The Genealogical World of Phylogenetic Networks

Biology, computational science, and networks in phylogenetic analysis

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December 16, 2014

22:30

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 beed 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, and 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.

December 14, 2014

16:30

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.


December 9, 2014

22:30

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.

December 7, 2014

16:30

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.

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.

December 2, 2014

22:30
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.

November 30, 2014

16:30

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 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 above. 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.

November 25, 2014

22:30

This the 300th post on this blog, and so I thought we might have a bit of a summary. Here is the early history of phylogenetic trees and networks as we currently know it. There may, of course, be as yet undetected sources. Details of each of these historical notes (including illustrations) can be found elsewhere in this blog — you can use the search feature in the right side-bar to find them.

Biology

Genealogies as pedigrees (the history of individuals) have a long history. For example, they appear in inscriptions concerning the pharaohs of Ancient Egypt, although these are very imprecise and have caused many headaches for modern scholars. They appear as chains of ancestors and descendants in the Old Testament of the Christian Bible, often contradicting each other and claiming impossible lifespans. Most importantly for modern usage, they were employed in the New Testament to legitimize Jesus as the messiah foretold in the Old Testament. The first known illustration of this appeared in c.400 AD, and it was actually a network, as there were two lineages leading to Jesus (via both Joseph and Mary).

The apparent success of this application (later called the Tree of Jesse, pictures of which started appearing in the 10th century) has meant that both royalty and the nobility have subsequently used pedigrees to assert their own right to be regal and noble. The first known illustration of this is from c.1000 AD, in which Cunigunde of Luxembourg's ancestry was traced in a tree-like manner to include Charlemagne, thus legitimizing her claim to being royal.

Also, up until 1215 AD marriage within seven degrees of separation was not allowed by the christian church, and intestate inheritance applied the same relationship limit. So, a record of blood ties among relatives was often needed; and these started appearing in family bibles, for example. The first recorded tree-like illustrated pedigree was for Lambert of Saint-Omer, which appeared in 1122 AD in his personal copy of his book Liber Floridus.

It seems obvious, then, to also construct genealogies for groups of organisms, which we now call phylogenies (a word coined by Ernst Haeckel in 1866). The Great Chain of Being was for a long time the most popular iconography for relationships, mainly because it neatly tied in with the Christian philosophy of a chain of intellectual ideas, leading from pragmatic earthly concerns and culminating in the idealistic heavens. Humans were, of course, at the head of the chain of earthly beings, and capable of ascending to the heavens.

However, this did not work from a purely observational point of view. Observed pedigrees were not linear, but branched with each generation and often fused again via marriage. Furthermore, biodiversity (the patterns among groups of organisms) also seemed to have multiple relationships. This lead Vitaliano Donati in 1750 (Della Storia Naturale Marina dell' Adriatico) to suggest that:
In addition, the links of the chain are joined in such a way within the links of another chain, that the natural progressions should have to be compared more to a net than to a chain, that net being, so to speak, woven with various threads which show, between them, changing communications, connections, and unions. [from the original Italian]He was not alone in this thought, although others chose different metaphors. For example, Carl von Linné in 1751 (Philosophia Botanica) wrote this:
All plants show affinities on either side, like territories in a geographical map. [from the original Latin]Neither author published a reticulating diagram to illustrate their thoughts, although one of Linné's students subsequently produced a version of his ideas in 1792 (Caroli a Linné, Praelectiones in Ordines Naturales Plantarum).

So, it was Georges-Louis Leclerc, Comte de Buffon, who produced the first empirical phylogeny in 1755 (Histoire Naturelle Générale et Particulière, Tome V). This was a network showing the evolutionary origin of domesticated dog breeds. This was followed by Antoine Nicolas Duchesne in 1766 (Histoire Naturelle des Fraisiers), who produced a network showing the evolutionary origin of strawberry cultivars. In both cases the evolutionary process illustrated by the reticulations in the network was hybridization. Note that both of these diagrams refer to within-species genealogies, rather than to relationships between species; and neither author seems to have contemplated the idea of among-species phylogenies.

Thus, in both theory and practice modern phylogenetic metaphors started as networks, not trees. It was Peter Simon Pallas in 1776 (Elenchus Zoophytorum) who first suggested using a tree as a simplified metaphor:
As Donati has already judiciously observed, the works of Nature are not connected in series in a Scale, but cohere in a Net. On the other hand, the whole system of organic bodies may be well represented by the likeness of a tree that immediately from the root divides both the simplest plants and animals, [but they remain] variously contiguous as they advance up the trunk, Animals and Vegetables; [from the origina Latin]Again, no diagram was forthcoming to illustrate this. It was Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, who finally produced an empirical phylogeny in 1809 (Philosophie Zoologique). This was a small tree showing the evolutionary relationships among the major groups of animals. However, it represented what we would now call transformational evolution, as Lamarck did not believe in extinction, and thus he showed one group transforming into another. This differed from both Buffon and Duchesne, who were illustrating a process of increasing diversity of groups. It also differed by referring to supra-species relationships.

For the next 50 years, diagrams showing biodiversity relationships illustrated what we now call patterns of affinity, rather than showing historical relationships. These affinity diagrams showed apparent similarities among groups of organisms, without any implication that the relationships were the result of evolutionary history. The majority of these diagrams were networks rather than trees, indicating that groups of organisms had observed similarities with several other groups.

It is Charles Darwin and Alfred Russel Wallace who are credited with introducing, in 1858, the idea that natural selection could be the important process by which new species arise, although the idea of natural selection itself had been "in the air" for more than half a century with respect to within-species variation. (In the case of Patrick Matthew, he had also suggested a role in the origin of new species; 1831, On Naval Timber and Arboriculture; with Critical Notes on Authors who have Recently Treated the Subject of Planting).

As was by now becoming a tradition, neither Darwin nor Wallace (nor Matthew) produced a diagram to illustrate their thoughts. Darwin did draw a theoretical diagram in his subsequent 1859 book (On the Origin of Species by Means of Natural Selection), but he used it to illustrate continuity of evolutionary descent and the processes of extinction and diversification, rather than strictly as representing a phylogeny. His famous "Tree of Life" metaphor had nothing to do with the diagram (it was a Biblical metaphor, to stimulate the imagination of his readers).

The first person to get into print what we could call an empirical diagram representing Darwin's idea was Johann Friedrich Theodor Müller in 1864 (Für Darwin), who drew a small (three-species) tree of amphipods. This was followed by St George Jackson Mivart in 1865 (Contributions towards a more complete knowledge of the axial skeleton in the primates. Proceedings of the Zoological Society of London 33: 545-592). This was a much more extensive diagram illustrating possible evolutionary relationships among primate species (including humans) based solely on their body skeleton.

