Free software for biologists pt. 5 –operating systems

If you’ve made it this far in the series then you’ll have already explored software for writing, analysing data, preparing figures and creating presentations, many of which are designed explicitly with scientists in mind. You’re clearly interested in learning how to make your computer work better, which is great. If you’re willing to do this then why not take the natural next step and choose an operating system for your computer which is designed with the scientific user in mind?

Put simply, Windows is not the ideal operating system for scientific computing. It takes up an unnecessarily large amount of space on your hard drive, uses your computer’s resources inefficiently, and slows down everything else you’re trying to do*. Ever wondered why you have to keep updating your anti-virus software, and worry about attachments or executable files? It’s because Windows is so large and unwieldy that it’s full of back-doors, loopholes and other vulnerabilities. You are not safe using Windows.**

What should you do? Macs are superior (and pretty), but also expensive, and free software solutions are preferable. The alternative is to install a Linux operating system. If this sounds intimidating, but you own a smartphone, then you may not realise that Android is actually a Linux operating system. Many games consoles such as the PlayStation, along with TVs and other devices, also run on Linux. Do you own a Chromebook? Linux. You’ve probably been a Linux user for some time without realising it.


I have no idea why the Linux avatar is a penguin. It just is.

If you’re coming out of Windows then you can get an operating system that looks and behaves almost identically. Try the popular Linux Mint or Mageia, which both offer complete desktops with many of the programs listed in earlier posts pre-installed. Mint is based on the Ubuntu distribution, which is another common Linux version, but has a default desktop environment that will take a few days to get used to. The best thing about Ubuntu is that there is a vast support network, and whatever problem you come across, however basic, a quick web search will show you how to resolve it in seconds.


Your Linux Mint desktop could look like this sample image from their website. See, Linux isn’t so intimidating after all.

Unlike Windows, all these distributions are free to download, easy to install, and everything works straight out of the box. Within a week you will be able to do everything you could do on Windows. Within two weeks you will be realising some of the benefits. Like any change, it takes a little time to get used to, but the investment is worth it. There are literally thousands of operating systems, each tailored to a particular group of users or devices. Rather than getting confused by them all, try one of the major distributions first, which offer plenty of support for beginners. Once you know what you need you can seek out an operating system that is specifically tailored for you (or, if you’re really brave, create one). Put the fun back into computing. Use Linux, BSD._001

Yeah, I know, may not look like the most exciting website in the world, but it does contain download links to every Linux OS you could imagine, and many more.

It’s possible to boot many of these distributions from a DVD or even a USB stick. This means you can try them out and see whether they suit before taking the plunge and installing them on your hard drive (remembering to back all your files up first, of course). If it doesn’t work out then take the DVD out of the computer and all will return to normal. An alternative, once you’ve set it up, is VirtualBox, which allows you to run a different distribution inside your existing operating system.

If you have an old computer which appears to have slowed down to a standstill thanks to all the Windows updates and is not capable of running the newer versions, don’t throw it away! This is exactly what manufacturers want you to do, and is why it’s not in their interests to have an efficient operating system. Making your computer obsolete is how they make more money. Try installing one of the smaller operating systems designed for low-powered computers like elementaryOS. You will get years more use out of your old hardware. A really basic OS like Puppy Linux will run even on the most ancient of computers, and if all you need to do are the basics then it might be good enough.

My preferred operating system is Arch, which has an accessible version Manjaro for moderately-experienced users. It’s not recommended for beginners though so try one of the above first. Why bother? Well, there’s an old adage among computer geeks that ‘if it isn’t broken, break it’. You learn a lot by having to build your OS from the ground up, making active decisions about how your computer is going to work, fixing mistakes as you go along. I won’t pretend that it saves time but there is a satisfaction to it***. Even if it means having to remember to update the kernel manually every now and again. One of its best features is the Arch User Repository, which contains a vast array of programs and tools, all a quick download away.

desktop 3_003

Behold the intimidating greyness that I favour on my laptop, mainly to minimise distractions, which is one of the advantages of the OpenBox window manager. Files and links on the desktop just stress me out.

As with every other article in this series, I’ve made it clear that you will need to spend a little time learning to use new tools in order to break out of your comfort zone. In this case there are great resources both online and from more traditional sources, such as the magazine Linux Format, which is written explicitly for the general Linux user in mind. You might outgrow it after a few years but it’s an excellent entry point. If you’re going to spend most of your working life in front of a computer then why not learn to use it properly?

