Tuesday, March 31, 2009

Natural Selection Studies Flawed?

Upcomming article at PNAS...

Repost from ScienceDaily:

Scientists at Penn State and the National Institute of Genetics in Japan have demonstrated that several statistical methods commonly used by biologists to detect natural selection at the molecular level tend to produce incorrect results.

"Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions," said Masatoshi Nei, Penn State Evan Pugh Professor of Biology and the team's leader. The team's results will be published in the Online Early Edition of the journal Proceedings of the National Academy of Sciences during the week ending Friday 3 April 2009 and also in the journal's print edition at a later date.

Nei said that many scientists who examine human evolution have used faulty statistical methods in their studies and, as a result, their conclusions could be wrong. For example, in one published study the scientists used a statistical method to demonstrate pervasive natural selection during human evolution. "This group documented adaptive evolution in many genes expressed in the brain, thyroid, and placenta, which are assumed to be important for human evolution," said Masafumi Nozawa, a postdoctoral fellow at Penn State and one of the paper's authors. "But if the statistical method that they used is not reliable, then their results also might not be reliable," added Nei. "Of course, we would never say that natural selection is not happening, but we are saying that these statistical methods can lead scientists to make erroneous inferences," he said.

The team examined the branch-site method and several types of site-prediction methods commonly used for statistical analyses of natural selection at the molecular level. The branch-site method enables scientists to determine whether or not natural selection has occurred within a particular gene, and the site-prediction method allows scientists to predict the exact location on a gene in which natural selection has occurred.

"Both of these methods are very popular among biologists because they appear to give valuable results about which genes have undergone natural selection," said Nei. "But neither of the methods seems to give an accurate picture of what's really going on."

Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

"These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences," said Nei. "But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time."

Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

A third author on the study is Yoshiyuki Suzuki, a researcher at the National Institute of Genetics in Japan. This research was supported by the National Institutes of Health.

Sunday, March 29, 2009

The Hunting Modes of a Wolf Spider

Taking a break from stalking prey amid the jungle of leaf litter in my front yard, this spider sprinted across my patio last Monday night. I managed to drop my compass next to him (the edge of which has a two inch ruler) and approximate his Cephalothorax-to-spinneret length at about 7/8 of an inch.

My best guess is Lycosa gulosa, though I’m somewhat doubtful due to the size of this beast… (If anyone else has an alternative ID be sure to let me know.)

Wolf Spiders are ferocious predators, and in captivity have been shown to scavenge as well as hunt. They hunt mostly by cruising; moving slowly and deliberately through high prey areas, taking precaution as to not raise the notice of local cockroaches, moths and other quarry. They also occasionally practice an ambush mode of hunting during which they remain motionless – or even actively conceal themselves – waiting for unwary meals to stumble on them.

The cruising and ambush styles of hunting have evolved specifically as counters to the sensory systems of prey species – to either avoid detection while on approach, or, to completely overwhelm the capabilities of the prey’s sense organs. As detailed in a recent article by Jérôme Casas, Thomas Steinmann and Olivier Dangles, “crickets, cockroaches and other orthropteroid insects are equipped with air-flow sensors (filiform hairs) at the rear end of their abdomen. They possess many short hairs, serving as acceleration sensors, and fewer long hairs (velocity sensors) on their cerci. These mechanosensors are among the most sensitive sensors in the animal kingdom, with action potentials triggered by less than one tenth the energy of a photon; indeed, the orthropteroid escape system, and in particular fluid flow sensing using filiform hairs, has maintained textbook-example status over many years. Thus, we hypothesised that spiders use the two different hunting strategies to cope with optimal air-flow detection by crickets.”

If you have an interest in spiders, or arthropods at all, check out The Aerodynamic Signature of Running Spiders to see the results of using Digital particle image velocity (DPIV) measurements of a running spider in an air tunnel to estimate prey response…

Casas, J., Steinmann, T., & Dangles, O. (2008). The Aerodynamic Signature of Running Spiders PLoS ONE, 3 (5) DOI: 10.1371/journal.pone.0002116

Ecosystem on a Log and Scarab Beetles - Field Photos

I wanted to share couple of interesting snapshots taken during the past week – well the snapshots themselves aren’t all that great, but what is depicted in them is pretty cool.

First, a section of an old log that now serving as a microcosm of biodiversity:

The fallen log is of the species Pinus elliottii (Slash Pine), as you can see from the photo, a new P. elliottii sapling has sprouted mid span. The sapling’s roots haven’t penetrated the base of the log and are fully contained within the rotting wood.

And if you take yet a slightly closer look,

You’ll notice that near the base of the sapling several other species of plants, grasses and mosses (including this week’s Wetland Plant of the Week - L. lucida) have made the log home. Though it’s difficult to see from the above images, there are also several ants, spiders and chiggers using the plants as habitat.

Using the fallen pine log for nutrients and structural support is interesting enough, but the story gets even better!

What is truly remarkable is that if you take a look to the right of the log in the first photo, you’ll notice a clearing of the foliage associated with a slight topographical depression. This depression actually functions as a waterway during periods of seasonal flooding!

Taking a look at the surrounding trees,

you’d find water stain lines more than a foot in elevation above the ground surface.

Considering that this entire site is less than five miles from the Gulf of Mexico and letting my imagination run a little wild (but not too much), I can easily envision a scenario in which such a log-microcosm serves as a platform in “rafting” plants and animals to far off places, thereby driving Natural Selection via a founding effect… It even has a ready made sail - the leaves of the pine sapling!

The other snapshot I felt deserved posting was a couple of Scarab Beetles (Family Scarabaeidae) battling for the privilege of rolling dung.

Being a still photo as opposed to a video, you may not be able to read the whole story in the above image, but what’s happening is that three "Tumblebugs" (Canthon spp.) are maneuvering a well-rounded ball of dung.

Male Scarab beetles proactively assist the females in collecting dung to be used for nest building. In exchange for help with rolling the dung balls back to the burrow, males may receive the opportunity to mate with the female, who will in turn lay a single egg on the dung ball.

Rolling the dung helps compact the material into a more stable base for larval development and at the same time provides a method for the most fit males to demonstrate their paternal skills in hopes of wining the affections of a potential mate.

In the picture above two males, both vying for an opportunity to mate, are attempting to impress the female – unfortunately for her, their back-and-forth rolling has landed her on her back under the ball of dung! She can just be made out under the upper left corner of the dung ball.

Saturday, March 28, 2009

The Rise of “Homo egocentricis”

Although it was literally a dark and stormy night, such weather conditions were but a novelty to the speaker – a scientist whom had spent the majority of his life scanning barren rocks and desiccated landscapes for fragments of fossil bone beneath the unrelenting and scorching sun of an East African desert. Yet, I can’t help but think that some level of instinctual fear naggingly tickled at his stomach as he approached the waiting crowd…

There was little doubt that villains - the arch enemies of reason and deniers of fact– concealed themselves among the many upstanding community members and university staff in attendance. This was, after all, Tallahassee, Florida. A city of the Southeastern Unite States, geographically located near the eastern extent of the so called “Bible belt.”

How would they react to being told that biological evolution is fact? Moreover, how would they respond to learning that Homo sapiens, despite an egocentric view of the world, have shared a common ancestry with other primates, and in fact, a common lineage with all life on Earth?

