Realism in systematics through biogeographical consilience

Renato S. Capellaria,* and Charles Morphy D. Santosb

aDepartamento de Biologia, Faculdade de Filosofia, Universidade de Sao Paulo, Ciencias e Letras de Ribeirao Preto, Av. Bandeirantes 3900, 14040-901,

Ribeirao Preto, Sao Paulo, Brazil; bUniversidade Federal do ABC, Centro de Ciencias Naturais e Humanas, Rua Santa Adelia 166,

Bairro Bangu, 09210-170, Santo Andre, SP, Brazil

Accepted 30 April 2011

Abstract

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionaryprocesses, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a definedcriterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historicalseries of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree oftruthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize thebiological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption thatrobust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa.

� The Willi Hennig Society 2011.

Instrumentalism is a philosophical defence of theo-retical hypotheses as being merely tools to generatepredictions, denying the need of an ontological com-mitment to scientific theories. Such hypotheses do notmake assertions or try to discover the underlyingmeaning of reality: the truth or falsity of a theoreticalsentence when compared with the observable world isirrelevant to instrumentalism (Leplin, 2001) and thequestion of whether theoretical terms (e.g. ‘‘clade’’,‘‘terminal taxa’’) must be thought of as actually refer-ring to existing entities can be neglected with no harm.Rieppel (2007) brought attention to the increasingtendency of an instrumentalist approach within system-atics. He is most concerned with the prominent status ofparsimony to achieve homologues, but also commentson a growing tendency to overemphasize the algorithmicsteps during phylogenetic analyses, e.g. in molecularsystematics, to the detriment of a more careful analysisof the final products of phylogenetic analyses, thecladograms. In his final remarks, he asks whethersystematists should be instrumentalists, stating that ‘‘a

realist perspective may be more difficult to argue intaxonomy, or phylogenetics, but would seem to be moreambitious as well as more attractive as it seeks toincrease the correspondence of scientific theories to theworld through their causal grounding’’ (Rieppel, 2007,p. 182; emphasis added). The aim of our commentary isto discuss briefly this ‘‘more attractive’’ approach inorder to suggest one possible starting point for furtherdevelopments. In our opinion, such an approach shouldbe based on a scientific realistic view as invoked byRieppel (2007) through the use of consilient biogeo-graphical hypotheses (Santos and Capellari, 2009) tomeasure the robustness of phylogenetic hypotheses,mainly according to Croizat�s (1964) statement thatevolution can be properly known only if its three aspects(form, space, and time) are concomitantly assessed.

Phylogenetic hypotheses are representations of thehierarchical structure of nature. In this sense, a gap isexpected between any phylogenetic inference and thenatural world shaped by historical evolutionary pro-cesses totally independent of human perception. Inpractice, however, such gap is overlooked. The onlyconcern during phylogenetic analyses is the congruenceamong characters under a defined criterion (parsimony

*Corresponding author:E-mail address: rscapellari@gmail.com

� The Willi Hennig Society 2011

Cladistics 28 (2012) 170–173

Cladistics

10.1111/j.1096-0031.2011.00363.x

or any other). It is just a matter of empirical adequacy ofsentences (Rieppel, 2007): the theory (cladogram) is aproduct of the coherence among the sentences (primaryhomology hypotheses). This is an instrumentalist per-spective: the measure of confirmation of the theory is notgiven by its accordance to the natural world, but ratherto the accordance among the sentences that compose thetheory. Although there seems to be no room forprediction in phylogenetic analyses (Rieppel et al.,2006; Rieppel, 2008) and, as said before, instrumentalismadvocates hypotheses only as tools to generate predic-tions, an instrumentalist perspective is a very pervasiveapproach throughout contemporary systematics. It isconducted in a manner similar to that proposed by theempiricist Bas van Fraassen in the so-called ‘‘construc-tive-empiricism’’ (see Vergara-Silva, 2009, and referencestherein). Under the constructive-empiricism perspective,theories are supposed to provide the greater empiricaladequacy among the statements they assemble, no aspectof realism being taken into account.