With that, my series is complete. Have I missed something out? Made a catastrophic error? Please let me know in the comments!

* To be fair to Microsoft, Windows 10 is much better in this regard. That said, if you don’t already have it then you’ll need to pay for an upgrade, which is unnecessary when there are free equivalents.

** If you think I’m kidding, and you’re currently on a laptop with an integral camera, read this. Then go away, find something to cover the camera, and come back. You’re also never completely safe on other operating systems, but their baseline security is much better. For the absolutely paranoid (or if you really need privacy and security), try the TAILS OS.

*** Right up until something goes snap when you need it most. For this reason I also have a computer in the office that runs safe, stable Debian, which is valued by many computer users for its reliability. It will always work even when I’ve messed up my main workstation.

Field notes from Mexico 6 — a botanist in the museum

On my last day in Mexico, my hosts kindly took me to see the National Museum of Anthropology in Mexico City. First of all — wow. It’s absolutely spectacular, and if you have even the slightest interest in human history, culture and archaeology then you should go. Much like the British Museum* in London, you simply can’t take in the whole place in a single day. In fact, you would struggle to do so in a week.

In a single afternoon I was only really able to take in two archaeological sections: the Mexica empire, and the civilisations of the Pacific coast. The former were characterised by a militaristic state, the latter by their complex cultures and fine crafts. In fact, I was even more focussed, as I was specifically looking for evidence of botanically-inspired features among the artefacts, and I found plenty.

Many of them, interestingly, were related to cacti. This surprised me. Although Central America is the cradle of cactus diversity, and they are the most distinctive feature of Mexican dry vegetation, they are also relatively unimportant as crops and a minor component of most systems. Evidently they were considered worthy of carving into stone though.

In the section on the Mexica, rulers of the Aztec Empire, there is an altar with an Opuntia (prickly pear) clearly depicted on the rear face. This distinctive cactus provides a useful resource: its pads, once cleaned of the spiny glochids**, are cooked as a vegetable, known today as nopales, a word which derives directly from the Nahuatl as spoken by the Aztecs. Likewise the fruit, tuna, is still harvested and eaten widely in Mexico. The name Opuntia itself, however, is from the reference by Theophrastus to a plant in the classical Greek city of Opus which could grow from a leaf that was stuck in the ground. He wasn’t talking about a cactus though, because although they are now invasive in some parts of the Mediterranean, they definitely hadn’t arrived there in 300 B.C.


Opuntia isn’t solely used for food though; one of its more surprising appearances was in a reconstruction of a burial chamber from La Cueva de la Candelaria, on the border between the modern states of Hidalgo and Durango, which was occupied around 1100–1300 AD. The bodies each rest upon a layer of Opuntia pads. It hardly seems like comfort — no-one would do that if they were alive — perhaps these were provisions for the journey beyond?

Other cacti have more entertaining functions, such as peyote (Lophophora williamsii), a favourite hallucinogen for ritual and recreational use. It appears as a design on a large pot, and also in my favourite piece in the museum, a ring of revellers surrounding a shaman who is clearly holding a cactus in his hand. Both are from the Tumbas de Tiro tradition of West Mexico (200–600 AD).

RIMG2623To finish off the cacti, how about this metre-tall carved columnar cactus, probably from the genus Cereus? I definitely coveted this for a corner of my living room. It’s thought to be a boundary marker between two territories, and has the face of a legendary Mexica leader carved into its base. What interests me is that this kind of cactus isn’t present in that area, at least not in the modern world. Was it chosen because it was a feature of the landscape back then, or alternatively because it would stand out as unusual?

Other plants have important cultural associations. I’ve mentioned Agave before on this trip, particularly with reference to the manufacture of the alcoholic beverage pulque. I learnt much more in the museum though. Pulque had its own god, Ome Tochtli, which translates as ‘Two Rabbit’. Adults were only permitted one drink of pulque in any sitting (size not specified), and drunkenness was heavily frowned upon, lest one lose control and fall under the violent spell of Cenzon Totochtin, or ‘Four Hundred Rabbits’ (which, wonderfully, is the name of a popular brand of mezcal). So remember kids, two rabbits good, four hundred rabbits bad.

