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mammothIt seems strikingly obvious that modern humans are a pretty big deal. In Pat Shipman’s The Invaders she argues that H. sapiens can be thought of as a top predator which is so efficient that it rearranges the whole ecosystem, wreaking havoc with the conventional trophic cascades. We can see this in the archaeological record. Humans arrive in Australia, and all sorts of cool marsupial species disappear. A similar phenomenon is attested for the New World. The more recent extinctions on islands such as Madagascar and New Zealand are well attested.

Nevertheless, many people still argue that the pattern of extinctions which we see over the Pleistocene and Holocene is not the outcome of human expansion, but climate change. In other words, they are not anthropogenic. Don’t believe me? Here’s a paper from a few years ago, Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability:

Examination of an under-exploited source of ancient DNA—small-mammal remains—identified previously unreported and unprecedented temporal population structuring of a species within Europe during the end-Pleistocene. That we identify a series of population extinctions throughout the Pleistocene from a small-mammal species demonstrates an extensive and prolonged diversity loss and suggests a nonsize-biased reduction in ecological stability during the last glaciation, a pattern consistent with climatic and environmental change as key drivers for changes in Late Pleistocene biodiversity.

You can find similar arguments for other particular regions and areas. For example, in North America. The mysterious hand of climate is everywhere. To some extent it reminds me of arguments about the Indo-European languages, and their origin. “Out of India” proponents make points which would be just as valid for the Greeks, e.g. the early Indians and Greeks did not have a memory of being from anywhere else. Obviously the Indo-European languages are unlikely to both originate in India and Greece, but when examining just one area the arguments can seem persuasive. What needs to happen when assessing probabilities though is to get a sense of the broader framework of prior information. The same applies to the mass extinctions of the past few hundred thousand years. A new preprint on bioRxiv tries to do this, Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns:

…Results: We find that current diversity patterns have been drastically modified by humans, mostly due to global extinctions and regional to local extirpations. Current and natural diversities exhibit marked deviations virtually everywhere outside sub-Saharan Africa. These differences are strongest for terrestrial megafauna, but also important for all mammals combined. The human-induced changes led to biases in estimates of environmental diversity drivers, especially for terrestrial megafauna, but also for all mammals combined. Main conclusions: Our results show that fundamental diversity patterns have been reshaped by human-driven extinctions and extirpations, highlighting humans as a major force in the Earth system. We thereby emphasize that estimating natural distributions and diversities is important to improve our understanding of the evolutionary and ecologically drivers of diversity as well as for providing a benchmark for conservation.

It’s a preprint, you can read the whole thing. Of course I’m broadly persuaded, since it only confirms rigorously what I already believed impressionistically.

Citation: Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns, Søren Faurby , Jens-Christian Svenning, doi:

• Category: Science • Tags: Ecology, Extinction 
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The domestication of the dog is a complex and unresolved topic. But at this point I am convinced that this is one domestication event which well predates agriculture. To some extent this is common sense. There are tentative archaeological finds of domestic dogs in the New World almost immediately after widespread human habitation of the Western hemisphere, >10,000 years ago. More concretely domestic dog DNA has been retrieved from ~9,250 year old coprolites in Texas. The distinctiveness of the New World dogs is well attested genetically. Eskimo dogs for example are nested in a well diverged clade with “ancient dogs” (e.g., Basenji), indicating their early separation from the main Eurasian stock. Additionally, from talking to a dog geneticist I am to understand that the Eskimo dogs themselves are likely new arrivals, and superseded older dog lineages in the far north.

These results suggest to me that by the late Pleistocene many of the hunter-gatherer populations of Eurasia existed in a symbiotic relationship with domestic dogs. I suspect that the dog lineages in fact predate the late Pleistocene, and the earliest tendencies toward coexistence with humans may date to before the Last Glacial Maximum. And yet an interesting sidelight to this is that in Australasia it seems that the native domestic dogs, the singing dog and the dingo, postdate agriculture, and derive from Southeast Asian dogs (arriving ~5,000 years ago). Clearly the story of the dogs of the world has several chapters. There are many debates about the exact location of the “first dogs,” whether in the Middle East or East Asia. These arguments often seem to place the date of origin of modern dog lineages in the very early Holocene, around the time of agriculture. This contradicts hints from archaeology, and is difficult to square with the likely arrival of dogs with the First Americans.

And yet in hindsight the pre-agricultural constraint of the geographic expanse of the dog shouldn’t be too surprising (Sub-Saharan African domestic and feral dogs seem to derive from Middle Eastern dogs who arrived through the Nile Valley during the Bronze Age). Wolves, from whom dogs derive, are creatures of the Palearctic ecozone. A later expansion into tropical Asia and Africa is less surprising, as perhaps the lifestyles of human populations in those regions were not congenial to canine hunting companions before agriculture. The phylogeny of dogs can tell us a lot about human migration. But the presence of absence of dogs can also tell us about the constraints of human societies, and how they reshaped their ecology.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology 
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One of my major gripes with my friends in ecology is that there is a tendency to look at every problem through the lens of ecological models. Garrett Hardin, who popularized the term “tragedy of the commons” is an exemplar of this. People in ecology often get irritated by the public confusion between it, a positive scientific discipline, and environmentalism, a normative set of beliefs (it doesn’t help when some environmentalist groups have names like “ecology movement”). But the fact is there are deep commonalities in terms of prior assumptions by both ecologists and environmentalists. Despite evolutionary ecology, the reality is that ecologists seem to be characterized by a mindset which posits limits to growth and a finite set of responses to the challenges of scarce resources. That is, the Malthusian paradigm.

I bring this up because despite the similarities between ecology and economics it strikes me that ecologists often have a difficult time admitting that the parameters of the model which they think they have a good grasp of may not always be fixed. Incentives and innovation can shift the dynamics radically. Consider George Monbiot’s about face on “peak oil,” We were wrong on peak oil. There’s enough to fry us all:

A report by the oil executive Leonardo Maugeri, published by Harvard University, provides compelling evidence that a new oil boom has begun. The constraints on oil supply over the past 10 years appear to have had more to do with money than geology. The low prices before 2003 had discouraged investors from developing difficult fields. The high prices of the past few years have changed that.

Maugeri’s analysis of projects in 23 countries suggests that global oil supplies are likely to rise by a net 17m barrels per day (to 110m) by 2020. This, he says, is “the largest potential addition to the world’s oil supply capacity since the 1980s”. The investments required to make this boom happen depend on a long-term price of $70 a barrel – the current cost of Brent crude is $95. Money is now flooding into new oil: a trillion dollars has been spent in the past two years; a record $600bn is lined up for 2012.

