New Species, More Diversity For Coffee – a Long Awaited “Breakthrough in Coffee Research”
- liberica
- 2 days ago
- 14 min read
Introduction: A Major Breakthrough in Coffee Research
In the world of coffee, constant advancements shape how we grow and enjoy our favorite brew. One of the most exciting developments recently came from a groundbreaking study on Coffea liberica, a species with much untapped potential. For years, little was known about the true diversity within Coffea liberica.
For over a century, Coffea liberica and Coffea var. dewevrei (Excelsa) have been known in the coffee world. However there was long-standing confusion, with Excelsa often considered just a variety of Liberica. A recent study published in Nature Plants has cleared up this confusion, confirming that Excelsa is, in fact, a separate species from Liberica. In an even more surprising development, the study also identifies a third species within the fromally known Liberica group, bringing the total number of recognized coffee species to 133n instead of 131. This discovery not only reshapes our understanding of coffee's genetic and ecological makeup but also highlights the promising role Coffea liberica, Coffea dewevrei (Excelsa) and Coffea Klainai could play in future coffee cultivation, especially in the face of climate change. Let’s break it down together:
What Happened
The future of the global coffee supply chain faces significant challenges, especially due to climate change. Smallholder farmers in tropical regions, who depend on coffee for income, are particularly at risk. Coffee farming mainly relies on two species: Arabica and Robusta. However, Coffea liberica, which includes Liberica and Excelsa, is becoming more important as it is increasingly cultivated in response to climate challenges. In Southeast Asia, Liberica is experiencing a comeback, while Excelsa is gaining popularity in regions like Uganda and South Sudan, where it thrives in hotter climates with less rainfall. Despite the growing interest in these species, the classification of Coffea liberica has been confusing, with conflicting views on whether it should be considered one species or more. This lack of clarity limits the species' potential for development and conservation, making it a key topic of study.
In this summary, Tobias Nicolas Seewer – Sheikh Salleh from Kebun Malaya explains and interprets the findings of the study titled “Genomic Data Define Species Delimitation in Liberica Coffee with Implications for Crop Development and Conservation,” published by A. P. Davis and colleagues. The information in this piece is based solely on the paper released on August 8th, 2025, in Nature Plants: https://www.nature.com/articles/s41477-025-02073-y. Any personal notes or insights shared at the end are clearly marked.
Main
The study reveals a revised classification for Coffea liberica, supported by genetic, morphological, and geographical analyses. It confirms that Coffea liberica should be divided into three distinct species: C. liberica (Liberica), C. dewevrei (Excelsa), and C. klainei. Previously, C. klainei was thought to be a synonym of C. liberica, but it is now recognized as its own species. This revision brings the total number of known coffee species from 131 to 133. Cameroon, now home to 18 species, has the highest number of indigenous coffee species in Africa, followed by Tanzania with 17 and Madagascar with 67.
Genetic Difference
Poligenomic analysis
The researchers used a tool called the “Angiosperms353 target capture kit” to analyze the genetic relationships between Coffea liberica and its related species. This kit allows researchers to focus on 353 specific genes found in the DNA of plants. By studying these genes, they can better understand how different coffee species are related.
How It Worked:
The researchers collected genetic data from 55 different coffee samples, then sequenced these 353 genes. They compared the DNA from different coffee species to see how much it differed. This kind of analysis helps identify whether the species are closely related or distinct from one another.
The Findings: The analysis showed that the species within Coffea liberica fall into three distinct genetic groups, or “clades”:
C. liberica (Liberica)
C. klainei
C. dewevrei (Excelsa)
These clades represent species that are genetically different from each other, meaning
they have distinct evolutionary lineages.
How Big Are the Differences?
The differences between these three species were significant enough to group them separately. The researchers used a tool called ASTRAL-III to create a "family tree" of these species based on their genetic data. The results showed that C. liberica and C. klainei are more closely related to each other than to C. dewevrei (Excelsa), but all three species are distinct. In genetic terms, this means they share a common ancestor but their genetic paths diverged long ago, leading to three separate species.
In summary, the researchers used the genetic tool to analyze key genes across these coffee species, confirming that C. liberica, C. klainei, and C. dewevrei (Excelsa) are separate species, though they share a distant common ancestor.
SNP (Single Nucleotide Polymorphism)
To explore the genetic structure and relationships of Coffea liberica, Coffea klainei, and Coffea dewevrei, the researchers looked at 2,240 SNPs (genetic markers) from the exon regions of 37 coffee samples. This allowed them to identify genetic differences between the species and better understand their evolutionary relationships.
What the Analysis Showed:
The genetic distance tree (a type of family tree based on genetic data) confirmed that the three species are distinct, supporting what was found in the earlier phylogenomic analysis. C. liberica and C. klainei are more closely related to each other than to C. dewevrei Excelsa.
