204 Works

Data from: Anatomical enablers and the evolution of C4 photosynthesis in grasses

Pascal-Antoine Christin, Colin P. Osborne, David S. Chatelet, J. Travis Columbus, Guillaume Besnard, Trevor R. Hodkinson, Laura M. Garrison, Maria S. Vorontsova & Erika J. Edwards
C4 photosynthesis is a series of anatomical and biochemical modifications to the typical C3 pathway that increases the productivity of plants in warm, sunny, and dry conditions. Despite its complexity, it evolved more than 62 times independently in flowering plants. However, C4 origins are absent from most plant lineages and clustered in others, suggesting that some characteristics increase C4 evolvability in certain phylogenetic groups. The C4 trait has evolved 22–24 times in grasses, and all...

Data from: Towards a worldwide wood economics spectrum

Amy E. Zanne, G. Lopez-Gonzalez, David A. Coomes, Jugo Ilic, Steven Jansen, Simon L. Lewis, Regis B. Miller, Nathan G. Swenson, Michael C. Wiemann & Jerome Chave
Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on...

Data from: Historical divergence versus contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians

Peter Schönswetter, Andreas Tribsch, Ovidiu Paun & Manuela Winkler
Although many species have similar total distributional ranges, they might be restricted to very different habitats and might have different phylogeographic histories. In the European Alps, our excellent knowledge of the evolutionary history of silicate-dwelling plants is contrasted by a virtual lack of data from limestone-dwelling plants. These two categories are expected to differ strongly with respect to their glacial history. The calcicole Ranunculus alpestris group comprises three diploid species of alpine habitats. Analyses of...

Data from: Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae)

Christine D. Bacon, William J. Baker & Mark P. Simmons
The study of three island groups of the palm tribe Trachycarpeae (Arecaceae/Palmae) permits both the analysis of each independent radiation and comparisons across the tribe to address general processes that drive island diversification. Phylogenetic relationships of Trachycarpeae were inferred from three plastid and three low-copy nuclear genes. The incongruent topological position of Brahea in CISP5 was hypothesized to be caused by duplication event and was addressed using uninode coding. The resulting phylogenetic trees were well-resolved...

Data from: Liverworts to the rescue: an investigation of their efficacy as mycorrhizal inoculum for vascular plants

Jill Kowal, Silvia Pressel, Jeffrey G. Duckett & Martin I. Bidartondo
Pezoloma ericae (D.J. Read) Baral, a widespread mycorrhizal fungus of plants in the Ericales, is known to form intracellular associations with several families of leafy liverworts (Schistochilaceae, Lepidoziaceae, Cephaloziaceae, Cephaloziellaceae) in vitro. The ecological significance of this link between vascular and non-vascular plants is unknown. Fungal symbionts were isolated from rhizoids of the leafy liverworts Cephalozia connivens (Dicks.) Lindb. and C. bicuspidata (L.) Dum. (Cephaloziaceae), as well as from the hair roots of two dominant...

Data from: Quantification of population sizes of large herbivores and their long-term functional role in ecosystems using dung fungal spores

Ambroise G. Baker, Perry Cornelissen, Shonil Bhagwat, Fransciscus W. M. Vera, Katherine J. Willis & Shonil A. Bhagwat
The relationship between large herbivore numbers and landscape cover over time is poorly understood. There are two schools of thought: one views large herbivores as relatively passive elements upon the landscape and the other as ecosystem engineers driving vegetation succession. The latter relationship has been used as an argument to support reintroductions of large herbivores onto many landscapes in order to increase vegetation heterogeneity and biodiversity through local-scale disturbance regimes. Most of the research examining...

Data from: Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography

William J. Baker, Thomas L. P. Couvreur & Thomas L.P. Couvreur
AIM: Palms (Arecaceae/Palmae) are a model group for evolutionary studies in the tropics. Family-wide data on taxonomy, phylogenetics and distribution are now available, but a general framework of palm evolution is still lacking. The overall aim of this study, published in two companion papers, is to seek evolutionary explanations for the geographical distribution of palm lineages and species diversity patterns at global and regional levels. In this first paper we undertake a detailed analysis of...

Data from: The origin and evolution of phototropins

Fay-Wei Li, Kathleen M. Pryer, Gane K.-S. Wong, Carl J. Rothfels, Michael Melkonian, Sarah Mathews, Juan C. Villarreal & Sean W. Graham
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent...

