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The Week in Botany 155

June 22, 2020

It's a bit of a change this week on Twitter. Last week was dominated by politics, this week there's been a return to science. There are some encouraging signs that it's not entirely a return to business as usual. While there were a lot more botanical stories and papers shared, there's still plenty on the Black Lives Matter movement in science.
At Botany One, we're having a few changes of our own. This was Anne Osterrieder's last week as editor of the site. She's moved to the Centre for Tropical Medicine and Global Health at Oxford, where she's currently very busy. The search for her replacement has been disrupted by COVID, so I can't tell you who is replacing her in the longer term.
However, as long as I'm not disrupted by COVID, I'll be back next week with another selection of the stories you're sharing on Twitter. Until then, stay safe.
Alun (webmaster@botany.one)

From Botany One

Creating the conservationists of the future in times of rapidly shifting baselines
Planting urban trees could also plant a seed of conservation in children.

From computer to field: can in silico modelling can help us to optimise rice for possible droughts?
Advances in computational models may allow us to quickly predict responses of important food crops to environmental stresses in the field, and to identify the genetic basis of these.

Tales of tea, still stirring emotions in 2020
Tea leaves might not predict the future, but they have a powerful connection to our past.

Image analysis of phytoliths can tell grass species apart
Tiny stones created in plants can help identified which plants were found in past habitats.

When weather becomes less predictable, so do reproductive traits
Both within a plant and within a population, trait variability increases with unpredictable precipitation.

Going below ground: how some of the diversity in plant root morphology arose
A major transition in plant growth habit may have driven evolution of certain root traits.

You get a better model of the forest when you look at the individual trees
The computing principle GIGO states that if the data you put into a model is garbage, then the output will be too. Jie Yang and colleagues have been tackling the problem of modeling of tropical tree growth. What data is the best data for these models?

Comparative genetic and epigenetic diversity of threatened wild plants
Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation.

The off-switch is not the on-switch for rhizome development in tall fescue
When drought passes the signals to restart the development of rhizomes in Festuca arundinacea are on different regulatory pathways to the signals that turned it off at the start of the drought.

Law enforcement and ecologists will need to trade information to combat trading in endangered plants say crime researchers
Online trading is increasing the damage done by illegal trading in plant material, but researchers have suggestions to reduce this.

Scientists suggest bringing a fresh set of eyes to the problem, 'When did the first flowers evolve?'
A disagreement on when flowers evolved could be solved by studying the real experts on pollination, the pollinators.



News and Views

How to Make Beautiful Tables in R
Data visualization in R is a huge topic (and one covered expertly in Kieran Healy’s Data Visualization: A Practical Introduction and Claus Wilke’s Fundamentals of Data Visualization). But what about tables? Fortunately for R users, there are many ways to create beautiful tables that effectively communicate your results.
R for the Rest of Us

Migratory Birds Like Native Berries Best
Even when fruits of invasive plants are abundant, migratory songbirds seek out native berries, according to new research.
Audubon

PhD (fully funded for European/UK student: fee, stipend, research budget)
Effects of land management practices on ecosystem functioning in complex agro-forestry systems in East Africa (Tanzania)
Newcastle, UK

I’m a Black Female Scientist. On My First Day of Work, a Colleague Threatened to Call the Cops on Me.
Raven Baxter recounts her time as a corporate research scientist at a drug company in western New York—a job she left in 2017 in part because of its toxic culture. Afterward, she went into academia as an assistant professor of biology at a community college, also in western New York, where on her first day a white co-worker threatened to call the police on her. Today, she is hopeful the uprising we’re seeing across the country will bring real, lasting change, including in higher education. Her story here has been edited and condensed.
Mother Jones

Director of science at Kew: it's time to decolonise botanical collections
For hundreds of years, rich countries in the north have exploited natural resources and human knowledge in the south. Colonial botanists would embark on dangerous expeditions in the name of science but were ultimately tasked with finding economically profitable plants. Much of Kew’s work in the 19th century focused on the movement of such plants around the British Empire, which means we too have a legacy that is deeply rooted in colonialism.
The Conversation

It's Time to Build a Truly Inclusive Outdoors
As the nation continues to confront racism, the birding community must embrace difficult conversations.
Audubon

Healthy Plants – Healthy People – Healthy Planet
Healthy Plants, Healthy People, Healthy Planet or HP³ is an ambitious vision to secure a safer, healthier and more sustainable future through the power of plant and microbial science.
John Innes Centre

Plant Ecology Group: News: Postdoc position
This initial contract is for 3 years, but there is possibility to extend the contract as stipulated in the Bavarian “Hochschulgesetz”.
Bayreuth, DE