RIMG2635Another impressive piece of Mexica sculpture was this calabaza (Cucurbita moschata), a relative of the modern pumpkin. This magnificent piece was the size of… well, a ripe pumpkin. Alongside maize, which appeared in countless exhibits, beans and chilli, this was one of the staple foods of the peoples of central Mexico.

Not all the exhibits were carved in stone. One of the most important documents held by the museum is the Botorini Codex, a long pictographic account painted on fig bark by an Aztec artist around 1530–1541, so not long after the Spanish arrived. It tells the legend of how the Aztec arrived in the Valley of Mexico after leaving their original home of Aztlan. They decided to settle there due to the abundance of resources, but their first action was, of course, to cut down the trees. This is a useful reminder that tropical deforestation is by no means a new phenomenon, even if its intensity has increased in the modern world. One puzzling mystery though: why does the tree have arms?


A section from the Botorini Codex illustrating the clearance of forests in the Valley of Mexico following the arrival of the ancestors of the Aztec.

Finally, I’ll finish with another Mexica carving. On first inspection it looks like a bird sitting in a stylised flowering tree. But look more closely and you’ll see that the bird is eating some kind of caterpillar. In other words, it’s an archaeological representation of a tritrophic interaction! Perhaps they would have been unsurprised by findings of ecologists in Panama 500 years later that birds protect trees from herbivory.


Bird eats caterpillar eats tree. Tritrophic interactions in archaeology!

* Which is an order of magnitude larger again, thanks largely to the pillaging of cultures around the world in the name of empire, such as in the notorious case of the Elgin Marbles.

** Bristly patches of spines on some cacti, which often have barbs and detach when touched. I recommend a bar of soap to remove them. Then throw away the bar of soap before anyone else uses it by accident.

Field notes from Mexico 5 – ghost plants


Monotropa uniflora in the understorey of an Abies religiosa forest, El Chico National Park, Hidalgo, Mexico. Thanks to Sarah Pierce for the ID.

On numerous occasions on our trip through the coniferous forests of Mexico on the #PinaceaeGo project, we’ve encountered a ghostly pale plant on the forest floor. Depending on where in the world you’re from, it might look very familiar; or totally unlike anything you’ve ever seen before. That in itself is part of the mystery surrounding this plant.

Monotropa uniflora is variously known as the ghost plant, corpse plant, or Indian Pipe. As its appearance suggests, it is parasitic, and does not contain any chlorophyll of its own for photosynthesis. Unlike most parasitic plants, however, it doesn’t obtain its energy from other plants. Instead, it is an unusual example of a mycoheterotroph— it steals sugars from mycorrhizal fungi in the soil which are themselves symbiotic partners of trees. In other words, the trees choose to associate with the fungi, providing them with sugars in return for soil nutrients. Monotropa hijacks this arrangement and takes from the mycorrhizae while offering nothing in return.

This indirect theft is what allows it to survive even in dense, dark forests, and to be associated with a range of forest types. While most parasitic plants target particular plant species, M. uniflora is highly specialised on a few species of mycorrhizal fungi from the Russulaceae. All these features set mycoheterotrophs apart from more common parasitic plants such as dodder (Cuscuta spp.) or broomrapes (from my favourite plant family, the Orobanchaceae**), which are direct parasites on other plants.

Confusion over the taxonomy of Monotropa has been long-standing. Prior to Linnaeus, a related species Monotropa hipopitys was actually included in the genus Orobanche. Early botanists must have thought that parasitism ranked as a higher criterion for organising plants than flower traits. For a while it had its own family, the Monotropaceae, but it is now incorporated into the Ericaceae, along with heathers and Rhododendron, which superficially look nothing like it.

Another of its bizarre features is what biogeographers refer to as a disjunct distribution. It occurs in all sorts of places worldwide, in Russia, North and South America, but with large gaps between them. Genetic evidence suggests that these are distinctive, but not enough to call them different species. How did they get to such widespread locations? Was it through their dust-like seeds, or linkages in previous climates, or human transportation? Even where it is found, it’s never very common, and appears only in certain seasons.

monotropoideaemap (1)

Global distribution of Monotropoideae (including Monotropa uniflora) from Kathleen Kron’s Ericaceae site.

It’s not often that one can come across the same distinctive species in so many places around the world. How did a species of heather come to evolve into a fungal parasite, to develop such a strange form, and to spread itself quite so far? Wherever you find it, it’s always going to be special and mysterious.

