Apples and Genetic Bottlenecks

This is the eleventh 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.

Genetic Diversity in Malus x domestica (Rosaceae) through Time in Response to Domestication by Briana L. Gross, Adam D. Henk, Christopher M. Richards, Gannara Fazio, and Gayle M. Volk

Domestication is a selection process. Plants with desirable traits are selected (consciously or unconsciously) and removed from the larger population to be grown out and selected from again. Over time, this series of selections results in a cultivated variety that differs substantially from the larger, origin population. This process, while yielding crop varieties that feed a growing population of humans, also results in a series of genetic bottlenecks, meaning they experience a reduction in genetic variation compared to their wild relatives.

There are two points were bottlenecks occur in the domestication process. The first takes place “during the initial domestication event as a subset of the wild population is brought into a cultivated setting.” This is called a “domestication bottleneck.” The second, known as an “improvement bottleneck,” happens when “modern, elite cultivars are selected from the broad variety of landraces [locally adapted varieties]” that were developed during the original domestication event. This stepwise reduction in genetic diversity “limits the options of plant breeders, even as they face the need to increase crop productivity and sustainability” in today’s changing climate.

Most of what we know about genetic bottlenecks during domestication is derived from studies of annual fruit and grain crops. However, “non-grain crops, and perennials in particular, respond to domestication or are domesticated in ways that are fundamentally different.” For this reason, the authors investigated genetic bottlenecks in apple (Malus x domestica), “one of the most widely distributed perennial fruit crops.” They then compared what they learned to other published studies of annual and perennial fruit crops in order to gain more insight into how genetic diversity is affected in these types of crops during domestication.

The common apple was domesticated in central Asia around 4,000 years ago and is a hybrid of at least three species: Malus sieversii, Malus orientalis, and Malus sylvestris. Today, apples are grown throughout the world, and there are more than 7,500 known cultivars with new cultivars being released regularly. Despite this impressive diversity, just fifteen cultivars make up 90% of apple production in the U.S. The authors of this study analyzed DNA from 11 of the 15 major cultivars as well as DNA from the three main wild progenitor species.

Malus x domestica 'Gala' - One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Malus x domestica ‘Gala’ – One of the top 15 apple varieties produced in the U.S. (photo credit: wikimedia commons)

Perennial fruit crops typically experience “mild genetic bottlenecks” compared to annual fruit crops, and the authors confirmed this to be the case with domesticated apples, finding “no significant reduction in genetic diversity through time across the last eight centuries.” Because apple cultivars are maintained by clonal propagation, they can often be traced back to when they were originally developed, making bottlenecks easier to observe. The authors found that “the most recently developed or described cultivars of apples show little to no reduction in genetic diversity compared with the most ancient cultivars.” Cultivars developed since the 1950’s show increased diversity, which may partly be the result of plant breeders introducing genes from another wild species, Malus floribunda.

After a review of the literature, the authors found that apples have retained the highest amount of genetic diversity through the domestication process compared to other fruits, both annual and perennial. More studies are needed in order to confirm the accuracy and extent of these findings; however, the unique story of apple domestication may help explain why it has been “particularly prone to retaining diversity through time.” First, it was widely distributed across Eurasia during its early days of domestication. Second, it experienced “admixture with cultivars” as it expanded its range. For example, after being introduced to North America, it became naturalized, resulting in gene flow occurring between naturalized individuals and cultivated varieties. Offspring of these populations (“chance seedlings”), were then selected, cloned, and became named cultivars.

Despite the mild genetic bottleneck observed in apples, the authors warned that a “dependence on a small number of cultivars” for the majority of U.S. apple production may be resulting in some loss of genetic variation. Relying on so few cultivars may leave apple production vulnerable to pests, diseases, and climate change. “Careful management” is advised as “the continued genetic resilience of the crop is dependent on the genetic diversity of cultivars that are present in living and cryopreserved collections around the world.”

Malus sylvestris (common crabapple) - One of the three main players involved in the apple domestication story (photo credit:

Blossoms of Malus sylvestris (common crabapple) – One of three main species involved in the history of apple domestication (photo credit:


The Legacy of a Leaky Dioecy

This is the second 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.

The Ecological Side of an Ethnobotanical Coin: Legacies in Historically Managed Trees by Nanci J. Ross, M. Henry H. Stevens, Andrew W. Rupiper, Ian Harkreader, and Laura A. Leben

As much as we like to think otherwise, pre-Colombian Native Americans altered the natural landscape in drastic and measurable ways. What we often consider an unaltered, pristine natural area before European colonization, actually has human fingerprints all throughout it. Determining just how deep these fingerprints go, however, is a challenge that requires careful and thorough anthropological and ecological studies.

Many such studies have been done, mostly at the community and ecosystem level. For example, Native Americans used fire extensively as a land management tool. This is how prairies were maintained as prairies. Today, forests in eastern North America that were once dominated by oaks have shifted over to maple dominated forests. This is largely (although not solely) because anthropogenic fires have ceased and wildfires are now suppressed. If fires had never been used as a management tool, would oaks (an important Native American food source) have ever maintained such dominance?

Native Americans participated in the domestication of numerous plant species. Much of this was done by way of – as Charles Darwin termed it – unconscious selection. Rather than selecting specific individuals and breeding them to achieve a desired type, they would simply discard undesirable plants and maintain desirable ones. Much of this selection, especially for woody, perennial species was done through land management techniques – such as fire – as opposed to typical cultivation. The authors of this article, interested in whether or not the “legacy” of this method of selection through land management could be observed today in an individual species, developed a preliminary study to begin to answer this question.

