Biology subjects

Kadereit, G.

Publications and source records attributed to Kadereit, G..

13 recordsLinked to original sources

bioRxiv2026

Floral scent diversity and evolution in deceptive Cypripedium, and post-pollination effects on floral scent and its biosynthesis in C. henryi

Background and Aims: Floral scent is a primary driver of pollinator attraction and reproductive isolation in deceptive orchids. Yet, little is known about the variation and evolution of scent in a phylogenetic framework and how pollination affects the biosynthesis and emission of scents in these lineages. This study characterizes scent diversity across Cypripedium, a genus of deceptive orchids, examines phylogenetic constraints, and investigates post-pollination effects on scent composition in one of the species. Methods: Floral volatile organic compounds (VOCs) were sampled from 31 Cypripedium taxa using dynamic headspace techniques, and analysed by gas chromatography coupled to mass spectrometry (GC/MS). Uni- and multivariate methods were used to analyse intra- and interspecific scent variation and test for phylogenetic signal in floral scent. Post-pollination effects on scent composition were experimentally tested in C. henryi using four pollination treatments, combined with RNA-seq analyses of floral tissues to examine transcriptional responses in VOC biosynthetic pathways. Key results: We detected 258 floral VOCs, revealing a high chemical diversity dominated by terpenoids, aliphatics, and aromatic compounds. Floral scent composition was highly species-specific, and closely related taxa often shared only few compounds. Scent composition differed among pollination groups, but these groups explained only a limited proportion of overall scent variation. We detected a significant but weak phylogenetic signal, suggesting limited evolutionary constraint in floral scent. Pollination had limited effect on C. henryis floral scent and volatile biosynthesis gene expression, despite a significant decrease in total scent emission after pollinium deposition. Transcriptional changes predominantly occurred in the petals rather than the labellum and staminode. Conclusion: Floral scent evolution in Cypripedium is characterized by high chemical diversity, and a weak phylogenetic constraint, consistent with variable selection in food-deceptive systems. The pollination study further suggests the absence of a strong, directed post-pollination effect on the floral scent of C. henryi. Keywords: Cypripedium; deceptive pollination; floral scent; volatile organic compounds (VOCs); phylogenetic signal; linalool; post-pollination effects; transcriptome profiles; differential gene expression; floral organs

plant biology↗

bioRxiv2026

Tracing Sticky Trails: The Historical Biogeography of Australia's Glandular Goose-foots (Dysphania, Chenopodioideae, Amaranthaceae)

AimThe overarching aim of this study is to reconstruct the spatiotemporal evolutionary history of Australian Dysphania, including testing the littoral connection hypothesis, assessing the role of reticulation, and identifying the major drivers of diversification within the lineage. LocationAustralia and New Zealand TaxonDysphania, Chenopodioideae, Amaranthaceae, Caryophyllales, Angiosperms MethodsUsing a DNA sequence dataset based on a target enrichment approach with custom baits designed for Chenopodioideae, we compared alternative biogeographic and ancestral habitat models to infer the spatiotemporal evolutionary history of Australian Dysphania. In addition, we applied several complementary analyses to assess concordance and conflict within our phylogenomic datasets, estimate ploidy levels, and compare ecological niches among closely related species. Results and Main conclusionsOur results reveal a close evolutionary relationship between Sub-Saharan African and Australian desert ephemerals and indicate that Australian Dysphania originated through an ancestral reticulation event. The last common ancestor reached northwestern Australia during the Miocene, occupied riverine desert habitats, and migrated eastward with their expansion, potentially undergoing ecological speciation. Four major Australian clades subsequently diversified across Miocene to Pleistocene landscapes, from riverine deserts to salt lake mosaics, with divergence likely driven by salinity gradients, flood regimes, and microhabitat partitioning rather than polyploidisation or geographic isolation.

plant biology↗

bioRxiv2026

Insights into the functional and genetic basis of heteranthery in Arthrostemma ciliatum Pav. ex D.Don (Melastomataceae)

