non-primate

Exponential growth is a feature of current human populations, and was may represent how the human population behaved during some episodes of its demographic history. However, "exponential" can mean different things to different people, if you're not used to thinking mathematically about growth. So I need to lay out some definitions:

It's not just any rodents, but the "highly social, intelligent" degus. And they don't use tools in their natural habitats, but were taught specially by researchers. But it's still pretty interesting:

After two months of practice, researchers say, the degus can move the rake as smoothly and efficiently as croupiers in any Las Vegas casino.

This is first time rodents have been trained to wield tools, said Atshushi Iriki, a neuroscientist, who led the experiments at the Laboratory for Symbolic Cognitive Development at the Riken Institute in Tokyo. But other species may soon join them.

While it has long been thought that tool use is a hallmark of higher intelligence, Dr. Iriki said, the brain structures that underlie such abilities may lie dormant in many animals with good hand-and-eye or paw-and-eye coordination. Training them to use tools in captivity provides insights into the plasticity of their brains, he said, and may shed light on how early humans evolved tool use in the first place.

A high degree of sociality also probably makes a difference to the ability to learn these behaviors.

In separate studies, they are examining gene expression in the brains of macaques and marmosets trained to use tools.

Mitochondrial phylogeography is a useful tool for the study of wild populations. But applying phylogeography to domestic species is more complicated....

A classic example of the use of mitochondrial DNA (mtDNA) diversity to infer the history of domestication refers to dogs (Canis familiaris). Four to six mitochondrial haplogroups (Hg) have been described in genetic studies of modern dogs, indicating recurrent domestication or backcrosses between domestic dogs and wild wolves (Canis lupus). Three of the major Hgs are distributed throughout the world, whereas one (D) is restricted to Europe, especially in breeds originating in Scandinavia. Similar patterns of fragmented genetic diversity have been used to argue for local domestication in other species. Such scenario could apply to dogs as they appear as early as 9000 years ago in Scandinavia, and as dogs and wolf remains have been found on the same sites (Malmström et al. 2008:4).

So, they sampled ancient DNA from Neolithic and medieval dog skeletons, to look for the D haplogroup, which would provide evidence that these ancient dogs had a unique and separate origin from other domesticated dogs elsewhere in the world.

Except, it wasn't there.

Our results indicate that Hg frequencies have been altered in Scandinavian dogs since their first arrival. Interestingly, while Hg C is overrepresented in our ancient material, there is a complete lack of the Scandinavian group D in our ancient dataset. Hg D is the one that could support a Scandinavian origin whereas Hg C is suggested to be of Asian origin. Thus, we find no obvious evidence for prehistoric canid domestication in Scandinavia. An external origin of Scandinavian dogs is supported by morphologic data, as even the oldest remains of dogs in Scandinavia were of smaller size than those of prehistoric and extant wolves. While canid domestication may have occurred in other parts of Europe, Scandinavian dogs were likely imported and had experienced a long period of morphological change under human control before they reached the Scandinavian peninsula (Malmström et al. 2008:7).

Fair enough -- the mitochondrial gene pool of Scandinavian dogs has rapidly changed under human influence during the last few thousand years. No word on where the D haplogroup that characterizes today's Scandinavian dogs has come from; whether introgression from local wolves or dogs elsewhere in Europe.

Why does this remind me of human evolution? Well, consider this 2005 paper by Wolfgang Haak and colleagues:

Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages.

I discussed this paper when it came out, noting that one explanation for the results is selection, either in favor of the N1a type in Neolithic farmers or against it later. The change in frequency in post-Neolithic Europeans is clearly not consistent with drift. On the basis of other genetic loci, migration from other populations cannot explain the catastrophic decline in frequency of the N1a type, which the ancient DNA data show was widespread across central Europe. So, there would appear to have been local selection against N1a.

The Scandinavian dogs are showing the inverse pattern -- a now-common mtDNA type was formerly not present at a measurable frequency, at least in the available sample of ancient dogs. With dogs, of course, there is every reason to expect selection imposed by humans. The only question is whether the selection was directly on the mtDNA itself, or whether the mtDNA has been carried along fortuitously with other selected genes. The extreme inbreeding under recent intensive breeding would allow either scenario -- unlike in humans, where no extreme inbreeding occurred.

I want to point out the parallels and differences clearly, because I'm writing this week about effective population sizes and inbreeding. There are many geneticists who hold out the possibility of extreme degrees of inbreeding in post-Neolithic humans. Genetic, archaeological and historic data -- not to mention common sense -- weigh against this possibility. However, many prefer to maintain a strict view that natural selection occurs rarely, if ever.

(via Dienekes)

References:

Malmström H, Vilà C, Gilbert MTP, Storå J, Willerslev E, Holmlund G, Gotherstrom A. 2008. Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evol Biol 8:71. doi:10.1186/1471-2148-8-71

Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tänzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J. 2005. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018. doi:10.1126/science.1118725

Charles Q. Choi reports on a new paper by Michael Richards and colleagues:

For the past 30 years, studies of their skulls, jaws and teeth suggested cave bears might have been largely herbivorous. In addition, the bones of central and western European cave bears matched those of vegetarians in having low levels of nitrogen-15, whose atomic nucleus has one more neutron than common nitrogen-14 does. Animals accumulate nitrogen-15 in their bodies, and animals that eat animals -- that is, carnivores -- build up more nitrogen-15 than herbivores do.

