine and much less pleasant alternative.

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Polar bear mama and cub.

Following their mother has prepared them for life at the pole, an ever changing land ruled by ice. Whether they are ready for the bigger changes that have begun to shape the ice worlds of our planet remains to be seen.

The Postdoc

When we started this blog, the majority of the contributors were graduate students. Now, everyone has moved onto other stages in their careers (good job! go team!). But as I was the youngest when we started, I am the only one who remains pre-PhD (but finishing up this spring!).

And as a result, I am thinking about/applying to postdoctoral positions. I have written a bit about the postdoctoral position in the grand scheme of academia (here and here(especially the second post, Jeremy really summed it up excellently)).

And adding to the stack of interesting reading, this post about how a new PI views postdocs and how their plight is viewed from someone recently on the other side.

from PhD comics

from PhD comics

 

Genetic Drift vs. Inbreeding

I got this question as part of my preliminary exam: “What effect does genetic drift have on inbreeding?”

It is a difficult question to answer, and one that I’ve thought on often over the years. So imagine my delight when over at the Molecular Ecologist (If you aren’t reading the Molecular Ecologist every week, you are missing out. Seriously. Go read all of it. Now) Patricia Pecnerova wrote an article addressing the complexities of this very question.

Check it out here. And read all their stuff.

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They are also doing a fundraising campaign, and have a cool logo (see above) which you can get on a tshirt or Mug.

Happy Anniversary, Planet Earth! Episode 5: “Deserts”

As the fifth episode of Planet Earth begins, it feels like you might have stepped onto another planet.

The Namib desert (flickr: mariusz kluzniak)

The Namib desert (flickr: mariusz kluzniak)

Desert landscapes have an alien, otherworldly feel to them; vast swaths of sand around the world have acted as the backdrop for NASA equipment tests, science fiction classics like 2001: A Space Odyssey, and, of course, supposed extraterrestrial activity. But despite their interstellar associations, deserts are very much of this planet. As narrator David Attenborough tells us, deserts cover a third of the Earth’s surface, and all of them are populated with life.

“Deserts” takes us into a world of extremes, where the environment can go from habitable to hostile in an instant. In this 10-year anniversary post we will relive the episode’s most intense moments, highlighting the incredible challenges that accompany life in Earth’s driest places. We will also take a look at the unique difficulties conservationists face in attempting to protect the organisms that inhabit these inhospitable regions.

Desert Survival is About Timing

In the deserts of our planet, extremes are the norm. Attenborough tells us that temperatures fluctuate annually in the Gobi Desert from -40° C in the winter to 50° C in the summer. Death Valley holds the record for highest temperature ever recorded, at 56.7° C. In the Sahara Desert, sandstorms to rival Mad Max can reduce visibility over regions the size of Great Britain for several days, and the resulting dust clouds can affect weather patterns around the world.

Things don’t happen in moderation here.

Good conditions are transient, and when they do occur, organisms must be ready to take full advantage of them. Timing is everything when you are trying to survive in the desert, a fact that is apparent in multiple segments of the “Deserts” episode. Kangaroos in Australia forage in the early morning when temperatures are moderate, but must find a tree that provides suitable shade from the sun before midday, lest they risk overheating. Scorpions and toads in the Sahara have almost no tolerance for the sun’s rays, and must emerge from shelter only at night.

The importance of timing shows up in somewhat unexpected ways as well. For example, wild camels have fine-tuned the timing of their breeding season to coincide with the onset of winter, when precipitation is the most abundant. In the Gobi Desert, snow covers the ground throughout the winter months, providing a reliable and widespread source of water for the camels. Planet Earth camera crews searched the Gobi for two months for these rare and elusive animals, finally obtaining fantastic footage of the bizarre mating rituals of the species.

The ephemeral nature of favorable conditions means that a single bout of resource availability must sustain desert plants and animals for long periods of time. In Namibia, a flash flood (one of just a handful that occur annually) produces a burst of vegetation growth. This rare resource attracts oryx to area, which in turn attract a family of lions. Attenborough tells us that a single oryx will sustain the entire lion family for a week. These infrequent bouts of productivity are key in maintaining life here, for a range of species.

