Saturday, April 18, 2009

The Fire Gene: One Organism’s Ability to Exploit Fire


Gazing across the tranquil landscape of the Big Cypress Preserve, nature seems to be in balance, unchanging and at peace - picturesque beyond any poetic description. Here, anthropogenic throngs of sharply angled concrete and glass edifices suspend their battle for roadside dominance and yield themselves to a sea of sparsely treed savanna, rolling prairies of grass, and randomly scattered islands of thickly vegetated hammocks; the perfect environment for a relaxing stroll, a picnic, or even a quick nap. All may appear calm within this enchanting panorama; however, the perceived tranquility is but a chimera. A mere illusion of serenity resulting from shortfalls in the ability of Homo sapiens’ photoreceptors to see beyond the narrow range of the electromagnetic spectrum called visible light, an inability to hear sound outside of 22000 Hertz, and the failure of the human olfactory system to nose its way into the vast chemo-landscape of pheromones and other volatile chemicals in which it is continuously assailed. If the sensory apparatus of Homo sapiens was keener - more finely calibrated – the landscape of the Big Cypress would appear very different.

Very different indeed, imagine the ecological interplay that could be interpreted if humans could see ultraviolet light through the eyes of a bee, smell pheromones from six-miles’ distance like a moth, or interpret chemical stimuli through soil like a plant… Far from serene, if viewed through time, adaptive maneuvers, survival strategies and arms races would be manifest in every action undertaken by the immense diversity of organisms on Earth. If these actions could be viewed more directly, the landscape would appear saturated with war. Even the plant community boundaries which demarcate prairie from savanna from hammock in the above described landscape are maintained by way of fierce battles waged over evolutionary time. These ecosystems, which appear stable and so pleasingly haphazardly scattered, are in fact tightly ordered armies of competing plants struggling for resources and existence. In these recurrent ecotonal conflicts one species has honed a new weapon – it has adapted to exploit the power of fire.

Naturally existing plant communities exist in a continuum of ecosystems which through evolution have adapted to almost every available habitat on the planet; from “box thorns” (Lycium pallidum) in Death Valley to fully aquatic hyacinths (Eichhornia paniculata) floating around the lakes of Brazil, genetic plasticity in plants is the product of natural selection. Although diverse habitats represent a surmountable challenge, a multitude of both biotic and abiotic factors determine the overall abundance (density), composition (diversity) and ultimate success of plant communities at any given location.

For example, looking across the landscape of the Big Cypress, densely concentrated hardwood trees form hammocks which, due to the broad area of their collective canopies, limit the amount of sunlight available to underlying herbaceous groundcover. This is a straight forward relationship - no sun reaching the ground means fewer plants on the ground. Following this rationale, if the tree canopy should be opened (by a storm, hurricane or by the death of older trees) and sunlight is able to temporarily penetrate to the floor, a rapid emergence of both herbaceous plants and new saplings would be predicted. This is precisely what happens; sunlight is the limiting resource, once made available, those plants best able to take advantage of the situation (through rapid growth) will be able to literally overshadow their competitors; plants with genetic compliments favoring a period of “initial rapid growth” are at an advantage and will be positively selected.

Extrapolating this scenario to the prairies of Big Cypress begs the question – why aren’t there any trees in the prairie?

Prairies, typically found on relatively low topographical gradients in Florida, have an abundance of soil nutrients and water; at least enough to support the enormous quantity of grasses and herbaceous plants currently found there. Additionally, from the perspective of a tree, grasses present little competition for sunlight. So, what is it that prevents trees from invading the prairie?

One often suggested possibility is that because prairies are occupied by dense populations of grasses - some of which more than six feet in height - young trees are prevented from taking hold; sort of like a reverse hammock scenario in which the grasses overshadow the young trees thereby starving them of sunlight instead of vice versa… This is plausible, but why wouldn’t trees take hold after wildfires? Wildfires have been historically inevitable in Florida and have the effect of clearing grasses long enough for those trees possessing an “initial rapid growth gene” in their arsenals to stake a claim.

Slash Pine (Pinus elliotti), for example, has just such an initial rapid growth gene. This permits the tree to take advantage of any opportunity to seize real estate, whether it is in a forest or a prairie. Slash Pine is even capable of expressing secondary needles in less than six month’s time – seedlings grow rapidly. Once present, this conifer could easily out-compete grasses for sunlight.

A quick word about wildfires: Florida’s climate cycle is punctuated by alternating dry and wet periods. November to February is the dry season, with relatively little precipitation, and is followed by heavy rains and thunderstorms (particularly near the coasts) during the months of June, July and August. The spring season, February through May, represents a transition from dry to wet, but during this period lightening strikes often cause wildfires due to the parched conditions of plants – parched, having just come out of the dry season. Regularity of climate has resulted in a cyclic “fire season” arriving during the early spring.

