# Architectural singularities in wild Coffea species: integrated morphological perspectives for climate-resilient coffee cultivation

Rickarlos Bezandry, Hery L T Ranarijaona, Marie Elodie Vavitsara, Sylvie Sabatier, Romain Guyot, Artemis Anest

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## To cite this version:

Rickarlos Bezandry, Hery L T Ranarijaona, Marie Elodie Vavitsara, Sylvie Sabatier, Romain Guyot, et al.. Architectural singularities in wild Coffea species: integrated morphological perspectives for climate-resilient coffee cultivation. Plant ecology & diversity, 2026, 10.1080/17550874.2026.2637118. hal-05522821

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Architectural singularities in wild *Coffea* species: integrated morphological
perspectives for climate-resilient coffee cultivation

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Rickarlos Bezandry¹,², Hery L. T. Ranarijaona², Marie E. Vavitsara², Sylvie Sabatier³,
Romain Guyot⁴ and Artemis Anest³*

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¹ Ecole Doctorale sur les Ecosystèmes Naturels (EDEN), Mahajanga, Madagascar; ²

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Faculté des Sciences de Technologie et de l'Environnement (FSTE), Université de
Mahajanga, Mahajanga, Madagascar; ³ AMAP, CIRAD, CNRS, INRAE, IRD, Univ

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Montpellier, Montpellier, France; 4 UMR DIADE, IRD, CIRAD, Université de Montpellier,
Montpellier, France

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*Corresponding author. Email: artemis.anest@umontpellier.fr.com

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ORCIDs

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Rickarlos Bezandry: 0000-0002-1316-9791

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Hery Lisy Tiana Ranarijaona: 0000-0002-7492-4850

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Romain Guyot: 0000-0002-7016-7485

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Marie Elodie Vavitsara: 0000-0001-9721-5689

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Artemis Anest: 0000-0002-6661-4406

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24 **Abstract**

25 **Background:** Global coffee production faces increasing threats from climate change, including rising
temperatures, prolonged droughts, and the spread of diseases. Wild coffee species, notably those
26 growing in seasonally highly arid environments in Madagascar, represent a critical genetic resource to
27 address these challenges. Understanding adaptive traits allowing these species to establish into arid
28 environments is essential to guide breeding strategies for creating resilient coffee varieties.
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30 **Aims:** We identified structural strategies likely to explain drought tolerance in wild Malagasy *Coffea*
31 species.

32 **Methods:** We used architectural analysis to describe three Baracoffea species, *Coffea ambongensis*,
33 *C. bissetiae*, and *C. boinensis*, and compare them to known cultivated Coffee. Structural and functional
34 traits were measured across developmental stages.

35 **Results:** Our results suggest that, in addition to rhythmic growth and terminal flowering on shoots,
36 Baracoffea species possess unique architectural characteristics including a complex architectural unit
37 made of four different stem types, reflecting a high level of functional specialisation. Species-specific
38 developmental strategies reflect different pathways into edifying plant architecture mainly depending
39 on primary and secondary growth trade-offs.

40 **Conclusion:** These findings highlight the architectural diversity of Baracoffea, identify potentially
41 important drivers of ecological adaptation through development pathways and therefore highlight the
42 potential of this group of species for breeding climate-resilient coffee varieties.

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44 **Key words**

45 Baracoffea, drought adaptation, Madagascar, plant architecture, plant functional trait

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48 **Introduction**

49 Coffee is a globally significant commodity and the cultivation of which is increasingly threatened by
50 climate change (Figure 1; Bracken et al. 2021, 2023): rising temperatures, altered precipitation
51 patterns, and extreme weather events impact coffee growth, development, and flavor (Girma 2023).
52 These changes are shifting suitable coffee-growing regions, with highland areas for *Coffea arabica* L.
53 becoming too warm and lowland regions for *Coffea canephora* Pierre ex A.Froehner experiencing
54 prolonged droughts and severe weather stress (Davis et al. 2012; Hamon et al. 2017). Projections
55 suggest a 50% reduction in coffee-suitable land by 2050 globally, with Indonesia expected to lose over
56 half of its Arabica-suitable area (Baker and Haggar 2007; Davis et al. 2012; Ramadhillah and Masjud
57 2024). Mitigation efforts, such as shade plantations and soil moisture control are commonly employed
58 (Ramadhillah and Masjud 2024), however, the widespread adoption of these strategies is limited by
59 financial, environmental, and technical challenges, particularly for smallholder farmers.

