Wednesday, May 30, 2012

Networks of genealogy


Phylogenetic trees, indicating evolutionary relationships among organisms, are usually considered to have derived, to one extent or another, from the concept of a family tree or pedigree (also called genealogy, généalogie, stammbaum, stamboom or levensboom, depending on your language), which depict the lineal descent from some single specified human ancestral couple. However, these diagrams are only trees if one sticks to lineal descent, historically usually the patrilineal lineage. As soon as one includes the (many) matrilinear lines, the diagram becomes a network, with inter-connections between different family trees. [See the later post Family trees, pedigrees and hybridization networks.]

When creating the first two published phylogenetic networks, this seems to have been the idea of both Buffon (1755) and Duchesne (1766). They each observed hybridization histories (in dogs and strawberries, respectively), and they drew diagrams showing both the male and female parents (presumably without knowing which was which). Thus, they apparently saw themselves as doing nothing unusual, and neither did their contemporaries. They were simply drawing pedigrees in which both the matrilineal and patrilineal relationships were shown.

It is only with historical hindsight that we can see that they did something conceptually new. The "usual" family genealogies showed (and still do show) predominantly the male lineages (which keep the family name, and thus are easier to trace), with the female lineages apparently appearing from nowhere at the point where they marry into the male lineage. What both Buffon and Duchesne did was show that both the male and female lines came from within the same group of organisms. (In modern parlance, this was both biologically more informative and politically more correct.)

However, this new idea was restricted to within-species relationships (dog breeds and strawberry cultivars), thus emphasizing the close conceptual relationship to a pedigree of individuals. The idea that reticulating evolutionary relationships might occur between species (possibly members of different higher taxonomic groups) was apparently not something that either Buffon or Duchesne considered.

Lamarck (1809) appears to have been the first to consider supra-species evolution, and he used a non-reticulating tree for his diagram rather than a reticulating network. His published trees differ from our modern diagrams in having contemporary higher-level taxonomic groups at both the internal and external nodes, so that each tree represents a transformation series among the groups (based on morphoclines). Thus, his trees were based on the idea of descent with modification but do not match our modern trees. (Basically, Lamarck did not believe in extinction, and thought that the disappearance of species was due to their transformation into new species.) The animal tree of Barbançois (1816) and the pre-Darwinian ornithology trees of Strickland (1841) and Wallace (1856) are direct descendants of this type of tree (see O'Hara 1988, Tassy 2011).

Darwin (1859) is usually credited as being the originator of modern phylogenetic trees, with contemporary taxa at the leaves and ancestors at the internal nodes. (Darwin firmly believed in extinction, so that the internal tree nodes represented the extinct ancestors of modern species.) However, he never published an empirical tree (although one appears in his notes and another in his letters); and it was left to Hilgendorf (1863), Mivart (1865), Gaudry (1866) and Haeckel (1866) to provide the first published ones. [This later blog post discusses the history of these first trees.]

The point of this long dissertation is that from 1750, when Vitaliano Donati first suggested that biological relationships might be represented as a network, almost all of the relationship diagrams were either (i) networks showing non-genealogical affinity, (ii) trees showing non-genealogical affinity (eg. those of Agassiz, Augier, Bronn, Hitchcock), or (iii) trees showing genealogy (eg. those of Gaudry, Haeckel, Hilgendorf, Lamarck, Mivart) (see Stevens 1994, Ragan 2009, Tassy 2011). Networks showing genealogy at the species level or above were notably absent.

This situation appears to have lasted until 1888. In that year Ferdinand Pax published a revision of the plant genus Primula. In it he provided 14 diagrams illustrating the relationships among the species within each section of the genus, plus one diagram illustrating the relationships among the sections. Almost all of these diagrams are networks rather than trees, as they show complex reticulating relationships. These are affinity networks as they do not represent genealogies, with three exceptions.

Page 186, Section Vernales.
Click to enlarge.

