Tuesday, December 30, 2014

When experts stray out of their field


This end-of-year post has nothing to do with networks, or even phylogenetics, although the general principle involved might apply to both. My point here is simply that experts sometime look foolish when they commentate on fields outside their own area of expertise.

As an introductory example, I remember reading a paper in a physics journal that tried to convince the readers that humans could potentially live forever. Unfortunately, the authors confused the concepts of lifespan and longevity, which is pretty basic stuff in population biology. Lifespan is the length of time for which humans normally live. We have more than doubled this over the past millenium, due to changes in sanitation, medication, surgery and safety. Longevity is the length of time for which humans are capable of living. We have not changed this by even one year, as it seems to be related to phenomena like programmed cell death. Changes in lifespan do not therefore entail changes in longevity; all that has happened is that our expected lifespan is now closer to our observed longevity than it previously has been.


More recently, an electrical engineer drifted into the field of literature while claiming to be a scientist — Mikhail Simkin (2013) Scientific evaluation of Charles Dickens. Journal of Quantitative Linguistics 20: 68-73. Sadly, his article displays neither of the characteristics of science (replication and control), nor does it appear to contribute anything much to literature.

As noted on his web page, the author had trouble publishing this article, and he has subsequently received "a flood of criticism", which he naively seems to believe he has rebutted at the Significance blog.

His intention was a simple one: a comparison of the writing style of Charles Dickens and that of Edward Bulwer (later known as Edward Bulwer-Lytton). His premise was: "Edward Bulwer-Lytton is the worst writer in history of letters ... In contrast, Charles Dickens is one of the best writers ever." He put online a quiz with "a dozen representative literary passages, written either by Bulwer-Lytton or by Dickens." The takers had to nominate the author of each quote. Simkin discovered that on average the votes were "about 50%, which is on the level of random guessing. This suggests that the quality of Dickens's prose is the same as that of Bulwer-Lytton." The results are shown in the graph above.

Simkin's intention seems to have been to demonstrate that currently revered and non-revered authors do not differ much in style, which is a contention that I see no reason to disagree with, but if so he has gone about showing this in a remarkably unscientific manner.

Let us take the premise first, for which the author provides no personal justification nor any reference to a published one. It seems patently true that the current fashion is for Dickens to be widely read but Bulwer not. This on its own means little, however, as even the Shakespearean works have had a century or so of being out of fashion, although not in the past couple of hundred years (to the dismay of anyone who has had an English-language education).

Was Bulwer a bad writer? Well, first, the results of Simkin's poll imply "no", at least in comparison to Dickens. But more importantly, many other sources say "no", as well. Indeed, Wikipedia makes a strong case both for his popularity in his own time, and for considerable influence on literature since then. Indeed, he is so 'obscure' that towns as far apart as Canada and Australia are named after him. His works are so 'poorly known' that we continue to use his expressions "pursuit of the almighty dollar" and "the pen is mightier than the sword". His works have been so 'derided' that several operas are based on his books, including one by Richard Wagner; and authors such as Edgar Allan Poe have paraphrased his words. His books are such 'poor examples' of English that people have felt compelled to translate them into Serbian, German, Russian, Norwegian, Swedish, French, Finnish, Spanish and Japanese, among other languages.

Clearly, the premise that Bulwer represents the nadir of English-language literature holds no water. He is currently obscure, but as John S. Moore has noted, the fact that he is not read does not mean that he is not worth reading.

Indeed, a scientist would immediately note the lack of replication here. Why are "best" and "worst" writers not replicated in the experiment? This would immediately address any possible mis-judgements about potential literary worth. It is repeated patterns that provide convincing evidence in science, not isolated pairwise comparisons. This poll is hardly a "scientific evaluation", as claimed by the author.

Now let us consider the experimental procedure. This consisted of choosing "representative literary passages", without any explanation for how this was done or what were the criteria for choice. Clearly, this choice is the key to the experiment. After all, all the experiment does is show that one can find passages by both Dickens and Bulwer that are hard to distinguish. That could very well be true of almost any pair of writers from the same culture (ie. country and century). The experimental comparison has thus not been controlled, as it would be in science.

What would experimental control look like in this case? Clearly, the issue is one of style, since authors vary their writing style depending on the book, the plot situation, and even the character involved. (One of Bulwer's passages is actually taken from the dialog of one of his characters, which hardly represents the author's own writing style!) The objective, then, must be to find passages that represent the range of styles present in the corpus of each writer. One might try grouping the passages into topics or styles, for example, or whether they describe actions or locations, etc.

Without either replication or control, this literary evaluation cannot be considered to be scientific. Sadly, on his website Simkin has several other so-called scientific comparisons within the arts, designed in exactly the same inadequate way.

As a final note, we can ask why was Bulwer chosen for this comparison in the first place? The choice seems to be almost solely due to various extant parodies of the opening of one of his books, Paul Clifford (1830): "It was a dark and stormy night; the rain fell in torrents ..." For example, this was chosen by Charles Schultz in his Peanuts cartoons, as the opening of one of Snoopy's failed attempts to be a world-reknowned author. The full sentence does not actually seem bad, although it tries to cram a bit much information into the number of words available. Thomas Hardy later tried the same thing, but with more success, in The Return of the Native (1878): "A Saturday afternoon in November was approaching the time of twilight ..."