Let’s take Monbiot’s assertion as a given, that we are not entering an era of hydrocarbon scarcity. Why? As he outlines increasing demand, flat supply, and higher profits, stimulated exploration and innovation, generating more supply. This isn’t rocket science, critics of peak oil were pointing out this likelihood back in the mid-2000s. What this reminds me of is evolution. A eternal and circuitous race across a fluctuating ‘adaptive landscape,’ with fitness target constantly shifting.

Of course evolutionary process is not such that anything is possible. This is still science, and science has limits. But evolutionary process is often surprising in its ingenuity. Similarly, over the past 250 years or so human ingenuity has been surprising. This doesn’t mean we should bet on this lasting forever, the Malthusian condition has been the norm for almost all of human history. But, we should never forget the power of innovation and incentives when we consider policies at the intersection of the environment and economics. I don’t get irritated when the general public operates with Malthusian assumptions. But I do get irritated when biologists, and especially ecologists, seem to act as if human economic history since 1800 simply hadn’t happened.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Environment, Environmentalism 
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A monkey frog

The Pith: The Amazon Rainforest has a lot of species because it’s been around for a very long time.

I really don’t know much about ecology, alas. So my understanding of evolution framed in its proper ecological context is a touch on the coarse side. When I say I don’t know much about ecology, I mean that I lack a thick network of descriptive detail. So that means that I have some rather simple models in my head, which upon closer inspection turn out to be false in many specific instances. That’s what you get for relying on theory. Today I ran into a paper which presented me with some mildly surprising results.

The question: why is the Amazon Rainforest characterized by such a diversity of species? If you’d asked me that question 1 hour ago I would have said that it was a matter of physics. That is, the physical parameters of a high but consistent rainfall and temperature regime. This means the basic energetic inputs into the biome is high, and its consistency allows the organisms to plan their life schedule efficiently, maximizing the inputs. All that naturally produces a lot of diversification in the “climax” ecosystem. To some extent I would acknowledge this was pretty much a “Just-So,” but I’d have thought it was a good shot, and probably representative of the internal logic of many people. But no, a new paper in Ecology Letters seems to imply that that the answer we must look to is history and not physics. From the perspective of someone who is rooted in are reductionist conception of evolutionary biology this isn’t the answer I was “rooting” for, but if it is, it is. What’s their logic?

First, the abstract, Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity:

What explains the striking variation in local species richness across the globe and the remarkable diversity of rainforest sites in Amazonia? Here, we apply a novel phylogenetic approach to these questions, using treefrogs (Hylidae) as a model system. Hylids show dramatic variation in local richness globally and incredible local diversity in Amazonia. We find that variation in local richness is not explained primarily by climatic factors, rates of diversification (speciation and extinction) nor morphological variation. Instead, local richness patterns are explained predominantly by the timing of colonization of each region, an d Amazonian megadiversity is linked to the long-term sympatry of multiple clades in that region. Our results also suggest intriguing interactions between clade diversification, trait evolution and the accumulation of local richness. Specifically, sympatry between clades seems to slow diversification and trait evolution, but prevents neither the accumulation of local richness over time nor the co-occurrence of similar species

Thankfully species richness is pretty easy to understand. It’s a count of the number of species in a given area. In this case they limited their count to a specific clade, the tree frogs. This clade seems to have a common ancestor ~60-80 million years before the present from which it descends.

Below is a phylogenetic tree (scaled to time on the horizontal) representing the relationships of contemporary tree frog species, as well as a distribution of the species across the world:

Visual inspection tells you immediately that Amazonia is overloaded with tree frog species. But to get at the question of what explains the variation in species richness the authors used standard statistical techniques relating predictors such as temperature and precipitation values to the outcome, species richness. The authors did find a relationship between precipitation and temperature and species richness. But once they controlled for phylogeny in their regression, that is, take into account history, the relationship went away. In other words the correlations may have been an artifact of the fact that the Amazon is warm and wet and rich with species. Controlling for the phylogeny of the clade, which is a record of contingent history, the expected picture relating physical parameters to diversification changes. The two panels above and to the left show the relationships between species richness (y-axis) and first colonization event. The left panel is pegged from the first colonization of any tree frog lineage, while the second sums up distinct colonization events by different clades (so the x-axis has a larger magnitude). The r-squared, the proportion of the variance of y explained by variance in x, is nearly 0.50 in the left and 0.70 in the right. That’s pretty good.

There’s some interesting material in the paper sympatry vs. allopatry in regards to the tree frogs. Basically, how they vary in size and diversity as a function of whether they co-occur in the same ecosystem or whether they’re physically separated (so allopatric speciation is when two lineages are separated while sympatric is when they are geographically overlapping but diverge anyhow, perhaps through occupation of differing niches).

But that’s not my primary concern or interest. How generalizable are these results form tree frogs? I don’t know this literature well. Surely someone has done a phylogenetic least squares with a lot of different clades and checked for this? If the results here are generalizable then the diversity of the Amazon ecosystem is in large part a function of its longer term stability and persistence. I have posited that at the “end of history” natural selection will have shaped an exceeding simply and energetically optimized biosphere, dominated by a few species. But in Amazon is a case in the opposite direction, as clade diversification increases as a function of the time of ecosystem integrity. Is this monotonic? In other words, is there going to be a time when a rare evolutionary event may given rise to a species which sweeps away all the accumulated variation?

Those are questions for the future I suppose.

Citation: Wiens JJ, Pyron RA, & Moen DS (2011). Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity. Ecology letters PMID: 21535341

Image credit: Colin Burnett

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Diversity, Ecology, Environment, Speciation 
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Foraminifera, Wikimedia Commons

The Pith: The tree if life is nourished by agon, but pruned by the gods. More literally, both interactions between living organisms and the changes in the environment impact the pulsing of speciation and extinction.