Actually, they responded remarkably well, much to the credit of Dr. Don Johanson.

By all accounts, the talk on Human Origins was a success. Dr. Johanson spoke with the confidence and familiarity that has made him a highly sought, world renowned lecturer and scientist.

He began the talk by discussing the development of his personal interest in anthropology as a child and quickly moved through a summary of the major fossil discoveries made during his lifetime - a true story of adventure and discovery. The lecture was given at an IMAX theater and included some fantastic images of hominid fossils and African landscapes; the presentation can be viewed in its entirety by going to the FSU Origins webpage HERE and clicking on the red-highlighted “Webcast” text to the right of Dr. Johanson’s photograph.

As a further suggestion, I’d recommend a quick look at a recent article by Kaye E. Reed of the Institute of Human Origins (which Don Johanson runs in Arizona) discussing the paleoecology of the Hadar hominin site in Ethiopia. The article discusses speciation and environmental transitions associated with Australopithecus afarensis.

Reed, K. (2008). Paleoecological patterns at the Hadar hominin site, Afar Regional State, Ethiopia Journal of Human Evolution, 54 (6), 743-768 DOI: 10.1016/j.jhevol.2007.08.013

Friday, March 27, 2009

Wetland Plant of the Week #10

Lyonia lucida


Member of the Ericacea. Facultative wet, evergreen shrub with reddish to deep pink flowers. Leaves have a distinctive vein that parrallels leaf margins.

Here's another snapshot of the same plant with a jumping spider on guard (Phidippus spp.?).

Both photographed yesterday in Levy County, Florida.

Monday, March 23, 2009

“Punctuated Equilibrium is Garbage”

A fantastic lecture given by E. O. Wilson at Florida State last night!

It was a privilege to listen to such a distinguished scientist, expert naturalist and exceptional author. If only I was half as sharp today as he is at 79… The amount of technical knowledge, understanding and wit that he possess is only exceeded by his passion for the natural world – a true asset to the scientific community and to the planet as a whole.

Rather than listen to my second hand droning, checkout the link below to view the webcast directly - Courtesy of Florida State University.

Also, be sure to scope the “E.O. Wilson Biophilia Center” which is scheduled to open September 12, 2009.

By clicking on the link below you’ll be able to hear Ed Wilson talk about Darwin’s four great works:

1. Journal of Researches into the Natural History and Geology of the Countries visited during the Voyage of HMS Beagle Round the World (1845)
2. On the Origin of Species (1859)

3. The Descent of Man; and Selection in Relation to Sex (1871)

4. The Expression of Emotions in Man and Animals (1872)

As well as topics like;

The John Wayne Vs Woody Allen Model of Sexual Selection…

The Birth of Modern Psychology…

The two Tribes of Biologists - the Functional biologist and the Natural Evolutionist…

Religion as a Byproduct of Warring Tribalism…

The Plight of the Honey Bee…

The Potential for Life on Europa…

And don’t forget to listen for my favorite quote of the talk, “Punctuated Equilibrium is Garbage.”

UPDATE: Click on "WEBCAST" under Ed's picture at the website Here to listen.

Humorous Dan Dennett Video

Dan Dennett: Cute, sexy, sweet and funny -- an evolutionary riddle

Sunday, March 22, 2009

Andean to Amazon, an Anuran Account

The tropical rainforests of the Americas are a hotspot of biodiversity and boasts the largest reservoir of amphibian diversity on the planet; but how did such variety arise in our slippery skinned friends?

If I would have been asked this question yesterday, my reply would have a bit different than it would be today – this after reading an article by Juan C. Santos of the Integrative Biology and Texas Natural Science Center recently published at PLoS.

“The unstable coexistence of lineages within a large community for extended periods of time has been hypothesized as a cause of Neotropical diversity. However, our results suggest that such a model is incomplete; rather, the complex pattern of diversification is strongly intertwined with paleogeographic events. Our inferences about the past history of the poison frogs using ancestral area reconstructions and diversification analyses provide new insights on speciation and extinction patterns in the Neotropics. Three species richness patterns are potential explanations for the extant diversity differences among regions of the Neotropics:

(1) high immigration into one region after suitable geoclimatic conditions are established;

(2) gradual in situ diversification of old endemic clades, regardless of the geoclimatic conditions, promoting species accumulation; or

(3) rapid in situ diversification of endemic clades after favorable geoclimatic conditions are established. We found that all three patterns might apply to different areas depending on historical context.

All extant Amazonian species descended from 14 lineages that dispersed into the Amazon Basin, mostly after the Miocene floodbasin system receded. The recurrent immigrations that originated mostly in the adjacent Andes, combined with an increased rate of diversification, explain the high α–diversity of Amazonia. Later, from the Miocene-Pliocene boundary to the present, a rapid in situ diversification gave rise to the extant Amazonian endemic biota. Therefore, most species in Amazonia originated in the last 10 MY. Moreover, lineages immigrating into Amazonia at <8.0>

The diversity in the Chocoan-Central American super-region derived from scattered immigrations from Andes to the early Chocoan rainforest during the late Miocene. However, starting at the Miocene-Pliocene boundary, significant orogenic events gave rise to the Central American archipelago followed by sea level fluctuations, which provided the conditions for repeated dispersal and vicariance events in pre-PLB islands. Evidence of rapid in situ diversification is supported by the high genetic diversity observed among poison frogs and other lineages especially between Western and Eastern Panamá. Interestingly, our results might explain the high β–diversity of other endemic clades within the Chocó-Central America super-region as originating initially from long-distance dispersals between disconnected islands, with diversification later during isolation by high sea levels.

The Andes have undergone extended in situ diversification since the late Eocene. However, our analyses also provided evidence of decline in the diversification rate since the middle Oligocene, which has important implications for history and conservation of the endemic Andean fauna. First, the Andes uplift at the Miocene–Pliocene boundary caused significant changes in the rate of diversification in the lowland transition zone. We found that several poison frog lineages distributed on one or both sides of the Andes had dispersed repeatedly before the Miocene uplift (i.e., five cross-Andean and five Northern to Central Andes migrations). Paleogeological evidence supports introgression of shallow seas across the northern Andes during the Miocene, suggesting a historical connection between the Amazon Basin and the Chocó. Second, the Pliocene Andean uplift (>2,000 m above sea level) formed a significant barrier to dispersal, because no other cross-Andean dispersals were found. The uplift also was associated with dramatic ecological changes and a decrease in diversification rates. These results suggest a role for niche conservatism, in that some lineages may have gone extinct because of failure to adapt. Alternatively, despite greater sampling effort in the Andes region than in other areas, we failed to find some previously common Andean species (e.g., Hyloxalus jacobuspetersi and the Ecuadorian H. lehmanni). Consequently, it is difficult to separate a natural decrease in diversification rates from the current trend of amphibian species extinctions at high altitudes due to anthropogenic habitat alteration, increased UV radiation, climate change, or pandemic infection. In contrast, the montane transition zones of the Andes and adjacent lowlands (Chocó and Amazonia) have become centers of rapid cladogenesis, and species richness in these transition zones might be underestimated because many Neotropical lineages have been shown to contain several cryptic species. Therefore, dispersals within or across the Andes diminished during the Pliocene, but diversification has intensified in the Andes-lowlands interface.

