Naef and Cephalopod Awareness Day

Cephlapodcast has announced the Second Annual Unofficial International Cephalopod Appreciation and Awareness Day. I wonder what Adolf Naef would have said?

Naef said a lot about cephalopods and their relationships. As a respected world authority on octopuses and their relatives, Naef has produced several texts that have until now only interested David and I in parts (mostly the systematic theory and methodology). Our only foray into the fascinating world of calamari occurred recently when were contacted by Jan Strugnell - a cephalopodist from the University of Cambridge and admirer of Naef's work. Jan had an interesting question - why did Naef's phylogeny and classification of Argonautoidea differ?

The Argonautoidea Lamarck, 1809 (paper nautiluses and their relatives) are divided into two subfamilies: Tremoctopodinae and Argonautinae. The former includes Alloposidae and Tremoctopodidae and, the latter Argonautidae and Ocythoidae. Naef produced the following diagram (Figure 1a) with the following accompanying text:

"The typical relationship between the 4 genera which form the family are shown in the following graph: i.e., the genera developed by secondary specialization from forms I-IV in a direct series.
The ideal or hypothetical form I corresponds to the type of the family; form II corresponds to the type of the 3 genera, form II to the type of the 2 highest genera. Form IV is the ancestral form of Argonauta. The forms derived from II and III are clearly natural groups which can be defined, despite the specialization of their recent representatives. The important morphological relationships, however, call for a division into 2 subfamiles by drawing a line between II and II, i.e. a distinction between lower (I) and a higher (II) stage of variation. This is, of course, arbitrary ... and is only intended to introduce order for practical purposes by stressing the essential and omit characters of less importance. This division stresses the distance between forms II and III and creates the two natural subfamiles: Tremoctopodinae and Argonautinae (Naef 1972: 732).

These two conflicting statements (one pictorial and one as text) pose an interesting problem. What does the diagram represent and what was Naef thinking?

Naef believed both subfamilies to be monophyletic (natural groups). What Naef did diagrammatically shows a transition from the Haeckelian tree-thinking to modern systematics.

In order to understand what Naef did we go to the introduction of his work on the Fauna and Flora of the Bay of Naples. Firstly the graph is a phylogenetic tree as we understand it today. Back in Naef's day (prior to molecular systematics) the graph was termed a 'genealogical' tree. Phylogenetic trees were considered to be true depictions of ancestor-descendant relationships, an idea rarely entertained today. In Naef's phylogenetic tree, we see that forms are placed at the nodes. Naef's forms are types, namely "an abstract but naturally possible form from which a multitude of actually existing forms may have developed ..." (Naef, 1972: 15). Forms are not ancestor-descendant relationships but rather abstract transitional series between basic and specialized forms based on the concept of metamorphosis. Incorporate theses points together and you have a tree depicting the transition of forms that relate directly to the relationships of the taxa on the branches.

Confused?

Naef is depicting a back-to-front cladogram. In Naef's diagram the forms are being shown to be transitional within a dichotomous framework (Figure 1b); very much like showing a character tree within a consensus tree at the same time. A modern representation of Naef's tree would place the forms at the nodes (Figure 1c). What at first appears to be a rooted phylogentic tree, turns out to be a poorly drawn cladogram that places too much emphasis on transitional forms than it does on taxic relationships.

Naef's tree represents a transitional period between Haeckel and Hennig. Naef attempted to save us from the Haeckel's 'oak' trees that later inspired the neoDarwinian Modern Synthesis by emphasizing the importance of natural (monophyletic) groups. Naef's methodological and theoretical work should also be celebrated on Cephalopod Awareness Day.

References

Naef, A. (1972). Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.

Natural and Artificial Classification: A reply to Wilkins

The following post is a reply to John Wilkin’s The philosophy of classification on his blog Evolving Thoughts.

An Uninformed Consensus

John Wilkins in his recent post believe that our view is "radical" because

"… they have presented some views on classification that do, indeed, differ from the received consensus."

We beg to differ.

In late 20th and early 21st century literature there are very few discussions on the nature of classification. Most revolves around explaining existing classifications (i.e. Reptilia) or in the defence of poorly defined taxonomic groups that fail to form groups (i.e., paraphly). It is these debates (i.e., paraphly versus monophyly) that would benefit from the discussions of early 20th and late 19th century morphologists, would did hold a consensus view of natural and artificial classifications. That consensus was this,

We then follow a Natural Method, which cannot be called a system, because it is destitute of any unity of principle. (Candolle & Sprengel, 1821)

It is our belief that the pursuit for explanations to existing classifications that ended this debate and therefore any consensus. Furthermore, it is the addition of homology = similarity that radically altered how we view classifications, leading to the almost Fukuyamaist statement that,

"I would say that the effort put into this controversy is further evidence that systematists do not have their priorities straight. In their day-to-day work they really do not make much use of classifications, but they show a strange obsession with fighting about them for reasons that seem to me to be an historical curiosity" (Felsenstein 2005)

Currently there is no consensus over natural or artificial classifications. The topic is a moot point and very few concern themselves with its relevance to 21st systematics and biogeography. As systematists we are more or less tied to the consensus of the past, namely to the literature of the 19th century and early 20th century. In that sense we are not “radicals", but rather “old fashioned”.

