Identifying garden murids: a case study in unfortunate naming

It's a bit dull, spending all day revising. I have a window which looks over the garden, but being a shared rental house it's not a very nice garden. It's mostly slabs and concrete, with a shed at the end and a strip of grass the dog uses to relieve himself. So the wildlife highlight is usually a pigeon. But not today!

A short while ago, I saw movement in front of the shed, too bouncy for a bird but sort of heavy for a leaf. I put my glasses on and glimpsed what looked like the most adorable baby rat as it bounded behind some junk. I've seen baby rats before, and I'm really not usually a mammal fan but they were just lovely. I think I have a soft spot for rats.

I caught sight of it again a few minutes later, snuffling around in the grass. I was surprised. Looking again, it had very mousy proportions, even for a juvenile. It was the right brownish colour for a mouse. But its body must have been a good ten centimetres long. Could this be a gigantic mouse species I'd never heard of? Or even a mutant metropolitan variety terrorising Londoners? It definitely didn't look like a rat.

This is a house mouse (all British mice have pretty much the same shape):

Source: https://commons.wikimedia.org/wiki/File:%D0%9C%D1%8B%D1%88%D1%8C_2.jpg

And this is a brown rat:

Source: https://www.flickr.com/photos/jean-jacquesboujot/9874371664

As well as being much bigger, brown rats have proportionally smaller heads, ears and eyes. Basically the more adorable, the more likely it is to be a mouse. This rodent in the garden was definitely on the mouse end of adorable.

So I got on the Internet and searched for mouse species in the UK. They really do all look quite similar, and the biggest (the yellow-necked1) only gets to about ten centimetres in total length. About half of that is tail. So it really shouldn't have been a mouse.

Then I thought of the black rat. They are smaller than brown, but were more or less wiped out centuries ago when the brown rats came in. And surely black rats are, like, black? But apparently there are brown colour morphs, and they are slowly regaining a foothold on this island2.

So could it have been a brown black rat? I think so. This is a black rat:

Source: https://www.flickr.com/photos/alexfiles/3872887266

Sure looks brown and mousy and adorable enough.

Rats and mice belong to the family Muridae. It seems to suffer from a bit of a naming problem.

• Black rats are not always black.
• Brown rats, Rattus norvegicus, didn't actually get to Norway until after being named after it3.
• Yellow-necked mice are distinguished from the very similar field mice by a yellow collar. 'Yellow' is really quite a stretch.

Source: https://www.woodlandtrust.org.uk/blogs/woodland-trust/2016/10/types-of-uk-mice/

• And finally, though not a murid and actually part of the squirrel group, surely edible dormice aren't really edible. Who could possibly eat a dormouse honestly

Source: https://pixabay.com/en/edible-dormouse-sleep-furry-sweet-1179703/

(Thus concludes probably the only post on furry mammals ever. Back to the interesting tetrapods next time.)

References
1 https://en.wikipedia.org/wiki/Yellow-necked_mouse
2 "The black rat, Rattus rattus, is believed to have made a comeback in the UK after one was found under a woman's fridge in Cornwall." http://news.bbc.co.uk/1/hi/uk/337680.stm 
3 https://en.wikipedia.org/wiki/Brown_rat#Naming_and_etymology

How to write scientific names

I'm a fan of dinosaurs. I'm also a biologist. So it was a fairly typical occurrence when my excitement at reading about a really cool discovery:
http://edition.cnn.com/2016/12/08/health/dinosaur-tail-trapped-in-amber-trnd
Was dampened by a technical error:
"The tail section belongs to a young coelurosaurian -- from the same group of dinosaurs as the predatory velociraptors and the tyrannosaurus."

I actually though it was a good article and the author got many technical points right, including what a coelurosaur is. I imagine they paid attention to those parts, and that the mistakes come from simply not realising anything was wrong. The errors are in the two species names.