No one can be a true “Renaissance Man” today. One has to pick & choose the set of focuses to which one must turn one’s labor to. Life is finite and subject to trade offs. My interest in evolutionary science as a child was triggered by a fascination with paleontology. In particular the megafauna of the Mesozoic and the Cenozoic, dinosaurs and other assorted reptilian lineages as well as the hosts of extinct and exotic mammals which are no more. Obviously I don’t put much time into those older interests at this point, and I’m as much of a civilian when I read Laelaps as you are. More generally when it comes to evolution I focus on the scale of microevolution rather than macroevolution. Evolutionary genetics and the like, rather than paleontology. This is in part because I lean toward a scale independence in evolutionary process, so that the critical issue for me has been to understand the fundamental lowest level dynamics at work. I’m a reductionist. I am not quite as confident about the ability to extrapolate so easily from evolutionary genetic phenomena upwards in scale as I was in the years past. But let’s set that aside for a moment, and take a stroll through macroevolution. When I speak of natural selection I often emphasize that much of this occurs through competition within a species. I do so because I believe that the ubiquity of this process is often not properly weighted by the public, where there is a focus on competition between species or the influence of exogenous environmental selective pressures. The intra- and inter- species competition dynamic can be bracketed into the unit of selection debate, as opposed to the exogenous shocks of climate and geology. The former are biotic and the latter are abiotic variables which shape the diversity and topology of the tree of life.

A new paper in Science attempts to quantify the effect of these two classes of variables on the evolutionary arc of a particular marine organism over the Cenozoic, roughly the last 65 million years since the extinction of the dinosaurs. Interplay Between Changing Climate and Species’ Ecology Drives Macroevolutionary Dynamics:

Ecological change provokes speciation and extinction, but our knowledge of the interplay among the biotic and abiotic drivers of macroevolution remains limited. Using the unparalleled fossil record of Cenozoic macroperforate planktonic foraminifera, we demonstrate that macroevolutionary dynamics depend on the interaction between species’ ecology and the changing climate. This interplay drives diversification but differs between speciation probability and extinction risk: Speciation was more strongly shaped by diversity dependence than by climate change, whereas the reverse was true for extinction. Crucially, no single ecology was optimal in all environments, and species with distinct ecologies had significantly different probabilities of speciation and extinction. The ensuing macroevolutionary dynamics depend fundamentally on the ecological structure of species’ assemblages.

The foraminifera went from 2 species early in the Cenozoic to over 30. Additionally, as noted in the paper they’re well sampled across the whole time period. It is a cliché that paleontology suffers from a deficit of thick data sets, but this seems far less the case with marine organisms which are numerous and mineralize copiously, such as the foraminifera. Ecology here seems to be defined both by position in the water column as well as morphology of the species. Presumably this intersection defines specific niches inhabited by the species of this lineage.

Figure 2 and 3 illustrate the primary results of this paper:

The scatter plots in figure 2 are pretty striking. Using one parameter there’s almost no prediction of clade growth. Remember that R-squared simply tells how how much of the variance of axis y can be explained by axis x. But, when you include the interaction between two variables, the R-squared starts to become significant. And when you have three variables, it isn’t too shabby at ~0.66. That means the interaction between clade diversity, climate, and ecology, can explain 2/3 of the variance in clade growth.

Diversity just measures inter-specific competition and interaction. A diversity focused model would predict that clades rapidly expand to fill available niches when it is low, and that one attains a steady state equilibrium when species richness has increased. Climate is rather self-evident. Finally, as I note above, ecology seems to be a compound of characteristics and indicates the positioning of a population in relation to others and their environment. In this paper the authors refer to the Red Queen’s Hypothesis, as well as the “Court Jester Model.” Honestly I don’t really know specifically what the latter is aside from what is mentioned in the paper. That certainly highlights my ignorance. But from what I can tell the Red Queen Hypothesis of evolutionary arms races correspond to biotic pressures, while the Court Jester Model denotes the climatic shocks and shifts which are outside of the closed system of species’ interactions.

So figure 2 shows that both forces are critical in determining the specific state of species’ richness. But the third figure illustrates that they have somewhat different roles. “E” is ecology and “C” climate, while “D” is diversity. You see that diversity (or lack of more accurately) correlates with speciation, while ecology & climate are more relevant for prediction of of extinction. The former is due to the “early burst” of adaptive radiation which occur in a low diversity state. Why is the diversity low? Probably because of a massive extinction event due to an exogenous shock. So the two classes of variables do influence each other, insofar as biotic dynamism surges in the wake of an abiotic perturbation.

Much of the above is common sense, and we understand it non-quantitatively. Of course both exogenous and endogenous dynamics are at work in shaping the specific nature of the tree of life. By exogenous, I’m referring to climatic shifts, comets, geologic activity, etc. By endogenous I’m referring to the cycles of interactions which might be triggered by a sequence of co-evolutionary arms races. Many readers of this weblog with some biological background will be familiar with chaotic phenomena bubbling out of purely endogenous parameters. In theory a cycle of extinctions and clade radiations could be due to endogenous processes. But the above data suggest that at least for life on earth, that is not so. Perhaps in a low energy universe trillions of years in the future, in a universe with few surprises, we’ll see purely closed ecosystems at work. But not right now. A surprise is always in the cards!

Citation: Ezard TH, Aze T, Pearson PN, & Purvis A (2011). Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science (New York, N.Y.), 332 (6027), 349-51 PMID: 21493859

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Evolution, Extinction, Speciation 
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A “cloud forest”

The lush image above is of a cloud forest biome. Can you guess where it is? The Arabian country of Oman! How’s that for a surprise? I had known of the Green Mountain of northeast Oman, which is ~3000 meters above sea level and receives ~15 inches of rain (enough for shrubby woodland), but was totally ignorant of Salalah mountains in western Oman. Apparently the region catches a bit of the monsoon, and so has a rainy season. And yet the cloud forests receive only ~15 inches of rainfall themselves! (300 mm) But the key is that apparently if you include condensation from fog and such the precipitation triples. So the physical nature of the forest produces a feedback loop which allows it to sustain itself.

Here’s a paper on the Omani cloud forest, how it maintains equilibrium, and possible threats.

Image Credit: storymary

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology 
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On this week’s ResearchBlogCast we discussed Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory (see my post reviewing it). The basic idea was to discuss a simple mathematical model which treated biological populations as something more than simply static constants buffeted by changes in physical parameters. In particular there’s often an implicit model that species exist at a particular and precise equipoise with an environment, and that when those environmental parameters are shifted that the species is in jeopardy unless it can track its optimal environment through migration.