BackgroundMelastomes are well known for their striking diversity in stamen morphologies mostly adapted to buzz pollination by bees. The variously modified connective appendages and heteranthery in the family have fascinated botanists for more than two centuries and a variety of functions associated with pollination have been discovered for these staminal traits over the years. The repeated evolutionary shifts in these traits have been linked to pollinator shifts, likely contributing to diversification in the family. The evolutionary lability of staminal traits, especially the connective morphology, led us to hypothesize that these traits might be controlled by relatively simple genetic mechanisms and we here take the first steps to test this hypothesis by using a comparative transcriptomics approach with Arthrostemma ciliatum as our model. We also tested the functional significance of heteranthery and whether the classical division of labour hypothesis holds true for this species by comparing the number, size and viability of pollen in the two stamen types. ResultsStaminal development of this species was studied and suitable stages for transcriptome comparisons were identified. Differential expression analyses between the morphologically distinct stamen whorls at four developmental stages showed the differential expression of several transcripts involved in stamen development/elongation. Pollen comparisons between the two whorls showed that the antepetalous/inner whorl stamens have a significantly higher number of pollen and higher germination rates while the antesepalous/outer whorl stamens have significantly larger pollen. ConclusionsWe identified Jasmonate and Gibberellin signalling pathway genes (JAZ, GID1, DELLA and ARF homologs), EPF/EPFL family genes, autophagy related genes (VPE homologs) and S Locus ELF homologs as putative candidates involved in causing staminal dimorphism in A. ciliatum. Our results indicate that, for the heterantherous morph of this species, the shorter stamens (antepetalous/inner whorl) have both pollinating and feeding functions contradicting the division of labour theory. We also report the possible existence of heterostyly in A. ciliatum as an outbreeding mechanism.

evolutionary biology↗

bioRxiv2025

Phylogenomics and Systematics of African Sesuvium (Aizoaceae)

Sesuvium (Sesuvioideae-Aizoaceae) comprises leaf succulent annual and perennial herbs distributed in coastal or saline sites of subtropical and tropical regions. Some species of the genus tolerate highly salinized or polluted soils and show soil-improving properties. Sesuvium shows high flexibility of photosynthetic types, including and integrating C3, C4, and CAM photosynthesis. Previous molecular phylogenetic studies failed to resolve the infrageneric relationships of the genus. However, a better understanding of the systematics of this group is a prerequisite for further evolutionary studies. We explored the suitability of genome skimming, including mainly herbarium material, to produce a robust phylogeny of the presumably young African clade of Sesuvium. The approach generated an average of 6,289 orthologs per genome skimming sample and 30 complete to mostly complete plastomes. The coalescent-based species tree, as well as the plastome tree, shows stable resolution at the backbone of the African Sesuvium clade. An annual C3 species, here newly described, is sister to a C4 clade that is subdivided into two subclades, one comprising the annual S. hydaspicum (incl. S. nyasicum) and the other three perennial species, S. crithmoides, S. congense, and S. sesuvioides. Within each of these two subclades, high gene tree discordance, mainly driven by gene tree estimation error, was found.

evolutionary biology↗

bioRxiv2024

Building a robust backbone for Astragalus (Fabaceae) using a clade-specific target enrichment bait set

Premise of the studyWith over 3100 species, Astragalus (Fabaceae) has long fascinated botanists as the largest genus of flowering plants. With an origin in the Middle Miocene, Astragalus has one of the highest diversification rates known in flowering plants. Comprehensive taxonomic treatments exist, and the genus is currently subdivided into 136 sections in the Old World and 93 sections in the New World based on morphological characters. Despite considerable efforts, a comprehensive and well-resolved phylogeny of the genus is still lacking. MethodsHere, we reconstruct the backbone phylogeny of Astragalus using a custom bait set capturing 819 loci specifically designed for a target enrichment approach in the Astragalean clade. We carefully selected a set of 107 taxa representing all major clades currently recognized in Astragalus. Of those, 80 newly sequenced taxa were obtained from herbarium specimens as old as 110 years. Key resultsWe retrieved all the targeted loci and additional off-target plastome sequences for all samples, including the 80 herbarium specimens. Our phylogenetic analysis reinforced the currently accepted backbone phylogeny of Astragalus with high support and unprecedented details, additionally providing insights into cytonuclear phylogenetic conflicts in the genus. Evidence for potential reticulate evolution was found, providing a possible explanation for the conflicts observed. ConclusionsThis work represents an important milestone in obtaining a comprehensive, herbarium-based phylogeny of Astragalus, which will constitute the base to study a wealth of relevant biological questions, for example, the still unanswered question of what drove the rapid diversification of Astragalus, with important repercussions on our understanding of diversification in natural contexts.

evolutionary biology↗

bioRxiv2024

A new phylogenetic framework for the genus Kalanchoe (Crassulaceae) and implications for infrageneric classification