Speaking of wildfires… Being a regular occurrence, they are often offered as another explanation for limiting the advance of trees into prairies. Although this suggestion is partially correct, it isn’t the whole story - in some instances trees have even wielded fire as a weapon to destroy its grass competitors.


4-19-09 UPDATE: The Second Half of this Post can be Viewed HERE.

Beckage, B., Gross, L., & Platt, W. (2006). Modelling responses of pine savannas to climate change and large-scale disturbance Applied Vegetation Science, 9 (1) DOI: 10.1658/1402-2001(2006)9[75:MROPST]2.0.CO;2


Nordlund, D., & Lewis, W. (1976). Terminology of chemical releasing stimuli in intraspecific and interspecific interactions Journal of Chemical Ecology, 2 (2), 211-220 DOI: 10.1007/BF00987744

Morse, A., Peterson, D., Islam-Faridi, M., Smith, K., Magbanua, Z., Garcia, S., Kubisiak, T., Amerson, H., Carlson, J., Nelson, C., & Davis, J. (2009). Evolution of Genome Size and Complexity in Pinus PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004332

Platt, W. J., J. M. Huffman, M. G. Slocum, and B. Beckage. In press. Fire regimes and trees in Florida dry prairie landscapes. In: Noss, R. & Singh, S. (eds.) Land of fire and water: The Florida dry prairie ecosystem. Avon Park Air Force Range and Department of Defense, Avon Park, FL,

US.Kabrick, John M.; Dey, Daniel C.; Gwaze, David, eds. Shortleaf pine restoration and ecology in the Ozarks: proceedings of a symposium; 2006 November 7-9; Springfield, MO. Gen. Tech. Rep. NRS-P-15. Newtown Square, PA: U.S. Department of Agriculture, Forest Service, Northern Research Station: 28-32.

Friday, April 17, 2009

Night Vision and DNA

Science Friday at NPR -

Why do some animals have much better night vision than others? We'll talk about new research tracing the root of improved night vision to the architecture of the DNA inside the photoreceptor rod cells of the animals' eyes. Writing in the journal Cell, researchers say that an unusual way of packing the DNA within the rod cell nuclei turns the nuclei themselves into into tiny light-collecting lenses. The structure prevents light from excessive scattering within the eyes, improving their light collecting efficiency.

Guests:
Jochen Guck Lecturer, Physics DepartmentUniversity of Cambridge

Click here to hear the broadcast.

Beautiful Data

Demonstration of the “AlloSphere,” an entirely new way to see and interpret scientific data - in full color and surround sound inside a massive metal sphere.

A 3D immersive theater that maps complex data in time and space.

Dive into the brain, feel electron spin, hear the music of the elements...


Thursday, April 16, 2009

New Study Merges Genetics, Demography and Paleoanthropology

Mitochondrial DNA from twelve Neanderthal fossil assemblages was sequenced, compared and correlated with morphological data from fossil skulls, limbs and dentary remains to render evidence for multiple demes of Neanderthals from across Asia and Europe.

According to the authors, this “…approach to Neanderthal variability, based on nucleotide sequences analysis, confirms from a genetic point of view the morphological variations between western and eastern Neanderthals and the existence of a southern group…”

The mtDNA portion of the study therefore supports prior determinations based on morphological analysis that at least three separate Neanderthal sub-groups (and possibly a fourth group from western Asia) emerged from an ancestral population approximately 130,000 years ago. Furthermore, there is evidence that these populations existed in a dynamic state of migration.


Figure 2. Neanderthal Group Distribution


Abstract:
The Neanderthals are a well-distinguished Middle Pleistocene population which inhabited a vast geographical area extending from Europe to western Asia and the Middle East. Since the 1950s paleoanthropological studies have suggested variability in this group. Different sub-groups have been identified in Western Europe, in southern Europe and in the Middle East. On the other hand, since 1997, research has been published in paleogenetics, carried out on 15 mtDNA sequences from 12 Neanderthals. In this paper we used a new methodology derived from different bioinformatic models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparisons between simulated results (obtained by BayesianSSC software) and those estimated from nucleotide sequences (obtained by DNAsp4 software). The conclusions of this study are consistent with existing paleoanthropological research and show that Neanderthals can be divided into at least three groups: one in western Europe, a second in the Southern area and a third in western Asia. Moreover, it seems from our results that the size of the Neanderthal population was not constant and that some migration occurred among the demes.