In some ways this would be mighty convenient for us if it were so. If species were static we wouldn’t have to worry about weeds becoming resistant to pesticide, or diseases wrecking havoc to our crops, and so forth. But biology is dynamic, both on the life history and evolutionary scale. I think it would benefit us to take this into account when we humans consider the value we place on conservation, and the decisions we make to maintain biodiversity. Kevin Zelnio pointed out that there have been worries about the disappearance of charismatic fauna for about a generation now, and though species such as the tiger and elephant are still endangered (and because of their relatively long generation times this is problematic), many species which we were told as children would become extinct by the time we were adults remain a presence today in the wild. Some of this is surely due to conservation after the awareness of the threats, but another issue may be that some of these species are more resilient than we think, or give them credit for. Dave Munger reminded us that in 2007 100,000 Lowland Gorillas “discovered”, tripling the numbers of the species immediately. One way of looking at it is that these gorillas were mighty lucky that they’d been unnoticed…but another issue may be that gorillas coevoled to some extent with hominids and may have some sense where to go to avoid human habitation.

This is not to recommend complacency. And I haven’t even broached the serious normative issues as to the value of biodiversity outside of its human utilitarian consequences. These are points over which reasonable people can discuss and differ. Rather, when we speak of the environmental and non-human life we often speak as if humanity and physical nature are the two active forces operative on a passive and static biological nature. This is obviously not true. Our species’ mastery of the physical sciences in the past 200 years has given us a sense of power over the biological world, but we shouldn’t get complacent, and we shouldn’t dismiss the resilience and cleverness of nature, though that resilience and cleverness does not always redound to our benefit.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Biodiversity, Ecology, Environment 
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Change is quite in the air today, whether it be climate change or human induced habitat shifts. What’s a species in the wild to do? Biologists naturally worry about loss of biodiversity a great deal, and many non-biologist humans rather high up on Maslow’s hierarchy of needs also care. And yet species loss, or the threat of extinction, seems too often to impinge upon public consciousness in a coarse categorical sense. For example the EPA classifications such as “threatened” or “endangered.” There are also vague general warnings or forebodings; warmer temperatures leading to mass extinctions as species can not track their optimal ecology and the like. And these warnings seem to err on the side of caution, as if populations of organisms are incapable of adapting, and all species are as particular as the panda.

That’s why I pointed to a recent paper in PLoS Biology, Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory below. I am somewhat familiar with one of the authors, Russell Lande, and his work in quantitative and ecological genetics, as well as population biology. I was also happy to note that the formal model here is rather spare, perhaps a nod to the lack of current abstraction in this particular area. Why start complex when you can start simple? Here’s their abstract:

Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. We use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. Two key parameters relating the environment to population biology have not yet received sufficient attention. Phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. Environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. We use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.

Their model here seems to be at counterpoint to something called “niche modelling” (yes, I am not on “home territory” here!), which operates under the assumption of species being optimized for a particular set of abiotic parameters, and focusing on the shifts of those parameters over space and time. So extinction risk may be predicted from a shift in climate and decrease or disappearance of potential habitat. The authors of this paper observe naturally that biological organisms are not quite so static, they exhibit both plasticity and adaptiveness within their own particular life history, as well as ability to evolve on a population wide level over time. If genetic evolution is thought of as a hill climbing algorithm I suppose a niche model presumes that the hill moves while the principal sits pat. This static vision of the tree of life seems at odds with development, behavior and evolution. The authors of this paper believe that a different formulation may be fruitful, and I am inclined to agree with them.

journal.pbio.1000357.e001As I observed above the formalism undergirding this paper is exceedingly simple. On the left-hand side you have the variable which determines the risk, or lack of risk, of extinction more or less, because it defines the maximum rate of environmental change where the population can be expected to persist. This makes intuitive sense, as extremely volatile environments would be difficult for species and individual organisms to track.Too much variation over a short period of time, and no species can bend with the winds of change rapidly enough. Here are the list of parameters in the formalism (taken from box 1 of the paper):

ηc – critical rate of environmental change: maximum rate of change which allows persistence of a population

B – environmental sensitivity of selection: change in the optimum phenotype with the environment. It’s a slope, so 0 means that the change in environment doesn’t change optimum phenotype, while a very high slope indicates a rapid shift of optimum. One presumes this is proportional to the power of natural selection

T – generation time: average age of parents of a cohort of newborn individuals. Big T means long generation times, small T means short ones

σ2 – phenotypic variance

h2 – heritability: the proportion of phenotypic variance in a trait due to additive genetic effects

r max intrinsic rate of increase: population growth rate in the absence of constraints

b – phenotypic plasticity: influence of the environment on individual phenotypes through development. Height is plastic; compare North Koreans vs. South Koreans

γ – stabilizing selection: this is basically selection pushing in from both directions away from the phenotypic optimum. The stronger the selection, the sharper the fitness gradient. Height exhibits some shallow stabilizing dynamics; the very tall and very short seem to be less fit

Examining the equation, and knowing the parameters, some relations which we comprehend intuitively become clear. The larger the denominator, the lower the rate of maximum environmental change which would allow for population persistence, so the higher the probability of extinction. Species with large T, long generation times, are at greater risk. Scenarios where the the environmental sensitivity to selection, B, is much greater than the ability of an organism to track its environment through phenotypic plasticity, b, increase the probability of extinction. Obviously selection takes some time to operate, assuming you have extant genetic variation, so if a sharp shift in environment with radical fitness implications occurs, and the species is unable to track this in any way, population size is going to crash and extinction may become imminent.

On the numerator you see that the more heritable variation you have, the higher ηc. The rate of adaptation is proportional to the amount of heritable phenotypic variation extant within the population, because selection needs variance away from the old optimum toward the new one to shift the population central tendency. In other words if selection doesn’t result in a change in the next generation because the trait isn’t passed on through genes, then that precludes the population being able to shift its median phenotype (though presumably if there is stochastic phenotypic variation from generation to generation it would be able to persist if enough individuals fell within the optimum range). The strength of stabilizing selection and rate of natural increase also weight in favor of population persistence. I presume in the former case it has to do with the efficacy of selection in shifting the phenotypic mean (i.e., it’s like heritability), while in the latter it seems that the ability to bounce back from population crashes would redound to a species’ benefit in scenarios of environmental volatility (selection may cause a great number of deaths per generation until a new equilibrium is attained).

journal.pbio.1000357.e002Of course a model like the one above has many approximations so as to approach a level of analytical tractability. They do address some of the interdependencies of the parameters, in particular the trade-offs of phenotypic plasticity. In this equation 1/ω2b quantifies the cost of plasticity, r 0 represents increase without any cost of plasticity. We’re basically talking about the “Jack-of-all-trades is a master of none” issue here. In a way this crops up when we’re talking of clonal vs. sexual lineages on an evolutionary genetic scale. The general line of thinking is that sexual lineages are at a short-term disadvantage because they’re less optimized for the environment, but when there’s a shift in the environment (or pathogen character) the clonal lineages are at much more risk because they don’t have much variation with which natural selection can work. What was once a sharper phenotypic optimum turns into a narrow and unscalable gully.

