More literature on trees and networks

In a previous blog post I listed some of the Books about the history of trees and networks. While I mentioned a review paper by Pascal Tassy, I did not list his earlier book on the subject, which actually pre-dates all of the books listed.

  

• Tassy, Pascal (1991) L'Arbre à Remonter le Temps. Paris: Christian Bourgois Éditeur. First edition. (1998) Paris: Diderot Éditeur. Second edition.

In French; paperback. A conceptual history of phylogenetics up to the end of the 20th century. Covers the development of ideas for the general public, with a few illustrations. Networks are barely mentioned.

In this context, there are also other sources that illustrate at least part of the history of trees and networks (along with textbooks covering systematics). These include:

Archibald, J. David (2009) Edward Hitchcock's pre-Darwinian (1840) "Tree of Life". Journal of the History of Biology 42: 561-592.

Bigoni, Francesca and Barsanti, Giulio (2011) Evolutionary trees and the rise of modern primatology: the forgotten contribution of St. George Mivart. Journal of Anthropological Sciences 89: 93-107.

Coggon, Jennifer (2002) Quinarianism after Darwin’s Origin: the circular system of William Hincks. Journal of the History of Biology 35: 5-42.

Gaffney, Eugene S. (1984) Historical analysis of theories of chelonian relationship. Systematic Zoology 33: 283-301.

Gontier, Nathalie (2011) Depicting the Tree of Life: the philosophical and historical roots of evolutionary tree diagrams. Evolution: Education and Outreach 4: 515-538.

Lam, Herman J. (1936) Phylogenetic symbols, past and present (being an apology for genealogical trees). Acta Biotheoretica 2: 153-194.

Nelson, Gareth and Platnick, Norman (1981) Systematics and Biogeography: Cladistics and Vicariance. Columbia Uni. Press, New York.

O’Hara, Robert J. (1988) Diagrammatic classifications of birds, 1819-1901: views of the natural system in 19th-century British ornithology. In: H. Ouellet (ed.) Acta XIX Congressus Internationalis Ornithologici, pp. 2746-2759. National Museum of Natural Sciences, Ottawa.

O’Hara, Robert J. (1991) Representations of the natural system in the nineteenth century. Biology and Philosophy 6: 255-274.

O'Hara, Robert J. (1996) Trees of history in systematics and philology. Memorie della Società Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano 27: 81-88.

Ragan, Mark A. (2009) Trees and networks before and after Darwin. Biology Direct 4: 43.

Stevens, Peter F. (1984) Metaphors and typology in the development of botanical systematics 1690-1960, or the art of putting new wine in old bottles. Taxon 33: 169-211.

Tassy, Pascal (2011) Trees before and after Darwin. Journal of Zoological Systematics and Evolutionary Research 49: 89-101.

Willmann, Rainer (2003) From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe. Cladistics 19: 449–479.

The Tree of Architecture

The following diagrams are taken from the book A History of Architecture on the Comparative Method for the Student, Craftsman, and Amateur. This book is considered to be "a canonical text that has played a formative role in the education of generations of architects" because it really does "cram everything into a single volume". The first edition of the book appeared in 1896, with the 20th edition appearing in 1996.

The first picture is from the 5th edition (1905), and the second one is from the 16th edition (1954).

As noted in the first figure, these trees purport to show the "evolution" of the various architectural styles. However, they do no such thing.

At the base of the tree trunk is a set of individual architectural styles that apparently led nowhere, while at the crown of the tree several styles are repeated. Each of the latter styles exist on two side-branches from the main trunk, each pair connected by vertical tendrils. So, this is a network, at least. However, the meaning of this network is not immediately obvious. Indeed, even a short perusal of the diagram should lead you to the idea that the meaning is contained more in cultural bias than in the actual history of architecture.

The history of the book itself is somewhat complex. The first edition was written by the father and son team of Banister Fletcher & Banister F. Fletcher. Subsequent editions were revised by Banister F. Fletcher (the son), with the 6th edition (1921) being rewritten by Fletcher and his first wife (who got no credit, even though the father's name was then dropped). After Fletcher's death in 1953, the 17th edition (1961) was revised by R.A. Cordingley, the 18th (1975) by James Palme, the 19th (1984) by John Musgrove, and the 20th (1996) by Dan Cruickshank. The tone and arrangement of the book was changed with each edition.

