Even deleting the chestnut blight won’t necessarily bring the chestnut tree back*
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Tag Archives: Taxonomic
A new challenge
A few years ago, Sharon Baruch-Mordo posted a provocative challenge. She called it the biodiversity challenge and offered it as an opportunity to write about the importance of your research in the context of biodiversity and conservation. The biodiversity challenge was a tough one. Not many graduate students are given training in science communication, and when we are, it’s usually targeted towards generating concise scientific prose that can be published in peer-reviewed journals. But the challenge is an important one. If we want to disseminate our knowledge, we have to be able to communicate it effectively. Well, you rose up to the challenge, and we were amazed by the quality and breadth of the results.
Today, BioDiverse Perspectives is emerging from a months-long torpor to issue a new challenge. We still want you to tell us what makes your research topic relevant. But we want you to evaluate the importance of your research from a different angle. What would happen if the thing you study were to disappear off of the face of the earth tomorrow? How would the world change if your research topic simply ceased to exist?
Tomorrow, your favorite focal biological unit of research (molecule, gene, organelle, organ, organism, ecosystem, general law of nature) will be deleted from the face of the earth. What are the implications?
We took the challenge. Next week we’ll be posting our results, and we challenge you to join in, too. You can upload your posts here. We will publish them all, in full, as we receive them, unedited, in all their glory.
May 9, 2016
Best of Biodiversity in 2014
![By Tsirtalis (Own work) [CC BY-SA 3.0], via Wikimedia Commons](http://www.biodiverseperspectives.com/wp-content/uploads/2014/12/Island_Night_Lizard_San_Nicolas_Island_California.-608x456.jpg)
Biodiversity success of 2014! The Island night lizard was delisted under the Endangered Species Act in 2014. Photo by Tsirtalis (Own work) [CC BY-SA 3.0], via Wikimedia Commons
Happy New Year! To put the cap on 2014, we’ve highlighted some of our favorite biodiversity research and stories from the year. We’d love to hear what rocked your 2014 – pass us the link in the comments section!
- Reconciling Diversification: Random Pulse Models of Speciation and Extinction
- Predicting rates of interspecific interaction from phylogenetic trees
- Tale of two phylogenies: comparative analyses of ecological interactions.
Hundreds of new species have been described this year all over the world. Here are some of my favorites:
- A fossilized skull of one of the largest mammals that walked along with the dinosaurs in the Late Cretaceous, was discovered in Madasgcar. The species named Vintana sertichi was a 9kg gondwanatherian herbivore, that reminds me of a coypu. Up to now, the only information we had about gondwanatherian mammals came from teeth and small pieces of jawbones;
- A new species of annual fish from southern Brazil, Austrolebias bagual (bagual is a term from the Pampas that means untamed, unbroken horse or unsocial);
- The mushroom looking animals, form the deep oceans of Australia, Dendrogramma.
- A montane forest dwelling Tapaculo, form northeastern Brazil.
- And the coolest one; a new species of tree frog from the Amazon has been named after the Prince of Darkness, Ozzy Osbourne.
At last, a couple of species have been declared extinct in 2014 (for more information see the timeline of extinctions):
- Acalypha wilderi, a small shrub that inhabited the Cook Islands.The species has not been seen since 1929, and it seems that it disappeared due to habitat modification;
- Stipax triangulifer. This is a “virtually unknown” arachnid species that was collected only once in 1894 in the Seychelles island of Mahe, and was never spotted again.
-Vinicius Bastazini
The Avian Phylogenomics Project, an international team with more than 200 researchers worked in a collective effort to sequence the whole genome of 45 bird species, comprising the main clades of modern birds. The project published 28 papers, in journals like Science, Gigascience and Genome Biology, in just one day! One of their key papers is Jarvis et al., “Whole -genome analysis resolve early branches in the tree of life of modern birds”. Among their main findings are: 1) Two events of speciation happened around 66 mya, just after the dinosaurs went extinct, giving origin to most of the birds we know nowadays; 2) Avian genome is very reduced, with few repetitive DNA; 3) Vocal learning evolved independently, at least twice; 4) Tooth loss happened from lost enamel mutations, around 116 mya. Nonetheless, the most important steps accomplished by the group, is a better representation of the phylogenetic relationship of birds, with some very impressive changes, e.g. falcons are closer relatives to parrots than to other group of prey birds like hawks. Several other fields of biology must benefit from this better solved piece in the puzzle of the tree of life, especially fields like ecology, which in the last years has investigated the phylogenetic structure of communities as a way to understand patterns of diversity on Earth and the processes determining them. Maybe two last very important messages from Jarvis et al. (and the other of papers resulting from this project) are that: 1) basic science (e.g. taxonomy) is an essential tool for the next big steps toward understanding life on Earth; and 2) improvements on scientific knowledge are more and more related to collective efforts of huge networks of scientist and institutions around the world, working together in ambitious projects.
