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Journal article
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity
Hybridisation has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing inter‐specific gene flow. However, hybridisation in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its... -
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
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Other
The Bean Bag Issue 67
The Bean Bag started in 1974 on the initiative of Charles (Bob) Gunn and Richard Cowan and the first printed issue was distributed 45 years ago in May 1975. The aim of the annual newsletter is to keep legume researchers informed about new publications, events and projects focused on the... -
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
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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
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Journal article
Pantropical diversification of padauk trees and relatives was influenced by biome‐switching and long‐distance dispersal.
Schley, Rowan J. ; Qin, Ming ; Vatanparast, Mohammad ; Malakasi, Panagiota ; Estrella, Manuel …
Angiosperms-353, BioGeoBEARS, Rosewood, Phylogenomics, Traits, Tropics, and Legumes
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Journal article
Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion.
Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach... -
Journal article
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life.
Dentinger, Bryn T. M. ; Gaya, Ester ; O'Brien, Heath ; Suz, Laura M. ; Lachlan, Robert …
Phylogenetic informativeness, Orthologue, Agaricales, Evolution, Vouchers, and Phylogenomics
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Journal article
Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus...Helmstetter, Andrew J. ; Kamga, Suzanne Mogue ; Bethune, Kevin ; Lautenschläger, Thea ; Zizka, Alexander …
Rain forests, Africa, Madagascar, Sequence capture, Exons, Phylogenomics, and Raphia
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Journal article
Phylogenetic Relationships Within the Hyper-Diverse Genus Eugenia (Myrtaceae: Myrteae) Based on Target Enrichment Sequencing.
is one of the most taxonomically challenging lineages of flowering plants, in which morphological delimitation has changed over the last few years resulting from recent phylogenetic study based on molecular data. Efforts, until now, have been limited to Sanger sequencing of mostly plastid markers. These phylogenetic studies indicate 11 clades...Giaretta, Augusto ; Murphy, Bruce ; Maurin, Olivier ; Mazine, Fiorella F. ; Sano, Paulo …
Target sequence capture, Myrtaceae, Eugenia, Phylogenomics, Hyb-Seq, and High-throughput sequencing
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Journal article
A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.
Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with...Woudstra, Yannick ; Viruel, Juan ; Fritzsche, Martin ; Bleazard, Thomas ; Mate, Ryan …
Aloe vera, Genetic markers, Phylogenomics, Plant genetics, and Next-generation sequencing
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Journal article
Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava.
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Journal article
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
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Journal article
Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.
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Journal article
New insights into intergeneric relationships of Hickeliinae (Poaceae: Bambusoideae) revealed by complete plastid genomes.
Rakotonasolo, Rivontsoa A. ; Dransfield, Soejatmi ; Haevermans, Thomas ; Ralimanana, Helene ; Vorontsova, Maria S. …
Plastome, Hickeliinae, Bamboo, Madagascar, Phylogenomics, and Paleotropical
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Journal article
Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae).
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation... -
Journal article
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... -
Journal article
Asteraceae as a model system for evolutionary studies: from fossils to genomes.
With c. 24 700 species (10% of all flowering plants), Asteraceae are one of the largest and most phenotypically diverse angiosperm families, with considerable economic and ecological importance. Asteraceae are distributed worldwide, from nearly polar latitudes all the way to the tropics, and occur across a diverse range of habitats...Palazzesi, Luis ; Pellicer, Jaume ; Barreda, Viviana D ; Loeuille, Benoît ; Mandel, Jennifer R …
Phylogenomics, Fossil record, Biogeography, Asteraceae, Evolution, Compositae, and Genome size
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Journal article
Genomic insights into rapid speciation within the world’s largest tree genus Syzygium.
Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects...Low, Yee Wen ; Rajaraman, Sitaram ; Tomlin, Crystal M. ; Ahmad, Joffre Ali ; Ardi, Wisnu H. …
Syzygium, Evolutionary genetics, Phylogenomics, Polyploidy in plants, and Comparative genomics
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Other
Bean Bag Issue 68
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Journal article
Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae).
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Journal article
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.
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Journal article
Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication.
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to... -
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Journal article
Phylogenetics of Ochna (Ochnaceae) and a new infrageneric classification.
Advances in high-throughput DNA sequencing are allowing faster and more affordable generation of molecular phylogenetic trees for many organisms. However, resolving relationships at species level is still challenging, particularly for taxonomically difficult groups. Until recently, the classification of Ochna had been based only on morphological data. Here, we present the...Shah, Toral ; Mashimba, Fandey H. ; Suleiman, Haji O. ; Mbailwa, Yahya S ; Schneider, Julio V …
Systematics, Style branching, Ochna, Phylogenomics, Anther dehiscence, Taxonomic revision, and HybSeq
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Journal article
Repeated evolution of pollination syndromes in a highly diverse bromeliad lineage is correlated with shifts in life form and habitat.
Mutualistic plant-pollinator interactions play a critical role in the diversification of flowering plants. The spatiotemporal correlates of such interactions can be understood in a phylogenetic context. Here, we generate ddRAD-seq data for the highly diverse Vriesea-Stigmatodon lineage to test for correlated trait evolution among pollination syndromes and life form, habitat... -
Journal article
Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories.
Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal... -
Journal article
Complementing model species with model clades.
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here... -
Journal article
Reinstatement and expansion of the genus Anatherum (Andropogoneae, Panicoideae, Poaceae).
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Journal article
Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa.
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Book chapter
2. Tribe Ceratonieae.
Lewis, Gwilym P.
Mimosoideae, Taxonomy, Classification, Ceratonieae, Leguminosae, Phylogenomics, Diversity, and Fabaceae
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Book chapter
10. Tribe Campsiandreae.
Lewis, Gwilym P.
Fabaceae, Diversity, Campsiandreae, Taxonomy, Classification, Phylogenomics, Leguminosae, and Mimosoideae
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Book chapter
16. Entada clade.
O’Donnell, Shawn A. ; Lewis, Gwilym P.
Fabaceae, Diversity, Entada, Taxonomy, Classification, Phylogenomics, Leguminosae, and Mimosoideae
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Book chapter
35. Samanea clade.
Lewis, Gwilym P.
Mimosoideae, Taxonomy, Classification, Leguminosae, Phylogenomics, Fabaceae, Neltuma, and Diversity
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Journal article
From southern Africa and beyond: Historical biogeography of a monocotyledonous bulbous geophyte.