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REPLY TO COMMENT BY THERIOT (2008) ON KACZMARSKA ET AL. (2006)1
Version of Record online: 26 AUG 2009
© 2009 Phycological Society of America
Journal of Phycology
Volume 45, Issue 4, pages 987–994, August 2009
How to Cite
Kaczmarska, I. and Medlin, L. K. (2009), REPLY TO COMMENT BY THERIOT (2008) ON KACZMARSKA ET AL. (2006). Journal of Phycology, 45: 987–994. doi: 10.1111/j.1529-8817.2009.00721.x
Received 20 March 2008. Accepted 29 May 2009.
- Issue online: 26 AUG 2009
- Version of Record online: 26 AUG 2009
Vol. 46, Issue 6, 1359, Version of Record online: 1 DEC 2010
Theriot (2008) aimed to demonstrate nontrivial errors in the inferences made regarding evolution of a morphological character (fultoportula, syn. “strutted process”) in thalassiosiroid diatoms published by Kaczmarska et al. (2006). He stated that phylogenetic principles were not upheld in Kaczmarska et al. (2006) because, apparently, our hypotheses were nonparsimonious. He demonstrated this conclusion by applying Patterson’s (1988) tests for homology. Contrary to his impression, our three hypotheses of fultoportula emergence, as ascribed in the goals of our paper (Kaczmarska et al. 2006, p. 122), are sound and consistent with parsimony as a methodological principle. Parsimony is a part of scientific methodology in general and not restricted to phylogenetic systematics (Sober 1988, p. 39; Brooks and McLennan 1991, p. 45).
For accuracy and clarity we will refer the reader to the specific contentious statements made by Kaczmarska et al. (2006) and Theriot (2008) in the following manner. The normal author-year citation will be supplemented by the page number, specific column of the text (either right column [RC] or left column [LC], when appropriate), and a number specifying the line of text when statements are short.
Using the same principles and criteria that Theriot (2008) advocates, we show that his conclusion is incorrect in the case of our tubular hypothesis, while our annular hypothesis is more parsimonious than the one he proposes (we appear to agree on the areolar hypothesis).
First of all, we wish to refer the reader to Kaczmarska et al. (2006, p. 135, LC 33), which gives clear indication that the presentation was made on an initial, original data set (no similar work was conducted prior to our initial submission in 2003). The analysis and hypotheses referred to taxa for which both molecular and morphological data were available (Kaczmarska et al. 2006, p. 127, RC 15–16) and within the framework of the sister relationship between thalassiosiroids and lithodesmioids (ibid., p. 122, RC 37). As much as possible, we refrained from assumptions where unsequenced species would fall onto a tree, however similar their valve morphology might be. Discoveries of unanticipated phylogenetic relationships inferred from molecular data and contradicting those inferred from morphology (including nonmonophyly of stephanodiscaceans first shown in our paper) warranted such caution.
In this rebuttal, we focus on the major contentious issues to show the patterns of errors and misrepresentations in Theriot’s (2008) presentation of our work and in his conclusions. We start with providing schematic illustration of the three discussed hypotheses (Figs. 1–3), as we proposed in our paper for comparison to Figure 4, illustrating the hypothesis that Theriot (2008, p. 831, RC 52, LC 1–20) claims is best supported. This analysis will follow with general comments relevant to the phylogenetic context in which we placed our work. In addition to major errors, Theriot (2008) contains many omissions and other lesser misrepresentations and mistakes describing our work. There are too many of these to address in point-by-point fashion without testing the patience of readers, but we will provide them on request.
Comments regarding the phylogenetic trees. Two issues brought up by Theriot require rebuttal. First, the claim that our alignments were not available to him (Theriot 2008, p. 822, LC 39) is not true. In fact, he received the requested NEXUS files in January 2006 from one of the authors (L. M.), in accordance with Journal of Phycology standards and policies. These files, which contain the bases selected for analyses from the aligned sequences in a format ready for analysis by PAUP and MrBayes, are the only type of files required to reproduce or additionally analyze any of our original molecular data. The alignment alone is insufficient because one does not know from the alignment which bases were selected for analyses.
