Coffea arabica
Creationists insist on seeing evolution as an event, not a process happening slowly over time, but there are a few rare examples where they are right - right by accident because few of them will have the courage to study evolutionary biology or even find out what it is and what processes cause it.
In the plant world, though not exclusively, new species arising by a single event such as hybridization between two related species which goes on to form a stable population that doesn't normally interbreed with either of the parent species, are fairly common. And one of them is the Arabica coffee plant, Coffea arabica, which is the result of a chance crossing between two diploid versions of Coffea canephora and Coffea eugenioides between 600,000 and 1,000,000 years ago to produce a state of allopolyploidia.
Because this represents such a narrow genetic bottle-neck with low genetic diversity, Arabic coffee is susceptible to infections and environmental hazards such as climate variability and soil conditions, so it needs carefully controlled conditions. It may well owe its long-term survival to the fact that it was cultivated by humans.
This was discovered by researchers at the University of Buffalo led by Victor Albert, Empire Innovation Professor in the Department of Biological Sciences, College of Arts and Sciences. Their paper is published, open access, in the journal Nature Genetics and their findings are explained in a University of Buffalo news release by Tom Dinki:
The key to growing coffee plants that can better resist climate change in the decades to come may lie in the ancient past.
Researchers co-led by UB have created what they say is the highest-quality reference genome to date of the world’s most popular coffee species, Arabica, unearthing secrets about its lineage that span millennia and continents.
Their findings, published April 15 in Nature Genetics, suggest that Coffea arabica developed more than 600,000 years ago in the forests of Ethiopia via natural mating between two other coffee species. Arabica’s population waxed and waned throughout Earth’s heating and cooling periods over thousands of years, the study found, before eventually being cultivated in Ethiopia and Yemen, and then spread over the globe.
Coffee giants like Starbucks and Tim Hortons exclusively use beans from Arabica plants to brew the millions of cups of coffee they serve every day, yet, in part due to a low genetic diversity stemming from a history of inbreeding and small population size, Arabica is susceptible to many pests and diseases, and can only be cultivated in a few places in the world where pathogen threats are lower and climate conditions are more favorable.We’ve used genomic information in plants alive today to go back in time and paint the most accurate picture possible of Arabica’s long history, as well as determine how modern cultivated varieties are related to each other.
Professor Victor Albert, co-corresponding author
Department of Biological Sciences
College of Arts and Sciences
University at Buffalo, Buffalo, NY, USA.From their new reference genome, accomplished using cutting-edge DNA sequencing technology and advanced data science, the team was able to sequence 39 Arabica varieties and even an 18th-century specimen used by Swedish naturalist Carl Linnaeus to name the species.A detailed understanding of the origins and breeding history of contemporary varieties are crucial to developing new Arabica cultivars better adapted to climate change.
Professor Victor Albert.
The reference genome is now available in a publicly available digital database.
Evolved without people’s helpWhile other public references for Arabica coffee do exist, the quality of our team’s work is extremely high. We used state-of-the-art genomics approaches — including long- and short-read high throughput DNA sequencing — to create the most advanced, complete and continuous Arabica reference genome to date.
Patrick Descombes, co-author
Société des Produits Nestlé SA
Nestlé Research, Lausanne, Switzerland.
Arabica is the source of approximately 60% of the world’s total coffee products, with its seeds helping millions start their day or stay up late. However, the initial crossbreeding that created it was done without any intervention from humans.
Arabica formed as a natural hybridization between Coffea canephora and Coffea eugenioides, whereupon it received two sets of chromosomes from each parent. Scientists have had a hard time pinpointing exactly when — and where — this allopolyploidization event took place, with estimates ranging everywhere from 10,000 to 1 million years ago.
To find evidence of the original event, UB researchers and their partners ran their various Arabica genomes through a computational modeling program to look for signatures of the species’ foundation.
The models show three population bottlenecks during Arabica’s history, with the oldest happening some 29,000 generations — or 610,000 years — ago. This suggests Arabica formed sometime before that, anywhere from 610,000 to 1 million years ago, researchers say.