Confusion between trees and networks reappeared at this time. In particular, Franz Martin Hilgendorf had produced an unpublished PhD thesis in 1863 (Beiträge zur Kenntniß des Süßwasserkalkes von Steinheim) during which he constructed an empirical network of relationships among extinct snail species; but he rejected this because it did not match the Darwinian idea of an evolutionary tree. He later collected more data, and instead published a phylogenetic tree in 1866 (Planorbis multiformis im Steinheimer Süßwasserkalk: ein beispiel von gestaltveränderung im laufe der zeit).

Thus, we last saw an explicit evolutionary network in 1766, referring to with-species variation. The first person to publish an evolutionary network showing relationships among species was apparently Ferdinand Albin Pax in 1888 (Monographische übersicht über die arten der gattung Primula. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 10: 75-241). He produced 14 networks of various primula species, apparently showing affinity relationships, but three of these also illustrate hybridization, which is strictly an evolutionary process.

Anthropology

Genealogies appear in anthropology as well as in biology. Any human creation can be considered to have a history of "descent with modification" if copies are passed from generation to generation (eg. languages, books, tales). For our purposes here, the most important historical developments were in linguistics (languages studies) and in stemmatology (manuscript studies).

Georg Stiernhielm appears to have been the first linguist to draw a genealogy, when he produced a small network of Germanic languages in 1671 (De Linguarum Origine Præfatio, the preface to his edition of Evangelia ab Ulfila Gothorum). This was followed by Félix Gallet in c.1800 (Arbre Généalogique des Langues Mortes et Vivantes), who produced a single broadsheet with a network of Indo-European languages.

Note that, as for biology, the modern metaphors started as networks, not trees. More importantly, note that Stiernhielm's diagram pre-dated Buffon's dog network by more than 80 years — evolutionary ideas were less revolutionary in linguistics than they were in biology.

Darwin explicitly noted a connection between language genealogies and biology genealogies in 1859. However, the first people to get into print what we could call empirical diagrams representing Darwin's idea did so before Darwin published anything on the subject. In 1853 František Ladislav Čelakovský published a tree depicting a history of the Slavic languages (Čtení o Srovnávací Mluvnici Slovanské na Universitě Pražskě), and Auguste Schleicher published one on the development of the Indo-Germanic language family (Die ersten Spaltungen des Indogermanischen Urvolkes. Allgemeine Monatsschrift für Wissenschaft und Literatur 1853: 786-787).

Stemmatology differs from linguistics and biology in first producing a tree rather than a network. Hans Samuel Collin and Carl Johan Schlyter produced this in 1827 (first volume of Corpus Iuris Sueo-Gotorum Antiqui), with a tree of relationships among hand-written copies of documents containing the Medieval laws of Sweden. This was also a tree that represented Darwin's genealogical idea, and so it may be considered to be the first one of that type to be published (ie. 25 years before Čelakovský and Schleicher, and 30 years before Darwin).

This early lead was followed by the first network in 1832, when Friedrich Wilhelm Ritschl's stemma of a book by Thomas Magister (Thomae Magistri sive Theoduli Monachi Ecloga vocum Atticarum) explicitly showed sources of contamination among the manuscript copies — that is, different parts of a manuscript were copied from different sources, rather strict ancestor-descendant copying.

Interestingly, the tree metaphor didn’t endure in anthropology as well as it did in biology. It was quickly replaced by alternative metaphors, such as wave, web, warp & weft, lattice and other continuously reticulating images. Horizontal flow of information has always been seen as a dominant force in anthropological histories.

Timeline

Networks

1671 Georg Stiernhielm — small language network
1750 Vitaliano Donati — biology network suggestion
1751 Carl von Linné — biology map suggestion
1755 Georges-Louis Leclerc, Comte de Buffon — intra-species network
1766 Antoine Nicolas Duchesne — intra-species network
1792 Carl von Linné — map
1800 Félix Gallet — language network
1832 Friedrich Wilhelm Ritschl — small manuscript network
1863 Franz Martin Hilgendorf — unpublished inter-species network
1888 Ferdinand Albin Pax — inter-species network

Trees

1776 Peter Simon Pallas — biology tree suggestion
1809 Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck — small inter-species tree
1827 Hans Samuel Collin and Carl Johan Schlyter — manuscript tree
1853 František Ladislav Čelakovský — language tree
1853 Auguste Schleicher — language tree
1859 Charles Robert Darwin — generalized tree
1864 Johann Friedrich Theodor Müller — small inter-species tree
1865 St George Jackson Mivart — large inter-species tree
1866 Franz Martin Hilgendorf — large inter-species tree

November 23, 2014

16:30

Infographics have become very popular in recent decades, with the advent of computer graphics packages. Infographics combine data and pictures, trying to produce an aesthetically pleasing but still informative presentation of numeric information. Recently, the following book appeared:
The Infographic History of the World (2013)
by Valentina D’Efilippo & James Ball
HarperCollins (UK) / Firefly Books (US)

A selection of the the infographics can be perused at the senior author's web page:
http://www.valentinadefilippo.co.uk/ihw/At the visual.ly blog the author also explains her intentions:
The Infographic History of the World is a new book that continues to push the field of infographics forward. Our task required research, organization and the selection of topics. Then, we needed to decide how to display data in order to tell a coherent and compelling story. We have never considered this to be an alternative to tons of books of history, but hopefully a refreshing interpretation of what history is about. With this book, we hope to lead readers on a journey, to interpret the data and find the implications that resonate with them. We don’t pretend that every set of data presents an unquestionable truth. And, rather than looking to define the world’s history, we were looking to present readers with an unconventional interpretation of the subject.Sadly, these good intentions have not always been achieved. As noted by a review at Amazon:
the book showcases *clever* ways of displaying data, not *clear* ways of displaying it ... Far too often I had to pore over the graphic to figure out what it was trying to say.What is worse for the readers of this blog, the information is not always correct. Consider this version of the Tree of Life, which has a long-standing tradition in systematics as one of the world's first examples of an infographic:

Click to enlarge.
Quite a number of the taxonomic labels are misplaced. You can check them for yourselves, but here is a selection of some of the surprising information contained in this infographic:
  • Amphibians are not Tetrapods
  • Humans are not Mammals
  • Mammals are not Amniotes
  • Turtles are not Reptiles
  • Lobe-finned fishes are not Sarcopterygians
  • Ray-finned fishes are not Bony Vertebrates
  • Charophytes are Land Plants
  • Hornworts are Vascular Plants
  • Ferns and Horsetails are not only Seed Plants they are Gymnosperms
  • Conifers, Gnetophytes, Gingko and Cycads are not Gymnosperms
 Clearly, little has been done to check the veracity of the information in this infographic, which completely defeats its purpose.

