Wednesday, August 20, 2014

The role of biblical genealogies in phylogenetics

Phylogeneticists treat the tree image as having special meaning for themselves. Conceptually, the tree is used as a metaphor for phylogenetic relationships among taxa, and mathematically it is used as a model to analyze phenotypic and genotypic data to uncover those relationships. Irrespective of whether this metaphor / model is adequate or not, it has a long history as part of phylogenetics (Pietsch 2012). Of particular interest ihas been Charles Darwin's reference to the "Tree of Life" as a simile, since that is clearly the key to the understanding of phylogenetics by the general public.

The principle on which phylogenetic trees are based seems to be the same as that for human genealogies. That is, phylogenies are conceptually the between-species homolog of within-species genealogies. As far as Western thought is concerned, human genealogies make their first important appearance in the Bible, with a rather specific purpose. The Bible contains many genealogies, mostly presented as chains of fathers and sons. For example, Genesis 5 lists the descendants of Adam+Eve down to Noah and his sons, which can be illustrated as a pair of chains (as shown in the first figure); and the rest of Genesis gets from there down to Moses' family, for which the genealogy can be illustrated as a complex tree.

The genealogy as listed in Genesis 5.
Cain's lineage was terminated by the Flood.

However, the theologically most important genealogies are those of Jesus, as recorded in Matthew 1:2-16 and Luke 3:23-38. Matthew apparently presents the genealogy through Joseph, who was Jesus' legal father; and Luke apparently traces Jesus' bloodline through Mary's father, Eli. These two lineages coalesc in David+Bathsheba, and from there they have a shared lineage back to Abraham. Their importance lies in their attempt to substantiate that Jesus' ancestry fulfils the biblical prophecies that the Messiah would be descended from Abraham (Genesis 12:3) through Isaac (Genesis 17:21) and Jacob (Genesis 28:14), and that he would be from the tribe of Judah (Genesis 49:8), the family of Jesse (Isaiah 11:1) and the house of David (Jeremiah 23:5).

That is, these genealogies legitimize Jesus as the prophesied Messiah. Following this lead, subsequent use of genealogies has commonly been to legitimize someone as a monarch, so that royal genealogies have been of vital political and social importance throughout recorded history (see the example in the next figure). This importance was not lost on the rest of the nobility, either, so that documented genealogies of most aristocratic families allow us to identify the first-born son of the first-born son, etc, and thus legitimize claimants to noble titles — genealogies are a way for nobles to assert their nobility.

The genealogy of the current royal family of Sweden.
The lineage of the recent monarchs is highlighted as a chain, with an aborted side-branch dashed.

If we focus solely on the line of descent involved in legitimization, then genealogies can be represented as a chain (as shown in the genealogy above). However, if we include the rest of the paternal lines of descent then family genealogies can be represented as a tree. However, if we include some or all of the maternal lineages as well, then family genealogies can be represented as a network. For example, the biblical genealogies only rarely name women, but where females are specifically named the genealogies actually form a reticulated network. Jacob produced offspring with both Rachel and Leah, who were his first cousins; and Isaac and Rebekah were first cousins once removed. Even Moses was the offspring of parents who were, depending on the biblical source consulted, either nephew-aunt, cousins, or first cousins once removed. These relationships cannot be represented in a tree. (See also the genealogy of the Spanish branch of the Habsburgs, who were kings of Spain from 1516 to 1700.)

This idea of genealogical networks was straightforward to transfer from humans to other species. Originally, biologists stuck pretty much to the idea of a chain of relationships among organisms, as presented in the early part of Genesis. Human genealogies were traced upwards to Adam and from there to God, and thus species relationships were traced upwards to God via humans. However, by the second half of the 1700s both trees and networks made their appearance as explicit suggestions for representing biological relationships. In particular, Buffon (1755) and Duchesne (1766) presented genealogical networks of dog breeds and strawberry cultivars, respectively.

However, these authors did not take the conceptual leap from within-species genealogies to between-species phylogenies. Indeed, they seem to have explicitly rejected the idea, confining themselves to relationships among "races". It was Charles Darwin and Alfred Russel Wallace, a century later, who first took this leap, apparently seeing the evolutionary continuum that connects genealogies to phylogenies. In this sense, they both took ideas that had been "in the air" for several decades, but previously applied only within species, and applied them to the origin of species themselves. [See note below.] Both of them, however, confined themselves to genealogical trees rather than using networks. It seems to me that it was Pax (1888) who first put the whole thing together, and produced inter-species phylogenetic networks (along with some intra-species ones).

In this sense, the biblical Tree of Life has only a peripheral relevance to phylogenetics. Darwin used it as a rhetorical device to arouse the interest of his audience, but it was actually the biblical genealogies that were of most practical importance to his evolutionary ideas. Apart from anything else, the original biblical tree was actually the lignum vitae (Tree of Eternal Life) not the arbor vitae (Tree of Life). Similarly, the tree from which Adam and Eve ate the forbidden fruit was the lignum scientiae boni et mali (Tree of Knowledge of Good and Evil), not the arbor scientiae (Tree of Knowledge) that was subsequently used as a metaphor for human knowledge.

Note.  Along with phylogenetic trees, Darwin and Wallace did not actually originate the idea of natural selection, which had previously been discussed by people such as James Hutton (1794), William Charles Wells (1818), Patrick Matthew (1831), Edward Blyth (1835) and Herbert Spencer (1852). However, this had been in relation to within-species diversity, whereas Wallace and Darwin applied the idea to the origin of between-species diversity (i.e. the origin of new species).


Buffon G-L de. 1755. Histoire naturelle générale et particulière, tome V. Paris: Imprimerie

Duchesne A.N. 1766. Histoire naturelle des fraisiers. Paris: Didot le Jeune & C.J. Panckoucke.

Pax F.A. 1888. Monographische übersicht über die arten der gattung Primula. Bot. Jahrb. Syst. Pflanzeng. Pflanzengeo. 10:75–241.

Pietsch T.W. 2012. Trees of life: a visual history of evolution. Baltimore: Johns Hopkins University Press.

Monday, August 18, 2014

Bioinformaticians' nightmares

These illustrations are from Alper Uzun's Biocomicals web site.

Bioinformaticians' dream

Bioinformaticians' reality