Still, black bears and brown bears are omnivores. This suggested that although some cave bears were largely vegetarian, others might have been more carnivorous.

New data from the Pestera cu Oase ("Cave with Bones") in the southwestern tip of the Carpathian mountains in Romania now hints most of its cave bears were significantly carnivorous, due to their high nitrogen-15 levels.

It's PNAS, so we won't see the paper for a while. I'll comment more fully here when it is available. Nitrogen-15 is the primary evidence for Neandertal carnivory also, although as I've noted (here and here), those interpretations face some complications.

A large source of nitrogen-15 is fish, which seems a likely source for the cave bears.

UPDATE (2008/01/08): I got the paper. The results show that the Oase cave bears have nitrogen-15 values ranging from a low overlapping with red deer up to a high midway through the wolves -- where higher means more carnivorous. There was one outlier with a very low nitrogen-15 ratio. The impressive thing is the range of values, which apparently exceeds the ranges in other species.

In comparison with other European cave bear samples, the Oase specimens are not alone in showing evidence of carnivory, but the vast majority of specimens from other sites (n=105) have values in the red deer range or lower.

Axes of variation

The paper suggests that the high nitrogen-15 in the Oase cave bears could not have come from the local ungulates (red deer and ibex) because their carbon-13 ratios are extremely different from those species. I think that's a fair speculation, but really there are too many dietary parameters to get an estimate from these two ratios. For example, a primarily vegetarian diet that included a significant amount of fish might explain both ratios (and the wide variation in nitrogen-15, since bears compete for fishing access).

But there are other possible axes of variation. Life history and behavioral variation can affect the isotope ratios. Some of the cave bears across Europe have very low (lower than ungulate) nitrogen-15 values. Hibernation has been suggested previously to explain the correlation of nitrogen-15 values with estimates of temperature, the idea being that bears facing colder winters are dormant for longer periods.

The hibernation story raises the question of the impact of long-term climate change on isotope ratios. The channel through which climate changes may affect the uptake of different isotopes into plants and animals is unclear -- it seems to involve temperature and rainfall as they modulate diet availability. Here's a chart of the carbon and nitrogen stable isotopes in Pleistocene Europe in three different carnivores:

Carbon (top) and nitrogen (bottom) stable isotopes in European herbivores (horse, cattle, and deer) over time. Figure 1 from Hedges et al. 2004.

None of this casts any doubt on the paper's results -- the Oase cave bears simply seem to have been higher on the food chain than most other cave bears sampled across Europe. I just raise them to note the demands that paleoecologists are placing on these isotope ratios. Especially when the species in question has substantial dietary flexibility, like bears, we should probably figure that diet choices are the largest component of variation. That means that we should probably be skeptical about the impact of smaller-scale variations, such as climate, unless there is very strong evidence for dietary stability over the relevant time scales.

Since many large European mammals were undergoing large range contractions or extinctions during this time period, we should expect that the surviving species may have undergone substantial changes in niche partitioning and dietary choices. Humans -- whose isotope ratios are in many ways the most interesting -- would be included in this number.

Bear paleoecology

I think the best passage from the paper is the end of the discussion, where the authors compare the dietary and ecological flexibility of extant ursids as a way of contextualizing the cave bears.

As a consequence of these ₁₅N values, the dietary ecology of modern, higher-latitude bears (excluding polar bears) is relevant for that of cave bears, especially the North American brown bears (U. arctos, including the Kodiak and grizzly bears) given their high-latitude range, body-size variation, occupation of regions with less human ecological impact than most of Eurasia, and extensive database. Brown bear diets range from almost completely vegetarian, including ones with substantial amounts of fruit/berries, to ones containing a substantial amount of fish and/or ungulate meat (19-21, 29, 30, 44, 45). All aspects of their omnivorous diets have limitations in availability, potential feeding rates, and nutritional value in any given environment; adequate weight gain for survival, reproduction, and hibernation therefore depends on a mix of as many food resources as are available (19, 21). Meat consumption, in particular, varies widely among and within brown bear populations, due, among non-maritime bears, to the availability of ungulate fauna (29, 30, 44, 45). Large adult males also appear to be more carnivorous than females or subadult bears (28, 29). North American black bears (U. americanus) appear to have similar plant/meat dietary proportions as brown bears (29), except that the larger brown bears are frequently more carnivorous when the prime meat is maritime (e.g., salmon) (46). This ecological flexibility of modern brown bears therefore makes an appropriate model to understand the range of isotopic values now available for European cave bears, both within and between site-specific samples (Richards et al. 2008:4).

Europe presents a problem of bear competition similar in many ways to the current North American case, in that different ecologically flexible species are differentiated by size. In North America, the larger brown bears exclude access to salmon fishing sites from the smaller black bears.