Second, Theriot casts doubt on the reproducibility of our trees and on the soundness of the relationship between Thalassiosirales and Lithodesmiales. In response, we draw attention to the most recent publication by Alverson et al. (2007, fig. 3; work performed in Theriot’s lab and coauthored by Theriot) where the main clades of thalassiosiroids (with greater taxon sampling and an additional gene) are very similar to those presented in Kaczmarska et al. (2006, fig. 7), with our Clades B, C, and D species clearly identifiable in Alverson et al. (2007, fig. 3) in the same sequence of divergence and species association for those species in common between the two studies. Kaczmarska et al. (2006) Clade F is also clearly recognizable. The major difference between the two papers is a better resolution of “assemblage E” and its relationship to Clade F in Alverson et al. (2007). Kaczmarska et al. (2006) clearly addressed the issues of the topological differences in recovered trees (fig. 6, pp. 129–30) and referred to their work as initial (Kaczmarska et al. 2006, p. 135, LC 33), in need of follow-up work with greater taxon sampling (p. 135, RC 47), and collegially refrained from including genera that at that time were under investigation in Theriot’s lab (p. 122, RC 54).
Furthermore, despite doubting the robustness (Theriot 2008, p. 831, RC 31, “Kaczmarska believes this to be robust…”) of the sister relationship between Lithodesmiales and Thalassiosirales shown in Kaczmarska et al. (2006), Theriot nonetheless writes (in Alverson et al. 2007, p. 195, LC 32) that “the four outgroup taxa were chosen because they consistently comprise the sister clade to Thalassiosirales.” All four of the outgroup taxa are lithodesmioids. The word “consistently” in that publication stands in stark contrast to his doubts expressed in Theriot (2008) regarding this very same relationship shown in our paper.
Kaczmarska et al. (2006, p. 122, RC 39, pp. 132–3, and table 3) clearly recognized and addressed the issues of H1 being dependent on lithodesmioids being a sister clade to thalassiosiroids. Sequence data available up to that date (nuclear-encoded SSU rRNA, plastid-encoded SSU rRNA, and mitochondrial cytochrome oxidase subunit 1) generated by independent laboratories (Medlin et al. 1997, Ehara et al. 2000, Kooistra et al. 2003) demonstrated support for lithodesmioids and thalassiosiroids as sister clades, and we did address exceptions in Kaczmarska et al. (2006, p. 132, RC 23). The most current work in Theriot’s own lab (Alverson et al. 2007) adds to the significance of this relationship.
Comments regarding our evolutionary inferences. Kaczmarska et al. (2006) discussed three hypotheses that could explain the origin of the fultoportula: tubular (H1), areolar (H2), and annular (H3) origin in the context of the sister relationship between lithodesmioid and thalassiosiroid diatoms recovered by molecular phylogeny, schematically illustrated in Figures 1–3. Two hypotheses (H2 and H3, and their permutations) have been known for nearly two decades, and as such we had to address them in our paper. The areolar (H2) hypothesis is known in two variants, one proposed by Syvertsen and Hasle (1982) and another by Round and Crawford (1984); we supported the latter.
The annular hypothesis (annular process and multistrutted process are two names for the same structure) involving some extinct diatoms grossly similar to frustule architecture seen among lithodesmioids was already developed and discussed extensively in earlier publications (Gersonde and Harwood 1990, Medlin et al. 2000). In accordance with Gersonde and Harwood (1990) and Medlin et al. (2000), the annular origin of the fultoportula (H3) was introduced in a broader evolutionary context than H1 and H2 and suggested a sequence of several stages, beginning with Lower Cretaceous and extinct species to modern diatoms to illustrate the hypothetical connection of extinct diatoms to extant lithodesmioids and thalassiosiroids, because no molecular data are available for these extinct species. Because of this fact, H3 involved additional scenarios, some published before (Gersonde and Harwood 1990, Medlin et al. 2000), others under investigation in (then unpublished) projects (Kühn et al. 2006, Sims et al. 2006), and thus were not taken beyond cursory presentation. In comparison of all three hypotheses (H1–H3), Kaczmarska et al. (2006, p. 134, RC 45) focused on the events immediately preceding emergence of the fultoportula (our H3) outside of the broader issue of evolution of central structures involving many extinct lineages (Gersonde and Harwood 1990, Medlin et al. 2000). The hypothesis of a tubular origin of fultoportulae (H1) was new, and thus needed and received the most detailed treatment.