In case you were wondering about genetic links to modern Homo sapiens, the study was limited to “…what occurred previous to the arrival of modern humans in the Neanderthal landscape and we therefore do not consider the potential phylogenetic relationship between Neanderthals and modern Humans.”

The article, in its entirety, is available at the below referenced link.

Fabre, V., Condemi, S., & Degioanni, A. (2009). Genetic Evidence of Geographical Groups among Neanderthals PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005151

Anti-Science and Ignorance Prevail – No on Stem Cell Research

State funding for embryonic stem cell research falls to the wayside at the State’s Capital today as Reps put politics and ignorance before science, ethics and public health during a debate at the Florida State University…

Rep. Eric Eisnaugle oppossed the research because his mommy said so…
“As much of a stake she has in this, she is absolutely against using public money to fund embryonic stem cell research,” said Eisnaugle.


And Miami Representative Anitere Flores decided to make a “definitive statement” in hopes of promoting misinformation and avoiding ethical challenges. Read her letter to Science and Ethics Chair Claire Thuning-Roberson - here.


Their arguments are as baseless and ignorant as the positions themselves.

Absolutely shameful, welcome to the south ya’ll !

Wetland Plant of the Week #13

Pistia stratiotes

"Water lettuce"

In Florida, this Obligate species is a non-native invasive.

Glazier (1996) describes P. stratiotes as a free-floating perennial of quiet ponds. It is stoloniferous, forms colonies, and has rosettes up to 15cms across. It has long, feathery, hanging roots. Its leaves are obovate to spathulate-oblong, truncate to emarginate at the apex, and long-cuneate at the base. Leaves are light green and velvety-hairy with many prominent longitudinal veins. Inflorescences are inconspicuous and up to 1.5cms long. Flowers are few, unisexual, and enclosed in a leaflike spathe.


Juvenile gator Concealed in the P. stratiotes

Emergence of a Predator

While checking out a floodplain along the Ochlocknee River yesterday, I ran into an emerging predator – a dragonfly.

Fresh from the naiad, this Darner (Family Aeschnidae) represents one of the largest and fastest dragonflies found anywhere in the world. After hatching from an egg, they immediately begin to feed on minnows, tadpoles, aquatic insects, and other small prey - including conspecifics (like siblings). Once reaching adulthood, they quickly become the scourge of mosquitoes and flies.

Naiad

Newly Emerged


Almost Ready to Hunt!


Reference:

Density-Dependent Cannibalism in Larval Dragonflies
Josh Van Buskirk
Ecology, Vol. 70, No. 5 (Oct., 1989), pp. 1442-1449
Published by:
Ecological Society of America
Stable URL:
http://www.jstor.org/stable/1938203

Sunday, April 12, 2009

“Extreme” Imperfection?

I just happened across a nifty little article from the Journal of Evolution: Education and Outreach. It discusses the fossil record, Darwin and other concepts such as “missing links” and transitional forms.

It’s jargon free and would be a good resource for teachers, or anyone interested in explaining to lay persons how fossils provide evidence for evolution.

It can be downloaded as a PDF - HERE.

Saturday, April 11, 2009

Cretaceous Multituberculata from Australia

Thomas H. Rich (et. al.), Curator of Vertebrate Paleontology at the Museum of Victoria in Melbourne, Australia, recently published a description of dentary fragments from a member of the Multituberculata in the Journal Acta Palaeolontologica Polonica.

Several mammalian families have previously been identified from the Aptian formation (where the current fossil was found), most of these are believed to represent species endemic to Australia; however one family – the Ornithorhynchidae – have also been found in Argentina. Ornithorhynchidae, a group of monotremes, have been used to provide evidence for mammalian dispersal between South America and Australia during the Mesozoic.

According to the authors, these prehistoric platypuses provide biogeographical clues because “[g]iven the relative geographic positions of Australia and South America during the Mesozoic, it is reasonable to expect that were it then possible to do so, at least one of these terrestrial mammals would have traversed the Antarctic landmasses, in one direction or the other…”


Abstract:
A dentary fragment containing a tiny left plagiaulacoid fourth lower premolar from the Early Cretaceous (Aptian) of Victoria provides the first evidence of the Multituberculata from Australia. This unique specimen represents a new genus and species, Corriebaatar marywaltersae, and is placed in a new family, Corriebaataridae. The Australian fossil, together with meagre records of multituberculates from South America, Africa, and Madagascar, reinforces the view that Multituberculata had a cosmopolitan distribution during the Mesozoic, with dispersal into eastern Gondwana probably occurring prior to enforcement of climatic barriers (indicated by marked differentiation in regional floras) in the Early Cretaceous.