But in Europe, the brown bears were the smaller species. That helps to make sense of the isotope results on Pleistocene European brown bears, which have even lower nitrogen-15 values than the cave bears (Bocherens et al. 2004).

As for the cave bears, I suppose not even pic-a-nic baskets are out of the question....

A genetic afterthought

There is also this:

Genetic Affinities. To provide additional confirmation of the morphological evidence, mitochondrial DNA (mtDNA) was extracted, amplified, and sequenced from 19 ursid samples (SI Table 2). All 19 individual sequences of the Peçstera cu Oase ursids show clear affinity to central European cave bear sequences (35) rather than to brown bears. They do not form a monophyletic group within cave bear mtDNA variation, and the range of the Oase bear haplotypes is spread throughout most of the variability known for central European cave bear populations from southern Germany, Austria, Croatia, and Slovakia (35-37).

If we expect to have any hope of working out the phylogeography of ancient humans (like Neandertals), then we have to be able to work out the movements of many ancient mammals. That's the only chance of cross-The cave bears look a bit like the Neandertal pattern -- probably not surprising since they are both medium-bodied omnivorous mammals. That's encouraging.

References:

Bocherens H, Argant A, Argant J, Billiou D, Crégut-Bonnoure E, Donat-Ayache B, Philippe M, Thinon M. 2004. Diet reconstruction of ancient brown bears (Ursus arctos) from Mont Ventoux (France) using bone collagen stable isotope biogeochemistry (¹³C, ¹⁵N). Can J Zool 82:576-586.

Hedges REM, Stevens RE, Richards MP. 2004. Bone as a stable isotope archive for local climatic information. Quatern Sci Rev 23:959-965. doi:doi:10.1016/j.quascirev.2003.06.022

Richards MP, Pacher M, Stiller M, Quilès J, Hofreiter M, Constantin S, Zilhão J, Trinkaus E. 2008. Isotopic evidence for omnivory among European cave bears: Late Pleistocene Ursus spelaeus from the Peçstera cu Oase, Romania. Proc Nat Acad Sci USA (online early) doi:10.1073/pnas.0711063105

At Nobel Intent, Jonathan Gitlin writes about the diversity of lab mice:

Now, scientists don't use just any mice; you couldn't trap one in your attic and then bring it to work. Instead, there are hundreds of inbred strains that are used. Creating such a strain involves mating sibling mice for at least 20 generations. By this point, almost all the genetic loci will be homozygous, that is, each of the two copies of each gene will be identical.

...

[A]ll of the inbred strains, and even the four wild-derived strains, are much closer genetically than previously thought. The study identified 8.27 million different single nucleotide polymorphisms (SNPs).  These SNPs are distributed along the genome, but those that are near each other are likely to be  inherited together as a group. By creating a map of these groups, or haplotypes, the researchers were able to look at the contributions of each of the four wild-derived strains to the 11 inbred strains, to attribute ancestry. They found that M. m. domesticus contributed the largest part of the 'HapMap,' with 68 percent. The other three wild strains each were responsible for between three and ten percent, with another ten percent of unknown origin, presumably coming from populations of wild mice not represented in the four wild-derived strains.

The whole post is interesting, tracing the development of mouse strains back through breeder Abbie Lathrop to their origins in wild mouse subspecies.

The original research is by Kelly Frazer and colleagues in Nature and Hyuna Yang et al. in Nature Genetics.

Like mathematician Terence Tao hasn't heard that one before, hyuk. But he gives a nice account of the Grants' work on introgressive hybridization of ground finches:

This was all very reasonable and predictable, but it led to an interesting puzzle - given the modest genetic pool of the Geospiza scandens population, how was it that both the small-beak genes and large-beak genes survived for millions of years, given that selective pressures tended to strongly favour one over the other every decade or so?

The answer, hypothesised and then confirmed by Grant and her collaborators, was introgressive hybridisation - the occasional sharing of genes between Geospiza scandens and Geospiza fortis due to interbreeding.

We didn't include the finches in our paper on introgression,, but it's a well-documented example. For the finches, the clear importance of reinforcement selection on the species barrier between the forms means that their species difference is greater than it would be in the absence of such selection -- and in my thinking probably greater than species barriers in early hominids.

(via Gene Expression)

Rutte and Taborsky report in PLoS Biology that their rats know how to be nice to others:

The evolution of cooperation is based on four general mechanisms: mutualism, where an action benefits all partners directly; kin selection, where related individuals are supported; "green beard" altruism that is based on a genetic correlation between altruism genes and respective markers; and reciprocal altruism, where helpful acts are contingent upon the likelihood of getting help in return. The latter mechanism is intriguing because it is prone to exploitation. In theory, reciprocal altruism may evolve by direct, indirect, "strong," and generalized reciprocity. Apart from direct reciprocity, where individuals base their behavior towards a partner on that partner's previous behavior towards themselves, and which works under only highly restrictive conditions, no other mechanism for reciprocity has been demonstrated among conspecifics in nonhuman animals. Here, we tested the propensity of wild-type Norway rats to help unknown conspecifics in response to help received from other unknown partners in an instrumental cooperative task. Anonymous receipt of help increased their propensity to help by more than 20%, revealing that nonhuman animals may indeed show generalized reciprocity. This mechanism causes altruistic behavior by previous social experience irrespective of partner identity. Generalized reciprocity is hence much simpler and therefore more likely to be important in nature than other reciprocity mechanisms.

