Category Archives: ecology

Natural History in the -omics era

by Hird

This post is a guest contribution by Michael Harvey, graduate student in Robb Brumfield‘s lab at the Museum of Natural Science at Louisiana State University. Mike studies avian evolution, phylogenomics, and Neotropical ornithology. 

Blackwater river…approximate Bayesian computation…dawn song…genomic islands…wing chord…target DNA enrichment…

My life as an evolutionary biologist straddles two worlds. I study the comparative phylogeography of Amazonian birds, and on the one hand my research involves laboratory and computational methods that push the limits of new technologies and analytical techniques, and on the other, expeditions to the tropics that are nearly indistinguishable from the natural history work conducted by Victorian era biologists. I am a PhD student at Louisiana State University, and for most of the year my work is in the lab and at my desk. For several months of the year, however, my work is general ornithological collecting expeditions to the Amazon Basin.

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Friday Coffee Break, St. Patty’s Style

by yoderjb

Irish Coffee

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

First of all, my deepest apologies for the lateness of this post.  As you may know I am a 4th year medical student and today was Match Day and I was deep in the throws of celebrating the completion of 4 years of medical education as well as learning where I will be training for the next three years in Family Medicine.   So, without further adieu, your links for this week.

CJ decided to that there were too many good links and had to share several.  First, as a skater herself she found an article relating to transmission of skin flora between close team mates and those competing in roller derby.  Next she decided to share how the sequester is going to affect science jobs and the next few years could be difficult.  But finally, a cool post on five animals that could possibly take over the world, which makes me look at spiders a little closer now.

Next, Jeremy likes the fact that new evidence from the Mars rover is favorable to the possibility of conditions that could have sustained life on the red planet.

From Sarah, some very cool slow mo predator vs. prey footage.  Gotta say this is pretty awesome!  She also found some up close and personal pics of jumping spiders.

From Noah, a video documenting several scientists as they inventory one of the worlds most biodiverse locations, the Yasuni Biosphere Reserve.

Finally, in the spirit of March Madness, from Devin comes a battle of the Mammals. “Mammal March Madness from the Mammal’s Suck blog. Although the tournament is purely fictional, the facts and natural history information given out during the extended live tweet rounds are amazing. The first rounds are already complete, but tune in for the exciting finals. Live action via twitter: @Mammals_Suck and general info via the website:”

A post about lizards on islands. But not the ones you’re probably thinking of.

by noahmattoon
Yemen Socotra Felletti 48_00

Socotran Adenium obesum

Evolutionary biologists are fascinated by islands. There are a number of reasons for this. Islands systems can act as natural evolutionary experiments. They are small, less biodiverse, and isolated, so their biota can often be treated as simplified models of more complex mainland ecosystems (e.g. Darwin’s finches on the island Daphne Major). Ecologically similar islands can also act as replicates, with related taxa playing out the same evolutionary scenarios over and over again in isolation (e.g. Caribbean Anolis). Or they can act as life preservers, providing isolated strongholds for ancient evolutionary lineages that have long been extinct in the rest of the world (e.g. the Tuatara of New Zealand).

The Socotra archipelago is a particularly interesting, but poorly studied island system. Socotra consists of four islands in the Indian Ocean. It is extremely isolated (150 miles from the horn of Africa, 240 miles from the Arabian Peninsula) yet it has a continental origin. That means it was once part of the supercontinent Gondwana and suggests that some species may have lived there since it first became an island (~17.6 million years ago). Socotra has a very high level of endemism, with 37% of its plant species and 90% of its reptiles occurring nowhere else. As the islands are very remote and in a politically unstable part of the world, most of this unique biodiversity has not been studied using modern techniques. The islands are rugged and mountainous, reaching 1500m elevation, and primarily classified as tropical desert, making for a fairly fantastical landscape. A recent paper by Goméz-Diaz et al. (2012) takes a broad-brush approach to characterizing a chunk of Socotra’s obscure diversity: the Hemidactylus geckos.

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Evolving invaders

by Yoder

This post is a guest contribution by Kathryn Turner, a PhD student at the University of British Columbia, who studies the evolution of invasive thistles. Kathryn writes about her scientific interests at the slyly named site Alien Plantation and tweets under the handle @KTInvasion.

