January 2025
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51 Reads
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January 2025
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51 Reads
January 2025
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603 Reads
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1 Citation
Grasses (Poaceae) comprise c . 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153‐tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910‐tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree–species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear–plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.
November 2024
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159 Reads
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1 Citation
Madagascar is a regional diversity centre of the plant genus Erica L. (heathers; anjavidy in Malagasy), with 35 species currently recognised. There is no modern taxonomic treatment of the group, and many collections remain unidentified. We review the taxonomic history of Malagasy Erica , built largely on the 1927 revision by Perrier de la Bâthie, who treated them as Philippia . We summarise diagnostic species descriptions and incorporate them into the Erica Identification Aid. There is clearly morphological variation that is poorly reflected in current species concepts and requires further study. Malagasy Erica most likely form a single radiation also encompassing species from the Mascarenes, according to published and new phylogenetic data. However, resolution within the group is poor, and most species remain unsequenced. Literature and specimen records show that Erica is found in all regions of Madagascar except the dry west and southwest, with the highest species richness on the high mountains. Habitats include the high-altitude “ericoid thickets”, shrubland–grassland mosaics in the central highlands and on the eastern coast, and Uapaca bojeri (tapia) savanna. The ecology of individual Erica species is insufficiently known. There may be both wind- and (currently undocumented) insect-pollinated species. Many Erica species are likely to be part of dynamic ecosystems with infrequent fire regimes. The paleorecord indicates a more widespread ericoid shrub vegetation during the last glacial period. Erica is mainly used as fuelwood, but local uses as tools and medicine have also been reported. None of the Malagasy species has had its conservation status assessed, but estimates suggest at least one-fifth of the species may be threatened. Taxonomic revision of the group, coupled with phylogenomics, is an urgent priority. This would also enable better assessments of ecological variation, local uses and conservation priorities.
October 2024
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135 Reads
Increasing genome size (GS) has been associated with slower rates of DNA replication and greater cellular nitrogen (N) and phosphorus demands. Despite most plant species having small genomes, the existence of larger GS species suggests that such costs may be negligible or represent benefits under certain conditions. Focussing on the widespread and diverse grass family (Poaceae), we used data on species' climatic niches and growth rates under different environmental conditions to test for growth costs or benefits associated with GS. The influence of photosynthetic pathway, life history and evolutionary history on grass GS was also explored. We found that evolutionary history, photosynthetic pathway and life history all influence the distribution of grass species' GS. Genomes were smaller in annual and C4 species, the latter allowing for small cells necessary for C4 leaf anatomy. We found larger GS were associated with high N availability and, for perennial species, low growth‐season temperature. Our findings reveal that GS is a globally important predictor of grass performance dependent on environmental conditions. The benefits for species with larger GS are likely due to associated larger cell sizes, allowing rapid biomass production where soil fertility meets N demands and/or when growth occurs via temperature‐independent cell expansion.
May 2024
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1,074 Reads
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1 Citation
Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. The nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree–species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.
April 2024
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4,169 Reads
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83 Citations
Nature
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5–7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes⁸. This 15-fold increase in genus-level sampling relative to comparable nuclear studies⁹ provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
February 2024
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148 Reads
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1 Citation
Annals of Botany
Background and Aims The grass genus Urochloa (Brachiaria) sensu lato 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 Megathyrsus 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. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus. Methods Using a target enrichment sequencing approach (Angiosperms353), we inferred a species level phylogeny for Urochloa s.l., encompassing 54 species (~40% of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits. Key Results Agricultural 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. Conclusions Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent 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 both to develop conservation strategies, and exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.
January 2024
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43 Reads
Disentangling contributions from environmental variables is crucial for explaining global biodiversity patterns. We use wavelet power spectra to separate wavelength-dependent trends across Earth’s surface. Spectra reveal scale- and location-dependent coherence between species richness and topography ( E ), annual precipitation ( Pn ), temperature ( Tm ) and temperature range ( ΔT ). >97% of richness of carnivorans, bats, songbirds, hummingbirds and amphibians resides at wavelengths >~10 km. 30-69% is generated at scales >~10 km. At these scales, richness across the Americas is anti-correlated with E and ΔT , and positively correlated with Pn and Tm . Carnivoran richness is incoherent with ΔT , suggesting insensitivity to temperature seasonality. Conversely, amphibian richness is anti-correlated with ΔT at large scales. At scales <~10 km, richness is highest within the tropics. Terrestrial plateaux exhibit coherence between carnivoran richness and E at scales ~10 km, reflecting contributions of orogeny/epeirogeny to biodiversity. Similar findings result from transects across other continents. Scale-dependent sensitivities of vertebrate populations to climate are revealed.