However, the award for sheer bravado surely goes to D.H. Lawrence, in his short story Tickets, Please! (1919), which starts with a paragraph consisting of a sentence of 118 words, followed by sentences of 15 words, 27 words and finally 113 words.** A plethora of commas, colons, semi-colons and dashes are needed to keep the meaning coherent in this page-long paragraph. You and I could not get away this, which is why Lawrence is considered to be one of the great English literary stylists. Apparently, Bulwer did not get away with it, either.

** My count is based on the original publication in The Strand magazine, which is slightly different to subsequent versions.

Thursday, December 25, 2014

Fast food and diet


Season's greetings.

For your Christmas reading, this blog usually provides a seasonally appropriate post on fast food, including to date: nutrition (McDonald's fast-food) and geography (Fast-food maps). This year, we will focus on the effects of fast food on people.

Defining fast-food is a bit of a trick. The U.S. Census of Retail Trade defines a fast-food establishment merely as one that does not offer table service. However, legislation recently passed in Los Angeles defines fast-food establishments as those that have a limited menu, items prepared in advance or heated quickly, no table service, and disposable wrappings or containers. Some people feel that these definitions should include all pizza restaurants, even those that do offer table service in addition to take-away (or take-out). The latter are sometimes distinguished as fast-casual restaurants rather than fast-food restaurants.

About 90% of Americans say they eat fast-food, including those who visit an establishment on average once per day. The main concern about the effect of fast-food, then, is on people's diet. By "diet" I mean the combination of foodstuffs consumed each day, which may or may not match what is known to be required for a healthy human. Fast-food rarely matches this diet, and so there must be some effect of eating the stuff.

In particular, fast-food has been implicated in what is now known within medicine as the "obesity epidemic" — the observation that an increasing proportion of the people in the developed world are formally classified as obese. The usual symptom of obesity is a body mass index (BMI) > 30 (overweight is 25-30, normal is 18.5-25). BMI is an approximate measure of body fat.

Obesity has risen rapidly in recent decades, but there is some evidence that the levels are now beginning to stabilize (Obesity Rates & Trends Overview). The main risk with obesity is its strong association with potentially fatal health problems, notably heart disease, stroke, high blood pressure, and diabetes. Indeed, it has been suggested that obesity may be the greatest cause of preventable death in the United States.


Demonstrating a relationship between fast-food and obesity is not hard, given the high sugar, carbohydrate, fat, and salt content of most of the food items. This results in the intake of more energy than the body uses, and this excess is stored as fat. This pattern shows up clearly in large-scale samples of prevalence, such as this one collated on the DataMasher site, where each point represents a state of the USA.


An obvious issue concerning fast-food is our ability, or lack of it, to understand just how many calories (or joules) there are in fast-food meals. The marketing people seem to have a clear idea about how different fast-food chains are presented in terms of their food quality, as shown in this Perceptual Map.


However, this perception is clearly not accurate in terms of calories, especially for Subway. An article in the British Medical Journal evaluated the ability of people to estimate the calorie content of the fast-food meal they had just purchased. As shown in the next graph, clearly in most cases there was a major under-estimate, and this was worst for the highest-calorie meals. The under-estimation of calorie content was largest among Subway diners. Diners at both Subway and Burger King showed greater under-estimation of meal calorie content than those at McDonald's, whereas diners at Dunkin' Donuts had less under-estimation. In other words, Subway is not as healthy for you as you think it is, but you already know how bad those Donuts are.


One response to this situation has been to insist that fast-food places advertise the calorie content of their food on the menu board itself. For example, it has been suggested that nutrition experts can compose apparently healthy meals based on the nutritional information provided in the menus of fast-food restaurant chains.

This will only have an effect, however, if people actually use this information when choosing their meal. An article in the Journal of Public Health suggested that most young people don't actually do so, and that people who eat fast-food most often are least likely to do so. Indeed, a report from Sandelman Associates showed that the only people who are likely to use calorie information regularly are those with a specific "calorie target" for their personal diet, as shown in this next chart.


Nevertheless, an article published in the British Medical Journal has reported a decrease in the energy content of fast-food purchases after the introduction of calorie information on the menu boards, except at Subway, where there was an increase. (before the labeling the Subway meals chosen had fewer calories than for the other chains but afterwards they had more!)

Another important feature of fast-food is the usually large portion sizes, which exacerbates the energy imbalance. An article in the Journal of the American Dietetic Association has shown that not only does modern fast-food exceed dietary standard serving sizes by at least a factor of 2, and sometimes by as much as 8, these serving sizes have increased dramatically over the past 50 years.

What is perhaps most surprising is the truly vast difference that can occur between servings of what is allegedly the same fast-food product, not only between countries but within a single country. The following graph is from an article in the International Journal of Obesity. It shows, for the named locations, the amounts of total fat in a meal consisting of 171 g McDonald's french fries and 160 g KFC chicken nuggets. The darker colour indicates the added amounts of industrially produced trans fat. The values in parenthesis are the amount of trans fat as a percentage of total fat.


On a somewhat different note, one of the main characteristics of fast-food is the focus on a sweet taste, rather than on a diversity of tastes. In contrast, traditional cooking in many cultures has focussed on mixing together a diversity of complementary ingredients. Indeed, this was the impetus for the formation of the Slow Food movement, founded "to prevent the disappearance of local food cultures and traditions ... and combat people's dwindling interest in the food they eat, where it comes from and how our food choices affect the world around us." (It was organized after a public demonstration at the intended site of a McDonald's franchise at the historic Spanish Steps, in Rome.)