60 While trying to address these challenges, coffee breeding programs remain constrained by the narrow
61 genetic base of cultivated varieties. The two cultivated coffee species, *Coffea arabica* and *Coffea
canephora*, belong to a single evolutionary lineage, hereafter referred to as the Mascarocoffea group.
62 *Coffea arabica*, for instance, originated from a small genetic group of individuals (primarily in Ethiopia
63 and Yemen) limiting its ability to adapt to new environmental stresses (Rakotomalala et al. 1992; Kang
64 et al. 2014). Similarly, while *Coffea canephora* exhibits greater genetic diversity, its adaptive potential
65 is still insufficient to face the magnitude of the effects of climate change. These genetic limitations
66 emphasise the critical need for alternative sources of biodiverse material (Guyot et al. 2016, 2020,
67 Bezandry et al. 2021a,b, 2023).
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69 Wild coffee species, particularly those endemic to Madagascar, represent a promising solution to
70 these challenges. Among them, the Baracoffea group (Figure 2) forms a sister clade to the
71 Mascarocoffea group. It comprises nine species, does not include any cultivated coffee species, and
72 express impressive drought tolerance, high-temperature resilience, pest resistance (Davis et al. 2008)
73 and low fertility soils tolerance (Davis and Rakotonasolo 2008; Bezandry et al. 2021). Although these
74 species cannot be directly incorporated into current breeding programs for cultivated coffee due to
75 their poor beverage quality attributes and distant phylogenetic position, the adaptive traits they
76 express constitute an invaluable source of knowledge. However, the potential of these species
77 remains poorly studied, especially due to limited interest associated with limited conservation efforts,
78 despite their high risk of extinction (Myers et al. 2000; Chadburn and Davis 2018) caused by
79 deforestation in Madagascar and the absence of *ex-situ* conservation programmes such as seed banks
80 or botanical gardens (Ormsby and Kaplin 2005; Davis and Rakotonasolo 2021).
In addition to broadening the potential spectrum of mobilisable genetic resources, protecting these species is also crucial to maintain functional diversity locally. Indeed, Davis et al. (2005) have identified that Baracoffea species display different morphological characteristics from those observed in cultivated *Coffea* and regional congeneric *Coffea* species, particularly long shoots with lateral flowering and short shoots with sympodial branching. These documented differences indicate that Baracoffea species follow a distinct organisation compared to that in other *Coffea* taxa. Such divergence suggests that additional, yet unexplored aspects of their structure may also differ, potentially bearing ecological or adaptive significance, which could therefore be analysed more deeply through the lens of plant architecture.

Plant architectural analysis is used to describe the branching rules that characterize the species-specific whole plant form, and the step through this form establishes during plant development (Hallé et al. 1978; Caraglio and Barthélémy, 1997, Barthelemy and Caraglio 2007). Within all the stems produced by a plant, this conceptual framework makes it possible to identify distinct “axis categories”, defined as groups of stems that share similar morphological features and associated biological functions and costs, and that clearly differ from stems belonging to other categories (Edelin, 1984, 1990). For example, “long shoots” require a high investment in wood while providing spatial exploration, while plants’ light acquisition efficiency is exponentially increased by the presence of specialised “short shoots” for which woody cost is neglectable (De Haldat et al. 2023). Plants, as sessile organisms, grow under constraints of resource acquisition, reproduction and defence against local disturbances (Lavorel et al. 1997). Millions of years spent facing these ecological constraints selected specific architectures reflecting what is the most challenging to grow, survive and reproduce. As a result, woody plants express a variety of architectural strategies through different branching patterns and thus that strongly varies in terms of functional capacity (Laurans et al. 2024). Notably, recent studies have demonstrated that modularity of plant architecture plays a key role in plant adaptation to survive in arid conditions: Anest et al. (2021) have shown *Euphorbia* species (Euphorbiaceae) growing in deserts evolved a particular capacity that allows individuals to occasionally sacrifice specific modules of the whole plant in order to ensure the survival of the genet when water availability becomes extremely limited. These findings suggest that trait associations at the whole plant scale hold many keys to improve our understanding of functional adaptations, nobility to drought tolerance, in plants.

While the cultivation of *Coffea* species is a major preoccupation in the context of accelerating ecological and climatic change (Figure 1; Bracken et al. 2021, 2023) until now, only limited attention has been given to plant architectural diversity in the *Coffea* genus, and how this could play a role in the distribution of species and ecological adaptation to extreme conditions. In this article, we
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addressed this gap by exploring the architectural and potentially adaptive traits of Baracoffea species that might explain their tolerance to extremely dry conditions, and thus their potential for future coffee improvement strategies.

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We hypothesised that Baracoffea species, in addition to exhibiting the previously documented morphological differences from cultivated *Coffea* (e.g., long shoots with lateral flowering and short shoots with sympodial branching), possess unique functional characteristics expressed through specific architectural traits of the entire plant. These traits, reflecting the organisation and differentiation of axes resulting from branching processes, may reveal adaptive strategies to the highly constrained environments in which these species evolved. By characterising the architecture of three Baracoffea species (*Coffea ambongensis* Leroy ex Davis & Rakotonasolo, *C. bissetiae* Davis and Rakotonasolo, and *C. boinensis* Davis & Rakotonasolo) and comparing them to existing architectural descriptions of other *Coffea* species, we aimed to identify structural traits potentially relevant for functional adaptation, which could inform strategies to enhance the resilience of cultivated coffee to climate-induced stresses.

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## Materials and methods

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### Study sites and environmental context

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The study was conducted in the north-western Boeny Region of Madagascar, part of the western phytogeographical domain (Figure S1; Guillaumet and Koechlin, 1971). This region is characterised by seasonally dry tropical forests with predominantly deciduous vegetation (MNP 2025). Water availability is the primary limiting factor for plant development in this area. The climate is tropical, dry and hot, strongly influenced by the monsoon.

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The study focused on two sites: Ankarafantsika National Park (PNA; longitude 46.57° to 47.28°; latitude -16.00° to -16.33°) and the Antsanitia forest (longitude 46.4° to 46.43°; latitude -15.55° to -15.58°. These sites were chosen for their contrasting ecological conditions and the presence of the Baracoffea species under study (Davis and Rakotonasolo 2008; Bezandry et al. 2021a).