Coffee plants have long been thought to have developed in Ethiopia, but varieties that the team collected around the Great Rift Valley, which stretches from Southeast Africa to Asia, displayed a clear geographic split. The wild varieties studied all originated from the western side, while the cultivated varieties all originated from the eastern side closest to the Bab al-Mandab strait that separates Africa and Yemen.In other words, the crossbreeding that created Arabica wasn’t something that humans did. It’s pretty clear that this polyploidy event predated modern humans and the cultivation of coffee.
Professor Victor Albert.
That would align with evidence that coffee cultivation may have started principally in Yemen, around the 15th century. Indian monk Baba Budan is believed to have smuggled the fabled “seven seeds” out of Yemen around 1600, establishing Indian Arabica cultivars and setting the stage for coffee’s global reach today.
How climate impacted Arabica’s populationIt looks like Yemeni coffee diversity may be the founder of all of the current major varieties. Coffee is not a crop that has been heavily crossbred, such as maize or wheat, to create new varieties. People mainly chose a variety they liked and then grew it. So the varieties we have today have probably been around for a long time.
Patrick Descombes.
East Africa’s geoclimatic history is well documented due to research on human origins, so researchers could contrast climate events with how the wild and cultivated Arabica populations fluctuated over time.
Modeling shows a long period of low population size between 20-100,000 years ago, which roughly coincides with an extended drought and cooler climate believed to have hit the region between 40-70,000 years ago. The population then increased during the African humid period, around 6-15,000 years ago, when growth conditions were likely more beneficial.
During this same time, around 30,000 years ago, the wild varieties and the varieties that would eventually become cultivated by humans split from each other.
Low genetic diversity threatens ArabicaThey still occasionally bred with each other, but likely stopped around the end of the African humid period and the widening of the strait due to rising sea levels around 8,000 to 9,000 years ago.
Assistant professor Jarkko Salojärvi, co-corresponding author
School of Biological Sciences
Nanyang Technological University, Singapore, Singapore.
Cultivated Arabica is estimated to have an effective population size of only 10,000 to 50,000 individuals. Its low genetic diversity means it could be completely decimated, like the monoculture Cavendish banana, by pathogens, such as coffee leaf rust, which causes $1-2 billion in losses annually.
The reference genome was able to shed more light on how one line of Arabica varieties obtained strong resistance to the disease.
The Timor variety formed in Southeast Asia as a spontaneous hybrid between Arabica and one of its parents, Coffea canephora. Also known as Robusta and used primarily for instant coffee, this species is more resistant to disease than Arabica.
[Professor] Albert … also co-led sequencing of the Robusta genome in 2014. Albert and collaborators’ current work also presents a highly improved version of the Robusta genome, as well as new sequence of Arabica’s other progenitor species, Coffea eugenioides.Thus, when Robusta hybridized itself back into Arabica on Timor, it brought some of its pathogen defense genes along with it.
Professor Victor Albert.
While breeders have tried replicating this crossbreeding to boost pathogen defense, the new Arabica reference genome allowed the present researchers to pinpoint a novel region harboring members of the RPP8 resistance gene family, as well as a general regulator of resistance genes, CPR1.
The genome provided other new findings as well, like which wild varieties are closest to modern, cultivated Arabica coffee. They also found that the Typica variety, an early Dutch cultivar originating from either India or Sri Lanka, is likely the parent of the Bourbon variety, principally cultivated by the French.These results suggest a novel target locus for potentially improving pathogen resistance in Arabica.
Assistant professor Jarkko Salojärvi.Our work has not been unlike reconstructing the family tree of a very important family.
Professor Victor Albert.
AbstractOther examples of speciation by hybridization include:
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
Main
Polyploidy is a powerful evolutionary force that has shaped genome evolution across many eukaryotic lineages, possibly offering adaptive advantages in times of global change1,2. Such whole-genome duplications (WGDs) are particularly characteristic of plants3, and a great proportion of crop species are polyploid4,5,6,7,8,9,10,11. Our understanding of genome evolution following WGD is still incomplete, but outcomes can include genomic shock, in terms of activation of cryptic transposable elements (TEs), subgenome-partitioned gene regulation or fractionation, homoeologous exchange (HE), meiotic instability and even karyotype variation8,12,13,14,15,16. Alternatively, few or none of the above phenomena can materialize, and the two subgenomes can coexist harmonically, gradually adapting to new ploidy levels17. Regardless, the most common fate of polyploids appears to be fractionation and eventual reversion to the diploid state18.
