Search Constraints
Search Results
-
Journal article
Estimation of species divergence times in presence of cross-species gene flow.
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies...Tiley, George P ; Flouri, Tomás ; Jiao, Xiyun ; Poelstra, Jelmer W. ; Xu, Bo …
Gene flow, Divergence time, Introgression, MSci model, Hybridization, and Multispecies coalescent
-
Journal article
The allopolyploid origin(s) and diversification of New Caledonian Grevillea (Proteaceae).
-
Journal article
The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data.
The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we... -
Journal article
Tropical environmental change in North Sumatra at the Last Glacial Maximum: Evidence from the stable isotope composition of cave guano.
-
Journal article
Multiple pre‐ and post‐zygotic components of reproductive isolation between two co‐occurring Lysimachia species.
-
Journal article
The mirror crack'd: both pigment and structure contribute to the glossy blue appearance of the mirror orchid, Ophrys speculum.
-
Journal article
Multiple origins of lipid‐based structural colors contribute to a gradient of fruit colors in Viburnum (Adoxaceae).
-
Journal article
SpyPhage: A Cell-Free TXTL Platform for Rapid Engineering of Targeted Phage Therapies.
-
Journal article
Matches and mismatches between the global distribution of major food crops and climate suitability.
Over the course of history, humans have moved crops from their regions of origin to new locations across the world. The social, cultural and economic drivers of these movements have generated differences not only between current distributions of crops and their climatic origins, but also between crop distributions and climate...Mahaut, Lucie ; Pironon, Samuel ; Barnagaud, Jean-Yves ; Bretagnolle, François ; Khoury, Colin K. …
Global agriculture, Climatic niche, Crop biogeography, Food crops, and Climate suitability
-
Journal article
The likely extinction of hundreds of palm species threatens their contributions to people and ecosystems.
Bellot, S. ; Lu, Y. ; Antonelli, A. ; Baker, W. J. ; Dransfield, J. …
Extinction, Ecosystem services, Economic botany, Biodiversity, Palmae, Ethnobotany, Palms, and Conservation biology
-
Journal article
Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia.
Dunning, Luke T. ; Olofsson, Jill K. ; Papadopulos, Alexander S. T. ; Hibdige, Samuel G. S. ; Hidalgo, Oriane …
Ecotypes, Hybridisation, Themeda triandra, Australia, and Chloroplast capture
-
Journal article
Stomatal Development and Gene Expression in Rice Florets.
Stomata play a fundamental role modulating the exchange of gases between plants and the atmosphere. These microscopic structures form in high numbers on the leaf epidermis and are also present on flowers. Although leaf stomata are well-studied, little attention has been paid to the development or function of floral stomata....Bertolino, Lígia T. ; Caine, Robert S. ; Zoulias, Nicholas ; Yin, Xiaojia ; Chater, Caspar C C …
Gene expression, Floral stomata, Rice, Stomata, Oryza, and Stomatal development
-
Journal article
A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons.
Wild progenitors of crops are important resources for breeding and for understanding domestication, but identifying them is difficult. Using an integrative approach, we discovered that a Sudanese form of melon with nonbitter whitish pulp, known as the Kordofan melon, is the closest relative of domesticated watermelons and a possible progenitor.... -
Journal article
Mixed Mating in Homostylous Species: Genetic and Experimental Evidence from an Alpine Plant with Variable Herkogamy, Primula halleri.
de Vos, Jurriaan M. ; Keller, Barbara ; Zhang, Li-Rui ; Nowak, Michael D. ; Conti, Elena
Alpine plants, Homostyly, Primula halleri, Reproduction, Flowers, Herkogamy, and Primula
-
Journal article
Timing and tempo of evolutionary diversification in a biodiversity hotspot: Primulaceae on Indian Ocean islands.
-
Journal article
Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions.
-
Journal article
Mediterranean origin and Miocene-Holocene Old World diversification of meadow fescues and ryegrasses (Festuca subgenus Schedonorus and Lolium).
-
Journal article
A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family elanthiaceae.
-
Journal article
The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae).
-
-
Journal article
Fungal diversity notes 491–602: taxonomic and phylogenetic contributions to fungal taxa.
-
Journal article
PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences.
Identification tool, internal transcribed spacer (ITS), Fungi, Molecular species identification, Probabilistic taxonomic assignment, Annotation, Data quality, and Environmental sequencing
-
-
-
-
Journal article
Fungal diversity notes 1387–1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa.
-
Journal article
Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota).
-
Journal article
Pangenome Graphs.
Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support...Eizenga, Jordan M. ; Novak, Adam M. ; Sibbesen, Jonas A. ; Heumos, Simon ; Ghaffaari, Ali …
-
Journal article
The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification.
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive...Carruthers, Tom ; Scotland, Robert W
Divergence time estimation, Phylogeny, Macroevolution, Diversification rates, and Macroevolutionary history
-
Journal article
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.
Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled...Tello-Ruiz, Marcela K ; Naithani, Sushma ; Gupta, Parul ; Olson, Andrew ; Wei, Sharon …
Major crops, Genomics, Model plants, Comparative genomics, Gramene, and Databases
-
Journal article
Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella.
Torres Jiménez, Maria Fernanda ; Prata, Eduardo M. B. ; Zizka, Alexander ; Cohn-Haft, Mario ; de Oliveira, Ayslaner V. G. …
Amazonia, Phylogenomics, Palmae, Mauritiella, and Africa
-
Journal article
The largest type study of Agaricales species to date: bringing identification and nomenclature of Phlegmacium (Cortinarius) into the DNA era.
Liimatainen, K. ; Niskanen, T. ; Dima, B. ; Kytövuori, I. ; Ammirati, J. F. …
Taxonomy, Typification, Diversity, Basidiomycota, ITS, and DNA barcoding
-
-
Journal article
Complex evolutionary history of two ecologically significant grass genera, Themeda and Heteropogon (Poaceae: Panicoideae: Andropogoneae).
Arthan, Watchara ; Dunning, Luke T. ; Besnard, Guillaume ; Manzi, Sophie ; Kellogg, Elizabeth A. …
Pleistocene, C4 grassland expansion, Phylogenomics, Plastomes, Anthistiriinae, and Dating
-
Journal article
Stomatal responses to carbon dioxide and light require abscisic acid catabolism in Arabidopsis
In plants, stomata control water loss and CO2 uptake. The aperture and density of stomatal pores, and hence the exchange of gases between the plant and the atmosphere, are controlled by internal factors such as the plant hormone abscisic acid (ABA) and external signals including light and CO2. In this...Movahedi, Mahsa ; Zoulias, Nicholas ; Casson, Stuart A. ; Sun, Peng ; Liang, Yun-Kuan …
-
Journal article
Fossil data support a pre-Cretaceous origin of flowering plants
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils....Silvestro, Daniele ; Bacon, Christine D. ; Ding, Wenna ; Zhang, Qiuyue ; Donoghue, Philip C. J. …
Evolution, Computational biology and bioinformatics , and Plant sciences
-
Journal article
A robust phylogenomic framework for the calamoid palms
Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550...Kuhnhäuser, Benedikt G. ; Bellot, Sidonie ; Couvreur, Thomas L.P. ; Dransfield, John ; Henderson, Andrew …
Systematics, Calamoideae, Phylogenomics, Gene tree conflict, Rattan, and Arecaceae
-
Journal article
Habitat specialisation controls ectomycorrhizal fungi above the treeline in the European Alps
Alpine habitats are one of the most vulnerable ecosystems to environmental change, however, little information is known about the drivers of plant–fungal interactions in these ecosystems and their resilience to climate change. We investigated the influence of the main drivers of ectomycorrhizal (EM) fungal communities along elevation and environmental gradients... -
Journal article
Repeat-sequence turnover shifts fundamentally in species with large genomes.
Given the 2,400-fold range of genome sizes (0.06–148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive...Novák, Petr ; Guignard, Maïté S. ; Neumann, Pavel ; Kelly, Laura J. ; Mlinarec, Jelena …
Species lineages, Genomes, Repeat turnover, Repeat-sequence content, and Genome size
-
Journal article
Identifying and mapping individual plants in a highly diverse high-elevation ecosystem using UAV imagery and deep learning
The identification and counting of plant individuals is essential for environmental monitoring. UAV based imagery offer ultra-fine spatial resolution and flexibility in data acquisition, and so provide a great opportunity to enhance current plant and in-situ field surveying. However, accurate mapping of individual plants from UAV imagery remains challenging, given...Zhang, Ce ; Atkinson, Peter M. ; George, Charles ; Wen, Zhaofei ; Diazgranados, Mauricio …
Scale sequence, Multi-scale deep learning , Residual U-Net, Semantic segmentation, and Páramos
-
Journal article
Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics
We studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the...Chave, Jerome ; Sothers, Cynthia ; Iribar, Amaia ; Suescun, Uxue ; Chase, Mark W …
tropical forest, phylogenetic inference, Amazonia, Malpighiales, and molecular dating
-
Journal article
A model-data fusion approach to analyse carbon dynamics in managed grasslands.
Grasslands are an important component of the global carbon (C) cycle, with a strong potential for C sequestration. However, an improved capacity to quantify grassland C stocks and monitor their variation in space and time, particularly in response to management, is needed in order to conserve and enhance grassland C...Myrgiotis, Vasileios ; Blei, Emanuel ; Clement, Rob ; Jones, Stephanie K. ; Keane, Ben …
Primary production, Grasslands, Carbon sequestration, United Kingdom, and Model-data fusion
-
Journal article
Floristics of forests across low nutrient soils in Sulawesi, Indonesia.
The island of Sulawesi formed from the joining of proto‐islands roughly three million years ago. Regions of zoological endemism, corresponding to the proto‐islands, have been reported. Sulawesi's tree communities, however, remain poorly documented. In better‐studied tropical regions, soil types similar to those found in Sulawesi often have distinctive tree communities....