Global change

The world has been shaped by…

…agriculture

When did hunter-gatherers begin the cultivation of plant species?

At the start of the Holocene (12,000 years ago)

What did these plants provide^?

Sources of food, fibre, and other uses

The earliest stages of crop domestication was probably the result of…

…unconscious innate behaviours - they will have unconsciously selected for certain types and varieties of plants (this eventually became more intentional).

How were these activities reinforced^?

They were reinforced by changes in behaviour at the end of the Pleistocene (due to climate change, decreases in availability of big game, and increasing human occupation of local habitats).

What did the transition from hunter-gatherers to early farmers entail?

More work, shorter stature, worse nutritional condition, and more disease in farming societies

What did farming (the transition of food production) allow?

It allowed people to settle next to permanent food sources, instead of migrating to follow seasonal food supplies.

What did this lead to^?

A human population explosion

Why^?

• The sedentary lifestyle allowed for shorter birth cycles

• A greater density of edible foods (compared to wild distributions) supported large populations

Why did sedentary lifestyles allow for shorter birth cycles?

Because babies did not need to be carried on migration, so families could have more

What did sedentary living and food cultivation permit?

The accumulation of technology diversification of crafts and vocation, social stratification, political centralisation, and standing armies (which eventually led to farmers displacing hunter-gatherers).

What is domestication?

The process of speciation and/or species transformation that occures when one species (the domesticator) begins to control the reproduction and dispersal of another species (the domesticated) in order to meet the needs of the former, most notably but not exclusively for food.

Domesticated crop species are the result of…

…evolutionary processes acting at distinctly human timescales rather than geological timescales

How can we view crop domestication and why?

As a sort of mutualistic relationship and an example of co-evolution because, in domestication, wild species are exposed to new selective environments associated with the practices of agriculture and cultivation, as well as selection arising from their use by humans.

Explain this relationship^.

• Plant species have adapted to human control and survival in human-manipulated environments to enhance the survival and reproduction of Homo sapiens

• Domestication also results in the increased fitness of the domesticated species, with massive increases in the population size

How does plant domestication compare to mammal domestication?

More species of plants were domesticated by Homo sapiens compared to mammals

Are Homo sapiens te only species that is known to domesticate other species?

No

Which other species do this^?

The attine ants (especially the leaf cutter ants) - they obligately depend on the cultivation of fungus gardens for food.

How can we describe the attine ant agriculture?

It is a symbiotic relationship between four separate organisms - the domesticator ants cultivate the domesticated funghi, and there is a parasitic fungus called Escovopsis that can infect the fungal gardens created by the ants, this is controlled by the fact that the ant will form a symbiotic relationship with a becterium (which will produce an antibiotic that controls the Escovopsis infestation).

It is quite common that plants produce…

…domatia - hollow swellings that can be inhabited by ants

What is the purpose of domatia^?

It serves to house the ants and are one aspect of a broader mutualism in which the ant gives the plant protection from predators and nutrients from faeces.

What does this relationship exist between^?

Between the ant Philidris nagasau and several species of the plant genus Squamelleria (an epiphytic plant that grows on other plants).

Describe this in more detail^.

• Philidris nagasau harvests unripe fruits of Squamelleria, extracts the seeds and then deliberately inserts the seeds into cracks of other host plants, so they can germinate

• As the young plants grow the ants protect them and defecate on them to provide fertiliser

• The ants preferentially sow the seeds on the sunny side of trees to ensure optimal growing conditions

What did Vavilov do?

He identified centres of origin for domesticated crop species according to the following characteristics:

• Centres of origin had a high co-occurrence of wild ancestors with their related domesticated species

• Centres of origin show a higher varietal diversity compared to other areas because the transport of domesticated crops to new areas of cultivation focused on a few favoured varieties and is associated with evolutionary bottlenecks

• Centres of origin have a long history of crop use

Where did expansions of domesticated crops tend to occur?

Along the east-west axis rather than the north-south axis (because areas at the same latitude share identical day-lengths and seasons).

What does this mean^?

Moving within the same latitudes requires less evolutionary change to domesticated species and less adaptation to associated technologies and cultivation practices.

What can we say due to the fact that many of the crops we grow are not evolutionary closely related?

There are multiple evolutionary origins of domestication

What are some evident hotspots of crop domestication?

• The order Poales which contains the grass family and most of our cereal crops

• The order Rosales which contains most of our temperate fruit species

• The order Fables which contains the family Fabaceae which includes all our legume crops and the Solanales which contains the family Solanaceae

Despite the fact that most crop plants are only very distantly related from each other…

…there are a set of traits that are common to nearly all of them

What does this mean^?