This topic was investigated in detail in an article published in Nature Scientific Reports. The authors produced the following network of food flavours.


Interestingly, they conclude that:
We introduce a flavor network that captures the flavor compounds shared by culinary ingredients. Western cuisines show a tendency to use ingredient pairs that share many flavor compounds, supporting the so-called food-pairing hypothesis. By contrast, East Asian cuisines tend to avoid compound-sharing ingredients.
There is diversity even in the amount of diversity.

Monday, December 22, 2014

Tattoo Monday X


Here are five more tattoos in our compilation of evolutionary tree tattoos from around the internet. For more examples of this circular design for a phylogenetic tree, in a variety of body locations, see Tattoo Monday, Tattoo Monday V, and Tattoo Monday VII.


Wednesday, December 17, 2014

Current methods for evolutionary networks


It has been noted before that we have a wide range of mathematical techniques available for producing data-display networks, most notably the many variants of splits graphs (see Huson & Scornavacca 2011). For example, NeighborNets and Consensus networks are commonly encountered in the phylogenetics literature, and Reduced median networks and Median-joining networks are commonly used for haplotype networks in population biology.

However, there are few techniques used to produce evolutionary networks. Studies of reticulate evolutionary histories, which include recombination networks, hybridization networks, introgression networks and HGT networks, have no unifying theme as yet. So, the biological literature has many papers in which biologists struggle with reticulate evolutionary histories using ad hoc collections of techniques, which often boil down to simply presenting incongruent phylogenetic trees from different datasets (see Morrison 2014a).

So, maybe a brief look at the current state of play with evolutionary networks would be useful. There are enough worthwhile techniques out there for people to be using them more often than they are.

Assumptions

Almost all current phylogenetic methods assume that the basic building unit is a non-recombining sequence block, for which the evolutionary history is strictly tree-like. We tend to call these blocks "genes" and their history "gene trees", but this is just for semantic convenience. In practice, we first collect data for various loci, and we then simply make the assumption that there is recombination between the loci but not within them. This is basically the assumption of independence between loci. At the limit, each nucleotide along a chromosome has a tree-like history, but for aggregations of nucleotides it is all assumptions.

Furthermore, we assume that there are no data errors that will confound any reconstruction of the phylogenetic trees. Possible sources of error include: incorrect data (e.g. contamination), inappropriate sampling (taxa or characters), and model mis-specification. Any of these errors will lead to stochastic variation at best and to bias at worst.

Gene-tree incongruence

Reticulate evolutionary processes lead to gene trees that are not all congruent. However, there are two other processes that have been widely recognized as also producing gene-tree incongruence, but which do not involve reticulation in the strict sense: incomplete lineage sorting (deep coalescence; ancestral polymorphism), and gene duplication-loss.

Many studies have now shown that stochastic variation due to ILS can be very large (see Degnan & Rosenberg 2009), and that this varies in relation to both the population sizes of the taxa and the times between divergence events. The expectation of completely congruent gene trees is thus very naive, even when the evolutionary history of the taxa has been strictly tree-like. A number of methods have been developed to reconstruct species trees in the face of ILS (Nakhleh 2013).

DL involves gene duplication (which can be repeated to create gene families) followed by selective gene loss. The phylogenetic history of the genes is usually presented as an unfolded species tree, where each gene copy has its own part of the tree. A number of methods have been developed to reconstruct gene DL histories given a "known" species tree, which is called gene-tree reconciliation (Szöllősi et al 2015). However, our interest here is in the reverse process, in which reconstructed but incongruent gene trees are combined into a single species tree, given a model of duplication and selective loss, which is called species-tree inference (which is the same as cophylogeny reconstruction; Drinkwater & Charleston 2014).

Reticulations

Known biological processes such as recombination, reassortment, hybridization, introgression and horizontal gene transfer all create reticulate phylogenetic histories. However, it is a moot point as to whether these processes can be distinguished from each other solely in the context of an evolutionary network (Holder et al 2001; Morrison 2015). These evolutionary processes operate by distinct biological mechanisms, but the evolutionary patterns that they create can all be rather similar. The processes all result in gene flow among contemporaneous organisms (usually called horizontal flow or transfer), whereas other evolutionary processes involve gene flow from parent to offspring (usually called vertical inheritance), including ILS and DL. These gene flows create incongruent gene histories, which we may detect directly in the data or via reconstructed gene trees. The patterns of incongruence do not necessarily allow us to infer the causal process.

There are a number of differences in pattern, but the consistency of these is doubtful. Polyploid hybridization produces the most distinctive pattern, because there is duplication of the genome in the hybrid. However, subsequent aneuploidy will serve to obscure this pattern. Homoploid hybridization nominally involves 50% of the genome coming from difference sources, while introgression ultimately involves a smaller percentage. However, in practice, genome mixtures vary continuously from 0 to 50%. HGT also involves a small percentage of the genome, but in theory it also can vary from 0 to 50%. Reassortment produces mixtures of viral genes, which can occur in such a great number that reconstructing the history is severely problematic.

So, in the absence of independent experimental evidence, distinguishing one form of evolutionary network from another is almost a matter of definition. This has become increasingly obvious in the methodological literature, where semantic confusion abounds.

For example, a network produced directly from a set of characters has usually been called a "recombination network", while one produced from a set of trees has usually been called a "hybridization network", irrespective of what processes the gene trees represent. Furthermore, models that add reticulation events to DL trees have usually referred to the horizontal gene flow as "HGT", whereas models that add reticulation events to ILS trees have usually referred to the horizontal gene flow as "hybridization" (Morrison 2014a). Studies of horizontal gene flow during human evolution have usually referred to "admixture", which is a more process-neutral term.