Principal Coordinate Analysis (PCoA) is a technique used to visualize the genetic differences. The results clearly showed the three species separating into different groups, with C. klainei positioned between C. liberica and C. dewevrei.
STRUCTURE analysis showed that the three species form distinct genetic clusters, but there were some exceptions. For example, a few samples from C. liberica (from Nigeria and Ivory Coast) showed some genetic overlap with C. klainei, which suggests that these populations may share a common ancestry. This is likely due to historical evolution, not recent mixing between species.
What the Results Mean:
The analysis confirmed that while C. liberica and C. klainei are genetically similar, they are separate species with no recent genetic exchange. The presence of some shared genetic traits (admixture) in a few samples is due to their historical evolutionary relationship, not human-driven crossbreeding.
These findings help clarify the genetic boundaries between these species and reinforce that they are distinct but related.
In short, the SNP analysis provided additional proof that Coffea liberica, Coffea klainei, and Coffea dewevrei are separate species, with C. liberica and C. klainei being more closely related to each other than to C. dewevrei. The analysis also highlighted a small amount of genetic overlap between C. liberica and C. klainei, likely due to shared ancestry.
Physical Differences Between the Three Coffee Species (Morphological Delimitation)
The researchers examined the physical characteristics of Coffea liberica, Coffea dewevrei (Excelsa), and Coffea klainei to determine how easily they can be distinguished based on their appearance.
The Findings:
Coffea dewevrei (Excelsa): Compared to C. liberica, C. dewevrei has:
Larger leaves that are longer and broader.
More flowers and fruits per branch.
Smaller fruits with thinner pulp (the flesh around the seed) and thinner parchment (the protective layer around the seed).
Smaller seeds.
Fewer flower parts, usually with five parts per flower (compared to six to nine in C. liberica).
Coffea klainei: This species is more similar to C. liberica, but it differs in:
Inflorescences (flower clusters) that are unbranched and have fewer flowers per cluster (1–3 flowers compared to 2–6 in C. liberica).
Fruit shape, which is more ellipsoid (compared to spherical to ellipsoid in C. liberica).
How Farmers and Coffee Professionals Can Distinguish the Species:
Experienced farmers and buyers can easily tell C. liberica from C. dewevrei based on differences in leaf size and shape, as well as the size and yield of the fruit and seeds. These distinctions are consistent with the morphological data found in the study.
In short, Coffea liberica, Coffea dewevrei, and Coffea klainei can be clearly identified by their physical traits, such as leaf size, flower and fruit characteristics, and seed size. These morphological differences provide additional support for classifying them as separate species.
Mapping the Natural Habitat and Elevation of Coffee these Species
The researchers looked at data from herbarium specimens to map the natural, wild distributions of Coffea liberica, Coffea klainei, and Coffea dewevrei. They focused on removing records from cultivated or self-sown coffee plants to ensure they only included wild populations.
Geographical Findings:
Coffea liberica: Found in Upper West Africa, including Sierra Leone, Liberia, Ivory Coast, Ghana, and Nigeria.
Coffea klainei: Found in West-Central Africa, including Cameroon, Gabon, Republic of Congo, and Angola (Cabinda).
Coffea dewevrei: Found in Central Africa, including the Republic of the Congo, Cameroon, Democratic Republic of Congo, Central African Republic, South Sudan, and Uganda.
The study showed a clear separation between the regions where C. liberica is found and where C. dewevrei Excelsa and C. klainei grow naturally. Interestingly, C. dewevrei Excelsa and C. klainei share overlapping areas, suggesting their populations are more closely related in terms of their geographical distribution. In other words: the study found that only Coffea dewevrei (Excelsa) and Coffea klainei share overlapping areas. There is a clear separation between the regions where Coffea liberica is found and where Coffea dewevrei and Coffea klainei grow. Thus, C. liberica does not overlap with C. dewevrei or C. klainei in its native distribution.
Elevation Patterns:
Coffea liberica and Coffea klainei are typically found at low elevations, with average elevations of about 386 meters for C. liberica and 273 meters for C. klainei.
Coffea dewevrei tends to grow at mid-elevations with an average of 653 meters.
In short, the three species of coffee are naturally found in distinct regions of Africa, with C. liberica in West Africa, C. klainei in West-Central Africa, and C. dewevrei in Central Africa. Additionally, the species grow at different elevations, with C. liberica and C. klainei at lower altitudes, and C. dewevrei at higher altitudes.
Climate Adaptation of Coffea liberica and Coffea dewevrei Excelsa
The researchers studied the climate factors that affect the growth, yield, and health of Coffea liberica (Liberica), Coffea dewevrei (Excelsa), and Coffea klainei. They compared key climate variables such as temperature and precipitation across the natural ranges of these species.