There are traits that have been selected for and enhanced by humans to make the plant more productive and nutritious, or more amenable to cultivation techniques.

What is this group of traits known as^?

The domestication syndrome

What traits do humans select for?

• Larger seed and fruit sizes

• Plants that are shorter and less bushy

• The absence of toxins and spines

• Synchronicity in both seed germination and ripening

• Reduced see shattering (the separation of the seed from the plant)

• Selection for self-fertilisation over outbreeding

Why do humans select for larger seed and fruit size?

So that a greater proportion of the plant resources are devoted to the part of the plant that humans eat

Why humans select for shorter and less bushy plants?

Because they are easier to access and less resources is wasted

Why have humans selected for synchronicity in both seed germination and ripening?

To ensure that cultivation cycles can be efficient and particular agricultural activities can be conducted simultaneously on the whole crop.

Why have humans selected for reduced seed shattering?

So that no valuable seeds and fruits are lost before or during the harvest

Why have humans selected for self-fertilisation over outbreeding?

To ensure that the crop is not dependent of variable presence of pollinators, and it also limits the potential for introgression of unwanted alleles and further ensures that the selected traits and beneficial alleles are retained.

What do the early stages of domestication include?

Unconscious selection by humans, which was subsequently replaced by more conscious selection, cultivation, and breeding.

What can we refer to these stages as?

Domestication (first stage) and diversification (second stage)

What is domestication?

The onset or initiation of the process of evolutionary divergence from the wild ancestral species

What is diversification?

The subsequent evolution of the domesticated species and related to the spread and adaptation of the domesticated species to different habitats, climates, and cultures.

What can we say about the differet traits?

Different traits come into play at different stages of the domestication process

What is the first stage (domestication)?

Onest of domestication - plant exploitation involved harvesting and stewardship of wild plants with favourable traits. Selection begins to occur for the new crop, resulting in its incipient isolation from its wil relative.

What are the stages of diversification?

• Increase in frequency of desired alleles - as selection continues and strengthens, populations with desirable alleles are amplified, and yield increases begin to be seen as well as a diversity of favoured phenotypes

• Adaptation of populations to new environments - as domesticated crops evolve and spread from their centre of origin, different crop varieties are selected for in different environments and cultures

• Deliberate breeding - different crop varieties are deliberately bred to maximise yield, ease of farming, uniformity, and quality

How can we describe these four stages in terms of maize?

• The merging distinction between wild ancestor teosinte and an early form of maize

• Increasing selection for desirable alleles, with a fair degree of variation as represented by the different pigments in these cobs

• Selection for different varieties by different cultures

• A modern varietal of maize as a result of dedicated breeding approaches

What do domesticated species offer?

A powerful model to study the early stages of species formation and subsequent diversification (to understand the speed of evolution and to explore how large morphological or phenotypic changes can occur over relatively short evolutionary time periods).

What is the origin of maize?

Zea mays

What is the wild ancestor of maize?

Teosinte (unusual because it doesn’t look anything like maize) (also a common name for ~4 species from the genus Zea).

How can we describe these species^?

One of them (Zea mays ssp. parviglumis) has a very close genetic relationship with the cultivated species Zea mays, and the two species are fully infertile and able to form fertile hybrids.

What are the main differences between maize and teosinte?

• Teosinte is highly branched

• Teosinte ear (female inflorescences) consist of 5-12 kernels and each kernel is wrapped in a stony hard casing (when mature, the ear breaks up and each kernel can be dispersed separately)

What is notable about the casing of teosinte ears?

The kernels are protected and they can survive the digestive tracts of animals

How do maize ears compare?

• They are larger (>500 kernels on each ear) and are naked without the stony casing

• The kernels are firmly attached, never become detached, and cannot be dispersed

The wild relatives of most crop plants look…

…similar to the human eye (maize and teosinte are an exception)

What do these morphological differences suggest^?

Because teosinte (Zea mays ssp. parviglumis) looks so different from modern corn, people originally thought it couldn’t possibly be its ancestor - but later, strong evidence from different sources proved that it actually is.

What was this evidence^?

• The inter-fertility of teosinte and Zea mays indicated there wasn o species barrier between them

• The use of DNA markers that samples a range of possible ancestors showed that Zea mays ssp. parviglumis was the closest living relative

• Karyotypes are nearly identical between teosinte and maize

Where was wheat first domesticated?

The fertile crescent (arguably the oldest of the crop domestication sites)

How can we describe the domestication history of wheat?