Rain is also infrequent in the Sonoran Desert. Consequently, the saguaro cactus is well-adapted to make the most of the brief Arizona monsoon season. The pleats on its trunk allow the cactus to expand, so that it can absorb as much of this valuable resource as possible- up to 5 tons! And if the cactus is good at collecting water, it’s even better at making it last; it can live off these stores through multiple months of drought.

A saguaro cactus (flickr: Michael Wilson)

A saguaro cactus (flickr: Michael Wilson)

When resources like water are so difficult to come by, one survival strategy utilized by many desert species is to rely on other organisms collect them first. In the Atacama, the only predictable source of water comes in the form of a fog generated by cold ocean currents. Coastal communities of plants called lomas collect the fog’s moisture, and provide life-sustaining hydration for a number of desert organisms. Guanacos eat cactus flowers for the water they contain, and coyotes lick dew off of moisture-loving lichens.

Interacting with other species can also be key if you are a traveler, trying to get across the depauperate desert environment as quickly as possible. For just four weeks during the summer, saguaro cacti bloom during the night. The timing of this event corresponds to the annual migration of the lesser long nosed bat. As bats travel across the Sonoran during their trip from Mexico to the United States, they subsist on nectar from the flowers, fertilizing the next generation of cacti along the way. The bats would have no hope of making it across if it wasn’t for this short-lived food source, and the saguaros in turn rely the bats for pollination.

While resources are fleeting in the desert, we learn that some elements of this ecosystem stick around for a surprisingly long time. For instance, star dunes in Namibia can reach up to 300 meters high. The sand at the peaks of these dunes is in almost constant motion thanks to the wind, but sand at the base may not have shifted for 5,000 years. In addition, locust eggs lie dormant for 20 years before they hatch, and seeds in Death Valley can wait for 30 years for favorable conditions before they sprout. A “superbloom” of wildflowers is currently taking place in Death Valley- what a fantastic way to celebrate the anniversary of Planet Earth!

The Curious World of Desert Conservation

In the desert ecosystem, organisms face a somewhat bizarre set of conservation challenges.

From the illicit underground cactus trade, to the legacy of nuclear weapons testing; from rabbits run amok in Australia, to the controversially brutal hemorrhagic disease released to control them; from a history of violent confrontations between the federal government and armed ranchers, to the endangered desert tortoise that first set those land disputes in motion- conservation in the desert has a strange and dramatic past.

In terms of scale, The Great Green Wall of Africa is as dramatic as conservation comes. An effort to counteract the ongoing effects of desertification, the Great Green Wall project proposes to plant a corridor of drought resistant trees along the southern edge of the Sahara. The Great Green Wall, if completed, will be really, really long: 4,750 mile long and 9 miles wide, to be exact. It’s a huge undertaking, with 12 nations currently in collaboration on the project. But if all goes to plan, the Great Green Wall will be quite an amazing feat of conservation.

Big game hunting presents another dramatic desert conservation issue. In 2014, Namibia issued a handful of licenses to hunt desert elephants. Desert elephants are distinct from African elephants, exhibiting a number of behavioral and morphological adaptations for desert life. These locally adapted animals are also exceedingly rare, with fewer than 100 individuals in Namibia. However, desert and African elephants are not technically considered separate species, and thus the Namibian government does not currently extend any additional protection to these populations. This controversy highlights the importance of species delimitation in conservation- an issue that is only more dramatic in the context of big game hunting.

A desert elephant (flickr: Vernon Swanepoel)

A desert elephant (flickr: Vernon Swanepoel)

The plants and animals of the desert are some of the planet’s most hardy, but even they can have difficulty rebounding from disturbance. In the Atacama, the life-sustaining lomas are at risk. Local people rely on the water-collecting capabilities of these plants for survival, but have also destroyed the majority of the vegetation to make way for agriculture. Researchers are attempting to replant one particular plant, called the tara tree, in hopes that it will help to rehabilitate these important communities. But new seedlings seem to have trouble taking hold within existing lomas. Lomas are home to 1,400 plant species, around half of which are endemic; their loss would be truly devastating to the region.