In contrast, given a scientific realistic view, phyloge-netic hypotheses or cladograms are scientific theoriesthat try to depict what once indeed happened in thenatural world, i.e. the historical series of cladogeneticevents among biological entities. Even though the linkbetween cladograms (a ‘‘scientific possibility’’) and thephylogeny (the ‘‘actual historical lineage of life’’) (Haber,2005, p. 833) is tied by an argument of theoreticalapproximation of the reality (i.e. we shall never know ifwe really found the true phylogeny), a bridge can bemade somehow between the mind-independent worldand its representation. Hence, phylogenetic systems arealways hypothetical as they are human constructs (aspointed out by Wagele, 2005), and are based on theattempt to recover and interpret the evolutionarypatterns and processes, respectively. According to thisview, as phylogenetic hypotheses emerge from theperception of the mind-independent natural-kind frame-work of the world, a parameter of reality should besearched for to give support to this theoretical approx-imation of the reality and, concomitantly, to the taxo-nomic groups inferred from cladograms.

The noticeable growth of instrumentalism in system-atics is probably associated with the great increase in thegeneration and availability of new databases (such asGenBank) as well as with new techniques and methodscreated to treat taxonomic data, a substantial propor-tion of them especially designed to deal with large datamatrices and large taxon samples. In recent decades, themassive adoption of numerical analyses has propitiateda boom in the number of papers presenting phylogenetichypotheses. Despite the ongoing development of newmeasures of clade support, there is modest questioningabout the reliability of the clades obtained in theseconjectures, in such a manner that the discussionregularly relies only on a methodological basis. It is

not a simple matter of quality of the phylogenetichypothesis obtained: it is common to find deep incon-gruence among distinct cladograms for a similar set oftaxa (quite different trees relating to the same taxa, usingthe same or different kinds of data). Nevertheless, thereis an underlying reality apart from our ability toreconstruct it, i.e. if there is a unique tree of life, asignificant proportion of the phylogenetic hypothesescurrently available must be simply wrong.

The challenge is to establish a form of measuring thedegree of reality (or truthfulness) of a cladogram. Asstated by Freckleton (2009, p. 45), ‘‘(…) [t]here are anumber of reasons why the phylogeny [i.e. the phylo-genetic hypothesis] might not accurately reflect history,or it is frequently the case that there is uncertainty suchthat different phylogenies are equally as well sup-ported’’. In fact, the phylogeny exists independently ofour perception, and the evolutionary theory aims toobtain an approximate description of the phylogeny. Inphylogenetic systematics, the characters (morphological,molecular, behavioural, ecological or any other kind ofdata) are mathematically analysed in order to provide aset of hypotheses of relationships resulting from imper-fect tree-reconstruction methods and from subjectivecriteria (Morrison, 2006). Neglecting the discussionabout the reliability of groups and their correspondenceto the natural world keeps systematics on the ground ofscientific instrumentalism.

Epistemologically, taxonomic groups are the outcomeof character analysis—those characters with usefulphylogenetic signal to be recognized as synapomorphies.The relationship between synapomorphies and the taxathey are supposed to be markers of was defined byNelson (2004, p. 133) who stated ‘‘that taxon andsynapomorphy are different names for the same thing’’.Although the strict relational equivalence betweenmonophyly and synapomorphy has been dismissed byAssis and Rieppel (2011), they are unquestionablyclosely related, as ‘‘synapomorphy is the empiricalrelation that supports hypotheses of phylogenetic rela-tionship’’ (Assis and Rieppel, 2011, p. 95). Yet, allhypotheses of homology (candidate synapomorphies)are restricted to the possibilities ascribed in the datamatrix (Grant and Kluge, 2004), and congruence ‘‘(…)do[es] all the work in sorting homology from homo-plasy’’ (Rieppel, 2007, p. 180). The phylogenetic practiceis therefore instrumentalist when assumptions of homol-ogy and homoplasy are exclusively related to issuesconcerning the use of algorithms.

Regarding Rieppel�s question ‘‘should systematists beinstrumentalist, or do they sometimes have no otherchoice?’’ (2007, p. 181, emphasis in original), it isreasonable to say that they have no choice during thealgorithmic step of the cladistic analysis. The cladogrambehaves as a simple summary of information related tothe data matrix, and is the best option among the whole

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set of possible trees. In this view, a cladogram is correct ifit is the end-product of adequate character identificationfollowed by careful analytical procedure. That is it.Respecting the procedure and the algorithms is thecondition to turn any cladogram into consistent science.However, if there is a firm belief that our phylogenetichypotheses are in fact representations of the naturalworld driven by evolutionary forces that are real, this isnot enough. The main point is: how to know that aphylogenetic inference has biological meaning apart fromits instrumentalist value, and how do we certify if it is areliable evolutionary scenario?As there is an intelligibilitygap between how the natural world is perceived and howit really is, ‘‘[h]ow then dowe know that our perception ofthe world is at all faithful to the way the world is?’’(Ladyman, 2002, p. 141). To achieve this goal, weadvocate the use of consilient biogeographical hypothesesin a post-analytical step, as briefly outlined below.