November 18, 2014

22:30

In a previous post I introduced the Great Stemma as the earliest known pedigree, being a genealogical view of biblical history (The first infographic was a genealogy). In it I noted that people were enclosed in circles, which were connected by lines showing relationships, much as we still do today. However, the lines combined marriage, parent-offspring and brotherly relationships without distinction. So, while it is a good first attempt, the Great Stemma leaves room for informational confusion, and this was not corrected at any time during its centuries of being copied. (In fact, confusion was increased through embellishments, deletions and modifications; but that is another story.)

To illustrate the potential problem of interpreting this early type of genealogy, I have included here a specific example.


The above excerpt from the Stemma shows the the children of Jacob by his wife Leah (who is shown at the top centre), and their subsequent children (ie. Leah's grandchildren). I have annotated the diagram to show parent-offspring (P), brother (B) and half-brother (HB) relationships. Note that all relationships are between males unless specified otherwise (so, half-brothers have the same father).

Leah is at the top [generation 1], with her six sons in a row below her (in birth order left to right), and her daughter to the side [generation 2]. Below this is the first-born son of each of the sons [generation 3], followed in columns down the page by their later sons, in birth order. Sons by later relationships are shown as half-brothers. At the bottom are two of Leah's great-grandchildren [generation 4].

Thus, the genealogical diagram does not effectively separate the generations visually, and parental and fraternal relationships are depicted in the same way. These days we solve this, of course, by keeping each generation as a single row and linking each child directly to the parent. It is easy to get used to the Stemma way of doing it, because it is fairly consistent about the arrangement. If there is confusion, then each circle does specify the relationship in words.

So, as I noted, this is a good first attempt, but some of the things that we now feel need distinguishing were not distinguished by the (unknown) original author.

However, the 24 extant copies of the Stemma are not identical, and two of them try to fit more information into Leah's family tree than is shown above. This information concerns the origin of the fourth generation, which is accurately depicted as far as it goes, but the above figure leaves out a lot. Some of the extra information is shown in the Stemma version below, which adds two extra people, both of them wives. I have annotated this version the same as the previous one, except that this pedigree adds one more relationship to the mix — marriage (M).


The extra details come from Genesis 38, which describes a set of relationships that would make a modern television soap-opera scriptwriter jealous. The story goes something like this (I have indicated the named people with letters in the diagram above, with Leah as L):
Judah (J) marries the [unnamed] daughter (W) of Shua. Judah and his wife have three children, Er (E), Onan (O), and Shelah (S). Er marries Tamar (T), but God kills him because he "was wicked in the sight of the Lord" (Gen. 38:7). Tamar becomes Onan's wife in accordance with the custom of the time, but he too is killed by God after he refuses to father children for his older brother's childless widow, and "spills his seed on the ground" instead (Gen. 38:8-10). Although Tamar should marry Shelah, the remaining brother, Judah does not consent, for fear of his son's life (Gen. 38:11). In response, after Judah's wife has died, Tamar deceives Judah into having intercourse with her, by pretending to be a prostitute (Gen. 38:12-23). When Judah discovers that Tamar is pregnant he prepares to have her killed, but recants and confesses when he finds out that he is the father (Gen. 38:24-26). The result is twin boys, Zerah (Z) and Perez (P) (Gen. 38:27), who are accepted as Judah's sons.Biblically, this story is important because Judah became the founder of the Tribe of Judah, one of the twelve Tribes of Israel. Their land encompassed most of the southern portion of the Land of Israel, including Jerusalem. Both the Book of Ruth and the Gospel of Matthew identify Tamar's son Perez as an ancestor of King David, which makes Judah and Tamar also ancestors of Jesus.

For our purposes here, though, the interesting thing is the confusion caused by trying to add the two marriage relationships to the pedigree. These are in no way distinguished visually from the paternal and fraternal relationships, although the circled text does specify the relationship in words. Today, we solve this potential confusion by using horizontal lines for marriage relationships and vertical lines for parent-offspring relationships.

Equally importantly, note that Tamar's (legal) relationship supplants the (biological) parent-offspring relationship between Judah and her sons — you would never conclude from the diagram that Perez was Judah's son, for example, rather than Er's. However, note the neat attempt to keep Tamar's children in a single column by putting one twin above her and one below (perhaps also signifying simultaneous birth).

The above part of this post was inspired by a blog post from Jean-Baptiste Piggin (The Tamar Storyboard). The first picture above is from an unnamed manuscript in the Biblioteca Medicea Laurenziana, Florence, Plut.20.54, dated c. 1050 AD. The second picture if from an unnamed manuscript in the Pierpont Morgan Library, New York, M.644, dated 940-945 AD.

Moving on, the scribes of that time tried to go even further in complicating simple genealogies, as shown in the next figure. This is drawn by Stephanus Garsia Placidus, and is taken from the Saint-Sever Beatus in the Bibliothèque Nationale de France, Paris, ms. lat 8878, dated c. 1060 AD.


It shows the non-Semitic (ie. polytheistic) part of Noah's family. Noah is at the top right (sacrificing two doves), with his son Japheth (J) to the left and son Ham (H) below. Their wives (W) are indicated by intersecting circles, rather than by lines, which is a more successful approach than in the Stemma. Their descendants are shown in roughly the same style as above, with the first-born son followed by the later ones in order (so that the P and B relationships are not clearly distinguished) — Japheth has seven sons and Ham has four.

However, the illustrator has also tried to include a lot of history in this genealogy. For example, the sons of Ham's son Cush end with Nimrod (N), who has a small essay attached to his name. Among other things, he founded Babel, the city that plays an important role later in the Bible. Moreover, the sons of Ham's son Canaan (C) are shown as a reticulating network rather than as a simple chain. This apparently represents their roles as founders of the 11 tribes who originally occupied the ancient Land of Canaan, and who were later driven out and enslaved by the Israelites. These lines thus represent later history rather than parental or fraternal relationships.

This diagram is thus not a simple pedigree, as we would usually leave it today.

November 16, 2014

16:30

The New Testament was originally written in Greek, and it apparently did not occur to the writers that a visualization of the many (and lengthy) Biblical genealogies would be helpful. They knew a lot about geometry but nothing about infographics.

Given the importance of the New Testament genealogies for the foundation of Christianity (see The role of biblical genealogies in phylogenetics), it is not at all surprising that eventually someone had a go at summarizing them all in one place. However, this did not happen until several centuries later, when the Bible was being translated into Latin. Perhaps this delay had something to do with the biblical prohibition on images.

The first known attempt to draw a biblical pedigree, rather than writing out the relationships as text, also appears to have been the first attempt at a genealogy of any sort. Jean-Baptiste Piggin has been researching this document since 2009, and he has remarkably extensive notes about it at his web site Macro-Typography. Piggin dates the document to sometime in the decades before 427 AD, which is surprisingly early and thus unique in its historical context (Late Antiquity).

