Phylogenetic Arts and Crafts

This is a guest post by Rachel Rodman.

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The foods we eat – namely fruits, vegetables, and grains – are all products of their own evolutionary stories. Some of the most well-known chapters in these stories are the most recent ones – dramatic changes in size and shape mediated by human selection.

One especially striking example is that of Brassica oleracea –the source of broccoli, cauliflower, kale, Brussels sprouts, kohlrabi, and cabbage. Each of these diverse vegetables belongs to the same species, and each is the product of a different kind of selection, exerted on different descendants of a common ancestor.

Corn is another famous chapter. The derivation of corn – with its thick cobs and juicy kernels developed from the ancestral grain teosinte, which it barely resembles – has been described as “arguably man’s first, and perhaps his greatest, feat of genetic engineering.”

But these, again, are recent chapters. Relatively. They unfolded over the course of consecutive human lifetimes –hundreds of years or thousands at the outset (sometimes much less). They are the final flourishes (for the moment) on a much older story — a story that significantly precedes agriculture as well as humans.

It is this older story that lies at the heart of truly deep differences, like those at play in the idiom “apples and oranges.” The contrast between these two fruits can be mapped according to many measures: taste, smell, texture, visual appearance, and so on. When used colloquially, the phrase serves as a proxy for unmanageable difference — to describe categories that differ along so many axes that they can no longer be meaningfully compared.

However, in evolutionary terms, the difference between apples and oranges is not ineffable. It is not a folksy aphorism or a Zen puzzle at which to throw up one’s hands. To the contrary, it can be temporalized and quantified; or at least estimated. In fact, in evolutionary terms, that difference comes down to about 100 million years. That is, at least, the date (give or take) when the last common ancestor of apples and oranges lived — a flowering plant from the mid-Cretaceous.

The best way to represent these deep stories is with a diagram called a phylogenetic tree. In a phylogenetic tree, each species is assigned its own line, and each of these lines is called a branch. Points at which two branches intersect represent the common ancestor of the species assigned to these branches.

Phylogenetic trees can serve many purposes. Their classical function is to communicate a hypothesis – a pattern of familial relationships supported by a particular set of data based on DNA sequence, fossils, or the physical characteristics of living organisms.

But here are two alternate reasons to build trees:

  • To inspire wonder
  • Or (my favorite) just because

To reflect these additional motivations – this conviction that trees are for everyone and for all occasions and that an evolutionary tree belongs on every street corner – when I build trees, I often avail myself of a range of non-traditional materials. I’ve written previously about creating edible trees using cake frosting and fruit, as well as building trees out of state symbols and popular songs. Now here are two additional building materials, which are arguably even more fun.

First: Stickers. This one is titled: “Like Apples and Oranges…and Bananas.”

Bananas split ways with the common ancestor of apples and oranges about 150 million years ago, 50 million years before the split between apples and oranges. On this tree, these relationships are represented like so: the banana branch diverges from the apple branch at a deeper position on the trunk, and the orange branch diverges from the apple branch at a shallower position. 

All of the data required to build this tree  (and essentially any tree) is available at TimeTree.orgOn TimeTree, select “Get Divergence Time For a Pair of Taxa” at the top of the page. This is where one can obtain a divergence time estimate for most pairs of species. The divergence time is an approximate date, millions of years ago, at which the organisms’ last common ancestors may have lived. For more heavy duty assistance, there is the “Load a List of Species” option at the bottom of the page. Here, one can upload a list of species names (.txt), and TimeTree will generate a complete tree – a schematic that can serve as a guide in patterning one’s own phylogenetic artwork.

Here, by way of additional illustration, are three more sticker trees, equally charming and equally mouthwatering:

Carrot, watermelon, broccoli, strawberry, and pear.

Onion, asparagus, tomato, cucumber, and cherry.

Raspberry, apricot, pea, grape, and green pepper.

Sticker trees are festive takes on traditional trees. They are brighter, livelier, and more lovely. But, like traditional trees, they are also 2D, restricted to a flat sheet of paper. To extend one’s phylogenetic art projects into three dimensions, one must modify the choice of materials. There are many options. The following 3D tree, for example, employs 13 pieces of plastic toy food, the accouterments of a typical play kitchen. Segments of yarn serve as branches.

Trees like these, made of stickers or toys, constitute playful takes on deep questions. In pencil and yarn, they sketch a network of primeval relationships. They tell the history of our foods, a narrative whose origins profoundly precede us, as well as our intention to selectively breed them. To the Way-Before, to the Way-Way-Way-Before, these projects give shape and color. If and where they succeed, it is because they manage to do two things at once: To communicate a vast biological saga extending across many millions of years, and to be completely cute. Perhaps best of all – and let it not go unmentioned – anyone can make them.

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Bio: Rachel Rodman has a Ph.D. in Arabidopsis genetics and presently aspires to recast all of art, literature, and popular culture in the form of a phylogenetic tree.

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Improving Perennial Crops with Genomics

This is the twelfth in a series of posts reviewing the 17 articles found in the October 2014 Special Issue of American Journal of Botany, Speaking of Food: Connecting Basic and Applied Science.

Genomics: A Potential Panacea for the Perennial Problem by Kendra A. McClure, Jason Sawler, Kyle M. Gardner, Daniel Money, and Sean Myles

Compared to annuals, a small but significant portion of our food comes from perennial crop plants. “Approximately one eighth of the world’s total food-producing surface area is dedicated to perennials,” and while that may seem relatively small, there is a good chance that some of your favorite things to eat or drink are perennial crops (apples, bananas, coffee, citrus, sugar cane, coconut, avocados, olives, grapes, cherries, almonds…just to name a few). However, making improvements to and introducing new cultivars of perennial crops is considerably more challenging compared to annual crops simply due to the nature of perennials. This puts perennial crops at greater risk to threats like pests and diseases, climate change, soil degradation, and water and land shortages. Advances in genomics, “the collection and use of DNA sequence information,” could change this.