In the discussion of the paper, the authors describe the results of other experiments that suggest rats are even more cooperative when repeated interactions occur:

In a follow-up study we tested whether the propensity to cooperate would be increased further when Norway rats interacted with a known partner who had helped them before [32]. As expected, this direct reciprocity caused even higher levels of cooperation than generalized reciprocity, i.e., a rat was 50.7% more likely to help a conspecific who had helped her before than an unknown rat after experiencing cooperation with anonymous partners. This is compatible with a "hierarchical information hypothesis" assuming that specific information about the helping propensity of a partner is used if available, but if not, anonymous social experience is used when deciding whether to cooperate or not [32], i.e., cooperation may ensue also when specific information is limited or costly to be obtained. A similar mechanism might operate in humans [29]. Theoretical models showed that the existence of direct reciprocity in a population will induce the evolution of generalized reciprocity [22], entailing much higher levels of cooperation overall.

Well, lab rats aren't necessarily the same as wild rats, so I suppose it's possible that these rats are doing unusual things compared to their natural habitat. But I'm not really surprised that rats would be capable of either general or direct reciprocity. The game theoretic basis of reciprocity is very simple, and can easily be implemented in a short algorithm. The hard part is when you try to be choosy about it -- determining exactly the right social situations in which a bias toward reciprocity pays off. Evolving the bias in a social species might be very easy. Finding that rats exhibit the behavior under some circumstances tends to confirm that this class of altruism may evolve readily, in even a modestly social species.

I take it as a suggestion that this probably isn't the main reason why humans evolved large brains...

References:

Rutte C, Taborsky M. 2007. Generalized reciprocity in rats. PLoS Biol 5:e196. doi:10.1371/journal.pbio.0050196

The NY Times gave a short writeup earlier this week to a paper about ancient DNA from arctic foxes:

"We wanted to know what happened with the Arctic foxes over the transition from the ice age to the current warm period," Dr. Dalen said. "When the tundra shifted up to Scandinavia and Siberia, did they move too?"

The researchers analyzed DNA from fossilized fox bones found at European ice age sites, and compared it with DNA from the current Scandinavian and Siberian populations. They found that there was no connection between the ancient and modern populations.

"They didn't move," Dr. Dalen said of the European animals. "That whole population is extinct."

The paper itself is a simple, 3-page read. The newsworthy element of the paper is its relationship to climate change -- with the implication that the current genetic diversity of many species will be lost if climate change restricts them to a limited part of their ranges. In the Pleistocene, habitat changes happened without humans getting in the way. So the observation that foxes didn't "track" the movement of their habitat as the glaciers receded means that today's species are very unlikely to do so, if climate zones move in the near future.

But I found a different implication to be more interesting. Arctic foxes that live in northern Scandinavia today are essentially occupying a refugium -- a shrunken fragment of their original habitat. The ancient DNA shows that foxes across northern France, Germany, and Russia were not mtDNA ancestors of today's Scandinavian foxes. While foxes occupy an interglacial refugium, we can look at their mirror image in the glacial refugia of European species; notably Neandertals.

During the height of the last glaciation, Neandertals appear to have been constrained to the southern tier of Europe -- possibly limited at some times to Iberia, Italy, Croatia and points further south. Usually, when people talk about these refugia, they mention northern European populations moving south. But Southern Europe was already full of Neandertals, and there probably was no moving south for the increasingly marginal populations of France, Germany, and other parts of northwest Europe when the climate deteriorated. If they followed the fox model, then northern Neandertal populations may have simply became extinct during each glacial maximum. Southern populations may have undergone substantial demographic turnover also, since glacial and interglacial conditions would have selected for different phenotypes for some characters.

There are many differences between arctic foxes and Neandertals in geographic range and life history, so it is certainly possible that Neandertals moving south maintained greater population continuity than the foxes moving north. Small mammals may grow their population faster than they can disperse over long distances. For Neandertals, that may be less true -- long-distance dispersal would certainly have been possible; the question is whether the population density of the southern refugia would have allowed it.

In general, I think the fox analogy is probably a good one, since carnivores have large home ranges and dispersal distances for their size. The home range size of arctic foxes today averages between 20 and 50 km² (Eberhardt et al. 1982; Landa et al. 1998), depending on the local habitat. Pups disperse outside their parents' home range for the most part, with a dispersal distance between 20 and 40 km (Strand 2000). The home ranges of Neandertals were larger,

The periodic reduction of Neandertals to glacial refugia in southern Europe would have set up a pattern of extinction and recolonization across most of Europe. This must have been a very important demographic force in Neandertal evolution -- since the continent underwent repeated episodes of climate change, possibly on a submillenial basis during the Late Pleistocene. During each range restriction, a nonrandom sample of southern European Neandertals survived and increased their relative gene frequencies compared to other Neandertals. Whenever conditions were suitable, this southern European population was the "first on the scene" to expand into the empty habitat of central and northwestern Europe. We can imagine some strong gene flow from outside Europe also, but the demographic growth of southern Europeans made their relative allele frequencies increase with a pulse every time the population expanded.