Similarity and Homology

Similarity, as expressed in the usual kinds of data matrices, is 11, or, the molecular version, AA is not a relation. The 11 and the AA are, if anything, homologues, the parts, the 'namesakes' as Owen called them. We see homology as a relation: 0(11), or the molecular version, G(AA). We stated earlier:

"...all molecular systematic studies are phenetic as they ignore relationship, that is, homology". One might expand that and say, "...all numerical systematic studies are phenetic as they ignore relationship, that is, homology."

This would be more accurate.

In response to John’s comment,

"I'm not sure I follow this. According to current usage, molecular systematics does rely on homologies: they have a number of special terms devoted to identifying them: paralogy, xenology and orthology. Of course, they often don't use homology properly. And to identify a homology in molecular biology you need to do some prior work; homology is an inference from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives homology from similarity".

In fact we would suggest that it would be more accurate to say:

"... molecular systematics does rely on HOMOLOGUES: they have a number of RELATIONS DERIVED FROM them: paralogy, xenology and orthology....And to identify a HOMOLOGUE in molecular biology you need to do some prior work; HOMOLOGUES ARE inferenceS from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives HOMOLOGUES from similarity ..."

This certainly is not radical. What we are suggesting is that de Candolle (1813) presented a very clear account of classification, an account still of significance today.

Haeckel and Classification

In our understanding, Ernst Haeckel did more than most to promote the genealogical view of species relationships. It might be fair to say that all our genealogical endeavours stem from Haeckel. Adolf Naef (1917, 1919)was the first to critique that viewpoint His interest was in natural classification. Hennig (1950), quite deliberately, focused on Naef. Thus, it might be fair to say that Hennig's efforts were directed towards rehabilitating Haeckel. Further, one might see Systematics and Biogeography (Nelson & Platnick, 1981) as a further detailed critique of Haeckel - if the most detailed critique available - and a restatement of de Candolle's viewpoints on classification. In this sense cladistics sensu Nelson & Platnick is of greater significance than cladistics sensu computer programs.

We would venture the suggestion that Sober (1988) mistook cladistics sensu Farris (parsimony sensu Farris) as if it was the generally accepted view (in the mid-1980s that might have been possible). In fact Sober deliberately excludes the more general view, as if the argument really was about parsimony versus likelihood, one algorithm versus another,

"Because this work is about phylogenetic inference, not classification, nothing will be said about the current controversy concerning so-called 'pattern' cladism." (Sober, 1988:8, footnote 7).

Thus, in our view, the more general study of classification exclude Sober's work as a relevant commentary on the matter.

References
Candolle, A.P., de, & Sprengel, K. 1978. Elements of the philosophy of plants. Reprint of the 1821 ed.. New York, NY.
Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik, Deutsche Zentralverlag, Berlin.
Naef, A. 1917. Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte "biogenetische Grundgesetz"), Verlag von Gustav Fischer, Jena.
Naef, A. 1919. Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen), Verlag von Gustav Fischer, Jena).
Nelson, G. & Platnick, N.I. 1981. Systematics and biogeography. Cladistics and vicariance. Columbia University Press, New York.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, Massachusetts.

Adolf Naef - A Potted Biography

Who was he?
Adolf Naef was a Swiss systematist, malacologist and a proponent of systematic morphology. He was born in Niederhelfenschwil on 1st May 1883 and passed away on May 11th 1949.

What did he do?
Naef studied at the University of Zurich, under the guidance of Arnold Lang (1855—1914), a former Professor of Jena University and close friend of Ernst Haeckel. Naef visited and worked in Anton Dorn’s Zoological Station in Naples, Italy in 1908, studying the squid Loligo vulgaris, the subject of his dissertation (Naef, 1909a, b). Naef returned to the Naples Zoological Station in the mid 1920s to study cephalopods, publishing a two-part monograph in the Station’s Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte (Fauna e Flora del Golfo di Napoli) series (Naef 1921d, 1923c, 1928, later translated into English, Naef, 1972a, 1972b, 2000), which formed the basis for his two short but significant monographs on systematic theory (Naef, 1917, 1919). In 1922 he became Professor at the University of Zagreb, and in 1927 was Professor of Zoology at the University of Cairo.