Recently, Santos and Capellari (2009) described anon-instrumentalist procedure to biogeographical anal-ysis based on the search for biogeographical reciprocalillumination and consilience. In their words: ‘‘To beconsilient, a general biogeographical hypothesis mustexplain phenomena not contemplated during its con-struction, as other taxonomic group distributions, theexistence (or absence) of fossil groups in certaingeological layers, and the phylogenetic relationshipswithin other taxa with shared—at some extent—distri-butional patterns. (…) [B]iogeographical consilience isas an evaluative criterion for the robustness of biogeo-graphical hypotheses when considered as scientifictheories, and not as simple descriptions of geographicalpatterns’’ (Santos and Capellari, 2009, p. 411). Consil-ience was first raised by William Whewell (1847) todesignate situations in which a causal explanatorytheory, initially constructed to explain a particular setof phenomena, provides an equally successful causalexplanation to other kinds of phenomena, different fromthose considered during the construction of the theory(Fisch, 1985). Accordingly, consilience would work asan evaluative criterion for the truth of a scientific theory(in the sense of a correspondence theory). Even if it isbeyond the capacity of science to reach the ‘‘truth’’,consilience can be seen as a ‘‘criterion of reality’’ for ascientific theory (Snyder, 2005a,b), given that a scientifictheory is an approximation to the truth about thereality. As it would seem improbable that phenomenadisconnected a priori were integrated in a theory purelyby chance, to discover the relationships among severaland distinct phenomena is a strong signal that their veracausa was found (Whewell, 1860). In this sense, as aconsilient theory explains more than its own set ofquestions, it can be considered more trustable than atheory that explains only predicted or known situations.Although the consilient approach shown in Santos andCapellari (2009) is interpreted as a guideline to historical

(and particularly cladistic) biogeography, the sameconsilient guidance could be used in the context ofphylogenetic analyses to move away from the pureinstrumentalism during the proposition of taxonomicgroups and their relationships. This biogeographicalapproach, especially regarding consilient hypotheses, isa complementary perspective to previous papers con-cerning realism (e.g. Ruse, 1979; Rieppel, 2007; Vergara-Silva, 2009) and also the lack of empirical foundation(e.g. Kearney and Rieppel, 2006; Rieppel and Kearney,2007; Assis, 2009) in systematics.

It is widely known that biogeography tries to identifypatterns of spatial evolution and the processes respon-sible for them (Platnick and Nelson, 1978). Thesequence of modifications of every area affects thedistribution of a substantial portion (sometimes thewhole) of the taxa occupying that area and, thus, suchtaxa will share a common biogeographical history.When taking consilient biogeographical hypotheses asquantifiers of the realism of our phylogenetic hypoth-eses, we are comparing the particular history of the taxaunder scrutiny with the history of the Earth—the spatialsequence of disjunctions in the context of evolution intime and space. The Whewellian vera causa reflects thesecommon causes intrinsically tied to and responsible forphenomena causally connected—the phenomena being,in this case, the groups originated through biologicalevolution. But it is the case that ‘‘causal relations implyreality: it is hard to imagine things that do not exist toenter into causal relations’’ (Rieppel, 2008, p. 270). Tofind correspondence between the biogeographical pat-tern of a given taxonomic group and a consilientbiogeographical hypothesis is then to find strongevidence to suppose the taxon shares a causal relation-ship with the history of Earth (see Fig. 1). Its trueexistence is fairly defensible.

Our proposal is based on the assumption that robustbiogeographical hypotheses, when associated withphylogenetic hypotheses, reveal the real evolutionaryhistory of taxa—or, at least, allows us to be close to thishistory. This realistic perspective ‘‘may be more difficultto argue in taxonomy’’ (Rieppel, 2007, p. 182), as onlytaxa with strong biogeographical signal could be com-pared with an already proposed consilient biogeograph-ical pattern. It is important to note that the congruencebetween a phylogenetic hypothesis and a biogeographicalhypothesis can be due to chance only—such cases shouldbe identified a priori (in this sense, the congruence amonglarge cladograms and broad biogeographical hypothesesis better). Besides, our approach relies exclusively onconsilient biogeographical hypotheses, bearing in mindthat some biogeographical inferences (or hypotheses), atleast those obtained via cladistic methods, are themselvesbased on phylogenetic hypotheses, which might suggesttautological reasoning. Consilient hypotheses escape thisbias. As they have been previously tested under different

