Biology subjects

Harpke, D.

Publications and source records attributed to Harpke, D..

8 recordsLinked to original sources

bioRxiv2026

Chromosomal variability in a clonal crop: Somaclonal change follows the emergence of triploid saffron crocus

(1) BackgroundSaffron crocus (Crocus sativus) is the source of saffron, the most expensive spice in the world. It evolved about 3000 years ago as a sterile triploid clone in Greece. Since then, saffron has spread across the globe, where regionally distinct practices of saffron cultivation have developed. Despite differences in morpho-physiological traits, genetic variability is low, if present at all. Here, we aim to resolve chromosomal and sequence-associated variability across saffron crocus cultivars from the crops main cultivation areas in Africa, Asia and Europe. (2) MethodsWe used genome-wide DNA polymorphisms obtained through genotyping-by-sequencing (GBS) of 33 saffron and 14 closely related Crocus accessions, which we place into a phylogenetic context. For karyotyping, we compare nine saffron accessions by multi-color fluorescent in situ hybridisation (FISH) with repetitive DNA probes. (3) Key resultsPhylogenetic analyses confirmed the single origin and clonal nature of all saffron accessions. We detected slight DNA differences among saffron crocus genotypes, which were minor compared with those in wild C. cartwrightianus populations. Still, the Iranian saffron accessions form a genetically very narrow group that differs from the other proveniences in population genetic analyses. However, chromosomes of some saffron accessions display variable FISH signals, likely resulting from gains and losses of tandemly repeated DNA. (4) Main conclusionsBased on the high genetic identity and small karyotypic differences, we confirm the clonal origin of the saffron accessions. Nevertheless, as we detected small and regional chromosomal variability, we conclude that at least four somaclonal saffron lineages emerged after saffrons origin. Societal Impact StatementFor millennia, many cultures developed cultivation practices and regional crop varieties. A notable case is saffron, the worlds most expensive spice that is harvested from stigmas of saffron crocus. This flower crop arose 3000 years ago in a singular genome triplication event and since then spread clonally across the globe. By identifying genetic and chromosomal variability in clonal saffron accessions, we highlight regional diversity, support the preservation of traditional knowledge, and underscore the risk of relying on only one clonal lineage. This informs strategies for saffron cultivation, linking cultural heritage with modern genomics to address biodiversity, evolution, and food security.

plant biology↗

bioRxiv2026

Drowning in a sandy ocean: Epiarenic growth of Tillandsia in the hyperarid Atacama Desert

The Atacama Desert hosts a unique ecosystem formed by the sand-dwelling Tillandsia landbeckii, which extends over hundreds of square kilometers. This vegetation relies primarily on fog as its main water source; however, aeolian sand also plays a crucial role in the long-term persistence of both the species and the overall plant community. The terrain is sloped and exposed to the prevailing wind direction. Tillandsia forms regular banding patterns oriented orthogonally to these landscape features. In this study, we aim to elucidate the abiotic-biotic interactions between sand properties and vegetation characteristics through a comparative approach. Three populations - Caldera, Oyarbide and Arica -, each spanning several square kilometers in the southern, central, and northern regions of the Chilean Atacama Desert, were selected to compare wind regimes, terrain structure, sand and substrate properties, and vegetation structure in order to identify common principles that maintain vegetation integrity. Data were collected from six climate stations, 1,246 substrate samples, population genomic data from 718 individuals, as well as satellite imagery and digital terrain models. Our findings demonstrate that regional wind systems transport sand from distant source areas, while near the ground, Tillandsia vegetation reduces wind velocity and traps sand, leading to the formation of moderately sorted sandy substrates that are similar across all three populations. Sites lacking or containing dead Tillandsia individuals often differ significantly in substrate characteristics. Genetic analyses indicate that Tillandsia populations exhibit strong spatial structure albeit recruiting high genetic diversity and an excess of heterozygosity, reflecting adaptation to the dynamic environmental conditions. We conclude that sand represents an essential component of this ecosystem, while Tillandsia, as the dominant biotic factor, actively shapes and maintains this distinctive desert environment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/707457v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@14529eforg.highwire.dtl.DTLVardef@1c42435org.highwire.dtl.DTLVardef@25147aorg.highwire.dtl.DTLVardef@639128_HPS_FORMAT_FIGEXP M_FIG C_FIG Generated based on own drawings and iterative improvements using ChatGPT while providing own peer-reviewed research contributions as input and baseline information (MAK). Short summaryWe exemplify unimodal regional wind systems facilitating sand transport toward Tillandsiales. Tillandsiales show a low-energy wind system allowing sand accumulation of predominant grain sizes available at each site. Thereby Tillandsia landbeckii modifies and maintains its own microenvironment. Genomic data reveal high clonality and excess of heterozygosity promoting fitness in a hyperarid environment, and abiotic factors drive the selection of diverse and adaptive Tillandsia phenotypes.

