The tree of life becomes clearer with Next-Generation sequencing

Since the dawn of molecular genetics, scientists have been developing new ways to reconstruct evolutionary relationships among organisms. While historically, taxonomy was a field that relied on comparative anatomy of living organisms, or even more challenging, comparative anatomy of fossils, the comparison of genetic code allows for precise measurements of relatedness among different species. However, sequencing an entire genome was, until quite recently, prohibitively expensive for everything except well-characterized model organisms, and therefore not a viable way to measure the evolutionary relatedness of, say, two rare species of fish.

Next-generation sequencing techniques are rapidly opening new doors in the field of genomics- making it faster, more efficient, and significantly cheaper to sequence entire genomes. Scientists are finally beginning to examine the geneti code of non-model, and even very rare organisms to determine their “evolutionary place” in the tree of life. For example, micrognathozoa is a small, wormlike invertebrate with complex jaw architecture. It was entirely unknown to science until 1994, when the first specimins were discovered on an island off the west coast of Greenland. From anatomical characteristics alone, micrognathozoa was impossible to place into any existing phylum, suggesting that it diverged from other modern relatives very deep in evolutionary history. Researchers at Brown University have recently collected samples of micronathozoa and are now sequencing its bulk DNA. They are hoping to identify specific genes that will allow them to properly place the bug in a phylogenetic tree.

In addition to simply classifying organisms based on relatedness, Next-Generation sequencing is allowing scientists to study evolutionary dynamics and discern how changes in gene expression patterns lead to the divergence of species. A particularly exciting new technique, known as RNA-seq, can be used to gauge genetic activity by measuring cDNA copy number. cDNA, or complementary DNA, is produced when genes are activated. The amount of cDNA in a sample therefore reflects the relative “usage” of that gene. This technology could provide answers to questions as fundamental as how flight or swimming evolved ona  genetic level- was the activity of certain genes upregulated or downregulated?

 

 

Reference: Elizabeth Pennisi, “Tracing the Tree of Life”. Science 331: 1005-1006.

Evolution in Action!

A really great interactive phylogenetic tree showing all major extant taxa on Earth today and their evolutionary relationships.

Tree of Life

Simulation of plant evolution

This video shows results from a research project involving simulated Darwinian evolutions of virtual block creatures

wyrd evolution

A population essentially evolves through the accumulation of random changes in its genetic makeup over time. These genetic changes modify organisms’ phenotypes, and over time change the distribution of traits in a population. Many traits which become prevalent in a population do so because they make the population more “evolutionarily fit”- better able survive and reproduce in its environment. Darwin coined the famous term “natural selection”to describe this phenomenon, though he wasn’t aware of the complex genetic mechanisms underlying it.

Evolutionary theory is anchored on the principle that the biology of the past has shaped the diversity we see today. Though countless examples in nature substantiate the important role of natural selection in evolution, it is important to understand that natural selection itself is not a conscious force. Rather, it is it is a pattern that produces predictable outcomes. Stochastic probability tells us that, over a long enough time and with large enough populations, traits that allow organisms to produce more offspring will come to dominate a population, simply because the individuals possessing these traits will pass along more of their genes into the next generation.

Because evolution by natural selection is not a conscious force, and because it must work to improve upon what already exists in nature, evolution cannot rapidly produce superanimals that are perfectly adapted to their environments. As the French biochemist Francois Jacob once eloquently described it, evolution is a tinkerer that works to improve upon what is already there, but its creative freedom is heavily constrained by existing body plans and biochemical pathways. Moreover, natural selection works to optimize organisms, not isolated systems. A trait that may seem advantageous, such as a genetic mutation producing enhanced night vision, may be helpful for a large predator on the Savannah, but useless for a cave fish that is rarely exposed to any sunlight and must use other sensory systems to perceive its environment. The cave fish would not develop improved eyesight because the selective advantage conferred by this ability would not outweigh its energetic costs.

As this last example begins to illustrate, natural selection is often working in concert with another force known as selective constraint. When a gene, biochemical pathway, or phenotypic trait is under selective constraint, it is maintained over evolutionary time. There are many reasons that selective constraint could operate. A biochemical pathway could be so fundamental to an organisms ability to survive that any small alterations to that pathway would be lethal. A limb or sensory organ could already be well suited for its environment, or the benefits of  making any changes to it may not outweigh the costs. A single mutation event in a gene encoding an essential protein could alter the protein’s structure and make it useless.

Natural selection and selective constraint are two important paradigms for understanding evolution. They are not the entire story, but they do help us to understand how evolution produces produces change but also propagates sameness. An alien visiting earth 3 billion years ago could not have imagined that the simple life he discovered would lead to the overwhelming diversity we see today. And yet in spite of all the novelty and innovation that has appeared over evolutionary time, this diversity has drawn upon itself, reaching outwards without  breaking its ties to the past.