* Here’s a pretty old review of this group of plants from 1994. If another has been published since then I’m unaware of it, and suggests that there might be scope for an update.

** One day I hope to retire to a herbarium and prepare a full review of the Orobanchaceae, so long as no-one else gets there first. I collect them on sight, wherever I am in the world. This is probably a pipe-dream. I’m never going to retire…

Field notes from Mexico 4 – tree farmers


Pico de Orizaba looms large over the landscape of Veracruz State, Mexico. From this vantage  point we’re still 3000 m from the summit.

There are two main crops grown on the northern slopes of Pico de Orizaba, a dormant volcano and the highest mountain in Mexico*. Unsurprisingly, one is maize, the standard subsistence crop in this region. The other is the pine tree Pinus patula.

We’ve spent two days this week getting to know the northern face of Pico de Orizaba, which is the side where the majority of coniferous species are found. As in so many parts of the world, our explorations are complicated because anywhere that’s accessible has been transformed by humans, which means that even if we can spot intact forests through the telescope, reaching them would be nigh-on impossible without a guide, climbing gear and a lot more time.

The first day was spent on the ridge tops, trying to get a view down into some of the valleys and find a promising route. This was a race against time as the cloud falls rapidly over the course of the day, shrouding everything in thick fog. Eventually we spotted some tall old-growth stands and reached a friendly village where they showed us the trail to reach them. We scouted a short way up the ridge but heavy rain put paid to any further adventures.

The next morning we set out to climb the narrow gorge which led to the forests we wanted to reach. On several occasions we hit waterfalls and had to turn back to climb around them. It also poured with rain for a large part of the day. Our determination was rewarded, however, when we finally emerged into some grand, full-stature forests of Pinus patula, mixed with some P. ayacahuite and Abies religiosa. It was a breathtaking sight and made the long climb worthwhile.

We weren’t the first to reach them though. All the way, our trail had been pock-marked by the hooves of donkeys. It soon became apparent that what we had reached was not an isolated remnant of forest but the current front line of an ongoing, small-scale logging operation.

The dominant cottage industry in this region is the manufacture of low-grade crates and pallets, the kind that are used to transport fruit and vegetables. Many households are surrounded by mounds of sawdust; often someone (usually a woman) is sat outside knocking together an endless series of crates. The improvised sawmill providing the planks is around the back. Their dominant raw material is Pinus patula.

Which brings me back to my comment at the start of the post about farming Pinus patula. Government grants have provided landowners in this area with thousands of seedlings of Pinus patula, which are now being planted all through the valleys. Men can be found peppered across the slopes, clearing the brash and shrubs away in order to plant yet more. The scheme has obviously been running for several decades because, in a few places, the trees are now reaching harvestable sizes.

I will confess to having mixed feelings about this. There is no doubt that the main driver of loss of these magnificent ancient forests has been the manufacture of cheap pine products. On the other hand they are, in some sense, being replaced, which means that the activity could in the longer-term become sustainable. Farmers are at least planting a native tree species, and one which clearly belongs in these valleys. It will act to reduce erosion, prevent flooding, and although not as good as old-growth stands, plantations will still provide habitat for many of the species that formerly inhabited the forests. The waste products — bark and other off-cuts — can be used as fuelwood to reduce their dependence on other sources such as charcoal. Finally, making crates provides a stable income for communities who have lived on and farmed these slopes for generations.

This landscape is so rugged, the topography so steep, that there will always remain some places where the native vegetation persists, out of reach of both donkey and chainsaw. These may only be small fragments but they are crucial in providing continuity, seed sources and safe redoubts from the encroachment of civilisation. I may never reach them or survey them, but I am glad to see them from my telescope, and know that they still exist.


This beautiful forest is under threat. But somewhere in these mountains others like it will remain, simply by virtue of their inaccessibility.

UPDATE: in between writing and posting this piece, the aftermath of Storm Earl led to multiple deaths in the area around Coscomatepec, where we were staying, due to flooding and landslides. It’s worth remembering that behind the headline figure of fatalities is always a larger story of survivors who have lost houses, crops, livestock; many villages will have been cut off. Mexico is a beautiful country but one with great disparities in wealth, and in this tragedy the heaviest burden will fall on those least able to cope.

* Its total height is 5,636 m, but most striking is its prominence, rising 4,922 m above the surrounding landscape. It really does stick out.