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Ankarafantsika (Figure S1), spanning 136,513 hectares, comprises primary and secondary dry forests located 115 km south of Mahajanga. Mean annual precipitation for the Ankarafantsika site was obtained from WorldClim v2.1 (Bio12; baseline 1970-2000) and compared to data from MadaClim (2023). Extracted values (2.5' resolution) were approximately 1,450-1,600 mm yr⁻¹ (WorldClim v2.1; Fick and Hijmans 2017; MadaClim 2023). The Park experiences two distinct seasons: a rainy season (November-April), with peak rainfall exceeding 500 mm in January (NASA POWER 2025), and a dry season (May-September), with rainfall as low as 5 mm in August. Average temperatures range from 22°C during the coolest months (June, July) to 29°C in October-December. Soils are predominantly

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sandy, derived from parent rock degradation, and prone to severe erosion (FAO 2025). Vegetation includes seven natural habitat types, such as dry deciduous forests, riparian forests, and xerophilous thickets, hosting over 830 plant species (443 genera and 111 families) with a 90% endemism rate (MNP 2025).

The second site, Antsanitia forest (Figure S1), represents degraded coastal forests and savannas. It covers 1,385 ha and was designated as a national reforestation reserve in 1955. Mean annual precipitation for the Antsanitia site (2.5' resolution) was approximately 1,250-1,350 mm yr⁻¹ (WorldClim v2.1; Fick and Hijmans 2017; MadaClim 2025). Similar to PNA, Antsanitia has a six-month-long rainy season with peak rainfall above 400 mm in January (NASA POWER 2025), and a dry season with monthly precipitation between 6-10 mm. Temperatures range from 24°C (July) to 28°C (October-December). The vegetation of Antsanitia includes coastal mangroves, savanna woodlands, and dry deciduous forests with drought-adapted species with around 68.6% being endemic (Rakotonandrasana et al. 2017, MNP 2025). Soils range from sandy-clay to sandy-loam textures (FAO 2025).

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## Species selection and sampling strategy

This study focused on three species of the genus *Coffea* from the Baracoffea group (Davis and Rakotonasolo 2008): *Coffea ambongensis*, *C. bissetiae*, and *C. boinensis* (Figure 2), naturally distributed across the study sites. These species were selected for their accessibility, their shared general traits with other Baracoffea species (such as deciduous leaves and terminal flowering), and their distinct ecological habitats.

*Coffea bissetiae* is typically found in shaded understories, whereas *C. boinensis* occupies intermediate habitats with moderate light exposure. *Coffea ambongensis* mostly grows in open areas, making it an ideal candidate for studying adaptations to arid conditions (Bezandry et al. 2021a,b).

*C. ambongensis* is found in the coastal and shrub forests of western Madagascar, particularly in Mahajanga Province (districts of Mahajanga II and Soalala). It grows on white sandy substrates at elevations of 0-30 m and is likely to flower and fruit between October and March. *C. bissetiae* is distributed along the western coast, in the districts of Marovoay, Mahajanga II, and Boriziny. It thrives in seasonally dry, deciduous forests on sandy or lateritic soils, at elevations of 10-240 m. *C. boinensis* is restricted to Ankarafantsika National Park, in seasonally dry, deciduous forests on white sandy soils at elevations of 170-210 m.

Observations of individuals from the three species were conducted based on their theoretical stages of maturity, classified by branching order (Andrianasolo 2012). Stage 1 represents unbranched individuals, Stage 2 includes individuals with one level of branching, Stage 3 features individuals with

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two levels of branching (branching on branching), and Stage 4 corresponds to adults with four orders of branches and that express sexuality. Selection criteria prioritised healthy individuals, free of visible damage, to ensure accurate representation of natural growth.

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Given the protected status of the species, non-destructive methods were employed, focusing on the observation and sketching of morphological traits. Efforts were made to examine as many individuals as possible across different locations and developmental stages to generate a comprehensive representation of each species.

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## Architectural analyses

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For each developmental stage, at least three individuals were observed, sketched, and photographed.

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Observations were conducted *in situ* in forest environments, both in Ankarafantsika and in Ankarafantsika. The architectural analyses were conducted following Sabatier (1999), Heuret et al. (2000), and Barthélémy and Caraglio (2007) to identify:

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1. The different axis categories present in each of the three Baracoffea species. The number of axis categories is generally indicative of functional specialization within a plant's body, as a higher number of axis categories reflects greater compartmentalization of functions (Caraglio and Barthélémy, 1997).

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Axis categories were identified using key morphological descriptors used to characterize whole-plant architecture (see Figure S2), including: (1) phyllotaxy, defined as the arrangement of leaves on each stem; (2) growth direction (vertical or horizontal) and symmetry (radial or bilateral) of each axis; (3) meristem activity, i.e. whether the meristem grows throughout the plant's life or dies after a defined period; (4) growth rhythmicity, referring to yearly interruptions in meristem activity; (5) spatial branching patterns, i.e. the location of branches on each stem; (6) temporal branching patterns, i.e. the timing of branch initiation on each stem; and (7) sexuality position, whether lateral or terminal on each stem when present (see Barthélémy and Caraglio 2007 for details and Figure S4). After being identified, axis categories were named from C1 (axis category 1) to C4 (axis category 4).

