Global change

What were the impacts of early farming?

Although early farming led to poorer health, it allowed for permanent settlement near reliable food sources (which enabled population growth and societal complexity)

It allowed for larger populations, fostered technological advancement, social hierarchies, and political organisation

It allowed farming societies to outcompete and displace hunter-gatherers

What is domestication?

Domestication is the process of speciation or species transformation that occurs 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 (usually but not exclusively for food)

Domestication represents a mutualistic, co-evolutionary relationship, where plants adapt to human environments
This increases human survival while the plant species gain fitness, population size, and global distribution

Insects can domesticate species as well
E.g. attine ants obligately depend on the cultivation of fungus gardens for food (when a daughter queen leaves the nest she must carry in her mouth a small amount of fungus so she can start her own garden)
E.g Philidris nagasau ants domesticate several species of the plant genus Squamelleria by planting their seeds in tree crevices and selecting sunny sites to maximise plant growth

What is the origin and evolution of domestication?

Centres of origin for domesticated species are characterised by the presence of both wild and domesticated species and high varietal diversity

Domesticated plants spread mainly through the expansion of farming populations - this spread was faster along east-west axes than north-south axes because regions at the same latitude share similar climates (reducing the need for crops to adapt to new conditions)

Crop plants have multiple evolutionary origins e.g. domestication hotspots are found in specific plant lineages

What are domestication syndromes?

A common set of traits which are shared across domesticated species and evolved due to human selection for productivity and ease of cultivation e.g. larger seeds and fruits, reduced branching, loss of toxins and spines, synchronised germination, reduced seed dispersal and shattering

What are the stages of domestication?

Stage 1 - onset of domestication, humans harvest wild plants with favourable traits

Stage 2 - increase in frequency of desired alleles, yield and phenotype diversity increases

Stage 3 - adaptation of populations to new environments, different crop varitieties are selected for in different environments and cultures

Stage 4 - deliberate breeding

This shows how domestication progressed from acidental to intentional crop development

How can we describe the domestication of maize?

Maize originated from its wild ancestor Teosinte (despite their very different appearances)

Teosinte has small, hard-coated kernels that disperse easily, while maize has large ears with many naked kernels that stay attached

Genetic evidece, including their ability to interbreed, DNA markers, and similar karyotypes, show that Zea mays spp. parviglumis is the closest wild ancestor of maize

How can we describe the domestication of wheat?

Wheat originated from the Fertile Crescent and its domestication involved complex hybridisations

Wild diploid wheats like T. monococcum hybridised with species such as T. speltoides to form tetraploid emmer wheat T. turgidum (which later hybridised with T. tauschii to give modern bread)

Domesticated wheats show key traits like larger grains and non-shattering ears

How can we describe the domestication of rice?

Asian rice was first domesticated in the Yangtze river in China from the wild progenitor Oryza rufipogon to produce japonica subspecies

Japonica rice spread to India where it hybridised with local Oryza nivara, leading to the evolution of the indica subspecies (the most widely grown rice)

Key domestication traits in rice include non-shattering seeds, loss of red colour, and erect growth

African rice was harvested separately and it lacks non-shattering due to different harvesting methods

How can we describe the domestication of apple?

The domestic apple was first domesticated from wild crabapples in central Asia

Apples spread westward and hybridised with local crabapples across Eurasia

Unlike many crops, apples are not self-fertilising and do not breed true from seed, so grafting became essential for propagating desirable varieties

What is the role of hybridisation and polyploidy in domestication?

When hybridisation is linked with polyploidy it can provide an instant speciation events that also reproductively isolates the new crop from its wild ancestors e.g. when a tetraploid species is formed it is difficult to then backcross to the diploids

Hybridisation can introduce novel genetic variation, aiding adaptation to new environments, especially through introgression with local species

Hybridisation can lead to heterosis or hybrid vigour, where the hybrid outperforms its parents

What can be said about whether traits are caused by a few genes with large effects or many genes with smalle effects?