Field notes from Mexico 3 — Pulque Party



Caution — drunkards. My favourite warning sign on the roads*. The source of their booze, the maguey plant, is on the left. Photo: Libertad Sanchez-Presa.

Once you leave the main roads and cities, a large amount of Mexican culture revolves around the Agave. Its most internationally renowned member is the blue agave, Agave tequilana, whose sugary heart is used to make tequila. A less well-known drink is mezcal, which can be made from a range of Agave species, and by small producers. This allows for a wide variety of styles and flavours, making it a more diverse and interesting drink than mass-market tequila.

In the region where we’ve been working, however, the dominant species is Agave americana, known as maguey. The plants are everywhere, either as dedicated plantations, scattered among crops, or surrounding houses and smallholdings. They’re not just a weed though; they are carefully tended and visited regularly to harvest the sugary sap from their core, known as aguamiel (honey water).


The heart of the maguey plant contains a pool of sugary sap (aguamiel). In this case it is protected from evaporation and contamination by a plug of igneous rock.

During our hunt for the lost firs, which was a great adventure, we ended up walking through a number of farms in the foothills. In one we met a local woman collecting her aguamiel, who showed us how it was done. The process is pretty simple: a coke bottle with a hole in the bottom and a tube attached is used to suck the liquid straight out of the core, then drained into a bucket. She then scrapes out any scum or accretions on the bottom of the core, which ensures that the plant continues to secrete more sap through what is effectively an open wound. Most of her teeth were missing, which can probably be attributed to a lifetime of doing this.


A local farmer near Metapec sucks the sap from the heart of a maguey plant using an improvised bottle with a tube attached.

She offered me some and, being generally willing to try everything, I naturally obliged. It’s sweet with a distinctive flavour, in this case enhanced by a number of dead flies which added an interesting mouth feel.

In some places you can buy the aguamiel pure, though one imagines they filter it first. Its most important value, however, is to be fermented into the mildly alcoholic** beverage pulque. As you drive through rural areas there are occasional improvised signs next to shacks declaring its availability. Pulque is sold by the litre***, dispensed into whatever container you have to hand. We’ve been using old plastic water bottles, though this makes them impossible to ever use for water again because the pulque leaves a lasting unpleasant odour in the bottle.

It’s best drunk fresh because it continues to ferment in the bottle, which shouldn’t be closed too tightly as the build-up of gas can cause it to explode, especially if you’re bumping along dirt roads as we tend to be. Left for too long it becomes viscous and unpleasant.

The drink is the favoured end-of-day beverage for labourers, serving the role that beer plays elsewhere in the world. It’s slightly sweet, frothy and refreshing. We’ve tried a number of pulque shacks and experienced the full range of quality. Some was delicious and moreish, another so bad that one sip had us spitting it out and feeling queasy for the rest of the day. We’ve been going for pulque natural, the pure version, although in many places you can buy it flavoured with fruit juices.

Pulque is also used to make the dish barbacoa, a speciality of the State of Higalgo, which is meat (usually pork) soaked in pulque, wrapped in maguey leaves and baked. The result is something like pulled pork; tender and juicy with a characteristic flavour. It can then be wrapped in a taco with the usual accompanying relishes.

Is there a potential mass market for pulque? Personally I doubt it. Achieving greater quality control and consistency would not be impossible, but the difficulties of transporting it and keeping it fresh mean it’s unlikely to supplant beer. In the villages and rural parts of the country, however, it remains an important part of daily life. It’s also a great way to finish a long, tiring day of fieldwork in the forest.

* Not, I should add, an official Mexican highways sign. Someone had stuck their own sign on top of the existing one. Drunkards of Mexico, we salute you.

** I sank a litre of it by myself a few nights ago. It didn’t get me anywhere even close to drunk but it did give me a vicious hangover. I won’t be trying that again.

*** We’ve paid 10–12 pesos per litre, which is around 50 pence.

Field notes from Mexico 2 — Lost Valley of the Firs

UPDATE: this post is followed by an embarrassing correction. I’m leaving the original in place, unchanged, because I don’t want to hide the fact that scientists sometimes (often) make mistakes, and are as prone to over-enthusiasm and optimism as anyone else. So please read on, and don’t judge us too harshly for admitting our errors. 

We have rediscovered Abies hidalgensis! This is an amazing find, and a real boost to the PinaceaeGo project. It took two solid days of hunting on inaccessible mountain slopes. To understand why this species is so important, we need to start at the beginning, with some fine detective work in the herbarium by awesome PhD student Libertad Sanchez-Presa.

