Genes and ancestry

Back in April, 23andme had a special offer by which you could get their personal genome screen for just the price of a one-year membership. Having read Gene Expression off and on for the last few years, I have gradually grown more interested in the world of personal genomics, but what really caught my attention was when Zack Ajmal started his Harappa Ancestry Project back in January. His focus on Indian ancestry really opened up new possibilities for me, and by following his blog (and paying more attention to Razib’s posts on the subject) I felt a great to desire to join in the fun.

So, back in April, I ordered my kit. And then I did nothing with it for a few weeks. It was nice to contemplate it, savour the sense of possibility. But there was also the matter of not eating, drinking or brushing your teeth within half an hour of giving the (saliva) sample. And it seemed like every time I realise that the kit was sitting there – I had just broken one of those rules. Eventually I got myself to do it, mailed off the kit, and a few days ago I finally got my results. And I was faced with a new question – now what?

The first set of results I got had to do with things like disease status and traits. I learned that I am likely to be at higher risk for some diseases, at lower risk for others. It was interesting observe my own reactions to these results – my initial reaction was to downplay both the negatives (the higher risks of certain diseases) while also downplaying the positives. The former makes sense – the odds of most of these things are low enough that even if my risk is higher, it’s still very small. On the other hand, even if my risk of Type II diabetes is about 20% lower than the average, it’s still shockingly high – mostly because the average risk is shockingly high. After a while though, I came back to the realisation that, with regards to the things that might pose a higher risk…well, I need to use that information to my advantage, keep an eye out for things (without being a hypochondriac) and maybe a little knowledge might let me catch a problem sooner, rather than later… (More later)

Names…

I suppose it’s time to stop calling this by the default My Blog that WordPress gave it. To be honest though, it’s a pretty descriptive name – it’s a blog, it’s mine…what more do you want?

I suppose some sense of the place might help. But what do I really want to do here? What’s my vision for this site? And how do you encapsulate it in a single phrase? OK, well, I can’t. Well…what about something clever? Something catchy? Something profound? Sounds great – now all I need is skill in coming up with clever, catchy names. If I could do that, wouldn’t I be making lots of money in marketing?

OK then – how about a reference to something that’s kinda cool and somewhat descriptive? Something with a distinctly Trini flavour. But what? I’m sure there are dozens of ‘river lime’ blogs and ‘rum shop’ blogs. “A Mayaro state of mind” would be nice. But it’s probably been done already. And, more importantly, I’m not shooting the breeze in Mayaro, and I’m not in that sort of a state. I don’t want peace with the universe, I want intellectual engagement. With a sense of what is Trini and botanically inclined, nature inclined.

And then I realised what I was looking for. The samaan tree – Samanea saman. For starters, it’s a really attractive tree with its open, spreading crown. Its long, almost horizontal branches are excellent hosts for epiphytes. The campus of the University of the West Indies in St. Augustine (Trinidad) was dotted with them when I was an undergrad, and (weather permitting) the grass under a samaan tree was a good place to sit and talk, sit and contemplate the world. With the added bonus of random small insects falling out of the tree above you.

The first meeting of the group that was to become the Association for Tropical Biology (and Conservation, in recent years) had their initial meeting in Trinidad, and it was the samaan tree outside the Sir Frank Stockdale Building on the UWI campus that has graced the cover of their journal, Biotropica, ever since.

Although not a native species, there is something very Trinidadian about the samaan tree. In many ways it speaks to an older, less industrialised time when people understood that trees mattered. It has a personal connection, in memories of my undergrad days at UWI. And it is connected with one of the pillars of Neotropical biology – the journal Biotropica.

So it is with that in mind that I have renamed this blog. Too pompous and self-indulgent? Maybe. But so be it.

What do evolutionary biologists study?

So what do evolutionary biologists study? Evolution is, in the minds of much of the public, ‘controversial”. In no small part, this is the doing of a large, vocal, well-funded anti-evolution movement. But responsibility also lies with the people who have taught evolution, who work in the field of evolution.

A lot of people see evolution as being pretty much the same as palaeontology. People dig up fossils and then come up with explanations for how these fossils are related. One person calls a certain fossil a human ancestor. Another says that is represents a distinct lineage. From the outside it just looks like a group of people with advanced degrees pontificating about a subject…specifically, the subject of origins. To look at it another way, it it seems rather a group of scholars discussing some esoteric element of theology.

