Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.10.750513

Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia

Kiew, R.·Fareed, F. S.·FOONG, L. C.·Tam, S. M.
View original source ↗Export metadata ↓

Abstract

Karsts of Southeast Asia cover ~400,000 km2, with tropical limestone karsts possessing highly biodiverse flora in many, varied microhabitats that are unique from lowland- and hill forests. Begonia L. is a pantropical mega-genus with ~1,550 described species to date, ideal for studying evolutionary patterns and factors driving tropical population- diversity and speciation. Begonias grow on multiple substrates including limestone and granite, sandstone, quartzite, on steep earth slopes and near streams in primary forests. Niche partitioning is commonly observed, resulting in many single-site endemic Begonia species especially on limestone karsts. Molecular phylogenetic analyses were performed on combined chloroplast ndhF-rpl32 and nuclear internal transcribed spacer ITS sequences that included 30 selected Begonia species representing all sections from Peninsular Malaysia (Pen. Msia; ten limestone-, thirteen forest- and seven granite species). Results of Bayesian inference and molecular dating showed evolution of Begonia from continental Asia into Pen. Msia during the mid-late Miocene period of ~ 10.65 mya (9.7 - 12.12 mya), with at least two independent dispersal events observed by the early splitting of the ancestral lineage into two major clades i.e. clades A- and B at 9.85 mya (HPD 9.7-10.36 mya) and 8.85 mya (HPD 7.7-11.23 mya) respectively; followed by multiple speciation events colonizing limestone- as well as non-limestone (forest, granite) habitats. Begonia speciation into limestone habitats occurred three times, with climate indicated as more important factor than substrate in diversification - clade A contained the Indian/Continental Asia (monsoon climate) species, i.e. Sect. Platycentrum and Parvibegonia, resolved slightly older than clade B where Sect. Petermannia, Jackia and Ridleyella formed a Sunda Shelf (equatorial climate) centred group. Strong population structuring by locality, common in Begonias, was also observed (e.g. B. kingiana, B. foxworthyi, B. nurii, B. sinuata), regardless of distribution. However, for widespread species (B. kingiana, B. sinuata) behavioural (physiological) inertia on niche evolution, and/or genome size variation and dynamics (genome evolution) may potentially explain species cohesion. Phylogenetics relationships are mostly concordant with current sectional classifications excepting Sect. Parvibegonia, Sect. Diploclinium and two paraphyletic species complexes. Conservation of Begonias and biodiverse limestone karsts in Malaysia remains concerning due to ongoing threats (large-scale quarrying/mining, human encroachment), and most are still without any legal protection.

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kiew, R., Fareed, F. S., FOONG, L. C., Tam, S. M.. 2026-09-13. Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia. https://doi.org/10.64898/2026.09.10.750513

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

RNA-guided nucleases (RGNs), such as Cas9 from Streptococcus pyogenes (SpCas9), are widely used for plant genome editing. Previous surveys for off-targeting, the modification of unintended targets with similarity to the intended target, indicate high specificity of SpCas9 in plant cells. However, off-targeting has not been assessed for efficiency-optimized editing systems combined with extensive multiplexing, which might increase the likelihood of cleavage at unintended sites. We therefore analyzed Arabidopsis thaliana lines that had been extensively mutagenized using zCas9i and up to 29 gRNAs addressing >45 target sites over several rounds of editing. Genomes were sequenced by short- and long-read technologies, and genome-wide variants were catalogued. Our pipeline for variant calling reliably detected RGN-induced mutations at on-targets. When excluding these on-target modifications, variants were detected in edited lines at frequencies similar to those previously reported for spontaneous mutations. In further analyses, we did not find any evidence for an origin of these variants from RGN activity. Our data are thus consistent with high specificity of SpCas9. In contrast, we detected genomic reorganization events upon editing at two complex loci, RPP1 and RPP7, encompassing multiple homologous genes, and also identified an allele by WGS that had escaped detection by amplicon sequencing. We conclude that, while off-targets may efficiently be avoided by selection of specific gRNAs, on-target modifications may be more extensive than intended, especially at complex loci and/or during multiplexing.

