Biology subjects

Renner, S. S.

Publications and source records attributed to Renner, S. S..

9 recordsLinked to original sources

bioRxiv2026

Ancient DNA reveals early use of melons in China's Song Dynasty

Melon (Cucumis melo L.) domestication is thought to have occurred independently once in Northeast Africa and twice in India, but archaeobotanical seed remains point to a possible additional domestication in China. Because Cucumis seeds are difficult to diagnose morphologically, genomic data from archaeological material are needed to evaluate these scenarios and reconstruct ancient melon traits. We sequenced two Song Dynasty melon seeds from Shuomen Gugang (China), recovering 4.6x and 1.7x nuclear genome coverage. Nuclear and chloroplast analyses place both seeds within cultivated C. melo from China, supporting introduction from the broader Asian domestication pool rather than independent Chinese domestication. To assess whether these seeds carried traits associated with sweet dessert melons, we examined loci underlying fruit phenotypes. Neither seed carried alleles for orange flesh; one harbored an allele linked to yellow/orange peel, the other possessed alleles associated with green flesh and reduced acidity. Since wild melons are monoecious, the presence of the derived andromonoecy allele in one seed, associated with rounder fruit shape, suggests early selection on fruit morphology. Together, these findings indicate that Song Dynasty melons were likely consumed as fresh or culinary fruits rather than as sweet dessert melons. Their flesh coloration resonates with Song-period aesthetic sensibilities, exemplified by jade-green celadon ceramics frequently crafted in melon-shaped forms. By anchoring East Asian archaeobotanical remains within modern melon genomic variation, this study provides a temporal framework for melon dispersal into China and shows how ancient genomics can illuminate past crop use.

evolutionary biology↗

bioRxiv2025

Developmental constraints mediate the summer solstice reversal of climate effects on European beech bud set

Accurate projections of temperate tree growing seasons under climate change require representing developmental constraints that determine tree resource allocation. Recent work has identified a phenological "switch point" after the summer solstice (21 June), with pre-solstice warming advancing autumn phenology and post-solstice warming delaying it. Here, we propose this switch is flexible and occurs at the compensatory point between the antagonistic effects of early-season development and late-season temperature. We performed trans-solstice climate manipulation experiments on potted European beech (Fagus sylvatica) saplings to test (i) how spring leaf-out timing and June-August temperatures influence end-of-season timing (bud set and leaf senescence [50% loss of leaf chlorophyll content]), and (ii) whether daytime and nighttime temperatures before and after the solstice have different effects, given that trees primarily grow at night. Bud set and leaf senescence responses were tightly coupled (R2 = 0.49), with bud responses being generally stronger. Each day delay in spring leaf-out delayed bud set by 0.24 {+/-} 0.06 days and senescence by 0.22 {+/-} 0.08 days. Post-solstice full-day cooling in July delayed autumn phenology in late-leafing individuals (bud set +4.9 {+/-} 2.6 days; senescence +3.1 {+/-} 2.8 days) but had negligible impact on early-leafing trees (bud set +1.4 {+/-} 2.6 days; leaf senescence +2.2 {+/-} 2.8 days). Conversely, August full-day cooling advanced both stages. Daytime cooling before the solstice had no effect, while after the solstice it advanced autumn phenology. Nighttime cooling always delayed bud set. These findings support the Solstice-as-Phenology-Switch model and highlight the central role of developmental progression in constraining growing seasons. Faster early-season development -especially under nighttime warming- moves trees past the switch earlier, increasing sensitivity to late-season cooling and thereby triggering earlier autumn phenology. To improve growing season length projections, phenology models should account for these developmentally-mediated and diel-specific temperature responses.

ecology↗

bioRxiv2023

Morphometrics and phylogenomics of coca (Erythroxylum spp.) illuminate its reticulate evolution, with implications for taxonomy

South American coca (Erythroxylum coca and E. novogranatense) has been a key-stone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half century, global demand for cocaine has placed this plant in the centre of armed conflict, deforestation, and explosive growth of illegal economies. While national and international agencies progress from a war on drugs policy model towards locally appropriate, data-informed strategies to tackle coca plantations, monitoring their expansion and composition remains essential. The principal means to identify coca plants is leaf morphology, yet the extent to which it is reflected in taxonomy is uncertain. Here, we analyse the consistency of the current naming system of coca and its four closest wild relatives (the coca clade), using morphometrics, phylogenomics, and population genomics. We include the name-bearing type specimens of cocas closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the rounder and more obovate leaves of certain coca varieties could be associated with domestication syndrome of this crop. Our phylogenomic data indicate gene flow involving monophyletic clades of E. gracilipes and the E. coca clade. These results further clarify the evolution of coca and support a taxonomic framework wherein E. gracilipes is retained as a single species. Our findings have implications for the development of cost-effective genotyping methods to effectively discriminate varieties of cultural significance from high-yielding cultivars fuelling the lucrative cocaine market.