In many, if not most, cases we might all be better off if network methods simply distinguish gene flow among contemporaries (horizontal) from gene inheritance between generations (vertical), rather than trying to infer a process — process inference can often best take place after network construction. This does not help anthropologists, of course, who are dealing with evolutionary networks where oblique gene flow is possible (so that they do not have Time inconsistency in evolutionary networks).

Methods

There seems to be a dichotomy of purposes to current method development, which are neatly summarized by the contrasting theoretical views of Mindell (2013) and Morrison (2014b). These views each recognize that evolutionary history involves both vertical and horizontal processes, but they reconstruct the resulting evolutionary patterns as a species tree and a species network, respectively. Obviously, this blog is dedicated to the latter point of view, but it is the former one (the so-called Tree of Life) that seems to currently dominate the literature.

Focussing on gene-tree inference, Szöllősi et al (2015) provide a comprehensive review of the various models that have been used to describe the dependence between gene trees and species trees. Essentially, gene trees are contained within the species tree, and they may differ from it in relative branch lengths and/or topology. The differences between genes and species are the result of population-level processes, often modeled using the coalescent. These authors recognize four current classes of probabilistic model that combine different evolutionary processes:
  • the DLCoal model, which combines coalescence and DL
  • the DTLSR model and the ODT model, both of which combine gene transfer and DL
  • models that combine hybridization and ILS
  • models of allopolyploidization.
When inferring species trees from gene trees (species-tree inference), we basically combine the scores for all of the gene trees, and then search for the species tree with the best overall score. This involves adding the scores in parsimony analyses, or multiplying the conditional probabilities in likelihood analyses (ie. maximum-likelihood or bayesian context). Many methods have been developed for inferring a species tree based on multi-locus data. These differ in whether the gene and species trees are estimated simultaneously or sequentially, and in how the gene trees are used to infer the species tree. Nakhleh (2013) and Szöllősi et al (2015) discuss both parsimony and likelihood methods for species-tree inference based on either ILS or DL models.

Extending these ideas to infer networks (rather than species trees) is a bit more tricky, and most of the work to date has involved combining hybridization and ILS. There has been no recent summary of the ideas. However, calculating the parsimony score of a network, given a set of gene-tree topologies, has been addressed by Yu et al (2011); and Yu et al (2013a) have extended these ideas to heuristically search the network space for the optimal network (the one that minimizes the number of extra reticulation lineages in a species tree). Furthermore, methods for computing the likelihood of a phylogenetic network, given a set of gene-tree topologies, have been devised by Yu et al (2012, 2013b); and Yu et al (2014) have extended these ideas to heuristically search for the maximum-likelihood network for limited cases of introgression or hybridization (since they differ only in degree).

There are also several methods that simply use gene-tree incongruence to infer reticulation events in a species network (Huson et al 2010). Basically, these methods combine gene trees into "hybridization networks" by minimizing the number of reticulations required for reconciliation, measured either by counting the reticulations or calculating the network level. The combinatorial optimization can be based on trees, triplets or clusters, using parsimony as the optimality criterion. These methods model homoploid hybridization by assuming that reticulation is the sole cause of all gene-tree incongruence. This means that they are likely to overestimate the amount of reticulation in a dataset when other processes are co-occurring.

The most completely developed network methods involve data for allopolyploid hybrids. Here, there are multiple copies of each gene, one in each copy of the genome, so that allopolyploid hybrids have more copies than do their diploid parent taxa. To construct a hybridization network topology, Huber et al (2006) developed a parsimony method based on first estimating a multi-labeled gene tree, and then searching for the single-labeled network that best accommodates the multiple gene patterns. The model has been extended to heuristically include ILS (Marcussen et al 2012), as well as dates for the internal nodes (Marcussen et al 2015). Jones et al (2013) have also developed models that incorporate ILS in a bayesian context, but only for the case of a single hybridization event between two diploid species (an allotetraploid).

Species-tree inference for a pair of gene phylogenies that may be networks not trees, has been considered in terms of parsimony by Drinkwater & Charleston (2014).

This brings us to the matter of introgression. The massive recent influx of genome-scale data for hominids has lead to the development of methods explicitly for the analysis of what is termed admixture among the lineages. These methods basically work by constructing a phylogenetic tree that includes admixture events, the topology inference being based on allele frequencies. There has been no formal comparison of the methods, and not much application to non-humans. Three such methods have been produced so far (Patterson et al 2012; Pickrell & Pritchard 2012; Lipson et al 2013).

Recombination has somewhat been the poor cousin to other causes of reticulation, as most network methods assume it to be absent. Nevertheless, Gusfield (2014) has recently provided an ample survey of the study methods available to date.

References

Degnan JH, Rosenberg NA (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24: 332-340.

Drinkwater B, Charleston MA (2014) An improved node mapping algorithm for the cophylogeny reconstruction problem. Coevolution 2: 1-17.

Gusfield D (2014) ReCombinatorics: the Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, Cambridge.

Holder MT, Anderson JA, Holloway AK (2001) Difficulties in detecting hybridization. Systematic Biology 50: 978-982.

Huber KT, Oxelman B, Lott M, Moulton V (2006) Reconstructing the evolutionary history of polyploids from multilabeled trees. Molecular Biology & Evolution 23: 1784-1791.

