Evolutionary biology in the 21st-century: from big theories to big facts

A few years ago I reflected that genomics has not really “revolutionized” evolutionary biology. In contrast, it arguably has revolutionary the science of medical genetics. The reason I said this is that because the big questions in the field were formulated in the 19th and 20th-centuries.

To a great extent, we’re recapitulating theoretical arguments of Huxley and Wallace (the power of selection), or Fisher and Wright (selection within structured populations). What has changed is that genomics allows for the more granular testing of predictions and models. In other words, evolutionary biology is illuminated by the surfeit of data of the 21st-century, rather than presenting to us startling new models.

The theoretical raw materials are present if you read old books and papers. It’s just that then testing those disputes were exceedingly difficult. Another way to state it is that what we suspected, we can now confirm or reject.

This, to me, explains why theoretical arguments are less vociferous and personal today than they were in the past. The data is there, so the race is to calculate.

On the genealogy of “Social Darwinism”

In my review of David Sloan Wilson’s This View of Life: Completing the Darwinian Revolution I observe that one of the author’s projects seems to be to educate a more general audience on a revisionist understanding of the history of evolutionary biology as applied to society:

…He notes that the opprobrium hurled at evolution’s application to social problems draws from Richard Hofstadter’s Social Darwinism in American Thought. Hofstadter was a man of left-wing commitments writing in 1944, as the war against Hitler’s regime was still a live concern. His was not a dispassionate scholarly analysis. He aimed to produce something which could be deployed in the fight against “racism, nationalism, or competitive strife.”

This View of Life highlights how men as diverse as Darwin, Herbert Spencer, Francis Galton, and Thomas Malthus were not united in their views, nor were they the cruel anti-humanitarians that their detractors portray them as (Hitler’s own views were scientifically inchoate at best, and ignorant at worst). Wilson’s arguments are familiar to libertarians in particular, many of whom have long argued that Hofstadter misrepresented classical liberals.

The argument for the defense that one encounters in This View of Life may not entirely convince, at least in the chapter-length treatment Wilson provides. The great evolutionary geneticist R. A. Fisher’s central work, Genetical Theory of Natural Selection, contains a long exposition of eugenicist thought as applied to humanity…

I noticed today that Devang Mehta has put up a review of the same book, and he’s far less positive than I (we notice the same problems, but I’m considerably more charitable). There are many points where I disagree on details of interpretation with Mehta, but I want to highlight the criticism of David Sloan Wilson’s treatment of Social Darwinism:

Of course, this sets off all sorts of alarm bells about “social Darwinism,” the 19th century idea that socially powerful individuals are innately better than weaker ones, which underpinned early 20th century theories of race, justified colonialism, and rationalized eugenics and Nazi-ism. Wilson is at least cognizant of this connotation, and in fact spends a whole chapter early in the book trying to persuade the reader that Nazis (and the eugenics movement) were actually not “social Darwinists.” He claims that social Darwinism was not a term adopted by eugenicists, but in fact used as a pejorative by their opponents. This is a bizarre argument; regardless of who came up with the label, the shoe fit. In fact, it was Darwin’s half-cousin, Francis Galton, clearly inspired by Darwin’s work, who sparked the eugenics movement, coining the term, and promoting the idea that eugenically “compatible” couples should be given incentives to marry and procreate. A modern understanding of evolution and genetics utterly refutes eugenicist ideas — but nevertheless, it’s important to not whitewash the field’s grim history.

Mehta zeroes in on exactly the same issue I alluded to above: the relationship between eugenics and what became evolutionary genetics is very close, and the two emerged at approximately the same time. But where I disagree with Mehta is assuming that “Social Darwinism” and eugenics were identical and substitutable. Mehta and the broader public seem to think this equality is warranted, but I disagree.

I was familiar with Richard Hofstadter’s misrepresentation of intellectual history through libertarian critiques long before I read histories of evolutionary biology. Obviously, libertarians take a very different from the stance of David Sloan Wilson. That people with such different ideological commitments agree on a misrepresentation of the historical record should make one come to attention, rather than dismiss Wilson’s attempt at revision as pure sophistry.

Many years ago I read Lee Alan Dugatkin’s book The Altruism Equation. It surveyed the early period, and how evolutionary thought shaped social thought, and it is far more diverse than the reductions to “Social Darwinism” we’re given.

This is relevant because my friend Eric Michael Johnson, a man of the Left himself, has done his own intellectual archaeology of the relationship between early evolutionary biology and social thought. A chapter of his Ph.D. thesis has now been published, The struggle for coexistence: Peter Kropotkin and the social ecology of science in Russia, Europe, and, England, 1859-1922. If you are curious about “Socialistic Darwinism”, then I suggest you read it. It shows exactly how Hofstadter overreached, and what he missed.

Sequence the thousands and your eyes shall be open

Charles Darwin’s The Origin of Species as an audacious work that birthed a whole discipline. But it had its failings. In particular, Darwin famously lacked the Mendelian model of genetic inheritance which easily maintained variation from generation to generation. The reason that variation is important is that it is one of the major raw materials which is required from biological diversification through adaptation (natural selection and the heritability of that variation being other important components). Mendelian genetics is defined by a rearrangement of discrete units of heredity, alleles of various genes, and so solves the problem of the maintenance of genetic variation.

