Anophthalmia in Mus musculus

If you look at Joe Felsenstein’s Google Scholar citations page, you’ll find jaw-droppingly high numbers, reflecting the importance of his contributions to evolutionary biology. However, inexplicably, a paper from early in his career, one of his most subtle and deep papers, is not listed there. Perhaps it was forgotten because it pertains to disciplines (mammalian behaviour, sensory physiology, and species interactions) in which Joe is relatively unknown. In going through my files I found a copy of it, which I have scanned and shown in the photograph here.

AnophthalmiaInMusMusculusJoe, sorry for any copyright violation.

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Haiku at #SSB2015

Cécile Ané and I talked about problems with comparative methods at #SSB2015 yesterday, from broken methods, to incomplete data, to intrinsically unreachable inferences. One of the unsolvable problems is that we (usually) can’t recognize trends without fossil data — e.g., a clade that has gradually had all its lineages increase in body size through time will end up presenting a facade in extant taxa the same as if the bodies had always been more or less that size. Rich FitzJohn explained it to me with the metaphor of a stream, and in trying to prepare an explanation for our audience, a haiku just popped into my head:

Leaves afloat on stream.
How fast? One glance tells me not.
Please, a second glance!

This led to other haikus. For the problem of pseudoreplication discussed recently by Rich and me, wherein a single clade can be mistakenly interpreted as showing many instances supporting correlation and diversification effects:

Leaves jump, fly, shout
Heed not their many lone cries!
It’s but one wind’s voice.

Our ability to understand diversification is severely hampered by our incomplete picture of phylogeny, with systematic errors in branch lengths from underparameterized models and nearly no information about extinction because of lack of fossils. For this:

Birds know leaves in sun
I know roots and furrowed trunk
Neither knows the tree

Over all, we need to let go of the hope to understand everything about the evolutionary process. There are many interesting problems we can solve, and insights into evolutionary processes we can gain.  But, there are also questions we will never be able to answer, either in principle, or because of lack of information.

In youth, I sought it all
Now I know a leaf, and smile
Beauty I can hold

We, as a field, need to look for and find those limits, and come to peace with them.

Limits of comparative methods at #SSB2015

One highlight of #SSB2015 was a series of debates organized to focus on key points of uncertainty or debate in the field of systematics and phylogeny: Better models vs. more data (Hillis vs. Rokas), species concepts (Simon vs. Mallet), and molecular divergence times (Marshall vs. Hedges). Cécile Ané and I were asked to debate comparative methods, but a debate did not suit us, and so we built a presentation together about the limits of comparative methods.

A successful but immature field shouts “Wow, look at what we can do!” A mature field ponders “What are the limits of what we can know?” After decades of almost unchecked enthusiasm, fuelled by oceans of new data and computational capabilities, we are waking up to our limits. The success in reconstructing phylogeny has perhaps made us overconfident, believing that we should have similar success in phylogenetic studies of ancestral states, character correlation and diversification. However, the optimism shouldn’t transfer: reconstructions of phylogeny itself gain their power from the entire genome, while methods using phylogeny to answer evolutionary questions usually have sample sizes limited to the number of species at best.

The presentation Cécile and I put together asked: What are our humbling limits in principle, in the style of Heisenberg’s Uncertainty and Gödel’s Undecidability? What are our unfortunate limits in practice, given the amount of data we can usually gather?  I’ll try to post a few more snippets from it.

Meeting in Ann Arbor, 1981 vs. #SSB2015

pheneticsCladisticsTShirtThe last time I was in Ann Arbor was 1981, for the simultaneous-but-separate meetings of the Hennig Society and the Numerical Taxonomy Society — long ago and a very different time. Those meetings represented warring factions.  Very few of us walked between buildings to attend both meetings, and those of us who did were no doubt noticed. My brother David had the brilliant idea of making T-shirts for the two primary belligerents (the cladists and the pheneticists) in the style of warring soft drinks. Since he made them, he got to choose which shirt to wear. Here is a photo of the two of us in the T-shirts, though two years later (thankfully, beards had been grown in the meantime). David’s in the “Cladistics..it’s the real thing” shirt.  I’m rather proud of our chutzpah for having worn those T-shirts to the meetings, and impressed at our survival.

This time in Ann Arbor, the Systematic Biology meeting has been full of great data and thoughtful discussion, a great blend of enthusiasm, hope, and caution. Lacey Knowles, Brian O’Meara, Dan Rabosky and team organized it perfectly in minimalist style: a single-sheet program, no swag, just discussions over round tables and intense lightning talks in rows.

The other change since 1981 has been the cost of meetings. Note the cost of the NT meeting registration on the scan shown here, and compare it to the last meeting you attended!

AnnArbor1981