Huson D, Rupp R, Scornavacca C (2010) Phylogenetic Networks: Concepts, Algorithms, and Applications. Cambridge University Press, Cambridge.

Huson DH, Scornavacca C (2011) A survey of combinatorial methods for phylogenetic networks. Genome Biology & Evolution 3: 23-35.

Jones G, Sagitov S, Oxelman B (2013) Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Systematic Biology 62: 467-478.

Lipson M, Loh P-R, Levin A, Reich D, Patterson N, Berger B (2013) Efficient moment-based inference of population admixture parameters and sources of gene flow. Molecular Biology & Evolution 30: 1788-1802.

Marcussen T, Heier L, Brysting AK, Oxelman B, Jakobsen KS (2015) From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae). Systematic Biology 64: 84-101.

Marcussen T, Jakobsen KS, Danihelka J, Ballard HE, Blaxland K, Brysting AK, Oxelman B (2012) Inferring species networks from gene trees in high-polyploid north American and Hawaiian violets (Viola, Violaceae). Systematic Biology 61: 107-126.

Mindell DP (2013) The Tree of Life: metaphor, model, and heuristic device. Systematic Biology 62: 479-489.

Morrison DA (2014a) Phylogenetic networks: a review of methods to display evolutionary history. Annual Research and Review in Biology 4: 1518-1543.

Morrison DA (2014b) Is the Tree of Life the best metaphor, model or heuristic for phylogenetics? Systematic Biology 63: 628-638.

Morrison DA (2015, in press) Pattern recognition in phylogenetics: trees and networks. In: Elloumi M, Iliopoulos CS, Wang JTL, Zomaya AY (eds) Pattern Recognition in Computational Molecular Biology: Techniques and Approaches. Wiley, New York.

Nakhleh L (2013) Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology & Evolution 28: 719-728.

Patterson NJ, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (2012) Ancient admixture in human history. Genetics 192: 1065-1093.

Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics 8: e1002967.

Szöllősi GJ, Tannier E, Daubin V, Boussau B (2015) The inference of gene trees with species trees. Systematic Biology 64: e42-e62.

Yu Y, Barnett RM, Nakhleh L (2013a) Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Systematic Biology 62: 738-751.

Yu Y, Degnan JH, Nakhleh L (2012) The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 8: e1002660.

Yu Y, Dong J, Liu KJ, Nakhleh L (2014) Maximum likelihood inference of reticulate evolutionary histories. Proceedings of the National Academy of Sciences of the USA 111: 16448-16453.

Yu Y, Ristic N, Nakhleh L (2013b) Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinformatics 14: S6.

Yu Y, Than C, Degnan JH, Nakhleh L (2011) Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. Systematic Biology 60: 138-149.

Monday, December 15, 2014

Update to Charles Darwin's unpublished tree sketches


This blog has previously reproduced some of the unpublished sketches by Charles Darwin that involve tree-like relationships:
  • Part 1 — collected notebooks and notes
  • Part 2 — a letter to Charles Lyell
  • Part 3 — a reconstruction from one of his books
Recently, the first two of these posts have been updated.

Part 1 was updated to include three new sketches. I had previously encountered references to them but had not located them amongst the online Darwin documentation.

Part 2 was updated to include information from a paper on the same topic that was published several months after the blog post itself.


Wednesday, December 10, 2014

Circular phylograms for phylogenetic networks


Phylogenetic trees have been drawn in many formats, including what are known as vertical, horizontal, multidirectional, radial, hyperbolic (restricted to interactive trees) and figurative (ie. looking like an actual tree). Radial, or circular, trees are used when there are many taxa — the root is placed at the centre, and the increasing length of the circumference is used to display the increasing number of nodes. An example is shown in the earlier blog post Why do we still use trees for the dog genealogy?

Here, I point out that the radial format also makes it much easier to display reticulations in an evolutionary network. My example comes from The Nam Family: a Study in Cacogenics (Arthur H. Estabrook and Charles B. Davenport. 1912. Eugenics Record Office Memoir No. 2. Cold Spring Harbor, NY). This book involves, among other things, a pedigree study of an extended family in New York state, with a large amount of inbreeding. Two large pedigrees are presented, representing the genealogies of two different parts of the extended family in a place called "Nam Hollow".


One of these pedigrees is drawn in the vertical format, with the earliest generations at the top. The other pedigree is drawn in the radial format, with the earliest generations in the centre.


The difference in choice of format seems to be a result of the fact that in the second case there is extensive reticulation within the earlier generations, and this is obviously much easier to display in the centre of a circle, with increasing circumference for the large number of descendants. Nevertheless, the first pedigree would also be easier to read in the radial format. It is surprising that this format is not used more often.

Eugenics

The study under discussion was one of several projects that arose from the eugenics movement in the USA. The reports include Hill Folk: Report on a Rural Community of Hereditary Defectives (Davenport. 1912), The Kallikak Family: a Study in the Heredity of Feeblemindedness (Henry Herbert Goddard. 1912), and The Jukes (Estabrook. 1916). Eugenics arose in the wake of research on Mendelian inheritance, applying it to the study of human societies. This was thus the initial phase of what we now call the study of human genetics, and large amounts of detailed data were collected in many parts of the world.