Species names (or scientific, or binomial names) are the pairs of words assigned to every species scientists have described. Taxonomy is the science of naming things. Taxonomists try their best not to get into what is and isn't a species (there are like thirty definitions) but, once something is recognised as needing a name, they decide how to name it. Official names allow scientists speaking different languages and living decades apart to talk about the same organism. They're super important.

Different organisms are covered by different codes of nomenclature (naming). Dinosaurs come under the International Code of Zoological Nomenclature. Apart from the one for viruses, the codes all follow very similar rules, including on how names should be written. It might seem trivial, but writing and formatting names properly is important. Standardisation makes it much easier to find things, and maintains the clarity of a single official name for each species.

So, here's how to write the scientific name of the world's favourite carnivorous dinosaur:

Tyrannosaurus rex

Or, as an abbreviation if you're sure the reader knows which species in the genus Tyrannosaurus you're talking about:

T. rex

• There are two parts. The first word is the genus name, the second is the specific name. Each genus can have multiple species. For example, Triceratops has two species: Triceratops horridus and Triceratops prorsus. Think of the genus as a noun and the species as an adjective.
• Dinosaurs are a bit strange because most people only know them by genus. Referring to an organism by just its genus name is fine, but remember that species in the same genus still have differences.
• The genus name is always capitalised. The specific name is never capitalised, even if it's a proper noun.
• If you abbreviate the genus name, treat it like any other abbreviated word and put a full stop at the end.
• Because the name refers to a category of organisms rather than individuals, you can't make the name plural. Triceratopses doesn't make sense. Use it like you would 'sheep' or 'deer'. For example, "my pyjamas are covered in Triceratops" (I wish).
• Finally, the name should always be in italics if typed. If handwritten, underline it instead because hand-written italics often isn't clear. But note that names of higher-ranking groups than genus or species, like family or kingdom, don't need italicising or underlining.

So, the quote from the article should have read:
"The tail section belongs to a young coelurosaurian -- from the same group of dinosaurs as the predatory Velociraptor and Tyrannosaurus."

And next time you read something about T-Rex, make like a taxonomist and feel disappointed. 

Banana preservation

Storing bananas in the fridge WORKS!

I'm eating one that's been in there for nearly a week, the skin is thin and dark brown, but it's like a slightly green banana on the inside, just as it was when it went in. Amazing. 

This has reminded me of a cautionary tale about banana preservation in another sense, told in several of my lectures over the years. I've looked up parts I don't remember in great detail, but most of this is the equivalent of biology student folk wisdom.

So. The humble banana is a striking example of the dangers of low genetic diversity. Genetic diversity describes how mixed the gene pool of a population is; how genetically similar the individuals are. The vast majority of plants are able to reproduce sexually, so new plants are made via some genetic mixing of their parents. This isn't about gene mutations per se, just new combinations of existing gene varieties. This keeps the population well mixed, and genetic diversity high (barring other factors I won't get into here). Wild bananas are no exception.

However, most cultivated bananas are. Here is a wild banana:

Source: https://commons.wikimedia.org/wiki/File:Banana_with_Seeds.jpg

And here is one you might buy in a shop:

Source: https://www.flickr.com/photos/carowallis1/1524840873

Wild bananas have large seeds. Due to a genetic quirk and encouraged by the fact that seeds aren't nice to eat, the seeds in the cultivated banana are so tiny I'm not even sure if they should be called seeds. They certainly won't grow into a plant1. New banana plants for plantations aren't grown from seed, but by cutting off part of a parent plant. The cut part can grow into an entire new plant quite happily - many plants can reproduce vegetatively like this. But most other plants use vegetative reproduction as a bonus and still make seeds. By not making seeds, cultivated bananas don't do any genetic mixing between generations. The daughter plants are clones of the parent. They miss out on the biggest force behind genetic diversity.

It is, in effect, a timebomb. Clones might be very well adapted to the current environment, but all of the population's eggs are in one basket, because if the environment changes all individuals have the same chance of suffering. There's no strange weirdo plant that struggled in normal conditions but happens to flourish in the new ones.