Because Theriot (2008) referred to our hypotheses using his own labeling system, for clarity we schematically illustrate our hypotheses in Figures 1–3 and compare these to Theriot’s best supported hypothesis shown in Figure 4. The closest correspondence between our hypotheses (H1–H3) and labels used by Theriot (2008) is the following: tubular hypothesis (H1) carries the same label in both papers; areolar hypothesis in our paper (H2) is discussed in Theriot (2008) on p. 830, LC 55 to p. 832, LC 1–12 as one scenario of his hypothesis 5; our annular hypothesis (H3) is referred to in Theriot (2008) in separate hypotheses. The closest correspondence between his inferences and our H3 is Theriot’s hypothesis 3. Theriot’s hypotheses 2 and 4 discuss ideas advanced in previous publications (Gersonde and Harwood 1990, Medlin et al. 2000) and was work we were aware of being performed in another laboratory (Kühn et al. 2006, Sims et al. 2006). For this reason, it was not advanced beyond general outline in our paper.
Tubular origin of fultoportula (H1 in Kaczmarska et al. 2006, fig. 1). This hypothesis is parsimonious, sound, and consistent with the data at hand, despite Theriot’s claim to the contrary. It is unclear why Theriot (2008) embarked on an argument regarding “ridges” in T. weissflogii (pp. 823–5). We can find no evidence that we suggested that this diatom has ridges. Consequently, those arguments are irrelevant to our H1. He is in error claiming that we suggest that the lithodesmioid ridge system is the evolutionary precursor to marginal fultoportulae (Theriot 2008, p. 823, RC 2); again, we did not claim this. See Kaczmarska et al. (2006, p. 127, LC 21–22 and p. 133, LC 15) for a clear indication of what we meant. We introduced “valve face protrusions” listing best-known formats (spines, tubular and hair-like protrusions, projections and siliceous flaps) when used for the first time. Later, we shortened the list of types of protrusions to “marginal ridges or fimbria” to avoid cumbersome repetition.
Theriot (2008, p. 824, LC 9–15) is incorrect in writing that we did not hypothesize positional and functional homology of fultoportulae and marginal protrusions. We did in several locations in Kaczmarska et al. (2006, table 3, p. 132, RC 56 and p. 134, LC 34–38). The hypothesis that marginal protrusions (not ridges) are homologues of fultoportulae (H1) is supported by functional and positional similarity of the characters, passing the test for similarity (Fig. 5, and text below). We hypothesized that a “process” (meaning a sequence of steps) whereby a marginal protrusion transformed into external tubes of fultoportulae might have resembled structures similar to those that are formed during valve morphogenesis in T. weissflogii. The term “margin” is used correctly in our writing (Round et al. 1990, pp. 280 and 290). Only two steps are required for a fultoportula in a tube to evolve from marginal protrusions (Fig. 1).
Theriot (2008) claims that the cell-linking function of fultoportulae is incongruent with our H1 (p. 825, LC 22–26). However, this paragraph of his paper is difficult to interpret because we both agree that in most of the taxa of interest, extrusion of chitin threads through the fultoportulae is used to join cells (compare Kaczmarska et al. 2006, p. 133, LC 40 and p. 135, LC 50 to Alverson et al. 2007, p. 194, RC 1–3). The most compelling claim of incongruence in Theriot (2008) makes reference to “14 independent losses” being required to resolve “Group G” taxa (Theriot 2008, p. 825, LC 56). However, because neither our original paper (Kaczmarska et al. 2006) nor Theriot (2008) contain a “Group G” in any tree, this critique is hard to rebut or even understand. In any case, when the cell-linking function of the fultoportulae (inclusive of their exudates, Hasle 1973, p. 68, LC 23) is correctly mapped onto the tree (Fig. 5), there is good internal consistency of this character distribution, thus passing the congruence test.
The hypothesized tubular origin of the fultoportula fails the conjunction test, sensu Patterson (1988) if we accept that “some of the forms similar to hypothesized intermediate stages in the evolution of the fultoportula within the external tube might have resembled an occluded process” (Kaczmarska et al. 2006, p. 133, LC 54). If occluded processes were taken as representing one of the early serial homologues of fultoportulae, the co-occurrence of fultoportulae and occluded processes fails the test of conjunction because Patterson (1988) does not recognize serial homologues as homologues in the strict sense (Theriot 2008, p. 822, LC 27). However, as discussed below, all the hypotheses fail this test, including the one Theriot regards as best supported.