Hence, most of Europe was a pulsed population sink. Significant source populations in southern Europe may have maintained substantially distinct allele frequencies than contemporary populations outside Europe, both as a result of restricted gene flow during glacials and as a result of strong selection for dispersal and colonizing ability. These conditions would explain a relatively strong mtDNA distinction between Neandertals and some contemporaries, in comparison to relatively slight autosomal and X chromosomal differences. The mtDNA is much more strongly affected by restricted and temporally intermittent gene flow because of its smaller effective size. In a growing and shrinking population, the effective size of mtDNA would have made it more strongly affected by drift than other loci. In effect, it may be the strongest signature of this evolutionary pattern.

That's what seems to be the story with the foxes. The ancient mtDNA shows a lack of close relationship between today's arctic foxes in Scandanavia and Pleistocene populations further south. The range contraction had a strong effect on mtDNA. It will be of interest to see if autosomal genes show a similar effect, or whether instead they share the Neandertal-modern pattern of slight differences.

So far, so good. But there are a couple of kinks. More later.

References:

Dalén L and 8 others. 2007. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc Nat Acad Sci USA 104:6726-6729. doi:10.1073/pnas.0701341104

Eberhardt LE, Hanson WC, Bengtson JL, Garrott RA, Hanson EE. 1982. Arctic fox home range characteristics in an oil-development area. J Wildlife Management 46:183-190.

Landa A, Strand O, Linnell JDC, Skogland T. 1998. Home-range size and altitude selection for arctic foxes and wolverines in an alpine environment. Can J Zool 76:448-457.

Strand O, Landa A, Linnell JDC, Zimmermann B, Skogland T. 2000. Social organization and parental behavior in the arctic fox. J Mammal 81:223-233. doi:10.1644/1545-1542(2000)081<0223:SOAPBI>2.0.CO;2

Who knew?

Termites actually social cockroaches

...

Researchers added that the cockroach penchant for coprophagy, or eating feces, could very well have led termites to evolve in the first place.

Yeeeaaah!

Larry Moran posts on glyphosate resistance in weed plants:

Roundup® (glyphosate) has been used to control weeds since 1974 [How Roundup® Works]. In all those years, the number of reported cases of resistant plants has been far below predictions. Only in the past ten years have Roundup®-resistant plants been identified and there are only 11 species of resistant weeds known at last count (Perez-Jones et al. (2007).

We now know from studies of the mechanism of resistance of the C4 EPSP synthase that resistance to glyphosate requires very special circumstances; namely, an enzyme active site that can exclude glyphosate while still allowing phosphoenolpyruvate to bind efficiently [The Molecular Basis of Roundup® Resistance]. Thus, with hindsight, it is perhaps not surprising that so few resistant plants have turned up.

This post and the earlier one outlining the biochemistry of glyphosate are very interesting to me (for reasons that will probably remain obscure!) and make a useful counterpoint to the more common tales of antibiotic resistance in bacteria.

I also found the linked 2004 article from Wired really interesting:

The Mystery of the Coca Plant That Wouldn't Die

by Joshua Davis

Over the past three years, rumors of a new strain of coca have circulated in the Colombian military. The new plant, samples of which are spread out on this table, goes by different names: supercoca, la millonaria. Here in the southern region it's known as Boliviana negra. The most impressive characteristic is not that it produces more leaves - though it does - but that it is resistant to glyphosate. The herbicide, known by its brand name, Roundup, is the key ingredient in the US-financed, billion-dollar aerial coca fumigation campaign that is a cornerstone of America's war on drugs.

One possible explanation: The farmers of the region may have used selective breeding to develop a hardier strain of coca. If a plant happened to demonstrate herbicide resistance, it would be more widely cultivated, and clippings would be either sold or, in many cases, given away or even stolen by other farmers. Such a peer-to-peer network could, over time, result in a coca crop that can withstand large-scale aerial spraying campaigns.

It's a long article, but very compelling. The scenario that comes out as likely in the end is a case of natural adaptive introgression:

Which points back to selective breeding. The implication is that the farmers' decentralized system of disseminating coca cuttings has been amazingly effective - more so than genetic engineering could hope to be. When one plant somewhere in the country demonstrated tolerance to glyphosate, cuttings were made and passed on to dealers and farmers, who could sell them quickly to farmers hoping to withstand the spraying. The best of the next generation was once again used for cuttings and distributed.

This technique - applied over four years - is now the most likely explanation for the arrival of Boliviana negra. By spraying so much territory, the US significantly increased the odds of generating beneficial mutations. There are numerous species of coca, further increasing the diversity of possible mutations. And in the Amazonian region, nature is particularly adaptive and resilient.

Could be true, but I couldn't find any later work confirming the existence of glyphosate resistance; just a lot of references to this one Wired article.