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2. The Architectural Unit of each species that characterises how each category is arranged within the plant body.

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3. The quantitative variations between each category across development stages including internode characteristics (length, diameter, number of internodes), leaf dimensions (length, width), and total height and basal diameter (Tables S1-S4).

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Additionally, the architecture (the axis categories descriptions and the structure of the architectural unit) of the two cultivated species, *C. arabica* and *C. canephora*, have been retrieved from the work of Hallé (2019) and Sabatier et al. (2011, 2019) for further interspecific comparison with the Baracoffea species.

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218 **Functional trait measurements**

219 Between March and July 2021, 65 individuals were sampled across the two sites. This included 25
220 individuals of *C. boinensis*, 26 of *C. bissetiae*, and 14 of *C. ambongensis*.

221 A total of 317 dry seeds were measured and weighed, including 222 seeds of *C. boinensis* sampled
222 from 12 individuals (ca. 20 seeds per individual), 69 seeds of *C. bissetiae* from 12 individuals (ca. 5
223 seeds per individual), and 26 seeds of *C. ambongensis* from eight individuals (ca. four seeds per
224 individual). The number of individuals sampled and seed collected for each species was based on the
225 availability of mature, seed-producing individuals in the population.

226 For foliar analysis, 960 dry leaves were measured, weighed, and scanned, distributed as follows: 300
227 leaves of *C. boinensis* collected in equal proportions from 25 individuals, 360 leaves of *C. bissetiae*
228 from 26 individuals, and 300 leaves of *C. ambongensis* from 14 individuals.

229 To identify the functional spectrum across the different axis categories identified through the
230 architectural analysis, leaf functional traits (leaf mass per area, LMA, and leaf dry-matter content,
231 LDMC) and seed mass (SM) and seed size were measured according to Perez-Harguindeguy et al.
232 (2013).

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234 **Statistical analyses**

235 The quantitative variables analysed included architectural traits (number of internodes per annual
236 shoot for each axis category: stem C1, branches C2, twigs C3), internode characteristics (length,
237 diameter, number of internodes), leaf dimensions (length, width), and whole-plant traits (total height
238 and basal diameter) across developmental stages (Tables S1-S4). Descriptive statistics (means,
239 standard deviations, variances) were computed to summarise the distribution of each variable within
240 and between species. Prior to selecting statistical procedures, we assessed whether data met
241 parametric assumptions using the Shapiro-Wilk test for normality and Bartlett's test for homogeneity
242 of variances; no data transformations were applied. When assumptions were satisfied, differences
243 between species or between axis categories were tested using Student's t-test or ANOVA; otherwise,
244 the Mann-Whitney or Kruskal-Wallis tests were used (e.g., comparisons of internode number across
245 axis types or across species). For each comparison the choice of statistical test followed the data
246 distribution: parametric tests (t-test or ANOVA) were used when assumptions were met, otherwise
247 non-parametric alternatives (Mann-Whitney or Kruskal-Wallis test) were applied, with appropriate
248 post-hoc tests. Significant effects were followed by Tukey's HSD test (parametric conditions) or Dunn's
249 test with Bonferroni adjustment (non-parametric conditions) for pairwise comparisons, as presented
250 in Tables S1-S4. Associations between variables (e.g., internode dimensions vs. leaf size) were
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assessed using Spearman's rank correlation when normality assumptions were not met. All analyses
were performed using R version 4.3.1 (R Core Team 2024).

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## Results

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### Architecture singularities of Baracoffea species with regards to cultivated Coffea

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All three Baracoffea species (*C. ambongensis*, *C. bissetiae* and *C. boinensis*) shared the same branching pattern on the primary stem as the cultivated species *C. arabica* and *C. canephora*. They all conformed to Roux's architectural model (sensu Hallé et al. 1978), which is characterised by a vertical primary stem (first axis category, C1) bearing horizontal branches originating from every axillary bud (second axis category, C2). In Roux's model, reproductive structures are borne laterally on branches and shoots (C3). Conversely, in all three Baracoffea species studied here, terminal flowers and fruits were found to be born on specialised short shoots (fourth axis category, C4; Figure S3) which are absent in cultivated *Coffea* trees (Figure 3).

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The main differences between Baracoffea species and other *Coffea* species (including the Mascarocoffea species group) lie in the structure of the architectural units, with four categories in Baracoffea compared to three in Mascarocoffea and all other *Coffea* species described so far. Additionally, growth rhythmicity differs; while most *Coffea* species display continuous growth without significant annual rhythm, Baracoffea species show rhythmic growth (Figure 4). Growth stops are marked by the formation of a bud protected by cataphylls (leaves transformed into scales), which allows the identification of annual shoots. In Baracoffea, buds associated with cataphylls do not develop into branches, representing another difference from *Coffea* species, in which all buds on primary stems develop into lateral branches.

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### Morphological variation in architecture

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Although qualitative characteristics in Baracoffea were shared across all three species, several traits differed quantitatively (Figure 4). Specifically, *C. ambongensis* was distinctive by producing only few internodes by annual shoots (mean 2.93 ± 0.59 cm, Table S1-S2) on the branches (C2), and shorter leaves (Table S4) on the stem (C1; mean 5.25± 1.32 cm) and twigs (C3; mean 6.64 ± 1.80 cm). Leaves were however wider on twigs (C3; 3.89 ± 1.01 cm) than those of other species, as well as having globally (all categories considered) higher LMA (Figure S4; 0.026 ± 0.005 g cm⁻²) and LDMC (0.37 ± 0.06 g). Finally, the seed size (length and width; Figure S5; 15.7 ± 1.4 and 11.35 ± 1.1 mm) and SM (0.53 ± 0.1 g) were significantly greater in *C. ambongensis* than in the other two Baracoffea species.

