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Extinction

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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: http://dx.doi.org/10.1101/017368

 
• Category: Science • Tags: Ecology, Extinction 
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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.

ResearchBlogging.org 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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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:

paramslande

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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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"