Biology subjects

Bellot, S.

Publications and source records attributed to Bellot, S..

9 recordsLinked to original sources

bioRxiv2025

Functional traits drive speciation in tropical palms through complex interactions between genome size, adaptation and allometry

O_LIThe importance of functional trait evolution and genome size on plant speciation are well established, but their interactive effects remain untested in a single comparative macroevolutionary framework. C_LIO_LIWe integrated phylogenetic, trait and genome size data for palms (Arecaceae) - a large pantropical family (>2600 species) with 167-fold variation in trait and 60-fold variation in genome size. We used structural equation modelling to test three key hypotheses: trait evolution promotes speciation (H1: trait flexibility hypothesis), and, speciation and trait evolution rates are constrained by allometry (H2: allometric constraint hypothesis) and genome size (H3: large genome constraint hypothesis). C_LIO_LIWe detected seven major speciation rate shifts during the ca. 110-million-year history of palms. Tip-derived speciation rates increased with faster evolution in leaves and plant height, supporting H1, whereas correlated evolution between trait evolution rates indirectly influenced speciation, supporting H2. Large genomes decreased plant height and stem diameter evolutionary rates, but increased leaf size evolution and speciation rates, thus partly supporting H3. C_LIO_LIOur findings illustrate how the complex interplay between genome size, allometry and trait evolvability affect speciation, emphasizing the importance of holistic approaches in macroevolution. Furthermore, our results point to potential general mechanisms driving speciation rates throughout the plant Tree of Life. C_LI

evolutionary biology↗

bioRxiv2024

Early Cretaceous Origin and Evolutionary History of Palms (Arecaceae) inferred from 1,033 Nuclear Genes and a New Synthesis of Fossil Evidence

AO_SCPLOWBSTRACTC_SCPLOWTropical rainforests are home to almost half of all known plant diversity, yet a shortfall in tropical plant phylogenetic hypotheses is hindering our understanding of how rainforests have formed and adapted to past global changes. Phylogenetic and historical biogeographic evidence from key rainforest lineages, including palms (Arecaceae), are required to illuminate the history of these ecosystems. However, our current understanding of the palm tree of life is based on uneven sampling of data from the plastid and nuclear genome, and numerous palm genera and palm fossils have been described or revised over the past decade, casting doubt on many palm relationships, ages and ancestral ranges inferred in previous studies. Here, we infer the phylogenetic relationships of all palm genera based on data from 1,033 nuclear genes generated using target sequence capture. Our palm tree of life is highly resolved and supported. Remaining areas of ambiguity reflect the complex dynamics of palm evolution, including many rapid diversification events in subfamily Arecoideae and putative cases of ancient reticulation throughout the family. We review the phylogenetic placement and age of hundreds of palm fossils and use a vetted selection to estimate divergence times and ancestral ranges for all palm genera. We show that the family is older than previously thought, likely first diversifying in the Early Cretaceous in Laurasia, and that three quarters of the genera had originated by the Oligocene. The early spread of palms across the world involved at least 40 long-distance dispersals across oceanic gaps. Dispersals away from northern latitudes vastly outnumber dispersals into these latitudes, consistent with the ancient affinity of palms for megathermal climates, and suggesting that global cooling during the Oligocene was a major constraint on early palm distribution. Our dated phylogenomic tree and curated fossil dataset provide a new foundation for evolutionary studies on palms, opening the door to deeper research on the rainforest biome in which they thrive.

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 Ecology of Palm Genomes: Repeat-associated genome size expansion is constrained by aridity

O_LIGenome size varies 2,400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat communities are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. C_LIO_LIWe measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically-informed linear models to explore relationships between repeat dynamics and environmental factors. C_LIO_LIWe show that palm genome size and repeat community composition are best explained by aridity. Specifically, EnSpm CACTA repeats were more abundant in palm species from wetter environments, which generally had larger genomes (>2.15Gbp/1C), suggesting amplification. In contrast, Ty1-copia Angela elements were more abundant in drier environments. C_LIO_LIOur results suggest water stress inhibits the expansion of repeats through selection on upper genome size limits. However, Ty1-copia Angela elements, which may associate with stress-response genes, have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat communities. C_LI

evolutionary biology↗

bioRxiv2021

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a "first pass" angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the worlds natural history collections.

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 phylogenomic analysis of Nepenthes (Nepenthaceae)

Nepenthaceae is one of the largest carnivorous plant families and features ecological and morphological adaptations indicating an impressive adaptive radiation. However, investigation of evolutionary and taxonomic questions is hindered by poor phylogenetic understanding, with previous molecular studies based on limited loci and taxa. We use high-throughput sequencing with a target-capture methodology based on a 353-loci, probe set to recover sequences for 197 samples, representing 151 described or putative Nepenthes species. Phylogenetic analyses were performed using supermatrix and maximum quartet species tree approaches. Our analyses confirm five Western outlier taxa, followed by N. danseri, as successively sister to the remainder of the group. We also find mostly consistent recovery of two major Southeast Asian clades. The first contains common or widespread lowland species plus a Wallacean-New Guinean clade. Within the second clade, sects. Insignes and Tentaculatae are well supported, while geographically defined clades representing Sumatra, Indochina, Peninsular Malaysia, Palawan, Mindanao and Borneo are also consistently recovered. However, we find considerable conflicting signal at the site and locus level, and often unstable backbone relationships. A handful of Bornean taxa are inconsistently placed and require further investigation. We make further suggestions for a modified infra-generic classification of genus Nepenthes.

evolutionary biology↗

bioRxiv2017

Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny

1) BackgroundSeed-banking (the ability to persist in the soil over many generations) is usually considered as a dormant stage where genotypes are \"stored\" as a bet-hedging strategy in response to unpredictable environments. However, seed dormancy may instead have consequences for the integrity of the DNA and generate novel mutations.\n\n2) MethodsWe address this paradox by building phylogenies based on the plastomes and nuclear ITS of species belonging to ten angiosperm clades. In each clade, the substitution rate (branch-length) of a seed-banking species is compared with that of a closely-related non-seed-banking species.\n\n3) ResultsSeed-banking species show as high or higher substitution rates than non-seedbanking species, and therefore mutations occur in dormant seeds at a rate at least as high as in above-ground plants. Moreover, seed born mutations have the same probability to reach fixation as those from above ground. Our results are robust to differences in selection, generation time, and polymorphism.\n\n4) ConclusionsMutations occurring in seeds, and thus seed-banking, affect the population diversity of plant species, and are observable at the macro-evolutionary scale. Our study has consequences for seed storage projects, since the stored seeds are likely to accumulate mutations at a higher rate than previously thought.

evolutionary biology↗