The tree has been analyzed in detail by Gülsüm Baydar Nalbantoglu (1998. Toward postcolonial openings: rereading Sir Banister Fletcher's "History of Architecture". Assemblage 35: 6-17). She notes the following:

Until the fourth edition of 1901, A History of Architecture had been a relatively modest survey of European styles. The fourth edition, however, appeared with an important difference: this time the book was divided into two sections, "The Historical Styles", which covered all the material from earlier editions, and "The Non-Historical Styles", which included Indian, Chinese, Japanese, Central American, and Saracenic architecture. 

The "Tree of Architecture" has a very solid upright trunk that is inscribed with the names of European styles and that branches out to hold various cultural / geographical locations. The nonhistorical styles, which unlike others remain undated, are supported by the "Western" trunk of the tree with no room to grow beyond the seventh-century mark. European architecture is the visible support for nonhistorical styles. Nonhistorical styles, grouped together, are decorative additions, they supplement the proper history of architecture that is based on the logic of construction. 

In the posthumously published seventeenth edition of 1961, the two parts were renamed "Ancient Architecture and the Western Succession" and "Architecture in the East", respectively. The nineteenth edition of 1987, on the other hand, consisted of seven parts based on chronology and geographical location. Cultures outside of Europe included "The Architecture of the Pre-Colonial Cultures outside Europe" and "The Architecture of the Colonial and Post-Colonial Periods outside Europe".

That is, "architecture" for the Banisters was defined as being about a building's construction, not its decoration. European cultures focused on construction, and they developed their styles through time. Other cultures focused on decoration, and were therefore not a proper part of architecture, and had no historical development. This is what the tree attempts to show.

This cultural bigotry was corrected in the final few editions of the book (after the Fletchers were no longer involved), where all architectural styles were considered more-or-less equal.

Rivers of Life, instead of trees

In an earlier blog post, I discussed some of the evocative Metaphors for evolutionary relationships, particularly reticulating ones.

In that post I listed the concept of a "braided river", and mentioned a 1994 paper by John Moore as my earliest source for the image. However, the metaphor actually goes back more than 100 years earlier. It occurs as the central metaphor in this quite remarkable book on comparative religion:

Forlong, J.G.R. (1883) Rivers of Life: or Sources and Streams of the Faiths of Man in All Lands, Showing the Evolution of Faiths from the Rudest Symbolisms to the Latest Spiritual Developments. 2 vols. Bernard Quaritch: London.

James George Roche Forlong was a Scottish engineer serving in the British army that occupied India during the 19th century. He apparently had a life-long interest in comparative religion, and his book arose from his personal experience of non-Christian religions (facilitated by his knowledge of several languages). The book involves a serious re-interpretation of the evolutionary history of world religions, as a series of six inter-connecting rivers running from ancient times into the modern world, each river representing a different type of worship.

The illustrative chart that accompanies the book can be viewed here. A low-resolution copy is shown below.

Books about the history of trees and networks

The standard references for the conceptual history of phylogenetic trees and networks are:

• Ragan, Mark A. (2009) Trees and networks before and after Darwin. Biology Direct 4: 43.
• Tassy, Passcal (2011) Trees before and after Darwin. Journal of Zoological Systematics and Evolutionary Research 49: 89-101.

Over the past 20 years, a number of books have appeared that expand upon this topic, which it is worthwhile to list here.

• Barsanti, Giulio (1992) La Scala, la Mappa, l'Albero: Immagini e Classificazioni Della Natura Fra Sei e Ottocento. Firenze: Sansoni Editore.

In Italian. A conceptual history of classification up to the time of Haeckel, and the beginning of phylogenetics. Covers the development of ideas and images equally. Networks are treated as "maps".

This is expanded from a preceding review article: (1988) Le immagini della natura: scale, mappe, alberi 1700-1800. Nuncius 3(1): 55-125. 

• Stevens, Peter F. (1994) The Development of Biological Systematics: Antoine-Laurent de Jussieu, Nature, and the Natural System. New York: Columbia University Press.