Unfortunately, the researchers greatly over-estimated the role of genetics in human behavior, attributing many of the by-products of poverty to "constitutional" characteristics. In particular, many of what we now consider to be environmental aspects of poverty were attributed to inbreeding (which is another feature common in poor communities). This is in contrast to previous studies of the same US families, such as that of Richard L. Dugdale (1874-1877. The Jukes: a Study in Crime, Pauperism, Disease and Heredity), which placed more emphasis on the environment as a factor in criminality, disease and poverty.

So, the eugenics researchers tended to collect data that we would now consider to be seriously biased, where the observations are inextricably confounded with interpretations. For example:
V-166 [person #166 in generation V] is a temperate, sociable, and licentious man, who married his cousin, V-183, a Nam-like, stolid shy, reticent, suspicious harlot. They had eight children ... All have the characteristic slowness in movement, and indolence and lack of ambition of the Nams. They vary little except that some are more reticent and shy than others, and there is some licentiousness. All are illiterate, and probably without the capacity for learning from books. VI-257, who is especially careless, disorderly, and shy, had an illegitimate son, who died of infantile diarrhea. Here again we see the uniformity resulting from inbreeding.
What was worse, the eugenics movement did not stop at mere scientific enquiry. They indulged, with governmental support, in what they politely called "social prophylaxis". For example:
Although our primary aim is the present the bare facts [!] we cannot altogether neglect the natural inquiry as to the proper treatment of such condition as we have described. Various possible modes of treatment will be considered.
First there is the method of laissez faire. The Nam community takes care of itself to a large extent; why do anything? Unfortunately, the community is not wholly isolated. From it families have gone to Minnesota and other points in the West and there formed new centers of degeneration. Harlots go forth from here and become prostitutes in our cities. The tendency to larceny, burglary, arson, assault, and murder have gone, with the wandering bodies in which they are incorporated, throughout the State and to great cities like New York. Nam Hollow is a social pest spot whose virus cannot be confined to its own limits. No state can afford to neglect such a breeding center of feeble-mindedness, alcoholism, sex-immorality, and infanticide as we have here. A rotten apple can infect the whole barrel of fruit. Unless we abandon the ideal of social progress throughout the State we must attempt an improvement here.
The authors seem to be almost foaming at the mouth by the end of their spiel. Option two, "improving the conditions of the persons in the Hollow" is dismissed as "supplying a veneer of good manners to a punky social body." Option three, "scattering the people" is seen as "fraught with danger". Nevertheless, this was the option preferred by the British government in the late 1700s and early 1800s, when they founded penal colonies in Australia for crimes like "stealing five cheeses". The assumption that poverty is hereditary certainly has a long history, and a wide geographical spread.

Option four, preventing the people from breeding, by isolating them, is the recommended one. The final note is: "Of course, asexualization would produce the same result; but it is doubtful if public sentiment would favor such treatment, quite within the province of the State though it be." We now know this to be a very naive conclusion. By the 1930s many western countries had active compulsory sterilization programs (see Wikipedia); and many still do, including states of the USA.

However, eugenics did have positive outcomes, among the obvious negative ones. For example, the first demonstration of simple Mendelian inheritance of a human medical condition concerned Unverricht-Lundborg disease, a form of epilepsy. This was first reported in 1891 by Heinrich Unverricht, in Estonia. However, it was Herman Lundborg, a Swedish physician, who first identified its genetic component (1903. Die progressive Myoclonus-Epilepsie (Unverricht’s Myoclonie). Almqvist and Wiksell, Uppsala).

He traced the ancestry of 17 affected people in one family from southern Sweden, showing that they were all descended from the same ancestors. The pedigree showed the pattern of disease occurrence expected from Mendelian inheritance of a single recessive locus. This study was facilitated by frequent inbreeding within the family (20% of households had first-cousin parents), which Lundborg referred to as "unwise marriages". We now know that the disease results from a mutation in the CCC-CGC-CCC-GCG repeat region of the cystatin B gene — unaffected people have 3-4 repeats while affected people have 40+ repeats.

Lunborg himself was an active member of the eugenics movement in Sweden (which was referred to as 'race biology'), and most of his writings about the epileptic family were as bad as those quoted above (their "degeneration" was attributed to the fact that "they distilled their own alcohol, and thus became drunkards"). He eventually became Professor for Racial Hygiene; and he was influential in the implementation of forced sterilization programs in Sweden, believing that "The future belongs to the racially fine people", which obviously included himself.

Monday, December 8, 2014

The first known pedigree of a non-noble family


I noted in an earlier post (The first royal pedigree) that interest in genealogy dates back to at least Roman times, where the so-called stemmata were displayed in homes, to distinguish between the patrician class (those with proven noble ancestry) and plebeians (commoners). We are not quite so ostentatious today, but the nobility are still just as snooty about their ancestry.

I also noted that the first known illustration of a noble pedigree is the Tabula Genealogica Carolingorum (c.1000 CE), which traces Cunigunde of Luxembourg's ancestry in a tree-like manner back to Charlemagne, and thence to the origin of the Carolingian dynasty in the mid 500s. This raises the question of the first known written pedigree not involving the nobility.

This appears to be a diagram labelled Genealogia Ouduini et Heimerici Decani Filii Sui, which dates from c. 1121 CE. This type of pedigree may have been relatively common among certain families at the time, but this seems to be the only surviving exemplar that has come down to us.


This diagram appears towards the end of the book Liber Floridus, composed by Lambert of Saint-Omer, who was canon of the city Church of Our Lady in Saint-Omer, in north-eastern France. The Universeitsbibliotheek at Ghent University owns the autograph of this work (ms. 92), i.e. the actual copy penned by the author himself; and it is in this copy that the author has inscribed his family pedigree (on folio 154r).

