Did Marine Mammals Merge Molecularly? Maybe.

Morphological convergence is one of the most striking patterns in evolution. Just among mammals there are spectacular and bizarre examples of distantly related species that share surprisingly similar adaptations. I bet you’ve heard of saber-toothed cats. But what about marsupial saber-toothed cats? Raccoons are surely familiar, but have you heard of raccoon dogs? Or the earless, eyeless oddity that is the golden mole, which somehow looks almost exactly like the equally earless and eyeless notoryctid marsupial mole? My favorite, though, might be the lesser hedgehog tenrec from Madagascar, which bears the same tiny coat of spiked armor as the common hedgehog but is more closely related to an elephant.

Skull from the marsupial saber-toothed “cat” Thylacosmilus.

Skull from a placental saber-toothed cat Smilodon.

Until recently, most scientists studying evolutionary convergence have focused on the converged phenotype (external appearance), but with the arrival of ever-cheaper DNA sequencing technologies, scientists can efficiently study patterns of convergent genotypes across thousands of genes in species that appear to have converged at the phenotypic level.

Now, I know dancing sharks are the preferred marine species of the moment, but allow me to reignite your interest in some other denizens of the sea. Last month, a team of researchers published a study in Nature examining how genes in three marine mammal lineages might have converged independently on the same solution to the very hard physiological problem of living in the ocean after millions of years evolving on land (Foote et al. 2015). Their results are hardly conclusive but do illustrate a compelling new way to think about and study convergence now that genomes are getting so cheap to produce.

Katy Perry and her dancing sharks at the 2015 Super Bowl

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Sex chromosomes in conflict

House mouse (by Wenfei Tong http://darwinsjackal.blogspot.com/)

House mouse (by Wenfei Tong)

Have you thought that not all the genes in your body might have the same evolutionary interests? The mouse Y chromosome has just been revealed after years of superhuman slog and turns out to be strikingly different from other non-recombining sex chromosomes in two main ways. Firstly, the mouse Y contains almost no DNA signatures of its past as a non sex chromosome. Secondly, most of it isn’t “junk”. Both these observations have shown just how much conflict within a genome can shape the evolution of entire chromosomes.

Figure from Sho et a. 2014, showing how much of the mouse Y contains recently evolved, repetitive coding sequences.

Figure from Sho et a. 2014, showing how much of the mouse Y contains recently evolved, repetitive coding sequences.

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How many phylogenies are there in a genome? Lots!

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.

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Friday coffee break

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.

From Sarah: For whales, taking in a mouthful of krill is more complicated than you might think.

A rorqual whale’s feeding lunge was “one of the largest biomechanical events on Earth”, said Dr Pyenson.

“This shows us how they do it so quickly, co-ordinating the inflation of the throat pouch with the opening of the jaws… and closing their mouth to prevent prey escaping – all in under 10 seconds.”

And from Jeremy: Will you live longer if you order an extra shot in that latte? Probably not.

During the time of the data collection (1995-2008), of the total 402,260 people, 52,515 of them died. At first blush, the risk of death (comparing the people who died to the people who didn’t and their demographics) was higher among the coffee drinkers.

But when you break it down, a large number of the heavy coffee drinkers (more than 2 cups/day) were also smokers, which is a very high risk of death in and of itself. When you controlled for the smokers, the authors got the OPPOSITE effect, this time coffee drinking (more than 2 cups per day), decreased the risk of mortality by 10% in males and 15% in females.

Friday coffee break

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.

From Sarah: Sequencing the genome of a 5,300-year-old body preserved in the ice of the Italian alps has revealed some interesting personal details.

The lactose intolerance makes sense, said Albert Zink, an anthropologist at the European Academy of Research in Bolzano, Italy, who was one of the study’s authors.

“In early times, there was no need to digest milk as an adult because there were no domesticated animals,” Dr. Zink said. “This genetic change took hundreds of years to occur.” [Link sic.]

And from Jeremy: An uprecedented study of genetic variation among the cells comprising individual tumors suggests that cancer genetics are going to get a lot more complicated before we understand them better.

Swanton found that even the primary tumour was surprisingly varied. He found 128 mutations among the various samples, but only a third of these were common to all of them. A quarter of the mutations were “private” ones – unique to a single sample.

The tumour had also split down two evolutionary lines. One area – part of R4 in the picture – had doubled its usual tally of chromosomes and seeded all the secondary tumours in the patient’s chest. The other branch had spawned the rest of the primary tumour. Even though this tumour looks like a single mass, whose cells all descended from a common ancestor, its different parts arehave all  evolved independently of one another.