– Jeferson Vizentin-Bugoni
Some of my favorites from 2014:
- The first meta-analysis of intraspecific diversity effects on higher-order processes.
- Grazers influence the genetic structure of phytoplankton in a pelagic predator-prey interaction.
- Ecological and evolutionary potential of plant traits related to nutrient cycling.
- The atlas of human admixture history.
– Kylla Benes
Forget horses, 2014 has been the year of the lichen. And although most readers are probably uninclined to overthrow thousands of years of Chinese tradition to make it so, I’m here to tell you why it’s worth the effort. Ecologists studying lichens have worked hard this year to push their traditionally esoteric research subject out into mainstream ecology. In honor of 2014’s listicle-mania, here are the top four ways that lichenologists have really broken the mold. You won’t believe what they found…
4. Lichens impact ecosystems at both micro and macroscales. From Porada et al comes a brand-new estimation of how lichens contribute to global biogeochemical cycles. Zooming in, Delgado-Baquerizo et al show that lichen species in biological soil crusts can cause fine-scale variation in the nutrients and microbes that reside under them.
3. Lichens are great for testing general ecological theory and models, both new and old. Pastore et al found no evidence for a competition-colonization tradeoff in the life-history traits of lichens inhabiting rocks over a 30+ year experiment. Time to lay this old idea to rest? From Ruete et al comes a cool new model for estimating dispersal rates in a metapopulation that is at disequilibrium from presence/absence data, patch ages, and past distributions. Because really, when aren’t we in a disequillibrial state? And yes, they tested it with lichens because epiphytes are great models of meta-structure.
2. We have discovered that lichens have traits too! Farber et al found that the performance of lichens with light-absorbing versus light-reflecting pigments recapitulated the distribution of these species along a vertical light gradient in boreal tree canopies. Lichens, however, may be more variable in their traits than plants or animals. Asplund & Wardle found that the community-level response of lichen N and P-content to a nutrient gradient occurs mainly intra-specifically, and not because of species turnover. Perhaps fungi are more flexible?
1. It’s been a great year for lichens’ better half- the algae and cyanobacteria that do all the photosynthesizing in the relationship. Although historically underappreciated by lichenologists, this year saw a barrage of papers exploring diversity of these “photobionts”, from across whole communities and large taxonomic groups (Lindgren et al, Nyati et al, Sadowska-Des et al) to genetic diversity within a single lichen individual (Dal Grande et al). It’s becoming increasingly evident that partner specificity and local adaptation among photobionts is a key determinant of whether a lichen-forming fungal species has a broad (Werth & Sork, Muggia et al) or narrow distribution (Dal Grande et al). With increasing interest in the ecology of microbial systems, the role of symbiosis in the community ecology of lichens is ripe for research. If 2014 was the year of the lichen, 2015 will be for their algae.
– Jes Coyle
2014 by the numbers:
This is what a hero looks like (Malagidris sofina)
221 – the number of new species described by CalAcademy of Sciences this year. I was particularly charmed by the description of the defensive behavior of the Hero Ant of Madagascar (Malagidris sofina), which hurls itself at invaders, kamikaze-style, knocking them off the nest. See for yourself.
2,218 – Number of plants and animals currently listed as threatened or endangered by the Endangered Species Act. There is an active recovery plan for about half of those.
1 – Number of species delisted under the ESA during 2014. The Island night lizard (Xantusia riversiana), the poster child of this post, was originally listed in 1977, and has benefitted from the removal of invasive mammals from the Channel Islands, and is considered recovered.
90% – Estimated population losses for the Monarch butterfly over the past two decades. They are now being considered for ESA listing.
1.6 million – Area (km²) proposed in 2014 as additions to marine protected areas worldwide, including Fiji, Gabon, Palau, and the US.
– Emily Grason
December 30, 2014
This biodiversity researcher used Flickr for data, and you won’t BELIEVE what happened next!
Is this a datum? Jewel Eyed Beetle (what kind? I don’t know! I’m a marine biologist not an entymologist!) near Corcovado NP, Costa Rica – hand for scale. Photo Credit: E. Grason – that’s right, I went to Costa Rica and it was totally amazingOMG!
No more feeling guilty about spending time on Facebook while eating your lunch at your desk! No more casually closing your laptop when your advisor walks by tryna act like you were just finishing the conclusions of your thesis! No more hiding in the Instagram closet – I welcome you to the 21st century where all of the world’s problems are solved (if not also caused) by social media!