This may recall to many of you the trend to keep hand-written records of pedigrees in the fly-leaves of family Bibles during the 1800s and early 1900s, particularly in English-speaking parts of the world. It does, however, seem to go a bit beyond this. Lambert repeatedly identifies himself in the text as the author of the book, and he also includes a portrait of himself writing his book, although this is apparently usual in medieval iconography.

The Liber Floridus (Book of Flowers) is literally an illustrated encyclopedia, rather than an encyclopedia with pictures. You will find copies of the illustrations all over the Internet, because Lambert was an imaginative and colorful illustrator. He was apparently concerned that uneducated people would lose access to important knowledge, and so (unlike his predecessors) he deliberately created a book that was accessible to almost everyone. It contains a curate's egg of information, including mythical biology (ie. a beastiary), selected history, and particularly biblical knowledge. It also contains an account of the genealogy of the Counts of Flanders, Lambert's local nobility, which may have inspired his personal account.

So, in his personal copy Lambert included a tree of his maternal ancestors going back to his great-great-grandfather Odwin, as shown in the first figure. It is rather scrappy and unclear, and so Jean-Baptiste Piggin has digitized a copy, as shown below.


There are c.80 names crammed into the compact space. As with other early pedigrees of which we have a record (eg. The first royal pedigree), the tree is rooted at the top and the family ramifies downwards. Like the Great Stemma (see How confusing were the first written genealogies?), siblings are grouped in short vertical lists, so that groups of first-names form family blocks that have only one connection to their parent. However, unlike either of these earlier genealogies, the names are not placed within segregating roundels, but simply exist as normal text.

Lambert is at the bottom centre, labelled as "qui librum fecit Lambertus filius Onulfi; Eva" [Lambert who produced the book, son of Onulph and Eva]. His lineage is traced back to Eva and her siblings, so that these are Lambert's maternal relatives. Why his mother and not his father is not directly explained, but the genealogy is listed as being that of Odwin and Heimericus the Dean, so that Heimericus is presumably the important progenitor (his family dominates the tree). Lambert does refer elsewhere in the book to his father, Onulph, who had been canon of the Church of Our Lady before him. Just in case you are left in any doubt about the purpose of the pedigree, the text at the top left of the figure specifies Lambert's direct lineage from Odwin to Heimericus the Dean to Baduif to Eva and thence himself.


How accurate this genealogy is is anyone's guess. Presumably it represents an oral tradition, even if many of the relatives continued to live close to each other. It was not until much later that formal records were kept. In Britain, for example, from 1538 King Henry VIII required that church ministers keep records of christenings, baptisms, marriages and burials; and civil registration did not became law until 1837. The Germanic lands began to keep similar sacramental records at roughly the same time as the British; and the Scandinavian countries followed suit. Thus, in most European countries it is the church parish registers that pre-date any civil record keeping. Otherwise, for commoners there have been only personal records.

Wednesday, December 3, 2014

Visual complexity and phylogenetic networks

Network diagrams have become rather commonplace in the modern world. Most of them are constructed along the same lines — observed entities (objects or concepts, or groups of them) are connected by lines showing observed relationships. Such visualizations are relatively easy to create using computers, and so they represent a relatively new form of visual data analysis. The complexity of the diagrams can be both seen and quantitatively analyzed, thus forming part of what is now grandiosely called "data mining and knowledge discovery".

The Visual Complexity project has been compiling an interesting set of online network visualizations. While the author (Manuel Lima) intends this to be "a unified resource space for anyone interested in the visualization of complex networks", at the moment it is simply a magpie collection of references to web pages. There are currently nearly 800 visualizations referenced, grouped into:
  • Art
  • Music
  • Biology
  • Food Webs
  • Transportation Networks
  • Business Networks
  • Social Networks
  • Political Networks
  • Computer Systems
  • Internet
  • World Wide Web
  • Pattern Recognition
  • Semantic Networks
  • Knowledge Networks
  • Multi-Domain Representation
  • Others
Our interest is in the Biology group, of course, where we have long known about networks, including food webs, which you will notice are grouped separately. There are currently 52 networks (plus 8 in the Food Web group), covering a wide range of topics, such as:
  • Gene interaction networks
  • Protein-protein interaction networks
  • Protein "homology" networks
  • Neuron networks
  • Haplotype blocks
  • Metabolic pathways
  • Genome maps
  • Physiology maps
  • Disease maps
  • Visualizing the aging process

This is all very well. However, we are specifically interested in phylogenetic networks, which are as old-fashioned as food webs. They differ significantly from these other biological networks. Phylogenies connect observed entities (objects, or groups of them) only indirectly, via unobserved nodes, with the lines representing inferred affinity or genealogical relationships. Only at the population level is it likely that all internal nodes, representing individuals, will be observed, and that their relationships might also be observed.

There are currently three phylogenies referenced by Visual Complexity:
Only the last of these is a network, the other two being trees. Sadly, the first one also contains a dead link, which is a problem common for most multi-year internet projects.

Unfortunately, the uniqueness of phylogenies among networks is not acknowledged by the Visual Complexity site. This is not unusual amongst network researchers, most of whom have never even heard of phylogenies. Moreover, many of the people who do seem to have heard of them often fail to understand them and their interpretation, so that they do not notice the fundamental difference. Nevertheless, phylogenetic networks are among the oldest type of recorded network, and there are certainly complex versions of them dating back to the 1700s (see those by Herman and by Batsch in Affinity networks updated).