Holotype of multituberculate mammal Corriebaatar marywaltersae gen. et sp. nov. from Flat Rocks, Wonthaggi Formation (Aptian), Australia (NMV P216655), a left dentary fragment with p4 and anterior root of m1 in labial (A), lingual (B), and occlusal (C) views. Artwork by P. Trusler.

THOMAS H. RICH,et al. (2009). An Australian multituberculate and its palaeobiogeographic implications Acta Palaeolontologica Polonica
The article is available as a PDF HERE.

Beck, R., Godthelp, H., Weisbecker, V., Archer, M., & Hand, S. (2008). Australia's Oldest Marsupial Fossils and their Biogeographical Implications PLoS ONE, 3 (3) DOI: 10.1371/journal.pone.0001858

Phylogenomics and Metazoan Evolution

During the course of constructing a “Tree of Life” based on more than 120 gene sequences and fifty-five different species, a group of scientists led by Gert Wörheide of Munich have reached two conclusions; one, all Porifera (sponges) share a common sponge-like ancestor, and two, that ancestor did not give rise to the Bilateria.

According to Wörheide, “If the ancestral animal would have had a sponge-like organization or body, as some earlier molecular studies repeatedly claimed, then we would all be descendents of such sponge-like organisms. This proposition generated a lot of attention in the past. But our results clearly disagree with it."


Abstract:
The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence order of the early branching taxa: the sponge groups, ctenophores, placozoans, cnidarians, and bilaterians. The ‘‘phylogenomic’’ approach has recently provided a robust picture for intrabilaterian relationships but not yet for more early branching metazoan clades. We have assembled a comprehensive 128 gene data set including newly generated sequence data from ctenophores, cnidarians, and all four main sponge groups. The resulting phylogeny yields two significant conclusions reviving old views that have been challenged in the molecular era: (1) that the sponges (Porifera) are monophyletic and not paraphyletic as repeatedly proposed, thus undermining the idea that ancestral metazoans had a sponge-like body plan; (2) that the most likely position for the ctenophores is together with the cnidarians in a ‘‘coelenterate’’ clade. The Porifera and the Placozoa branch basally with respect to a moderately supported ‘‘eumetazoan’’ clade containing the three taxa with nervous system and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early diverging phyla.


Phylogenomics is the science of comparing genetic compliments, such as genes, nucleotides or entire genomes from different species, and through the application of statistics determining the “best fit” in terms of any evolutionary history (phylogeny) that the organisms share. Frequently these studies result in multiple “possible fits” and determining the most parsimonious model isn’t always a simple task, but in the case of this current study, it appears that the bar has been raised.



(A) Schematic section of an adult sponge (bottom) and SEM picture showing a choanocyte, the sponge collar cell (top, choanocyte from Chelonaplysilla noevus, Demospongiae). The arrows indicate the direction of circulation of water in the aquiferous system of the sponge. Abbreviations: atr, atrial cavity; cb, cell body; cc, choanocyte chamber; col, collar of microvilli; ex, exhalant canal; fl, flagellum; in, inhalant canal; mes, mesohyl; osc, osculum (or exhalant orifice); ost, ostium (or inhalant orifice); pin, pinacoderm (thin epithelial layer, limiting the sponge body on its external surface and within the canals); sp, spicule.


(B) Most parsimonious scenario for the evolution of sponge body plan characters, imposed on a scheme of sponge paraphyly.


(C) Most parsimonious scenario assuming sponge monophyly.


In (B) and (C), the gray branches indicate the presence of sponge body plan characters (aquiferous system, internalized choanocyte chambers, pinacoderm) and the black branches indicate the absence of these characters. The gray horizontal line indicates character acquisition; the hollow horizontal line indicates character loss. ‘‘Sponges 1, 2, and 3’’ correspond to the major lineages (silicisponges, homoscleromorphs, and calcisponges), of which exact branching order varies among published studies recovering sponge paraphyly.


Incidentally, if your interested in the search for the urbilaterian (common ancestor of Bilateria), I’d recommend a look at a recent paper by Neil Shubin, Cliff Tabin and Sean Carroll titled Deep homology and the origins of evolutionary novelty. This article was published this past February in Nature.



Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., & Quéinnec, E. (2009). Phylogenomics Revives Traditional Views on Deep Animal Relationships Current Biology DOI: 10.1016/j.cub.2009.02.052

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty Nature, 457 (7231), 818-823 DOI: 10.1038/nature07891

Friday, April 10, 2009

Eugenie Scott on Texas Schools

Today on NPR's Science Friday, Eugenie Scott talks about the Texas School Board and its endorsement of ignorance. Audio HERE.

Recorded Today.

People don’t understand science

I missed this post earlier in the week - good stuff!

Science IS Imagination