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*C. bissetiae* was distinct by having the highest total height (Table S4; mean 358.73 ± 104.14 cm), the highest number of internodes by annual shoots (Table S2-S3) on branches and twigs (C2 and C3;

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respectively 4.35 ± 1.67 and 3.48 ± 1.22) and longer leaves (Table S4) on the stem (C1; 7.58 ± 1.29 cm).
Leaves were significantly smaller on twigs (C3; 7.19 ± 1.52 cm). LMA, Figure S4; 0.010 ± 0.005 g/cm²) and LDMC (0.07 ± 0.004 g) are also significantly the lowest. Finally, the seed size (length and width; respectively 6.33 ± 0.4 cm; 5.68 ± 0.3 cm) and SM (Figure S5; 0.06 ± 0.002 g) were significantly the smallest of the three species.

C. boinensis was characterised by the lowest total height (Table S4; mean 190.61 ± 31.8 cm), and the lowest number of internodes by annual shoots (Table S1-S2) on twigs (C3; 2.53 ± 1.29). Its leaves were significantly longer on twigs (C3; 9.21 ± 1.52 cm) and associated with higher leaf area on C3 (Figure S6; 39.72 ± 1.2 cm²). LMA (Figure S4; 0.016 ± 0.005 g cm⁻²) and LDMC (0.26 ± 0.03 g cm⁻²) were also significantly lower than C. ambongensis and higher than C. bissetiae, as well as the seed size (length and width; respectively 14.32 ± 1.1 and 10.17 ± 0.9) and SM (Figure S5; 0.29 ± 0.06 g).

Despite similar overall architectures, quantitative morphological differences led to distinct shapes among the three species. Analysing developmental strategies demonstrated that these differences were not established following the same pattern over the lifespan of the species.

## Developmental strategies in Baracoffea

All three species showed an ontogenetic path with similar developmental stages whereby Stage 1 corresponds to the seedling stage, when the plant is unbranched (only C1 present); Stage 2 corresponds to the establishment of the first lateral branches (acquisition of C2 axis category); Stage 3 corresponds to the acquisition point at which twigs develop (acquisition of C3 axis category); and Stage 4 is characterised by the appearance of short shoots (C4), the expression of sexuality, and the full development of adult individuals. Whereas all the morphological events defining the stages appeared in the same order in the three species, quantitative morphological variations shaped each species along a distinct trajectory across stages (Figure 5).

During Stage 1, *C. bissetiae* was significantly taller (14.10 ± 7.80 cm, Table S4) and had a thinner stem diameter (0.21 ± 0.05 cm) than other species. *C. boinensis* was the smallest (7.05 ± 3.77 cm), and *C. ambongensis* had the thickest stem (0.22 ± 0.08 cm). After reaching Stage 2, all species showed a similar height (average of 78.8 ± 26.16 cm). *C. ambongensis* remained having the thickest stem diameter (1.65 ± 0.1 cm) while *C. boinensis* had the thinnest stem diameter (0.48 ± 0.33 cm). This pattern persisted into Stage 3, with similar differences among species. After reaching Stage 4 and maturity (reproductive functions expressed), *C. bissetiae* was significantly taller than the other species (358.7 ± 104.1 cm) and *C. boinensis* was the smallest (190.6 ± 31.8 cm). All species had a similar stem diameter (average of 3.18 ± 0.88 cm).
At the species level, *C. ambongensis* showed progressive growth in both height and stem diameter across all developmental stages (Strategy “C-C”, i.e., Constant growth in height and diameter from one stage to the next). Growth from Stage 1 to 2 and from Stage 2 to 3 was steady, without sudden shifts in growth patterns. In contrast, *C. bissetiae* showed non-uniform growth; it invested strongly in secondary growth during the Stage 1 (W: Widening of the stem), followed by a phase of pronounced primary growth in height during the Stage 2 (H, increase in Height), resulting in what is hereafter referred to as the “W-H” trajectory. Conversely, *C. boinensis* followed the opposite pattern, with strong primary growth in height during the Stage 1, followed by strong secondary growth in stem diameter during the second stage producing what is hereafter referred to the “H-W” trajectory.

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## Discussion

We identified unique sets of characters in wild coffee species of the Baracoffea group that reflect their adaptive potential to the extreme environments. Baracoffea species differ markedly from other *Coffea* species in their rhythmic growth, with periodic growth pauses during which branches do not develop, and in having a more complex and functionally specialised architecture than cultivated *Coffea* species.

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### Seasonality of the environment and rhythmicity of plant growth

Drought tolerance and avoidance are two main strategies that have evolved in plants in water limited conditions (Ordoñez et al. 2010). Drought tolerance involves mechanisms such as water storage (e.g., succulence) that maintain physiological processes while water availability is limited. In contrast, drought avoidance delays deficit of water by synchronising physiological activities such as photosynthesis with favourable conditions (e.g., CAM photosynthesis, annual life cycle, deciduous foliage; Tomlinson et al. 2013). The morphological traits of Baracoffea species, compared to Mascarocoffea, suggest that Baracoffea has adopted the drought avoidance strategy (Reich and Borchert, 1984). Additionally, drought avoidance in Baracoffea is associated with growth cessation during unfavourable periods, resulting in rhythmic growth (Figure 3). This growth pattern alternates between a growth phase during favourable seasons, producing annual shoots, and a dormancy phase during dry seasons, marked by closer internodes, the presence of cataphylls, or reduced pith size. This markedly differs from the continuous growth of Mascarocoffea.

