Monthly Archives: November 2010

PHYLIP and phylogeny inference

PHYLIP Phylogeny

PHYLIP Phylogeny

The PHYlogeny Inference Package, PHYLIP, written by Joe Felsenstein (University of Washington) has reached the milestone of being 30 years old. Almost every recent volume of Annals of Botany has papers using this program for analysis of data, among the 32,000 papers that cite it published since 1980. There are few software packages that have stood the test of time over so many generations of computers – I have been using it regularly since I was a PhD student. Developed long before WIMP (windows, icons, mouse, pointer) interfaces, PHYLIP still retains its modular simplicity and versatility. You are much less likely to end up with garbage-in, garbage-out, none of the algorithms is proprietary, there is a gigantic literature associated with the program, and the documentation is a model of clarity. I always feel uncomfortable with the big modern informatics analysis packages where you are so ‘protected’ (or is that ‘unprotected’?) from the algorithms, and the PHYLIP methods have a robust (if sometimes controversial) literature behind them.

Over this period, Dr Felsenstein has continued with the extension of the program, and as well as the documentation, there is a Phylip Facebook pages, where he responds to every enquiry from the most basic to most advanced. Despite the widespread use of PHYLIP and value to a wide community, the anti-acknowledgements at the bottom of the Credits page also make interesting reading, showing just how difficult the funding of development and publication of such a widely used method can be.

Because of its straightforward nature, I use PHYLIP regularly in courses – at the basic level through one of the many web-interfaces so downloading and installation is not needed. One of my uses is shown at www.BS1008.molcyt.com : the students score a number of leaf characters from trees and shrubs, which classifies evergreens (Quercus ilex and Osmanthus) together, and then compare that with DNA data which follows a natural classification and oaks lie together. Another easily visualized application of PHYLIP for teaching is to work out relationships between Scotch whiskies. A book by the second most famous Michael Jackson (after, that is, the editor of AoB Plants) classifies 109 different malt whisky types on the basis of 68 organoleptic qualities (colour, nose, body, palate and finish), and Lapointe and, Legendre published a “Classification of Pure Malt Scotch Whiskies.” (Applied Statistics. 1994; 43(1):237; http://dx.doi.org/10.2307/2986124 (archive repository version available here; data matrix for analysis is here at Pierre Legendre’s website, and he has another related paper on distance matrices between malt whiskies).

So happy birthday PHYLIP, and congratulations to your creator.

Edit 1 Dec: add link to malt whisky (not whiskey) datamatrix.

Peter Bradbury from USDA, Cornell, also notes other useful SNP analysis programs:

TASSEL, http://www.maizegenetics.net/tassel EMMA, http://mouse.cs.ucla.edu/ PLINK, http://pngu.mgh.harvard.edu/~purcell/plink/ Haploview, http://www.broadinstitute.org/haploview

There is also PowerMarker, http://statgen.ncsu.edu/powermarker/ which I use in courses too and allows simple pasting of Excel formatted data.

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Dramatic improvement to a top-tool

A blog and manuscript in “Serials Review” discuss the versatility and coverage of Google Scholar. It’s now my first search point – fast access to the original manuscripts (Pubmed, in particular, note!), short excerpt, versatile ‘advanced search’ doing what is expected, useful citation count to judge importance. And now the coverage (including paper repositories) is excellent. (link)

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Patterns of resource allocation in a dioecious species

Patterns of resource allocation in a dioecious species
Patterns of resource allocation in a dioecious species

Resource allocation between vegetative and reproductive growth will vary over time, and dioecious species may also adopt different strategies for allocation between male and female plants. Sanchez Vilas and Pannell show that males and females of the annual Mercurialis annua differ in temporal patterns of resource allocation to roots, shoots and reproduction. These differences are likely to be the consequence of the different demands for resources required for producing pollen versus seeds at different times.

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I’m stealing this presentation

The social web isn’t just limited to blogs, Facebook and Twitter. Slideshare is a great place to look for presentations on all sorts of things. I’ve been particularly impressed by this presentation about how to give a PowerPoint presentation.

