Biology subjects

Zuntini, A. R.

Publications and source records attributed to Zuntini, A. R..

9 recordsLinked to original sources

bioRxiv2026

A large phylogenetic tree for euphyllophytes

PremiseMolecular datasets for estimating phylogenetic trees increasingly include more species and gene regions. Often trees are constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly expanding datasets. MethodsWe generated a phylogenetic tree (and 1,000 bootstrap trees) with divergence times that span euphyllophytes. To do this, we integrated taxonomically broad dated backbone phylogenies with species-level trees generated from phylogenetic analysis of individual clades. Datasets for species-level trees were assembled using PyPHLAWD. ResultsThe resulting dated phylogenetic tree includes: 121,641 angiosperm species; 1,026 gymnosperms; and 5,603 ferns. This is the largest euphyllophyte phylogenetic tree constructed to date. Topological uncertainty spikes at the start of the Cretaceous and gradually increases during the Cenozoic. Uncertainty in age estimates gradually increases in the Cenozoic but increases dramatically in the most recent 5 Myrs. DiscussionThis dated phylogenetic framework can underpin evolutionary studies spanning euphyllophytes, and enable the integration of insights from the recent to the distant past. Our approach also enables the tree to be easily updated in the future to reflect future increases in data availability, and systematic and taxonomic advances within specific clades.

plant biology↗

bioRxiv2025

Trait-dependent diversification and spatio-ecological limits drive angiosperm diversity unevenness across the Canary Islands archipelago

Island biotas often show highly uneven species richness among lineages, influenced by clade age, diversification rates, and/or spatio-ecological limits. However, disentangling these drivers has been challenging due to the lack of comprehensive datasets across multiple lineages in the same geographical arena. The flora of the Canary Islands includes hundreds of plant lineages with contrasting species richness and harbours the highest number of species that evolved their woodiness in-situ ("insular woodiness"). Here, we present a phylogenomic reconstruction for Canary Island angiosperms and show that diversity unevenness in the flora is not driven by lineage age but by trait-dependent diversification and spatio-ecological limits. Our phylogenomic dataset, based on 1,244 newly generated and 501 published DNA sequences for 669 Canary Island species and 771 closely related mainland taxa, allows us to simultaneously study 435 plant lineages ([~]50% of total). Applying dynamic stochastic modelling, we find the flora is shaped by high extinction and colonisation rates, maintaining a macroevolutionary equilibrium. Additionally, insular woody lineages exhibit higher diversification rates than the remaining flora. Our results suggest the uneven diversity of a highly dynamic insular region can be explained by the interaction of trait evolution and ecological constraints, providing insights into island biodiversity dynamics.

evolutionary biology↗

bioRxiv2024

Towards a phylogenomic classification of Magnoliidae

PremiseMagnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. MethodsHere we present the first comprehensive phylogenomic analysis of Magnoliidae as a whole, sampling 235 species from 199 (74%) genera and representing all families and most previously accepted subfamilies and tribes. We analyze newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies. ResultsWhile our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we find support for the position of Hydnoraceae as sister to the remainder of Piperales and, for the first time, resolve the backbone of relationships among most genera of Myristicaceae. ConclusionsAlthough some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step towards reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for Magnoliidae, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.

evolutionary biology↗

bioRxiv2023

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats

O_LIPoales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times. C_LIO_LIWe sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution. C_LIO_LIDiversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories. C_LIO_LIThe Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats. C_LI

ecology↗

bioRxiv2023

Phylogenomic analysis reveals the evolutionary origins of five independent clades of forage grasses within the African genus Urochloa

Background and AimsThe grass genus Urochloa (Brachiaria) includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America, and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis, and M. maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems, and frequent polyploidy are widely shared within the genus. The combination of these traits likely favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. MethodsUsing a target enrichment sequencing approach (Angiosperms353 baits), we inferred a species level phylogeny for Urochloa sensu lato, encompassing 57 species ([~]50% of the genus) and outgroups. We determined the phylogenetic placement of agriculturally important species and identify their closest wild relatives. Further, we mapped key traits associated with forage crop potential to the species tree, exploring trait distribution across the genus. Key ResultsAgricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis, and large seeds) independently evolved in forage clades. ConclusionsUrochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. The African continent is the centre of origin for these clades and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives needs to be better assessed to improve sustainability in Urochloa cultivar production.

evolutionary biology↗

bioRxiv2023

New to Ehretiaceae: Keraunea. Re-evaluation of a genus of climbers from Brazil.