Importantly, the pedigree is actually an infographic in the modern sense, in that the figure itself conveys almost all of the information, with the text acting as a supplement. Thus, a single image allows the viewer to grasp the overview (of biblical history in this case), as well as providing access to the details. This is an idea that did not really catch on until the Medieval period, when Latin manuscripts started to use images as pedagogic devices, in addition to their textual descriptions. An obvious example is the so-called Tree of Porphyry in logic, which was first described in words by Porphyry of Tyre in c. 270 AD (Isagoge), sketched by Boëthius c. 520 AD (In Porphyrium Commentariorum), and finally reproduced as an actual tree diagram in Medieval manuscripts (being named arbor Porphyrii by Petrus Hispanus in 1240, in Summulae Logicales).


Sadly, there is no extant copy of this early biblical pedigree, and so we do not know who produced it or exactly when; nor do we have any of the copies made during the following 500 years. We do, however, have 24 complete or partial copies from the period 950-1250, many of them incorporated into Spanish editions of the Bible. Piggin has studied these copies extensively, and tried to reconstruct what he thinks the original document most probably looked like.

Piggin reconstructs the document (shown above), which he calls the Great Stemma, as a single scroll made from papyrus, designed to be unrolled and read from the upper left towards the middle right. All extant copies, however, break the figure up into sections, for inclusion as pages in a parchment manuscript (a codex) typical of the Medieval period.

Reconstruction was not an easy task, given the later modifications, digressions and embellishments, made with each successive hand-drawn copy. In particular, the process of reducing the long scroll to sequential pages apparently introduced many errors; and subsequent modifications degraded the logic of the original intention. Incidentally, embellishments do not improve the communication of information (see Mistaken improvements), and nor necessarily do modifications, since in this case they often created contradictions.

Above is a schematic overview of the reconstructed original scroll, but you can zoom in to all of the details by visiting Piggin's original reconstruction. Each circle represents one person (out of 540), with connecting lines showing their genealogical relationships — marriage, parent-offspring or brotherly (these are inter-mixed). Time is read left to right along the top (Adam is at the top-left), with vertical excursions downwards for lineages that do not lead to Jesus (who is at the middle-right). Note that the pedigree is drawn using nodes and lines, as we still do, but it is not drawn anything like a tree (ie. a "family tree"). Indeed, it is actually a network, since two ancestral lineages converge on Jesus (via Joseph and Mary).

The diagram also has a distinct timeline superimposed, shown as the elements without circles, which attempts to synchronize biblical events with contemporaneous secular history. So, Piggin notes that the Stemma it is "not just a genealogy, but a graphic version of the universal chronicles which attempted in antiquity to cross reference the histories of different civilizations to establish an overview of Middle Eastern and Graeco-Roman history." However, the timeline is not calibrated in any way (ie. time changes are not constant).

Below, I have included pages from some of the extant manuscripts, to show their variety after more than 500 years of scribes making copies.


The above figure is the first page from the Roda Codex, in the Real Academia de la Historia (Madrid) cod.78 (dated 990 AD). This is the start of the genealogy, with Adam at the top-left, and illustrating his family.


The above figure is the third page from an unnamed manuscript in the Pierpont Morgan Library (New York) M.644 (dated 940-945 AD). This one shows Noah and his non-Semite descendants.


The above figure is the final page from an unnamed manuscript in the Plutei collection at the Biblioteca Medicea Laurenzian (Florence) Plut.20.54 (dated 1050 AD). This shows the incarnation of Jesus, at the end of the genealogy, illustrating the confluence of the lineages described by Matthew (at the top) and Luke (at the bottom).

Piggin notes that here may actually have been few early copies of the Stemma, because of the difficulty of transcribing illustrations by hand. That is, it is very difficult to accurately hand-copy a diagram, as opposed to copying text (where only the words matter not their visual style). Indeed, to what extent did the scribes actually understand that they needed a precise copy? Copying complex technical drawings requires careful measurement and layout, and yet some of the copies seem to have been very badly planned. Piggin suggests that "the serious corruption done to the Great Stemma early in its diffusion led to it ultimately being discarded and begun all over again by medieval writers such as Peter of Poitiers." The reference is to the Compendium Historiae in Genealogia Christi by Petrus Pictaviensis (Peter of Poitiers) produced in c.1185 AD, and for which there are many extant copies dated from that time to 1650 AD — he used long rolls for his genealogies.

Finally, Piggin even has a suggestion for a small ancient board game that might have provided inspiration for the form of the infographic (see Board Game). This is important, because there are no known prior models for constructing such a diagram — apart from geometry, no-one had previously produced an image that illustrated non-corporeal ideas.


Footnote: The word stemma referred originally to an ancient Roman genealogy (displayed in noble homes), which is roughly how it is used by Piggin. However, these days the word is more commonly used in anthropology to refer to a genealogy of manuscript copies. A genealogy of manuscripts is more properly called a stemma codicum.

November 11, 2014

22:30

The draft Minimum Information about a Phylogenetic Analysis standard (Leebens-Mack et al. 2006) suggests that all relevant information about each and every published phylogenetics analysis should be archived, so that it can be scrutinized by later researchers, either for validation or for re-use. The issues here are both preservation of the information (data and analysis protocols) and open access to it.

In this blog we have already pointed out that there has been criticism of the bioinformatics part of this archiving, where there have been repeated claims that many computer programs are poorly maintained (Poor bioinformatics?) as well as poorly archived (Archiving of bioinformatics software).

Anyone who has ever tried to get data out of a biologist will know that the data-related part of the standard is no better. My own success rate, at requesting data from all areas of biology not just phylogenetics, is less than 20% over the past 25 years. The responses have been, in order: (i) no response (>50%), (ii) "a student / postdoc / colleague has the data not me", and (iii) "I have moved recently and don't know where the data are". My most recent attempt, to get the data from Collard et al. (2006), was ultimately unsuccessful even after several attempts.


For phylogenetics, this situation has recently been quantified and analyzed by Magee et al. (2014). They tried to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 published studies. Of these, 54 (25%) had at least some part of the data (alignment or tree) archived in an online repository, and 91 (42%) were obtained by direct solicitation, but in 72 (33%) of cases nothing could be obtained even after three requests. Overall, complete datasets (both tree and alignment) were available for only 40% of the studies.

The authors note that the data were more likely to be deposited in online archives and/ or shared upon request when the publishing journal has a strong data-sharing policy. Furthermore, there has been a positive impact of recent policy initiatives and infrastructural changes involving data repositories. The TreeBASE phylogenetic-data repository has existed for more than 20 years, but its use has been sporadic. However, the recent establishment of the Joint Data Archiving Policy by a consortium of journals, which requires the submission of data to online archives as a condition of publication, and the concomitant establishment of the Dryad repository for evolutionary and ecological data, has seen a surge in the archiving of data.