Neurophilosophy has really come to life in the last few weeks. A post earlier this week described the neural circuitry that controls swimming in zebrafish, from work published in Nature. Today's post takes the evolution of motion up to tetrapods, with a description of a robotic salamander and what it tells scientists about motor control systems.

And this post about rat metacognition covers the Current Biology paper by Foote and Crystal so I don't have to:

Jonathan Crystal and Allison Foote, of the University of Georgia’s Department of Psychology, taught rats to associate two different auditory stimuli with different levers. A short burst of static, lasting around 2 seconds, was associated with one lever, and a longer burst, lasting up to 8 seconds, with another. In the second phase of the trials, the sounds were played back to the rats. When the lever associated with each sound was correctly pressed, the rats were given a large reward - 6 food pellets. But if the wrong lever was pressed, they received no reward. The rats were also given the option to decline taking the test - they learnt that they could retrieve a smaller reward - 3 food pellets - without making a decision about which lever to press, by poking their snout through an aperture in a food trough.

During the test phase, the rats were presented with the short and long bursts of static, as well as with bursts of intermediate length, and their responses were recorded. When the length of the sound burst was unambiguous (i.e. either short or long) they ignored the food trough and pressed the lever associated with the sound, so that they received the large reward. But when sounds of an intermediate length (approximately 3 seconds) were played, the rats frequently declined to take the test, and chose instead to retrieve food pellets from the food trough, suggesting that the rats knew that they did not know how to respond in the duration discrimination test.

The paper concludes that the rats have a concept of what they know they know -- that is, a metacognitive concept. My students this week told me that rats are smart; I suppose it's true enough.

References:

Foote, AL, Crystal, JD. 2007. Metacognition in the rat. Curr. Biol. doi:10.1016/j.cub.2007.01.061

This is interesting:

Scientists had previously placed the skill of "future-planning" into the exclusively human category. Recent studies have revealed some planning smarts in primates such as apes, but most other animals were perceived as only capable of putting their immediate needs on center stage.

Nicola Clayton et al. rigged it so that some scrub jays had a diet that was predictable in certain ways:

On alternate mornings for six days, eight scrub jays experienced one of two compartments. In one compartment, the birds were always given breakfast, and in the other they were not.

In the evening, after this training period, the scientists allowed the birds to feast freely on pine nuts, which are suitable for hoarding. The birds planned for a breakfast-free morning by hiding much more food in the bare compartment compared with the "breakfast" one. The prudent squirreling away reveals an understanding of future needs, the researchers say.

In a similar experiment, the scrub jays hung out in either a compartment with peanuts or one with dog kibble on alternate mornings. After several days, the birds were allowed to travel between compartments. This time the forward thinkers planned for a balanced diet and buried peanuts in the kibble enclosure and kibble in the peanut compartment.

Thoughts:

1. There are plenty of people willing to argue that Neandertals couldn't do this kind of planning. That's clearly wrong -- planning isn't all that difficult under the right informational circumstances. The birds surely aren't alone, although their caching behavior does prime them for diet-relating planning.

2. Here, the utility of planning is not only to ensure adequate total food intake, but also to enable a better balance of different foods. From the standpoint of nutritional ecology, it makes sense that an animal would be adapted to plan its activities to broaden diet, where possible. This also is very relevant to early hominids.

A nice post on bee dancing and the bee sensory system at Neurophilosophy. From an information perspective, here we have a good example of adapting a nervous and sensory system to maximize information transfer through a given channel. In this case, the channel is defined by the frequency of bee wingbeats, particularly during the waggle dance. The critical sensory apparatus of the antennae turns out to be a simple machine for picking up these signals.

It was found that the antennae of mature worker bees are most sensitive to sounds with a frequency of between 250-300 Hz, and that the frequency and timing of the flagellar vibrations are accurately translated into the neural responses of the sensory cells in the Johnson's organ. The worker bees' hearing is therefore perfectly tuned to detect the movements of other bees, and the auditory system is ideal for listening in on the sounds made by other workers performing a dance no more than several millimetres away.

The extra twist is that worker bees differentiate their activities by age, and only older bees can hear the waggle dance at maximal efficiency. Younger bees who don't forage for food also don't have the sensitivity in the right range of frequencies.

It's a simple model with ontogenetic change in information receptivity.

References

Tsujiuchi, S., et al (2007). Dynamic range compression in the honey bee auditory system toward waggle dance sounds. PLoS One 2: e234. doi:10.1371/journal.pone.0000234.

You have to have a pretty weird science story to get traction this week, and Reuters serves one up:

Gene swap makes boy flies fight like girls

The researchers swapped the male and female versions of the gene in fruit flies and observed the consequences. Males with the feminine gene used female fighting tactics, while the females with the masculine gene fought like the boys.