• It started with a number of diploid wheats (one of which was called Triticum monococcum)

• T. monococcum (or likely a close relative of T. urartu) hybridised with another species (probably T. speltoides)

• This hybridisation gave rise to emmer wheat and a tetraploid wheat (T. turgidum)

• The tetraploid emmer wheat hybridised with another diploid wheat (T. tauschii) to give the modern bread wheat (Triticum aestivum)

How can we describe T. monococcum?

This was itself cultivated as a crop and is called einkorn wheat (it is still in cultivation today but is largely considered to be a relict crop).

What are the domestication traits of domesticated wheats?

• Enlargement of the grain

• The evolution of a non-shattering phenotype via a toughened rachis that lacks abscission zones

• Threshing is required to remove the grains after harvest

• In T. aestivum there are higher amounts of the protein gluten, which give its visco-elastic properties and ensure it is useful for making various types of dough

How can we describe the domestication history of rice?

• Asian rice was domesticated from a wild progenitor (Oryza rufipogon) in China and gave rise to a subspecies or variety group called japonica

• Separately, cultures in India were also harvesting the related wild species Oryza nivara (may have been cultivating, but no evidence of domestication)

• Japonica rice began to arrive in India (likely transported along ancient silk roads)

• The introduction of japonica led to hybridisation and introgression with the local Oryza nivara or some proto-domesticated species

• Introgression of japonia led to the evolution of a subspecies indica which is now the dominant rice group grown

What does the domestication sydrome in rice include?

• The evolution of non-shattering

• The loss of red colour in the pericarp of the seed

• The emergence of a more erect growth form

• Rice has also been domesticated separately in Africa (Oryza glaberrima), but non-shattering has not evolved in this instance because the rice is not harvested by sickles but using baskets

How can we describe the domestication history of apples?

• Apples were domesticated from wild apples (crabapples, specifically Malus sieversii)

• The domestication history starts in the Tien Shan mountains of central Asia

How can we describe the migration of apples?

• Apples were probably sprad outside of central Asia by migrating humans who travelled along ancient silk roads

• As apples were moved outside of central Asia, the apples were crossed with local crab apples (e.g. Malus baccata, M. orientalis, M. sylvestris)

What can be said about Malus domestica?

Unlike many domesticated crops, M. domestica is not self-fertilising and has weak pollen incompatability mechanisms (it will accept pollen from a range of different species).

What are the consequences of this^?

It doesn’t breed true from seed (if you plant the seed of your favourite apple, it is unlikely to taste the same or as good).

What was a key development for the domestication of the apple?

Grafting, which allowed the vegetative propagation and amplification of desirable lines.

What are the roles that hybridisation can play?

• When linked with a polyploidy event, it can provide an instant speciation event that also reprodutively isolated the new crop from its wild ancestors (e.g. if a tetraploid forms it is difficult to backcross to the diploids

• It can result in the rapid addition of novel alleles and novel genetic combinations that can provide the raw material for further adaptation (beneficial for when a crop is migrated into new environments and habitats, and introgression with local species can quickly provide alleles that are already adapted to the local climatic conditions)

• It is common to see heterosis or hybrid vigour where the hybrid outperforms its parents (a function of heterozygosity)

What allows us to understand the genetic basis of the phenotypic differences between maize and teosinte?

Their ability to interbreed and produce fertile F1 and F2 allows for a QTL

How does a QTL work?

• A QTL analysis helps identify which parts of the genome influence a specific trait

• Parents are crossed to give heterozygous F1 generation, and the F1 individuals are crossed to give F2 generation

• They track how both the traits and genetic markers appear in the offspring

• If a marker shows up more often in plants with a certain trait, it’s likely near a gene affecting that trait

• This method showed that major differences between maize and teosinte, like branching, are controlled by just a few key genes

What did QTL show us regarding other differences between maize and teosinte?

• At the locus teosinte branched1 (tb1), the teosinte allele confers a highly branched plant and the maize allele a less-branched plant

• At the locus teosinte glume architecture1, the teosinte alleles confers covered grains and the maize allele confers uncovered grains

• At the locus grassy tillers 1 (gt1), the teosinte allele confers multople ears per branch and the maize allele a single ear per branch

How can we describe tb1 in more detail?

• It encodes a TCP transcription factor (there is no difference in the coding sequence of this trancription factor between teosinte and maize but its expression patterns are different)

• tb1 represses axillary meristems

• In maize, expression of tb1 is elevated cimpared to teosinte

What is the metaphor of the tape of life?

Stephen J Gould = if the tape of evolution life on earth was replayed, then it would not turn out the same, and humans would not have evolved.