Background and AimsKalanchoe is a diverse genus in the Crassulaceae, with a centre of diversity in Madagascar and sub-Saharan Africa. The genus is known for its popularity in horticulture, its use as a model system for research on CAM photosynthesis and vegetative reproduction, its high invasive potential, and its use in traditional medicine. The genus-rank circumscription and infrageneric classification of Kalanchoe has been the subject of debate for centuries, especially regarding the status and rank of what is now treated as K. subg. Bryophyllum and K. subg. Kitchingia. We aim to generate a densely sampled phylogeny of Kalanchoe s.l. and evaluate the current infrageneric classification system. MethodsWe inferred a phylogenetic tree for Kalanchoe using a ddRAD sequencing approach, covering 70% of taxa and four out of five subgenera currently recognised in the genus. Key ResultsWe recovered four well-supported clades, partially corresponding to the current subgeneric classification. Kalanchoe subg. Calophygia resolves as sister to the rest of the genus. The relationships among the three remaining clades, however, receive less support. The predominantly mainland African K. subg. Kalanchoe forms a strongly supported clade that resolves as sister to K. subg. Bryophyllum. These two clades are together sister to a clade containing mainly species from K. subg. Kitchingia and K. sect. Pubescentes. ConclusionsThe current subgeneric classification of Kalanchoe is partially backed up by our phylogenetic tree but requires further refinement. The tree topology suggests a Malagasy origin of the genus and one dispersal event to the African mainland, with subsequent dispersal from continental Africa to the Arabian Peninsula and Southeast Asia. The formation of bulbils on the leaf margin is restricted to a larger clade within K. subg. Bryophyllum and thus only evolved once. Our tree provides a framework for further taxonomic, evolutionary, and physiological research on the genus.

evolutionary biology↗

bioRxiv2024

Systematics of the fleshy-fruited Sonerileae (Melastomataceae)

With approximately 1080 species, Sonerileae is the second largest tribe in the Melastomataceae. Approximately 40% of Sonerileae species belong to fleshy-fruited genera (Catanthera, Heteroblemma, Kendrickia, Medinilla, Pachycentria, and Plethiandra). Relatively few species, especially of the fleshy-fruited taxa, have been sampled for phylogenetic study. Consequently, there is huge uncertainty resulting in many unanswered questions about their evolutionary history, including the monophyly of the largest genus, Medinilla. In this study, the phylogeny of the fleshy-fruited Sonerileae was reconstructed using 385 nuclear and 81 plastid protein-coding loci recovered from target capture. Our study revealed that the fleshy fruited Sonerileae are polyphyletic and belong to three lineages. Kendrickia is sister to an Afrotropical endemic clade. Heteroblemma and Catanthera belong to a second clade and are most closely related to some Phyllagathis and Driessenia species. Medinilla forms a third clade, and includes Pachycentria and Plethiandra. Within Medinilla, fifteen clades are identified and characterized. To make Medinilla monophyletic, the genus is redefined to include Pachycentria and Plethiandra. Major lineages identified within Medinilla lay the groundwork for an infrageneric classification system. Areas of the phylogenetic tree with high conflict or weak sampling are identified to aid further studies in the tribe.

plant biology↗

bioRxiv2024

Target Enrichment Data Uncovers Rapid Radiation, Whole Genome Duplication, and Extensive Hybridization in Slipper Orchid Genus Cypripedium L.

Background and AimsCypripedium is the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny of Cypripedium and explore its evolutionary history using target capture data for the first time. MethodsWe used the orchid-specific bait set Orchidaceae963 in combination with transcriptomic data to reconstruct the phylogeny of Cypripedium based on 913 nuclear loci, covering all 13 sections. Subsequently, we investigated discordance among nuclear and chloroplast trees, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified potential gene (genome) duplication and hybridization events. Key ResultsAll sections were recovered as monophyletic, contrary to the two subsections within sect. Cypripedium. The two subclades within this section did not correspond to its subsections but matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect. Cypripedium, which can be attributed to hybridization events detected based on phylogenetic network analyses, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Oligocene ([~]30 Ma), with a lineage of potentially hybrid origin spreading to the Old World in the Early Miocene ([~]22 Ma). The rapid radiation at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition ([~]15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution within Cypripedium. ConclusionsOur study provided novel insights into the evolutionary history of Cypripedium based on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

evolutionary biology↗

bioRxiv2023

C4-like Sesuvium sesuvioides (Aizoaceae) exhibits CAM in cotyledons and putative C4+CAM metabolism in adult leaves as revealed by transcriptome analysis