‘Intersectional Environmentalist’ Platform by Leah Thomas Launches
In an Instagram post last month, Leah Thomas, a climate activist better known online as Green Girl Leah, popularized the phrase “intersectional environmentalism,” a form of climate justice that “advocates for both the protection of people and the planet.” Now, just a few weeks later, what simply started as a social media post about an inclusive, anti-racist branch of environmentalism is already blossoming into a new fixture of the current environmental activism zeitgeist. 
GreenMatters

Embrace wilder farming to restore nature on a grand scale
Last spring I visited the Pennines. It is as bleak a landscape as you’ll find anywhere in Britain, until you arrive at a place called Geltsdale, where the tenant farmer decided ten years ago to swap his intensive sheep enterprise for a herd of native longhorn cattle.
Reaction



Scientific Papers

Fire as a Selective Agent for both Serotiny and Nonserotiny Over Space and Time
Serotiny is the prolonged storage of seeds in closed cones or fruits held within the crown of woody plants. It is widespread throughout fireprone vegetation with a predominantly winter rainfall, especially in Mediterrnanean-type ecosystems (MTEs). Nonstorage is a feature of fireprone vegetation with summer-dominant rainfall or nonfireprone vegetation. Serotiny confers fitness benefits on an individual when fire return intervals fall between age to reproductive maturity and the plant life span. The level of serotiny within and between species varies greatly along a continuum indicating highly plastic responses to different environmental conditions. Lamont et al. review how and why the traits that underpin this reproductive syndrome evolved and continue to control the occurrence of species in contemporary landscapes.
Critical Reviews in Plant Sciences

Does Tweeting Improve Citations? One-Year Results From the TSSMN Prospective Randomized Trial
One-year follow-up of this TSSMN prospective randomized trial importantly demonstrates that tweeting results in significantly more article citations over time, highlighting the durable scholarly impact of social media activity.
The Annals of Thoracic Surgery

Land‐use history determines ecosystem services and conservation value in tropical agroforestry
Based on a conceptual framework, Martin et al. recommend to (a) promote agroforestry on suitable open land, (b) maintain tree cover in existing forest‐derived agroforests, and (c) conserve remaining forests. Land‐use history should be incorporated into land‐use policy to avoid incentivizing forest degradation and to harness the potential of agroforestry for ecosystem services and biodiversity.
Conservation Letters

Multidimensional gene regulatory landscape of a bacterial pathogen in plants
Nobori et al. simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. They found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of the bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial messenger RNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence.
Nature Plants

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species
The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Gibson and Moyle use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modelling [SEM] and generalized dissimilarity modelling [GDM]) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms [SNPs]) with climate and geography, among 140 wild accessions.
Molecular Ecology

A multiple ion-uptake phenotyping platform reveals shared mechanisms that affect nutrient uptake by maize roots
Growth and branching of roots lead to effective root placement to acquire nutrients, but relatively less is known about absorption of nutrients at the root surface from the soil solution. This knowledge gap could be alleviated by understanding sources of genetic variation for short-term nutrient uptake on a root length basis. A new modular platform for high-throughput phenotyping of multiple ion uptake kinetics was designed to determine nutrient uptake rates in Zea mays. Using this system, uptake rates were characterized for the crop macronutrients nitrate, ammonium, potassium, phosphate and sulfate among the Nested Association Mapping (NAM) population founder lines. The data revealed that substantial genetic variation exists for multiple ion uptake rates in maize. Interestingly, specific nutrient uptake rates (nutrient uptake rate per length of root) were found to be both heritable and distinct from total uptake and plant size. The specific uptake rates of each nutrient were positively correlated with one another and with specific root respiration (root respiration rate per length of root), indicating that uptake is governed by shared mechanisms.
bioRxiv

The proteome landscape of the kingdoms of life
Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported, advances in mass-spectrometry-based proteomics have enabled increasingly comprehensive identification and quantification of the human proteome. However, there have been few comparisons across species, in stark contrast with genomics initiatives. Müller et al. use an advanced proteomics workflow—in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system—for the in-depth study of 100 taxonomically diverse organisms.
Nature

A singleton NLR of recent origin causes hybrid necrosis in Arabidopsis thaliana
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. Barragan et al. investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR disease resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11).
bioRxiv

Mutation bias shapes gene evolution in Arabidopsis thaliana
Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness and evolutionary optimization of genic mutation rates remains controversial. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve. To test this possibility, Monroe et al. used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome.
bioRxiv

The origins of flowering plants and pollinators
For more than a century there has been a fascination with the surprisingly rapid rise and early diversity of flowering plants (angiosperms). Darwin described the seemingly explosive diversification of angiosperms as an “abominable mystery,” and debates continue about the origin and processes driving angiosperm speciation.
Science


     

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