STEAL THIS PRESENTATION!
View more presentations from @JESSEDEE.
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Methods for analysing the response of vegetation to land use

Methods for analysing the response of vegetation to land use
Methods for analysing the response of vegetation to land use

The assessment of ecological gradients and functional composition of plant communities will affect subsequent predictions as to how those communities will react to disturbances. Focusing on leaf dry matter content (LDMC), Duru et al. compare methods for assessing the impact of different disturbances and nutrient conditions upon functional characteristics of 69 grassland communities. They find that estimates based on a database of plant traits correlate well with actual measurements provided that variations in temperature are taken into account, and that the N-Ellenberg index out-performs methods based on plant nutrient content.

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Plant Anatomist Elizabeth Cutter dies

Plant anatomist and developmental biologist Elizabeth Cutter died in October 2010. She published seminal experimental work on pteridophyte development and on organogenesis (including 11 papers in Annals of Botany), and is well known for her important textbook, “Plant Anatomy: Experiment and Interpretation”. Obituary at: the Guardian

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Phylogeny and biogeography of Allium

Allium nanodes of subgenus Anguinum from China
Allium nanodes of subgenus Anguinum from China

Allium is one of the largest moncotyledonous genera and has been subject to many phylogenetic studies; however, species endemic to China have often been neglected. Based on ITS and chloroplast rps16 intron data, Li et al. find that Allium is monophyletic and consists of three major clades, but some subgenera are not monophyletic. The high genetic distances imply that Allium is of ancient origin. A taxonomic synopsis is proposed that divides Chinese Allium into 13 subgenera and 34 sections.

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The roadside botanist, bananas and cassava biodiversity

Roadside Botany ...

Roadside Botany ...

 

This week’s roadside botany in the Brazilian Cerrado: eleven wild species of cassava, Manihot, extensive bananas and exceptional biodiversity. The morning showed the remarkable cassava plant breeding project in the context of EMBRAPA Cerrados, and their evaluation programme for Musa genotypes, while the afternoon looked at wild species.

In a tour led by Luiz Carvalho (part of the FAO/IAEA programme – see blog), Eduardo Alano Vieira introduced us to the large cassava (manihot, manioc or tapioca) crossing programme, involving 30000 seedlings per year and some novel characteristics: not just yield, biotic and abiotic stress resistance, but including sugary as well as starchy forms, those with altered post-harvest physiological deterioration (PPD) and

Segregating trial plots of F3 cassava crosses

Segregating trial plots of F3 cassava crosses

 

with a range of colours from important micronutrients or provitamins – illustrations here show root sections.

Cassava roots varying in colour and starch/sugar content

Cassava roots varying in colour and starch/sugar content

 

We went on to see the banana genotype evaluation collection, with Tadeu Graciolli Guimaraes. We had the chance to eat the various genotypes the researchers have been working with. One banana genotype was rather flavourless and starchy (Prata Ana), but two others emphasized what we in the temperate countries miss: Garantida II with citrus flavours overlaying a sweet smooth texture, while Caipira had a more savoury and vanilla custard taste. But the research project (presented in Portugal earlier this year – Tadeu Graciolli Guimaraes et al. Yield and agronomical behaviou of banana (Musa spp.) genotypes in Brazil’s Central plateau. In: INTERNATIONAL HORTICULTURAL CONGRESS, 28., 2010, p. 749, (see http://bit.ly/hmMF0q [PDF]) was a model of its type: 22 Musa genotypes are being grown at more than 20 locations without any inputs and being evaluated for a substantial number of agronomic, disease, yield and other traits. This type of experiment needs careful management. In fact, the plants were remarkably healthy (not least because this is not a banana-growing area and largely disease free), although there were gaps where the six replicates of genotype Maca had died from Fusarium (Panama disease) within a few months of planting.

Banana genotypes

Banana genotypes

 

Of the remaining genotypes, only one showed serious yellow sigatoka (there is no black sigatoka [seen in this field - text addition made May 2011] in Brazil – “yet” as Andrew James from CICY in Mexico reminded us several times!).