Finally, the Visual Complexity site does not yet have much from anthropology (as distinct from the social sciences in general) or anything from linguistics (other than programming languages!). These are promising areas for studies of visual complexity.

Monday, December 1, 2014

The first royal pedigree


I mentioned in a previous post that genealogies first appeared as human pedigrees, initially based on biblical histories (The role of biblical genealogies in phylogenetics). However, such ideas were also adopted by the Roman nobility as stemmata (literally, garlands connecting portraits of ancestors) to be displayed in their homes. The latter pedigrees were used to assert the nobility of the nobles by right of family descent — stemmata distinguished between the patrician class (those with noble ancestry) and plebeians (commoners). This usage continues to this day, in most parts of the world.

However, there are no extant pedigrees (of real people) from the earliest times. The first preserved written records appear towards the end of the first millenium CE, when family chronicles began to be written by clerics in the courts or monasteries of northern France. For example, the Genealogia Arnulfi Comitis [Genealogy of Count Arnould] was compiled between 951 and 959 CE by the Benedictine monk Witger, listing the pedigree of the counts of Flanders. It was preserved at the abbey of Saint Bertin, and is reproduced in Monumenta Germaniae Historica, Tomus IX (1851) pp. 302-304.

This development seems to have been as much a response to the feudal inheritance system (automatic consanguineous inheritance of fiefs) as it was a concern for familial prestige or preserving the memory of ancestors. Legitimacy of succession was the key motif, not history. It might have been this motivation that lead to the use of diagrams, as these illustrate the succession in unambiguous terms.


The first known illustration of a pedigree is the Tabula Genealogica Carolingorum from c.1000 CE. Here, Cunigunde of Luxembourg's ancestry is traced in a tree-like manner to include Charlemagne, thus legitimizing her claim to being of royal descent. Cunigunde (c.975-1040) married Henry, Duke of Bavaria, in 999. He became King Henry II of Germany ("Rex Romanorum") in 1002, at which point she became Queen consort of Germany (1002-1024); and when he was crowned Holy Roman Emperor ("Romanorum Imperator") in 1014, which was the tradition for the King of Germany, she became Empress consort of the Holy Roman Empire (1014-1024). Henry died in 1024, and Conrad II was elected to succeed him.

Cunigunde's ancestry is thus of some practical importance. Being able to trace that ancestry to Charlemagne ("Charles the Great") is of especial interest, as it made her a descendant of the Carolingian dynasty. Charlemagne (c.742-814 CE) was the last great ruler of a united Western Europe. When his son, Louis the Pious (778–840), died, his own sons fought over the succession. The resulting Treaty of Verdun (843) divided the Carolingian Empire into three kingdoms, without any consideration for linguistic or cultural groupings. Europe has been arguing over national boundaries ever since; and the European Union is thus the first serious attempt to return to Carolingian times for more than 1,100 years.


The oldest copy of the Tabula Genealogica Carolingorum is shown in the first figure. It is from the Bayerischen Staatsbibliothek, in Munich. BSB Clm 29880(6. Since it is almost unreadable, Jean-Baptiste Piggin has digitized a copy, as shown above.

The pedigree is drawn very like an upside-down tree. (Actually, it looks like a chandelier hanging from the ceiling.) The ancestors of Charlemagne form a trunk at the top, and his descendants fan out as tree branches at the bottom. Cunigunde herself is at the bottom-left, labelled "Cynigund imperatrix" [empress]. She is thus part of the seventh generation from Charlemagne (labelled "Karolus rex" and also "imperator in Frantia"). Her connection is through Louis the Pious' second son, who became "Karolus rex Francie et Hispaniae". Her ten siblings are not shown.

Charlemagne's ancestors are traced back 200 years, to the mid 500s CE. The ancestry as shown is via the male lineage back to Arnulf of Metz (c.582-640). However, the person listed at the root of the pedigree, Arnoald of Metz (c.540/560-c.611), is disputed — he may have been the father of Arnulf's wife (Doda), rather than of Arnulf himself.

Cunigunde's husband is shown in a separate pedigree of seven people at the bottom right. He is labelled "Heinricus dux Baioariae" — the rest is unreadable but Piggin transcribes it as "postea imperator" [later emperor].


There is also an annotated transcription in the Monumenta Germaniae Historica, Tomus II (1829) p.314, as shown in the third figure. This is taken from the copy in the Codicum Manuscriptorum Bibliothecae Regiae Monacensis. It is displayed in a much more conventional modern form; and it lists Henry as "Romanorum imperator".

Piggin notes that another version of the pedigree was drawn between 1101 and 1111 CE at the monastery of Prüm and bound into the Liber Aureus, a book of important Prüm documents. Finally, there is also a version of the pedigree that tries to hint at a divine origin for the nobles, as shown in the figure below. This is from the Chronicon Universale at the Thüringer Universitäts- und Landesbibliothek, in Jena, Codex Bose quarto 19 fol. 152v. Several editions of this book were produced between 1100 and 1125 CE.


In noble pedigrees, the presence of sacred progenitors who sanctify the lineage is not uncommon, as this legitimizes the nobility in religious as well as secular terms. Interestingly, this idea seems to trace all the way back to the Ancient Greeks, who employed genealogy to prove descent from a god or goddess.