C. liberica (Liberica) and C. dewevrei (Excelsa) were introduced to agriculture less than 200 years ago, while C. klainei remains largely undomesticated. Therefore, the study compared the natural climate conditions for these species, not specifically their domesticated growing environments. Since C. klainei is rarely cultivated, there is less data on how it performs in domesticated conditions. Thus, the study did look at C. klainei but focused more on the climate factors of C. liberica and C. dewevrei in both their wild and agricultural environments.
Findings:
When comparing climate conditions:
The average annual temperature for C. liberica is 24.6°C and for C. dewevrei Excelsa is 24.4°C.
C. liberica experiences more precipitation (simplyfied rain) during the wet season, while C. dewevrei has less precipitation but a more even distribution throughout the year
C. liberica tends to have longer and more severe dry seasons, while C. dewevrei grows in areas with shorter dry seasons and more consistent rainfall.
Precipitation refers to any form of water, such as rain, snow, sleet, or hail, that falls from the atmosphere to the Earth's surface. In the context of the study, precipitation is a key climate parameter that affects the growth and development of coffee plants. The amount and distribution of rainfall (or lack thereof) throughout the year play a significant role in determining where certain coffee species can grow and how well they thrive. For instance, some species of coffee may be adapted to areas with more rainfall, while others may be more tolerant of drought conditions or a more seasonal distribution of rain. |
Precipitation differences:
C. liberica requires higher annual precipitation (2,215 mm) compared to C. dewevrei (1,678 mm). However, C. liberica is more adapted to a seasonal rainfall pattern and may be more drought-tolerant.
C. dewevrei is found in areas with both open-canopy and closed-canopy forests and may access underground or surface water during drier months, helping it thrive in areas with lower overall rainfall.
The climate conditions for C. dewevrei allow it to grow in more varied environments, suggesting it has greater climate adaptability compared to C. liberica and C. klainei.
Comparing with Other Coffee Species:
C. liberica and C. dewevrei are adapted to warmer temperatures compared to Arabica and Robusta, and both can tolerate relatively high levels of water and show better drought tolerance than C. canephora (Robusta).
However these findings excluded the experience done by farmers in other regions of the world. To better understand how these species will perform in different climates, field trials across various locations and conditions will be necessary. This will help further explore their climate preferences and whether they can be cultivated in areas that are becoming too hot or dry for traditional coffee species like Arabica and Robusta.
In short, Coffea liberica and Coffea dewevrei Excelsa thrive under different precipitation patterns, with C. liberica needing more rain but adapted to drier seasons, and C. dewevrei growing in more stable climates with shorter dry seasons. Furthermore C. dewevrei shows strong drought tolerance, making it more adaptable to varying climates.
Changing the Status Quo and What Does This Mean
Breeding and Cultivation Potential of Liberica and Excelsa
In this study, researchers delved deep into both the genetic and physical characteristics of Coffea liberica (Liberica) and Coffea dewevrei (Excelsa). To uncover the distinctive traits of these species and explore how these could be harnessed to improve coffee breeding and development. By studying their genetic makeup and morphology, the team was able to identify key differences between these two species — differences that could play a crucial role in shaping the future of coffee farming.
Genetic Profiles and Physical Traits:
C. liberica and C. dewevrei not only have distinct genetic profiles, but these differences are also reflected in their physical traits. For instance, they vary in leaf shape, fruit size, and seed characteristics, all of which can influence the ease of cultivation, harvest, and processing.
Superior Yields of Excelsa:
When it comes to productivity, Excelsa (C. dewevrei) stands out. It produces a higher yield per tree, with more fruits, thanks to its thinner pulp and parchment. These traits make Excelsa easier to process, aligning it more closely with the handling methods used for Arabica and Robusta. Moreover, its smaller seeds are particularly better-suited for the after harvest processes etc.
Flavour and Market Differentiation:
One of the most exciting aspects of these new species is their distinct flavour profiles. The contrasting tastes between Liberica and Excelsa open up opportunities for market differentiation, giving consumers more diversity, more choices and allowing producers to target specific markets based on taste preferences.
Climate Adaptation and Agricultural Potential:
C. liberica is more adapted to lower elevations with higher rainfall and longer dry seasons, whereas Excelsa flourishes in higher elevations with a more consistent rainfall pattern. This makes each species uniquely suited to different climates and growing conditions. As climate change continues to affect traditional coffee-growing regions, these two species are emerging as valuable alternatives for farming areas where Arabica and Robusta are struggling to thrive.
In fact, Excelsa has already started replacing Robusta in places like Uganda, where shifting climate patterns have made traditional robusta farming more challenging.
Breeding Potential:
One of the most exciting possibilities highlighted by the study is the potential for hybridization between Coffea liberica and Coffea dewevrei (Excelsa). These two species share a close genetic relationship, which makes crossbreeding a promising avenue. Reports suggest that hybrids of these two species could bring greater vigor and higher yields, but genetic confirmation is still needed to validate these findings.