Diospyros – a genus in the ebony family (Ebenaceae) consisting of around 500 species – is mainly pantropical with a few species occurring in temperate regions. One temperate species is Diospyros virginiana – common persimmon – which “has a broad distribution throughout the United States from Connecticut south to Florida and west to the eastern edge of Nebraska.” Persimmons were used and managed extensively by Native Americans; however, they are “now viewed as a rare, weedy, wild fruit tree that is known primarily by hobbyists and wild harvesters.”

Fruits of common persimmon, Diospyros virginiana )photo credit: Wikimedia commons)

Fruits of common persimmon, Diospyros virginiana (photo credit: wikimedia commons)

D. virginiana is a dioecious species, meaning that it produces male flowers and female flower on separate individuals. Despite this, some individuals have been reported bearing both male and female flowers while others have been seen having perfect flowers along with either male or female flowers. Some trees have even been reported to be dioecious one year and then having perfect flowers and/or some combination of male, female, and perfect flowers the next year. This variation from the norm – what the authors call “leaky dioecy” – can either be a result of artificial selection or environmental pressures. The authors hypothesized that “leaky dioecy in D. virginiana is a result of historical selection by Native Americans for trees with copious fruit production.” This preliminary study was designed to see if climate and soil conditions might be the reason for the observed “sex expression.”

Skipping ahead, the authors found “no compelling evidence…to suggest segregation due to environmental factors,” signaling them to “move forward in [their] investigation of potential long-term impacts of historical management on the evolution of reproductive traits in American persimmon without the noise of a strong environmental driver.” The authors go on to discuss challenges in their study, including the length of time since “extensive management” making it hard to “uncover a signal of precontact management” and the limitations of having to rely on herbarium specimens. Either way, it is a worthy study to pursue. Even if it does not reveal the full story of how Native Americans managed persimmons in pre-colonial times, further insight into “adaptive flexibility in reproductive systems of long-lived perennial species” and other interesting things that persimmons might teach us will be well worth the effort.

Characteristic bark of common persimmon, Diospyros virginiana (photo credit:

Characteristic bark of common persimmon, Diospyros virginiana (photo credit:


Figs and Fig Wasps

Recently I was listening to a past episode of Caustic Soda Podcast in which the hosts briefly discussed fig wasps. I was intrigued by this discussion, having previously never heard of fig wasps, and so I did a little research. As it turns out, what I am about to share with you here is just the tip of the iceberg. The relationship between figs and fig wasps is a complex topic, to the extent where you could easily spend a lifetime studying this relationship and there would still be more to discover.

Ficus is a genus of plants in the  family Moraceae that consists of trees, shrubs, and vines. They are commonly referred to as figs, and there are between 755 and 850 described species of them (depending on the source). The majority of fig species are found in tropical regions, however many of them are found in temperate regions as well. The domesticated fig (Ficus carica), also known as common fig, is widely cultivated throughout the world for its fruit.

common fig

Ficus carica – common fig

photo credit: wikimedia commons

The fruit of figs, also called a fig, is a multiple fruit because it is formed from a cluster of flowers. A fruit is formed by each flower in the cluster, but they all grow together to form what appears to be a single fruit. Now here is where it starts to get bizarre. The flowers of figs are contained inside a structure called a syconium, which is essentially a modified fleshy stem. The syconium looks like an immature fig. Because they are contained inside syconia, the flowers are not visible from the outside, yet they must be pollinated in order to produce seeds and mature fruits.

This is where the fig wasps come in. “Fig wasp” is a term that refers to all species of chalcid wasps that breed exclusively inside of figs. Fig wasps are in the order Hymenoptera (superfamily Chalcidoidea) and represent at least five families of insects. Figs and fig wasps have coevolved over tens of millions of years, meaning that each species of fig could potentially have a specific species of fig wasp with which it has developed a mutualistic relationship. However, pollinator host sharing and host switching occurs frequently.

Fig wasps are tiny, mere millimeters in length, so they are not the same sort of wasps that you’ll find buzzing around you, disrupting your summer picnic. Fig wasps have to be small though, because in order to pollinate fig flowers they must find their way into a fig. Fortunately, there is a small opening at the base of the fig called an ostiole that has been adapted just for them. What follows is a very basic description of the interaction between fig and fig wasp – remember with the incredible diversity of figs and fig wasps, the specifics are sure to be equally diverse.

First a female wasp carrying the pollen of a fig from which she has recently emerged discovers a fig that is ready to be pollinated. She finds the ostiole and begins to enter the fig. She is tiny, but so is the opening, and so her wings and antennae are ripped off in the process. No worries though, she won’t be needing them anymore. Inside the fig there are two types of flowers – ones with long styles and others with short styles. The female wasp begins to lay her eggs inside the flowers, however she is not able to lay eggs inside the flowers with the long styles. Instead, these flowers get pollinated by the wasp. After all her eggs are laid, the female wasp dies. The fig wasp larvae develop inside galls in the ovaries of the fig flowers, and they emerge from the galls once they have matured into adults. The adult males mate with the females and then begin the arduous task of chewing through the wall of the fig in order to let the females out. After completing this task, they die. The females then leave the figs, bringing pollen with them, and search for a fig of their own to enter and lay eggs. And the cycle continues.

But there is so much more to the story. For example, there are non-pollinating fig wasps that breed inside of figs but do not assist in pollination – freeloaders essentially. And how is the cycle different if the species is monoecious (male and female flowers on the same plant) compared to dioecious (male and female flowers on different plants)? It’s too much to cover here, but visit for more information. FigWeb is an excellent resource for learning all about the bizarre and fascinating world of the fig and fig wasp relationship. Also check out the PBS documentary, The Queen of Trees.

This is the first of hopefully many posts on plant and insect interactions. Leave a comment and let me know what plant and insect interactions interest you.