Abies hidalgensis was first described in 1995 by a Hungarian botanist following a collecting expedition the previous year*. Unlike all the other ‘new’ species described in that paper, it survived subsequent critical review by Aljos Farjon, the world expert on conifers and a notorious lumper**. Libertad uncovered the type specimen in the National Herbarium of Mexico at UNAM in Mexico City. Everything about this species sounded dubious. The description of the collection locality didn’t match the co-ordinates, which were 30 km away. It was supposedly found at 2300 m altitude, whereas we haven’t seen Abies below 3000 m anywhere else in the country. Most of all, this is an arid area, and firs are usually found in dense, damp, dark forests. Nothing we saw on Google Earth suggested that such a location existed. She decided that this mysterious species was worth tracking down.


This is the duplicate specimen of Abies hidalgensis held in the Kew herbarium (obtained via HerbWeb). That label is all the information we had to go on.

Our journey began with a drive up from Puebla to Tulancingo in the state of Hidalgo, where we spent the night. An early start took us to the vicinity of Metapec, a small village to the south of the mountain range where the species was described. From there we took dirt roads as far as we could towards the location described on the sheet, though the details couldn’t be matched to the actual landscape.

For one day we hacked up and down gulleys and over ridges, sweating in the heat. We saw some amazing stuff: a huge tarantula hawk wasp killing a large spider then dragging it away; a wild Mammillaria cactus with edible fruits, which we ate; some oak ‘apples’ (really galls formed by insects) large enough to deserve the name; and an array of spectacular mushrooms. Some of our findings will be the subject of a future post.

What we didn’t see were any fir trees. More concerning was that we didn’t even see any habitat where Abies was likely to be found. There was plenty of dry pine forest and scrubland, but even scanning the slopes and plunging into the valleys revealed no firs or even evidence that they might once have been there. By late afternoon we were tired and disheartened. Had the species disappeared? Did the collector get their field notes mixed up?  Was it an elaborate hoax? All sorts of explanations ran through our minds.

Typing the co-ordinates into my GPS gave a location 30 km away in the state of Veracruz. This was a long way from the site description, but it was at least up in higher mountains where Abies might more plausibly be found. There was nothing for it; we had to look. The actual driving distance was more like 50 km, ending up on dirt tracks in remote villages. All we found were large plantations of exotic trees that the locals referred to as ‘Chinese pine’ (perhaps Pinus koraiensis?). If the Abies had been there once then there was no sign of it now, nor of any native vegetation. We drove back, 100 km of wasted effort.

All the way back to Metapec we were haunted by visions of Abies in the forests around us. More than once we screeched to a halt, convinced that one or other of us had spotted something, only to discover it was just another Cupressus lusitanica. 

As we drove past the ridges we had been exploring earlier in the day, it was late evening, and the setting sun was illuminating the slopes. Sarah spotted some conical trees unlike anything we had seen that day. We pulled out the telescope and peered through the dusty haze. There was definitely something up there, tucked away in an inaccessible valley… but we had become rather jaded by our earlier experiences and were no longer willing to trust our eyes. Besides, it was 10 km away, and there was no hope of making it up that evening.

The next day we had plans to inspect another site, but made the difficult decision to try again, one last time. If it was there then it would be remarkable; if not then we were all ready to remove it from our biogeographical analyses as an aberration. We started out from a different point, navigating through the slopes towards the valley Sarah had identified from the road.

Emerging onto a ridge crest, it was Sarah who again noticed something unusual. On the next ridge north of us, atop an escarpment a few hundred metres away, a small tree was poking up with a distinctive conical form. It was only around two metres tall and, squinting through the telescope, it looked like it just might be an Abies. Reaching it would be extremely dangerous though. We pressed on.

We climbed further up until we reached a high ridge at 2600 m close to our target location. It was lunchtime and we were tired and hungry. We dropped bags and looked around the typical oak-alder forest. Libertad pointed towards something growing in the understorey. Could it be?


Sarah celebrates finding the first Abies seedling. It’s just to the right of her.