plant biology↗

bioRxiv2022

Mobile stamens enhance pollen dispersal by scaring floral visitors away

Animal-pollinated plants have to get pollen to a conspecific stigma while protecting it from getting eaten. We provide experimental evidence that touch-sensitive stamens function in (i) enhancing pollen export and (ii) reducing pollen loss to thieves. Stamens of Berberis and Mahonia are inserted between paired nectar glands and when touched by an insects tongue rapidly snap forward so that their valvate anthers press pollen on the insects tongue or face. We immobilized the stamens in otherwise unmodified flowers and studied pollen transfer in the field and under enclosed conditions. On flowers with immobilized stamens, the commonest bee visitor stayed up to 3.6x longer, yet removed 1.3x fewer pollen grains and deposited 2.1x fewer grains on stigmas per visit. Self-pollen from a single stamen hitting the stigma amounted to 6% of the grains received from single bee visits. Bees discarded pollen passively placed on their bodies, likely because of its berberine content; nectar has no berberine. Syrphid flies fed on both nectar and pollen, taking more when stamens were immobilized. Pollen-tracking experiments in two species showed that mobile-stamen-flowers donate pollen to many more recipients. These results demonstrate another mechanism by which plants simultaneously meter out their pollen and reduce pollen theft. HighlightsO_LIStamens that snap forward when triggered by a flower visitor may serve to meter out pollen, scare away pollen thieves, or place pollen more accurately. C_LIO_LIWe tested these hypotheses by experimentally immobilizing all six stamens in numerous flowers of Berberis and Mahonia species in the field and under enclosed conditions. C_LIO_LIIn flowers with immobilized stamens, the commonest bee species stayed up to 3.6x longer, yet removed 1.3x fewer pollen grains and deposited 2.1x fewer grains on stigmas per visit. Mobile stamens exported their pollen to significantly more neighboring flowers. C_LI Graphic abstractBehaviour and pollen transfer after flower visitors received a beating on the tongue or in the face by the forward-snapping stamens of Berberis. Stamens only snap forward if their filament basis is touched by an insect tongue. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/498951v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1dff517org.highwire.dtl.DTLVardef@53f369org.highwire.dtl.DTLVardef@1918627org.highwire.dtl.DTLVardef@fe9447_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2021

iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software specifically targeted at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The alpha version (iTaxoTools 0.1) distributed with this paper contains GUI versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files and tables; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses.

evolutionary biology↗

bioRxiv2020

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

O_LIThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies. C_LIO_LIWe addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species. C_LIO_LIThe ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris. C_LIO_LIOur study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species. C_LI

evolutionary biology↗

bioRxiv2020

Evidence for dosage compensation in Coccinia grandis, a plant with a highly heteromorphic XY system

Some ~15.000 angiosperms are dioecious, but mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped and the transmission patterns of SNPs then analysed. In the >1300 sex-linked genes studied, X-Y divergence was 0.13 - 0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.

plant biology↗

bioRxiv2019

A 3500-year-old leaf from a Pharaonic tomb reveals that New Kingdom Egyptians were cultivating domesticated watermelon

Domestication of the watermelon (Citrullus lanatus) has alternatively been placed in South Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence coming from Libya and Egypt. The geographic origin and domestication of watermelons has therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-year-old Citrullus leaf from a mummys sarcophagus and skimmed genomes for representatives of the seven extant species of Citrullus, we show that modern cultivars and the ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom Egyptians were cultivating domesticated watermelons. The genomic data also identify extant Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated watermelons.\n\nSignificance statementWith some 197.8 million tons in 2017, watermelon, Citrullus lanatus, is among the Worlds most important crops, yet its area of origin and domestication have remained unclear, with competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a Pharaonic sarcophagus and performed genome skimming for representatives of all other Citrullus species to compare key genes involved in fruit bitterness and color. White-fleshed, non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form (but no wild forms), implying that 18th Dynasty Egyptians were cultivating domesticated watermelon by 3500 years ago.

evolutionary biology↗

bioRxiv2018

Loss of leaf-out and flowering synchrony under global warming

The temporal overlap of phenological stages, phenological synchrony, crucially influences ecosystem functioning. For flowering, among-individual synchrony influences gene flow. For leaf-out, it affects interactions with herbivores and competing plants. If individuals differ in their reaction to the ongoing change in global climate, this should affect population-level synchrony. Here, we use climate-manipulation experiments, Pan-European long-term (>15 years) observations, and common garden monitoring data on up to 72 woody and herbaceous species to study the effects of increasing temperatures on the extent of within-population leaf-out and flowering synchrony. Warmer temperatures reduce in situ leaf-out and flowering synchrony by up to 55%, and experiments on European beech provide a mechanism for how individual genetic differences may explain this finding. The rapid loss of reproductive and vegetative synchrony in European plants predicts changes in their gene flow and trophic interactions, but community-wide consequences remain largely unknown.

ecology↗