Tuesday, May 22, 2012

Networks of affinity rather than genealogy

To date, published phylogenetic networks have been of two distinct types: (i) non-directional networks showing affinity among taxa, and (ii) directed networks showing genealogical relationships among taxa. In previous posts I have discussed what are apparently the first two networks of the latter type (1755 and 1766), which illustrate hybridization relationships among domesticated breeds / cultivars.

Today, I wish to point out that the vast majority of the networks published from 1750-1900 were actually of the first type. Indeed, the third explicitly genealogical network appears to date from 1888, whereas more than a dozen networks of the affinity type are known.

There is little point in trying to formally define what biologists have meant by "affinity", since it seems to vary greatly. However, it has usually referred to some sort of attraction or connection between taxa (and their characteristics), sometimes described as similar to the laws regulating the combinations of elements that form compounds in chemistry. It has usually been the basis of some sort of "natural system" of classification (as opposed to some artificial grouping of organisms, eg. utilitarian): "an arrangement that groups organisms of the same kind more closely to each other than either of them is to any organism of another kind" (Cuvier 1817). In modern terminology, affinity originally included evaluation of both homology and analogy, and therefore affinity was a more general relationship than evolutionary history, and it does not necessarily correlate well with it. Genealogy also appears to be a much looser form of connection between taxa than was originally imagined by some of the seekers of affinity connections.

The important point here, however, is that affinity was usually imagined as being multi-facetted, so that any diagram of affinities showed multiple connections among the taxa: relationships between groups were very definitively reticulating, and it was considered impossible to form a linear series because emphasizing a relationship in one direction necessarily entailed simultaneously breaking relationships in another (de Jussieu 1843; see Stevens 1994 p. 98). Hence, the diagrams were networks rather than trees. (Trees have a long history as a metaphor for arranging human ideas, but not for representing affinity; Gontier 2011.) Indeed, network diagrams may out-number tree illustrations from 1750-1900 (Stevens 1994, Ragan 2009, Tassy 2011), if one excludes dichotomous keys for the identification of taxa. These network diagrams lacked any directionality, as affinities between taxa were considered to be symmetrical (unlike genealogical relationships). Notably, when interpreting their diagrams the authors either fail to mention genealogy, or they implicitly or explicitly exclude it.

The importance that I see in these historical networks is that they match closely the modern idea of unrooted data-display networks. They are not a form of exploratory data analysis, of course, because they were intended to express the author's ideas about biological relationships rather than to reveal previously unquantified patterns in the data; but they certainly are not rooted evolutionary networks. Thus, the dichotomy that I see in contemporary usage of the expression "phylogenetic network" apparently has a long history, and it needs to be recognized. (There are also all sorts of other historical representations of reticulate relationships, some intended to be solid figures with faces, others were interlocking circles or radiating hexagons or nested ovals, and some were explicitly referred to as maps. Most of these could be converted to a network representation.)

Affinity Networks

[Note: the following list has been updated in a later blog post: Affinity networks updated]

Here is a list of the publications from 1750-1900 containing affinity networks that I know about. I have indicated my source, and I have also linked to an online copy of the diagram. (I have extracted some of the figures from Gallica, Google Books or the Biodiversity Heritage Library, where they are otherwise unavailable.)