Vijay Barve recently provided me with all of the ammunition I need to justify the the time I already waste online in a recent Ecological Informatics paper. He advocates for the utility of social networking sites in the landscape of Digital Accessible Knowledge. That is: scientists should take advantage of all the hobbyist wildlife photographers out there who post on Flickr, Facebook, Picasa (and LOLcats?). Increasingly, photos are tagged with metadata such as time stamps and are geo-referenced with the location, facilitating inference on changes in species occurence over time and space.
This is, of course, all part of the big data push in biodiversity, and we have discussed other avenues for increasing the quantity of biodiversity data on this blog previously: including making museum collections “available” online (that is, making the data about specimens available, see our Diverse Introspectives conversations with Sharlene Santana), and training an army of volunteers to go be our scientific eyes and ears (The potential of citizen science). Eavesdropping on the online bragging about who saw what on which amazing vacation to Iceland/Bolivia/Antarctica/The Maldives(1) seems like a logical next step.
Barve uses to case studies to compare the quantity and quality of data to another currently-available online data repository, the Global Biodiversity Information Facility (GBIF). Species occurrence data for both the Monarch Butterfly (Danaus plexippus), and the snowy owl (Bubo scandiacus – (2)) were extracted from Flickr as well as GBIF, to explore geographic distribution of the two organisms.
For the Monarch (Figure 1), GBIF and Flickr yielded similar numbers of geo-referenced records/photos, depending on whether the common or scientific name was used as the search term (3). However, for the Snowy Owl (Figure 2), GBIF outperformed Flickr by an order of magnitude. This presumes, I think correctly, that the records are really only useful if they can tell us something about distribution or location of the observation. The author also points out a number of errors in the Flickr data, either misidentifications, or tangential references (as when a user names the Monarch for comparison with whatever the picture is actually of), but doesn’t quantify how much this would reduce the total number of valid observations.
Figure 1. Figure 2 from Barve 2014 showing records of Monarch from GBIF (grey circles) and Flickr (+: searches for the common name; o: searches for the genus and species name;-)
In the case of the Snowy Owl, it’s likely that some of the pictures were taken at zoos. However, both examples also show several cases where the data from Flickr exceed the spatial extent of the data from GBIF, and might actually improve our knowledge of the distribution of the animals, such as central Europe for the Monarch, and southern Europe for the owl. It’s also apparent from these figures that scientists go many places that tourists are not as eager to spend time, like Nunavut.
Figure 2. Figure 3 from Barve. Distribution of observations of Snowy Owl from Flickr and GBIF. Symbols as for Figure 1.
So it’s clear to me that there is potential here, but there is still a long way to go in making this a usable technology. If I were a cynic, I might argue that the data monkey on Ecology’s back has finally driven us to rock bottom, and we are so thirsty for data that we will find a way to subsist off of literally the lowest grade of information. If we consider biodiversity data on a scale that represents the trade-off between quantity and quality, E.O. Wilson would be on one end, on his knees staring at ants through a magnifying glass, and the guy bragging about how big the bass was he caught via Facebook would be on the other (4).
Some other considerations I think might be relevant:
- What is the quality of the geographic data on social media sites? On some sites, the data from the capture device (phone, camera, etc) is used, but on others, you can drop a pin by hand. How good is your memory of exactly where you were in the Amazon?
- *Cough, cough* Biasedtowardcharismaticmegafauna. Yes, butterflies count as charismatic at least.
- It’s unclear whether European organisms will invoke the “right to be forgotten” which could impose serious geographic bias on distributions.
I can see, however, that this type of information could be useful for keeping track of rapidly-emerging natural events, such as the irruption of the snowy owl discussed in the paper, or for identifying areas where additional research should be directed. Certainly this mountain of information could be used for something. If nothing else, I almost always enjoy just flipping through the photos and appreciating the diversity for what it is – totally effective clickbait.
- How did I not know that there is a Wallace’s Line cruise?! This is now on my bucket list and you will see how amazing it was on my Picasa page.
- Bubo is a pretty funny genus name (sorry orthithologists, you probably get this all the time). And while the first thing that popped into my head was Bubotuber juice from Harry Potter, I subsequently realized that a different phonetic association might occur to teenaged boys, but not because they know their Greek. Turns out the etymology of the word Bubo is even more likely to make middle schoolers giggle than I originally suspected since it evidently comes from “swelling of the groin”.