If I’m correct, that might explain a good deal of how American (especially evangelicals) see evolution. To American Protestants, theology and christology tend to be a very personal endeavours. The Protestant Reformation led to the translation of the Bible into the tongues of the common people. Not only were they able to read the words for themselves, they were also encouraged to come to their own conclusions about it. Looking in from the outside, it’s easy to see evangelical and fundamentalist churches telling their members what they should believe about a number of important issues. But most churches also tell people that they should find their own meaning in scripture. If you aren’t willing to take your own pastor’s word on the meaning of everything in the Bible, why should you take the word of some ivory-tower intellectual who (a) almost certainly knows nothing of the life experience of people like you, (b) is just one voice among many, each of whom has a different view of what this fossil means, and (c) is probably an atheist with an agenda to undermine Christianity and morality.

Now, obviously, this approach is entirely incorrect. Science isn’t a collection of equally valid ideas – some ideas are demonstrably better than others, while others are demonstrably worse. The diversity of views that anti-evolutionists speak of, just doesn’t exist. More importantly, there is no hierarchy imposing orthodoxy.

But more people don’t understand this. And sometimes, I suspect, evolution defenders miss this point entirely. [More later]

Bob Ricklefs: My Life as a Naturalist

Robert Ricklefs gave the American Society of Naturalists‘ Presidential Address today at Evolution 2011. For me, this was one of the high points of the entire conference. In a meeting where ecologists and tropical biologists were fairly thin on the ground, it was great to see someone speak who had such standing, not only as an ecologist, but also someone who had done some of his best work on the biogeography of the insular Caribbean.

Ricklefs talked about what it meant to be a “naturalist”. Naturalists and natural history have gone out of fashion in the last half century. Naturalists were Victorian field biologists, especially the amateur biologists and explorers who played such an important role in the early development of fields like ecology, evolution and taxonomy. But as growing academic disciplines in the second half of the twentieth century, these fields felt the need to divorce themselves from their antecedents in “natural history” and claim their place as rigorous academic disciplines. In his memoir Naturalist, E.O. Wilson spoke of some of the challenges that organismal biologists faced in the early years of the age of DNA, when they were labelled ‘stamp collectors’ and portrayed as a field being superseded by molecular biologists. It was against that backdrop that the fields of ecology, evolution and systematics transformed themselves into hard, quantitative scientific disciplines in the second half of the twentieth century. Modern systematics is about building consensus trees based on genetic data, and evolutionary biologists talk about SNPs and haplotypes. You can be an organismal biologist who has never seen your organism in the wild.

It was against a backdrop such as this that Ricklefs presented his talk. Direct observations of nature – direct experience of nature – is important for the progress of ecology and evolutionary biology. Most people realise, at least on some level, that observations of nature are an important means by which hypotheses can be generated. Broad theories and models of how the world work also have their roots in observations of the natural world. But, as Ricklefs pointed out, we also need to test our theories and models against nature, ensure that our explanations aren’t only internally coherent and logical, but that they also work when presented with the real world.

In addition to his own work on taxon cycles in Caribbean bird species, Ricklefs also discussed Steve Hubbell’s Unified Neutral Theory of Biodiversity and Biogeography. Hubbell’s neutral theory is a rather interesting idea. in essence, it suggests that tree species are competitively neutral, and that species diversity in tropical forests is maintained by a a mixture of random drift and speciation. Ricklefs expressed the opinion that Hubbell’s neutral theory, which has been around for a decade, probably has another decade before it fades into obscurity, as these things tend to do in ecology. The flaws in the neutral theory, he said, are seen when the theory is confronted with data.

Opening reception

For most people, Evolution 2011 got off to a start tonight with the opening reception at the Sam Noble Oklahoma Museum of Natural History (SNOMNH).* Upon arrival, we met long registration lines which threatened to spill out the building into the 100°F (38°C) outdoors. Luckily, since we had registered early, we were directed past the lines directly into the main hall. It’s a familiar space where I’ve attended many receptions and seen many distinguished speakers. In his portion of the welcome address, College of Arts and Sciences Dean, Paul Bell, reminisced about the opening of the museum 11 years ago, when Stephen Jay Gould stood and spoke on the very spot where Bell was now speaking. Bell raised an issue that came up many times in conversation tonight – the importance of science education and the embattled status of evolution in the state of Oklahoma today.