These findings suggest that Baracoffea species have diverged structurally from Mascarocoffea of Madagascar (Andrianasolo 2012) and from most *Coffea* species (Hallé et al. 1978; Okoma 2019) through the selection of structural traits supporting drought avoidance, such as deciduous foliage and rhythmic growth (Figure 2, 3). The seasonal leaf shedding in Baracoffea requires renewal of leaves in

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each favourable season; at the opposite of Mascarocoffea, which retains its foliage during the whole year. This renewal is facilitated by the short specialised shoots of the Baracofea species.

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## Complexity and functions in plant architecture

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The structural complexity of Baracoffea, with four specialised axis types, likely reflects a higher degree of functional specialisation than other *Coffea* species, which have only three different axis categories, and where branches are simultaneously responsible for exploration, assimilation, and reproduction.

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The acquisition of a new axis category, the highly specialised short shoots, may have improved both assimilative and reproductive functions in Baracoffea by enabling the production of a high annual number of leaves and flowers by producing many short, resource cost-effective shoots, thereby reducing the establishment cost in new stem tissue (De Haldat et al. 2023; Dörken and Stützel 2009).

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Being deciduous, Baracoffea species must renew their leaves each growth season, which represents a significant investment of resources in environments where water is limited. The low-cost production of leaves and flowers in Baracoffea was likely a major adaptive advantage in arid environments, allowing the plants to maintain high functional efficiency under slow metabolism and limited water and carbon resources (Reich 2014), and highlighting the adaptive value of their specialised axis architecture.

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Despite these new traits, Baracoffea species retain continuous branching, a characteristic common among *Coffea* species in which all buds on the primary stem develop into branches (Andrianasolo 2012; Hallé et al. 1978; Okoma and Sabatier 2018). A possible functional advantage of this continuous branching is that it improves resource exploitation during the rainy season, notably by increasing the number of short shoots and thus photosynthetic capacity. However, it may also simply reflect a strong developmental constraint on this branching pattern within the *Coffea* genus, which does not compromise species fitness in arid environments (Anest et al. 2021).

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## Ontogenetic trajectories, avoidance and resilience

377

While all three Baracofea species studied grow in the dry environment of Madagascar (Bezandry et al. 2023), differences in local ecological conditions are likely reflected in their specific developmental trajectories. In closed environments, such as the Ankarafantsika sites where light availability is low, *C. bissetiae* develops a tall stem, higher than other species, with numerous internodes, optimising vertical growth to compete for light. Juvenile stages display slow primary growth, suggesting different behaviour than that usually characterising pioneer species that adopt rapid growth in height and diameter (Armani et al. 2019) and suggesting this species is adapted to low light availability conditions (Figure 5).

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In contrast, in more open environments (such as in Antsanitia), species develop with different strategies. *C. ambongensis* has a very constant growth, suggesting that water is probably the single main limiting factor in these systems. Conversely, *C. boinensis* displays a very rapid growth in height before slowing down after reaching the second and third establishment stages. These results emphasise the possibility of evolutionary divergence of the Baracoffea group (Rimlinger et al. 2020) and the genetic potential of wild coffee species to establish into diverse ecological conditions by shifting resource investment into different functions throughout their ontogeny.

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## Functional implications for breeding

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Our findings reveal a strong functional specialisation in both space and time for the three Baracoffea species. Assimilation and reproduction functions are spatially separated from mechanical support and exploration functions, and performed by structures with little wood, and thus requiring limited carbon investment, which is indirectly constrained by low water availability (Reich 2014; De Haldat et al. 2023). On the other hand, mechanical support and exploration functions, operated by the primary stem, branches and long shoots, are separated in time as the developmental strategy selected for the three species follows either a slow-fast, fast-slow, or medium-medium pathway (Reich 2014). The latter pattern might reflect the need to cope with a series of constraints: while water is limited in every habitat, species growing under a closed canopy may benefit from rapid primary growth during the establishment stage, allowing them to compete in the canopy. However, this constrains them in their investment in secondary growth due to limited water availability, and consequently, limited carbon resources. Integrating species-specific developmental strategy could therefore help anticipate the responses of coffee varieties to environmental constraints, based on their developmental stage traits and ecological factors that have selected these characteristics (Lauri 2021; Maurin et al. 2023; Anest et al. 2024), offering predictive tools for breeding programmes aiming at improving resilience in cultivated coffee trees.

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By demonstrating how Baracoffea species combine short, low-cost shoots, which enable the annual production of leaves and flowers with minimal wood and water investment, with flexible growth trajectories that modulate stem height and secondary growth according to light and water availability, our findings show how specific architectural traits maximise resource use and reproductive output under drought and low-light conditions. These results highlight the potential of wild coffee species to withstand climatic variability and provide valuable knowledge for breeding strategies aiming for more resilient cultivated *Coffea*. Additionally, the presence of short shoots in Baracoffea allows an exponential increase in the number of flowers and fruiting sites compared to Mascarocoffea species,
418

which lack these specialised axes, partially compensating for the lower seed production associated
with their stress-tolerant investment in vegetative protective traits.