ResearchBlogging.orgInvasive species are a big problem. A real big problem. In the US alone, invasive species cost nearly $120 billion in damages per year (Pimentel 2005). 42% of species on the Threatened and Endangered list are there primarily because of invasive species.

Which leaves us with two questions. First, most obviously, how is it that a species is able to come into a new environment that it is not adapted to, surrounded by new environmental conditions and foreign biological interactions, and thrive? Thrive so exaggeratedly, that it can out-compete and displace species which have been there for millennia, adapting precisely to those environmental conditions and biological interactions? How can an individual survive to propagate a population? How can any species accomplish this? Second, less obviously: why can’t more species do it? Humans transport animals and seeds (and spores and larvae, etc, etc) around all the time, but only 10% establish self-sustaining populations, and only 1% spread to new habitats, becoming potentially invasive; this is known as the ‘tens rule’ (Williamson 1993) – a funny ‘rule of thumb’ for which I could never quite figure out the math.

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Ecological complexity breeds evolutionary complication

by Yoder


ResearchBlogging.orgIt is a truth universally acknowledged in evolutionary biology, that one species interacting with another species, must be having some effect on that other species’ evolution.

Actually, that’s not really true. Biologists generally agree that predators, prey, parasites, and competitors can exert natural selection on the other species they encounter, but we’re still not sure how much those interactions matter over millions of years of evolutionary history.

On the one hand, groups of species that are engaged in tight coevolutionary relationships are also very diverse, which could mean that coevolution causes diversity. But it could be that the other way around: diversity could create coevolutionary specificity, if larger groups of closely-related species are forced into narower interactions to avoid competing with each other.

Part of the problem is that it’s hard to study a species evolving over time without interacting with any other species—how can we identify the effect of coevolution if we can’t see what happens in its absence? If only we could force some critters to evolve with and without other critters, and compare the results after many generations …

Oh, wait. That is totally possible. And the results have just been published.

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The paradox of the prickly: Why grow thorns if they don’t work?

by Yoder

This post is a guest contribution by Colin Beale, a research fellow at the University of York who studies ecology in Tanzania. Colin writes about the living community of the savannah, from butterflies to wildebeests, with co-blogger Ethan Kinsey at Safari Ecology. If you have an idea for a post, and you’d like to contribute to Nothing in Biology Makes Sense, e-mail Jeremy to inquire.

Giraffes lick leaves from between the thorns.

Spinescent. Now there’s a word! It simply means having spines and one of the first things many visitors to the African savannah notice is that everything is covered in thorns. Or, in other words, Africa is spinescent. It’s not a wise idea to brush past a bush when you’re walking, and you certainly want to keep arms and legs inside a car through narrow tracks. These are thorns that puncture heavy-duty car tyres, let alone delicate skin. But why is the savanna so much thornier than many of the places visitors come from? Or even than other biomes within Africa, such as the forests?

At one level the answer is obvious—there are an awful lot of animals that like to eat bushes and trees in the savanna. Any tree that wants to avoid this would probably be well advised to grow thorns or have some other type of defence mechanism to protect itself. But then again, perhaps the answer isn’t so obvious: all those animals that like to eat bushes seem to be eating the bushes perfectly happily despite the thorns. So why bother having thorns in the first place? There’s certainly a serious cost to having thorns: plants that don’t need to grow them have been shown in experiments to produce more fruits. So if animals eat the plants with thorns anyway, why pay this cost?

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A post about inbreeding depression in which I make no reference to the movie “Deliverance.”

by noahmattoon
Bighorn sheep (Ovis canadensis) at Glacier National Park in Montana. Photo by Noah Reid.

As humanity spreads out over the globe, finding ever more clever ways to domesticate wild landscapes and harness natural processes to its will, many species of wildlife find their natural distributions becoming fragmented.  Iconic North American species such as grizzly bears, red-cockaded woodpeckers, and the American burying beetle today inhabit only small fractions of the ranges they occupied only 100 years ago. A result of this fragmentation is that many individuals exist in small, isolated populations.  In these populations, a curious phenomenon often emerges, one that can only be understood in light of some basic evolutionary theory.  That phenomenon is known as inbreeding depression, and it refers to the decline in average fitness of individuals in a shrinking population.