With an estimated production of 10 million metric tons per year, coffee is one of the most traded commodities in the world. The most broadly appreciated coffee is produced from the allotetraploid species Coffea arabica, especially from cultivars belonging to the Bourbon or Typica lineages and their hybrids19. C. arabica (2n = 4x = 44 chromosomes) resulted from a natural hybridization event between the ancestors of present-day Coffea canephora (Robusta coffee, subgenome CC (subCC)) and Coffea eugenioides (subgenome EE (subEE)), each with 2n = 2x = 22. The founding WGD has previously been dated to between 10,000 and 1 million years ago20,21,22,23, with the Robusta-derived subgenome of C. arabica most closely related to C. canephora accessions from northern Uganda24. Arabica cultivation was initiated in fifteenth- to sixteenth-century Yemen (Extended Data Fig. 1). Around 1600, the so-called seven seeds were smuggled out of Yemen25, establishing Indian C. arabica cultivar lineages. A century later, the Dutch began cultivating Arabica in Southeast Asia—thus setting up the founders of the contemporary Typica group. One plant, shipped to Amsterdam in 1706, was used to establish Arabica cultivation in the Caribbean in 1723. Independently, the French cultivated Arabica on the island of Bourbon (presently Réunion)26, and the descendants of a single plant that survived by 1720 form the contemporary Bourbon group. Contemporary Arabica cultivars descend from these Typica or Bourbon lineages, except for a few wild ecotypes with origins in natural forests in Ethiopia. Due to its recent allotetraploid origin and strong bottlenecks during its history, cultivated C. arabica harbors a particularly low genetic diversity20 and is susceptible to many plant pests and diseases, such as coffee leaf rust (Hemileia vastatrix). As a result, the classic Bourbon–Typica lineages can be cultivated successfully in only a few regions around the world. Fortunately, a spontaneous C. canephora × C. arabica hybrid resistant to H. vastatrix was identified on the island of Timor27 in 1927. Many modern Arabicas contain C. canephora introgressions derived from this hybrid, ensuring rust resistance, but having also unwanted side effects, such as decreased beverage quality28.
Modern genomic tools and a detailed understanding of the origin and breeding history of contemporary varieties are vital to developing new Arabica cultivars, better adapted to climate change and agricultural practices29,30,31. Here, we present chromosome-level assemblies of C. arabica and representatives of its progenitor species, C. canephora (Robusta) and C. eugenioides (hereafter Eugenioides). Whole-genome resequencing data of 41 wild and cultivated accessions facilitated in-depth analysis of Arabica history and dissemination routes, as well as the identification of candidate genomic regions associated with pathogen resistance.
- Sunflowers: Helianthus anomalus is a species of sunflower that arose through hybridization between two parent species, Helianthus annuus and Helianthus petiolaris. This new species exhibits traits not present in either parent, such as increased drought tolerance.
- Butterflies: The butterfly species Heliconius heurippa emerged as a result of hybridization between Heliconius cydno and Heliconius melpomene. This hybrid species has distinct color patterns and behaviors compared to its parent species.
- Cichlid Fish: In Africa's East African Rift Lakes, such as Lake Malawi, hybridization between different cichlid species has led to the formation of new species. For instance, the "Mbuna" cichlids have diversified through hybridization events, giving rise to numerous distinct species.
- Hawthorn Trees: In the genus Crataegus, hybridization events between different species have contributed to the emergence of new species. For example, Crataegus × lavallei is a hybrid between Crataegus monogyna and Crataegus laevigata, exhibiting characteristics intermediate between its parents.
- Daisies: The Oxford ragwort (Senecio squalidus) is a species that arose through hybridization between two parental species, Senecio vulgaris and Senecio cambrensis. This hybrid has become established as a distinct species, exhibiting unique traits and ecological preferences. It is now common along roadsides in and around Oxford.
- London's Pride: Saxifraga × urbium, also known as London Pride or St. Patrick's Cabbage, arose from the cross between Saxifraga umbrosa and Saxifraga spathularis. Saxifraga × urbium is a popular garden plant valued for its attractive rosettes of evergreen foliage and delicate pink flowers. It exemplifies how hybridization can lead to the creation of new ornamental varieties, often with desirable traits inherited from both parent species.
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Illustrated by Catherine Webber-Hounslow.
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