Author: Yana Eglit

To summarise Week 3:

Tue – intro to phylogenies with Wayne Maddison; discussed some basics of speciation and evolutionary processes as well, in addition to stressing a non-hierarchical view of diversity and evolution (ie. no ‘ladder’ of progression)

Recommended reference for more phylogeny stuff: TR Gregory 2008 Evol Edu Outreach: ‘Understanding evolutionary trees’

For more info on the proper use of the term ‘basal’, see Krell & Cranston 2004 Sys Entomol: ‘Which side of the tree is more basal? — this is for the biologists among us especially! Many of us are guilty of abusing that term…although I’d think it’s ok as long as the other parties all know how phylogenies actually work, as a bit of a dirty illegal shortcut…

Thu – went over some further MURC info, brainstormed ideas for the short presentations, and then discussed that evol psych paper claiming depression is adaptive. Aside from the issues of the paper pertaining to psychology itself, the evolutionary reasoning was rather sketchy. The take-home message was that an adaptationist just-so story can be fairly easily created for just about anything, and just because we can make one up doesn’t mean it’s a useful explanation.

Hypotheses and fitness landscapes

Competing hypotheses and parsimony

Since this topic was brought up in class, I say useful because it’s rather difficult to experimentally reject a hypothesis about something in the past, and adaptationist stories are hard to support either way. We evaluate their likeliness based on understandings of modern organisms (ie. a good hypothesis should have some biological implications we’d be able to trace); but since we’re using ‘functional biology’ (biochem, mol biol, cell biol, physiol, genetics, etc) to explain many of those features anyway, why not just stay with the neutral explanation unless otherwise necessary?

First off, a brief summary of week 2:

– Greg Bole gave us a great introduction to evolutionary biology focusing on replicators,defining the latter as a ‘stable pattern that can replicate itself’ (well-said, I think!); this opens up a wide territory for exploring what constitutes a replicator and how it applies outside biology.

– We also discussed levels of selection, more or less agreeing that the basic level of explanation should be on the gene (or, to generalise, replicator?) level; a higher level of organisation can be evoked in cases where gene-centred explanations fail (need specific examples; group selection to be discussed in more detail later)

– Fundamentals of biological evolution (molecular, and a touch of population genetics) were discussed very briefly, to give an idea of how evolution actually physically works in biology. Molecular (incl neutral) evolution will be covered in greater detail later; speciation and some population biology should be discussed tomorrow; but it would be nice to learn a little more about the mechanics of selection (population genetics stuff, etc), as I, for one, am absolutely clueless in that field*.

* This may be hard to believe, but there was for a long time (and still lingers) this divide between botanists and zoologists. This divide did not just happen on a taxonomic level — the approaches to evolutionary biology were fundamentally different in the two disciplines! Zoologists tend to focus more on speciation, selection, etc; ie. the actual mechanisms of how species diverge with a very population-based approach. Botanists, on the other hand, are obsessed with phylogenies and have a greater inclination to play with molecular evolution. It’s quite hilarious how the disciplines are all influenced tremendously by their histories, and this does have an impact on how we view and understand certain subjects!

This week, we should get a thorough grasp on phylogenies, focusing on how to read them correctly, but also something about how they’re made and what they actually mean. Some vile misconceptions (eg. the wretched progressive ‘ladder’ view of evolution) shall be ruthlessly despensed with. On Thursday, we should discuss the psychology paper, and spend the remaining time brainstorming some project ideas for the proposal due next week. (I’m as worried as you guys are, despite having known about this months ago…! Still have no idea/too many ideas for a topic…both simultaneously, somehow…)

And now, a response to Scott’s post on language and phylogenies: (too long to post as a comment…)

For one thing, phylogenies actually originated in linguistics. But perhaps what you mean is, do all languages fit on a single nice phylogeny? It’s interesting that you bring up creoles and pidgins — I find that example simply fascinating, and almost took language acquisition (LING452 methinks), except that it would’ve been a bit much that term. I guess a biological analogue to language learning/acquisition could be embryonic development:

It may help to think of languages as mature organisms, including genetics, epigenetics and various stuff that happened to them during their own lifetime. Some of that stuff is clearly inherited, some is murky, some has little influence on the progeny (among animals the example would be losing a limb). So, by analogy, one’s personal language* would also have some traits that are heritable, and some that are not. The language is still recogniseable as a ‘species’, if you will, but has some idiosyncratic streaks to it.

*One unfortunate thing is that Chomsky, who pretty much ruled the field of linguistics for decades, didn’t care much for individual variation within a language, and focused on the ‘pure’ language (or dialect) itself. Some linguists today are beginning to realise that was not such a good idea…

Now, in the case of pidgins and creoles, a pidgin would be sort of like mashing various parts of mature biological organisms together. This is seldom possible in the biological world, not spontaneously anyway. I say ‘seldom’ because things like grafting of both plants and some single cell organisms can generate these weird chimaeric hybrids. In the case of single celled organisms, this could actually be somewhat heritable, via cellular inheritance. But that’s murky ground. So biological ‘pidgins’ could be possible.

Creoles, on the other hand, are like mashing various parts of a mature biological organism together AND creating a whole new stable lineage that way. The gut reaction would be to call that ridiculous, but…luckily for us, biology is about as messy as linguistics, if not more so. Endosymbiosis is one complication where you actually get gene transfer between genomes, and the chimaeric organisms persist (there’s some stunningly complex stories out there, such as an organism with 6 different extant genome compartments (nuclei, plastids, mitochondria); in land plants we have cases of hybridisation between closely related species. The endosymbiosis case may be somewhat VERY LOOSELY analogous to creolisation, as we have multiple unrelated genomes and cells working in a single compartment, forming a single organism. It may be a stretch though.

Next up: what is an organism? =D

By the way, in April, Ford Doolittle (Dalhousie)  is giving a talk at the biodiversity research seminar (about constructive neutral evolution AFAIK); he’s a major MAJOR oponent of the bacterial tree; that is, he argues that because of all the lateral gene transfer (ie, between lineages rather than down along them), the tree concept fails for bacteria. It’s a long raging war, and if you guys are interested we could explore it. But in any case, closer to the day (it’s end of April, if I recall) I can remind you guys again, and highly recommend his talk. Afterwards, if there’s time, perhaps you could even pester him about LGT and the tree of life stuff.

Sorry for the really long post…