Inbreeding depression is essentially a result of individuals in small, isolated populations being more likely to mate with close relatives.  It’s well known that mating with close relatives produces less fit offspring, and the aggregate effect in natural populations is seen as low average fitness and an ensuing low population growth rate.  This can be a serious problem in populations subject to conservation efforts because even after protective measures have been taken (removing threats, restoring habitat) recovery can be hindered by inbreeding depression.  Inbreeding depression is slightly more complicated than this, however, because it is not consistently seen in all small populations.  In some island populations with very small population sizes (such as the Chatham Robin, Petroica traversi) inbreeding depression has not been observed (Jamieson et al. 2006).

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Christmas is upon us, what field guide, obscure tome and biography of Darwin would you bring to a far away island?

by williamgodsoe

I’ve been looking through my bookshelf and would like your help with a bit of a thought experiment. In evolution and ecology we are often concerned about when we can see past the complexities of the natural world and get to general, reliable knowledge. In a sense this is a matter of taking lots and lots of information and boiling it down to a small set of facts that we think “really” matter. Due to a recent job change I’ve had to get rid of a large section of my book collection and I would like chat with you guys about which pieces of biology were “general” enough to take on a long voyage.

Sure the question “what book would you take to a far away island” is supposed to be clichéd, but this June the question became quite literal for me. I was working at a post doc at the National Institute for Mathematical and Biological Synthesis at the University of Tennessee in Knoxville (USA) and was offered a job as a lecturer at the at the University of Canterbury in Christchurch New Zealand. The job had a lot of what I was looking for, a chance to do research, some teaching and an amazing local to think about biology. The one thing that this job did not include was a hefty budget to move my huge collection of books to a distant hemisphere.

Me tramping in New Zealand.

People who know me well will realize how painful this would have been. I am a compulsive buyer of field guides and if I spend more than a day or two in some new place I immediately track down the nearest visitor center and pick up a copy of any field guide I can find. When Jeremy Yoder found out I was moving to Tennessee he gave me (not entirely in jest) a guide to an obscure group of algae in Great Smoky Mountains National park as a going away present. That book (and many more) are now residing in my parent’s basement separated from the few biology books that I thought would help me when I moved to a new hemisphere. Let me tell you about how useful I have found nature guides, hefty biology books and Darwin biographies.

First, two examples of field guides:

WEEDS- Sadly enough it is pretty easy to transfer knowledge of weedy plants to my new home in New Zealand. I didn’t take a field guide to the weeds of North America with me, but inside the city of Christchurch this would have been quite in handy.  I now have a student working on mallows http://en.wikipedia.org/wiki/Malva, a plant I recognized immediately from North America. Mustard plants, docks http://en.wikipedia.org/wiki/Rumex and invasive garden species like the mint in my garden are all thriving here as they would in many parts of North America. I would argue that this is not because ecologists have a great general understanding of weedy biology, rather it is because humans have now moved a massive number of weedy plants throughout cruddy sites in cities throughout the world.

TREES- The native trees here blow my mind. I’ve bought a few beautiful guides to the trees of New Zealand, but they are so different from everything I’ve ever seen before that no field guide from North America will be any help. The best I can say is that there are rhyming patterns in the trees here. In dry sites you will find Cabbage Trees, which looks surprisingly like the Joshua trees I’ve studied in North America. When you climb up in the mountains here you get into beautiful southern beech forests that remind me just a bit of the Douglass fir forest in the Pacific Northwest.

Cabbage tree, Canterbury New Zealand

Joshua Tree, California

Now for the heft:

To be a scientist means reading a huge number of books on seemingly arcane topics. Let me give you some preliminary notes on whether these books have helped me to make sense of biology in my new home.