Genes are quite convenient as instruments of evolutionary bookkeeping, and one reason that John Maynard Smith believed that biologists had an advantage over economists in their deployment of game theory. He believed that genes were superior to various attempts by economists to measure “utility.”

Obviously, evolution is not just genes. But, if you are an evolutionary geneticist, then evolution for all practical purposes is defined by changes in frequencies of genetic variants over time.

Until very recently the genetic currency fed into the theoretical machine of evolutionary genetics was precious. There was a great deal of scarcity. A few model organisms, and a few loci. The birth of genomics meant that many common and “important” organisms were sequenced en masse. But the revolution left most of the tree of life untouched.

That is going to change very soon, as geonomicists begin to churn out sequences of a huge number of species. More importantly, they will begin to have population-scale datasets of many species.

This is a step forward from comparing single genomes of various species in a comparative sense. With population genomics researchers can inspect dynamics within numerous species across their whole genomes. This is a big deal. A lot of old questions regarding the generality and specificity, the inevitability and contingency, could be answered within a generation.

Endless Tigers Most Beautiful


The Thylacine, or the Tasmanian Tiger, is a tragic story that we all know (or should know!). Too late did humans realize how precious it was, a large(ish) marsupial carnivore endemic to Tasmania. Hunted to extinction, the last one died because it was not properly taken care of.

The Tasmanian Tiger is an example of why science is not just instrumental. That is, science is not simply the handmaid of engineering. Most people with an interest in biology have some instinctive reaction to the Tasmanian Tiger and what happened. There’s a natural pathos in it.

If you read The Monkey’s Voyage you know that the marsupials of South America probably derive from a single dispersal event. Genetics has determined that the South American Monito del monte is the most basal of the superorder Australidelphia, which includes all Australasian marsupials. That means instead of the single South American marsupial of this superorder being due to a migration from Australia, the Australian lineages diversified from a single South American ancestor. The Monito del monte is the last living descendent of this once extensive clade.

This means that all of the vareigated marsupials of Australia probably diversified during the Cenozoic, even though the divergence between marsupials and placental mammals dates deep into the Mesozoic. The Koala, the Kangaro, and the Tasmania Devil, all derive from the same source.

Well, a new paper in Nature: Ecology & Evolution does something quite neat, they sequence the whole genome of a Tasmanian Tiger! Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore:

The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

The authors are saying that the clear morphological convergences between Tasmania Tigers and canids, which are obvious to anyone with eyes, aren’t detectable in similar sequence identity in regions of the genome known to be functional relevant to the characteristics of interest. Instead of sequence identity they suggest that rather the morphology is being controlled by evoutionary genetic process of cis-regulatory adaptation.

In the Mike Lynch vs. Sean Carroll debate of about ten years back, they’re saying that Sean Carroll was right (see this Hoekstra & Coyne paper for a different take).

Part of the issue here is probably the sort of traits they’re focused on. There seems to be something about the gross morphological characteristics humans find salient that make them the target of cis-regulatory mediated evolutionary processes.

Finally, they suggest with a PSMC plot that Tasmanian Tiger populations crashed around 70,000 years ago, well before Australian Aboriginals arrived. First, I’m not sure that I trust the 70,000 number to be precise enough that we can say it doesn’t overalp with human arrival. But second, is it me, or does every PSMC look like the pot above? It’s probably some sort of publication bias, as you don’t put in PSMC figures if they don’t show a bottleneck. But I’m kind of getting tired of it.

Our time in the sun

The New York Times has a story up, After the Dinosaurs’ Demise, Many Mammals Seized the Day. It’s a write-up of a new paper that is open access, Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction.

This research illustrates how computational power has changed evolutionary biology. There has long been an intuitive verbal model that mammals were ancestrally night-adapted creatures based on aspects of their biology, as well as the evolutionary reality that for most of the lineages’ existence they were overshadowed by dinosaurs (remember, more than half of our evolutionary history predates the Cenozoic).

But today we do more than posit models which match and predict the fossil (or genetic) data. Computationally intensive phylogenetic frameworks are tested using extant lineages to generate probabilities of given scenarios generating the data we see given particular models. Something like the Reversible-jump Markov chain Monte Carlo (which is used in this paper) could actually be done manually…if a phylogeneticist had thousands of slaves to do all the computations. Obviously, the emergence of powerful computers accessible to all really changed the game in terms of analytic power.

And yet I wonder about the sense of precision that people gain from these methods. Verbal models are necessarily vague. When you give a probability of a given hypothesis being 0.71, that gives understanding a solidity. But is it warranted? Though researchers understand all the individual moving parts of the phylogenetic framework, only a computer can really bring it all together.

It’s something to consider. This is to a great extent the future of evolutionary biology. Positing models, and put it into a calculating machine like Leibniz dreamed of.

Citation: Temporal Niche Expansion In Mammals From A Nocturnal Ancestor After Dinosaur Extinction
Roi Maor, Tamar Dayan, Henry Ferguson-Gow, Kate Jones

Addendum: This is stupid of me, but only after reading the above paper did I reflect that most amniotes are diurnal and that mammals are the exception. Think about it, birds. And reptiles are probably more sluggish at night.