Deserts, with their reputation as barren wastelands, may not seem like obvious targets of conservation. Desert flora and fauna face extreme conditions on an everyday basis, and the added strain of human impacts makes survival all the more difficult for these organisms. But on the bright side, evidence suggests that our effects on deserts can be successfully mitigated. In the case of the once-threatened Eureka dune grass, limiting the use of off-road vehicles in particular regions of Death Valley has been enough to allow populations of the plant to reestablish.

Life in this unique desert ecosystem defies all odds, and protective measures will be key for helping it to persist into the future.

Be sure to stick with us as we continue our celebration of Planet Earth’s 10-year anniversary! Check out our posts on “From Pole to Pole,” “Mountains,” “Fresh Water,” and “Caves.” Next week we’ll be looking at the polar opposite of deserts: ice worlds!

 

The Tully Monster

In 1955 Francis Tully found a fossil 50 miles south of Chicago that looked like “an obese foot-long earthworm with a trunk and a spade shaped tail”. See below.

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When Mr Tully brought his discovery to the field museum, where they had no idea what it was either (but they named it Tullimostrum gregarium, which is latin for “Tully Monster”). Or what it might be related to. Or what animal group it belonged in. What they did know was that this strange monster wasn’t rare, in fact specimens started cropping up all over the place.

50 years, and 1200 specimens later, Victoria McCoy and a team of scientist have solved this very puzzling mystery. Read about it over at the Atlantic, or the original paper here.

The insignificance of the significant pvalue

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We’re told early and often that this means that your data is significant. But statisticians and biologists that are statistically inclined, while tell you (and have been telling us for awhile) that this is a completely arbitrary figure. Like most tools, in statistics if you use the pvalue incorrectly you’re doing yourself and your science a disservice.

And the American Statistics Association agreed, and disagreed. Last week they released an AWESOME statement on p-values.

Read the original, or the equally excellent synopsis over at the Molecular Ecologist (I can’t give that blog enough love…)

xkcd comics

xkcd comics

Happy Anniversay, Planet Earth! Episode 4: Caves

This is our planet’s final frontier. An inner world where only the most adventurous dare to go.

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The episode opens with shots of BASE jumpers being swallowed by the Cave of Swallows in Mexico – the largest cave shaft in the world. Throughout this episode, we’re treated to seeing some of the least explored or just most stunning places on Earth – Deer Cave in Borneo, the cenotes of Mexico’s Yucatan Peninsula, Poor Knight’s Island in New Zealand and Lechuguilla – a gypsum crystal filled wonderland with clear water pools near Carlsbad, New Mexico. We’re also shown the bizarre and slightly creepy cave specialists that frequently share slightly disturbing characteristics like eyelessness, albinism and bioluminescence.

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I’m tempted to assume that caves are one of the environments least affected by climate change. I mean, they’re frequently underground and thus climatically buffered and away from most human-associated changes. It may even turn out that their isolation is beneficial to humans. For example, researchers in 2012 found bacteria in Lechuguilla that are resistant to many of the antibiotics we currently use to treat infections – but not because we brought them there. These bacteria have never been exposed to human sources of antibiotics but were all resistant to between one and 14 (!) currently used antibiotics. This means (1) they were exposed to antibiotics inside the pristine cave and (2) they’ve evolved to get around those compounds. “This has important clinical implications. It suggests that there are far more antibiotics in the environment that could be found and used to treat currently untreatable infections.” says Gerry Wright (scientific director of the Michael G. DeGroote Institute for Infectious Disease Research at McMaster University). I don’t want to overstate these findings but caves could hold the key to stopping the antibiotic resistant apocalypse!

Since Planet Earth first aired many new caves have been discovered. Including “the cave so huge it has it’s own weather system” – the first pictures of Er Wang Dong in China came out in 2013 and it’s amazing to see something so large be discovered on our increasingly small planet. Explorers in the Czech Republic believe they have found the world’s deepest underwater cave, measuring in at over 1200 feet down. And Son Doong in Vietnam was discovered in 2009 – another mammoth cave, 2.5 miles long with some passageways being over 600 feet high. (A digital tour can be found here.)