As more loci are identified by QTL analyses, what is now becoming possible?

We can now compare the genetic basis of convergent traits across multiple unrelated crop species.

How can we describe seed shattering?

• The retention of seed on cereal crops occurs via the suppression of the abcission zone

• In the crop Sorghum, abcission is regulated by a YABBY transcription factir caled shattering1 (in which three mutations in domesticated Sorghum bicolor prevent shattering)

• Loss of shattering in maize is the result of mutations in the same gene

• In rice, the copy of sh1 is also involved in preventing shattering but is a minor contributing locus

How can we describe glutinous grains?

• Sticky rice is sticky because it has limited amounts of amylose and higher amount of amylopectin

• In rice, the sticky phenotype has arisen through mutations in an amylose biosynthesis gene called waxy

How can we describe loss of colour?

• E.g. white grapes evolved from purple grapes due to mutations in a MYB transcription factor that controls the anthocyanin genes that confer colour in grapes

• In the unrelated crop species Amaranthus, the white seeds have been selected for (again through mutations in a MYB transcription factor that controls antgocyanin production

What is food security?

A concept used to think systemically about how and why malnutrition arises and what can be done to address and prevent it.

What underlies this concept^?

A moral ideology that can be linked to realising the international goal of food as a human right

What are the four components to food security?

• Food availability (enough nutritious food of sufficient quality needs to be available to people for their consumption)

• Food access (individuals and households must be able to acquire sufficient food to be able to eat a healthy, nutritious diet, or have access to sufficient resources needed to grow their own food)

• Food utilisation (people must have access to a sufficient quantity and diversity of foods to meet their nutritional needs but must also be able to eat and properly metabolise such food)

• Stability (food must be available and accessible to people in an enduring way rather than temporarily)

What is the ‘perfect storm’?

It will result from shortages of food, energy, and water

What has led to global food security being at risk?

• Increases in population size and wealth

• Reductions in improvement in crop yields

• The impact of climate change on land availability

• Conflicts with demands to set land aside either to produce biofuels or to maintain biodiversity and store carbon

What happened as populations grew in wealth?

Their use of meat as a primary foodstuff increases (conversion of plant calories to animal calories has a maximum efficiency of 10%).

What’s a further contrainst on increasing crop yield?

The availability of land on which to farm

What land factors must we consider^?

• Soil type

• Elevation

• Climate

• Ardification

• Desertification

• Increased urbanisation threatens arable land

• The use of land for the production of biofuels

What is a genetic bottleneck?

A rapid reduction in the effective size of a population that may occur through a variety of causes

What do bottlenecks do?

They reduce the variation in the gene pool of a population, so that less genetic diversity is present to pass onto future generations (this can be linked to an overall reduced robustness in the population, impairing its ability to survive future challenges that may require adaptation e.g. climate change).

How can we increase genetic diversity?

Gene flow from another population or alternatively genetic diversity may slowly accumulate again

When can a bottleneck occur?

When a small group is reproductively isolated from a main population e.g. through a founder effect (founder effects can occur at a number of stages in the domestication process).

Following the initial bottleneck of domestication crops, what happened?

Diversity levels may have increased through unconscious or conscious selection in different local ecological situation, and through introgression from the wild population.

When might a second potential bottleneck occur?

When crops are introduced outside of their centre of domestication, where a smaller diversity of the domesticated crops is used as the genetic basis for the new location.

What are is the progenitor?

The progenitor wild species

What is a crop wild relative?

Wild plant taxon that has an indirect use derived from its relatively close genetic relationship to a crop.

What do crop wil relatives represent?

A vast reservoir of lost genetic diversity that our Neolithic ancestors left behind.

What might this include^?

Genes for resistance to high temperatures, pests and diseases, taste, nutrition, and yield.

What has this led to^?

The use of introgression in crop breeding (to introduce these genes).

What’s an example of introgression?

Introgressing Oryza nivara in Oryza sativa subsp indica provide extensive resistance to a pathogen called grassy stunt virus across south-east Asia.

The use of wild crop progenitors in plant breeding is based on…

…the wild relatives having been collected, being available to breeders, and not having gone extinct.

Why is introgressing diploid progenitor spcies into an already polyploid crop such as hexaploid wheat?

Because the progeny will be sterile triploids

What is one approach to overcome this?

Resynthesising polyploids

What does this entail^?

You ‘go back’ to that moment in time when the initial hybridisation happened in nature, use your knowledge of the evolutionary history of the crop species, and re-create the polyploid with the original progenitors.