In summary, in contrast to Theriot’s claims, we show that H1 passes the functional similarity test and congruence test (Kaczmarska et al. 2006, table 3, p. 132, RC 56, and p. 134, LC 34–38; and Fig. 5 in this presentation). Theriot (2008) overlooks the fact that the first diagnostic character of Lithodesmiales is its bilabiate process and not their marginal protrusions (ridges being only one of the types present), and a combination of characters to define taxa is often used in diatom taxonomy (Round et al. 1990). We concur that H1, as all hypotheses in science, is sensitive to taxon sampling, irrespective of the approach.
Areolar origin of fultoportula (H2 in Kaczmarska et al. 2006, fig. 2). Kaczmarska et al. (2006, p. 133, RC 20) explicitly state that fultoportulae might have evolved from areolae more directly and illustrate a clear structural resemblance between the two (Kaczmarska et al. 2006, fig. 3d), as also suggested by Round and Crawford (1984) by modification of the basal cribra (two steps in Fig. 2). We did not hypothesize that areolar fultoportulae were derived via an occluded process; Syvertsen and Hasle (1982, text fig. 6) did. Consequently, Theriot’s arguments (2008, pp. 829–30) regarding serial homology of the occluded process and areolae is irrelevant to our hypothesis H2. Whenever appropriate, we gave credit to the work of Syvertsen and Hasle (1982), even though we did not support their hypothesis.
The purpose of Theriot’s criticisms of Syvertsen and Hasle (1982) in our paper is unclear to us. We stated and illustrated (Kaczmarska et al. 2006, p. 133, RC 20, fig. 3d) which of the two previously published hypotheses relating fultoportulae to areolae we follow. We clearly stated that this hypothesis recognizes structural similarity (passes similarity test) between areolae and fultoportulae and requires only simple modifications. Theriot arrived at the same conclusion and could not reject the hypothesis that fultoportulae might have evolved from areolae via modification of the cribra, just as we did and others before us. H2 passes the congruence test (as Theriot 2008 agrees) but fails the conjunction test (as did H1; Theriot’s best supported hypothesis also fails). The areolar origin of the fultoportula is just as well supported as is H1 once errors and misrepresentations of Theriot (2008) are dispensed with.
Annular origin of fultoportula (H3 in Kaczmarska et al. 2006, fig. 3). Disagreement here centers on the evolutionary significance of ancient structures called either multistrutted or annular processes. We felt compelled to include H3 in our discussion because of the published record of this hypothesis, even though we had no molecular data to substantiate the phylogenetic relationship between the extinct and extant diatoms considered in our paper. “Multistrutted” and “annular” processes were discovered independently by Hasle and Syvertsen (1985) and Nikolaev and Strelnikova (1987), respectively. It therefore appears that the “obvious” similarity (Theriot 2008, p. 826, LC 53) of this process to the fultoportula was obvious to Hasle and Syvertsen but not to Nikolaev and Strelnikova. The process is known in extinct diatoms from the genera Thalassiosiropsis and Gladiopsis. Similar to H1 and H2, the annular hypothesis passes similarity and congruence tests but fails the conjunction test, because areolae and annular processes co-occur on the same valves.