So, all in all, things have been no better on the bio side than the informatics side of bioinformatics.

Stoltzfus et al. (2012) have identified a number of possible barriers to successful data archiving, including lack of awareness of options and policies, perception that benefits do not justify burden, and an active desire to restrict data access. Importantly, there are also a number of practical issues even for those people who do wish to archive their data:
  • inconvenience of gathering complete data and metadata
  • inconvenience of format conversions needed for archiving
  • frustration when some data don't fit the archive's data model
  • poor and undocumented archive submission interfaces.
For the readers of this blog, issue three is possibly the most important one — all current repositories are based on a tree model for phylogenetics, and therefore network phylogenies are frustrating to deal with.

In order to improve the overall situation, there are explicit suggestions from Cranston et al. (2014) for best practices when archiving. They have ten simple guidelines that, if followed, will result in you providing open access to your data and analyses, even if the publishing journal does not force you to do it.

Footnote: I have been reminded that archiving data in PDF format is inappropriate. Trying to extract text (such as a dataset) from a PDF file can be difficult, because there is no standard format for storing the text. Consequently, different PDF readers will extract the text in different ways, and it is possible that in all cases the output will need extensive manual re-formatting, in order to recover the original text formatting that went into the PDF file. In my experience, Google Chrome may do the least-worst job.

References

Collard M, Shennan SJ, Tehrani JJ (2006) Branching, blending, and the evolution of cultural similarities and differences among human populations. Evolution and Human Behavior 27: 169-184.

Cranston K, Harmon LJ, O'Leary MA, Lisle C (2014) Best practices for data sharing in phylogenetic research. PLoS Currents Jun 19;6.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjölander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 10: 231-237.

Magee AF, May MR, Moore BR (2014) The dawn of open access to phylogenetic data. PLoS One 9: e110268.

Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes 5: 574.

November 9, 2014

16:30

Trees can be many things: objects, symbols, art, or information.

As objects, they act as homes and shelter, they provide food and oxygen, and they bind soil to hold topography in place. They even provide somewhere to sit while you are waiting to discover gravity. Their most famous use as symbols is the Tree of Life, which recurs in many cultures throughout the world. This was later extended to the Tree of Knowledge, a potent intellectual symbol throughout Western history. In the modern world this latter use has been expanded, so that trees are mathematical representations of the relationships among information.

Trees have also long played a role in art, which continues in the modern works of, for example, Vincent van Gogh and Gustav Klimt.

My first introduction to this was the book The Tree (1979, Aurum Press, UK / Little, Brown and Co, USA) by John Fowles (text) and Frank Horvat (photographs). This is a meditation on the connection between the natural world and human creativity. Horvat provides moody views of trees with (almost) no human objects in sight, and Fowles (the novelist) provides a provocative essay on trees as representations of art, revealing in his usual erudite manner that he particularly dislikes the "taming the wild" aspects of horticulture and science.


More recently, there has been the hand-lithographed book The Night Life of Trees (2006, Tara Books, Chennai, India). This contains a series of tribal-art images from three Gond people of central India (Bhajju Shyam, Durga Bai and Ramsingh Urveti). (And yes, the land of the Gond is Gondwanaland, which was the source of our name for the southern land masses.)

The Gond people have previously decorated their house walls and floors with traditional tattoos and motifs; and these motifs have made their way onto paper as modern representations of the tribal art form. Other tribal art forms that have followed a similar transfomation include the Aboriginal art of Australia, which bears a strong stylistic resemblance to some of the Gond art.

The Gonds are traditionally forest dwellers, and so the lives of humans and trees have been seen as closely entwined. Their lore suggests that trees are hard at work during the day providing shelter and nourishment, but at night they finally rest and their spirits are revealed. It is these spirits that the artists have tried to capture in their book.

I have reproduced two of the images here, because it is clear that the inter-twining reveals a very network-like aspect of the trees. The accompanying text is taken from the book.

Snakes and Earth

The earth is held in the coils of the snake goddess. And the roots of trees coil around the earth too, holding it in place. If you want to depict the earth, you can show it in the form of a snake. It is the same thing.



The Binding Tree

Mahalain trees are found deep inside the thickest jungles, holding each other in a tight embrace. Because it clings and binds so well, Mahalain bark is known for its strength. Our ancestors from earliest times searched for it in the deep jungles and used it to build houses. A house built well with Mahalain bark is said to last a hundred years.


Both books are worth seeking out if you value art as well as science. The Gond book is now in its 9th hardback edition, and is widely available in bookstores. The Fowles book (without the photographs) is currently available as a 30th anniversary paperback edition; but you are better off finding a second-hand hardback with the pictures.

Finally, just by way of contrast, here is the Albero Trinità from Joachim of Fiore's Liber Figurarum (published in 1202), a book that uses many different visualizations to display human knowledge.


My daughter was the inspiration for writing this blog post.

November 5, 2014

19:00

For those of you who have missed it, the magazine Nature has recently looked at the 100 most highly cited science papers of all time (across all fields):
van Noorden R, Maher B, Nuzzo R (2014) The top 100 papers: Nature explores the most-cited research of all time. Nature 514: 550-553.The list is dominated by biology papers, with biochemical laboratory techniques taking all of the top spots. However, it also worth noting that bioinformatics papers produce a very good showing, and so I have extracted 10 of them here.

If you have ever wondered what phylogenetic tree-building method is most used then it is at #20, while the most-used tree-building program is at #45 (having got there in only 7 years). You may also wonder why sequence alignment programs (#10 & #28 for Clustal; #12 & #14 for BLAST) do much better than tree-building programs (#45 for MEGA; #75 for GCG; #100 for MrBayes).

As for journals, the papers appeared in Nucleic Acids Research (4), Molecular Biology & Evolution (2), Bioinformatics (2), Journal of Molecular Biology (1) and Evolution (1). This list only partally matches their Journal Citation Reports current 5-Year Impact Factors: 8.378, 10.494, 6.968, 3.795 and 5.469, respectively.


Rank: 10 Citations: 40,289
Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson, J. D., Higgins, D. G. & Gibson, T. J
Nucleic Acids Res. 22, 4673–4680 (1994).

Rank: 12 Citations: 38,380
Basic local alignment search tool.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.
J. Mol. Biol. 215, 403–410 (1990).

Rank: 14 Citations: 36,410
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
Altschul, S. F. et al.
Nucleic Acids Res. 25, 3389–3402 (1997).

Rank: 20 Citations: 30,176
The neighbor-joining method: A new method for reconstructing phylogenetic trees.
Saitou, N. & Nei, M.
Mol. Biol. Evol. 4, 406–425 (1987).