She ran over and confirmed — we had an Abies! In fact, they were all around us. But at this altitude, in this vegetation, was extremely peculiar. It wasn’t anything like the normal conditions for Abies, nor in fact much like the site description from the herbarium records. None of this made much sense. As we descended down the opposite, north-facing side of the ridge, they were everywhere. The tallest individuals exceeded 20 m in height and 50 cm in diameter, with a range of sizes and plentiful seedlings. But they were growing in dry, open conditions, on a ridge with cacti nearby; how was this possible?

We only had a few hours before we needed to return home. In that time we managed to collect herbarium specimens, tissue samples in alcohol for genetic analyses, trait data for our own work and core two large stems***.  The steepness of the slopes, peppered with escarpments, made it impossible to descend far into the valley below, but we could see more Abies down there and on the opposite slope. Talking to a local farmer later that evening it sounds as though another route into the valley exists, which we may explore next time. We left as late as was safe, exhilarated and exhausted, and also a little frustrated at not being able to stay longer and collect more data.


Two large, healthy specimens of Abies hidalgensis, right on an exposed ridge top. This is not where we would have expected to find them.

What now? We have the trait data we were looking for, and can confirm not only the presence of this species but also its exact location. Our samples will be sent to local herbariums and experts; hopefully the tissue samples will allow a systematist to determine the true place of this species on a phylogeny and identify its nearest relatives. We are also a little puzzled by the cones, which don’t look much like those on the existing herbarium specimens.

That’s not where this story should end though. The species is listed as vulnerable on the IUCN Red List, which is reasonable given that the range of this population can be no more than two square kilometres. One hot summer and a severe forest fire could severely deplete its numbers, a disaster which becomes increasingly likely in a warming climate. Having found the species again, we now bear some responsibility to do something about it.


So far as we know, these two valleys encompass the global range of Abies hidalgensis. Rumour has it that there are some more close to the village of Agua Blanca to the north, but we were unable to confirm this.

What this action should be is something we will need to discuss. Perhaps we could undertake a comprehensive mapping exercise and population estimate; press for the designation of a protected area; collect seeds or propagate live material for ex situ conservation; set up a mapped forest dynamics plot… all could be the subject of future work.

Personally, I think the most important outcome should be a local education campaign. We spoke to many locals and farmers over the course of the two days, yet only one knew about the species. These are people for whom this forest is on their doorstep, who use it to hunt or collect firewood and mushrooms. Realising that their forest contains a tree of global importance and interest should be a matter of great pride, and will be the key to ensuring that it remains well protected.


Libertad’s plant press contains that most precious of cargoes: herbarium specimens of Abies hidalgensis, the first to be collected for over 20 years, linked to a much greater amount of contextual information and data on the individual trees.

* Their visit is described briefly in this paper. They didn’t manage to see a great deal on their two trips up the mountain.

** Taxonomists are often broadly stereotyped as ‘splitters’ or ‘lumpers’. Splitters have a propensity to declare new species on the basis of fine differences among populations, sometimes as much through wishful thinking as meaningful variation. Lumpers review these designations and collapse them into single species. Splitters don’t like lumpers because they take ‘their’ species away. This tension has been present throughout the history of taxonomy.

*** Coring carries a small risk to the tree, and therefore should only be performed with a good reason and where you can be confident that there are plenty of individuals. From these cores we can determine the growth rates of the trees and look for any indication of climate dependence or changes over time.

IMPORTANT UPDATE (18 August 2016)

Well, as the new header on this post might have given away, we didn’t actually find Abies hidalgensis. We had grown increasingly suspicious of our collection over the days that followed, and on depositing the specimens in the herbarium at Monterrey, our fears were confirmed. We had actually collected Pseudotsuga menziesii. 

How did three experienced plant ecologists come to make such a big mistake? There are a few mitigating factors. Psuedotsuga  wasn’t previously recorded in this area, so we weren’t expecting to see it. We were tired, clutching at straws, and perhaps too ready to leap at anything that looked like an Abies. Finally, they aren’t that easy to tell apart. I should be embarrassed because I know Pseudotsuga menziesii well from North America (its common name is Douglas fir), but the local Mexican type actually looks very different, and some botanists have tried to designate it as a different species. I won’t comment on this other than to say that the accepted approach is to consider it as a single species with sub-specific variants and a high degree of morphological variation.

Where does this leave Abies hidalgensis? We still don’t know. The original collection records for the type specimens are contradictory and bear little resemblance to the landscape of the area. We tried everywhere that sounded roughly right, or that looked like it might be Abies habitat, and a lot of places that weren’t, just in case. We did everything we could to find this species in the time available and failed. Is it actually there at all? Was it ever? We are back to having some serious doubts about the very existence of this species.