- It’s unclear to me how much the list of Flickr occurrences based on a query of the common name overlapped with the list of Flickr photos tagged with the genus and species names. Presumably some photos had both.
- I think a fruitful area of discussion at cocktail parties (j/k, grad student happy hours) might be the area in between. Here, rank the following in terms of where you think they fall on the quality/quantity of data spectrum:
- Graduate students
- Undergrads
- Faculty
- Citizen Scientists
- Private Sector Scientists
- Parents who help graduate students collect data for their projects
- Internet Trolls responding to articles about science
December 2, 2014
Why Conservation? Communicating Applied Biodiversity Science
Applied Biodiversity Science Program – Texas A&M University
You might have a favorite science writer. Mine are David Quammen, Bill Bryson, Carl Sagan, and Tim Flannery. Others may be more inclined to read Pulitzer Prize-winning and nominated authors like Jonathan Weiner, Siddhartha Mukherjee, or James Gleick, MacArthur-fellow Atul Gawande, or consummate greats like E. O. Wilson, Richard Dawkins, Stephen J. Gould, and Oliver Sacks. Or perhaps books aren’t all you’re interested in. In that case you may be a fan of Carl Zimmer’s blogging or the stories and editorials from journalists/authors Malcolm Gladwell or Stephen J. Dubner.
It’s likely you’ve read at least one of these authors. Like most readers you were probably impressed by how well they articulated the complexities and subtleties of their topic: everything from astrophysics to evolution, cancer, neurology, chaos theory, economics, and psychology. If you find an author who draws you into a topic that wouldn’t otherwise gain your attention, particularly an unfamiliar scientific discipline, take notice. Take stock of what they have accomplished by gaining your interest and curiosity. As George Gopen and Judith Swan stated in their 1990 for American Scientific, “the fundamental purpose of scientific discourse is not the mere presentation of information and thought, but rather its actual communication.” Good communication requires gaining the reader’s attention. Attention requires garnering interest and curiosity.
In our ever-connected world with vast communication and social networking ability, we have the ability to do just that. We possess the tools to communicate science to a diversity of people in a diversity of ways.
As a member of the Applied Biodiversity Science Program (ABS) at Texas A&M University I find myself in a position where communicating science is an imperative for success. The ABS program is graduate program originally funded by the National Science Foundation as part of their Integrative Graduate Education and Research Traineeship (IGERT) program. The principle mission of ABS at Texas A&M is to achieve integration between biodiversity research in the social and natural sciences with on-the-ground conservation practices and stakeholders.
To that end, a foundational component of ABS is to communicate across scientific disciplines with various institutional actors to facilitate broader impacts across the realm of conservation. In essence, the ABS Program seeks to produce applied scientists who can communicate effectively across disciplines. A natural corollary of this goal is the ability to communicate science outside the realm of science. In this respect, our ABS Perspectives Series is intended to communicate more broadly and inclusively who applied biodiversity conservationists are, what we study, where we conduct research, how we conduct research, and why we are doing it. The current issue of the ABS Perspectives Series, features experiences from the Caribbean, the United States, Sénégal, Ecuador, Nicaragua, and Costa Rica. Contributions cover topics ranging from captive parrot re-wilding with pirates to blogging in the Nicaraguan forest with limited Internet access.
Perhaps more importantly, the ABS Perspective Series wants to reach out and share ABS student and faculty experiences with a diverse readership to raise awareness of biodiversity conservation issues. Outreach is an important axiom of actionable science, especially outreach that informs, improves and influences management and policy. I consider both the ABS Perspectives Series and BioDiverse Perspectives outreach initiatives to communicate the biodiversity conservation mission to the general public, communities where our research has been conducted, fellow academics and practitioners, and institutions that can provide logistics, infrastructure, and support. We must intend to make and practice making our research accessible and intriguing to everyone.
November 18, 2014
Flump side of the moon
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!
An article published in PLOS ONE on Wednesday describes a new genus (Dendrogramma) of benthic organisms that, based on preliminary morphological data, have been classified at Metazoa incertae sedis. This basically means we know they’re animals, but we couldn’t tell you which phyla they belong to. The fact that we can’t find a taxonomic place for these critters, along with the absence of available genetic data, let’s me think that we haven’t heard the last of Dendrogramma.
National Geographic released a troubling story last week detailing the decline of Icelandic seabird colonies and what that means for their respective global populations.
A study in Science, representing the work of researchers from across the U.S., documents the genetic composition of the microbiomes associated with human homes. Major findings include that humans tend to be the “primary bacterial vector,” and that we should be paying much less in rent based on the amount of additional bacterial occupants within our own private domicile. – Nate Johnson
September 5, 2014