November 2023
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701 Reads
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17 Citations
Poales 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 six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We 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 regionalisation analyses, historical biogeography and ancestral state estimations. Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, 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. Smaller families display unique and often divergent evolutionary trajectories. The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.
October 2023
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3,208 Reads
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75 Citations
What grows where? Knowledge about where to find particular species in nature must have been key to the survival of humans throughout our evolution. Over time, and as people colonised new land masses and habitats, interactions with the local biota led to a wealth of combined traditional and scientific wisdom about the distributions of species and their many uses. Fast-forward to the present day, and much of our current scientific knowledge of global plant and fungal diversity comes from specimens hosted by the world’s herbaria and fungaria, of which there are more than 3,000. But despite this wealth of knowledge and collections, one might be surprised to learn that, to date, we have not been able to answer one of the most fundamental questions in plant and fungal diversity with confidence – namely, how many species are there globally and in different parts of the world? The consequences of our insufficient knowledge on biodiversity and distribution are manifold. Scientists may have drawn biased – or possibly even incorrect – conclusions on the patterns and underlying drivers of diversity. Beyond the impacts of knowledge gaps and inaccuracies on efforts to answer fundamental scientific questions, there are serious implications for conservation given that several targets in the Kunming–Montreal Global Biodiversity Framework, such as those related to protecting and restoring biodiverse habitats, rely on having robust biodiversity data. To tackle this challenge, this fifth edition of State of the World’s Plants and Fungi, from the Royal Botanic Gardens, Kew (RBG Kew), focuses on the latest knowledge on the diversity and geographical distribution of plants and fungi. It relies on two major advances. The first is the release of the World Checklist of Vascular Plants complete with geographical distributions for all known species – a landmark achievement, led by RBG Kew’s Rafaël Govaerts, which took more than 35 years of meticulous and highly collaborative work. And the second is the extraction of a wealth of new information on fungal diversity from analyses of environmental DNA in soil samples across the world, combined with morphological and molecular evidence from fungarium specimens. In the following chapters, we present compelling stories demonstrating what we have learned from these and related sources of data, and how this understanding can help us foster future research and conservation. This report is based on groundbreaking research papers from many international teams of scientists. They are co-released in a collection of open-access articles titled ‘Global Plant Diversity and Distribution’ from the journals New Phytologist and Plants, People, Planet, and a review of global fungal diversity in the Annual Review of Environment and Resources. We are grateful to the Sfumato Foundation for financial support, the journals’ editorial boards, the expert reviewers, and all authors and other contributors to this important, timely and fruitful collaboration. Just as our early ancestors needed to know what grows where for their own survival, so plants and fungi need us to know where they grow – to enable us to safeguard their continued existence for generations to come.
... Though C 4 grasslands expanded later in the record during a drier period and again when human impact increased, it is important to note that open and mosaic ecosystems dominated by a matrix of grasslands and ericoid shrubland are a natural part of the highlands landscape. Conserving these ecosystems is worthwhile, especially the ericoid shrubland, which deserves focused research priorities (Hackel et al., 2024). These habitats should not be assumed to be degraded and replanted as part of the government's afforestation programme, which primarily focuses on the Central Highland's open spaces (Lacroix et al., 2016). ...
November 2024
... Some organismal groups possess nearly complete phylogenies, such as birds (e.g., Jetz et al., 2012;Jarvis et al., 2014;Prum et al., 2015) and flowering plants (Guo et al., 2023). For example, Zuntini et al. (2024) recently produced a groundbreaking phylogenomic tree of life encompassing more than half of known angiosperm genera. ...
April 2024
Nature
... Más allá de características estructurales y fisiológicas únicas, hay atributos ecológicos que hacen a los hongos un sistema de estudio particularmente complejo e interesante para la filosofía de la biología. Para empezar, su enorme biodiversidad, ya que se estima que podrían existir hasta 6,28 millones de especies de hongos en el planeta (Baldrian et al., 2022), aunque solamente han sido descritas un poco más de 155 mil (Antonelli et al., 2023). En general, ha resultado difícil aplicar los conceptos tradicionales de especie (por ejemplo, basados en reproducción sexual) a organismos diferentes a animales y plantas, lo que explicaría -en parte-esta enorme diversidad fúngica no clasificada ('dark taxa'), particularmente en el suelo (Anthony et al., 2023). ...