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Cave research in the last ten years has also resulted in one of the biggest discoveries of the decade – sitting in the bottom of the Rising Star Cave system in South Africa, a team of 7 spelunkers found thousands of fossils belonging to at least 15 individuals from a new species of human ancestor, Homo naledi. The placement of H. naledi on the Hominid phylogenetic tree and the questions surrounding this amazing discovery (particularly – how did so many individuals become located in a single, difficult to access place? Did H. naledi dispose of their dead?) have been exciting questions that are transformative for what we know about human evolution. (Read more about the expedition here or some of the National Geographic coverage here.)

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Not all cave news is happy, unfortunately. Climate change and human habits are affecting ground water and ground water affects caves, both new and old. A particularly sad example is from the Ayalon Cave, discovered in 2006 near Ramle, Israel. The good news: inside the cave, researchers discovered a new species of blind cave scorpion, named Akrav israchanani (after the men who discovered it). The bad news: all 10 specimens had been dead since the 1990s, when intensive pumping of groundwater changed the level of underground water, possibly altering the scorpion’s food chain and driving it to extinction. More good news, though: some parts of the cave system remain intact and another 7 species of arthropods were found in the cave (including some new species) – the challenge now is to protect the cave and its inhabitants from their own discovery.

Here’s a link to the full episode – check it out!

Happy Anniversary Planet Earth pt 3: “Fresh Water”

All live on land is dependent on Fresh water, but it is only 3% of all water available on earth, as David Attenborough reminds us in the opening lines of the third episode of Planet Earth.

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Unlike some of the other Planet Earth episodes, this one is clearly a journey. We follow fresh water from where it condenses at the top of mountains, down to where it eventually meets oceans, with a slight detour to talk about some epic lakes on the way.

We start in the mountains of Venezulua, the epic Mountain plateaus that inspired Arthor Conan Doyle’s Lost World. At these heights, it rains a ton. The ocean air gets pushed up to great heights, the air condenses and falls as rain by the gallons. We’re talking about a tropical down pour every day of the year.

From there it cascades down, “from humble streams to mighty rivers”, until we get a view of Angel falls (the inspiration for Paradise Falls in the Pixar movie Up).

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Where only the strong thrive

After landing on the ground, we move into my favorite part of the episode, embracing the uncharismatic minifauna. The fresh water is full of energy, and low in nutrient making life difficult. And yet somehow invertebrates thrive, clinging on to the rocks for dear life. Hellgrammites, with their busy gills to extract oxygen and Bamboo shrimp filter out particles as they rush by using their fanlike forearms. And although they may not be small, no one can say that the Giant Salamander is charismatic. With a face only a mother could love, they can grow up to 2 meters long and are one of the only predators in these rough waters. With poor eyesight, they more than make up for it using the sensory nodes on their face and body.

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Damn dam building

Similar to salmon, the giant salamanders swim upstream to spawn. Their migrations is increasingly being blocked by dam-building. Ramps and staircases are being added to allow them to move upstream, but the impediment has effected the population. To see one possible solution, I would like to draw your attention to the salmon cannon:

I give you, the salmon cannon.

I give you, the salmon cannon.

Water: The epic battle for life

Next we enter the segment of this episode that I’d like to call “Ichthys/Herps vs. Mammal”. We have ahead of us a series of monumental battles between predator and prey that take place in or near fresh water.

We begin with salmon, known to travel hundreds of miles back to their spawning grounds to reproduce (see above note about the salmon cannon facilitating this migration). But, low and behold, where there are happy breeding salmon, there are also hungry bears ready to eat them. In this episode we get almost face to face with a grizzly bear, swimming along looking for that oh so delicious tasty morsel. And what’s more, he’s brought along two adorable cubs to teach to hunt. And maybe share his food.

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As we leave the mountains, the fresh water warms and begins to support more life. In comes the world’s most social otter in India. They rub coats, fish together, and ward off predators together. First, we see the otters diving gracefully to catch, and teaching their young otters to fish as well. The social otters are together able to defend themselves against a 4 m long crocodile.  While at first the otters seem hopelessly outmatched (and if they were alone, they most likely would be) but as a group they successfully put him in his place.

Finally our river starts to meander slowly across the planes of east Africa. No longer as dynamic and destructive, but the life source for millions of wildebeests. Where the wildebeest go to drink the crucially important water, the Nile crocodiles (5 m long?!) feast on the abundance. While these two creatures are seemingly well matching in size and ability, these massive crocodiles are shown to repeatedly catch and devour their prey.

