A Brave New Ecology

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Onsite assessment, analysis and classification of natural areas and natural communities is the job of the community ecologist while infield. Depending on specialty and employer, the variables measured by these scientists could range from the organic content of soils, to tree canopy invertebrate biodiversity, or anything in between; it’s a physical job and deals with evaluation of natural systems, organic and inorganic, as they exist and function contemporaneously - or at least that’s the traditional role of these scientists. Currently things may be changing; no longer are community ecologists limited to the quantitative and qualitative assessment of systems as they exist at hand, now, thanks to advances in our understanding of genomics and phylogeny, evolution is entering into the equations of ecology.

Charles Darwin recognized that phenotypic and ecological similarity existed between species with shared ancestry. This relationship between environmental fit and evolutionary history created a paradox in his mind; if ecologically and genealogically similar, shouldn’t species exhibit the same resource needs and be found coexisting in habitats where those resources are present? But at the same time, shouldn’t direct competition for those resources of mutual necessity push the organisms in different directions and towards acquisition of divergent characteristics?

Does the phylogenic history of a species factor into a currently evaluated ecological system, or are hydrology, soil chemistry, biodiversity, trophic interaction and anthropogenic effects the only variables of concern to the community ecologist?

This dilemma has been evident throughout the history of ecology. It has effectively resulted in a linear continuum of thought in which one side supports a model of ecological assembly that accounts for the interplay of species through evolutionary time; at the other side of the spectrum, ecological systems are viewed as a minute snapshot of the temporal range with organismal and physical components that are to be measured in situ, without a concern for past or future directionality. On the whole, this continuum is now showing bias towards the inclusion of evolution.

More and more ecologists are coming to place value on the interaction of species within the temporarily fluctuating biological and physical environments in which they are submersed. Through complex nutrient cycling and resource accusation processes organisms alter the physical world around them and in so doing interact with other organisms via competitive and mutualistic dynamics. These newly altered physical environments, freshly acquired mutualisms and recently incepted rivalries provide direct feedback to the original organism forcing additional change and adaptation – just as the ecological picture was becoming clear, it changes again.

Recognizing the links between biological organisms and the physical environment as they exist over deep time and with respect given to spatial biogeography, dispersion and phylogeny is essential to the future of the field. Further developing of methodologies and techniques that incorporate these highly complex dynamics into tools that can be utilized by in-field ecologists should be – will be – an important step in conserving the world’s biota well into the future, particularly on a planet with a rapidly expanding human population and a quickly changing climate.

Cavender-Bares, J., Kozak, K., Fine, P., & Kembel, S. (2009). The merging of community ecology and phylogenetic biology Ecology Letters DOI: 10.1111/j.1461-0248.2009.01314.x

Harmon, L., Matthews, B., Des Roches, S., Chase, J., Shurin, J., & Schluter, D. (2009). Evolutionary diversification in stickleback affects ecosystem functioning Nature, 458 (7242), 1167-1170 DOI: 10.1038/nature07974

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