Although some of the oldest lineages of poison frogs originated in the Guiana Shield and the Venezuelan Highlands (>30 species), our results suggest extended in situ diversification followed by a decline in the rate of diversification of endemic clades in both areas since the early Miocene. Along the same lines, the Guiana Shield has high poison frog endemism, which is mostly restricted to the summits of the sandstone tepuis, while recent Amazonian poison frog immigrants occupy lowlands adjacent to the tepuis. Our results suggest that the decline of endemic Guianan diversity might be associated with ecological changes in habitat due to the collapse of the ancient tepuis and repeated dispersals from Amazonian lineages since the Pliocene. However, the diversity of poison frogs in the Guiana Shield is only beginning to be revealed. In contrast, diversification in the Venezuelan region most likely reflects the oldest vicariant event in Dendrobatidae, at 40.9 MYA. The costal ranges of Mérida, Cordillera de la Costa, and Paria peninsula are species rich but their total area is less than 5% of that of the Amazon Basin. No lineage of this endemic fauna has dispersed out to other regions since the early radiation of the poison frog family in the late Eocene. However, Eocene floristic paleoecological reconstruction of the Venezuelan Highlands area showed that it was more diverse than at present, suggesting that the ancestral habitat of the first poison frogs might have been lowland. The depauperate dendrobatid fauna of the Venezuelan llanos and Brazilian Shield plateau is puzzling, but might be related to Holocene aridity.

The recurring dispersals to Amazonia suggests that a large part of dendrobatid diversity results from repeated immigration waves at <10.0>

Santos, J., Coloma, L., Summers, K., Caldwell, J., Ree, R., & Cannatella, D. (2009). Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages PLoS Biology, 7 (3) DOI: 10.1371/journal.pbio.1000056

Saturday, March 21, 2009

The Adventures of Darwin, Alfred Wallace & Henry Bates

Lecture filmed 3/19/2009 at Florida State University as part of the Origins 2009 Celebration.

UPDATE: Click on "Webcast" under Sean's picture (here) to view.

Sean Carroll retraces the epic adventures of three scientists - Darwin, Alfred Wallace & Henry Bates – as they develop their ideas on evolution during the golden age of the theory’s development. Carroll then proposes that we are currently in a second golden age of learning.

To skip introductions, jump to about the 14:30 minute mark.

Wednesday, March 18, 2009

Octopus Fossils from the Cretaceous

Cool fossil find!

New finds of 95 million year old fossils reveal much earlier origins of modern octopuses. These are among the rarest and unlikeliest of fossils. The chances of an octopus corpse surviving long enough to be fossilized are so small that prior to this discovery only a single fossil species was known, and from fewer specimens than octopuses have legs.

Everyone knows what an octopus is. Even if you have never encountered one in the flesh, the eight arms, suckers, and sack-like body are almost as familiar a body-plan as the four legs, tail and head of cats and dogs. Unlike our vertebrate cousins, however, octopuses don't have a well-developed skeleton, and while this famously allows them to squeeze into spaces that a more robust animal could not, it does create problems for scientists interested in evolutionary history. When did octopuses acquire their characteristic body-plan, for example? Nobody really knows, because fossil octopuses are rarer than, well, pretty much any very rare thing you care to mention.

The body of an octopus is composed almost entirely of muscle and skin, and when an octopus dies, it quickly decays and liquefies into a slimy blob. After just a few days there will be nothing left at all. And that assumes that the fresh carcass is not consumed almost immediately by hungry scavengers. The result is that preservation of an octopus as a fossil is about as unlikely as finding a fossil sneeze, and none of the 200-300 species of octopus known today has ever been found in fossilized form. Until now, that is.

Palaeontologists have just identified three new species of fossil octopus discovered in Cretaceous rocks in Lebanon. The five specimens, described in the latest issue of the journal Palaeontology, are 95 million years old but, astonishingly, preserve the octopuses' eight arms with traces of muscles and those characteristic rows of suckers. Even traces of the ink and internal gills are present in some specimens.

'These are sensational fossils, extraordinarily well preserved' says Dirk Fuchs of the Freie University Berlin, lead author of the report. But what surprised the scientists most was how similar the specimens are to modern octopus: 'these things are 95 million years old, yet one of the fossils is almost indistinguishable from living species." This provides important evolutionary information. "The more primitive relatives of octopuses had fleshy fins along their bodies. The new fossils are so well preserved that they show, like living octopus, that they didn't have these structures.' This pushes back the origins of modern octopus by tens of millions of years, and while this is scientifically significant, perhaps the most remarkable thing about these fossils is that they exist at all.



Fuchs et al. New Octopods (Cephalopoda: Coleoidea) from the Late Cretaceous (Upper Cenomanian) of Hakel and Hadjoula, Lebanon. Palaeontology, 2009; 52 (1): 65 DOI: 10.1111/j.1475-4983.2008.00828.x

Monday, March 16, 2009

Wetland Plant of the Week #9

Senecio glabellus

[Yellow flower heads to left of Cypress knees]


Obligate member of the Asteraceae. Tall, glabrous annual with single hollow stem. Leaves are alternate and lobed. Flowers are golden yellow.

Photo taken two weeks ago in Brevard County, Florida.

Closeup of Leaves

Symbiosis and Evolution in Aphids

Below is a hodgepodge of info discussing the symbiotic relationship between pea aphids (Acyrthosiphon pisum) and the bacteria Buchnera aphidicola as it relates to adaptation and evolution. By and large, the discussion centers on recent research by Naruo Nikoh and Atsushi Nakabachi; however several other sources are listed at the bottom of this post – including the Douglas Lab’s website which is a great place to follow-up on the latest aphid-symbiosis research.

Most aphids host mutualistic bacteria, Buchnera aphidicola, which live inside specialized cells called bacteriocytes. Buchnera are vital to the aphids well being as they provide essential amino acids that are scarce in its diet. Now research published in the open access journal BMC Biology suggests that the aphids' ability to host Buchnera depends on genes they acquired from yet another species of bacteria via lateral gene transfer (LGT).

symbiotic bacteria Buchnera are located in specialized cells
called bacteriocytes (shown green in figure) in the aphid body cavity. [Drawing by Tomás Lazo]

Atsushi Nakabachi from Japan's RIKEN institute with his colleagues had previously uncovered two clusters of mRNA sequences from the bacteriocyte of the pea aphid Acyrthosiphon pisum that were encoded in the aphid genome, but similar to bacterial genes. Naruo Nikoh from The Open University of Japan and Nakabachi determined these sequences in full for more detailed analysis, and used real-time quantitative RT-PCR experiments to investigate the genes' expression levels in the aphid bacteriocytes.

Phylogenetic Analysis (Figure 3 - From Article)

The evidence points to LGT from bacteria to aphids. Genetic family trees show that one of the genes came from a bacterium closely related to Wolbachia, a common inherited symbiotic microbe, which infects a high proportion of insects. The aphid strain used for the study is free from Wolbachia and other closely related bacteria, but the transferred gene could be a remnant of an infection in the distant past. The evidence suggests that the aphids use these acquired genes to host Buchnera, which has lost many genes that appear to be essential for bacterial life. The association between aphids and Buchnera is over 100 million years old, and has evolved so that today neither the bacteria nor the host can reproduce without the other.