I can remember several unfortunate cases (as no doubt can the others involved) where I have stopped a bus full of molecular biologists and rushed off into the field margins, or declined the coffee on offer after a long drive to have the chance to botanize in the area around a motorway service station (on at least two occasions, on different continents, picking up armed guards in the process). So then off to some real roadside botany – the first part along 4×4 tracks, but the second part involving the verges of a 6-lane highway (see opening illustration). The highway margins gave an excellent view of the purpose of the storage root of cassava. Unlike many other vegetatively propagated crops, root segments do not grow to new plants, but provide storage for rapid regrowth of the plant after the spring rains, or after fire damage.

Wild manihot regrowth soon after fire

Wild manihot regrowth soon after fire

 

The area we walked through had been burned less than a month ago, but was completely green. While my swiss-army knife was more than up to cutting the cultivated roots, the Manihot vericosa and M. gracilis of the afternoon involved cutting through wood. Why did the root change from woody to starchy? Surely the function of a starch store is different from a woody root store.

Manihot stipularis - a tiny species

Manihot stipularis - a tiny species

 

Later, we got to see the miniature Manihot stipularis - a plant flowering when smaller than a finger, contrasting with the morning’s cultivars reaching up to 3m.

Woody storage root of Manihot violacea

Woody storage root of Manihot violacea

 

Interestingly, the road verge had been burnt about three weeks before our visit, so we could see the high level of regeneration – allowing classic pictures of the cerrado vegetation. What fantastic diversity, and I hope threats can be mitigated (see Ratter et al., 1987; and more recently Collevatti et al. 2009 Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub).

 

Campo Cerrado vegetation, Brazil

Campo Cerrado vegetation, Brasil

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The origin of modern Botany and the Infinite Monkey Cage

Robin Ince and Brian Cox in the Infinite Monkey Cage

Robin Ince and Brian Cox in the Infinite Monkey Cage

Some ideas work and some ideas don’t. Sticking Prof Brian Cox and Robin Ince together for half an hour each week works. The Infinite Monkey Cage is their weekly show on Radio 4 (available worldwide as a podcast) where they discuss topics with various guests. Last week Andy Hamilton in for a chat about the Apocalypse. These week they talk with the chemist Professor Tony Ryan, social sciences researcher Aleks Krotoski and comedian Paul Foot to ask if the modern world is a force for good or evil.

That means defining what the modern world is. Tony Ryan went for the Haber-Bosch process marking the start of the modern world in 1908 due to the ability to create fertiliser. He made a good case for the process being imperative for the modern world Aleks Krotoski choose the invention of the printing press in 1440. So I thought as post I could ask when you thought the modern era for Botany started. It sounds like a good idea, but I don’t think it works.

The plan was that you could argue for The Origin of Species, or Mendel’s genetics or the modern synthesis as marking the watershed for modern Botany. Alternatively you could look back at the great voyages of exploration, like Joseph Banks’ trip around the world. Other disciplines have discussions about their origins. Did modern Physics start with Galileo or Newton? But Botanists seem to be fairly unified in where modern Botany starts.

There seems to be a convergence on 1753 and the publication of Species Plantarum by Carl Linnaeus. Recently Fay and Chase published in Annals of Botany on Orchid biology: from Linnaeus via Darwin to the 21st century. This is clearly marking modern Botany between Linnaeus and now. It’s a view that groups such as the Linnean Society agree with, obviously. We also recently published Linnaean sources and concepts of orchids by Jarvis and Cribb, which looks at what makes Linnaeus special.

This bothers me. Usually when I come to an easy solution to a matter of opinion it’s a good sign I’ve not been thinking hard enough. So does anyone have any other contenders? I’ve found this paper on The Concept of the Genus on JSTOR, but I don’t have access to it. Google Scholar hints that it argues some Linnaean concepts actually date from much earlier.

Alternatively could you argue that modern Botany has yet to start? Linnaeus gave us taxonomy, but is cladistics a superior approach and taxonomy holding us back? This might not make sense though as Grant argues that one system is not necessarily right and the other wrong in his paper Incongruence between cladistic and taxonomic systems in AJB.

Do the origins of Botany lack the controversy that you find in other sciences? If so what does that say about Botany as a science?

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