Figure 2 illustrates some of the implications of particular parameters in relation to trade-offs:


There’s a lot of explanatory text, as they cite various literature which may, or may not, support their model. Clearly the presentation here is aimed toward goading people into testing their formalism, and to see if it has any utility. I know that those who cherish biodiversity would prefer that we preserve everything (assuming we can actually record all the species), but reality will likely impose upon us particular constraints, and trade-offs. In a cost vs. benefit calculus this sort model may be useful. Which species are likely to be able to track the environmental changes to some extent? Which species are unlikely to be able to track the changes? What are the probabilities? And so forth.

I’ll let the authors conclude:

Our aim was to describe an approach based on evolutionary and demographic mechanisms that can be used to make predictions on population persistence in a changing environment and to highlight the most important variables to measure. While this approach is obviously more costly and time-consuming than niche modelling, its results are also likely to be more useful for specific purposes because it explicitly incorporates the factors that limit population response to environmental change.

The feasibility of such a mechanistic approach has been demonstrated by a few recent studies. Deutsch et al…used thermal tolerance curves to predict the fitness consequence of climate change for many species of terrestrial insects across latitudes, but without explicitly considering phenotypic plasticity or genetic evolution. Kearney et al…combined biophysical models of energy transfers with measures of heritability of egg desiccation to predict how climate change would affect the distribution of the mosquito Aedes aegiptii in Australia. Egg desiccation was treated as a threshold trait, but the possibility of phenotypic plasticity or evolution of the threshold was not considered. These encouraging efforts call for more empirical studies where genetic evolution and phenotypic plasticity are combined with demography to make predictions about population persistence in a changing environment. The simple approach we have outlined is a necessary step towards a more specific and comprehensive understanding of the influence of environmental change on population extinction.

Citation: Chevin L-M, Lande R, & Mace GM (2010). Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory PLoS Biol : 10.1371/journal.pbio.1000357

(Republished from Discover/GNXP by permission of author or representative)
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100413162914-largeI’m still a sucker for stories like this, Only Known Living Population of Rare Dwarf Lemur Discovered:

Researchers have discovered the world’s only known living population of Sibree’s Dwarf Lemur, a rare lemur known only in eastern Madagascar. The discovery of approximately a thousand of these lemurs was made by Mitchell Irwin, a Research Associate at McGill University, and colleagues from the German Primate Centre in Göttingen Germany; the University of Antananarivo in Madagascar; and the University of Massachusetts.

The species was first discovered in Madagascar in 1896, but this tiny, nocturnal dwarf lemur was never studied throughout the 20th century. Following the destruction of its only known rainforest habitat, scientists had no idea whether the species still existed in the wild — or even whether it was a distinct species….

Living today is much more awesome than the 19th century overall, but, we’ve mapped the whole world, and have a good sense of all the large animals (at least the upper bound, unfortunately the number seems to be dropping). Call me mammal-centric, but I feel that we have tapped out most of the zoological wonder of our planet. Is it too much to say that the terrestrial domain now involves mostly the counting of beetles? (I exaggerate!) But sometimes there’s a lemur in Madagascar or a rare ungulate in Vietnam, and we get a sense of the wonder which once was (along with all the -isms which we now abhor!). Could you imagine the blog posts that Carl Zimmer or Ed Yong could have written about the discovery of the Platypus? Actually, they’d probably end up narrating a special on the National Geographic Channel….

Here’s the original paper: MtDNA and nDNA corroborate existence of sympatric dwarf lemur species at Tsinjoarivo, eastern Madagascar.

Credit: Image courtesy of McGill University

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Zoology 
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pleistocene_brain_sizeJohn Hawks has an excellent post rebutting some misinformation and confusion on the part of Colin Blakemore, an Oxford neurobiologist. Blakemore asserts that:

* There was a sharp spike in cranial capacity ~200,000 years ago, on the order of 30%

* And, that the large brain was not deleterious despite its large caloric footprint (25% of our calories service the brain) because the “environment of early humans was so clement and rich in resources”

Hawks refutes the first by simply reposting the chart the above (x axis = years before present, y axis = cranial capacity). It’s rather straightforward, I don’t know the paleoanthropology with any great depth, but the gradual rise in hominin cranial capacity has always been a “mystery” waiting to be solved (see Grooming, Gossip, and the Evolution of Language and The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature). Blakemore may have new data, but as they say, “bring it.” Until then the consensus is what it is (the hominins with the greatest cranial capacities for what it’s worth were Neandertals, and even anatomically modern humans have tended toward smaller cranial capacities since the end of the last Ice Age along with a general trend toward smaller size).

But the second issue is particularly confusing, as Blakemore should have taken an ecology course at some point in his eduction if he’s a biologist (though perhaps not). One of the problems that I often have with biologists is that they are exceedingly Malthusian in their thinking, and so have a difficult time internalizing the contemporary realities of post-Malthusian economics (see Knowledge and the Wealth of Nations: A Story of Economic Discovery).Innovation and economic growth combined with declining population growth have changed the game in fundamental ways. And yet still the biological predisposition to think in Malthusian terms is correct for our species for almost its whole history.*

A “tropical paradise” is only a tropical paradise if you have a modicum of affluence, leisure, and, modern medicine. Easter Island is to a great extent a reductio ad absurdum of pre-modern man and gifted with a clement regime. Easter Island’s weather is mild, the monthly low is 18/65 °C/°F and the monthly high is 28/82 °C/°F. The rainfall is 1,118/44 mm/in. But constrained on an island the original Polynesians famously transformed it into a Malthusian case-study. We literally breed up to the limits of growth, squeezing ourselves against the margins of subsistence.

I can think of only one way in which Blakemore’s thesis that the environment of early humans was rich in resources might hold, at least on a per capita basis: the anatomically modern humans of Africa exhibited bourgeois values and had low time preference. In other words, their population was always kept below ecological carrying capacity through forethought and social planning, since there is no evidence for much technological innovation which would have resulted in economic growth to generate surplus. My main qualm with this thesis is that it seems to put the cart before the horse, since one presupposes that a robust modern cognitive capacity is usually necessary for this sort of behavior.

* Malthus’ biggest mistake was probably that he did not anticipate the demographic transition, whereby gains in economic growth were not absorbed by gains in population.