It is, of course a very valid concern. Several anti-evolution bills lost or died in committee this session through the hard work of groups like the Oklahomans for Excellence in Science Education. Sure, there’s a religious and political basis for much of the hostility to evolution in Oklahoma, but there’s also an element of ignorance as to what evolutionary biology is. What, someone asked, do evolutionary biologists do? This isn’t really an evolution-specific question. Few members of the general public could answer what any specific sub-field of knowledge actually studies. But creationists have done a good job of exploiting this particular hole in ‘common knowledge’. All evolution does is look at fossils and guess at how the fossils evolved, right? And it’s not really a science because you can’t do any experiments. A little ignorance, reinforced by a few creationist memes, and suddenly people “know” that evolution is not a science. So why are all these people here in Oklahoma – to engage in socialist plots against God-fearing Americans?

The real answer, of course, is fairly easy to find. But would the public be able to deduce anything from it? The first set of talks, spread across eight concurrent sessions include

  • Introduction to models of character state-dependent diversification
  • Variable environments, fluctuating selection and the stability of breeding partnerships in birds
  • Rapid adaptation to anthropogenic environments via hybridization?: Invasive hybrid watermilfoil genotypes are more common than parental genotypes in herbicide-treated lakes
  • Wedge effects: the shape of dispersal barriers and spatial population genetics
  • The evolutionary tale of the largest C4 eudicot lineage: North American desert origin, highly reticulated evolution and extraordinary Hawaiian Island radiation in the Chamaesyce clade of Euphorbia (Euphorbiaceae)
  • The genetic architecture of a difference in male genital morphology between Drosophila mauritiana and D. sechellia
  • Evidence of a resident species of Plasmodium in the Galapagos avifauna
  • Evolutionary genomics of biofilm adaptation and diversification

While I’m sure the average person might have a hard time figuring out what the practical applications of any of this might be, a few things are evidence – no dinosaurs, no fossils.

I find myself wondering – would that really help? Would the public be any more positively inclined to the study of evolution if you could show them that it’s not just a group of people trying to disprove the existence of God.Or would the conversation simply switch to “wasteful spending”?

The opening reception was pretty good. I met Carl Zimmer, one of the best science writers out there. Wine and beer were available at the reception, but only with a drink ticket. Since there were only spaces for tonight, attendees were limited to two alcoholic drinks. I’m sure there are a lot of good reasons, but when I jokingly said something about it to one of the people behind the bar, he replied “well it is a museum”. That led to a rather hilarious image of crowds of drunken evolutionary biologists rampaging through the museum and reclassifying things based on rival phylogenetic hypotheses.

*Try saying S-N-O-M-N-H. The first challenge is the difficulty in remembering the acronym. Usually it works the other way – you remember AMNH, and use that to remind yourself ‘American Museum of Natural History’. Here though, you need to remember “Sam Noble Museum of Natural History”, and cross-check that with the sequence of letters that’s coming out of your mouth. Already, mnemonic fail. But there’s also the sequence of letters. Sure, AMNH has the same sequence, but with only four letters you say each one separately. Here though, you end up with words; ess’no em’naitch. Funny-sounding words.

Evolution 2011

The 2011 Evolution meetings are in town. Four days of scientific presentations on evolutionary biology, a field whose very existence many creationists would cast into doubt. Today was just the initial things – arrival, registrations, and workshops for K-12 teachers in Oklahoma. I headed over in the late morning, registered, and perused the (only partially set-up) displays by merchants. It is, I have learned, an important part of meetings. I love all things book-related, so browsing books and journals and chatting with publishers reps are fun.

Next up – the opening reception at the Sam Noble Oklahoma Museum of Natural History. I was planning to walk over there – it’s about a 20-minute walk, and at 7 pm it should have cooled down enough to make for a pleasant walk. Which just goes to show that I still don’t understand Oklahoma weather. At 7 pm it’s still 100°F (38°C). Granted, that’s down from 104°F (40°C), but it’s still ridiculously warm. And while I still expect the sun to set by 6 pm, it does nothing of the sort in Oklahoma in summer.

The conference proceedings look interesting. It’s not an ESA or ATBC meeting, but a lot of it is still within my general area of interest (and some isn’t. I don’t care about tools for building phylogenies, even if I do care about phylogenies – I’m a consumer of systematics, not a producer.) Anyway, scientific meetings are fun, any way you put it…

That went well…

I jumped out of hiding, bright-eyed and bushy-tailed, ready to take the world of blogging by storm. But somehow, nothing happened. Not a word appeared on my exciting new blog. Why?