Data from: X-rays and virtual taphonomy resolve the first Cissus (Vitaceae) macrofossils from Africa as early diverging members of the genus

Neil F. Adams, Margaret E. Collinson, Selena Y. Smith, Marion K. Bamford, Félix Forest, Panagiota Malakasi, Federica Marone & Dan Sykes
PREMISE OF THE STUDY: Fossilized seeds similar to Cissus (Vitaceae) have been recognized from the Miocene of Kenya, though some were previously assigned to the Menispermaceae. We undertook a comparative survey of extant African Cissus seeds to identify the fossils and consider their implications for the evolution and biogeography of Cissus and for African early Miocene paleoenvironments. METHODS: Micro-computed tomography (µCT) and synchrotron-based X-ray tomographic microscopy (SRXTM) were used to study seed morphology and anatomy....

Data from: Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy

Luke T. Dunning, Helen Hipperson, William J. Baker, Roger K. Butlin, Céline Devaux, Ian Hutton, Javier Igea, Alexander S. T. Papadopulos, Xueping Quan, Carole M. Smadja, Colin G. N. Turnbull & Vincent Savolainen
Ecological speciation requires divergent selection, reproductive isolation, and a genetic mechanism to link the two. We examined the role of gene expression and coding sequence evolution in this process using two species of Howea palms that have diverged sympatrically on Lord Howe Island, Australia. These palms are associated with distinct soil types and have displaced flowering times, representing an ideal candidate for ecological speciation. We generated large amounts of RNA-Seq data from multiple individuals and...

Data from: Extensive variation, but not local adaptation in an Australian alpine daisy

Megan J. Hirst, Jason P. Sexton & Ary A. Hoffmann
Alpine plants often occupy diverse habitats within a similar elevation range, but most research on local adaptation in these plants has focused on elevation gradients. In testing for habitat-related local adaptation, local effects on seed quality and initial plant growth should be considered in designs that encompass multiple populations and habitats. We tested for local adaptation across alpine habitats in a morphologically variable daisy species, Brachyscome decipiens, in the Bogong High Plains in Victoria, Australia....

Data from: Exploiting mycorrhizas in broad daylight: partial mycoheterotrophy is a common nutritional strategy in meadow orchids.

Julienne M.I. Schiebold, Martin I. Bidartondo, Florian Lenhard, Andreas Makiola, Gerhard Gebauer & Julienne M.-I. Schiebold
Partial mycoheterotrophy (PMH) is a nutritional mode in which plants utilize organic matter, i.e. carbon, both from photosynthesis and a fungal source. The latter reverses the direction of plant-to-fungus carbon flow as usually assumed in mycorrhizal mutualisms. Based on significant enrichment in the heavy isotope 13C, a growing number of PMH orchid species have been identified. These PMH orchids are mostly associated with fungi simultaneously forming ectomycorrhizas with forest trees. In contrast, the much more...

Identifying drivers of forest resilience in long-term records from the Neotropics

Carole Adolf, Carolina Tovar, Nicola Kühn, Hermann Behling, Juan Carlos Berrío, Gabriela Dominguez-Vázquez, Blanca Figueroa-Rangel, Zaire Gonzalez-Carranza, Gerald Alexander Islebe, Henry Hooghiemstra, Hector Neff, Miguel Olvera-Vargas, Bronwen Whitney, Matthew J. Wooller & Kathy J. Willis
Here we use 30 long-term, high-resolution palaeoecological records from Mexico, Central and South America to address two hypotheses regarding possible drivers of resilience in tropical forests as measured in terms of recovery rates from previous disturbances. First, we hypothesise that faster recovery rates are associated with regions of higher biodiversity, as suggested by the insurance hypothesis. And second, that resilience is due to intrinsic abiotic factors that are location specific, thus regions presently displaying resilience...

Continued adaptation of C4 photosynthesis after an initial burst of changes in the Andropogoneae grasses

Matheus Bianconi, Jan Hackel, Maria Vorontsova, Adriana Alberti, Watchara Arthan, Sean Burke, Melvin Duvall, Elizabeth Kellogg, Sébastien Lavergne, Michael McKain, Alexandre Meunier, Colin Osborne, Paweena Traiperm, Pascal-Antoine Christin & Guillaume Besnard
C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ~ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related...

Data from: A genome for gnetophytes and early evolution of seed plants

Tao Wan, Zhi-Ming Liu, Ling-Fei Li, Andrew R. Leitch, Ilia J. Leitch, Rolf Lohaus, Zhong-Jian Liu, Hai-Ping Xin, Yan-Bing Gong, Yang Liu, Wen-Cai Wang, Ling-Yun Chen, Yong Yang, Laura J. Kelly, Ji Yang, Jin-Ling Huang, Zhen Li, Ping Liu, Li Zhang, Hong-Mei Liu, Hui Wang, Shu-Han Deng, Meng Liu, Ji Li, Lu Ma … & Xiao-Ming Wang
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel...