(Republished from Discover/GNXP by permission of author or representative)
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The Middle-to-Upper Palaeolithic transition in Cova Gran (Catalunya, Spain) and the extinction of Neanderthals in the Iberian Peninsula:

The excavations carried out in Cova Gran de Santa Linya (Southeastern PrePyrenees, Catalunya, Spain) have unearthed a new archaeological sequence attributable to the Middle Palaeoloithic/Upper Palaeolithic (MP/UP) transition. This article presents data on the stratigraphy, archaeology, and 14C AMS dates of three Early Upper Palaeolithic and four Late Middle Palaeolithic levels excavated in Cova Gran. All these archaeological levels fall within the 34-32 ka time span, the temporal frame in which major events of Neanderthal extinction took place. The earliest Early Upper Palaeolithic (497D) and the latest Middle Palaeolithic (S1B) levels in Cova Gran are separated by a sterile gap and permit pinpointing the time period in which the Mousterian disappeared from Northeastern Spain. Technological differences between the Early Upper Palaeolithic and Late Middle Palaeolithic industries in Cova Gran support a cultural rupture between the two periods. A series of 12 14C AMS dates prompts reflections on the validity of reconstructions based on radiocarbon data. Thus, results from excavations in Cova Gran lead us to discuss the scenarios relating the MP/UP transition in the Iberian Peninsula, a region considered a refuge of late Neanderthal populations.

ScienceDaily has a lot more. Here’s the important point I think:

The samples obtained at Cova Gran using Carbon 14 dating refer to a period of between 34,000 and 32,000 years in which this biological replacement in the Western Mediterranean can be located in time, although the study regards as relative the use of Carbon 14 for dating materials from the period of transition of the Middle to Upper Palaeolithic period( 40,000 and 30,000).
The results also support the hypothesis that there was neither interaction nor coexistence between the two species.

There’s long been a model that modern humans replaced Neandertals without coming into direct conflict with them. The model would be that modern humans simply disrupted the ecology which the Neandertals depended upon. It seems a bit too pat for me, but considering the very low population densities of hunter-gatherers, and in particular Neandertals, perhaps it is possible.
Citation: The Middle-to-Upper Palaeolithic transition in Cova Gran (Catalunya, Spain) and the extinction of Neanderthals in the Iberian Peninsula, doi:10.1016/j.jhevol.2009.09.002

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Evolution 
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Is the Hobbit’s Brain Unfeasibly Small?:

Brain expansion began early in primate evolution and has occurred in all major groups, suggesting a strong selective advantage to increased brainpower in most primate lineages. Despite this overall trend, however, Mundy and his colleagues have identified several branches/lineages within each major group that have shown decreasing brain and body mass as they evolve, for example in marmosets and mouse lemurs.
According to Mundy, “We find that, under reasonable assumptions, the reduction in brain size during the evolution of Homo floresiensis is not unusual in comparison to these other primates. Along with other recent studies on the effects of ‘island dwarfism’ in other mammals, these results support the hypothesis that the small brain of Homo floresiensis was adapted to local ecological conditions on Flores.”

The paper will show up in BMC Biology at some point. The main question I have is in regards to the purported tool use of the Hobbits. I can believe that a local adaptation toward small brains, Idiocracy-writ large, occurred. Brains are metabolically expensive, and it isn’t as if the history of life on earth has shown the massive long-term benefits of being highly encephalized (though I think one can make a case that there has been a modest trend, with primates, and especially H. sapiens as extreme outliers above the trend). But could small brained creatures maintain the relatively advanced toolkit which the Hobbit finds have been associated with? Seems to me that there’s a high probability here of some sort of contamination, but I’ll be happy to be put in my place by anthropologists in-the-know….

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Evolution 
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Modern civilization has extremely deleterious consequences in regards to species richness, primarily through destruction of habitat. Because of these negative aspects of modernity hunter-gatherers have been idealized as a model of humanity at equilibrium with their ecology. 1491: New Revelations of the Americas Before Columbus lays out the revisionist, and to some extent now mainstream, argument that the American wilderness which European settlers encountered was actually an instance of “re-wilding” in the wake of native demographic collapse due to disease. But setting this case aside, what about Australia? Its fauna was even more exotic to Eurasian sensibilities, and the Australian Aboriginals do not seem to have ever shifted away from obligate hunter-gatherer lifestyles. Perhaps they truly were at equilibrium with their environment, judging from the fact that Australia has so many endemic species.
I think the argument that Australian Aboriginals were at some equilibrium is correct; but only because the havoc that they wrought upon the native ecosystem was relatively deep in the past. The particular destructiveness of modern civilization is a function of its progressiveness and the constant roil of its development. Pre-modern societies characterized by Malthusian conditions whereby population growth was “checked” by natural limitations were static enough over the long term that after an initial transient period of ecological instability a new equilibrium had time to settle in. If humanity is an environmental condition, Malthusian humanity is like a storm which passes. Post-Malthusian humanity is like a perpetual hurricane.
A new paper in Science speaks to the specific case of Australia. And Then There Were None?:

Giant marsupials, reptiles, and flightless birds once inhabited Australia (see the first figure). But 23 of the 24 genera of these megafauna disappeared in the late Pleistocene (125 to 12 thousand years ago). Most Australian megafauna appear to have survived until 51 to 40 thousand years ago, with human impact by hunting or vegetation change proposed as the extinction drivers…Yet, one site has stood out as an anomaly: Cuddie Springs in interior New South Wales. Persistent claims have been made that this site contains megafauna fossils associated with stone tools in sediments deposited 40 to 30 thousand years ago…thus indicating prolonged overlap between people and megafauna. These claims have been challenged…based on concerns about possible reworking of fossils from older deposits. To resolve this conundrum, Grün et al…have now directly dated the fossils themselves. The results provide no evidence for the late survival of megafauna at the site.