According to Nakabachi,
"the cases presented here are of special interest in that these transferred bacterial genes not only retain their functionality, but are highly expressed in the bacteriocyte that is differentiated so as to harbour Buchnera, which lack such genes."
LGT (also referred to as horizontal gene transfer) occurs when genetic material from one organism finds its way into another organism other than its offspring. Genetic engineering uses LGT deliberately, but there is increasing evidence that LGT has taken place in many organisms (usually between unicellular organisms) naturally. This has caused a major shift in how biologists view genetic family trees.

Symbiotic relationships have a great deal to teach us regarding evolution.Such interdependent relationships are not unusual in the natural world. What is unusual, report Helen Dunbar, Nancy Moran, and colleagues in a new study published [last year] in the open access journal PLoS Biology, is that a single point mutation in Buchnera's genome can have consequences for its aphid partner that are sometimes detrimental, and sometimes beneficial.

The authors probe Buchnera's and A. pisum's ability to tolerate heat. When exposed to high temperatures, Buchnera is supposed to activate special "heat-shock" genes whose products help to protect proteins from heat-related degradation. By using microarrays to assess activity of A. pisum and Buchnera genes, the researchers discovered that after a four-hour exposure to 35 °C temperature, some of their laboratory strains of Buchnera upregulated the heat-shock genes, but others did not. Further analysis showed the genetic basis for the difference: a single missing nucleotide in an adenine-filled stretch of DNA, called a promoter, that's involved in activating the heat-shock gene. Testing at a range of temperatures from 15 °C to 35 °C showed that activation of the heat-shock gene was consistently lower in the lines with the missing nucleotide than in the normal bacteria.

What does this mean for A. pisum's ability to tolerate tough conditions? To answer that, the researchers asked whether exposing juvenile aphid hosts of Buchnera with either long or short promoters to four hours of high temperatures (35 or 38 °C) affected their ability to reproduce. They found that few of the aphids with bacteria bearing short promoters reproduced after the heat treatment, while those with bacteria bearing the longer promoters had no trouble. In addition, aphids that had been exposed to the high temperatures and had the short-promoter-bearing bacteria weighed less as adults and had far fewer Buchnera inside them than did their counterparts with long-promoter-bearing bacteria.

Given these seemingly huge disadvantages to dropping a single adenine, it's hard to believe the mutation could last long in a Buchnera population. Yet, by sequencing and comparing the Buchnera associated with various A. pisum lines, the researchers discovered that the short-promoter option had arisen and been fixed twice in laboratory stock and was also found at frequencies of 21% and 13%, respectively, in bacteria in field-collected aphids from Wisconsin and New York.

Population genetic theory predicts that when a mutation is maintained in a population at high frequencies, it likely confers some benefit to its bearer. What could be the advantage of carrying a gene that causes one to lose the ability to reproduce at high temperatures?

A clue to the answer comes from the wild populations in which the mutation was not found: those living in Arizona and Utah. Could the bacterial mutation confer a competitive advantage that's only relevant in cooler climates? To find that out, the researchers performed a second test using a range of four-hour exposure temperatures. They discovered that short-promoter bacteria-bearing aphids produced progeny faster than did the normal ones when raised at 15 °C or 20 °C. Thus, though aphids containing bacterial symbionts with the heat-shock-promoter mutation fare worse than normal aphids after exposure to high temperatures, they do better under cool conditions, giving the mutation a selective advantage that causes it to be maintained in the population.

In addition to their explorations of A. pisum and its Buchnera, Moran's team also looked for and found multiple-adenine stretches related to heat-shock genes in Buchnera symbiotic with other aphid species. This offers fertile ground for further study of the intriguing interplay among aphids, bacteria, and temperature.

Sources: Eureka Alert, PhysOrg and Douglas Lab

Nikoh, N., & Nakabachi, A. (2009). Aphids acquired symbiotic genes via lateral gene transfer BMC Biology, 7 (1) DOI: 10.1186/1741-7007-7-12

Dunbar, H., Wilson, A., Ferguson, N., & Moran, N. (2007). Aphid Thermal Tolerance Is Governed by a Point Mutation in Bacterial Symbionts PLoS Biology, 5 (5) DOI: 10.1371/journal.pbio.0050096

Saturday, March 14, 2009

Trilobites, Paleoecology and Anomalocaris

The “Explosion,” as the Cambrian Diversification is commonly referred, occurred approximately a half-billion years ago and is represented by the rapid appearance of about fifty phyla of animals. Present day scientists through the study of numerous fossils, as well as, genetic research have identified this uprising from the Kingdom Animalia and have come to the astonishing conclusion that the entire event lasted, at the very most, a mere ten million years. Most would agree that this seems an extremely minute quantity of time to permit such an all-encompassing radiation, which is one reason why this event is not only a topic of current research, but also one of heated debate.

A linear representation of animal evolution would certainly have a spike near the geologic time of the Cambrian Explosion. All present day phyla (i.e. body-plans, or animal “designs”) arose during that time (with the exception of Bryozoa) including that of the most abundant animal, and second most abundant organism (following only bacteria) on earth today, the arthropods.

One of the groups to rise from the Cambrian is the Phylum Arthropoda. Today the most common arthropods are the insects, but in pre-history, deep in geologic time, the title of most abundant arthropod may quite possibly have gone to the class Trilobita.

Trilobites are without a doubt one of the most easily recognized fossils in modern times, their abundance and variety have played a key role in paleontology as they act as wonderful index fossils. Variation in trilobites covers a wide range of morphological deviation, but most hold a few key characteristics in common. These common morphological characteristics include the division of the trilobite exoskeleton into three distinct regions, those being the head, (cephalon), the main body (thorax) and the tail (pygidium). These regions, especially the cephalon, have distinct sub-features that aid in the identification of individual trilobites, some of which are diagramed below in Figure 1.


Trilobites were structurally similar to many modern day arthropods; they possessed jointed appendages and hard exoskeletons, which fortunately - in conjunction with the process of molting - provided us with numerous high quality fossils today. The trilobites ranged in size from mere millimeters to over two-feet in length. They occupied primarily calm, deep waters were there was an abundance of fine silts which they plowed through with their flattened cephalons in order to search out rich debris to be used as a food source. Some trilobites however were most certainly predators, and many may have occupied other niches as well. They appeared (or they apparently appeared - some evidence suggests that they may have earlier origins) early in the Cambrian, reached their zenith in the late Cambrian and then began diversifying up till the Permian during which time they became extinct. There have been estimates of greater than 20,000 species of these incredibly successful Paleozoic marine arthropods - making classification rather tedious at times with new finds occurring on a regular basis. Luckily, some fossils retain sufficient detail as to render their classification relatively certain; however fossils don’t always readily describe the ways in which organisms interacted within their ecosystems.

This is one reason why Jennifer Dunne, et al, conducted research focused towards delineating the food-webs and niche interactions of species identified from the Chengjiang and Burgess Shales. From the Author’s Summary of Compilation and Network Analyses of Cambrian Food Webs,

“Our analyses show that for most aspects of network structure, the Early Cambrian Chengjiang Shale and Middle Cambrian Burgess Shale food webs are very similar to modern webs. This suggests that there are strong and enduring constraints on the organization of feeding interactions in ecosystems. However, a few differences, particularly in the Chengjiang Shale web, suggest that some aspects of network structure were still in flux during early phases of de novo ecosystem construction.”