Maize and teosinte can interbreed so we can use QTL analysis to identify genomic regions associated with specific traits, and studies found that major differences, like plant branching could be traced to a few genomic regions (a small number of genes with large effesct play a role in domestication)

E.g. tb1 (teosinte branched1) affects plant branching via changes in gene expression
tga1 (teosinte glume architecture1) influences grain casing
gt1 (grassy tillers1) affects the number of ears per branch

Recent studies using genome sequencing also show that many genes also exhibit signs of selection (many small effects contribute cumulatively to other traits)

What can be said about convergent evolution in domestication?

It shows that different species under similar selection pressures, can evolve similar traits (domestication syndromes) and by identifying the genes behind these traits, researchers can investigate whether unrelated crops have evolved similar genetic changes

Similar genes often underlie convergent traits across unrelated species

• Branching = tb1 suppresses branching in maize and also affects millet and barley

• Seed shattering = sh1 gene regulates seed abcission in Sorghum (via mutations), maize (via gene fusion and inactivation), and rice (along with the effect of other genes)

• Glutinous grains = waxy gene reduces amylose and increases stickiness and has independently mutated in rice, millet, and barley

• Colour = loss of pigmentation is due to mutations in MYB transcription factors affecting grape colour and white seed colour

What can be said about global food security?

Food availability = sufficient nutritious food must exist

Food access = people must be able to obtain or grow in

Food utilisation = food must meet nutritional needs and be metabolised effectively

Stability = these conditions must be consistent over time

Concerns regarding this are due to population growth, increasing wealth (which drives demand for resource-intensive meat), climate change, land degradation, and competition for land use

Yield growth is now slowing

Land availability is constrained by urbanisation, land degradation, biofuel production, and climate change

What is the role of bottlenecks?

A genetic bottleneck is a reduction in population size that leads to loss of genetic diversity, reducing a population’s ability to adapt to future challenges

Diversity may recover slowly through gene flow from other populations

In the domestication bottleneck, only a small portion of wild species’ genetic diversity was originally selected by early farmers, limiting the gene pool of the cultivated crop

Additional bottlenecks can occur during dispersal, when crops are introduced to new regions using only a subset of existing diversity

These processes have led to reduced allelic diversity in modern crops, making it harder for breeders to develop new varieties with important traits like disease or pest resistance

Why are ancestral progenitors and other Crop Wil Relatives (CWRs) important?

Comparing modern crops to their wild progenitors helps uncover key domestication traits

Many crops remain inter-fertile with their wild relatives, which enables researchers to study the genetic basis of these traits

Identifying progenitors also has practical applications, as it offers a way o reintroduce genetic diversity lost during domestication bottlenecks

How can we use wild relatives in crop improvement?

CWRs are undomesticated plants closely related to crops, holding valuable genetic diversity during domestication

These offer genes for drought and heat tolerance, disease and pest resistance, and traits related to nutrition, yield, and flavour

Breeders often use CWRs through introgression e.g. resistance to grassy stunt virus in rice from Oryza nivara, and disease resistance in tomatoes

Many CWRs are under threat from climate change, habitat loss, nitrogen deposition, and invasive species
Identifying and conserving wild relatives, including seed banking, is essential for ensuring they remain available for future crop improvement

Why do polyploids present major breeding challenges?

Triploid crops are sterile and propagated vegetatively, making them vulnerable due to low genetic diversity

In polyploid crops, crossing them with diploid relatives results in sterile triploid offspring

A solution is to resynthesise polyploids by recreating original hybridisation events using the crop’s ancestral progenitors e.g. crossing T. turgidum with T. tauschii to mimic the natural formation of hexaploid wheat
These sterile crops can be treated with colchicine, a chemical that doubles chromosomes and restores fertility
The resulting synthetic polyploids can then be bred with modern varieties, allowing new genetic diversity to be introduced

What are orphan crops?

Orphan crops are lesser-known, regionally important plants that are not widely traded but are crucial for local diets and the incomes of smallholder farmers

They have undergone little domestication or improvement, so there is growing interest in accelerating the domestication of these underutilised crops to diversift agriculture and improve global food security

How can we speed up domestication?