plant biology↗
bioRxiv2026

Seeding paradise: germination ecophysiology of Xyris paradisiaca Wand. (Xyridaceae), an endangered endemic species from Central Brazil

Seed ecophysiology is essential for understanding plant regeneration and developing effective conservation and ecological restoration strategies, yet knowledge remains scarce for most threatened Cerrado species. We characterised the germination niche, desiccation tolerance and storage behaviour of Xyris paradisiaca (Xyridaceae), an Endangered species endemic to Central Brazil, to assess whether its restricted distribution is associated with narrow germination requirements and to inform seed-based conservation. Germination was tested across light regimes, constant temperatures, decreasing water potentials and short-duration heat shocks, while thermal- and hydro-time models were used to quantify thermal and hydric thresholds. Seeds exhibited an absolute light requirement but broad abiotic tolerances. Germination remained >87% between 15 and 40 {degrees}C, with estimated cardinal temperatures of Tb = 8.94 {degrees}C, To = 33.13 {degrees}C and Tc = 45.53 {degrees}C. Germination remained similar to the control down to -0.6 MPa and exceeded 40% at -1.0 MPa, with a median base water potential of {Psi}b = -1.03 MPa. Germination also remained high after 1-min heat shocks up to 200 {degrees}C. Seeds were desiccation tolerant, with 100% germination after drying and a viability loss index of -0.04, and germination remained >90% after 24 months of ambient storage. Thus, the highly restricted distribution of X. paradisiaca is not driven by a narrow physiological germination niche. Its broad environmental tolerances, desiccation tolerance and favourable storage behaviour also highlight its unexplored potential for seed-based restoration, propagation and ex situ conservation.

plant biology↗
bioRxiv2026

Planted origin of shade trees: a robust determinant of cocoa yield among smallholder farmers in Cote d'Ivoire

CONTEXT: While the agroeconomic literature on the determinants of cocoa yield among West African smallholders is abundant, it remains dominated by descriptive studies or work conducted at an aggregated regional scale, leaving open the question of the role of shade-tree management practices at the scale of the individual plantation. OBJECTIVE: This study tests whether shade-tree management practices and the farmer's socio-demographic profile explain variation in cocoa yield, using a nationwide sample of 409 plantations covering, for the first time, the three major Ivorian production zones (loops) (98, 151 and 160 plantations for loops 1, 2 and 3, respectively). METHODS: A univariate screening of 27 variables, a mixed model with a random intercept by village, a production-function specification, LASSO variable selection, and a random forest were applied, all evaluated by 5-fold cross-validation. RESULTS AND CONCLUSIONS: The five approaches converge on a robust result: the deliberately planted origin of shade trees (as opposed to a residual or spontaneous origin) is the strongest and most stable determinant of yield, with a mean gap of 332 versus 183 kg/ha/year. This effect withstands four successive robustness checks: it remains significant after simultaneous adjustment for age, plantation size, production zone, technical extension, and farmer education; it is not driven by a handful of extreme plantations; it holds within each of the three production zones taken separately rather than in only one of them; and, taken in isolation, it retains a positive out-of-sample predictive power (cross-validated R2=8776; 0.05). A second group of robust determinants of more modest magnitude emerges for agricultural technical extension (ANADER/CNRA/SATMACI) and farmer education level; shade-tree alignment shows a signal in the same direction, consistent with recent independent work in Cote d'Ivoire, but becomes statistically marginal once adjusted for these other factors. The full multivariate model reaches a cross-validated R2 of around 0.07-0.08. SIGNIFICANCE: This signal, undetectable in an analysis restricted to loop 1 alone (n=98) for lack of statistical power, confirms the value of nationwide sampling for detecting modest but real agronomic determinants, and argues for integrating shade-tree origin into agroforestry extension programmes.

plant biology↗