Archive for the 'Genetics' category

Climate change, invasives and extinction in Thoreau's Woods

...I walk encouraged between the tufts of Purple Wood-Grass, over the sandy fields, and along the edge of the Shrub-Oaks, glad to recognize these simple contemporaries. With thoughts cutting a broad swathe I “get” them, with horse-raking thoughts I gather them into windrows. The fine-eared poet may hear the whetting of my scythe. These two were almost the first grasses that I learned to distinguish, for I had not known by how many friends I was surrounded — I had seen them simply as grasses standing. 

From "Autumnal Tints" by Henry David Thoreau The Atlantic Monthly October 1862. In this photo from 1908, the rocks mark the location of his cabin in relation to Walden Pond.

ResearchBlogging.orgAround 1851, after completing the retreat that inspired Walden, Thoreau had taken his interest in nature and made it a more scientific part of his work routine, walking the woods and fields around Concord, Massachusetts recording his observations of plants and animals through the seasons in the area. He paid particularly close attention to the flowering days of local plants, which has been of interest to the scientific community of late.

The data that Thoreau collected is meticulous enough to be considered a viable, useful data source by modern researchers. Thoreau's records of the area's wildlife have been carried on by others, providing us with over 150 years of data regarding the phenology of Northeast American flora; that is, life cycle events like fruiting or flowering days or migration and how these events are influenced by the seasons and the climate. Simply put, after 150 years of suffering the effects of disturbance and climate change, the natural communities of Concord are not quite the forests and fields of yore.

In the past two years or so there have been a handful of studies based on the data set that Thoreau started. In February 2008, Rushing and Primack published a study in Ecology discussing how global warming had affected flowering times in Concord. The average temperature has increased in the area by approximately 2.4° C since 1852, which has, on average, pushed flowering times up by 7 days since Thoreau's time. It was also observed that two non-native plants common in the Northeast, St. John’s wort (Hypericum perforatum) and highbush blueberry (Vaccinium corymbosum), could be useful as bioindicators of the future effects of climate change due to how quickly they responded to the changing temperatures; their mean first flowering days shifted forward approximately three days per 1° C increase in temperature.*

Later that year, Willis et al. published a study in PNAS using the data set started by Thoreau, this time looking at the data from a phylogenetic perspective. It was shown that flowering time was strongly correlated with abundance and that the species seemingly incapable of a relatively quick response to the change in climate were declining. The pattern is phylogenetically selective, strong evidence of climate change as an extinction risk.

In the near term, this pattern of phylogenetic selectivity is likely to have an accelerated impact on the loss of species diversity: groups of closely related species are being selectively trimmed from the Tree of Life, rather than individual species being randomly pruned from its tips.

A more recent study from Willis and his colleagues published in PLoSONE takes a look at how these flowering times differ between native and non-native species, determining how each has been able to respond over the past 150 years. It was previously demonstrated that the non-natives St. John's wort and highbush blueberry have been apt conformers to the changing climate, but neither are considered invasive.

The researchers placed the Concord flora in four comparative categories for analysis - Native vs. non-native, Native vs. non-native, non-invasive, Native vs. invasive, Non-native, non-invasive vs. invasive - and examined phenologically and ecologically important traits such as plant weight at maturity and flower diameter.


The results are remarkable, and reveal another layer of danger to native plants in the area. In general, non-natives were shown to adapt to changing temperatures better than the natives. Invasive species are particularly apt; they flower 11 days earlier than natives and 9 days earlier than the non-native, non-invasives. The results of the study also backed up earlier evidence that abundance was tied to earlier flowering days; invasives displayed greater relative abundance than the natives and non-native, non-invasives. But in general, non-natives in the area are equipped with certain traits that better prepare them for changes in climate.

Already the Concord area has lost about 27 percent of the species that once inhabited Thoreau's woods and another 36 percent have become incredibly rare. If the projections of 1.1° - 6.4° C increases in average temperature over the next century are correct, this trend will continue, progressively selecting traits that promote invasive growth and pushing natives that much closer to extinction.

*It's not always a boon for the flowering days of plants to be pushed forward in the season. If flowering too early, they may miss their pollinators or succumb to a late frost.

Willis, C., Ruhfel, B., Primack, R., Miller-Rushing, A., Losos, J., & Davis, C. (2010). Favorable Climate Change Response Explains Non-Native Species' Success in Thoreau's Woods PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008878

Willis CG, Ruhfel B, Primack RB, Miller-Rushing AJ, & Davis CC (2008). Phylogenetic patterns of species loss in Thoreau's woods are driven by climate change. Proceedings of the National Academy of Sciences of the United States of America, 105 (44), 17029-33 PMID: 18955707

Miller-Rushing AJ, & Primack RB (2008). Global warming and flowering times in Thoreau's Concord: a community perspective. Ecology, 89 (2), 332-41 PMID: 18409423

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Why Spiders Aren't Insects IV: Molecular Homology

Photo by: Gerald Yuvailos

This is the fourth part in an ongoing series discussing the distinction and evolution of spiders and other arthropods.
Part I, part II and part III have led up to this point:

In the last post of this series, we established that spiders descended from marine arthropods called the eurypterids, distinct and separate from insects, appearing in the fossil record in the late Silurian/early Devonian, about 425 million years ago.

The cladogram we used to analyze the spider's history was based on the organism's morphological characteristics, that is, visible structures like chelicerae and book lungs that can be tied to other organisms that possess the same structures. Limulus (the extant horseshoe crab) has both of these structures and predates the spiders, placing them further back in the chelicerates' evolutionary history.