This discovery paves the way for the development of interspecies breeding programs that could significantly improve coffee production. By combining the strengths of both species, these programs could create more resilient coffee varieties, better suited to the challenges posed by climate change and shifting environmental conditions.
It isn’t 1% but 0.01% - Current Global Status:
It’s important to correct a common misconception about the global role of Coffea liberica and Coffea dewevrei. Historically, it was assumed that Liberica made up around 1% of global coffee production—a figure based on data from the late 19th century when C. liberica was one of the most important coffee varieties alongside Arabica. By the mid-20th century, however, C. liberica was reported to account for about 1% or less of global coffee production.
Today, however, C. liberica and C. dewevrei represent far less than 1,000 metric tons of coffee, making up only 0.01% of global coffee exports. Despite this, their cultivation is on the rise, particularly in new regions like Uganda, South Sudan, India, and Southeast Asia. This expansion is a sign of these species' growing importance as viable alternatives for coffee farming in areas where Arabica and Robusta face climate challenges, providing farmers with the opportunity to diversify and sustain coffee production.
Extinction Risk: Protecting Coffee’s Biodiversity
The revised taxonomic classification and updated understanding of the indigenous distribution of Coffea liberica shows a significant reduction in its range. The extent of occurrence (EOO) for C. liberica has decreased by an alarming 94.8%, from 6.8 million km² to just 352,310 km². Similarly, the area of occurrence (AOO), or the actual area where the species is found, has dropped by 92.9%, from 736 km² to only 52 km².
Under the current IUCN Red List assessment, C. liberica is listed in 17 countries, but the updated species delimitation reduces this to just five: Sierra Leone, Liberia, Ivory Coast, Ghana, and Nigeria. Deforestation and land-use changes have significantly impacted its populations in these regions, with most of the coffee’s historical range now being fragmented or extirpated. For example, in Sierra Leone, recent searches failed to locate C. liberica in areas where it was previously recorded, like Kasewe Hills, where it was last seen in 1913.
In light of these findings, the species may need to be reclassified from its current status of ‘Least Concern’ to ‘Vulnerable’ under IUCN criteria. In contrast, C. dewevrei (Excelsa) is still classified as ‘Least Concern’ despite facing some forest loss.
C. klainei also faces a serious risk, with an AOO of just 76 km², which may qualify it for a ‘Vulnerable’ status as well. However, more research is needed before any final assessment can be made.
In summary, stronger conservation efforts are crucial to prevent the decline of all three species, especially C. liberica, to secure their role in global coffee sustainability and biodiversity.
Personal Notes by Kebun Malaya; Written by Tobias
When I first read the study reclassifying Coffea liberica into three distinct species, I felt genuinely thrilled. This wasn’t just a surprise; it was something I had been anticipating for a while. The separation was long overdue, especially for those of us who work with Liberica and Excelsa. The new species classification, which now includes C. klainei, brings clarity and emphasizes the diversity within the coffee world. It's essential for research and cultivation, allowing us to approach each species with a better understanding of their unique potentials. It’s not just about splitting them apart – it’s about unlocking new opportunities and recognizing their worth individually.
For coffee farming, especially in Southeast Asia, this study will offer a chance for better cultivation strategies. With clearer distinctions between these species, farmers can target the specific growing conditions each one thrives in. This clarity could lead to more precise farming practices, which is especially important in the face of climate change. As these species thrive at different elevations, we can now make informed decisions about where to plant them, opening up new potential regions for coffee cultivation, particularly in places that were previously unsuitable for coffee production due to climate shifts.
For Kebun Malaya, these findings align perfectly with how we’ve always viewed Liberica and Excelsa. We've always recognized their differences, even when the industry didn't, and we’ve made efforts to highlight these distinctions. Now, with a more diverse portfolio, we can further explore the potential of each species, giving us more flexibility in developing our offerings. The clarity this study brings will allow us to better prepare for future challenges and give us a deeper understanding of the unique characteristics of each coffee type.
The coffee industry, especially in terms of climate change, can benefit immensely from this study. While it's not the sole solution to climate issues, these species, with their adaptability to different climates, provide an important piece of the puzzle. It’s a move toward greater diversity, which I believe is the key to ensuring the future of coffee. Arabica and Robusta have their roles, but the introduction of more resilient species could help us navigate the impacts of climate change on coffee farming.
Finally, I hope the coffee community takes away the importance of understanding the differences between Liberica, Excelsa, and the newly defined C. klainei. This study provides a foundation for better post-harvest processing machinery, more informed breeding programs, and opportunities for farmers to improve yield and quality. For consumers, it brings an exciting variety of flavors, and for farmers, it could mean more opportunities and greater job security in an evolving coffee world.