Morphological phylogenetics

After weeks of travelling back and forth from another campus for computing and ecology, I'm now back at the NHM. An hour's commute each way never seemed so gentle.

This week is phylogenetics, starting in the same way the field did by completely ignoring DNA. We've been learning how to turn the morphological variation you see in organisms into hard facts that a computer can use to compare them, and through comparing many many features, suggest their evolutionary relationships. With molecular data you typically have a fixed number of characters: the base at this point in the sequence can only be A, C, T or G, for example. But there's a real art to choosing and defining morphological characters, as I found out yesterday.

In the practical session we were given a set of taxa to describe. My group came up with our set of characters and we ran the analysis and got a fairly nice cladogram, for something that took an hour. Most taxa had a clear set of relatives and you could trace the evolution of some of our characters back to common ancestors.

When I got back, I decided to ramp it up a notch, adding 16 taxa and changing some of the characters. I experimented with lots of different character arrangements, mostly unsuccessful. This not-brilliant cladogram was the result:

Did I mention the taxa were biscuits?

The methods used by morphological phylogenetics just assume there's an evolutionary relationship between the items you describe. One of my classmates apparently did one on screws.

So, to the science:

It seems most of the finger biscuits are closely related (yellow), and the two chocolate chip cookies have come out as sister taxa (green) as expected. Interestingly, the sandwich condition seems to have evolved multiple times, as it crops up all over the cladogram. The single-layer sandwich fingers (red) probably evolved the finger shape independently of the other fingers.

But, the tree has failed to recognise the close relationships between hobnobs and coated and uncoated digestives respectively; I feel these are unlikely to be convergences but represent true homology. It also failed to recover many deeper-level relationships, leaving a very large polytomy of most round biscuits. The single exception is the Viennese whirl as the basalmost biscuit (the jaffa cake is the outgroup). This is interesting, as the Viennese finger has come out as one of the most derived, so here the Viennese resemblance is likely to be convergent.

In conclusion, this analysis has revealed only a few useful characters with which biscuits can be classified, and these are still apparently subject to homoplasy. It is recommended that molecular methods be applied to offer a different perspective. Sadly, DNA extraction from biscuits is not an active field of research.

Let the young make mistakes

This morning, a pair of woodpigeons dropped into the garden. It led me to much biological speculation.

I tried to take some photos:

The flash was on

There's a robin

The key picture

Some readers may see a problem - these do not look like wood pigeons. There are a few differences probably beyond the scope of this questionable photo, like their big dark eyes and drab beaks, but it's clear that they lack the flashy collar. Wood pigeons have a bright white patch on the sides of their neck, with green iridescence around the back. This is because these birds are juveniles.

A typical reason for a juvenile to look different to an adult is sexual maturity: it makes no sense for a bird to have flashy colours to show off to potential mates if it's not interested in finding one, especially if the colours will interfere with its camouflage. This could definitely apply to these pigeons, even if pigeons are not known for camouflage (despite today's prevalence of grey concrete). But the adults aren't sexually dimorphic - males and females look the same - and flashy colours are almost always associated with just one sex. And watching them, it does seem to be females accepting or rejecting males rather than both having to look attractive. So what else could flashy colour be used for?

I've forgotten where, but I think I've read that another species of bird has a white patch near its head just like wood pigeons. It lives in groups, and the patch is a signal to its flockmates: when the bird suddenly takes off, the movement of the patch is very visible, so the rest of the flock can quickly follow. This makes sense if the first bird has spotted a predator, and it's in the interest of the flockmates to escape too. The white tails of deer and rabbits probably does the same job.

But importantly, the juveniles of this bird species also didn't have the patch. It only grows in with the adult feathers. So, a juvenile could take off and the other birds wouldn't necessarily feel the urge to follow. This might be selected for if juveniles are very prone to false positives: flying away from predators that don't actually exist. Ignoring the inexperienced younguns would save the adults (mostly family, if this speculation is going to make biological sense) lots of energy. Vervet monkeys, known for their different alarm calls that refer to different types of predator, will also usually ignore calls from juveniles. So, maybe these juvenile pigeons lacked the flashy collar not because they're pretty young to be searching for that kind of fun, but because it pays for their parents to ignore them. Anthropomorphise from that what you will.



Note: robins (photo two) also have very different colouration as juveniles. They're mottled brown, lacking the bright white and orange of adults. Adults of both sexes use their colours in competition over territories and can be very aggressive. Another unsourced factoid: 10% of robin deaths are caused by other robins. Lacking the colours might save the juveniles from being attacked by bigger birds before they need to find a territory. Maybe anthropomorphised robins would wait until voting age to reveal their political leanings.

In the park II: what actually was in the park

Answers (highlight the text to see):
[A] Crow
[B] Nothing
[C] Nothing
[D] Crow
[E] Ring-neck parakeet
[F] Snake

Very surprising to see a reptile out on a cold autumn morning, but it wasn't moving much.

Yesterday I went to the other local park and the two highlights were a squirrel missing half its tail and a rat climbing out of a bin. But it was genuinely a very nice place.

Much more interesting than squirrels

In the park I

In a rare burst of free time, I've been exploring the local green space. I went out early in the morning with my camera to see what non-squirrel creatures I could find.

Now, read carefully.

This is a game.

The combination of my photography and the sheer lack of wildlife makes this a great opportunity for spotting. What's the animal (if there is one)? Answers in the next post!

[A]

[B]

[C]

[D]

[E]

[F]