Category: Ecology

Dogs, domesticated before agriculture

By Razib Khan | October 21, 2012 11:27 pm

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from talking to a dog geneticist I am to understand that the Eskimo dogs themselves are likely new arrivals, and superseded older dog lineages in the far north.

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MORE ABOUT: Domestic dogs

Evolutionary pressures, within and without

By Razib Khan | April 20, 2011 1:16 am

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.orgI 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:

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CATEGORIZED UNDER: Ecology, Evolution

A cloud forest in….

By Razib Khan | December 10, 2010 1:22 am

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

MORE ABOUT: Cloud Forest

The dynamism of nature

By Razib Khan | May 4, 2010 1:06 am

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.
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CATEGORIZED UNDER: Ecology, Environment

Modeling the probabilities of extinction

By Razib Khan | April 29, 2010 3:05 am

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.

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Shadows of menageries past

By Razib Khan | April 14, 2010 11:08 am

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


Thomas Malthus was right. Mostly

By Razib Khan | March 29, 2010 4:38 pm

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).

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Apartheid of Iberian Neandertals & modern humans

By Razib Khan | March 16, 2010 12:44 am

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

CATEGORIZED UNDER: Ecology, Evolution

Hobbits small brains not so anomolous

By Razib Khan | January 27, 2010 2:35 am

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….

CATEGORIZED UNDER: Ecology, Evolution

Time never forgot the land

By Razib Khan | January 22, 2010 1:15 am

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?:

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CATEGORIZED UNDER: Anthroplogy, Ecology

Minke whales not undergoing rapid demographic expansion

By Razib Khan | January 18, 2010 4:47 pm

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

CATEGORIZED UNDER: Ecology, Genetics

Contagious Tasmanian Devil cancer

By Razib Khan | December 31, 2009 7:24 pm

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.

CATEGORIZED UNDER: Ecology, Genetics

When mammoths roamed (rarely)

By Razib Khan | December 22, 2009 6:02 pm

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.


I for one welcome our future cephalopod overlords!

By Razib Khan | December 15, 2009 5:13 am

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)


Apocalypse 73,000 B.C.

By Razib Khan | November 24, 2009 1:07 am

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 C3 forest was replaced by wooded to open C4 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

CATEGORIZED UNDER: Anthroplogy, Ecology, Evolution

When mammoths roamed

By Razib Khan | November 21, 2009 1:19 am

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 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.


Ancient DNA & the moa

By Razib Khan | November 18, 2009 10:54 pm

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.

CATEGORIZED UNDER: Ecology, Evolution

Best paper title I've seen in a while

By Razib Khan | November 4, 2009 3:58 pm

Cooperation and individuality among man-eating lions.


The root of all anti-evolutionism

By Razib Khan | September 29, 2009 6:57 pm

The Religious Landscape Survey has a lot of data various denominations. Recently I noticed something weird about Mormons; they are very anti-evolution, as well as anti-universalist in their views on salvation, according to this survey. These are notable views because Mormons don’t have well established attitudes on evolution from on high (which is why Mitt Romney expressed anti-Creationist sentiments without any blowback during the 2007-2008 campaign), and, their religious tradition actually seems to have been influenced by American Universalism, and so an exclusive attitude toward salvation is rather strange. In the case of the latter one could fudge the issue by noting Mormons believe in levels of heaven, and only Mormons themselves have access to the highest level (in particular, male Mormons who become divine). But in the soteriology of Mormonism I am to understand that only a tiny minority of human beings will spend eternity in hell (the “Outer Darkness”). So what’s up with the Mormon response to this question? I think it has to do with social identification, as Mormons are now operational adjuncts to the culture of conservative Protestantism (rejection of the theses of Charles Darwin is apparently more pervasive now than it was in the 1930s on the BYU campus according to surveys published in The Creationists).
I wanted to relate attitudes toward evolution as they depend on other parameters. I created indices by converting ordinal variables into integers, so that Conservatives = 1, Moderates = 0 and Liberals = -1. I weighted by the proportions, so that if a group was -0.5 in terms of political index that mean it was somewhat more liberal than not. You should be able to figure out the meaning of the signs simply by how the groups associate with each other, though I went left to right in the tables in the Religious Landscape Survey positive to negative (1, 0, -1, or 2, 1, 0, -1, -2, etc.). I estimated WORDSUM means by looking at the means for each educational class in the GSS and weighting appropriately (for black churches I used black WORDSUM means).

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Why ligers are huge

By Razib Khan | September 27, 2009 7:10 pm

liger3.pngBelieve it or not, tigers are not the largest big cat. Ligers are (you might remember ligers from Napoleon Dynamite). Why? It has to do with the weirdness that occurs when you hybridize across two lineages which have been distinctive for millions of years, but not so long so as not to be able to produce viable offspring (in fact, many ligers are fertile as well). Here’s the explanation:

Imprinted genes are under greater selective pressure than normal genes. This is because only one copy is active at a time. Any variations in that copy will be expressed. There is no “back-up copy” to mask its effects. As a result, imprinted genes evolve more rapidly than other genes. And imprinting patterns — which genes are silenced in the eggs and sperm — also evolve quickly. They can be quite different in closely related species.
Lions and tigers don’t normally meet in nature. But they can get along very well in captivity, where they sometimes produce hybrid offspring. The offspring look different, depending on who the mother is. A male lion and a female tiger produce a liger – the biggest of the big cats. A male tiger and a female lion produce a tigon, a cat that is about the same size as its parents.
The difference in size and appearance between ligers and tigons is due in part to the parents’ differently imprinted genes. Other animals can also hybridize, with similar results. For example, a horse and a donkey can produce a mule or a hinny.

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CATEGORIZED UNDER: Ecology, Evolution

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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