Rank: 28 Citations: 24,098
The CLUSTAL_X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.
Nucleic Acids Res. 25, 4876–4882 (1997).

Rank: 41 Citations: 21,373
Confidence limits on phylogenies: an approach using the bootstrap.
Felsenstein, J.
Evolution 39, 783–791 (1985).

Rank: 45 Citations: 18,286
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura, K., Dudley, J., Nei, M. & Kumar, S.
Mol. Biol. Evol. 24, 1596–1599 (2007).

Rank: 75 Citations: 14,226
A comprehensive set of sequence analysis programs for the VAX.
Devereux, J., Haeberli, P. & Smithies, O.
Nucleic Acids Res. 12, 387–395 (1984).

Rank: 76 Citations: 14,099
MODELTEST: Testing the model of DNA substitution.
Posada, D. & Crandall, K. A.
Bioinformatics 14, 817–818 (1998).

Rank: 100 Citations: 12,209
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Ronquist, F. & Huelsenbeck, J. P.
Bioinformatics 19, 1572–1574 (2003).

November 3, 2014

02:16

In a recent article (by myself, Leo van Iersel, Nela Lekić and Simone Linz) we stumbled upon the following problem which appears to touch upon some interesting biological issues.

A rooted triplet xy|z is a rooted binary tree in which x and y have a common parent p, p is a child of the root, and z is the other child of the root. A rooted phylogenetic tree T displays (informally: agrees with) xy|z if the common ancestor of x and y is a strict descendant of the common ancestor of x and z (or y and z). See the figure below: the tree on the right displays triplet xy|z.


Suppose we are given a set of rooted triplets S on a set X of taxa. Suppose we have reason to believe that the set of triplets S have been obtained from different sources (e.g. genes), where the genes have different evolutionary histories due to reticulate phenomena. This means that, for a given subset of 3 taxa {x,y,z} from X, S will contain zero, one, two or three of the possible triplets {xy|z, xz|y, yz|x}.

Crucially, suppose we do not know which gene generated each triplet in S. This might sound artificial, but if some of the rooted triplets have been generated from phenotypic data, or have been obtained from inherently complex data (such as metagenomic data), then the genomic origins of the triplets might not be readily available.

Under such circumstances it is tempting to obtain a lower bound on the number of incongruent gene topologies by answering the following question. What is the minimum number of blocks that we can partition the triplets into, such that the triplets in each block are compatible with a tree (i.e. can all be displayed by the same tree)? It's easy to see that the worst case is when all 3(n 3) possible triplet topologies are present in S, where n is the number of elements in X. Let tau(n) denote this worst case.

We computed tau(n) exactly for small n. For n equal to 3 or 4, tau(n) is 3. For 5

October 28, 2014

23:30

It is well known that reticulations in phylogenetic networks can reflect variation in data sets from many sources, not only gene flow during evolutionary history. These other sources are presumably unwanted in the analysis when they are due to estimation errors. Such errors include incorrect data, inappropriate sampling, and model mis-specification.

For molecular data, one of the more obvious sources of model mis-specification is an incorrect multiple sequence alignment. This reflects wrong assessments of primary homology among the characters, so that the wrong residues are aligned in the columns. This particular issue seems not to have been addressed in the network literature in any systematic way.

However, it is obviously rather important. After all, who needs a phylogenetic network that reflects mis-alignment rather than evolutionary history? One approach to this issue would be to have some sort of measurement of our confidence in the alignment columns, which could be taken into account when the network is constructed.

One practical problem with this approach is that there has been a veritable cottage industry developing such measurements, which would need to be assessed for their suitability. So, I thought that I might list some of them here, along with a brief description of what they measure. The list is comprehensive but not necessarily exhaustive — it consists of ones for which there was at some stage a computer program (there are others that have never been named). Most of the methods are designed specifically for amino-acid sequences, so that not all of them can be used for nucleotides.


There are basically two types of measurement: (1) quantitative scoring schemes, which provide a reliability score for each aligned position, and (2) selection schemes, which select a subset of the aligned positions as being reliably aligned. So, I have divided the list roughly into these two groups.

QUANTITATIVE

WET
Dopazo J (1997) A new index to find regions showing an unexpected variability or conservation in sequence alignments. Computer Applications in the Biosciences 13: 313-317.
— evolutionary index is based on conservativeness of amino acid differences as predicted from nucleotide differences

ClustalX
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882.
— quality is based on conservativeness of amino acid differences

Coffee
Notredame C, Holm L, Higgins DG (1998) COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14: 407-422.
— score represents consistency among global and local alignments

AL2CO
Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700-712.
— conservation is based on weighted entropy

BAli-Phy
Redelings BD, Suchard MA (2005) Joint Bayesian estimation of alignment and phylogeny. Systematic Biology 54: 401-418.
— approximate probability that the letter is homologous to the ancestral residue in its column

MUMSA
Lassmann T, Sonnhammer EL (2005) Automatic assessment of alignment quality. Nucleic Acids Research 33: 7120-7128.
— consistency based on overlap of alignments from several programs

HoT score
Landan G, Graur D (2007) Heads or tails: a simple reliability check for multiple sequence alignments. Molecular Biology and Evolution 24: 1380-1383.
— measures uncertainty due to co-optimal alignments

FSA
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L (2009) Fast Statistical Alignment. PLoS Computational Biology 5: e1000392.
— several scores based on HMM consistency, certainty, expected accuracy, expected sensitivity, expected specificity

Guidance
Penn O, Privman E, Landan G, Graur D, Pupko T (2010) An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27: 1759-1767.
— robustness to guide tree uncertainty

PSAR
Kim J, Ma J (2011) PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Research 39: 6359-6368.
— agreement with probabilistic sampling of suboptimal alignments

Zorro
Wu M, Chatterji S, Eisen JA (2012) Accounting for alignment uncertainty in phylogenomics. PLoS One 7: e30288.
— pair Hidden Markov Model to model the sequence evolution and uses the model to calculate the posterior probabilities that residues of a column are correctly aligned

TCS
Chang J-M, Di Tommaso P, Notredame C (2014) TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Molecular Biology and Evolution 31: 1625-1637.
— transitive consistency score is an extended version of the Coffee scoring scheme


SELECTION

OSA
Martin MJ, Gonzâlez-Candelas F, Sobrino F, Dopazo J (1995) A method for determining the position and size of optimal sequence regions for phylogenetic analysis. Journal of Molecular Evolution 41: 1128-1138.
— locates the smallest blocks with similar pairwise genetic distances to the whole alignment

Gblocks
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17: 540-552.
— selected blocks are based on conservation of identity