  • 1774 Johann Philipp Rühling "Ordines Naturales Plantarum Commentatio Botanica" [Ragan Fig. 7, Stevens Fig. 12]
  • 1783 Johann Hermann "Tabula affinitatum animalium" [Ragan Fig. 8]
  • 1802 August Johann Georg Carl Batsch "Tabula Affinitatum Regni Vegetabilis" [Ragan Fig. 9]
  • 1825 Adrien-Henri-Laurent de Jussieu "Sur le groupe des Rutacées." Mémoires du Muséum d'Histoire Naturelle 12: 384-542 [Ragan Fig. 13, Stevens Fig. 10]
  • 1826 Augustin-Pyramus de Candolle "Mémoires sur la Famille des Légumineuses. Quatrième Mémoire. Division de la Famille des Légumineuses" [Stevens Fig. 14]
  • 1841 Eduard Fenzl "Darstellung und Erläuterung vier minder bekannter, ihrer Stellung im natürlichen Systeme nach bisher zweifelhaft gebliebener, Pflanzen-Gattungen." Denkschriften der Königlich-Baierischen Botanischen Gesellschaft zu Regensburg 3: 153-270 [Stevens, figure]
  • 1843 Adrien-Henri-Laurent de Jussieu "Monographie de la famille des Malpighiacées." Archives du Muséum d'Histoire Naturelle 3: 5-151 [Stevens, figure]
  • 1872 Alexander Andrejewitch von Bunge "Die gattung Acantholimon Boiss." Mémoires du Academie Imperiale des Sciences de St Pétersbourg Série 7 18(2): 1-72 [Stevens Fig. 19]
  • 1873 George Bentham "Notes on the classification, history, and geographical distribution of Compositae." Botanical Journal of the Linnean Society 13: 335-577 [Stevens Fig. 20]
  • 1888 Ferdinand Albin Pax "Monographische übersicht über die arten der gattung Primula." Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 10: 75-241 [Stevens, there are 15 figures]
  • 1889 Julien Vesque "Epharmosis, sive Materiae ad Instruendam Anatomiam Systematis Naturalis. Pars Prima. Folia Capparearum" [Stevens, figure]
  • 1889 Julien Vesque "Epharmosis, sive Materiae ad Instruendam Anatomiam Systematis Naturalis. Pars Secunda. Genitalia Foliaque Garciniearum et Calophyllearum" [Stevens, figure]
  • 1890 Franz Georg Philipp Buchenau "Monographia Juncacearum." Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 12: 1-495 [Stevens, figure]
  • 1893 Georg Klebs "Flagellatenstudien, Theil II." Zeitschrift für Wissenschaftliche Zoologie 55: 353-445 [Ragan Fig. 26]
  • 1895 Olga Tchouproff "Quelques notes sur l'anatomie systématique des Acanthacées." Bulletin de l'Herbier Boissier 3: 550-560 [Stevens, figure]
  • 1896 Nicolai Ivanovich Kusnezov "Subgenus Eugentiana Kusnez. generis Gentiana Tournef." Acta Horti Petropolitani 15: 1-507 [Ragan, Stevens Fig. 18]
  • 1898 Émile Constant Perrot "Anatomie comparée des Gentianacées." Annales des Sciences Naturelles: Botanique, Série 8, 7: 105-292 [Stevens, figure]

It seems important to note that these affinity networks continued to be produced after 1859, when phylogenetic trees in the modern context were introduced by Charles Darwin (ie. internal nodes represent ancestors and the leaves represent existing taxa). Clearly, affinity and genealogical inheritance did not become synonymous concepts until much later.

Also, other early authors described biological relationships as being like a reticulating network, without any necessarily genealogical interpretation, even though they apparently did not themselves produce network diagrams. (It seems that only 5 of the first 11 historical references to network relationships provided a diagram.) Here are some known examples (with source):

  • 1750 Vitaliano Donati "Della Storia Naturale Marina dell' Adriatico" [Ragan]
  • 1792 Giuseppe Olivi "Zoologia Adriatica" [Ragan]
  • 1802 Gottfried Reinhold Treviranus "Biologie, oder Philosophie der Lebenden Natur für Naturforscher und Aerzte, Band 1" [Ragan]
  • 1824 Johann Heinrich Friedrich Link "Elementa Philosophiae Botanicae" [Stevens]
  • 1828 Georges Cuvier "Histoire Naturelle des Poissons, Tome Premier" [Ragan]
  • 1836 Constantin Rafinesque "Flora Telluriana" [Stevens]

Note that it was apparently Vitaliano Donati who, 5 years before Buffon drew his dog genealogy, first suggested that biological relationships are like a network, although he did not provide an explicit diagram to illustrate this idea.


Cuvier G. (1817) Le Règne Animal Distribué d'Après son Organisation, Tome Premier. Deterville, Paris.

de Jussieu A.-H.-L. (1843) Cours Elémentaire d'Histoire Naturelle. Fortin Masson et Langlois & Leclerc, Paris.

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

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

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

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

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