Because breeding efforts to improve perennial crops is so challenging, “only a small number of elite varieties become popular, and the amount of genetic diversity represented by commercially successful cultivars is therefore often low.” This suggests that there is incredible potential for improvement in these crops, as long as major hurdles can be overcome. Following is a list of some of those hurdles:

  • Time – Most perennial crops have “extended juvenile phases,” meaning they won’t produce fruit for as much as ten years, considerably delaying evaluation of the final product.
  • Space – Perennial crops, especially trees, are large compared to annual crops, so the area required for evaluation is extensive.
  • Infrastructure – “Many perennials require trellis systems, extensive land preparation, and substantial costs for specialized equipment and skilled horticultural labor.”
  • Complex Evaluations – Automated assessments are “either unavailable or poorly developed,” so evaluations that include “size, shape, color, firmness, texture, aroma, sugars, tannins, and acidity” require “tasting panels” to ensure that the final product “satisfies consumer demands.” This process is expensive, and it differs depending on whether the crop will be consumed fresh or processed.
  • Vegetative Propagation – “Many perennials suffer from severe inbreeding depression when selfed,” so cultivars are maintained through vegetative propagation. This is a plus, because it means that the fruits of perennial crops are reliably uniform, so growers and consumers know what to expect year after year. However, this also means that while pests and pathogens evolve, the crops do not, making them more susceptible to such threats. Additionally, the “long histories” of certain cultivars “discourages [growers] from undergoing the risk of trying recently developed cultivars.”
  • Consumer Preferences – “Consumers often exhibit an irrational reverence for ancient or heirloom varieties,” despite the fact that the development of new varieties can result in crops that are higher yielding, resistant to pests and diseases, tastier, more nutritious, more suitable for storage, and require fewer chemical inputs. This obsession with traditional varieties leaves a “tremendous amount of untapped genetic potential for the improvement of perennial crops.”
"Modern avocado breeding still depends heavily on open-pollination because of the difficulty associated with making controlled crosses." (photo credit: wikimedia commons)

“Modern avocado breeding still depends heavily on open-pollination because of the difficulty associated with making controlled crosses.” (photo credit: wikimedia commons)

Apart from issues of social and cultural preference, the challenge of breeding perennial crops comes down to time and money. Advances in genomics can help offset both of these things. Using DNA-based predictions, a plant’s phenotype can be determined at the seed or seedling stage. Genomics techniques can also be “used to reduce the generation time thereby enabling combinations of desirable traits to be combined on a timescale that is more similar to annual crops.” Below are summaries of specific areas discussed in the paper for using genomics in perennial crop breeding programs:

  • Reduction of Generation Time – This can be done using transgenic technology in ways that do not result in transgenic (GMO) cultivars. One method uses virus-induced gene silencing, in which a host plant is infected with “a virus that is genetically modified to carry a host gene;” the host plant then “attacks itself and uses its own endogenous system to silence the expression of one of its own genes.” Early flowering in apples has been induced after seedlings were inoculated with apple latent spherical virus that expresses a flowering gene derived from Arabidopsis thaliana.
  • Genetic Modification – Advances in genomics have brought us transgenic technology, and several commercial crops have been genetically modified using this technology. Most of them are annuals, but one perennial in particular, SunUp papaya, has been a major success. Its resistance to ringspot virus rescued the papaya industry from a devastating pathogen that “almost completely destroyed the industry in Hawaii.” Consumer disapproval, however, poses a major obstacle to commercial production of genetically modified organisms, and unless this changes, “their widespread use is unlikely.”
  • Marker-Assisted Selection – This is the “primary use of genomics in breeding.” The time between initial plant crosses and the introduction of a new cultivar can be dramatically shortened when genetic markers are used to determine the phenotypes of adult plants at the seedling stage. This technology is also useful when crossing domesticated plants with wild relatives, since genetic markers can be used to determine when desired traits are present in the offspring.
  • Ancestry Selection – After crosses with wild relatives, offspring may “perform poorly because wild germplasm often harbors numerous traits that negatively affect performance.” To overcome this, the offspring is crossed with cultivated plants until undesirable traits are eliminated. This is called backcrossing. Using marker-assisted selection, breeders can “select a small number of offspring in each generation that carry both the desired trait from the wild and the most cultivated ancestry.”
  • Genomic Selection – The success of marker-assisted selection is greatest when used for traits that are controlled by one or a few genes. However, many traits involve a complex set of genes. Genomic selection is a new technique that “uses dense, genome-wide marker data to predict phenotypes and screen offspring.” It is “especially useful for predicting complex traits controlled by many small-effect genes.” Genomic selection is in its infancy, so there are kinks to work out, but it is a promising technology for perennial crop breeding efforts.

The use of genomics will not replace every aspect of traditional perennial crop breeding and “should be viewed as a potential supplement…rather than a substitute.” Geneticists and plant breeders are encouraged to work together to develop and implement these technologies in a concerted effort to improve the crop plants that help feed the world.

"Despite the remarkable phenotypic and genotypic diversity in bananas," the Cavendish banana is responsible for the "vast majority" of banana production. (photo credit: wikimedia commons)

“Despite the remarkable phenotypic and genotypic diversity in bananas,” the Cavendish banana is responsible for the “vast majority” of banana production. (photo credit: wikimedia commons)