Not having written anything for such a long time, I felt the need to come back with a bang. And two papers seemed to offer the opportunity to do just that – He & Hubbell’s controversial article Species–area relationships always overestimate extinction rates from habitat loss seemed like the perfect opportunity to write about something I know more than a little. Then came Davis et al.’s Don’t judge species on their origins. That article was especially timely – it appeared just a day or two after I read Scott Carroll’s Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems. Carroll is one of Davis’ 18 coauthors and his ‘conciliation biology’ is an excellent introduction to the subject. The Davis et al. article, on the other hand, lacks nuance. More to the point though, the controversy it generated made it a great topic to blog about. It seemed really promising.

But then ten days passed. I wrote something for my Ramjohn family site, but that, for now, is a closed blog with perhaps one member other than myself. I tried to get started here. And I realised something. I’m not a blogger. I’m no longer comfortable throwing up short posts, throwing up a few links, shooting a half-formed idea out into the blogosphere. Not even here, where no one is going to read it.

If you feel the need to write something coherent, writing can be really hard. So what happens now? Do I learn to blog again? Do I stop blogging, but continue writing? Or does this just the world of stillborn blogs? Time will tell.

Welcome!

Almost a year since my last blog post at Further Thoughts, and more than four years since my first post at that site, I’m ready to try something new.

One of the main reasons I stopped blogging was a rising perfectionism. Blogging stopped being an amusing diversion and started to be work. To make matters worse, I gradually began to expect more of myself. As a result, posts that once took minutes started to take hours to compose. Anything that lingered that long was likely to end up stuck, permanently, as a draft.

The end of my blogging made me somewhat happier, but it robbed me of my voice. There was so many times that I wanted to express an opinion about something, but I knew that before I did that, I needed to finish some big post. Which never got done.

I’m hoping that I will do better this time…

Human impacts on pre-Columbian tropical forests

When European naturalists first visited the New World Tropics they saw vast forests that seemed untouched by humans. While indigenous people often lived in these forests, their populations were small. This led to a perception of tropical forests as primeval, “virgin” forests. In the last few decades, this perception has changed – large areas now covered by mature forests have a history of cultivation. In many cases, “primeval” forests are less than 500 years old.

La Selva biological station in Costa Rica is one of the premier research stations for Neotropical biology. Prior to archaeological study of the site, much of it was assumed to be free of human influence. However, the discovery of pre-Columbian artefacts led to the discovery that the site had been occupied at least 3000 years ago. Charcoal was more abundant in alluvial terraces (flatter areas with deeper, more fertile soil) and less abundant in the less fertile upland soils. A chronology, established by Sol (2000)*, divided the La Selva into four archaeological phases: La Cabaña 1000 – 1550 CE; La Selva 500 – 1000 CE; El Bosque 300 BCE– 500 CE; La Montaña 1500 –300 BCE.

To better understand the history of the site, Lisa Kennedy of Virginia Tech and Sally Horn of the University of Tennessee, Knoxville, undertook a study of sediment cores extracted from the Cantarra swamp*, a 0.5 ha wetland dominated by perennial herbs. They used pollen, charcoal and macrofossils to reconstruct the environmental history of the site. Wetlands are frequently used to reconstruct vegetation histories. As sediments accumulate in bodies of water, plant pollen, fern spores and charcoal fragments are trapped. Pollen coats are extremely tough, and decay takes place very slowly in waterlogged soils. If the vegetation surrounding the site changes, different types of pollen will be deposited into the site. Someone with the patience to sort through these cores can observe thousands of years of history in a few metres of sediment.

The most obvious evidence of human activity is the presence of corn (Zea mays subsp. mays) pollen. Corn is a cultivated species which does very poorly without human intervention. Thus, the presence of corn pollen in the wetland sediments is direct evidence of agriculture. Corn pollen shows up from 880 CE to somewhere between the mid-1600s and mid-1800s. Pollen of other species like Amaranths, Asteraceae (the sunflower family), and other grasses and herbs also peak during and before the “corn zone”, often at the same time that charcoal density peaks. This may also reflect cultivation, although it could represent weedy species establishing after fires. Corn pollen was found in sediments about 1300 years older at another lake about 2 kn distance from this one. The authors suggested that disturbance in this time period at Cantarra swamp may have represented the cultivation of root crops (which don’t leave the kind of pollen signature that corn does.

As a forest ecologist, I find some of the “other evidence of disturbance” to be the most interesting. There are several peaks of Cecropia pollen, and to a lesser extent Trema pollen. These are fast-growing species that are usually associated with large gaps in the forest – specifically the type that human agricultural activities may have suggested. Other peaks of pollen belonging to forest species suggests that periods of forest recovery were interspersed with the cultivated times.