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classes of evidence and are able to explain otherphenomena not contemplated earlier, consilient hypo-theses come closer to the real structure of the naturalworld. Although a phylogenetic analysis aims to identifymonophyletic groups, these groups are, in fact, productsof evolution. Accordingly, after obtaining a phylogenetichypothesis, its congruence with consilient biogeograph-ical hypotheses may suggest that the phylogenetic patternis not just the result of a well-conducted algorithmicprotocol for phylogenetic analysis, which is instrumen-talist in essence, but depicts a meaningful evolutionaryscenario. To understand evolution in Croizat�s (1964)sense, systematics should encompass a broad realisticview apart from its instrumentalist analytical procedures.Biogeographical consilience, in this context, is a form toapproximate phylogenetic hypotheses to the real mean-ing of the natural world.

Acknowledgements

We thank Eduardo Almeida (USP, Brazil) and twoanonymous reviewers for comments on an earlierversion of this commentary.

References

Assis, L.C.S., 2009. Coherence, correspondence, and the renaissance ofmorphology in phylogenetic systematics. Cladistics 25, 528–544.

Assis, L.C.S., Rieppel, O., 2011. Are monophyly and synapomorphythe same or different? Revisiting the role of morphology inphylogenetic systematics. Cladistics 27, 94–102.

Croizat, L., 1964. Space, Time, Form: The Biological Synthesis.Published by the author, Caracas.

Fisch, M., 1985. Whewell�s consilience of inductions—an evaluation.Philos. Sci. 52, 239–255.

Freckleton, R.P., 2009. A Darwinian approach to community ecology.Front. Biogeogr. 1.2, 44–46.

Grant, T., Kluge, A.G., 2004. Transformation series as an ideographiccharacter concept. Cladistics 20, 29–31.

Haber, M.H., 2005. On probability and systematics: possibility,probability, and phylogenetic inference. Syst. Biol. 54, 831–841.

Kearney, M., Rieppel, O., 2006. Rejecting the ‘‘given’’ in systematics.Cladistics 22, 369–377.

Ladyman, J., 2002. Understanding Philosophy of Science. Routledge,New York.

Leplin, J., 2001. Realism and instrumentalism. In: Newton-Smith,W.H. (Ed.), A Companion to the Philosophy of Science. BlackwellPublishers, Oxford, pp. 393–401.

Morrison, D.A., 2006. Phylogenetic supertrees. Syst. Biol. 55, 530–532.Nelson, G., 2004. Cladistics: its arrested development. In: Williams,

D.M., Forey, P.L. (Eds.), Milestones in Systematics. CRC Press,Boca Raton, FL, pp. 127–147.

Platnick, N.I., Nelson, G., 1978. A method of analysis for historicalbiogeography. Syst. Zool. 27, 1–16.

Rieppel, O., 2007. The nature of parsimony and instrumentalism insystematics. J. Zool. Evol. Res. 45, 177–183.

Rieppel, O., 2008. Hypothetico-deductivism in systematics: fact orfiction? Pap. Avulsos Zool. 48, 263–273.

Rieppel, O., Kearney, M., 2007. The poverty of taxonomic characters.Biol. Philos. 22, 95–113.

Rieppel, O., Rieppel, M., Rieppel, L., 2006. Logic in systematics. J.Zoolog. Syst. Evol. Res. 44, 186–192.

Ruse, M., 1979. Falsiability, consilience, and systematics. Syst. Zool.29, 530–536.

Santos, C.M.D., Capellari, R.S., 2009. On reciprocal illumination andconsilience in biogeography. Evol. Biol. 36, 407–415.

Snyder, L.J., 2005a. Consilience, confirmation and realism. In:Achinstein, P. (Ed.), Scientific Evidence: Philosophical Theoriesand Applications. The Johns Hopkins University Press, Baltimoreand London, pp. 129–148.

Snyder, L.J., 2005b. Confirmation for a modest realism. Philos. Sci. 72,839–849.

Vergara-Silva, F., 2009. Pattern cladistics and the ‘‘Realism–Antire-alism Debate’’ in the philosophy of biology. Acta Biotheor. 57,269–294.

Wagele, J.W., 2005. Foundations of Phylogenetic Systematics. Fried-rich Pfeil, Munich.

Whewell, W., 1847. The Philosophy of Inductive Sciences FoundedUpon Their History, 2nd edn. John W. Parker, London.

Whewell, W., 1860. The Philosophy of Discovery. John W. Parker,London.

Fig. 1. An overview of the biogeographical approach to realism in systematics.

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