In another paleoecology related story, Mariel Schotenfeld from the University of Massachusetts Amherst has challenged the widely held idea that Anomalocaris preyed on trilobites.


From upcomming G.S.A. agenda: “The Cambrian animal Anomalocaris is hypothesized to have eaten trilobites and other biomineralized prey. The lack of broken or abraded teeth on the plates comprising examination of the mouth apparatus of Anomalocaris suggests that it may not have had the ability to break the exoskeletons of any hard-shelled animal. SEM – EDS of the mouth apparatus from Burgess Shale specimens, indicate that the 32 plates are composed of organic carbon, suggesting they were originally unmineralized cuticle.

Mechanical properties of these plates were analyzed using CAD modeling and Finite Element Analysis. Poisson's ratio and Young's modulus of potential Anomalocaris plates, as well as density and fracture strength used for the FEA analyses, were estimated using a range of modern-day arthropods. Two end-member values were used both to approximate the range of strengths exhibited by Anomalocaris' cuticle, and also to encompass the range of exoskeleton strength likely exhibited by trilobites. The hardest skeletal values are from wet lobster (Homarus americanus) crusher claw cuticle; these are most likely to deform in a brittle manner. The softest are from adult dung beetle (Copris ochus) cuticles. In order to bite and successfully break the calcified cuticle of a trilobite, Anomalocaris' mouth plates would have needed to withstand forces that are greater than those required to fracture a trilobite exoskeleton. Results demonstrate that the teeth-like structures of the mouth plates should have deformed or broken when less than 90 N of force was applied perpendicular to the plates.

Additionally, documented trilobite malformations were compared to modern and extinct arthropod malformations. Abnormal trilobites previously attributed to predation of Anomalocaris might also be interpreted as molting failures or genetic mutations; such malformations occur with similar frequency in modern marine clawed lobsters, brachyuran decapods, and limulids. Furthermore, there is no direct evidence for Anomalocaris' feeding habits such as gut contents.”

Dunne, J., Williams, R., Martinez, N., Wood, R., & Erwin, D. (2008). Compilation and Network Analyses of Cambrian Food Webs PLoS Biology, 6 (4) DOI: 10.1371/journal.pbio.0060102

Friday, March 13, 2009

19 Leopold Leadership Fellows Named by Woods Institute

Woods Institute Names 19 Leopard Fellows;


Kevin Arrigo, Department of Environmental Earth System Science, Stanford. Role of polar marine microalgae in global biogeochemical cycling.

Brendan Bohannan, Department of Biology, University of Oregon. Microbial biodiversity; response of microbial communities to environmental change.

David Breshears, School of Natural Resources, University of Arizona. Dieback of woodlands in response to severe drought.

Anne Chin, Department of Geography, University of Oregon. Dynamics of dryland rivers affected by urban development; dynamics of headwater mountain streams.

Simon Donner, Department of Geography, University of British Columbia. Effects of climate change and land use change on ecosystems.

Victoria Fabry, Department of Biological Sciences, California State University-San Marcos. Impact of ocean acidification on marine ecosystems.

Margot Gerritsen, Department of Energy Resources Engineering, Stanford. Optimization of environmentally friendly oil production processes, carbon sequestration and tidal energy systems.

Gretchen Hofmann, Department of Ecology, Evolution and Marine Biology, University of California-Santa Barbara. Impacts of ocean acidification on marine populations.

Madhu Khanna, Department of Agricultural and Consumer Economics, University of Illinois at Urbana-Champaign. Economic mechanisms for encouraging voluntary corporate environmental initiatives; environmental and economic implications of biofuel mandates, subsidies and tariffs.

David Lea, Department of Earth Science, UC-Santa Barbara. Implications of paleoclimate data for understanding and predicting climate change.

Laura Meyerson, Department of Natural Resources Science, University of Rhode Island. Identification of native plant populations at risk of extinction from invasive plant species.

Paige Novak, Department of Civil Engineering, University of Minnesota. Contamination of water and wastewater by estrogen compounds.

Dov Sax, Department of Ecology and Evolutionary Biology and Center for Environmental Studies, Brown University. Species extinction; evaluation of "assisted migration" as policy.

Karen Seto, School of Forestry and Environmental Studies, Yale University. Impacts of urban growth.

Whendee Silver, Department of Environmental Science, Policy and Management, UC-Berkeley. Land use management effects on climate change; impact of tropical reforestation.

U. Rashid Sumaila, Fisheries Centre, University of British Columbia. Economics of fishing and impacts on marine conservation policies.

Jeanne VanBriesen, Department of Civil and Environmental Engineering, Carnegie Mellon University. Drinking-water safety.

Jianguo "Jingle" Wu, School of Life Sciences and School of Sustainability, Arizona State University. Urbanization and its ecological effects in Arizona; biodiversity and ecosystem function in Mongolia.

Luis Zambrano González, Department of Zoology, Instituto de Biología, Universidad Nacional Autónoma de México. Dynamics of freshwater fish populations.

Rap Music and Evo Devo

Monday, March 9, 2009

Stem Cells the Vatican and Monty Python

Pope Benedict: ''all Catholics, especially legislators, jurists and those responsible for the common good of society' to promote human life from conception to death”

Philadelphia Archbishop Cardinal Justin Rigali: ''This action is morally wrong because it encourages the destruction of innocent human life, treating vulnerable human beings as mere products to be harvested''

United States' Bishops' Conference: ''a sad victory of politics over science and ethics''

Osservatore Romano: “immoral and superfluous''

So in lay terms…

Wetland Plant of the Week #8

Limnobium spongia

"American Frog's-Bit"

American frog’s-bit is a Florida native, obligate monocot and member of the Hydrocharitaceae that can be found as either rooted or free floating.

Christopher Taylor from Catalogue of Organisms has does a magnificent job at detailing some characteristic taxonomy of the Hydrocharitaceae in a recent blog post – I very much encourage you to take a look!

To my astonishment, I didn’t have any pictures of Limnobium in my personal collection; this photo was pirated from the University of Florida’s Center for Aquatic and Invasive Plants website here.

Sunday, March 8, 2009

Sexual Competition and Lemurs

Ivan Norscia, Daniela Antonacci and Elisabetta Palagi recently published an article in which inter- and intrasexual competition between wild prosimians is examined from the perspective of economic power distributions and as a metaphor for financial markets.

[Lemur, Propithecus verreauxi]

Essentially, their findings indicate that competition for females by males typically manifests as an “olfactory tournament” in which males try to “out bid” rivals by more proactively scent marking. This strategy accurately reflects dominance between males and is less costly than engaging in combative or otherwise aggressive behaviors.

Intersexual competition (male-female selection) in the lemur is accomplished via a strategy of “commodity exchange” in which males offering the best resources (food) or services (grooming) are preferred and ultimately gain advantage through more frequent copulations.

The article (available here) is clearly written and is jargon free; it could have just as easily appeared in a Pop-Sci magazine as a journal. For this reason, as well as to compliment my prior posts discussing sexual selection, I’ve pasted the Introduction and Videos below.