This is very interesting stuff. We are too inclined to interpret forests as “primeval”. In many cases, what our eyes see as ancient is only a few centuries old. It is important to understand that if we want to construct realistic models of forest dynamics.

  1. Sol, C., R. F. 2000. Asentamientos prehispánicos en la Reserva Biológica La
    Selva, Sarapiquí, Costa Rica: Sistemas de explotación de recursos naturales
    en un bosque tropical lluvioso. Licenciatura thesis, School of Anthropology and Sociology, University of Costa Rica.
  2. Lisa M. Kennedy, Sally P. Horn. A Late Holocene Pollen and Charcoal Record from La Selva Biological Station, Costa Rica. Biotropica (OnlineEarly Articles). doi:10.1111/j.1744-7429.2007.00334.x

What is natural? Reinterpreting rivers in the eastern US

[Repost from my old blog]
One of the fundamental questions faced in ecological restoration is that of trying to find a “natural” baseline to work towards. This is especially true in Europe and eastern North America – these are the areas where so much fundamental ecological work was done, but by the time this work was done, they were modified to the point where it was often impossible to distinguish “natural” from anthropogenic.

I’ve always been a little confused by streams. As a terrestrial ecologist, steams often seem to be these alien things that intrude into the landscape. It isn’t that bodies of water are themselves incomprehensible, but rather, the way that they interact with the terrestrial landscape. Too often, they just don’t seem to add up – it always feels like current processes couldn’t produce what I see. Turns out that, at least in eastern North America, I’m at least partly correct to feel that way.

In a paper published in the January 18, 2008 issue of Science Robert Walter and Dorothy Merrits of Franklin and Marshall College examined the established ideas about the characteristic form of rivers in the Mid-Atlantic and Western parts of the United States. The norm is seen to be a single meandering channel with a gravel bottom and alternating riffles and pools, often with a channel that is deeply incised into the surrounding streambanks. These streams flow through “valley flats” – broad deposits that fill the valley. The stream cuts into these relatively coarse deposits. These deposits were interpreted to have been deposited when the river floods, while the valley was thought to have been produced by the stream as it meandered across the valley. (That’s what I was taught in high school geography). However, many observations seemed inconsistent with these explanations. Modern flood patterns don’t deposit the type or amount of sediments that are observed in these valleys. In addition, Walter and Merritts observed that the tops of historic milldams (which were typically built 2.5 to 3.7 m tall) were at the level of the valley flats which suggested that the valley flats had been deposited in recent times, after the dams were built.

Dam construction began with European settlement. Until they were replaced by steam engines in the twentieth century forges, furnaces, mining operations and mills were driven by water from millponds. Walter and Merritts estimated that there are 16,000 – 18,000 millponds in Pennsylvania, covering a period of over 200 years. Since millponds were built early in the settlement period, they rapidly silted up as the surrounding landscape was deforested. In the late 1800s and early 1900s newer dams were built along streams that had breached older dams. Many of these dams have also breached, leading to an even more complex pattern.

When the dug into the valley flats, Walter and Merritts found several metres of sediment on top of soils characteristic of wetlands. These soils are rich in organic material and sometimes include tree stumps and the remains of corduroy roads – roads made of logs or planks on swampy ground. By digging trenches across the entire valley, they were able to get a sense of the entire river, and were able to conclude that:

The characteristics of the presettlement sediments and organicmaterial suggest that valley bottoms were broad, forested wetlands(alder shrub-scrub) with small, shallow (<1-m) anabranchingand chain-of-pool streams that experienced frequent overbankflow, which is consistent with accounts by early explorers ofubiquitous swampy meadows and marshes fed by springs at thebase of valley side-slopes

Walter and Merritts conclude by saying

These conclusions change the interpretation of hydraulic geometryin eastern U.S. streams that is based on the archetype of an”ideal meandering river form” and imply the need to reconsidercurrent procedures for stream restoration that rely on referencereach conditions and the assumption that eroding channel banksare natural and replenishable. The current condition of singlegravel-bedded channels with high, fine-grained banks and relativelydry valley-flat surfaces disconnected from groundwater is instark contrast to the presettlement condition of swampy meadows(shrub-scrub) and shallow anabranching streams described here.

These observations also have important implications for European rivers, were millpond construction dates back to the 1100s. It also makes me rethink Trinidadian streams and rivers – but that needs to be a separate blog post.

Walter, R.C., Merritts, D.J. (2008). Natural Streams and the Legacy of Water-Powered Mills. Science, 319(5861), 299-304. DOI: 10.1126/science.1151716