A conceptual history of classification and phylogenetics, mainly as related to plants. Focuses on the early development of ideas within biosystematics, with accompanying illustrations. Networks are effectively treated as variants of trees.

• Pietsch, Theodore W. (2012) Trees of Life: a Visual History of Evolution. Baltimore: Johns Hopkins University Press.

A richly illustrated history of trees, with a few networks. Focuses on the illustrations, with some accompanying text. The best source to see what people have drawn in the way of trees, but weaker on networks.

• Minaka, Nobuhiro, and Sugiyama, Kunihiko (2012) Phylogeny Mandala: Chain, Tree, and Network. Tokyo: NTT Publishing.

In Japanese. Covers the development of the tree metaphor (with a few networks), as related to pedigrees, phylogenies, and knowledge representation in general. The breadth of the topic is indicated in the "mandala" of the title, which is "a generic term for any diagram, chart or geometric pattern that represents the cosmos metaphysically or symbolically".

• Archibald, J. David (2014) Aristotle's Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. New York: Columbia University Press.

A conceptual history of trees, with a few networks. Focuses on the development of the ideas, with accompanying illustrations. Starts with pedigrees, and proceeds from there to phylogenies. The best coverage of phylogeny concepts, but explicitly treats networks as "trees with reticulations".

See also this later post:
More literature on trees and networks

One of the "joys" of blogging

A few years ago I wrote a few guest posts on the Guest Blogge at the Scientopia site (as described in the post Moonlighting at Scientopia). That blog has been inactive since 2013. Unfortunately, gremlins have since crept into the system, and all of my posts are no longer credited to me. The by-line for all of the posts is now "Christina Pikas" rather than "David Morrison". She is the author of a different blog at Scientopia, Christina's LIS Rant.

I hope that this sort of thing does not happen with my online research publications, as well !

Another early noble pedigree

In a few recent blog posts I have discussed the early history of pedigrees, noting that they were usually presented as descent trees (with an ancestor at the top and the descendants below), although some later ones reversed this arrangement. This does not match our description of them as "family trees", of course, because the root of the pedigree is at the top.

I present here another early example, if for no other reason than that I have spent the past hour trying to decipher it. It is a Genealogy of the Saxon Dynasty, particularly the Ottonians. The picture is from the Chronica Sancti Pantaleonis, produced by the Benedictine monastery of Saint Pantaleon in Cologne in 1237 CE, which was itself based on the Chronica Regia Coloniensis [Royal Chronicle of Cologne], first compiled about 1177 CE in Michaelsberg Abbey, Siegburg.

Heinricus rex and Methildis regina are the founding couple in the double circle. Henry the Fowler did not himself become Holy Roman Emperor, but he created a situation where his descendants could do so, and did. They are numbered in the next diagram in the order in which they ruled. Number 9 is missing, this being Lothair II, who was not part of the family.

There are several things to note:

• The interesting use of illustrative medallions, which seems to have been not uncommon at the time.
• The consequent difficulty the illustrator has had in fitting the pedigree into the page, even though most of the descendants have been left out.
• The pedigree is explicitly designed to establish noble ancestry, but females are included even when they are not in the direct line of descent.
• The rulers nominally change families, from the Ottonian to the Hohenstaufen to the Salian dynasties, as a result of females in the direct line of descent.
• Number 4 is Henry II, who made an appearance in an earlier post as the husband of Cunigunde of Luxembourg (The first royal pedigree).
• Number 11 is Frederick I Barbarossa, who also made an appearance in an earlier post (Does it matter which way up a tree is drawn?).
• The latter two points make it clear that the earliest written pedigrees were all closely related genealogically, and involved the attempts by certain parts of the German nobility to take control of the Holy Roman Empire, consisting at that time of what is now mostly Germany and Italy. Family descent was an important part of establishing who got to rule next.

Anna Maria Redfield — the first woman to draw a tree of biodiversity

It might be nice to live in a world where the mere fact that you are male or female does not attract attention to you within your profession. But while we are waiting for that day, you might like to ask yourself about women in systematics. David Archibald suggests that the tree produced by Anna Maria Redfield is "the first tree – creationist or evolutionary – by a woman and may well be the only such tree by a woman until well into the twentieth century."