SOAP
Löytynoja A, Milinkovitch MC (2001) SOAP, cleaning multiple alignments from unstable blocks. Bioinformatics 17: 573-574.
— stability is measured with respect to variation in the Clustal gap-opening and gap-extension penalties

NorMD
Thompson JD, Plewniak F, Ripp R, Thierry J-C, Poch O (2001) Towards a reliable objective function for multiple sequence alignments. Journal of Molecular Biology 314: 937-951.
— normalized mean distance is based on pairwise distances

Shift score
Cline M, Hughey R, Karplus K (2002) Predicting reliable regions in protein sequence alignments. Bioinformatics 18: 306-314.
— uses information from near-optimal alignments

LumberJack
Lawrence CJ, Zmasek CM, Dawe RK, Malmberg RL (2004) LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. Bioinformatics 20: 1977–1979.
— identifies blocks that have their phylogenetic tree being most similar to that of the whole alignment

Noisy
Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF. (2008) Noisy: identification of problematic columns in multiple sequence alignments. Algorithms in Molecular Biology 3: 7.
— identification of phylogenetically uninformative homoplastic sites from compatibilities in a circular split system

trimAl
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972-1973.
— proportion of sequences with a gap, level of amino acid similarity, level of consistency across different (user-provided) alignments

SVM
Blouin C, Perry S, Lavell A, Susko E, Roger AJ. (2009) Reproducing the manual annotation of multiple sequence alignments using a SVM classifier. Bioinformatics 25: 3093-3098.
— support vector machine reproduces manual annotations from other alignments

BMGE
Criscuolo A, Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology 10: 210.
— calculates entropy-like scores weighted by similarity matrices

Aliscore
Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, Wägele JW, Misof B (2010) Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Frontiers in Zoology 7: 10.
— consensus profiles identify dominating patterns of nonrandom similarity

SR
Rajan V (2013) A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments. Molecular Biology and Evolution 30: 689-712.
— compatible subsplits define clusters of sites which are then removed based on evolutionary rate

October 26, 2014

17:30

Charles Darwin and Alfred Russel Wallace are usually credited with independently developing the idea that natural selection could be the important process by which new species arise, although history has apportioned most of the fame to Darwin alone.

In the first edition of his most famous book Darwin (1859) cited no sources, and credited no-one except Thomas Malthus as a source of ideas. He was criticized for this, and from the third edition onwards he provided a historical essay mentioning a few more names.

The basic issue is that the idea of natural selection had been "in the air" for more than half a century, but only with respect to within-species variation. It was Darwin and Wallace who took the leap to consider between-species variation, on the basis that there is no historical boundary defining species — all individuals trace their ancestry back through a whole series of ancestors, including those who existed before the origin of their current species. That is, phylogenies trace back to the origin of life not just to the origin of each species.

So, who were the people who published, however briefly, a comment noting the idea of within-species natural selection? Joachim Dagg, of the Natural History Apostils blog, has recently been writing a series of posts discussing many of those publications that contain a clear description of selection. Here I have provided a convenient overview, in time order, with links to Joachim's blog for those of you who want more information.



Joseph Townsend
  • (1786, republished in 1817) A Dissertation on the Poor Laws, by a Well-wisher to Mankind. London: Ridgways.
— a brief mention of selection in relation to the Poor Laws, not organic evolution, but he seems to have inspired Thomas Mathus (1798) Essay on the Principle of Population, the critical work cited by both Darwin and Wallace (Malthus does not write about heritable variation, and therefore does not cover selection)
Link 1 - Link 2

James Hutton
  • (1794) Investigation of the Principles of Knowledge and of the Progress of Reason, from Sense to Science and Philosophy. Volume 2. Edinburgh: Strahan & Cadell. [section 13, chapter 3]
— advocated the idea of what we now call microevolution, especially in relation to agriculture, and suggested natural selection as the mechanism
Link 1

William Charles Wells
  • (1813) An Account of a White Female, Part of Whose Skin Resembles that of a Negro. [talk]
  • (1818) Two Essays: One Upon Single Vision with Two Eyes; the other on Dew. [plus] An Account of a Female of the White Race of Mankind, Part of Whose Skin Resembles that of a Negro. Edinburgh: Archibald Constable.
— a talk read before the Royal Society of London in 1813, and apparently referenced by Adams, but not put into print until 1818 — discusses selection in relation to human skin color
Link 1 - Link 2

Joseph Adams
  • (1814) A Treatise on the Supposed Hereditary Properties of Diseases. London: J. Callow.
— does not actually use the expression "selection" but briefly describes the process in relation to climate-related human variation, tucked away in the notes
Link 1 - Link 2 - Link 3

Patrick Matthew
  • (1831) On Naval Timber and Arboriculture; with Critical Notes on Authors who have Recently Treated the Subject of Planting. Edinburgh: Adam Black.
— explicitly used the phrase "natural process of selection" in relation to the origin of timber varieties, with a discussion tucked away in an appendix — as noted by Joachim Dagg, Matthew explicitly included the possible origin of new species via selection, thus being a literal predecessor of Darwin and Wallace, although they appear to have been unaware of his work
Link 1 - Link 2 - Link 3

John C. Loudon
  • (1832) [Book review of] Matthew, Patrick: On Naval Timber and Arboriculture; with Critical Notes on Authors who have recently treated the Subject of Planting. The Gardener's Magazine 8: 702-703.
— a book review mentioning Matthew's idea of natural selection (he was the only contemporary commenter to do so) and noted it explicitly as being concerned with "the origin of species and varieties"
Link 1 - Link 2

Edward Blyth
  • (1835) An attempt to classify the "varieties" of animals, with observations on the marked seasonal and other changes which naturally take place in various British species, and which do not constitute varieties. The Magazine of Natural History 8: 40-53.*
  • (1836) Observations on the various seasonal and other external changes which regularly take place in birds, more particularly in those which occur in Britain; with remarks on their great importance in indicating the true affinities of species; and upon the natural system of arrangement. The Magazine of Natural History 9: 393-409.*
  • (1837) On the psychological distinctions between man and all other animals; and the consequent diversity of human influence over the inferior ranks of creation, from any mutual or reciprocal influence exercised among the latter. The Magazine of Natural History, new series, 1: 1-9.*
— discusses the effects of artificial selection, but describes the process in nature as restoring organisms in the wild to their archetype (rather than forming new species)
Link 1

Herbert Spencer
  • (1852) A theory of population, deduced from the general law of animal fertility. Westminster Review 57: 468-501.
— published his article in order to show that the adaptedness or fitness of organisms results from the principle discussed by Malthus — Spencer later coined the expression "survival of the fittest" as a synonym of natural selection (in 1862)
Link 1


* Full title: The Magazine of Natural History and Journal of Zoology, Botany, Mineralogy, Geology, and Meteorology

October 21, 2014

22:30

Phylogenomics, the idea of applying genomic data to phylogenetic studies, has been around for quite a while now (Eisen 1998), although it was probably Rokas et al. (2003) who drew the first widespread attention among phylogeneticists. Molecular phylogenetics started off using the sequence of a single locus (often small-subunit rRNA) as the data, and slowly progressed from there to multiple loci. Currently, it is considered good practice to use half-a-dozen loci, sampling the main genomes (nucleus, mitochondrion, plastid); and genomics offers the possibility of a fast and cost-effective means of generating large amounts of multi-locus sequence data.