Homologous bones from human (I), dog (II), pig (III), cow (IV), tapir (V) and horse (VI):
r — Radius, u — Ulna, a — Scaphoid, b — Lunare, c — Triquetrum, d — Trapezium,
e — Trapezoid, f — Capitatum, g — Hamatum, p — Pisiforme

Paleontologists call this comparison of physical characteristics homology (coined by Richard Owen an anatomist and, ironically an opponent of Darwin). The mouth parts of a spider are homologous to the mouth parts of Limulus because of the cherlicae's exact form and function. This is a different designation than analogy; analogous structures may function in the same way, but they are different in form because of their different lineage. For this reason, scientists call analogy an artificial classification system.

A good example of analogous structures are wings from bat and bird. They perform the same function in varying degrees, but they have evolved very different forms. A bat's wing is basically a modified mammal hand, while the bird wing is a modified tetrapod arm.

Homology is essential in building an organism's phylogeny (evolutionary history). More recently, geneticists have employed this classification technique to analyze and find similarities among the less visible traits in life, RNA (ribonucleic acid) and the building blocks of proteins, amino acids.

Think of these cellular chemicals this way: If DNA is the blueprint of life, RNA is the builder and its materials are amino acids. When these amino acids are placed in the correct sequence by RNA, they become proteins, the framework of our body. And, since the genetic code for protein constructions is nearly universal*, geneticists can compare entire swaths of RNA from one organism to those of another and find homology at the molecular level.

Here's an example (sequences are greatly abbreviated for the sake of our sanity):

Organism 1: ACGC-CCCCC
Organism 2: ACGC-CCCUC
Organism 3: ACGU-CUCUC

Basically, from noting the differences in each RNA sequence, and determining the homologous sequences (such as the ACGU sequence above), a cladogram can be constructed that shows common ancestry without the murky distinctions that sometimes cloud the comparison of bones to bones, or mouth parts to mouth parts.

The problem with this molecular system of analysis is that it often provides vastly different cladograms than the ones crafted through morphological analysis. This is not necessarily the case between the spiders and and Limulus, the molecular evidence supports the fossil record's interpretation of ancestry, but it calls into question the descent of insects from chelicerates like spiders.

In short, the molecular evidence agrees with the morphological evidence: spiders are more closely related to horseshoe crabs than insects. But where and when did the insects arise?

Next time we'll tackle the more recent movements to elucidate the phylogeny of arthropods, including a discussion on the significance Hox genes and evolutionary-developmental biology (evo-devo).

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Why Spiders Aren't Insects III: The Evolutionary Advantages of Mass Extinction

So far we have established that spiders are distinct from insects for two reasons: physiology (mouth parts, body plan, respiratory structures) and more importantly, evolutionary history (or phylogeny, as scientists call it).

But where did spider's come from? How did they crawl out of the water as euryterids and speciate (become a distinct organism that cannot interbreed)?

The answer, like many in invertebrate paleontology, is cloudy. Organisms without hard, thick shells rarely become fossilized. In fact, for any organism's parts to become fossilized, even vertebrates, is a profound rarity, as Bill Bryson illustrates in A Short History of Nearly Everything:

Only about one bone in a billion, it is thought, ever becomes fossilized. If that is so, it means that the complete fossil legacy of all the Americans alive today - that's 270 million people with 206 bones each - will only be about fifty bones, one quarter of a complete skeleton.

Needless to say, invertebrate paleontologists are having a heck of a time piecing things together from such a paltry fossil record. But that doesn't mean there's no evidence.

According to morphological and geological evidence, and therefore directly observable comparison, spiders and their brethren descended from the eurypterids, many of which were sea-going creatures. The eurypterids arose in the Ordovician, a period that began with the decimation of perhaps 60% of all marine life, and consequently ended with another more devastating cataclysm, which which some paleontologists rank as the second most destructive extinction event in the history of the world (by extinction of family). This has become known, quite appropriately, as the end-Ordovician event.

Mass extinctions make room for the evolution of unique characteristics as dictated by an organism's environment, and the environment changed drastically for the eurypterids at the end of the Ordovician. Glaciers began to creep down from the upper latitude, as the greenhouse gas carbon dioxide was depleted from the atmosphere, reducing the Earth's ability to trap the sun's heat energy. As the glaciers encroached, sea levels dropped and global temperatures cooled. This rapid progression decimated habitats, and destroyed a species' equilibrium with its environment.

But the end-Ordovician event was comprised of two parts: glaciation and then a period melting, an interglacial. Temperatures warmed once more, glaciers melted, flooding the land, and raising sea levels once more. The world had completely lost almost 50 percent of the families of life, but the ancestors of the spiders had survived. The Silurian period had begun, and new ecological niches were available for exploitation, a habitat opportunity that eventually would produce the spider.

That's about how it stands from a morphological perspective. But more recently scientists have been delving into molecular evidence and crafting very different explanations of not only the rise of the spider, but the vast diversification of arthropods in general.

Next time we'll address the new cladograms produce by this molecular evidence, and what ramifications it might have in interpreting the diaspora of the most abundant creatures on the planet.

*Interestingly enough, we are in the middle of an interglacial right now, the Holocene. Much like the success of the spider, our current interglacial, which began about 16,000 years ago, may have contributed to the ultimate "success" of Homo sapiens.


Pechenik, J. A. (2000). Biology of the Invertebrates. : McGraw Hill Companies.

Gradstein, Felix, James Ogg, and Alan Smith, eds., 2004. A Geologic Time Scale 2004 (Cambridge University Press)

Baez, J. (2005). Temperature. Retrieved July 18, 2006, from

Webby, Barry D. and Mary L. Droser, eds., 2004. The Great Ordovician Biodiversification Event

University of Bristol. (2004). Fossil chelicerates and evolution. Retrieved July 18, 2006, from

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