We definitively place Keraunea, a genus of showy forest climbers from remnants of the Mata Atlantica of Brazil, in Ehretiaceae. Previously Keraunea had been ascribed to Convolvulaceae based on morphology, or divided between Malpighiaceae and Ehretiaceae based on molecular analyses (polyphyletic). Keraunea is morphologically anomalous in the Ehretiaceae, having fruits which are held in the centre of a large wing-like bract by adnation of the pedicel, and due the stem-twining habit of some species. However, morphologically Keraunea shares two apomorphies with monotypic Cortesia Cav., halophytic shrubs of Argentina: 1) "two parted endocarps" (the fruit contains two endocarps each with two 1-seeded cells, while four 1-seeded endocarps are plesiomorphic in Ehretiaceae) and 2) a large bract that subtends the flower (absence of bracts is plesiomorphic in Ehretiaceae). A combined tree using four markers (ITS, trnL-F, rbcL and matK) places the three species of Keraunea sampled unambiguously in a clade with Ehretia + Cortesia + Halgania and monophyly for Keraunea is shown with high support. In an ITS tree Keraunea is sister to Cortesia with low support. We expand the generic description of Keraunea including the first account of the internal fruit structures and the seed, and present new data on the vegetative architecture including variation within the genus, some species being stem twiners while one species at least, is described as a scandent shrub. Keraunea lombardiana, previously included within K. brasiliensis, is formally described from Minas Gerais and Bahia as the third species of the genus and both these species are described. In all five species are recognised but two, known to us only from digital images, are not formally described because sufficiently detailed descriptions cannot be made. All five species are mapped, and provisional conservation assessments are recorded, of either Endangered or Critically Endangered. The state of Bahia, with three species, has the highest species diversity, mainly in dry forest. Three species appear confined to moist coastal forest, extending southwards from Bahia to the state of Rio de Janeiro. Keraunea remains incompletely known. Not one of the species has both anthetic flowers and fruits described. Studies on pollen, germination, anatomy, embryology and phytochemisty are entirely lacking. Field observations of pollination, seed dispersal and phenology are also required. However, the most urgent requirement is undoubtedly a formal taxonomic revision based on a full herbarium search and targeted fieldwork, with full IUCN 2012 extinction risk assessments for each taxon. This is urgent because it seems that all the taxa that we present in this paper (and more that can be expected to be found) appear to be highly range restricted and generally not to occur in protected areas, and so appear to be highly threatened.

plant biology↗

bioRxiv2022

From southern Africa and beyond: historical biogeography of the Ledebouriinae (Scilloideae, Asparagaceae)

AimWithin sub-Saharan Africa, plants inhabiting more seasonal and arid landscapes showcase unique distributional patterns that hint at fascinating evolutionary histories. The Ledebouriinae (Scilloideae, Asparagaceae) are widespread throughout such climates in sub-Saharan Africa, and Madagascar, the Middle East, India, and Sri Lanka. Long-distance dispersal has been hypothesized as leading to such a widespread distribution; however, low taxon sampling and taxonomic uncertainties have made uncovering the history of the Ledebouriinae difficult. Here, using the most comprehensive sampling of the lineage to date, we hypothesize that both vicariance and dispersal events impacted the biogeographical history of these bulbous monocots within and outside of Africa. LocationSub-Saharan Africa, Madagascar, Asia TaxonLedebouriinae (Scilloideae, Asparagaceae) MethodsWe infer age estimates using penalized likelihood as implemented in treePL. Capitalizing on our broad geographic sampling, we use BioGeoBEARS to reconstruct ancestral ranges and investigate the role of vicariance and dispersal. ResultsOur results suggest the Ledebouriinae originated within the past [~]30 myr in southeastern sub-Saharan Africa, with the major subclades arising soon thereafter. Although long-distance dispersal cannot be fully ruled out, our results lead us to hypothesize vicariance was the major process responsible for the current distribution of Ledebouria in Eurasia. We recover two distinct Ledebouria groups that overlap in eastern Africa, but are divided into mostly northern and southern clades with divergent biogeographical histories, and each showing an independent dispersal to Madagascar. A similar north-south split is seen in Drimiopsis. Additionally, we recover a complex biogeographic history in the predominantly sub-Saharan African Ledebouria clade, with a rapid radiation estimated at [~]14 mya. Main conclusionsWe recover evidence to suggest that the expansion of seasonal rainfall and aridity in sub-Saharan Africa, coupled with orogeny, may have fostered the diversification of the Ledebouriinae and many subclades. Miocene-driven aridification may have caused fragmentation of a once widespread distribution that led to their occurrence in Eurasia.

evolutionary biology↗

bioRxiv2022

Global Phylogeny of the Brassicaceae Provides Important Insights into Gene Discordance

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

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↗