This is a guest post by Daniela Vergara, a postdoctoral researcher studying the genomic architecture of hybrid species of sunflowers and Cannabis in Nolan Kane’s Lab at the University of Colorado, Boulder. Daniela also blogs about science at A Ciencia Abierta. Check out her blog for a spanish version of this post.
Cannabis is definitely a cool plant. It has fun names like matanuska thunderfuck, jesus OG or trainwreck and it has been trendy among humans for a very long time (humans have utilized it for thousands of years). Despite this long history, and the fact that Cannabis is the most widely used recreational drug in the world , the genomics and the general the biology of these plants have only been partially studied. At the Cannabis Genomic Research Initiative (CGRI) at the University of Colorado Boulder we want to study this genus of plants for several reasons, including: (i) its medical significance, (ii) its importance in the biofuel, fiber, oil, textile and food industries, (iii) its long co-evolutionary relationship with humans as an ancient crop, and (iv) in general, because it is an exciting emerging study system in evolutionary biology.
Why should evolutionary biologists be excited about studying Cannabis?
In my part of North America, spring is finally underway after a long slog of a winter. The trees lining the streets of my Minneapolis neighborhood are lacy-green with budding leaves, flowerbeds all over the University of Minnesota campus are yellow and red and pink with daffodils and tulips, and violets are popping up in the edges of lawns everywhere I look.
Of course, all of this colorful display isn’t for my benefit. Showy flowers are an adaptation to attract animal pollinators. Some flowers are quite precisely matched to a single species of pollinator, but most flowers have lots of visitors. These less specialized flowers are still adapted for their attractive function, though—and this is the origin of pollination syndromes.
You know the type. Big, brown eyes. Cute, little nose. Long, striped tail.
Tamias amoenus canicaudus, Steptoe Butte, WA, photo: Noah M Reid
Chipmunks are adorable and one of the more easily viewed yet still kind of exotic North American mammals (in my opinion). I worked on red-tailed chipmunks for my Master’s degree at the University of Idaho with Jack Sullivan. Sullivan (et al.) just published a review of all the chipmunk research that’s taken place in his lab over the past 10 years or so. Central to the review is the concept of divergence with gene flow (DGF), but let’s start with some back story.
Figure 4 from Tehrani 2013. The result of a network analysis among fairy tales. The large number of well spaced network connections from the East Asian group is suggestive of blending between the other two major groups.
In a pretty interesting example of cross fertilization between scientific disciplines, a recently published paper by Jashmid Tehrani uses phylogenetic methods borrowed from evolutionary biology to construct an “evolutionary tree” of fables related to Little Red Riding Hood.
Tales typical of Riding Hood are found mostly in Europe, but a series of stories sharing some features are found in Africa (involving an Ogre) and East Asia (The Tiger Grandmother). These have sometimes been considered to be part of the Riding Hood group, but there has been debate over whether or not they actually belong to another, closely related group found in Europe and the Middle East known as The Wolf and the Kids.
This week we have a guest post by Jessica Oswald a graduate student at the Florida Museum of Natural History at the University of Florida. She works on the biogeography of neotropical birds using fossil, ecological, and molecular genetic data.
As an avian paleontologist, digging through fossils is to me like birding with a time machine. These fossils help us paint a picture of where modern forms came from and how different ancient species were from modern-day birds, especially intermediate forms. These outliers and in-betweeners are interesting because they hint at all sorts of morphological diversity that we don’t even know or expect, and give us a window into the past and how different diversity, communities, and climatic conditions and landscapes were from what we are familiar with today.
This paper (Ksepka et al. 2013) on an early bird in the Swift-hummingbird clade does both of these things by exhibiting an odd morphology that we don’t see in modern birds, and helps us understand how the uniquely specialized wing shapes in modern swifts and hummingbirds arose from their common ancestor.
Members of the order Apodiformes: treeswifts (Hemiprocnidae), true swifts (Apodidae), and hummingbirds (Trochilidae), are aerial marvels. Swifts are able to reach the highest speeds during level flight (Chantler 1999) and hummingbirds are well known for their hovering abilities and their sideways and backward flight. Swifts and hummingbirds, while sharing the same wing bone characteristics, have different lengths of flight feathers, resulting in different wing shapes across the group, which allows them to perform their different aerial feats. Hummingbirds have shorter wings relative to their body size compared to swifts, resulting in their hovering abilities. These different wing shapes are well suited for their modern functions, but we have almost no fossils from this group, so we don’t know how the wing shapes diverged, or anything about the ecology of ancient species in this lineage.
It would seem that between the global hitchhiking of feral pigs with human migration, America’s absurd obsession with bacon and the possible emergence of pandemic influenza via recombination of human and porcine strains, the past, present and future of our civilization are inextricably linked to that of the domestic pig. With that in mind, let’s have a look at a recent paper on the evolutionary history of the genus Sus by Frantz et al. 2013.
Domestic pigs are in the family Suidae, which includes the babirusas, warthogs, the endangered pygmy hog (whose generic name is, Porcula, seems a likely candidate for America’s next tragic children’s cereal) and the domestic pig’s close relatives in the genus Sus. Depending on where you draw the lines, there are around 7 species in Sus. With the exception of the wild boar (Sus scrofa) their natural ranges are restricted to Southeast Asia west of Wallace’s Line. Extant species of Sus have diversified recently (sharing a common ancestor ~5 million years ago) and the species are all thought capable of producing viable hybrid offspring. Most species are restricted to single islands or island complexes in Southeast Asia (such as Borneo, Java and the Philippines). Previous phylogenetic estimates of the genus are in conflict over the relationships among species.