419

420

However, using wild *Coffea* species in breeding constitutes a significant challenge, as structural data
on wild *Coffea* individuals are sparse, and these species are increasingly rare in their natural habitats.

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422

It is now acknowledged that many wild *Coffea* species are critically endangered (Davis et al. 2018) and
Baracoffea species might reach this critical threshold if no measure is taken (Canon and Lerdau 2023).

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424

For this reason, it is critical to emphasise the importance of understanding the functioning and
adaptations of these wild species, to highlight the value of preserving their genetic resources as a
potential means to counteract the effects of climate change on coffee production (Gay 2006; Jawo
2022).

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429

Further requirements for breeding resistant and resilience Coffea varieties

430

Our study highlights the potential of making use of structural and functional adaptations of wild coffee
species in addressing the challenges of climate change and improving the sustainability of coffee
production. Hybridisation between cultivated *Coffea* species and Malagasy Baracoffea presents both
opportunities and challenges. While hybridisation between Malagasy and African coffee species is
generally characterised by low fertility, some successful crosses occur, particularly with *C. arabica*
(Charrier, 1976). Additionally, high hybridisation success rates do not necessarily predict high hybrid
fertility, which is crucial when considering the introgression of traits from wild Baracoffea species
(Louarn, 1992). This suggests that any viable hybrids could serve as a foundation for conventional
breeding strategies aimed at improving key agronomic traits.

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To explore the potential of Baracoffea architectural traits for improving drought resilience in
cultivated *Coffea* species, small-scale, targeted hybridisation experiments could be conducted under
controlled conditions. However, historical attempts highlight significant biological constraints. In the
1970s (Charrier 1976) crosses between Mascarocoffea species and cultivated coffee produced
extremely low F1 fertility (between 1 and 2 fertile flowers per 1,000 in crosses between *C. canephora*
and Mascarocoffea species, ca. 0.1–0.2%), reaching at best 1% under favourable conditions. This
pronounced sterility represents a major bottleneck that must be overcome. More promising results
were obtained with *C. eugenioides* and *C. arabica*, suggesting that alternative breeding strategies may
be more effective. One option would be to first hybridise Mascarocoffea species with phylogenetically
closer African *Coffea* species (notably from East Africa) and subsequently backcross the resulting
hybrids with cultivated lines such as *C. canephora* (Charrier 1976). Within this framework, efforts
should focus on producing a limited number of viable F1 hybrids, monitoring the expression of key
architectural traits (short shoots, leaf renewal, growth rhythm), and assessing F1 viability and residual

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451
452 fertility to evaluate the feasibility of partial trait fixation. In parallel, bean quality parameters (caffeine
453 content, size, and other agronomic traits) must be evaluated to ensure that architectural and
454 functional gains do not compromise production standards. Although constrained by intrinsic hybrid
455 sterility and the rarity of wild Baracoffea taxa, such a stepwise introgression strategy would clarify
456 which traits are realistically transferable to cultivated germplasm and help structure breeding
457 programmes for water-limited and climatically unstable environments. In addition, other architectural
458 traits, such as the reiteration strategy of species (i.e., the functional magnitude, Laurans et al. 2024)
459 as well as root system structure (Stokes et al. 2009) may also have contributed to the adaptation of
460 *Coffea* (s.l.) to arid environments and should be of interest for further studies.

461 Integrating structural and functional knowledge into wild coffee conservation strategies and breeding
462 programmes could provide perspectives to secure the future of coffee as a global commodity. A
463 multidisciplinary approach that combines genomics, agronomy, ecology and evolution together with
464 experimentation will be essential for achieving this goal, ensuring that coffee cultivation remains
465 viable in the face of mounting climate challenges.
466

466
467

468 Acknowledgments

469 Rickalors Bezandry is sponsored by Rufford foundation grant n39692-1 and the French government
470 grant awarded by the Service de coopération et d'action culturelle (SCAC) in Madagascar (N°104008W
471 and N°122007W).

472 We are grateful to Madagascar National Parks (MNP) for allowing this research to be conducted.

473 This work has been made possible thanks to the Directorate of protected areas, renewable natural
474 resources and ecosystems of Madagascar (Direction des aire protégées, des ressources naturelles
475 renouvelables et des écosystèmes de Madagascar) research permit delivered
476 N°270/24/SG/DAPRNE/SCBE.Re.

477 The authors gratefully acknowledge the support of the French Embassy in Madagascar and the
478 Cooperation and Cultural Action Service (SCAC).

479 Rickarlos Bezandry has received the support of IRN LiStat (Statistics for Life Sciences and Ecology), the
480 "Institut de Recherche pour le Développement" (IRD) and The French Agricultural Research Centre for
481 International Development (CIRAD).

482 The authors thanks Frank RAKOTONASOLO for his help in the identification of Baracoffea species.

483

484 Notes on contributors
485

Rickarlos Bezandry's research focuses on the genetic diversity and drought adaptation of wild endemic coffee species (Baracoffea) from Madagascar, to understand their resilience to arid conditions and support conservation and climate-resilient coffee cultivation.