The co-occurrence of C4 and CAM photosynthesis in a single species seems to be unusual and rare, probably because of the difficulty to co-regulate both pathways effectively. Nevertheless, it represents a unique chance in gaining new insights into the evolution and regulation of these complex pathways. Comparative transcriptomics using RNA-seq revealed C4-like and CAM photosynthesis in Sesuvium sesuvioides (Aizoaceae) leaves and cotyledons, respectively. When compared to cotyledons, phosphoenolpyruvate carboxylase 4 (PEPC4) and some key C4 genes were found to be up regulated in leaves. During the day, the expression of NADP-dependent malic enzyme (NADP-ME) was significantly higher in cotyledons than in leaves. The acidity titration confirmed higher acidity in the morning than in the previous evening indicating the induction of weak CAM in cotyledons by environmental conditions. Comparison of the leaves of S. sesuvioides (C4-like) and S. portulacastrum (C3) revealed that PEPC1 was significantly higher in S. sesuvioides, while PEPC3 and PEPC4 were up-regulated in S. portulacastrum. Finally, potential key regulatory elements involved in the C4 and CAM pathways were identified. These findings provide a new species in which C4 and CAM co-occur and raises the question if this phenomenon is indeed so rare or just hard to detect and probably more common in succulent C4 lineages. HighlightC4 and CAM metabolism co-occur in the C4-like species Sesuvium sesuvioides (Aizoaceae).

plant biology↗

bioRxiv2022

Exploring the possible role of hybridization in the evolution of photosynthetic pathways in Flaveria (Asteraceae), the prime model of C4 photosynthesis evolution

Flaveria (Asteraceae) is the prime model for the study of C4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C3-C4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of trait shifts during C4 evolution. To assess the possible role of hybridization in C4 evolution in Flaveria, we re-analyzed transcriptome data of 17 Flaveria species to infer the extent of gene tree discordance and possible reticulation events. We found massive gene tree discordance as well as reticulation along the backbone and within clades containing C3-C4 intermediate and C4-like species. An early hybridization event between two C3 species might have triggered C4 evolution in the genus. The clade containing all C4 species plus the C4-like species F. vaginata and F. palmeri is robust but of hybrid origin involving F. angustifolia and F. sonorensis (both C3-C4 intermediate) as parental lineages. Hybridization seems to be a driver of C4 evolution in Flaveria and likely promoted the fast acquisition of C4 traits. This new insight can be used in further exploring C4 evolution and can inform C4 bioengineering efforts.

evolutionary biology↗

bioRxiv2021

On the hybrid origin of the C2 Salsola divaricata agg. (Amaranthaceae) from C3 and C4 parental lineages

O_LIC2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 can be interpreted as an evolutionary precursor of C4 and/or as the result of hybridization between a C3 and C4 lineage. C_LIO_LIWe compared the expression of photosynthetic traits among populations of the Salsola divaricata agg. (C2) from humid subtropical to arid habitats on the coasts of the Canary Islands and Morocco and subjected them to salt and drought treatments. We screened for enhanced C4-like expression of traits related to habitat or treatment. We estimated species trees with a transcriptome dataset of Salsoleae and explored patterns of gene tree discordance. With phylogenetic networks and hybridization analyses we tested for hybrid origin of the Salsola divaricata agg. C_LIO_LIWe observed distinct independent variation of photosynthetic traits within and among populations and no clear evidence for selection towards C4-like trait expression in more stressful habitats or treatments. We found reticulation and gene tree incongruence in Salsoleae supporting a putative hybrid origin of the Salsola divaricata agg. C_LIO_LIC2 photosynthesis in the Salsola divaricata agg. combines traits inherited from its C3 and C4 parental lineages and seems evolutionarily stable, possibly well adapted to a wide climatic amplitude. C_LI

evolutionary biology↗

bioRxiv2021

Insights into regulation of C2 and C4 photosynthesis in Amaranthaceae/Chenopodiaceae using RNA-Seq

Amaranthaceae (incl. Chenopodiaceae) show an immense diversity of C4 syndromes. More than 15 independent origins of C4 photosynthesis, partly in halophytic and/or succulent lineages, and the largest number of C4 species in eudicots signify the importance of this angiosperm lineage in C4 evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldia diffusa (C3), Sedobassia sedoides (C2), and Bassia prostrata (C4). Results show that B. prostrata belongs to the NADP-ME type and core genes encoding for C4 cycle are significantly up-regulated when compared to Sed. sedoides and T. diffusa, Sedobassia sedoides and B. prostrata share a number of up-regulated C4-related genes, however, two C4 transporters (DIT and TPT) are found significantly up-regulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C3 specific TFs is higher in C2 species as compared to C4 species, instead the C2 species show their own set of up-regulated TFs. Taken together, our study indicates that the hypothesis of the C2 photosynthesis as a proxy towards C4 photosynthesis is questionable in Sed. sedoides and more in favour of an independent evolutionary stable-state. HighlightTranscript expression profiles of C2 species are distinct and best explained as representing an independent evolutionary stable state.

plant biology↗

bioRxiv2019

Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The dataset included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations.

evolutionary biology↗