Here’s the original paper on the Cuddie River site, ESR and U-series analyses of faunal material from Cuddie Springs, NSW, Australia: implications for the timing of the extinction of the Australian megafauna:

The timing and cause of late Pleistocene faunal extinctions in Australia are subjects of a debate that has become polarised by two vigorously defended views. One contends that the late Pleistocene extinction was a short event caused by humans colonising the Australian continent, whereas the other promotes a gradual demise of the fauna, over a period of at least 10-20 ka, due to a combination of climatic changes and ecological pressures by humans. Cuddie Springs is central to this debate as it is the only site known in continental Australia where archaeological and megafauna remains co-occur.
We have analysed more than 60 bones and teeth from the site by laser ablation ICP-MS to determine U, and Th concentrations and distributions, and those with sufficiently high U concentrations were analysed for U-series isotopes. Twenty-nine teeth were analysed by ESR. These new results, as well as previously published geochronological data, contradict the hypothesis that the clastic sediments of Stratigraphic Unit 6 (SU6) are in primary context with the faunal, archaeological and other materials found in SU6, and that all have ages consistent with the optically stimulated luminescence (OSL) estimates of 30-36 ka. These young OSL results were used to argue for a relatively recent age of the extinct fauna. Our results imply that SU6 is either significantly older than the OSL results, or that a large fraction of the faunal material and the charcoal found in SU6 was derived from older, lateral deposits.
Our U and Th laser ablation ICPMS results as well as the REE profiles reported by Trueman et al. [2008. Comparing rates of recystallisation and the potential for preservation of biomolecules from the distribution of trace elements in fossil bones. C.R. Palevol. General Paleontology (Taphonomy and Fossilization) 7, 145-158] contradict the interpretation of previously reported rare earth element compositions of bones, and the argument based thereon for the primary context of faunal material and clastic sediments in SU6 layers.

ScienceDaily has more. Truly veni, vidi, vici is the story of man. The difference with modern man is that the exponent for the last two comes from 1 to ∞. We arrive. And see & conquer. We see & conquer. We see & conquer….
ESR and U-series analyses of faunal material from Cuddie Springs, NSW, Australia: implications for the timing of the extinction of the Australian megafauna, doi:10.1016/j.quascirev.2009.11.004
And Then There Were None?, Science 327 (5964), 420. [DOI: 10.1126/science.1185517]
Note: The arrival of the dingo in the past 10,000 years to Australia resulted in a second wave of extinctions, the “Tasmanian Tiger” was extant on mainland Australia until about 2,000 years ago. Tasmania was separated from the Australian mainland before the arrival of the dingo, ergo, the persistence of large carnivorous marsupials down to modern period.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Ecology 
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Are Antarctic minke whales unusually abundant because of 20th century whaling?:

Severe declines in megafauna worldwide illuminate the role of top predators in ecosystem structure. In the Antarctic, the Krill Surplus Hypothesis posits that the killing of more than 2 million large whales led to competitive release for smaller krill-eating species like the Antarctic minke whale. If true, the current size of the Antarctic minke whale population may be unusually high as an indirect result of whaling. Here, we estimate the long-term population size of the Antarctic minke whale prior to whaling by sequencing 11 nuclear genetic markers from 52 modern samples purchased in Japanese meat markets. We use coalescent simulations to explore the potential influence of population substructure and find that even though our samples are drawn from a limited geographic area, our estimate reflects ocean-wide genetic diversity. Using Bayesian estimates of the mutation rate and coalescent-based analyses of genetic diversity across loci, we calculate the long-term population size of the Antarctic minke whale to be 670 000 individuals (95% confidence interval: 374 000-1 150 000). Our estimate of long-term abundance is similar to, or greater than, contemporary abundance estimates, suggesting that managing Antarctic ecosystems under the assumption that Antarctic minke whales are unusually abundant is not warranted.

Populations, such as humans, who have expanded rapidly from a small population tend to exhibit a particular genetic signature. ScienceDaily has more on this particular paper.
Citation: Are Antarctic minke whales unusually abundant because of 20th century whaling?, doi: 10.1111/j.1365-294X.2009.04447.x

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Genetics 
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Carl Zimmer has a nice write up of the a new paper in Science which characterizes the nature of the cells which are manifest during devil facial tumor disease. The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer:

The Tasmanian devil, a marsupial carnivore, is endangered because of the emergence of a transmissible cancer known as devil facial tumor disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, a mitochondrial genome analysis, and deep sequencing of the DFTD transcriptome and microRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor and suggest that the disease is of Schwann cell origin. On the basis of these results, we have generated a diagnostic marker for DFTD and identify a suite of genes relevant to DFTD pathology and transmission. We provide a genomic data set for the Tasmanian devil that is applicable to cancer diagnosis, disease evolution, and conservation biology.

In Carl’s article, he reports:

The cancer, devil’s facial tumor disease, is transmitted when the animals bite one another’s faces during fights. It grows rapidly, choking off the animal’s mouth and spreading to other organs. The disease has wiped out 60 percent of all Tasmanian devils since it was first observed in 1996, and some ecologists predict that it could obliterate the entire wild population within 35 years.

I think that the ecologists need to be careful here, as the public might think that the cancer itself is going to be the immediate proximate cause of extinction. Rather, it seems more likely that the disease will reduce the numbers of the devils, of which there are on the order of 10 to 100 thousand on the island. And small populations, say less than a 1,000, are subject to random fluctuations in population size which could drive them to extinction (imagine a short-term climatic regime which reduces the food supply). It seems that some individuals are already immune to the disease, so over time if nature took its course the population would probably bounce back. Projecting extinction because of disease necessarily and sufficiently is just part of the linear fallacy, which isn’t really good at predicting over the long term in biological contexts. Australia still has rabbits. It’s called evolution.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Genetics 
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Brian Switek, The extended twilight of the mammoths:

So, if the team’s analysis is correct, both mammoths and horses lived in the interior of Alaska between about 11,000 and 7,000 years ago. This is significantly more recent than the youngest fossil remains of horses and mammoths, dated between 15,000 and 13,000 years ago. There are at least two factors that might contribute to this disparity. The first is that fossils from this more recent time were preserved but have not yet been found. More likely, though, is that the populations of both mammoths and horses had dwindled to the point where fossil preservation was becoming increasingly unlikely. There were so few of them that the death of an individual in circumstances amenable to preservation was becoming rarer and rarer.
Either way, this discovery has important implications for the extinction of horses and mammoths in North America. Based upon the fossil data alone it had been hypothesized that both disappeared around the time that humans became established in North America.* Some have taken this association to suggest that humans engaged in a blitzkrieg in which naive New World megamammals were quickly dispatched by the human hunters. If the new evidence is correct, though, humans did not wipe out horses and mammoths overnight. Instead humans lived alongside dwindling populations in Alaska for thousands of years. Likewise, these new findings also contradict the favored hypothesis of one of the study’s authors, Ross MacPhee, who previously proposed that some kind of “hyperdisease” carried by humans (or animals that traveled with humans) quickly wiped out these animals. The pattern of extinction was obviously more protracted.