NOTE- I removed references for ease of reading; please refer to the original article linked above for corroboration.

"In biology, as well as in economics and politics, power is a key concept for understanding asymmetrical dyadic relationships. Distributive power can originate from both dominance (when force is used) and leverage (when the use of force is not possible). An individual has leverage over another when that individual possesses something that the other needs but cannot acquire through coercion. In this case, trading becomes essential for mutually beneficial interactions within social groups, both in economical and biological markets. An important feature of market models is that the expected future gains are actively influenced by playing off potential partners against each other. The typical game theory approach includes only two players and, although this is changing within economics as well as biology, the classical models do not take into account partner choice. In contrast, the biological market theory includes multi-player models, that is theoretical games with at least three or more “players” (traders, in the market systems). Two or more classes of traders (sex classes, rank classes, etc.) exchange commodities in biological markets to their mutual benefit. Different group members can offer different kinds of commodities in exchange for alternative ones that they do not currently possess. Usually, competition acts as the driving force within the same trader class (including all members offering the same kind of commodity) while cooperation can occur between different trader classes.


Male countermarking behaviour on a female scent deposition

In the mating market, the balance of power tilts in favour of females whenever males cannot force females into mating (as it happens in sexually monomorphic species or when females form coalitions). Consequently, males depend on females for breeding opportunities and must compete to prove their superiority to females, thus increasing their possibility to be selected. Males can engage in both contest competition via physical/ritualized fighting and outbidding competition, in which a male plays off rivals by making a better offer. In the latter case, males can secure the favours of a female by advertising their quality (e.g. the dominance status) through visual or olfactory displays and/or by being more generous than others in providing a commodity in exchange for female access (competitive altruism). One of the most valuable commodity that can be offered in social mammal groups is grooming, which is used for parasite removal, stress reduction, and as social cement to start, consolidate, or repair relationships. Grooming is a commodity that can be exchanged for itself or for breeding opportunities.


Copulation followed by a grooming session

Sociality is widespread among mammals and particularly among anthropoid primates (monkeys and apes). In prosimians (the most ancestral group of primates) sociality is the exception more than the rule. Among Malagasy prosimians (lemurs), few species combine a powerful olfactory system (retained from basal mammals) and puzzling features like group living, female priority over resources, and absence of sexual dimorphism. Such combination of features makes gregarious lemurs the ideal model to understand the biological bases of mate selection by females, who cannot be accessed by force or using food as exchange commodity. In particular, we selected the diurnal species Propithecus verreauxi of south/southwest Madagascar to find out which male strategies are successful to maximize breeding opportunities."


Copulation in which intromission and thrusting were unambiguously observed

Ivan Norscia, Daniela Antonacci, Elisabetta Palagi (2009). Mating First, Mating More: Biological Market Fluctuation in a Wild Prosimian PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004679

Saturday, March 7, 2009

Academic Freedom Act Cartoon in Florida Newspaper

The Gainesville Sun posted an editorial and political cartoon criticizing the Education Academic Freedom Act bill filed in Florida.

Also blogged at Florida Citizens for Science.

Way to go Mary Bahr!

From Letter:

Imagine our society without computer networks, electronics, chemistry and modern medicine. Both our lives and economy would be greatly diminished. Biotechnology has created nearly 600 new businesses in medicine, the environment and agriculture in Florida with jobs that pay almost twice the State average. State economic adviser Enterprise Florida has labeled biotechnology a High Impact Industry and recommends legislators make sure we “provide students with the needed skills to work in biotechnology companies and market Florida as a hub for life science research and business development.”

Unfortunately At least one legislator has ignored Enterprise Florida’s advice. State Sen. Stephen Wise, of Clay County, is attacking science in Florida with his Critical Analysis bill SB 2396. Similar bills have been used to introduce Intelligent Design Creationism into science classrooms. Senator Wise recently reported in the Florida Times Union he wishes to do exactly that.

Leaders ranging from a Republican federal judge to the Pope have declared Intelligent Design a religious belief, not a scientific theory, making its introduction into a science classroom unconstitutional. In addition to irresponsibly putting our struggling school districts at risk of millions of dollars in law suits, Senator Wise is attacking the scientific basis of Florida’s Biotechnology economic expansion.

Biotechnology, which promises a more sustainable future, strategies to counteract climate change, medical benefits to prolong and enrich lives and high paying jobs, rests on the framework for modern biology known as the Scientific Theory of Evolution. Our new State Science Standards call for thorough examination of all aspects of science, but critical analysis does not include falsely claiming a religious belief as a scientific theory. Confusing Florida students about the nature of science will not lead to informed citizen scientists required for a prosperous future for Florida. Oppose Critical Analysis Bill SB 2396

Mary Bahr,


Friday, March 6, 2009

Isotopes Used in Tracking Migration and Dispersal of Birds

During last week’s post discussing vertebrates as indicators of climate fluctuation (linked here) isotopes were described as a significant tool in reconstructing the evolutionary and ecological histories of organisms. Today, Megan J. Sellick, et al, published an article in PLoS One discussing the value of using hydrogen and strontium isotopes, taken from the feathers of tree swallows, to track migratory dispersion.

Tree Swallow (Tachycineta bicolor)

The research (linked here) revealed that stable hydrogen isotopes were indicative of the latitude of molting sites and strontium was linked to the longitude of geological features found in proximity to the area where feathers were grown. Taken together, modeling revealed that, “these isotopes have the potential to provide predictable and complementary markers for estimating long-distance animal movements.”

GRAPHIC: Geographic variation of (a) dD and (b) 87Sr/86Sr values in Tree Swallow feathers. Contour maps were produced by ordinary kriging and are based on mean values in primary flight feathers at 18 breeding sites (denoted by black circles).

Megan J. Sellick, T. Kurt Kyser, Michael B. Wunder, Don Chipley, D. Ryan Norris (2009). Geographic Variation of Strontium and Hydrogen Isotopes in Avian Tissue: Implications for Tracking Migration and Dispersal PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004735

Wetland Plant of the Week #7

Iris hexagona

"Prairie Iris"

Obligate, perennial monocot common to swamps and marshes in southeast U.S.

Photographed yesterday near Melbourne, Florida.

Thursday, March 5, 2009

Cross Dressing Lizards

Young male lizards in South Africa imitate females to fool aggressive older males into leaving them alone, in an example of transvestism in the natural world, researchers have found.

The lizards not only avoid fights but gain access to females under the nose of their more macho rivals, the South African and Australian researchers discovered.

They found that young male Augrabies flat lizards delayed displaying the extravagant coloration of sexually-mature males until they were able to defend themselves adequately.

"Experienced males will chase and bite their young rivals," said associate professor Martin Whiting of Johannesburg's University of the Witwatersrand.

"By delaying the onset of colour to a more convenient period, these males, termed she-males, are making the best of a bad situation."

Australian National University associate professor Scott Keogh said opting to become transvestites for a period offered young males a dual advantage.

"They can avoid potentially dangerous bouts with dominant males and still have access to normally inaccessible females," he said.

But, as with large hands and an Adam's apple in the human world, there is a flaw in the lizards' transvestite transformation.