The story doesn't explain why there are male and female "versions" of the gene, but the actual research by Vrontou et al. sheds some light:

We speculated that the fruitless (fru) gene might be involved in specifying these sex differences in aggression and dominance. This inference was based on fru's critical role in another sex-specific social behavior, male courtship, as well as on an earlier report of anomalous interactions in fru mutant males that were subsequently found to be characteristic of normal female fights. The fru gene produces multiple transcripts, all of which are thought to encode zinc-finger transcription factors. Transcripts from the distal P1 promoter are sex-specifically spliced, resulting in male-specific mRNAs that encode full-length Fru proteins (FruM) and female-specific mRNAs that are evidently not translated. We previously generated alleles of fru that are constitutively spliced in either the male (fruM) or female (fruF) mode, irrespective of the sex of the fly. An additional control allele (fruC) is subject to normal sex-specific splicing.

Anyway, doing the switch-up between the male expressed version and the female nontranslated version causes a reversal of gender roles in these fights. Actually, the research paper has a much more flavorful description of these than the Reuters article:

Under the appropriate conditions, pairs of male or female flies will fight each other, displaying a distinctive set of aggressive behaviors (Supplementary Videos 1 and 2 online). Some of these behavioral components are common to both male and female fights, such as low-intensity 'fencing.' Other components, particularly those of higher intensity, are much more frequent in one sex than the other. For example, 'lunging' and 'boxing' are mostly seen in male fights, whereas 'shoving' and 'head-butting' are characteristic of female fights.

Oh yes, you read that correctly. The supplementary info includes videos.

And how can you not watch with a set-up like this?

They set up the insect world's equivalent to a steel-cage match - a chamber with glass walls and a lid with air holes, a dish of fly food and a mate - and sent in the combatants. But when they used a live female fly as a lure for the males, she often would just fly off.

"My student discovered when he transferred the female to the dish and accidentally crushed her head that the males didn't care whether she had a head or not. That's a true story of what led us to cutting the heads of the females off in subsequent studies," Kravitz said. "They'll court the dead, headless female fly, and try to copulate with her sometimes."

I must admit, it is more interesting than I thought fruit fly fights would end up being. They actually do "box" each other!

I can't tell what they're fighting on, though -- maybe it's one of those new candles from Glah-day...

References:

Vrontou E, Nilsen SP, Demir E, Kravitz EA, Dickson BJ. 2006. fruitless regulates aggression and dominance in Drosophila. Nature Neurosci Early online DOI link

I got in a conversation today about this paper by Régis Debruyne:

Recent molecular phylogenies of the African elephants suggest that there is an evolutionary structure within Loxodonta africana. Some nuclear results (Roca et al., 2001) support the separation of the forest African elephant subspecies L. a. cyclotis as a species distinct from the savannah elephant L. a. africana, on the basis of the recognition of both forming highly divergent (reciprocally monophyletic) clades. Conversely, a mitochondrial survey (Eggert et al., 2002), while admitting a geographic partitioning of the genetic structure within African elephants, suggests retaining the status quo. They recognize three diagnosible entities (western, central and south-eastern Africa) with non-overlapping ranges within L. africana sensu lato. In order to address these conflicting views (historical fragmentation and speciation or isolation by distance, respectively), we have sequenced two datasets of 1961 bp (for 50 elephants) and about 3700 bp, respectively (for 20 elephants) of the mitochondrial DNA for both forms of elephants (cyclotis and africana). They span the cytochrome b gene, the control region and several RNAs. When compared with former mtDNA data, they provide the most comprehensive view of the African elephant phylogeny (78 mtDNA haplotypes, of which 44 are new) and provide the first insight into populations from the Democratic Republic of Congo. The genetic diversity of mtDNA was appraised and the stability of alternative phylogenetic trees was investigated. Our results are inconsistent with both those prior studies. They revealed two highly divergent molecular clades referred to as F and S, that do not conform to the morphological delineations of cyclotis and africana. A non-negligible proportion of specimens of L. a. africana display haplotypes prevailing in forest elephant populations (clade F). The geographic distribution of clades and areas of their co-occurrence support the hypothesis of incomplete isolation between forest and savannah African elephant populations, followed by recurrent interbreeding between the two forms. We state that the conclusions of prior studies resulted from insufficient character and/or geographic sampling. We conclude that there is no satisfying argument which can recognize two or more species of African elephants. We briefly comment on the meaning of such an attitude in a conservation viewpoint.

The basic problem here was sampling. Earlier, smaller samples suggested strong geographic partitioning; larger samples (in this case, only of a single gene) were sufficient to show lots of interbreeding.

With apes, we see this conflict not only with respect to sampling density but also with respect to different loci. Chimpanzees, gorillas, and orangutans have all been argued to have very high genetic differentiation between subspecies, but this evidence suggesting great genetic differences has been mtDNA and Y chromosomal. Datasets of nuclear loci have more or less looked like more recent genetic differentiation, with more evidence of mixture.

Part of this pattern is entirely expected. Because of the smaller effective size of mtDNA, the effective rate of migration is a fourth that of the autosomes. This means that the genetic differences between populations ought to be four times higher.

But the genetic divergences shouldn't be older -- in fact, the mtDNA should have a more recent coalescence age than the autosomes. In particular, if two popluations diverged from a single ancestral population at time t generations in the past, then the mtDNA divergence date on expectation will be t + N/2, while the mean divergence date for autosomal loci will be t + 2N.