COEVOLUTION- I’ve spent a lot of my research time trying to understanding when reciprocal adaptation between species (coevolution) matters in nature. As a result I’ve brought a copy of John Thompson’s The Geographic Mosaic of Coevolution with me. The first thing that strikes me about this subject is that many of the examples John uses are not from this part of the world. New Zealand has no Yucca moths, no super toxic newts, and no colorful Heliconia butterflies. The natural history of New Zealand is amazing but fewer people have studied coevolution here (note however that contributor Devin Drown has done super cool stuff on this topic in New Zealand). As a result I am really not sure how to apply thinking on coevolution to what I see around me. What this book might help me to do is to expect the unexpected. Reading this academic work you get the sense that under every log, and inside every bog there is some bizarre way that one species evolves to deal with another species. The book makes me feel like the world is a very noisy place and that can at least be an incentive to get messy and closely watch the happenings of the natural world.

SPECIATION- I’ve brought a copy of Coyne and Orr’s book Speciation that is a fairly recent synthesis of what we know about the origin of new species. I actually think some of the arguments in this guide are a handy starting point for thinking about diversity in an unfamiliar part of the world. To take one example, as I learn more about the species in New Zealand I keep in the back of my head one of the main theses of this book, that newly formed species tend to occur in somewhat different geographic regions. I don’t want to go into all the technical details in this book, but I do think there are a number of generalizations in this book that will come in handy as I start to think about the nitty gritty of differences among species in my new home.

For the record I also brought the first volume of Janet Browne’s biography of Charles Darwin Voyaging. I won’t claim that this has done much for my biology, though it is an affecting portrait of biologists. I enjoy both the stories of Darwin as a quirky kid going on natural history expeditions, and the text on Darwin’s worldwide exploration, to localities that include New Zealand. I would guess that I am not the only biologist who sits at a whiteboard/computer screen/thermo cycler and dreams about some hiking trip looking at actual living things. Also any one looking for a last minute Christmas present I still don’t have volume two…

That makes up a snappy list of some of the books that made the cut and are still sitting on my shelf. I think my takeaway is that most things in biology don’t make sense… but some do. Some of the things we learn about biology in one place are worth carting to the far edges of the word. In other cases there is nothing to do but stand back and be amazed at how dramatically different living things are in each new place. Does any one else want to join me in this navel gazing? Which biology books do you guys sling around with you on adventures? Any books that help things make sense? Any one want to make a case that the next time I travel I should ensure I’m carrying a copy of your research with me?

The Kea, the world's only alpine parrot... only in New Zealand

My gut microbiota made me do it!

by Hird

Our bodies are teeming with bacteria: for every one human cell in your body, there are at least 10 microbial cells. That’s about 100,000,000,000,000 microbes – what are they all doing?

The communities of microorganisms that live on or in a particular host are called the microbiota, and are responsible for a lot of physiological and biochemical functions. It’s probably no surprise that the gut microbiota digest complex molecules we’ve eaten and they keep pathogens from colonizing our bodies (most of the time). They synthesize vitamins and amino acids that we can’t make ourselves. Recent studies have shown that variation in gut microbiota are associated with obesity, diabetes, normal brain development and insulin signaling (which has a downstream affects on body size and developmental rate). But there’s one effect that variation in microbiota can have on their host that is particularly fascinating to me: they can influence host mate choice.

In 1989, Diane Dodd reared fruit flies (Drosophila pseudoobscura) from a common stock on two different food sources: starch and maltose. She found that after multiple generations of isolation on their separate substrates, starch-flies preferred to mate with starch-flies and maltose-flies preferred to mate with maltose-flies. The result was robust and repeatable, but the reason why and its mechanism were unknown.

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A post on one of biology’s most confounding riddles: the latitudinal gradient in biodiversity.

by noahmattoon

A beautiful, but comparatively species poor forest in eastern Oregon

Explaining global patterns of biodiversity is a fundamental goal in biology. Understanding how the tens of millions of species on earth have arranged themselves into populations, communities, and ecosystems, is critical for conserving them in the face of a rapidly growing human population and global climate change.

ResearchBlogging.orgThe latitudinal gradient in species diversity is perhaps the most famous such pattern, and it has confounded biologists for decades. Almost invariably across taxonomic groups, hemispheres and continents, as one moves from polar regions towards the equator, species diversity increases (see the figure for a depiction of global bird diversity). The concept of diversity here can be broken down into three parts: “alpha diversity” or the diversity of species in a single location; “beta diversity”, or the turnover of species observed when moving among locations; and “gamma diversity” or the diversity of species found in an entire region. The latitudinal diversity gradient holds true for all three elements.
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