Anna Maria Redfield (1800-1888, née Treadwell) is described in these terms by Michon Scott's Strange Science web site:

Born at the dawn of the 19th century, Anna Maria Redfield earned the equivalent of a master's degree from the first U.S. institution of higher learning devoted to female students: Ingham University, and became perhaps the first woman to design a tree-like diagram of animal life. Although tree-like, her diagram didn't show common ancestry but instead showed the "embranchements" established by Georges Cuvier: vertebrates, arthropods, mollusks, and "radiata" (today classified as cnidarian and echinoderm phyla). To be fair, this diagram was published before Darwin's Origin of Species but later editions of her work made no mention of evolution either. Instead, she wrote about our simian cousins, "The teeth, bones and muscles of the monkey decisively forbid the conclusion that he could by any ordinary natural process, ever be expanded into a Man." Still, her elegant work is great fun to behold even now.

The tree-like diagram (shown in miniature above) was a wall chart (1.56 x 1.56 m) called A General View of the Animal Kingdom, published in 1857 by E.B. and E.C. Kellogg, New York. It is heavily illustrated with images of the taxa, their names, and brief notes: eg. "Man alone can articulate sounds, and is capable of improving his faculties or advancing his condition". Only three lithograph copies of the original tree are now known, one of which was sold at auction by Christie's in 2005 for £7,200.

The following year the same publishers produced a companion volume to the chart, called Zoölogical Science, or Nature in Living Forms: Adapted to Elucidate the Chart of the Animal Kingdom, and designed for the higher seminaries, common schools, libraries, and the family circle (1858, reprinted 1860, 1865, 1874). A copy is available in the Biodiversity Heritage Library. Only 57 original copies of the book are now known.

This book of 743 pages is richly illustrated, the artist being unacknowledged in the first edition but credited as E.D. Maltbie from then on. (He is presumably responsible for the chart as well.) The book has the frontispiece shown below, which is an edited version of the base of the tree.

Redfield and her chart have recently been discussed by Susan Butts (2011. Conservation of the Anna Maria Redfield wall chart: A General View of the Animal Kingdom. Society for the Preservation of Natural History Collections Newsletter 25(1): 18-19). She notes:

The wall chart is a masterpiece, with intricate and accurate illustrations of representatives of the animal kingdom portrayed as a Tree of Life, which illuminates the relationships of the major groups of organisms. It is an important document in the study of biology and in the pioneering work of women in science. The wall chart has eloquent phrases, which express a Victorian humanistic view of nature (often intermingled with anthropomorphism, biblical overtones, and the biological superiority of humans).

Redfield's views on evolution are clear from her book, indicating that the relationships shown represent affinity not evolution:

There is no evidence whatever that one species has succeeded, or been the result of transmutation of a former species.

Butts notes that unfortunately Redfield "remains a relatively minor and poorly recorded figure in the history of women in science, let alone biological and evolution studies in general."

The kabbalistic Tree of Life is a network

The Tree of Life and the Tree of Knowledge are images that have appeared in many cultures throughout the world. They are often combined as a cosmic or world tree, with the tree of knowledge supporting the heavens and earth and the tree of life connecting all living beings. However, the word "tree" is obviously rather nebulous in these images, and it can take many forms.

In the christian Bible these trees appear in the garden of Eden in a more restricted form as the Tree of Eternal Life and the Tree of Knowledge of Good and Evil. Even here, though, it is not clear whether they are one and the same tree. For example, only one tree is mentioned in the book of Revelation, when promising a new Eden.

The Tree of Knowledge was co-opted in Medieval times as a symbol of learning, and a metaphor for arranging all human knowledge, the Arbor Scientiae (see Relationship trees drawn like real trees). This idea was adopted by biology in the 1700s, where trees were used as metaphors for the relationships among biological species. In modern parlance, these depicted affinity or phenetic relationships, and so they represented knowledge (not life). In the mid 1800s Charles Darwin (in the Origin of Species) took this pre-existing tree idea and instead made it represent evolutionary relationships among species. In the process he re-named it the Tree of Life, thus once again uniting the Tree of LIfe and the Tree of Knowledge. We have been stuck with the ToL name ever since.