So the greater genetic differentiation of the ape subspecies is quite expected, but the older mtDNA divergence times are not.

Or are they?

Let's alter the assumptions. Instead of supposing that the populations diverged from a single ancestral population at time t, let's instead suppose that they have always had the same population structure as today; with partially isolated subspecies sharing some gene flow.

In this model, the mtDNA differentiation will be higher than the autosomal differentiation.

Also in this model, the mtDNA genetic divergence between the populations will be substantially older than the average divergence of autosomal loci. This is because the more limited gene flow for the mtDNA impedes its coalescence, as we look toward the past.

In other words, a long-term structure of limited gene flow between populations will generate the pattern where the mtDNA has a high divergence date and high population differentiation, at the same time that autosomes have lower average divergence dates and low population differentiation.

Is this important? Stay tuned.

References:

Debruyne R. 2005. A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants. Cladistics 21:31-50. DOI link

It's a short piece by John Noble Wilford, and there may be little more to say:

Remains of the extinct dwarf buffalo were found 50 years ago in a cave on Cebu, an island in the Philippines, but were not brought to the attention of scientists at the Field Museum in Chicago until recent years. They determined that the animal, which they named Bubalus cebuensis, weighed about 350 pounds and stood only two and a half feet at the shoulders.

The researchers were unable to date the fossils but thought it unlikely that they were more than a few tens of thousands of years old. A different species of dwarf buffalo lives today on Mindoro Island in the Philippines. But at 500 pounds, it is large compared to the extinct Cebu dwarf.

I find the biogeography of the Philippines and Sulawesi to be fascinating. Some mammals got there (notably pigs and monkeys on Sulawesi), while others didn't -- even those that you might expect to have because they are on Java and Sumatra. There are endemic buffalo in the Philippines now (notably the tamarao). It seems interesting that the buffalo of Java are feral, and there the native large bovid is a species of cattle, the gauteng.

I guess the thing is that there were dispersal barriers besides water in the region, so that even dispersing animals did so within relatively limited ranges. Geology is not the only answer with respect to these dispersals, and that is a lesson that is very relevant to the Flores case, although not in the way that Wilford points out.

Charles Siebert of the Times had a story this weekend about aggression by young bull elephants. It has a name now, HEC (human-elephant conflict). And it has taken a chilling turn:

Still, it is not only the increasing number of these incidents that is causing alarm but also the singular perversity -- for want of a less anthropocentric term -- of recent elephant aggression. Since the early 1990's, for example, young male elephants in Pilanesberg National Park and the Hluhluwe-Umfolozi Game Reserve in South Africa have been raping and killing rhinoceroses; this abnormal behavior, according to a 2001 study in the journal Pachyderm, has been reported in "a number of reserves" in the region. In July of last year, officials in Pilanesberg shot three young male elephants who were responsible for the killings of 63 rhinos, as well as attacks on people in safari vehicles. In Addo Elephant National Park, also in South Africa, up to 90 percent of male elephant deaths are now attributable to other male elephants, compared with a rate of 6 percent in more stable elephant communities.

Personally, I think that 6 percent is impressively high -- that is a huge toll in a species with such long life histories.

In human deaths:

In the Indian state Jharkhand near the western border of Bangladesh, 300 people were killed by elephants between 2000 and 2004. In the past 12 years, elephants have killed 605 people in Assam, a state in northeastern India, 239 of them since 2001; 265 elephants have died in that same period, the majority of them as a result of retaliation by angry villagers, who have used everything from poison-tipped arrows to laced food to exact their revenge. In Africa, reports of human-elephant conflicts appear almost daily, from Zambia to Tanzania, from Uganda to Sierra Leone, where 300 villagers evacuated their homes last year because of unprovoked elephant attacks.

It's a long story that goes into the study of elephant social behavior and relates psychological trauma in elephants to the mechanisms underlying it in humans. There's also a fascinating account of the time that a man-killing circus elephant was hanged (yes, hanged) for the crime.

UPDATE (10/10/2006): From Reuters:

Indians flee as elephants search for dead friend

RANCHI, India - Thousands of people in eastern India have fled their homes in fear as elephants crash through villages looking for one of their herd, which fell into a ditch and drowned over the weekend, officials said Tuesday.

Residents of Banta in Jharkhand state gave the 17-year-old female elephant a quiet burial three days ago, but 14 marauding elephants have been raiding the village ever since.

I find it eerily creepy the way that the journalists in these stories have chosen to anthropomorphize the elephants. Now, to be sure the elephant reactions may well involve a very similar psychological process to humans in similar situations (loss of companions, crowding in unfamiliar habitat). But here they are described in almost exactly the same terms that one would describe humans in the same situation (fighting off encroaching development, dealing with losses at the hands of other people):

With forest cover dwindling in eastern India, elephants and other animals regularly leave their forest homes in search of food, triggering conflict with locals.

The description of the rhino-raping is one of the few elements that really stand out as inhuman, and that's why it is so striking. But these stories have a very consistent theme, and it is a theme taken straight from Edgar Rice Burroughs. Somebody should teach these journalists better.