“You: on the earth’s surface. so young. so dynamic. full of life and suggesting a world of possibility. Me: subterranean. really old. fossilized, almost. intriguing but slightly inscrutable. We brushed past each other in Rabosky and Matute (2013). I thought there was something there, but in the blink of a p-value you were gone.”
One of the perennial questions in evolutionary biology is “What factors determine how many species are on earth?” Researchers take numerous approaches to get at this very big question. One is to look for correlations between attributes of organisms, the environments they inhabit, or geologic history and rates of species diversification. This the study of macroevolution, and it is based on the idea that the discovery of these correlations on large scales (often using datasets with hundreds to thousands of species with deep histories spanning tens of millions of years) would be a powerful indicator of the factors governing species richness. Another approach is to study speciation on a small scale, to examine sets of closely related populations currently in the process of diverging. The thought is that if we can observe the forces driving divergence in contemporary populations, we can use those observations to develop a more general understanding.
In the evolutionary history of big herbivores and the carnivores that prey upon them, the phrase “arms race” is only technically a metaphor. Antelope and zebras are literally born to run, and many of the things that chase them, like wild dogs or cheetahs, are either masters of endurance or champion sprinters. The evolutionary story almost writes itself: over millions of years of chasing, and being chased, whenever the predators evolved to become faster, the prey were selected to run even faster—until a cat evolves that can go from 0 to 60 faster than my Volkswagen Rabbit.
Except of course there’s more to life than running for your life. An antelope’s frame is under more demands than evading cheetahs—it also needs to travel long distances to follow food availability with the shifting rainy season. In fact, the North American fossil record suggests that big herbivores on that continent evolved long legs for distance running millions of years before there were predators able to chase after them. And then again, not all predators run their prey down; lions, for instance, prefer to pounce from ambush.
In a paper recently released online ahead of print in the journal Evolution, Jakob Bro-Jørgensen sets out to disentangle exactly these competing explanations.
** Hey y’all – it has come to my attention that the article this post is criticizing might have been more of a tongue-in-cheek textual criticism than a literal hypothesis (like I treated it). Instead of it being “this is what we think is true” opinion, I think it’s more of a “this interpretation of the Bible is more justified by the natural world”. Read at your own risk and sorry for my confusion. – S.Hird **
During his Society of Systematic Biologists presidential address at this year’s Evolution meeting, Jack Sullivan mentioned a rather…unusual…article. (Well, letter, technically.) Congenital Human Baculum Deficiency, by Scott Gilbert and Ziony Zevit was published in the American Journal of Medical Genetics in 2001; it describes their hypothesis that Genesis 2:21-23 doesn’t mean Eve came from one of Adam’s ribs, she came from his baculum.
Walruses have bacula almost 2 feet long – it is required that a picture of a walrus accompany any discussion of bacula.
What’s that, you say? Baculum is the technical term for the penis bone. Many mammals have one – presumably to aid in sexual intercourse. For mammals that mate infrequently, prolonged intercourse ups the chances that a particular male sires some babies. For mammals that must mate quickly, the baculum provides immediate rigidity. And for all mammals, keeping the urethra straight while copulating is imperative, so maybe it’s there to prevent a kink in the works, so to speak. The truth is, there are a lot of hypotheses about what bacula do but – as you might imagine – they’re kind of difficult to test. Regardless, our nearest evolutionary neighbors, the great apes, all have bacula, as do most other primates. Gilbert and Zevit cite this– the fact that our baculum is missing – as evidence for their argument. Which goes like this:
- A rib seems like an unlikely origin for Eve because male and female humans have the same number of ribs.
- Ribs also lack “intrinsic generative capacity”, which penises have “in practice, in mythology, and in the popular imagination”.
- Most mammals – and especially primates – have bacula, humans do not.
- It is therefore “probable” that Adam’s baculum was removed to make Eve, and not a rib.
The authors then continue to support their argument with alternate translations of the Hebrew word for “rib” (which they say could mean “support beam”) and claim the raphe of the human male scrotum is what Genesis 2:21 is referring to when it says “The Lord God closed up the flesh.”** I’m almost convinced!
One candidate for the original “evolutionary tree”—the only figure illustrating the first edition of The Origin of Species. Image via Wikimedia Commons.
Biologists have been constructing trees since before we knew why tree-shapes made such convenient organizing structures for living things. Since Charles Darwin (and Alfred Russel Wallace) first made the case that diverse groups of living species arise from common ancestors, we understand that tree-like relationships reflect this common descent, so that if we can infer the specific structure of those relationship-trees, or phylogenies, we can begin to draw conclusions about how individual species evolved to be what they are today.
Back in the day, we had to estimate phylogenies using directly observable characteristics—measurements of particular parts of particular bones (for mammals), or the shape of the antennae (for butterflies), or the capacity to synthesize lysine (for paramecia). If species that are more recently related tend, on average, to look more similar than each other, this kind of morphological data can be useful. But! When you’re setting out to reconstruct a phylogeny from a whole pile of morphological measurements—dietary preferences, tooth counts, fur color, wing length—what do you do when different traits support different relationship structures? Different traits will naturally change at different rates over evolutionary time, and it’s rarely obvious what those rates are.
Starting in about the 1970s, though, it became increasingly straightforward to directly compare the genetic codes of differnt species. That’s appealing for several reasons: first, because DNA is as direct a marker of inheritance as you can find, it provides a record that’s independent of potentially misleading, morphological similiarities. Second, because DNA sequences have only four character states—the good old “bases” adenine, guainine, thiamine, and cytosine—it’s more tractable to estimate how they change over time.