At about the same time as the rise of the Arbor Scientiae, a combined Tree of Life and Tree of Knowledge also appeared as the central mystical symbol of the Kabbalah of esoteric Judaism, consisting of the 10 Sephirot (enumerations). It is shown above in its full modern form. This is a reinterpretation of the Hebrew Bible, conceptually representing a list the attributes of God (how God emanates).

In the Kabbalist view, both of the trees in the biblical garden of Eden were alternative perspectives of the Sephirot. The 10 Sephirot are arranged into three columns, with 22 Paths of Connection. As a tree, it has roots above and branches below. To quote Wikipedia:

Its diagrammatic representation, arranged in 3 columns/pillars, derives from Christian and esoteric sources and is not known to the earlier Jewish tradition. The tree, visually or conceptually, represents as a series of divine emanations God's creation itself ex nihilo, the nature of revealed divinity, the human soul, and the spiritual path of ascent by man. In this way, Kabbalists developed the symbol into a full model of reality, using the tree to depict a map of Creation.

My main point here is that by combining two conceptual trees this icon is clearly a network, unlike most other conceptual trees such as the dichotomous Tree of Knowledge.

The Kabbalah started without an image, being described solely in words. The diagram of the Tree used by modern Jewish Kabbalists is usually based on the diagram published in the print edition of Rabbi Moses Cordovero's Pardes Rimonim from 1591 [composed 1548], and sometimes called the "Safed Tree". It is shown in the next figure.

One of the earliest illustrations comes from the 1516 Portae Lucis of Paolo Riccio, a Latin translation of Joseph ben Abraham Gikatilla's most influential kabbalistic work, Sha'are Orah (Gates of Light) from the 1300s. It is shown in the next figure.

There are actually two modern version of the Kabbalah. The one shown here in the first illustration has the crossing diagonals lower down than does the one shown in the second illustration. The one with two diagonals at the bottom is an earlier version that is still favoured by Hermetic Kabbalists. Both made their first public appearance in the Pardes Rimonim.

Does it matter which way up a tree is drawn?

To a modern phylogeneticist the answer to this question is obviously "no". Phylogenetic trees occur in the literature with their root at the top, the left or the bottom, and more rarely on the right. The graph has the same interpretation no matter where the root is placed, as all of the edges are implicitly directed away from the root. The tree can even be circular, with the root in the centre and the tree radiating outwards.

However, this was not always so for genealogies, and indeed this freedom seems to be a product of the past 200 years or so. The history of tree orientation has been discussed in detail by Christiane Klapisch-Zuber (1991. The genesis of the family tree. I Tatti Studies in the Italian Renaissance 4: 105-129).

Originally, genealogies were drawn with the root at the top, as shown in previous blog posts: The first royal pedigree, and The first known pedigree of a non-noble family. These pedigree trees (ie. genealogies of individuals) have a particular ancestor at the root of the "tree", so that the tree expands forwards in time down the page, to increasing numbers of descendants at the leaves (ie. a "descent tree"). This made linguistic sense, because people "descended" from the ancestor down the page. In European languages pages are read top to bottom, and so the natural reading order was the same as the time sequence.

However, this arrangement makes no sense if one refers to the graph as a "tree". Trees have their root at the bottom, not the top. Trying to draw the pedigree as a tree while retaining the original orientation could lead to unusual results, as shown in the first figure, from the end of the 1300s CE (from Universitätsbibliothek, Innsbruck, ms. 590, folio 116r). This is actually an Arbor Consanguinitatis rather than an empirical pedigree — it shows the various relatives of a nominated individual (the man pictured in the center) and their degree of relationship to that person. These diagrams have been used to compute which relatives can marry without committing incest, or which can inherit if a person dies intestate. Jean-Baptiste Piggin, at his web site Macro-Typography, has noted that the earliest known examples are from the 400s CE.

In order to match a real tree, the genealogy has to be read from bottom to top. This implies an ascent through time, instead, with a spreading out of the family upwards through time.

The first known empirical pedigree in which the ancestor is at the base is the Genealogia Welforum, the pedigree of a dynasty of German nobles and rulers (Dukes of Bavaria, and Holy Roman Emperors, successors of the Carolingians). The earliest known example, drawn as part of the Historia Welforum [Welf Chronicle], is shown in the second figure (from Hessische Landesbibliothek, Fulda, ms. D.11 folio 13v). The original text version of the pedigree is dated 1167-1184 CE, with the miniatures added sometime from 1185-1191 CE.