plant biology↗

bioRxiv2025

An area-resolved phylogeography of bulbous barley (Hordeum bulbosum; Poaceae)

Hordeum bulbosum, the closest relative of barley (H. vulgare), is an important source of resistance genes for cereals in the Triticeae. This perennial and mainly outcrossing species occurs with two cytotypes: diploids thrive in the western and central parts of the Mediterranean, while autotetraploids extend from Greece mainly eastwards to western Asia. To elucidate H. bulbosums origin, colonization patterns, population relationships, and distinctions between the two cytotypes, we determined ploidy and performed genotyping-by-sequencing analyses on 314 individuals from across the species distribution range. Our results revealed two distinct lineages within diploid H. bulbosum: individuals from Libya vs. all other diploids. Southeastern Italian populations were the origin for the species expansion eastward into Albania/Greece and westward into mainland Italy, Sicily/Sardinia, Tunisia, and Spain. The tetraploid cytotype originated early in the evolution of the species, thus retaining alleles found in extant Libyan diploids. Tetraploids underwent local introgression from diploids in Greece, where also a secondary origin of tetraploids was detected. We found that ecoclimatic conditions alone cannot account for the clear geographic separation of the cytotypes, as habitats across much of the central Mediterranean would be suitable for both. We conclude that minority cytotype exclusion is the most plausible explanation for the distinct distribution patterns observed. While both cytotypes are morphologically indistinguishable, diploid populations typically occur in scattered stands within their range, while tetraploids tend to form larger, often contiguous populations.

evolutionary biology↗

bioRxiv2023

Genome-wide SNP data reveal recent population structure of Huidobria fruticosa (Loasaceae), a paleo-endemic lineage from the Atacama Desert

The Atacama Desert is a biodiversity hotspot of neo-endemic radiation, where long-term aridity and complex physiographic processes create a unique environmental setting. Current species assemblages are mainly concentrated in highly patchy loma formations, and plant populations occurring in these are often geographically isolated from each other. Despite a general consensus on long-term aridity in the Atacama, climatological and geological evidence points to repeated climate change, making the Atacama Desert an ideal system for studying population genetic processes in highly unstable habitats. We are analyzing the genetic structure within and between populations of Huidobria fruticosa, a paleo-endemic lineage of the Atacama Desert, to shed new light on its biogeographic history and broaden our understanding of the evolution of life in extreme aridity, as well as plant evolution in response to a changing environment. To do this, we analyzed SNP data from genotyping-by-sequencing of 354 individuals from 21 populations. Our results suggest that, despite being an ancient lineage, the current population structure of Huidobria fruticosa only reflects changing abiotic conditions over the last 2 million years. We therefore conclude that the present distribution, together with the evolutionary processes documented here, is the result of climatic fluctuations and prolonged periods of hyperaridity during the Pleistocene. Building on this understanding, our findings contribute to a global narrative that highlights the complex interplay between climate change and evolutionary dynamics, and emphasize the importance of deserts as living laboratories for deciphering how species have historically adapted to some of the most extreme habitats on Earth.

evolutionary biology↗

bioRxiv2023

Genetic diversity of the Atacama Desert shrub Huidobria chilensis in the context of geography and climate