Our H1 and H2 place the evolving fultoportula onto valve architecture consistent with known Thalassiosirales, sister to Lithodesmiales (as stated in our goals, p. 122, RC 40–44) and nearly all modern diatoms; they have rimoportulae. The lack of rimoportulae in diatoms carrying annular processes was the main concern we had in 2003 (when Theriot reviewed this manuscript for the first time) and still have, even though morphological transformations needed to derive fultoportulae from annular processes are simple (Fig. 3, two steps), as we said before. However, no currently known species carry both annular processes and rimoportulae. Theriot (2008) claims that the annular process as an intermediate between areolae and fultoportulae is the most parsimonious solution (Fig. 4). For Theriot’s hypothesis to have happened, one of two possibilities must have occurred before thalassiosiroid diatoms evolved: (i) either the lineage bearing an annular process lost rimoportulae after they separated from the last common ancestor with thalassiosiroids, sometime before the Lower Cretaceous when no known diatom carried rimoportulae, or (ii) the thalassiosiroids evolved from an annular-process-bearing, rimoportula-less lineage and acquired it independently. Theriot (2008, p. 831, LC 1–5) seems to support the first scenario, illustrated in Figure 4. Kaczmarska et al. (2006, p. 134, RC 42–44) considered the second scenario (Fig. 3). Comparing Figures 1 through 3, it is apparent that to derive the fultoportula from the annular process (Fig. 3) is as parsimonious as to derive this portula from marginal protrusions, via enclosures with pores (Fig. 1), or directly from an areola with cribra modifications (Fig. 2); all take only two steps. All are more parsimonious than the sequence of steps suggested by Theriot (2008) involving both the areola and annular process (Fig. 4), which takes four steps. Our hypotheses H1 and H2 place the fultoportula in the context of modern diatoms with the sister relationship between Lithodesmiales and Thalassiosirales and is supported by molecular data (Medlin et al. 1997, Ehara et al. 2000, Kooistra et al. 2003, Kaczmarska et al. 2006, Alverson et al. 2007; the latter obtained by Theriot’s lab and with him as coauthor).
Theriot (2008) misquotes Sims (1994) as supporting his point of view. She did not support a close relationship between Thalassiosiropsis and Gladiopsis. She wrote that these diatoms differ in several important respects and thus are not as closely related as previous work suggested (Sims 1994, pp. 181, 185, and abstract). Theriot (2008) is apparently unaware of two extinct genera carrying stratigraphically younger and structurally simpler fultoportulae described from Early Miocene in Japan (Komura 1996), which bear on the understanding of the origin of the fultoportula. Kaczmarska and Ehrman (2008) provided description of an even older fultoportula from an Early Oligocene diatom (the same as the unnamed diatom in Kaczmarska et al. 2006) and showed how structurally simple fultoportular satellite pores are integrated into the perforation pattern of the valve mantle, consistent with nonannular emergence of the fultoportula. Accepting that fultoportulae are present in extinct species described exclusively from light microscope investigation as Theriot suggests should be taken with caution as quite a few of these “thalassiosiroids” have been reassigned to non-fultoportulate genera (Gleser et al. 1988, Barron 2005).
In summary, it requires only two steps to derive the fultoportula from the annular process under our H3. Only two steps are also required under either of our hypotheses H1 and H2. All are equally parsimonious, as we stated in our paper. With four necessary steps to derive fultoportulae from areolae via the annular process, Theriot’s favored hypothesis (Fig. 4) is less parsimonious compared to those discussed in our paper, with or without the sister relationship between Thalassiosirales and Lithodesmiales. The relationship between the two sister clades is supported by molecular data (as stated in Kaczmarska et al. 2006) and has gained further support in the more recent publication from Theriot’s own lab (Alverson et al. 2007), making consideration of the origin of the fultoportula outside this relationship contrary to existing scientific evidence obtained independently in several laboratories.
Comments of general philosophical nature. First of all, we take strong exception to Theriot’s (2008) implications that the principle of parsimony and critical examination of similarity (with intent to formulate a proposition of homology) can only be practiced within the conceptual and methodological framework of cladistics. “Lex parsimoniae” is a tool of logical analysis known for centuries and used by many fields of science and philosophy; it is not reserved for phylogenetic analyses conducted in a cladistic framework. Cladists also agree that parsimony, as a methodological principle is a part of scientific methodology in general (Sober 1988, p. 39; Brooks and McLennan 1991, p. 45). The latter authors write that “use of parsimony in phylogenetic systematics is no different from its use in any other branch of biology or any other science.” Therefore, there is no reason to speculate that the principle of parsimony was not followed in our work even if Patterson (1988) was not.
Similarly, deductive reasoning is also nothing new to science (having roots in the work of Aristotle), nor is logic or critical evaluation of soundness, completeness, and internal consistency of the data set at hand and are not reserved for specific types of studies (e.g., phylogenetic analysis performed with application of cladistic techniques). These are well-established, rigorous tools in scientific methodology (phylogenetic systematics being one of the fields using them with a very specific vocabulary) routinely used by scientists, including Kaczmarska et al. (2006). These methods leave no room for “expert opinions.”