As for our error, it’s an excellent demonstration of why scientists publish in journals rather than online blogs. When we submit a paper, as we would eventually have done, our findings go through many layers of careful scrutiny. It takes a long time, and many ideas fall by the wayside in the process. It’s easy to dash off a small blog post in the evening with a beer and claim quick credit, but were these to be treated as findings equivalent to published articles, it would carry the risk of mistakes ending up in the body of scientific knowledge. So you should never automatically trust a blog post, press release or similar non-standard means of transmitting a scientific finding. It may get more attention than a paper published years later, but it carries a high risk of being wrong, as we were.

Still, we had fun :o)

Field notes from Mexico 1 — Pinaceae Go!

For the next five weeks I’m based in Puebla, Mexico. It’s a beautiful location: an historic city (the centre is a World Heritage Site) surrounded by spectacular archaeological sites and with a horizon dominated by snow-capped volcanoes*. There’s not much time for tourism though; we have a packed itinerary.

The first three weeks will be taken up with a single mission: collecting trait data from as many Mexican coniferous species as we can find. Hence the nickname of the trip, Pinaceae Go!** Because finding real trees is way more fun than hunting virtual creatures on your mobile phone. We also stand a chance of spotting the legendary volcano rabbit, which sounds as though it should be a Pokémon.


The Pinaceae Go team — myself, ecologist Dr Sarah Pierce and PhD student Libertad Sanchez-Presa. And, in the background, the real object of interest: Abies religiosa on La Malinche volcano.

Why Mexico? The reason is that the country is the centre of global diversity of conifers. Of the 120 recognised species of Pinus worldwide,  49 occur in Mexico***. The country also holds 7 of the 18 species of Cupressus, 8 of 48 species of Abies, one each of the four species of Pseudotsuga and Calocedrus, 3 of the 38 species of Picea and 20 of the 68 species of Juniperus. That’s quite a haul. Of those seven important genera, Mexico alone contains 30% of  global species richness.

So what? There are other centres of tree diversity all around the world. Why is this one in Mexico special?

The reason this particular hotspot baffles me is that current opinion in forest ecology suggests that conifers can’t reach high levels of species richness. This is because classical theory argues that conifers don’t have the flexibility of traits and growth forms available to broad-leaved trees. Conifers all have roughly similar branching patterns, leaves**** and wood. It’s relatively easy to understand how multiple broad-leaved tree species can coexist by having distinctive traits to reduce the degree of competition among them. Such a wide range of variation simply doesn’t exist in conifers.

This account may appear compelling to a temperate ecologist, who will know of the vast boreal forests containing only a couple of coniferous tree species. It falls apart when faced with the montane forests of Mexico.

To illustrate the scale of the problem, our very first sampling location provided a perfect example. We drove along a dirt track up the side of the famous active volcano Popocatépetl, stopping at around 3000 m altitude to have a look around the forests. It didn’t take long to start building our database. Within 100 m of the road we were able to sample five species of Pinus, one Abies and a Cupressus. We weren’t even trying very hard; this was an introductory walk to test our methods rather than a systematic sample.

Ultimately the questions Libertad would like to answer include:

  • At what spatial scales does the coexistence of so many species of conifer occur? Are they growing side-by-side, or specialising on distinct types of habitat?
  • Do the traits of conifers determine which species are found in coexistence? Do these traits change among locations or depending on the presence of other competing species?
  •  What drives patterns of species and trait diversity in conifers on biogeographical scales?

We’re only at the beginning of this project; Libertad is still in the first year of her PhD and this is the first fieldwork we’ve done. A large amount of trait data is in the literature already, along with the Mexican national forest survey. We’ve been processing all this information over the last few months. Our aim for this trip is to supplement this with missing species and new locations. Gotta catch them all…

* Your view of snow-capped volcanoes may depend upon air quality.

** Conifers include the pines (Pinaceae), hence the trip nickname. Conifer Go would have been more accurate, but wouldn’t have sounded as good.

*** Let’s not get into arguments over taxonomy. We’re following the opinion of Aljos Farjon, generally acknowledged as the world expert on conifer systematics, and bane of splitters.

*** Yes, they are still leaves, even if they are colloquially referred to as needles.