Review papers are beginning to appear based explicitly on next-generation sequencing (NGS), such as those of Lemmon & Lemmon (2013) and McCormack et al. (2013), replacing the earlier work of Philippe et al. (2005), and there are suggestions for how phylogenetics analyses might need to change in response to NGS data (Chan and Ragan 2013). These all treat phylogenomics as being very similar to traditional molecular phylogenetics, in the sense that many people are expecting phylogenomics to provide tree-like resolution of questions that remain unresolved with the current smaller datasets. In the words of Rokas et al. (2003), phylogenomics is intent on "resolving incongruence in molecular phylogenies". That is, incongruent gene trees are seen as the major obstacle to be overcome by phylogenetics data analysis (see also Jeffroy et al. 2006).

However, this might be a naive expectation. After all, the existing phylogenetic conflicts are there for a reason. If we cannot resolve certain parts of organismal history in terms of a phylogenetic tree when we use the current levels of multi-locus data (say

October 19, 2014

16:30

Some time ago I wrote a blog post about The bourbon family forest, which contained a collection of trees that, rather than being genealogical trees, instead showed the corporate ownership of American whiskey.

Here is a similar arrangement for "the six companies that make 50% of the world's beer", produced by David Yanofsky at the Quartz blog. As before, the vertical axis is actually a time scale, but the trees are only marginally family trees in the genealogical sense. Note that there is a reticulation between two of the trees for the "Scottish & Newcastle" entry, although this was apparently followed immediately by a subsequent divergence.


Nevertheless, roughly the same sort of information could actually be presented as proper genealogies. Here is an example form Philip Howard's blog, restricted to American beer. Note that the genealogies refer to the joining of branches through time, rather than their splitting. There are two reticulation events, one of which also refers to the "Scottish & Newcastle" entry.


It is also worth noting the use of other types of network by Philip Howard, to look at:

October 14, 2014

22:30

Periodically, mathematicians and other computationalists produce lists of what they refer to as "Open Problems" in their particular field. Phylogenetics is no exception. We have had a few on this blog before today (e.g.  An open question about computational complexity; Phylogenetic network Millennium problems).

I thought that I should draw your attention to the fact that last year, Barbara Holland produced a few of her own (2013. The rise of statistical phylogenetics. Australian and New Zealand Journal of Statistics 55: 205-220). These are:

Open problem 1: What is the natural analogue of a confidence interval for a phylogenetic tree?

Open problem 2: What are useful residual diagnostics for phylogenetic models?

Open problem 3: What makes a good phylogenetic model?

Open problem 4: Should DAGs be acceptable objects for inference or should network methods be restricted to exploratory data analysis?

It is obviously the latter problem that is of most interest to us here:
DAGs [directed acyclic graphs] can be constructed by beginning with a good tree and then progressively adding edges until the fit between the model and the data is deemed good enough or there is no sufficient improvement in fit by continuing to add edges. The trouble with using DAGs to define mixture models is that this approach doesn’t actually capture the biological processes of interest within the model. The sorts of things we’d like the data to tell us are what is the relative rate of recombination events or hybridisation events to mutation events or speciation events. The danger with using phylogenetic networks in an "add an extra edge until the fit is good enough" approach is that by giving ourselves the capacity to explain everything we risk explaining nothing. At some point have we stopped doing inference and got back to just summarising our data? In phylogenetics we rely on our models for their explanatory power — in the context of network evolution we need to make careful decisions about what biological processes should be included within the model such that inferences about reticulate (non-treelike) processes of evolution can be brought within the realm of stochastic uncertainty rather than being left as a source of inductive uncertainty. This is not a straightforward task, and will require the collaboration of evolutionary biologists and statisticians.One of the principal issues here is that it is almost impossible to consistently distinguish one reticulation process from another based on the structure of the resulting network. These processes all produce gene flow in the biological world, and they all appear as reticulations in the graphical representation of a network. In practice, phylogenetic analysis may boil down to only two biological processes in the model (vertical gene inheritance and horizontal gene flow), followed by biologists trying to sort out the details with post hoc analyses. Deep coalescence and gene duplication are part of the vertical inheritance, while hybridization, introgression, horizontal gene flow and recombination are part of gene flow. It would be nice to think that this model would simplify network analyses.

October 12, 2014

16:30

Some years ago Larisa Lehmer, Bruce Ragsdale, John Daniel, Edwin Hayashi and Robert Kvalstad published a medical report about an ingested plastic bag closure caught in someone's colon (Plastic bag clip discovered in partial colectomy accompanying proposal for phylogenic plastic bag clip classification. BMJ Case Reports 2011). This sounds quite painful.


What is more interesting, though, is that the report was accompanied by a phylogenetic and taxonomic evaluation of plastic ties in general, which the authors named Occlupanids.


Note that the proposed morphological changes in the phylogeny match Cope's Rule of phyletic size increase, as discussed in a previous blog post (Steven Jay Gould was wrong).


Shortly afterwards, one of the authors, John Daniel, set up a web page with a more detailed analysis, under the guise of the Holotypic Occlupanid Research Group (HORG).

Among a lot of other interesting information, there is a revised phylogenetic analysis.


Given the data, it seems fairly clear that the genealogical relationship among these objects is reticulate, and that the trees should thus actually be networks. This follows from the simple fact that these phylogenies are rather uninformative (they are bushes showing a few character transformation series). Also, note that contemporary taxa are ancestors, so that the diagrams are more like population networks than species networks.

These ties are used for packets of sliced bread (a relatively recent invention), and so there has been an explosion of Occlupanid forms as they occupy a new adaptive zone. This is a classic instance of recent speciation that is not yet complete. Occlupanids have now reached pest proportions, except where governments have instituted erradication programmes (such as Europe, where they are no longer found).

Part of the difficulty of analysis is that the objects shown constitute only a small part of the known diversity of Occlupanids (e.g. see this photo and this one). There are a number of manufacturers, and their products constitute separate historical lineages. Morphological features have been transferred from one lineage to another, which is a classic case of reticulate history that has not been taken into account in the above phylogenies.

Indeed, the HORG page is not the only detailed web resource about bread ties — see also the now-defunct but fascinating Transactoid page.