The problem for cultivated bananas came in the 1950s, when the nigh-indestructible fungus that causes Panama disease arrived in Central America. Most plantations used just one cultivar, 'Gros Michel' ('Fat Michael' - I wish I knew where that came from). Cultivars tend to have low genetic diversity as it is, but Gros Michel plants are virtually identical. Panama disease slaughtered them all with equal lack of mercy.

It must have been terrible to be a banana farmer. Your entire plantation could have been gone in a puff of spores. As far as I know, the epidemic didn't spread to the other banana centres of the world, but it was a very real possibility and Gros Michels as far away as East Asia were in peril.

Fortunately, it was discovered that a different cultivar did show resistance to Panama disease. This was Cavendish, which can be traced back to an Englishman who grew them in Derbyshire in the 1830s. So, growers across the world replaced their plantations of Gros Michel with those of Cavendish, and the crisis was over.

Do you notice a problem with this solution? Cavendish bananas are no more generically diverse than Gros Michel. That they happened to be resistant to Panama disease in the 50s does not make them intrinsically healthier plants. In fact, a new race of Panama disease is currently wreaking havoc among Cavendish bananas in Asia, Africa and Australia, enough that its Wikipedia page has a section titled 'Cavendish devastation era'. Solutions are being sought in hybrids with other bananas, searches for wild relatives, genetic engineering... all methods of changing the genetics of plants that have become hopeless at changing themselves. I really hope a sustainable fix is found soon.


*Despite their size, banana plants aren't trees, just very large plants. To be a tree, a plant needs to form wood, which requires secondary growth. This is basically when a stem can grow wider as well as longer.

Pretty graphs in R

I've lately been learning about macroecology and macroevolution, which consider ecology and evolution on big scales of time and/or space. There's a lot of debate about how comparable these big-scale processes are to little ones. There's lots of data on small-scale processes because they can be experimented on and studied within a timeframe that you can get money for, but macro isn't so easy. Most of what I've been doing has been modelling: taking big datasets and asking what things we can draw out and make predictions from, and whether those predictions make sense. And a very popular tool for modelling in biology is, of course, R.

After three years of being taught R, on and off, I'd hoped to be somewhat proficient now, but alas no. However, I did use instructions to make some very pretty graphs.

1. A species accumulation curve

This tracks species found by effort put in to find them. The dark line is the estimate, the light blob the confidence we have in it, so the more species found the more certain the estimate is. You'd expect to find more species if you look in more places; eventually pretty much all species will be found no matter how much effort you put in, so the graph plateaus. Mine hasn't quite plateaued yet, but it's close.

What's interesting is that, in real life, you'll never know the exact total number of species in your area, but looking at a species accumulation curve can give you a good estimate. It tells you whether future collectors should bring shoeboxes or shipping containers. Incidentally, this data is imaginary and based on Pokemon, which are traditionally collected in neither.


2. A radial phylogeny of fish

The lady who wrote this practical has a thing for colours that some may consider unpublishable.


3. Histograms of mildly interesting traits in primates

The relationship between adult body mass and gestation length in primates might not be especially interesting, but R's col=rainbow() sure is.


4. A horribly complicated boxplot

Still with the primate data, this looks at home range size by primate family. Only four names of fifteen fit. Looks like a boxplot dance party. A rare specimen of boxplot excitement.


5. Ancestral state reconstructions of the social structure of magical creatures

This analysis used a phylogeny to predict whether the common ancestors of all of these taxa (J. K. Rowling taxa) were more likely to be solitary or social. Mostly, I love the large number of tiny pretty pies. Tiny pies are great.


6. A textbook bad graph

A textbook bad graph.


7. A mean phylorate plot for diversification rate in marsupials

This basically summarises the average diversification rate for each group on the tree. This tree is of marsupials (with monotremes as the little outgroup at the bottom) but it's far too big to have readable tip labels. In conclusion, kangaroos are red hot.


8. The nine credible distinct shift configurations for diversification rate in marsupials

Gonna be honest, I don't remember what this means, but it would make a super pattern for shower curtains.