52 Works

Campanula rotundifolia cytotype, distribution and first flowering dates

J. Wilson, A. Perry, Shepherd, M. Duran-Castillo, CE. Jeffree & S. Cavers
This dataset comprises information of location and cytotype of over 1300 samples of Campanula rotundifolia L. from the northern hemisphere (mostly from Britain and Ireland) and data from a common garden study in which British and Irish cytotypes were grown together and their flowering phenology and growth were assessed. Campanula rotundifolia L. is a widespread polyploid perennial herbaceous plant, with diploid, tetraploid, pentaploid and hexaploid cytotypes.

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Data from: Graphs in phylogenetic comparative analysis: Anscombe’s quartet revisited

Liam J. Revell, Klaus Schliep, Eugenio Valderrama & James E. Richardson
1. In 1973 the statistician Francis Anscombe used a clever set of bivariate datasets (now known as Anscombe’s quartet) to illustrate the importance of graphing data as a component of statistical analyses. In his example, each of the four datasets yielded identical regression coefficients and model fits, and yet when visualized revealed strikingly different patterns of covariation between x and y. 2. Phylogenetic comparative methods are statistical methods too, yet visualizing the data and phylogeny...

Data from: Evolution of angiosperm pollen. 6. the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales

Zhi-Bin Tao, Alexandra H. Wortley, Lu Lu, De-Zhu Li, Hong Wang & Stephen Blackmore
Analyzing pollen morphological data on a contemporary phylogenetic framework can enhance our understanding of the distribution, diversity, and evolution of palynological characters. In this paper, the sixth in a series detailing pollen morphological characters across angiosperms, we focus on the Celastrales, Oxalidales, and Malpighiales (COM) clade and Zygophyllales, together comprising ca. 20,000 species in 47 families within fabids. We first examined pollen grains from 21 species with light, scanning electron, and transmission electron microscopy, to...

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...

Life history evolution, species differences and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

Max Brown, Natacha Frachon, Edgar Wong & Alex Twyford
Premise of the study: Species delimitation in parasitic organisms is challenging as traits used in the identification of species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We test whether Euphrasia species show reliable trait differences, investigate whether these differences correspond to life history trade-offs between growth and reproduction, and quantify plasticity in response to...

Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora

Jialiang Li, Yujiao Zhang, Markus Ruhsam, Richard Ian Milne, Yi Wang, Dayu Wu, Shiyu Jia, Tongzhou Tao & Kangshan Mao
The eastern Asia (EA) – eastern North America (ENA) disjunction is a typical and well known biogeographic. Although its origin has been the topic of many studies, some new insights will arise when more complex evolutionary histories are revealed using phylogenomic methods. Here, we used targeted exon capture and sequenced >1,000 single copy nuclear, plus 73 chloroplast genes, to resolve interspecific relationships and the biogeographic history of an intercontinental disjunct genus Thuja. Two separate clades...

Data from: Applying plant DNA barcodes to identify species of Parnassia (Parnassiaceae)

Jun-Bo Yang, Yi-Ping Wang, Michael Möller, Lian-Ming Gao & Ding Wu
DNA barcoding is a technique to identity species by using standardized DNA sequences. In the present study, a total of 105 samples, representing 30 Parnassia species were collected to test the effectiveness of four proposed DNA barcodes (rbcL, matK, trnH-psbA and ITS) for species identification. Our results demonstrated that all four candidate DNA markers have a maximum level of primer universality and sequencing success. As single DNA marker, ITS region provided the highest species resolution...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Moses C. Wambulwa, Muditha K. Meegahakumbura, Samson Kamunya, Alice Muchugi, Michael Moller, Jie Liu, Jian-Chu Xu, Sailesh Ranjitkar, De-Zhu Li & Lian-Ming Gao
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used...

Data from: Low genetic diversity in small leading edge populations of a European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria

Galya Petrova, Stefan Petrov & Michael Möller
Ramonda serbica Panč. (Gesneriaceae) is an endangered endemic species of the Balkan Peninsula. It has been the subject of several studies in the past, but has not yet been investigated in terms of its genetic variation. Here, an Inter Simple Sequence Repeat (ISSR) analysis was performed to determine the genetic diversity of five populations sampled from the geographically eastern fringe of its range in northwestern Bulgaria. We found low levels of genetic diversity and significant...

Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

Li Feng, Markus Ruhsam, Yi-Han Wang, Zhong-Hu Li & Xu-Mei Wang
Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographic structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants we used population...