486

487

488

Hery L. T. Ranarijaona studies plant biodiversity and botanical ecology, especially Madagascar's native plant species and vegetation conservation.

489

490

Marie E. Vavitsara research focuses on the diversity and evolution of wild *Coffea* species, particularly their adaptation and phylogenetic history in Madagascar.

491

492

Sylvie Sabatier investigates plant morphology and ecological adaptation in trees.

493

Romain Guyot works on the evolutionary history and genetic diversity of wild coffee species to understand their adaptation and diversification.

494

495

Artemis Anest's research focuses plant morphological and functional diversity, integrating plant architecture, biogeography, and macroevolutionary frameworks.

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498

## Author contribution

499

RB, SS et AA planned and designed the research, RB conducted data collection and processing. RB and AA analysed data. RB and AA wrote the manuscript. HLTR, MEV, and RG revised the manuscript.

500

501

502

## Data availability statement

503

The data associated with this article can be provided upon request to the authors.

504

505

## Supporting Information

506

Supporting Information associated to this article includes:

507

### Supporting tables

508

**Table S1.** Average number of internodes per annual shoot and between species

509

**Table S2.** Average number of internodes per annual shoot by type of axis within the same species

510

**Table S3.** Comparison of internodes and leaves for species at stage 4

511

**Table S4.** Description and comparison of species based on total height and basal diameter variables.

512

513

### Supporting figures

514

**Figure S1.** Location of the two main study sites.

515

**Figure S2.** Some of the architectural descriptors commonly used in architectural analyses.

516

**Figure S3:** Short shoots bearing terminal sexuality in *Coffea ambongensis*, *Coffea boinensis* and *Coffea bissetiae*.

517

518

**Figure S4.** Average LSDM and LMA by species.
519 **Figure S5.** Average values of seed traits.

520 **Figure S6.** Average leaf area (length x width, in cm²) by axis category.

521

522

523 **Supporting notes**

524 **Notes S1.** Architectural and morphological description of *Coffea ambongensis*.

525 **Notes S2.** Architectural and morphological description of *Coffea bissetiae*.

526 **Notes S3.** Architectural and morphological description of *Coffea boinensis*.

527

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759
<figure><img src="image_3.png" /></figure>

Figure 1: Map of the predictions in land surface temperature differences between now and 2050, modified from Di Lorenzo (2015). Targets (red dots) were added to indicate the top 10 coffee-producing countries (ICO, 2023).

<figure><img src="image_4.png" /></figure>

Figure 2: Whole plants of three Baracoffea species: (a) *Coffea ambongensis* Leroy ex Davis & Rakotonasolo, (b) *Coffea bissetiae* Davis & Rakotonasolo, and (c) *Coffea boinensis* Davis & Rakotonasolo. Details of short shoots for each species are shown in (d) *C. ambongensis*, (e) *C. bissetiae*, and (f) *C. boinensis*. Photographic credits: Rickarlos Bezandry.
<figure><img src="image_5.png" /><figcaption>Figure 3: Three different architectures in genus Coffea. 1) Unbranched stem with lateral flowering in *Coffea macrocarpa*, modified from Hallé (Hallé, 2019); 2) Typical Roux model in *C. arabica*, *C. canephora et C. liberica* modified from Hallé (Hallé, 2019), made of a monopodial (built by a unique meristem) orthotropic (vertically growing with a radial symmetry) stem with continuous branching forming tiers of monopodial plagiotropic (horizontally growing with a bilateral symmetry) branches which lateral flowering on the stem and branches; 3) Variation of the Roux model in *C. ambongensis*, *C. bissetiae* and *C. boinensis* (this study), where sexuality is located in terminal position of short sympodial (successively branched from terminal buds) shoots, and growth is rhythmical. A detailed description of all tree species is available in Notes S1 to S3.</figcaption></figure>
<figure><img src="image_6.png" /><figcaption>Figure 4: Scheme and summary of morphological variation in the three Baracoffea species. Letters (a, b, c) indicate the results of post-hoc pairwise comparisons. Categories sharing the same letter do not differ significantly, whereas different letters indicate significant differences. The color code reflects the relative magnitude of the values: Dark green with "a" = significantly highest values, Medium green with "b" = intermediate, significantly different from both "a" and "c", Light green with "c" = significantly lowest values. The values shown correspond to the mean trait values, with detailed results and statistical tests provided in the Supporting Tables S1-4. * Significant, ** Highly significant, *** Very highly significant.</figcaption></figure>
<figure><img src="image_7.png" /><figcaption>Figure 5: Scheme and summary of morphological variations in the three Baracoffea species across different developmental stages. Each line represents a different stage; stages 1, 2, and 4 are shown, whereas stage 3 is omitted as no significant differences were observed between stages 2 and 3. "DGH": diameter at ground level. Letters indicate the results of post-hoc pairwise tests and are associated with colors: "a" with dark green = significantly higher values, "b" with light green = significantly lower values, "c" with white = intermediate values significantly different from both</figcaption></figure>
extremes; grey colour indicates no significant difference. All statistical test outputs and mean trait
values are provided in the Supporting Tables S1-4. "Strategy" indicates interpreted growth strategies
between stages, where C = Constant growth in height and width, H = Rapid growth in height, and Rapid
growth in width. "Primary growth" correspond to growth in height (resulting from apical meristem
activity), and "secondary growth" refers to growth in diameter (resulting from cambial activity).