Dominant males can detect transvestite's male hormones with their sensitive tongues, even if they are taken in by their female appearance.

University of Sydney researcher Jonathan Webb said this meant the she-males needed to be nimble to avoid advances from dominant males smitten by their fake female allure.
"Males are fooled by looks, but not by scent," he said.

"She-males are able to maintain this deception by staying one step ahead of a prying male, and thereby avoiding a nosey tongue that might give the game away."

The research was published in the journal Proceedings of the Royal Society.

Source: here

Tuesday, March 3, 2009

Federal Government and Science - Harold Varmus

Harold Varmus on John Stewart - Federal Money for Research, Science under Bush...

Sunday, March 1, 2009

Vertebrate Proxies of Climate Change

Haphazardly racing around the net while pumped-up on Peet’s Sumatra coffee (so good!), I noticed that Jessica Blois and Elizabeth Hadley have an article being published in the Annual Review of Earth and Planetary Sciences this upcoming May. This is great news for me, because I have an interest in Cenozoic climate change and these folks are experts in the subject area; however, unfortunately for any readers of this blog lacking sufficient caffeine-ation, this post may seem a bit rambling… Consider it a refresher on vertebrate proxies of climate change.

"Organisms change through time. " - At first read this simple four-word sentence may seem rather barren of substance but within its basic grammar there exists a world of profound scientific insight and understanding. Evolution lies at the center of our biological universe, its principles are essential to science, and by grasping these principles we are able to efficiently navigate the worlds of ecology, paleontology and other life-linked sciences. Paleontologists and paleobiologists often utilize the ideas and tenants of organismal change as tools to decipher the remnants and records of past life in aspirations of better understanding not only biology and life, but also as a means of interpreting the physical history of our beloved planet Earth - the fundamental constants of chemistry and climate.

Numerous factors or mechanisms may signal biological change; natural selection, genetic drift and other gene flow can all introduce variation into a population, but these are merely the effects, or end products of change, what physically lies at the source of the process - what environmental factor triggered or was driving the selection, drift and flow?
What if, for example, some physical barrier was removed from a geographic region, thereby permitting the migration of a herd into previously unchartered lands, or the founding of a new population? Would the organisms – and their fossil remnants - be disrupted in such a way as to leave clues behind explaining the reason for increased rate of change or distribution? Less temporally dramatic, what if the seasonality of a region changed in such a way as to lengthen the mating season, or change the territoriality of a species? Would these events, be recorded in the fossil record? Undoubtedly yes!

Responsiveness of Vertebrates to Environment
Many studies of vertebrates have suggested that climate is the single best indicator of modern species richness. Over the past decade several different theories have been suggested in hopes of establishing a clear and precise relationship between organismal change and the environment. Some of these hypotheses are relatively familiar, such as Van Valen’s “Red Queen model,” and Vrba’s “Turnover-pulse model,” but others less so… Regardless, the majority of these models work to resolve one key question; how synchronous are climate and biotic change?

Vertebrates, and in particular mammals, are highly responsive to changes in the environment. Climate fluctuation can lead to an incredible amount of variation in the diet choice, distribution and even morphology of vertebrates. Even within Humans, biological anthropologists have identified trends associated with body size and appendage length based on climate; they refer to this correlation as Bermand and Allan’s Rule. It suggests that human populations occupying regions closer to the equator statistically contain individuals with larger body size and longer limbs relative to those who inhabit more pole-ward regions. This variation has arisen primarily to promote more efficient thermoregulation as to reduce body heat loss in cooler regions, and to promote cooling in warmer climates. Some vertebrates posses even finer genetic plasticity changing morphologically with what could be termed “hair triggers.”

One of the most highly variable vertebrates is the Pocket gopher (Thomomys spp). These gophers have been intensively studied as indicators of environmental change. Their populations, and individual morphology, have been shown to vary with in a period of less than ten years. The most easily recognized change in morphology is their body size - which fluctuates with everything from altitude to diet. Body size, in turn, has a noticeable effect on territory, fertility of females and distribution of the population (Hadly, 1996). These physiological changes, and the fossils they have left behind, have been intensely studied in relation to Late-Holocene Climatic changes.
Thomomys spp

One site in particular, Lamar Cave, located with in the boundaries of Yellowstone National Park, has been used by Elizabeth Hadley to make correlations to such historic climate changes as the Medieval Warm Period (MWP). Through comparison of fossil dental plates with those of modern descendants, Hadley has been able to demonstrate that during the MWP pocket gophers of this region had the smallest body size than at any other point in the paleontological record. Using similar comparisons she was also able to identify trends in morphology that correlated with the Little Ice Age (LIA) and other events including neoglaciation (Hadly, 1996). The response of vertebrates is not limited to the highly plastic morphology of pocket gophers. Many other vertebrates respond equally as readily to climate change. However, morphological change is not necessarily required of a species in order for it to serve as a climate proxy. During their lifespan, all organisms make detailed records of their environment. Through the fundamental life processes of cellular growth and repair vertebrates have the potential to generate detailed records of their environment. Just as the old cliché exemplifies, “you are what you eat.” This record can later be resurrected and deciphered from their fossil remains to help clarify the picture of the climate and chemistry they endured while alive.

Examinations of isotopic records are commonplace for many paleontologists. Uncountable volumes have been written on Foram 18-O isotopes and their relationship to periods of increased glaciation, or similar correlations of speleothems and 13-C, but accurate isotopic records of both of these elements can be obtained from other sources as well - including vertebrates.

Carbonate apatite is a primary constituent of both skeletal bones and dentition in the vertebrates. It is incorporated into the organism through diet and water uptake. The process is riddled with various “vital effects” but has nonetheless been found to be very accurate. In fact, many conservationist use this isotopic signature in vertebrates to better decipher the life histories of contemporary vertebrates in hopes of aiding in their preservation. For example, remains from the world’s largest cavefish (Milyeringa veritas) have been used by Australian conservationists to better examine and comprehend the environment and ecosystem which the fish inhabits. The cavefish lives in deep columns of water that are rich in dissolved limestone. The depths of the water column posses various corresponding incremental concentrations of dissolved materials and by examining the isotopic signatures of the fish’s skeletal apatite, conservationists were able to discover the exact depth the fish occupies.

Milyeringa veritas

Uptake of elements within vertebrates (O, C, Sr & others) generates a highly detailed record of environmentally available isotopes, and as one might guess, availability is indicative of climate.

As another example, Thure Cerling and others at the University of Utah have refined the technique of laser ablation to such quality and precision that they can use it to vaporize the apatite found in vertebrate teeth, and then analyze the gas to determine its isotopic components. They can examine the teeth to such resolution as to be able to report the dietary preferences of mammals between C3 and C4 plants. Previously, samples of fossil teeth or skeletal structures were far to rare to permit them to be thrown into a TIMS for examination, but now that laser ablation has reached such a high level of efficiency isotopic analysis can be made in the smallest and rarest of specimens with minimum impact on the fossil itself. Laser ablation can be used to examine the minute layer of enamel on the smallest of rodents and the most voluble of fossils on display at museums with little difficulty.