Furthermore, similarity of structure (or function) has been used to infer homology ever since Darwin wrote about “descent with modification” from common ancestry, yet Theriot (2008, p. 826, RC 31) claims that homology cannot even be proposed without reference to Patterson (1988). However, similarity “cannot be considered as a test of homology because it constitutes the very source of primary homology propositions. It cannot possibly refute a conjecture that was derived from it in the first place” (de Pinna 1991, p. 377). Rather than a test, it appears to be a case of circular reasoning. Similarity (form, function, etc.) is what compels evolutionary biologists to postulate homology, with or without Patterson (1988).
Two other Pattersonian tests for homology, conjunction and congruence, have long been challenged by many examples where they do not apply (Roth 1984, Cronquist 1987, Wagner 1989, Williams 1992, Butler and Saidel 2000, Hull 2003,Cracraft 2005, Rutishauser and Moline 2005) and specific cases discussed below. The conjunction test is “violated” by numerous organisms where homologues co-occur on the same individual in great numbers and with numerous intermediates, for example, leaves and sepals, or stamens and petals in countless species of flowering plants, microphylls and sporophylls in lycopods, megaphylls and sporophylls in ferns, all sorts of modifications of leaves for a variety of purposes in terrestrial plants, scutes and feathers on birds, limbs of vertebrates, and so forth (Ruvinsky and Gibson-Brown 2000, Honma and Goto 2001, Irish and Litt 2005). These cases question the universal usefulness and “absolute” scientific validity of the test, particularly in the strict Pattersonian sense, as Theriot (2008, p. 822, LC 27) advocates. We observe that all of our hypotheses, as well as Theriot’s favorite, fail this test.
Even a test as useful as the test of congruence (internal consistency is a commonly tested property in any investigated logical system) has been shown to detect false homoplasies in cases where molecular homology is otherwise well established, for example, transspecific and transgeneric polymorphisms (Ward et al. 2002, Igic et al. 2006). It is now well documented that molecular “blueprints” for structures, metabolic pathways, or even body parts are not erased from the genome of the organism (and thus lineages) upon their phenotypical “disappearance” in individuals and species (Ward et al. 2002, Charlesworth et al. 2005, Igic et al. 2006) but are available for redeployment and modification(s) in later divergences (e.g., Malakowski 2000, 2003, Irish and Litt 2005, Borowsky 2008). We therefore acknowledge that our understanding of the genetic mechanisms behind the “disappearances” and “reappearances” of putative homologues is still too limited to accept that all character losses involve total deletion of gene sequence(s), whereas all gains mean independent acquisition of the gene sequence(s) of the character. The “massive independent gains/losses” of the characters if our hypothesis H1 were to be accepted (Theriot 2008, e.g., p. 825, LC 56 and p. 830, LC 12) clearly speaks of the latter context. We use the examples above primarily to expose weaknesses in Theriot’s approach and then only as a possibility that merits consideration.
A set of fundamental assumptions, limitations resulting from those assumptions, and a discussion of when cladistic parsimony should or could not be applied in phylogenetic reconstructions are nicely spelled out by Mishler and Theriot (2000, p. 49). This balanced perspective is missing from recent critiques of our work (Theriot 2008).
Conclusions. We wish to emphasize that we welcome scientific and philosophical debate from a basis of accuracy and fact. We do object to our work being misrepresented as unscientific because we postulated homology “with no reference to Patterson (1988).” We also show that alleged weaknesses of our molecular analyses are present only in Theriot’s (2008) writing, whereas published data (including Theriot’s own publications) support the tree topology from Kaczmarska et al. (2006) and the sister relationship between Lithodesmiales and Thalassiosirales, providing a morphology independent framework to assess putative homology among species examined. Theriot cannot be right in both perceptions, casting doubt on the quality of our analysis and at the same time publishing his own work showing basically the same trees. We show that our hypotheses were sound within the goals we defined and data we had available in 2002–2003 when work was performed, that they stand up to scrutiny, and, in actuality, are more parsimonious than Theriot’s preferred hypothesis of fultoportula emergence involving extinct diatoms with an annular process.
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