Data from: Multiple independent origins of intermediate species between Sorbus aucuparia and S. hybrida (Rosaceae) in the Baltic region

Joel Levin, Michael F. Fay, Jaume Pellicer & Mikael Hedrén
Populations intermediate between the diploid and sexual Sorbus aucuparia and the tetraploid and facultative apomictic Sorbus hybrida are scattered in coastal regions of southern Scandinavia. Our aims were to investigate whether these populations were of local and independent origins, whether they were morphologically and molecularly distinct from each other and whether they could give rise to constant offspring by apomixis. Six intermediate populations from the Baltic Sea basin were studied for variation at nuclear and...

Data from: C4 anatomy can evolve via a single developmental change

Marjorie R. Lundgren, Luke T. Dunning, Jill K. Olofsson, Jose J. Moreno Villena, Jacques W. Bouvier, Tammy L. Sage, Roxana Khosravesh, Stefanie Sultmanis, Matt Stata, Brad S. Ripley, Maria S. Vorontsova, Guillaume Besnard, Claire Adams, Nicholas Cuff, Anthony Mapaura, Matheus E. Bianconi, Christine M. Long, Pascal-Antoine Christin, Colin P. Osborne, Roxana Khoshravesh & Jose J. Moreno-Villena
C4 photosynthesis boosts productivity in warm environments. Paradoxically, this complex physiological process evolved independently in numerous plant lineages, despite requiring specialized leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non-C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata....

Data from: A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Juan Viruel, Nicolas Le Galliot, Samuel Pironon, Jean Pierre Suc, Gonzalo Nieto Feliner, Fatma Lakhal-Mirleau, Marianick Juin, Marjorie Selva, Magda Bou Dagher-Kharrat, Lahcen Ouahmane, Stefano La Malfa, Katia Diadema, Hervé Sanguin, Frédéric Médail & Alex Baumel
Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated...

Data from: Conservation of the threatened species Pulsatilla vulgaris Mill. (pasqueflower) is aided by reproductive system and polyploidy

Roberta Gargiulo, Gemma Worswick, Corinne Arnold, Lindsay Pike, Robyn S. Cowan, Kate A. Hardwick, Ted Chapman & Michael F. Fay
Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using ten nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations is not as evident as expected from demographic trends....

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Matheus Bianconi, Luke Dunning, Emma Curran, Oriane Hidalgo, Robyn Powell, Sahr Mian, Ilia Leitch, Marjorie Lundgren, Sophie Manzi, Maria Vorontsova, Guillaume Besnard, Colin Osborne, Jill Olofsson & Pascal-Antoine Christin
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during, and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy...

Data from : Historical legacies and ecological determinants of grass naturalizations worldwide

Anne-Christine Monnet, Maria S. Vorontsova, Rafaël H. A. Govaerts, Jens-Christian Svenning & Brody Sandel
The global distribution of exotic species is the result of abiotic, biotic and dispersal filtering processes that shape the movement and success of species outside their native range. In this study we aim to understand how these filtering processes drive the fluxes of grass species among regions, the factors that influence which species establish outside of their native range, and where they do so. We used national and subnational checklists of native and introduced grass...

Fire and grazing determined grasslands of central Madagascar represent ancient assemblages

Cedrique Solofondranohatra, Maria Vorontsova, Gareth Hempson, Jan Hackel, Stuart Cable, Vololoniaina Jeannoda & Caroline Lehmann
The ecology of Madagascar’s grasslands is under-investigated and the dearth of ecological understanding of how disturbance by fire and grazing shapes these grasslands stems from a perception that disturbance shaped Malagasy grasslands only after human arrival. However, worldwide, fire and grazing shape tropical grasslands over ecological and evolutionary timescales, and it is curious Madagascar should be a global anomaly. We examined the functional and community ecology of Madagascar’s grasslands across 71 communities in the Central...

Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

Jonna Eriksson, Christine Bacon, Dominic Bennett, Bernard Pfeil, Bengt Oxelman & Alexandre Antonelli
Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e., genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal...

The evolutionary history of sedges (Cyperaceae) in Madagascar

Isabel Larridon, Daniel Spalink, Pedro Jiménez-Mejías, José Ignacio Márquez-Corro, Santiago Martín-Bravo & Marcial Escudero
Aim: Madagascar is renowned for its unparalleled biodiversity and endemism. With many ecosystems under threat, research is urgently needed on its unique plant diversity. This applies both to Madagascar’s forests and treeless vegetation types. Sedges (Cyperaceae) are among the top ten species-richest angiosperm families in Madagascar (310 native species, 38% endemic), of which two thirds occur in open habitats. We aimed to infer the evolutionary history of sedges in Madagascar, by estimating the number, age...

The implications of interrelated assumptions on estimates of divergence times and rates of diversification

Tom Carruthers & Robert Scotland
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 assessment of the key variables that underpin analyses in this field – including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling....

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