The figures on pages 186, 202 and 233 all explicitly indicate hybridization relationships among the species. The hybrid species are indicated by a cross (rather than a circle), and they are connected to their nominated parents by dashed lines (as used by both Buffon and Duchesne). Some of the suggested relationships are quite complex, with two hybrid species deriving from the same parents.

Page 202, Section Farinosae.
Click to enlarge.

This thus seems to be the first publication of a hybridization network involving species rather than sub-specific relationships. Quite why it took more than 130 years from Buffon's innovation to take this next step is not clear. Perhaps it had something to do with the contemporary focus on genealogical trees of animals, particularly vertebrates, which traditionally have been considered to show little evidence of inter-specific hybridization (unlike plants, where there is considerable evidence).

Page 233, Section Auricula.Click to enlarge.

It seems to me to be important to emphasize the historical distinction between affinity and genealogy networks. This distinction continues in phylogenetic networks today, with rooted networks explicitly representing genealogy and unrooted networks representing similarity of a more general sort. Almost all of the published phylogenetic networks of the past 20 years have been unrooted, and therefore logically cannot represent historical relationships. (The root indicates the time direction of the genealogy, and time goes in only one direction, so that we have Time's Arrow not Time's Boomerang.) These unrooted networks can be (and usually are) a valuable tool for helping to understand phylogenetic history, but they do not represent evolution directly.

References

Barbançois, Charles-Hélion de (1816) Observations sur la filiation des animaux, depuis le polype jusqu'au singe. Journal de Physique, de Chimie, d'histoire Naturelle et des Arts 82: 444-448.

Buffon, Georges-Louis Leclerc, comte de (1755) Histoire Naturelle Générale et Particulière, tome V. Imprimerie Royale, Paris.

Darwin, Charles Robert (1859) On the Origin of Species. John Murray, London.

Donati, Vitaliano (1750) Della Storia Naturale Marina dell' Adriatico. Francesco Storti, Venezia.

Duchesne, Antoine Nicolas (1766) Histoire Naturelle des Fraisiers. Didot le jeune & C.J. Panckoucke, Paris.

Gaudry, Albert (1866) Considérations Générales sur les Animaux Fossiles de Pikermi. F. Savy, Paris.

Haeckel, Ernst Heinrich (1866) Generelle Morphologie der Organismen. Reimer, Berlin.

Hilgendorf, Franz Martin (1863) Beiträge zur Kenntniß des Süßwasserkalkes von Steinheim. Unpublished PhD Dissertation. Philosophische Fakultät, Universität Tübingen, 42 pp.**

Lamarck, Jean-Baptiste de Monet, chevalier de (1809) Philosophie Zoologique. Dentu et l'Auteur, Paris.

Mivart, St George Jackson (1865) Contributions towards a more complete knowledge of the axial skeleton in the Primates. Proceedings of the Zoological Society of London 33: 545-592.

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.

Pax, Ferdinand Albin (1888) Monographische übersicht über die arten der gattung Primula. Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 10: 75-241.

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

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

Strickland, Hugh Edwin (1841) On the true method of discovering the natural system in zoology and botany. Annals and Magazine of Natural History 6: 184-194.

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

Wallace, Alfred Russel (1856) Attempts at a natural arrangement of birds. Annals and Magazine of Natural History 18: 193-216.

** See this later post for information about this thesis.
[This was read as a paper before the Royal Prussian Academy of Sciences on July 19 1866, and was then published separately as:
   Hilgendorf F. (1866) Planorbis multiformis im Steinheimer Süßwasserkalk. Ein Beispiel von Gestaltveränderung im Laufe der Zeit. Buchhandlung von W. Weber, Berlin, 36 pp.
The paper then appeared as a regular part of the Academy's journal:
   Hilgendorf F. (1867) Über Planorbis multiformis im Steinheimer Süsswasserkalk. Monatsberichte der Königliche Preussischen Akademie der Wissenschaften zu Berlin 1866: 474-504.
So, you can take your pick as to the formal publication date of the tree.]

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