What’s the big idea?
Naef’s studies were framed within Systematische Morphologie (Systematic morphology) (Naef, 1917, 1919), the details he sketched out as early as 1913:

“Phylogenetic and natural systematics deal with the same factual material, and although each has different basic concepts, both disciplines can be united in a single concept because their objects are so similar. I have therefore proposed the name ‘systematic morphology’ for this concept (Naef, 1913: 344)…It is intended to show that there is an inner relationship between natural systematics and (comparative) morphology” (Naef, 1921-23: 7, from the English translation, Naef, 1972a: 12).

Naef’s concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813). Naef expressed it as so:

“For decades, phylogenetics lacked a valid methodological basis and developed on the decayed trunk of a withering tradition rooted in the idealistic morphology and the systematics of pre-Darwinian times. There was talk of systematic ‘tact’ and morphological ‘instinct’, terms which were felt rather than understood and consequently insufficient to form the frame of a science which required sound definitions and clearly formulated principles” (Naef, 1921-23, pp. 6-7, from the English translation, Naef, 1972, p. 12).

And thus was born ‘Systematische Morphologie’, perhaps the beginnings of cladistics, in its most general form (of which more in a further post). Towards the end of his career, Naef published several detailed accounts of ‘Systematische Morphologie’ (Naef, 1931a, b, 1933a), including a succinct summary in the widely read 2nd edition of the Handwörterbuch der Naturwissenschaften (Naef, 1933b).

Naef might be considered a man out of time – as might many morphologists today, relative to the explosion of molecular data. In Naef’s day palaeontology and the post World War II hegemony of the modern synthesis was attracting the young minds. Today it is molecular systematics and DNA barcoding – versions of artificial classifications.

References

Candolle, A.-P. de (1813). Théorie élémentaire de la botanique ou exposition des principes de la classification naturelle et de l'art de décrire et d'étudier les végétaux. Deterville, Paris.
Naef, A. (1909a). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Jenaische Zeitschrift für Naturwissenschaft, 45, N.F. 38:221—266.
Naef, A. (1909b). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Inaugural-Dissertation, Univers. Zurich, 46pp.
Naef, A. (1913). Studien zur generellen Morphologie der Mollusken. 2. Teil. Das Cölomsystem in seinen topographischen Berziehungen. Ergebnisse und Fortschritte der Zoologie 3: 329—462.
Naef, A. (1917). Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte “biogenetische Grundgesetz”). Verlag von Gustav Fischer, Jena.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Naef, A. (1921—23). Die Cephalopoden (Systematik). In: Fauna e Flora del Golfo di Napoli, Monograph 35 (I-1), Pubblicazioni della Stazione Zoologica di Napoli. R. Friedländer and Sohn, Berlin, pp. 1—863.
Naef, A. 1931a. Allgemeine Morphologie. I. Die Gestalt als Begriff und Idee, pp. 77—118 in Bolk, L, Göppert, E., Kallius, E. & Lubosch, W., (editors) Handbuch der vergleichenden Anatomie der Wirbeltiere 1. Berlin: Urban & Schwarzenberg.
Naef, A. 1931b. Phylogenie der Tiere, pp. 1—200 in Baur, E., & Hartmann, M., (editors) Handbuch der Vererbungswissenschaft, Gebrüder Borntraeger, Berlin 13 (3i).
Naef, A. 1933a. Die Vorstufen der Menschwerdung. Eine anschauliche Darstellung der menschlichen Stammesgeschichte und eine kritische Betrachtung ihrer allgemeinen Voraussetzungen. Jena: Verlag von Gustav Fischer.
Naef, A. 1933b. Cephalopoda, pp. 293—310 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 2. Jena: Verlag von Gustav Fischer.
Naef, A. 1933c. Morphologie der Tierre (Allegmeines und Grundsätzliches), pp. 3—17 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 7. Jena: Verlag von Gustav Fischer.
Naef, A. 1972a. Cephalopoda. Fauna and Flora of the Bay of Naples (Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte), Monograph 35, Part I, [Vol. I], Fascicle I. Smithsonian Institute Libraries, Washington.
Naef, A. 1972b. Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.
Naef, A. 2000. Cephalopoda. Embryology. Fauna and Flora of the Bay of Naples [Fauna und Flora des Golfes von Naepel]. Monograph 35. Part I, Vol. II [Final part of the Monograph No. 35], pp. 3-461. Washington, Smithsonian.