Tag Archives: phylogeny

Nothing in Biology Makes Sense: On the origins of bacon

Posted on by
Pig Photo by mgabelmann.

Over at Nothing in Biology Makes Sense! Noah Reid takes a look at a new study of the recent evolutionary history of pigs:

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.

Because domestic pigs are prone to going feral and getting, um, re-familiarized with their wild relatives, unravelling their history using genetic data is tricky business. To see what the new study found, go read the whole thing.◼

Nothing in Biology Makes Sense: God’s AIC score

Posted on by
The creation of Adam. Image via Web Gallery of Art.

This week at Nothing in Biology Makes Sense! Noah Reid takes a cue from Bill Nye the Science Guy and applies information theory to test whether a model of divine intervention fits a simple phylogenetic dataset.

Without getting into the details, we can think of information theoretic criteria for model selection as formally implementing Occam’s Razor: the simplest model with the most explanatory power is to be preferred. By preferring simple models, you guard against overinterpreting data, a pitfall that can make models poor predictors of new observations.

So, I realized as long as we can formulate any mathematical model of “The Hand of God”, rejectable or not, we can compare it to an evolutionary model in this framework. If, as Nye suggests, evolutionary theory is simple and powerful, and creationism is a model of fantastical complexity that doesn’t much improve our understanding of the data, information theory would help us sort that out.

If you want to settle the whole evolution-versus-creationism thing once and for all (okay, not really), or just learn how biologists use information theory to select models (really!), go read the whole thing.◼

Nothing in Biology Makes Sense: The evolution of lizards on islands. No, not those lizards.

Posted on by
Hemidactylus granti. Photo via Nothing in Biology Makes Sense!

Over at the collaborative science blog Nothing in Biology Makes Sense!, Noah Reid describes a new study dissecting the evolutionary history of island-dwelling lizards—not the field model Caribbean Anolis, but geckoes in the genus Hemidactylus, living on islands in the Indian Ocean.

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.

To find out how some of those endemic reptiles got to Socotra, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of polar bears’ origins

Posted on by
Polar bear. Photo by ucumari.

This week at the collaborative blog Nothing in Biology Makes Sense, contributor Noah Reid goes in-depth on the recent study pinpointing the historical origins of polar bears, and why it’s taken the most recent systematic methods to correctly pinpoint them.

From 2008 to 2010, a series of algorithms were published that could take data from multiple genes and infer the history of whole populations, a drastic improvement over previous methods that could only identify the history of single genes (e.g. mtDNA). With these methods in mind, a group of researchers gathered data from 14 nuclear genes for multiple extant brown and polar bear populations (Hailer 2012). … the new data analyzed with the new method suggested that polar bears diverged far earlier than previously thought (around 600 thousand years ago) and that they were no longer closely related to the southeast Alaska population, but rather to the common ancestor of all brown bear populations.

For more details, including a nice brief explanation of why it can be important to use multiple genes in reconstructing relationships among species, go read the whole thing.◼

And another thing …

Posted on by

Regarding that adaptive fairytale about the “runner’s high”—over at Distributed Ecology, Ted Hart points out that it doesn’t make much sense in phylogenetic context, either.

What would be really interesting is to see where this trait maps across the phylogeny. Is it a conserved trait that was selected for in some ancestor? That would point to the fact that maybe it has nothing to do with running. The authors are mute about phylogeny, but eCB’s could alternatively be the ancestral character state, and really the interesting question is why did ferrets evolve the loss of this state? On the other hand maybe the trait evolved multiple times, and that also is really interesting to ask how that happened. But either phylogenetic scenario undermine the central thesis of Raichlen.

You’ll want to read the whole thing, natch.◼