Survival in hyperarid deserts is a major challenge for plant life, requiring the development of evolutionary strategies. The Atacama Desert presents harsh conditions such as limited rainfall, crusted soils, high soil salinity, high altitude, and intense solar radiation. These conditions, together with paleoclimatic variability since the past millions of years, have influenced the genetic structure and connectivity of plant populations, resulting in a diverse flora with high endemism. However, the diversification of most lineages appears to be relatively recent, in contrast to proposed age of the Atacama Desert and the onset, evolution and expansion of hyperarid conditions since the Late Oligocene and Early Miocene. A prominent exception is the Atacama paleoendemic Huidobria chilensis (Loasaceae), which is thought to be adapted to such conditions since the Eocene. Still, the environmental limits and thresholds for life in the Atacama remain poorly understood. To investigate the genetic structure in relation to the history of the Atacama Desert, we studied 186 individuals from 11 populations using genotyping-by-sequencing (GBS). Genome-wide single nucleotide polymorphisms (SNPs) were analyzed for population structure and genetic diversity. We identified three genetic clusters corresponding to geographic regions: the coastal region south of Tocopilla, the Coastal Cordillera around Chanaral, and the Copiapo watershed in the south. These clusters as well as genetic diversity were analyzed alongside rainfall, altitude, and landscape data. Although the genetic data generally supports isolation by distance as a major factor for genetic variation between populations, the study also reveals the influence of the topography on the distribution of H. chilensis and highlights the role of hydrologically connected watersheds and rivers in plant migration and colonization. This shapes the species evolutionary trajectory and genetic diversity. Understanding these patterns provides insights into the adaptation and survival strategies of plants in extreme desert environments such as the Atacama.

genetics↗

bioRxiv2023

Cytogeography of Gagea bohemica (Liliaceae) outside the Mediterranean: two ploidy levels, spatial differentiation of cytotypes, and occurrence of mixed-ploidy populations

Gagea bohemica s. lat. is a morphologically and karyologically highly variable group with many morphologically similar "narrow" taxa currently considered as a single variable species. It is predominantly distributed in Mediterranean and warmer parts of temperate belt of Europe. The large-scale data on its cytogeography and population cytotype structure which could provide a basis for taxonomy is lacking, only scattered data on ploidy have been published from various parts of its range. In this study, we sampled 106 populations in broader Central Europe, the northeastern Balkan Peninsula and the northwestern Black Sea coast in order to analyse their ploidy level, genome size and pollen stainability. Two cytotypes, i.e., tetraploid (2n = 48) and pentaploid (2n = 60), were found in the study area using chromosome counting and flow cytometry, both in pure and mixed-ploidy populations. Pure pentaploid populations are mainly distributed in Austria, Czechia, northwestern Hungary and Slovakia while tetraploid cytotype in pure and mixed-ploidy populations forming two lineages which are concentrated into two disjunct geographical areas: a western lineage in Germany and Switzerland, and an eastern one in Bulgaria, southeastern Hungary, northern Greece, Romania, Serbia and Ukraine. The two lineages differ in their genome size regardless of their ploidy, indicating their independent origin. Analysis of pollen stainability using a modified Alexander stain revealed an unusual pattern with tetraploids having a lower pollen stainability (mean 44.29 %) than pentaploids (mean 70.70 %) but the western and eastern populations differed again from each other.

plant biology↗

bioRxiv2022

Two new species of Crocus series Scardici from the western Balkans

Crocus series Scardici has only two members, C. scardicus and C. pelistericus distributed at higher elevations in the Balkan Peninsula. In the course of our research, we discovered two new species growing on alpine meadows and pastures in the serpentine massifs in Albania and limestones in North Macedonia, respectively. The morphology and phylogenetic analyses (two nuclear single-copy markers, nrITS, two chloroplast markers) place the new species within series Scardici. Both new species are closely related to C. scardicus, but morphologically and ecologically clearly differentiated. We also measured genome sizes for all series Scardici species and report here the largest genomes found up to now in crocuses. The impact of different habitat types and isolation on separate mountain ranges in this alpine group of plants is discussed, too.

evolutionary biology↗

bioRxiv2019

Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wild Crocus cartwrightianus

Crocus sativus is the source of saffron, which is made from dried stigmas of the plant. It is a male-sterile triploid that ever since its origin has been propagated vegetatively. The mode of evolution and area of origin of saffron are matters of long-lasting debates. Here we analyzed chloroplast genomes, genotyping-by-sequencing (GBS) data, nuclear single-copy genes, and genome sizes to solve these controversial issues. We could place 99.3% of saffron GBS alleles in Crocus cartwrightianus, a species occurring in southern mainland Greece and on Aegean islands, identifying it as the sole progenitor of saffron. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the wild C. cartwrightianus population south of Athens as most similar to C. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes of C. cartwrightianus. Vegetative propagation prevented afterwards segregation of the favorable traits of saffron.

evolutionary biology↗