Stay away from the humans and you’ll be fine

The freshwater, social and crocodile destroying otters seen in this episode are facing threats from construction of large-scale hydroelectic projects (see above problem with damn dams). With humans over fishing their prey, polluting the water, and poaching their soft fur, these otters have seen serious population decline, and are listed as endangered.

The biggest problem Nile crocodiles face? They have a tendency to attack and eat humans, who in turn try to shoot the massive apex predator. They are responsible for hundreds of deaths each year, which ultimately gets them shot. Despite this, the population size is not threatened. More threatened than crocodiles, are wildebeests. Their massive migrations require open land. A fence was erected between the wildebeest and their watering hole by the Botswanan authorities, and it killed thousands of wildebeests reducing the herd by 90%.

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Detour: Check out these lakes!

While most rivers run to the sea, some drain into lakes. Because in general the Planet Earth series tends to focus on the extremes (largest mountains, smallest insect, etc), we start by visiting some of the largest lakes, and then work our way up to the biggest. The first three are in Africa, and Lake Malawi, Lake Tanganyika and Lake Victoria. The fish life in these lakes contain insane amounts of biodiversity. There  are 850 different cichlids alone, all evolved from one ancestral species (adaptive radiations anyone?). The males make craters to impress females, while others brood their young in their mouths for predators.

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Next we drop to the bottom of Lake Malawi, only to race back to the top. The floor is 700 m deep, where in the anoxic water allow the lake fly midges to hide from predators. They then rise to the surface for the most epic looking mating ritual I have ever seen invertebrates do. The density of flies are so intense they look like columns of smoke, instead of columns of flies mating. As the smoke clears, the flies fall to the lake surface, and die.

The worlds largest lake, or next stop, is a lake the has everything. Seriously if you want to study any biological question, study Lake Baikal. It contains a forest of sponges, the worlds only freshwater seal, and goofy looking crustaceans.

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Endemic Fish are the Most at Risk

Of the 850 species of cichlid, 184 are vunerable, 52 are endangered and 106 are critically endangered. Additionally, many are thought to be extinct. This is largely due to the introduction of the Nile perch in Lake Victoria, which decimated a lot of cichlid populations.

The biggest threat to the vast diversity of life in Lake Baikal is pollutants. A pulp and paper mill plant was constructed in 1966 directly on the shoreline. It was successfully shut down in 2008 (YAY!) but reopened in 2010 (BOO!). Luckily, it continued to be unprofitable and closed for good in 2013. It has now been turned into an nature reserve.

The Biggest of Big Rivers

Back on track heading toward the ocean, we start talking about the worlds most epic river, the Amazon. There are more fish species described within this massive river than in the Atlantic Ocean. The boto dolphins drive many different species of fish before them in a a wave of death. To attract the females, male dolphins carry large objects in their mouths, such as branches, or rocks.

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In the flat flood planes of the Amazon the river annually overflows its river and generates the worlds largest wetland. Remember those stories about pirañas in your childhood? They are more scary in person as we find out in our next segment. Ready to pick off any fish, a feeding frenzy develops in seconds, stripping a fish to the bone in minutes.

The Amazon in Trouble

While the pirañas and boto dolphin populations are not listed as endangered (although the dolphin has flirted with that title before), the amazon river faces various threats from dams (I’m seeing a pattern here…), mining, overfishing, and deforestation sending various pollutants into the river.

Want more updates/celebrations of this fantastic series? Check out the previous posts (From Pole to Pole and Mountains) and come back next week as we head down into Caves.

 

Introducing a new resource for ecology and evolutionary biology

Gina Baucom and Meghan Duffy noted and lamented the lack of female scientist getting the big ecology and evolution awards.

And then they decided to do something about it.

I give you DiversifyEEB, a list of female and/or underrepresented minority researchers in Ecology and Evolution. The idea is to have a go to list of minorities in the scientific community who are willing to give a talk at conferences or seminar series. So if you’re organizing a conference and thinking “How can I make my invited speakers more diverse?”, consult this list. There is now a way.

Go read all about the motivation and the list itself over at Dynamic Ecology.

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