Researchers can understand domestication syndrome traits and their sequence of emergence and they can identify homologous genes that control similar traits across different crops

Some domestication traits are caused by the same genes in different species and by identifying these homologous genes, scientists can use them as candidate genes in related, undomesticated crops to guide genetic changes

Traditional crop breeding takes a long time due to the randomness of recombination and the difficulty in removing unwanted genetic material

Modern genome editing tools like CRISPR/Cas allow precise, targeted changes to domestication genes, enabling rapid domestication of orphan crops e.g. scientists used CRISPR/Cas9 on the wild tomato to modify six known domestication genes

How can we engineer nitrogen fixation in cereal crops?

Nitrogen fixation is carried out by symbiotic bacteria in the roots of certain flowering plants, but not in cereal crops, which rely heavily on fertilisers

Although cereals diverged before nodulation evolved, evidence suggests they may still possess the ancestral predisposition to support engineered nitrogen fixation

Nodulation has evolved independently multiple times, showing convergent evolutionary pathways that might be mimicked through genetic engineering

Genes used in nodulation often overlap with those in arbuscular mycorrhizal symbiosis (a more widespread trait found in cereals)

Key hormones involved in root development also regulate nodulation, which further imply that cereals already possess parts of the required machinery

Engineering nitrogen fixation in cereal plants may be possible by reactivating or modifying these ancestral genetic pathways

What is the difference between taming and domestication?

Taming = a learned behaviour in individual animals, where they become accustomed to humans

Domestication = an evolutionary process (which often involves human control)

What is notable about the domestication of animals?

Their origins aew mainly in southern Eurasia - mainly around the Fertile crescent (not in Africa, as was the origin of humans)

We can gather evidence for the time and place of domestication using zooarchaeology (e.g. body size or sexual dimorphism changes)

Genetic evidence from ancient DNA can also help but hybridisation with wild relatives can obscure timelines and origins

How can we explain the main origin of domestication being in Eurasia?

Anna Karenina principle = many specific biological and ecological traits must align for domestication to be possible (and failure in any one trait makes domestication unlikely) and Eurasia had many species that met these requirements

Animal domestication likely began accidentally

• Commensal pathway - animals like dogs and cats approached humans, attracted by waste or shelter

• Prey pathway - humans began managing hunted animals - leading to control over breeding

The Fertile crescent provides suitable conditions for these key traits to evolve

(Riahi, 2022) offers an alternative hypothesis and suggests that extinction risks influenced domestication
In Africa, long-term co-evolution made prey too wary to domesticate
In the Americas, humans cause extinction too quickly for domestication
In Eurasia, animals were naive enough to manage, but not as vulnerable that they vanished before domestication even began

What does domestication select for?

It primarily selects for tameness, but other traits will also evolve (domestication syndromes)

These other traits appeared as side effects of selecting for tameness, possibly due to changes in neural crest cells during development (a group of cells that influence the formation of the skull and parts of the nervous system)

Genomic studies have identified which genes are linked to these changes
E.g. in pigs, the MC1R gene shows camoflague-preserving mutations in wild boar, but many new colour mutations in domestic pigs due to relaxed selection and later artifical selection

Domestication starts with selecting tame behaviour, but also produces many unexpected changes

What was the silver fox experiment?

This was an experiment that selected only for tameness but showed that many traits of the domestication syndrome also emerged, suggesting that these traits don’t require direct selection

One theory is that selecting for tameness unintentionally selects for neoteny (retention of juvenile traits)

Another theory suggests that reduced function of neural crest cells underlies the syndrome (these features are linked to changes in neural crest cells)
Althought this ideas has genetic support, these domestication syndrome traits are inconsistently expressed and mostly vomplete only in dogs

Have humans domesticated themselves?

Some argue that humans have self-domesticated, evolving traits like reduced aggression, smaller teeth, and more social cooperation

This may have happened not through external control, but by natural selection favouring tamer, more cooperative individuals

These changes may not reflect domestication, just broader social evolution

Some argue that humans might still be wild, but that they have just developed strong emotional control to function in complex societies