Clearly, this diagram is only sketchily like a tree, with many of the people placed along the main trunk, and medallions hanging off for other relatives. This seems to arise from the pedigree's origin as prose, and the subsequent literal illustration of that prose.

The ancestor is labeled "Welf Primus", and he apparently lived in the time of Charlemagne (the best known of the Carolingian dynasty). The empty space at the top of the chart was apparently intended for a picture of Emperor Frederick I Barbarossa, of the House of Hohenstaufen. The woman at the top right is Henry the Black's daughter Judith, who was the mother of Barbarossa. Intriguingly, the final bend of the Welf trunk to the left, combined with Barbarossa at the top, seems to imply that it is the descendants of Barbarossa who continue the Welf lineage, rather than those bearing the Welf name.

Historically, it seems to have been the proliferation, after about 1200 CE, of illustrations of the biblical Tree of Jesse that popularized the idea of "pedigrees as trees". The next figure shows such a tree from c. 1320 CE (from a Speculum Humanae Salvationis manuscript, Kremsen ms. 243/55). Jesse lies at the base of the tree, and the tree actually arises from him. His descendants then ascend to Jesus, shown at the crucifixion, with Heaven illustrated at the top. The tree thus uses Christ's pedigree to symbolize the ascent of humans to heaven (via his crucifixion), rather than simply the descent of humans through time. That is, the tree correctly represents ascent (as well as descent).

This leaves us contemplating just when we added the final twist to the iconography, by putting a single descendant at the base of the tree, and having the ancestors branching out above as leaves (ie. an "ascent tree"). This means that time flows from the top to bottom of the figure, even though the tree is oriented from bottom to top. This is quite illogical as an analogy, given that the base of a real tree is the origin of its growth (see Goofy genealogies). This particular iconography is not used for phylogenies but is very commonly used for pedigrees.

I have no idea when this first occurred. However, David Archibald (2014. Aristotle's Ladder, Darwin's Tree: The Evolution of Visual Metaphors for Biological Order. Columbia Uni Press) draws attention to a very tree-like pedigree of Ludwig (Louis III), fifth Duke of Württemberg, from the late 1500s, shown here as the final figure (from Württembergisches Landesmuseum, Stuttgart). Ludwig is at the base of the tree, and ironically he had no descendants (although he married twice). His parents are above him in the tree (Christoph, Duke of Württemberg, to the left, and Anna Maria von Brandenburg-Ansbach, to the right), followed by four further ancestral generations. Note the leaves and hanging fruits, which highlight the tree metaphor.

Update to Charles Darwin's unpublished tree sketches

This blog has previously reproduced some of the unpublished sketches by Charles Darwin that involve tree-like relationships:

• Part 1 — collected notebooks and notes
• Part 2 — a letter to Charles Lyell
• Part 3 — a reconstruction from one of his books

Recently, the first two of these posts have been updated.

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

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

The first known pedigree of a non-noble family

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

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

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

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

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

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

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

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

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

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

The first royal pedigree

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

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

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

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

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

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

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

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

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

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

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

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

An outline history of phylogenetic trees and networks

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 August 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

How confusing were the first written genealogies?

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.

The first infographic was a genealogy (c. 400 AD)

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 Old and 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), and elsewhere there are 13 simultaneous appearances of the same person in two places (to avoid complicated connections; see Reducing networks to trees).

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).

[Note: There is an update about the reconstruction in this blog post: The origin of an idea: reducing networks to trees]

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.

Massive citations of bioinformatics in biology papers

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 partially 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
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Bioinformatics 19, 1572–1574 (2003).

Predecessors of Charles Darwin

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 (related to heritable variation within species), 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 [until Matthew advertised it to the world after Darwin published his book: (1860) Nature's law of selection. Gardeners' Chronicle and Agricultural Gazette (7 April): 312-313]
Link 1 - Link 2 - Link 3 - Link 4 - Link 5
You can learn more about him at The Patrick Matthew Project.

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 known 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