As a side note - many scientists have recently discovered that skeletal tissues, which possess apatite, are very susceptible to diagenic processes that can cause recrystalization and alter results, but dental samples seem to be far more reliable when it comes to maintaining their original isotopic signatures. This coupled with the knowledge acquired in the past few decades in regards to the incorporation of specific 18-O and 13-C isotopes into biological entities has brought to light a highly detailed and accurate record of climate change.

Similar techniques have been used to examine bone fragments from marine vertebrates. Some alteration of samples occurs during fossil formation in paleo-seawater environments which forces users of this technique to integrate other proxies of isotopic variation in their final estimates as a “check,” but as the technique begins to advance some of this error is likely to be eliminated. Others have also verified the validity of the use of dental enamel as an isotopic record. Schmitz and his colleagues examined fossil shark teeth from two different locations in Mississippi (one strata being mixed marine, the other brackish-water). Both samples demonstrated nearly identical isotopic signatures, even though they had been deposited in different strata, one with a high salinity concentration - previously shown to accelerate diagenesis. They also examined skeletal remains from marine vertebrates, but there seemed to be a significant error associated with those found in the marine strata.

Isotopic signatures can be very useful in the interpretation of paleoclimate, but in certain cases the mere presence of an organism at a given location - biogeography - can report volumes of information in regards to past climate.

The vertebrate fossil record can be extrapolated in terms of the diversity, divergence and variation of distinct animal groups over a geographic region to display, with accuracy, the impact of environmental change. Similarly, known vertebrate biogeographic patterns can be used to demonstrate specific climatic fluctuation both locally and on the global scale.

The Cenozoic has been marked by tremendous variation of climate. During the early portions of the Cenozoic high temperatures were the standard with the highest to be found in the Early to Middle Eocene, since then a falling temperature trend has been the rule. It was during the Eocene-Oligocene transition that Antarctica became isolated and sea levels dropped dramatically with the accumulation of ice caps, this had the effect of changing terrestrial habitats significantly. Throughout the Cenozoic, similar patterns of fluctuating glacioeustatic sea level events would continue to occur. Evidence of this can be found across the globe.

Thailand, in South-East Asia, is one of many regions that accurately record these glacioeustatic events through its vertebrate fossil record. Thailand is especially significant in that it separates two distinct biogeographical regions (Fig 1). The Indochinese region is located to the north of Thailand and the Sundaic region is located to the south. These two regions have significantly different climates and zoological compositions. Up until about 800kyr B.P. fluctuation of sea level was somewhat constant in the region of Thailand, with the average being somewhere around 70m below the modern, and the greatest change being no more than 100m below the modern. However, near the 800kyr B.P. mark level dropped more dramatically, some fluctuations going as low as 170m below modern sea levels. This had the effect of constructing a land bridge between the Indochinese and Sundaic biogeographical regions, thus permitting the migration of a large variety of animals, including mammals. Through careful comparison of the fossils these migrating animals left behind, and the extant species found in both the Indochinese and Sundaic regions, certain conclusions can be established in regards to their phylogenies. The presence of fossil mammals with Indochinese affinity in the Sundaic regions, and the presence of Sundaic mammals in Indochina suggest some mode of migration in the past that is prevented in modern times by the sea acting as a barrier. Through radio dating of remains, an estimated time for the existence of the land bridge can be calculated, thus the fossil mammals provide dates for periods of reduced sea levels, and in turn, periods of increased glaciation.

FIGURE 1--- Land bridge linking distinct biogeographical regions in Thailand
Thailand is not unique in its ability to provide vertebrate proxies of climate change. Similar scenarios have been played out across the globe. Grenada offers another example of vertebrate biogeography acting as an indicator of sea level change due to increased glaciation.

Grenada has a rather sparse population of indigenous mammals at present, and bats represent the majority of these species. However, paleontologists have recently uncovered a variety of fossil mammals near the Grenadine coast dating from the Pliocene. These species, such as representative capybaras and sloth, did not arise independently on Grenada and then become extinct. Their lineages suggest that they arrived on Grenada from the South American mainland, where their descendants can still be found today. Grenada is located on the Southern Antilles Arc Platform, an elongate sub ocean structure that extends some 180km. This arc provides a base for several small islands and at its closest point comes to with in 40km of South America. During the Pliocene, a combination of low sea levels and tectonic activity provided a land bridge that may have conjoined Grenada with South America thus allowing for the migration of mammals. Through accurate dating of these fossil remains and of the associated tectonic activity estimates for late Pliocene glaciations can be made.

Through biogeographic research, other evidence can be in found with the target of determining periods of climatic change that are independent of sea level, and glacioeustaic events. Many other factors can have the effect of generating temporary corridors that permit faunal exchange. A “corridor” is simply a narrow tract, or pathway, which allows for the exchange of animals from one side to another. These corridors can be created by various means, including the growth of a forest.

The western Canadian ice-free corridor is a continuous tract of land that extends from Alberta, Northward to the Arctic Ocean (fig 2). This corridor separates Eastern and Central Canada from the Western Coastal portions of the Country. At one point in the past this corridor was closed to faunal exchange do to the advancing Laurentide ice sheet; however, near the close of the Pleistocene the ice retreated significantly enough to open the corridor temporarily, before finally closing again. This second closing of the corridor was not due to advancing ice caps, but rather to the growth of Boreal forests.

FIGURE 2---- Ice-free corridor, shaded region

These forests impeded the exchange of fauna between the Bering Strait (and in turn Asia) located in the North West, and Eastern Canada. This meant that any faunal exchange would need to occur between the Plains of the United States and the Bering Strait, which, as coincidence would have it, was a corridor itself. Evidence for this “faunal funneling” can be found through out the plains. The presence of fossil mammals such as wooly mammoths, camels, horses, buffalo, lemmings and even lions give support for the corridor closing during this period. These animals marked their migratory trails with their very own remains, which are now found as fossils - littering their previous routes. Through accurate dating it can be determined exactly when this western Canadian corridor was closed by the growth of forests, and reductively, when climate would support such lush growth.

Interpretation of paleoclimate is a highly important field of study. Not only is it required to better understand the physical and biological history of our planet, but also to endow us with the knowledge needed to prepare for tomorrows’ inevitable changes. The Cenozoic has been marked by extreme change of temperature and climate as a whole, many such changes visible on a short-term scale. This period in geological history has seen everything from periods of hot and dry, to glaciation. To better understand the past and future effects on humans we must discover how it impacted the existence of other animals, in particular, other mammals. To better understand their evolutionary responses to climate, careful analysis of their fossil record must be made. Their physiology, morphology, biochemistry and even behavioral responses record every detail of their natural histories and the climates that they endured. Organisms change through time; the trick to rendering these records lays in the accurate translation of their fossil remains. To accomplish this end, the vertebrate indicators of climate change are an essential and indispensable tool and I very much look forward to reading more about them in May.


Alberdi, M. et al. 2001. Vertebrate taphonomy in circum-lake environments: Three cases in the Guadix-Baza Basin (Granada, Spain). Paleogeogrphy, Paleoclimatology, Paleoecology. 165:1-26.

Badgley, C; Behrensmeyer, A. 1995. Preservational, Paleoecological and evolutionary patterns in the Paleogene of Wyoming-Montana and the Neogene of Pakistan. Paleogeography, Paleoclimatology, Paleoecology. 115: 319-340.

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