Reference:
Filosofía Fungi
October 2023
... Despite their value, monographs are lacking for many plant genera (Grace et al., 2021) but are also not fully explored for understanding changing plant distributions over time, which goes to show that we do not know much about global plant diversity (Cornwell et al., 2019;Ondo et al., 2024). Advances in digitizing herbarium specimens, combined with machine learning and community science initiatives such as iNat, can expedite the completion of monographs for all species in plant superfamilies with large global distributions such as legumes, grasses, orchids, and Bromeliaceae (Goettsch et al., 2015;Zizka et al., 2020;Grace et al., 2021;de Lutio et al., 2022;Elliott et al., 2024;Pérez-Escobar et al., 2024). ...
November 2023
... Most studies that examined richness-environment relationship of terrestrial vertebrates were confined to one or two tetrapod classes (Allen et al., 2002;Araújo et al., 2008;Barreto et al., 2019;Costa et al., 2007;Evans et al., 2005;Foody, 2004;Fritz et al., 2016;Kerr & Packer, 1997;Qian et al., 2007;Rahbek & Graves, 2001;Rodríguez et al., 2005), or involve birds, mammals, and amphibians (Belmaker & Jetz, 2011;Bohdalková et al., 2021;Buckley & Jetz, 2007;Davies et al., 2007;Gouveia et al., 2013;Grenyer et al., 2006;Gudex-Cross et al., 2022;Hawkins et al., 2007Hawkins et al., , 2012Hortal et al., 2008;O'Malley et al., 2023;Wu & Liang, 2018). Studies that incorporate all tetrapods (including reptiles) have usually been confined to one region (Currie, 1991;Lewin et al., 2016;Powney et al., 2010;Tallowin et al., 2017;. ...
May 2023
Global Ecology and Biogeography
... In addition, pronounced ecological gradients favor the diversification of species and explain the high number of micro-endemism within many taxa (Vences et al., 2009;Vorontsova et al., 2016). However, this ecological richness is under constant threat due to escalating rates of deforestation, land degradation, and persistent socio-economic challenges (Vieilledent et al., 2018;Ralimanana et al., 2022). Madagascar continues to have one of the highest poverty and malnutrition rates in the world, widespread food insecurity and is among the African countries most affected by climate change (Borgerson et al., 2016;Golden et al., 2016;Kappeler et al., 2022). ...
December 2022
Science
... Northwest Madagascar is a noted hotspot for marine biodiversity (Antonelli et al. 2022). The island of Nosy Be is a popular marine tourism destination (Ziegler et al. 2021), known for its populations of large planktivores such as Omura's whales (Balaenoptera omurai; Cerchio et al. 2015) and whale sharks (Rhincodon typus; Diamant et al. 2021). ...
December 2022
Science
... Species of this genus typically form ectomycorrhizal symbiotic associations with a wide range of host trees, primarily including Pinus spp., Castanopsis spp., Picea spp., Larix spp., Fagus spp., and Castanea spp. [5][6][7]. These fungi inhabit a diverse array of ecosystems, ranging from Arctic tundra to tropical forests, and play a crucial role in forest development and the maintenance of the ecological balance [8,9]. ...
July 2022
... Los procesos anagenéticos que modifican la distribución entre dos eventos de especiación son la dispersión y la extinción. Estos métodos tienen la ventaja de modelar el movimiento y establecimiento de especies en una nueva área geográfica que deja una marca en la filogenia (Hackel y Sanmartín, 2021), lo cual podría ser aplicado al espacio ambiental. Sin embargo, no hemos encontrado publicaciones donde se aplique. ...
August 2021
Trends in Ecology & Evolution
... Heteropogon diverged from Cymbopogon ~ 8.84 Ma, and the divergence between H. contortus and Themeda is estimated at ~ 7.6 Ma. In T. triandra, the Asian and Australian populations diverged from the African taxon by ~ 1.15 Ma (Arthan et al. 2021; also see Christin et al. 2014). Thus, although shifts in climate and genetic drift may have affected grass populations, it is evident that some of the grasses have been around for a very long time (see Bredenkamp et al. 2002). ...
August 2021
Botanical Journal of the Linnean Society