Biology subjects

Chomicki, G.

Publications and source records attributed to Chomicki, G..

12 recordsLinked to original sources

bioRxiv2026

Stemona genomes illuminate fatty acid partitioning between seeds and elaiosomes mediating wasp dispersal

O_LISeed dispersal by wasps (vespicochory) is documented in five angiosperm families, with phylogenies suggesting that most vespicochorous lineages evolved from ant-dispersed (myrmecochorous) ancestors. While recent work has identified cues attracting wasp dispersers, the molecular basis remains unclear. C_LIO_LITo shed light on the molecular basis of vespicochory, we generated chromosome-level genomes for the wasp-dispersed Stemona tuberosa, and its close ant-dispersed relative S. mairei. Combining comparative genomic, transcriptomic, lipidomic, and functional analyses, we ask (i) how chemical elaiosome differentiation occurs during seed development, and (ii) how key mutualism-associated genes evolved in Stemona. C_LIO_LIWe show that elaiosomes up-regulate stearoyl-ACP {Delta}9 desaturases (SAD) and accumulate oleic acid and 1,2-diolein, which serve both as food rewards and as precursors for CER1/3-mediated biosynthesis of (Z)-9-tricosene, the key wasp attractant. By contrast, high expression of FatB and DGAT1 in seeds is associated with medium-chain fatty acids (MCFAs) production. Comparative genomics indicates conservation of these genes across Stemona, with S. tuberosa-specific FatB expansion and SAD/CER1/3 repertoire divergence. C_LIO_LIOur work supports a model for elaiosome-seed fatty-acid differentiation linking recruitment and nourishment in vespicochory. Given that oleic acid and 1,2-diolein are also key cues in myrmecochory, this shared biochemical basis may help explain how vespicochory evolves from ant-dispersed ancestors. C_LI

evolutionary biology↗

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↗

bioRxiv2023

The Origin And Speciation Of Orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their geographical origin, historical spread across the globe, and hotspots of speciation remain uncertain due to the lack of a broad phylogenomic framework. We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and [~]7% (1,921) of the currently 29,524 accepted species. We then use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distribution data through the World Checklist of Vascular Plants. Orchids most recent common ancestor is traced back to the Late Cretaceous in Laurasia. The modern Southeast Asian range of subfamily Apostasioideae is interpreted as relictual, matching the history of numerous clades that went extinct at higher latitudes following the global climate cooled during the Oligocene. Despite their ancient origins, modern orchid species diversity mainly originated over the last 5 Ma, with the fastest speciation rates found in south-eastern Central America. Our results substantially alter our understanding of the geographic origin of orchids, previously proposed as Australian, and further pinpoint the role of Central American as a region of recent and explosive speciation.

evolutionary biology↗

bioRxiv2021

The origin and drivers of Neotropical plant and tetrapod diversification

The origins and evolution of the outstanding Neotropical biodiversity are still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we evaluate four evolutionary scenarios assuming different diversification trajectories and drivers of Neotropical diversification, and assess their variation across Neotropical regions and taxa. Our analysis of 150 phylogenies (12,512 species) of seed plants and tetrapods reveals that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity also account for 21% and 9% of Neotropical diversity, respectively. We identify five biogeographic areas that represent distinctive units of long-term Neotropical evolution (Pan-Amazonia, Dry Diagonal, Bahama-Antilles, Galapagos, and an elsewhere region) and find that diversity dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ substantially across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with climate change, with potential implications for future adaptation and ecosystem resilience.

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

Hundreds of nuclear and plastid loci yield insights into orchid relationships

Premise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated. MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes. Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes. ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

evolutionary 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↗

bioRxiv2017

From tree tops to the ground: reversals to terrestrial habit in Galeandra orchids (Epidendroideae: Catasetinae)

The colonization of the epiphytic niche of tropical forest canopies played an important role in orchids extraordinary diversification in the Neotropics. However, reversals to the terrestrial habit occurred sparsely in species of Epidendroideae. To better understand which factors might have been involved in reversals to terrestrial habits in the predominantly epiphytic Epidendroideae, we investigate Galeandra diversification in time and space. We hypothesized that the reversal to the terrestrial habitat is linked to the origin of open vegetation habitats in South America. We generated a time-calibrated phylogeny based on a matrix of 17 out of 20 species of Galeandra plus outgroups and seven DNA markers. We found that Galeandra originated towards end of the Miocene, about 10 Ma in Amazonia (including the Guiana Shield). The terrestrial clade originated synchronously with the rise of dry vegetation biomes, suggesting that aridification during the last 5 million years dramatically impacted the diversification of epiphytic lineages in the Neotropics. Habit is correlated with floral spur lengths and geographic range size. The longer spurs and narrower ranges are found in epiphytic species: probably adapted to a specialized pollination mode, associated to the long-tongued Euglossini bees, which also prefer forested habits. The terrestrial species presents variable floral spurs and wide distribution ranges, with evidence of self-pollination, suggesting the loss of specialized pollination system and concomitant range expansion.

evolutionary biology↗

bioRxiv2017

Multiple Geographical Origins of Environmental Sex Determination enhanced the diversification of Darwins Favourite Orchids

Environmental sex determination (ESD) - a change in sexual function during an individual life span driven by environmental cues - is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative mating systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.

evolutionary biology↗

bioRxiv2017

Experimental signal dissection and method sensitivity analyses reaffirm the potential of fossils and morphology in the resolution of seed plant phylogeny

The placement of angiosperms and Gnetales in seed plant phylogeny remains one of the most enigmatic problems in plant evolution, with morphological analyses (which have usually included fossils) and molecular analyses pointing to very distinct topologies. Almost all morphology-based phylogenies group angiosperms with Gnetales and certain extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in published seed plant morphological datasets. We use parsimony, Bayesian inference, and maximum likelihood approaches, combined with a number of experiments with the data, to address the morphological-molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and model based approaches with morphological datasets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction, consistent across a range of methodological approaches. Thus, there is a signal for the grouping of Gnetales with conifers in morphological matrices, but it was swamped by convergence between angiosperms and Gnetales, both situated on long branches. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Even when a clade including angiosperms and Gnetales is still weakly supported by parsimony, model-based approaches favor a clade of Gnetales and conifers, presumably because they are more resistant to long branch attraction. Inclusion of fossil taxa weakens rather than strengthens support for a relationship of angiosperms and Gnetales. Our analyses finally reconcile morphology with molecules in favoring a relationship of Gnetales to conifers, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.

evolutionary biology↗

bioRxiv2017

Recent origin of Neotropical orchids in the world’s richest plant biodiversity hotspot

* The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the worlds plant species, in only 1% of the worlds land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.\n\n* We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.\n\n* We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.\n\n* Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.

evolutionary biology↗

bioRxiv2017

The improbable journeys of epiphytic plants across the Andes: Historical biogeography of Cycnoches (Catasetinae, Orchidaceae)

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical organisms. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models with and without founder-event speciation, we infer that the most recent common ancestor of Cycnoches may have originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, such biological exchange occurred well after major mountain building periods. The Andes have not acted as an impassable barrier for epiphytic lowland lineages such as orchids having a great potential for effortless dispersal because of the very light, anemochorous seeds.

evolutionary biology↗