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The Week in Botany 34

February 12, 2018

The stories here are picked by looking at what people following @botanyone on Twitter are sharing - and then cutting out the political stories. The result is there's usually something that catches me by surprise each week. This week though has quite a few stories I would have overlooked. In particular, there's the article on Clustering Algorithms. I appreciate mathematical tools are important for biologists but I don't go out of my way to look for them. It's an example of how building a strong network on Twitter can highlight important articles you might otherwise miss.

From Botany One

Integrative approaches to understanding angiosperm origins and diversity
The rise of angiosperms should be studied as part of the global increase in biodiversity.

The Hungry Gap: Food for temperate February and March
Have we banished the hungry gap? Pat Heslop-Harrison has been talking to BBC Radio Leicester.

Clover, broccoli, and an AIDS-busting plant
Nigel Chaffey starts a series celebrating the human life-sustaining potential of plants…

What are holocentric chromosomes good for?
Possessing holocentric chromosomes may confer an advantage in clastogenic conditions and environments.

Unexpected flowers in the Jurassic
Did flowering plants appear earlier than the fossil record indicates? Two papers independently conclude they did - and suggest what fossil evidence we should look for.

Dispersal and establishment of vascular epiphytes in modified landscapes
In a recent study published in AoB PLANTS, Einzmann and Zotz experimentally studied four vital dispersal steps of a vascular epiphyte in human modified-landscapes. Their findings suggest a high capacity for dispersal and successful early establishment for anemochorous species

Contemporary Citation Classics in Plant Sciences – Journals, Authors and Affiliations
Previously Philip White described the compilation of a list of 517 contemporary Citation Classics in Plant Sciences (1992-2017) and tempted the reader with the prospect of revealing more about the authors, journals and organisations represented in these papers. So, as promised, here is some detail.

All the world’s plants are in here (well, almost…)
A review of Plants of the World: An Illustrated Encyclopedia of Vascular Plants by Maarten JM Christenhusz, Michael F Fay and Mark W Chase, 2017. Kew Publishing/University of Chicago Press

Hydraulic architecture of Eucalyptus grandis
A comprehensive understanding of the systems behind vertical transport of water in tall trees is crucial when predicting the susceptibility of these long-lived organisms to drought.

Call for Papers: Special issue on the Ecology and Evolution of Plant Reproduction

Botanists have long been fascinated by the extraordinary diversity in flowering plant reproductive patterns and have sought to understand theecological processes and genetic mechanisms influencing plant mating. Over the last five years, research progress in this discipline has rapidly accelerated. Important new insights in this field often combine elegant theoretical models with innovative field and laboratory experiments. Annals of Botany will release a Special Issue on the Ecology and Evolution of Plant Reproduction in January 2019, and it will highlight papers from 3 symposia at the XIX International Botanical Congress in Shenzhen, China. See the full call for papers for more information.

News and Views

Bacteria invented genetic engineering — we made it controversial
In the past 50 years, three major discoveries have fueled the field of genetic engineering. Together, they’ve revolutionized medicine and agriculture. Individually, they’ve sparked controversy.
Alliance for Science

I Spent Two Years Trying to Fix the Gender Imbalance in My Stories
Here’s what I’ve learned, and why I did it.
The Atlantic

How Do Infections Spread In Plants?
Plant Pathology for grades 4-8.
Science Friday

The 5 Clustering Algorithms Data Scientists Need to Know
Clustering is a Machine Learning technique that involves the grouping of data points. Given a set of data points, we can use a clustering algorithm to classify each data point into a specific group.
Towards Data Science

Lost World Discovered in Twilight of Chinese Caves
I never expected to be working in caves, that is, until I started to study nettles in Southwest China with Guangxi botanist Wei Yi-Gang. When Wei suggested that we collect in a local cave I was not hopeful. However, that first visit transported me to another world, an eerie moonscape in which plants thrived in powdery ‘soil’ and perpetual twilight. 
Tropical Botany

Wait nearly over for Golden Rice release in Bangladesh
Beta carotene-rich grain key to fight vitamin-A deficiency
United News of Bangladesh

Winning photos from the International Garden Photographer of the Year 2018
A picture of the vast ecological region known as the Cerrado in Brazil has won first place in this year's International Garden Photographer of the Year.
BBC News

DNA story of when life first gave us lemons
All citrus fruits can trace their roots to the southeast foothills of the Himalayas, according to DNA evidence.
BBC News

Debate blooms over anatomy of the world’s first flower
Some researchers say that statistical prediction of the ancestral blossom yielded an unlikely structure.

Invasive pests are the greatest threat to the survival of the world’s ash species
This is no better highlighted than in North America where an invasive pest, the emerald ash borer, originally from Asia, has devastated previously abundant and dominant ash tree populations. 

Call for papers: Developing sustainable bioenergy crops for future climates

Rapid progress has been made over the last five years with respect to emerging new genomic technologies for crop improvement and this Annals of Botany Special Issue will be devoted to highlighting the latest findings and considering the potential of these technologies for the future deployment of bioenergy crops in the face of climate change. At the same time, cutting-edge research that provides insights into the complex plant traits underpinning drought tolerance and response to other abiotic and biotic stresses is required for these relatively new crops. Knowledge in this area will be brought together in this Special Issue, and there will be a focus on recent advances in high throughput phenotyping to unravel these complex responses. See the full call for papers for more information.

Scientific Papers

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution
Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial.
New Phytologist

Conservation stories from the front lines
In this issue of PLOS Biology, we highlight the deeply human side of research in a new collection, “Conservation Stories from the Front Lines.” These narratives present peer-reviewed and robust science but also include the muddy boots and bloody knees, ravaging mosquitoes, crushing disappointment, and occasional euphoria their authors experienced. 
PLOS Biology

Ancient duons may underpin spatial patterning of gene expression in C4 leaves
We describe an ancient regulatory code that patterns the gene expression required for the efficient C4 pathway.

Genomics of the origin and evolution of Citrus
We describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons.

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
We sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. 
Nature Communications

Potential for re-emergence of wheat stem rust in the United Kingdom
We investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. 
Communications Biology

Discovery of a diverse cave flora in China
Few studies document plants in caves. Our field observations of a widespread and seemingly angiosperm-rich cave flora in SW China lead us to test the following hypotheses, 1) SW China caves contain a diverse vascular plant flora, 2) that this is a relic of a largely absent forest type lacking endemic species, and 3) that the light environment plants occupy in caves is not distinct from non-cave habitats.

CRootBox: a structural–functional modelling framework for root systems
CRootBox is a fast and flexible functional–structural root model that is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of roots on soil.
Annals of Botany

Seed ingestion and germination in rattlesnakes: overlooked agents of rescue and secondary dispersal
Seed-laden rodents are commonly consumed by snakes as they forage, but unlike raptors, coyotes, bobcats, and other endothermic predators which eat rodents and are known or implicated to be secondary seed dispersers, the role of snakes in seed dispersal remains unexplored.​
Proc Royal Soc B.


Next week and onwards

It would be nice if I could get the French version of Botany One working by the end of the week. We've been working on this for a while but the problem isn't so much translation of the articles as the fiddly parts of the interface. At the moment the computer is convinced today is lundi 12th of février.

Once we can get this right we'll look at adding a few more languages. I've started with French because we already have plenty of French in the system. If there's a language you'd like us to prioritise, then get in touch with Anne at and we'll do what we can.



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