Data from: Origin of angiosperms and the puzzle of the Jurassic gap

Hong-Tao Li, Ting-Shuang Yi, Lian-Ming Gao, Peng-Fei Ma, Ting Zhang, Jun-Bo Yang, Matthew A. Gitzendanner, Peter W. Fritsch, Jie Cai, Yang Luo, Hong Wang, Michelle Van Der Bank, Shu-Dong Zhang, Qing-Feng Wang, Jian Wang, Zhi-Rong Zhang, Chao-Nan Fu, Jing Yang, Peter M. Hollingsworth, Mark W. Chase, Douglas E. Soltis, Pamela S. Soltis & De-Zhu Li
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated...

Data from: Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya-Hengduan Mountains region

Xie He, Kevin Burgess, Xuefei Yang, Antje Ahrends, Lian-Ming Gao & De-Zhu Li
Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic...

Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu, Matthew G. Johnson, Cymon J. Cox, Rafael Medina, Nicolas Devos, Alain Vanderpoorten, Lars Hedenäs, Neil E. Bell, James R. Shevock, Blanka Aguero, Dietmar Quandt, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30...

Data from: Resolution, conflict and rate shifts: Insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae)

Zhi-Qiong Mo, Chao-Nan Fu, Ming-Shu Zhu, Richard I. Milne, Jun-Bo Yang, Jie Cai, Han-Tao Qin, Wei Zheng, Peter M. Hollingsworth, De-Zhu Li & Lian-Ming Gao
Background and Aims Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya–Hengduan Mountains where the genus is most diverse. Methods We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to...

Data from: Recent colonization of the Galapagos by the tree Geoffroea spinosa Jacq. (Leguminosae)

Sofia Caetano, Mathias Currat, R. Toby Pennington, Darién Prado, Laurent Excoffier & Yamama Naciri
This study puts together genetic data and an Approximate Bayesian Computation (ABC) approach to infer the time at which the tree Geoffroea spinosa colonized the Galápagos Islands. The genetic diversity and differentiation between Peru and Galápagos population samples, estimated using three chloroplast spacers and six microsatellite loci, reveal significant differences between two mainland regions separated by the Andes mountains (Inter Andean versus Pacific Coast) as well as a significant genetic differentiation of island populations. Microsatellites...

Data from: Hybridisation in closely related Rhododendron species: half of all species differentiating markers experience serious transmission ratio distortion

Tobias Marczewski, David F. Chamberlain & Richard I. Milne
An increasing number of studies of hybridization in recent years have revealed that complete reproductive isolation between species is frequently not finalized in more or less closely related organisms. Most of these species do, however, seem to retain their phenotypical characteristics despite the implication of gene flow, highlighting the remaining gap in our knowledge of how much of an organism's genome is permeable to gene flow, and which factors promote or prevent hybridization. We used...

Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Pablo Fuentes-Utrilla, Martin Venturas, Peter M. Hollingsworth, Jane Squirrell, Carmen Collada, Graham N. Stone & Luis Gil
Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity...

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer & Sarah Mathews
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is...

Data from: Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

Fabien L. Condamine, A.J. Harris, Junlin Chen, Bo Pan, Michael Moeller, Van Sam Hoang, Ming Kang, Hanghui Kong & AJ Harris
Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to...

Data from: Tiny niches and translocations: the challenge of identifying suitable recipient sites for small and immobile species

Rob W. Brooker, Mark J. Brewer, Andrea J. Britton, Antonia Eastwood, Christopher Ellis, Alessandro Gimona, Laura Poggio & David R. Genney
Assisted colonisation, one form of species translocation, has been proposed as a tool for helping species to track suitable conditions in a changing climate. There are considerable practical challenges associated with it, including predicting where to place translocated individuals. This problem may be particularly big for small and immobile species, where small-scale micro-environmental conditions de-couple them from environmental conditions as projected in large-scale climate models. To investigate this problem we developed a survey-based model to...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Data from: Macroevolutionary patterns in overexpression of tyrosine: an anti-herbivore defense in a speciose tropical tree genus, Inga (Fabaceae)

Phyllis D. Coley, María‐José Endara, Gabrielle Ghabash, Catherine A. Kidner, James A. Nicholls, R. Toby Pennington, Anthony G. Mills, Abrianna J. Soule, Maristerra R. Lemes, Graham N. Stone & Thomas A. Kursar
Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here, we examine the evolution of overexpression of the essential amino acid, L‐tyrosine and its role as a defence against herbivores. We examined overexpression of tyrosine in 97 species of Inga (Fabaceae), a genus of...

Data from: Tracking of host defenses and phylogeny during the radiation of Neotropical Inga-Feeding sawflies (Hymenoptera; Argidae)

María-José Endara, James A. Nicholls, Phyllis D. Coley, Dale L. Forrister, Gordon C. Younkin, Kyle G. Dexter, Catherine A. Kidner, R. Toby Pennington, Graham N. Stone & Thomas A. Kursar
Coevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny...

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