This seems about right. Excuse the analogy, but it sometimes seems that models of human-caused extinction of mega-fauna portray ancient hunter-gatherers as Einsatzgruppen, and the mega-fauna as Jews and Communists. Though genocides of human populations in the concerted manner of the Germans against the Jews, Gypsies and other groups during World War II have occurred periodically, more often what we see is a slow wearing down and attrition of marginal groups at the expense of dominant ones.
It seems a plausible model that when mega-fauna were plentiful hunters would focus on them, but once the mega-fauna became rare naturally the return on investment would decrease and it would become rational to shift to other prey organisms. This implies that many mega-fauna likely persisted in isolated pockets as relict populations, and may have been killed off only far later, or perhaps even succumbed to a natural environmental calamity. In another era the last herds of wild horses would probably have gone extinct due to drought, or perhaps been hunted down by a random group of humans who had no idea that they were decreasing the biological diversity of the planet.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology 
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octpus.pngCool new report in Current Biology, Defensive tool use in a coconut-carrying octopus:

The use of tools has become a benchmark for cognitive sophistication. Originally regarded as a defining feature of our species, tool-use behaviours have subsequently been revealed in other primates and a growing spectrum of mammals and birds…Among invertebrates, however, the acquisition of items that are deployed later has not previously been reported. We repeatedly observed soft-sediment dwelling octopuses carrying around coconut shell halves, assembling them as a shelter only when needed. Whilst being carried, the shells offer no protection and place a requirement on the carrier to use a novel and cumbersome form of locomotion — ‘stilt-walking’.

No surprise that when we are looking to a violation of an old “human exceptional” character (though tool-use seems to have been violated a fair amount now by any interpretation) that the cephalopod would step up to the plate. I’ve heard of weird behavior by octopuses in laboratories which begs to be anthropomorphized, but no one denies that this is one taxa which has some brains. Who says you need a notochord to be a “higher animal”? Anyone who’s read a fair amount of science fiction also is aware that cephalopods are one of the more exotic, but still frequent, candidate earth lineages which might potentially rise to sapience. Fore all the aquatic species who have the glimmer of intelligence cybernetics might offer up some potential avenues of freedom and leveling the playing field with the terrestrials.
Citation: Defensive tool use in a coconut-carrying octopus, Finn, Julian K.; Tregenza, Tom; Norman, Mark D. doi:10.1016/j.cub.2009.10.052 (volume 19 issue 23 pp.R1069 – R1070)

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology 
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FuturePundit points me to a new paper on the Toba explosion, Environmental impact of the 73 ka Toba super-eruption in South Asia:

The cooling effects of historic volcanic eruptions on world climate are well known but the impacts of even bigger prehistoric eruptions are still shrouded in mystery. The eruption of Toba volcano in northern Sumatra some 73,000 years ago was the largest explosive eruption of the past two million years, with a Volcanic Explosivity Index of magnitude 8, but its impact on climate has been controversial. In order to resolve this issue, we have analysed pollen from a marine core in the Bay of Bengal with stratified Toba ash, and the carbon isotopic composition of soil carbonates directly above and below the ash in three sites on a 400 km transect across central India. Pollen evidence shows that the eruption was followed by initial cooling and prolonged desiccation, reflected in a decline in tree cover in India and the adjacent region. Carbon isotopes show that C 3 forest was replaced by wooded to open C 4 grassland in central India. Our results demonstrate that the Toba eruption caused climatic cooling and prolonged deforestation in South Asia, and challenge claims of minimal impact on tropical ecosystems and human populations.

The Toba caldera is in Sumatra, but the ashfall in India was on the order of 15 centimeters to 6 feet. This might also be relevant to human evolution, The super-eruption of Toba, did it cause a human bottleneck?.
Citation Martin A.J. Williamsa, Stanley H. Ambroseb, Sander van der Kaarsc, Carsten Ruehlemannd, Umesh Chattopadhyayae, Jagannath Pale and Parth R. Chauhanf, Environmental impact of the 73 ka Toba super-eruption in South Asia, doi:10.1016/j.palaeo.2009.10.009

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Anthropology, Ecology, Evolution 
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Pleistocene Megafaunal Collapse, Novel Plant Communities, and Enhanced Fire Regimes in North America:

Although the North American megafaunal extinctions and the formation of novel plant communities are well-known features of the last deglaciation, the causal relationships between these phenomena are unclear. Using the dung fungus Sporormiella and other paleoecological proxies from Appleman Lake, Indiana, and several New York sites, we established that the megafaunal decline closely preceded enhanced fire regimes and the development of plant communities that have no modern analogs. The loss of keystone megaherbivores may thus have altered ecosystem structure and function by the release of palatable hardwoods from herbivory pressure and by fuel accumulation. Megafaunal populations collapsed from 14,800 to 13,700 years ago, well before the final extinctions and during the Bølling-Allerød warm period. Human impacts remain plausible, but the decline predates Younger Dryas cooling and the extraterrestrial impact event proposed to have occurred 12,900 years ago.

Ed Yong has the bases covered:

What about humans, those pesky slayers of animals? Some scientists believed that North America’s Clovis people specialised in hunting big mammals, causing a “blitzkrieg” of spear-throwing that drove many species to extinction. But these hunters only arrive in North America between 13,300 and 12,900 years ago, around a thousand years after the population crashes had begun.
If people were responsible, they must have been pre-Clovis settlers. There’s growing evidence that such humans were around, but they weren’t common or specialised. They may have contributed to the beasts’ downfall, while Clovis hunting technology delivered a coup de grace to already faltering populati0ons.
By analysing the sediment at Appleman lake – spores, pollen, charcoal and all – Gill has replayed the history of the site, spanning the last 17,000 years. Her data rule out a few theories, but as she says, they “[do] not conclusively resolve the debate” about climate causes versus human ones. It’s possible that similar studies at different sites and other continents will help to provide more clues.

A complex story like this is perhaps more common than an event such as the extinction of the passenger pigeons. Populations of organisms often go through cycles in census size, whether due to environmental variation or coevolutionary dynamics with parasites. Consider the example of the" href="">Tasmania devil, the disease which it is susceptible to is not the doing of humans, but the introduction of dingos (probably by humans) mean that the species is restricted to Tasmania. Additionally, humans have laid claim to much of the habitat of the devil (or what was the habitat of the devil). When a virulent disease hits, the devil has a much smaller margin of error than it had before. It could be that recent megafaunal extinctions are ultimately due to humans, even if they are not always proximately due to humans.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology 
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The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography:

…We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20-30 Ma. The data reveal that the patterns of genetic diversity within and between different moa clades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5-8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

“Subfossil” means that it hasn’t totally fossilized and one can extract organic material from the remains.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Ecology, Evolution 
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Razib Khan
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