1 From: Dr. hab. Joanna LENARCZYK, Ph.D.
W. Szafer Institute of Botany Polish Academy of Sciences Lubicz 46
31-512 Kraków, Poland
To: Doc. RNDr. Yvonne NEMCOVA, Ph.D., FRSC Chair of the examination board
Faculty of Science Charles University
Doctoral Study Department Albertov 6
128 00 Praha 2, The Czech Republic
Review of Kateřina Woodard’s Ph.D. dissertation
Mgr. Kateřina Woodard submitted in 2023 Ph.D. dissertation entitled “Quantitative shape analysis of diatom frustules: asymmetry, allometry and morphospace structure”.
Summary of the dissertation
The main content of the dissertation are three published papers and one book chapter submitted to
“Biological Shape Analysis – Proceeding of the International Symposium”. The papers were published over a relatively long period of time (2016–2022); this is acceptable considering the maternity leave of K. Woodard in this period. I appreciate that the papers were published in recognized international peer-reviewed journals (Diatom Research and Symmetry with Impact Factors 1.4–2.940) and the fact that K. Woodard is the first author in each of the three articles and in the book chapter, and wrote all the manuscripts. Her main contribution in completing the research was attested by her supervisor prof.
RNDr. Jiří Neustupa, Ph.D.
The dissertation focuses on the phenomenon of shape dynamics in selected algal taxa of pennate diatoms (Bacillariophyceae) using semilandmark based geometric morphometric methods, which have only sporadically been used in diatom analysis before. The subject studied by the Ph.D. candidate is ambitious because it requires both experimental (sometimes laborious and time consuming) and numeric-analytic skills and effort.
The List of scientific articles included in the dissertation, the Authors’ Contributions and the short Abstract are followed by the 18-page Introduction chapter, including 7 pages of a rich list of references dating from the 19th century up to 2023.
The thesis of the dissertation is not clearly defined. The Introduction chapter lacks the statement of research problem, or at least of clearly defined scientific aims. Instead, the candidate presents the main topics of research she conducted and describes the peculiar diatom morphology, life cycle, allometry, types of symmetry and asymmetric deviations in this algal group.
The studies presented in the three articles and in the book chapter were based on a variety of materials, including algal strains, a sample from environment and iconographic documentation of diatoms published in the literature. The first publication shows that circularity and shape variation of valves increases with decreasing cell size, whereas asymmetry does not change in a few naviculoid genera. The important result of the next article is that directional asymmetry (DA) in two Luticola poulickovae strains is significant, indicating a previously unknown systematic asymmetry in this species, which may be related to the ornamentation of the central area of its valves. According to the authors, DA was analysed in diatoms for the first time. The third publication, on the other hand, shows that bilateral asymmetry in Eunotia bilunaris complex occurring in natural conditions increases in the asexual diminution series and is mostly confined to central parts of the ventral valve outlines. Based on the rich iconographic documentation comprising seventy Eunotia species, the submitted book chapter illustrates that ontogenetic shape changes are relatively conservative across the genus level, especially in species mostly characterized by the Eunotia bilunaris-like morphology, whereas only a
2
few other species, often with more complex shapes, have divergent trajectories in the ontological morphospace. According to the authors, this may indicate the potential of these species for morphological and evolutionary diversification. This claim does not seem to be sufficiently grounded in the dissertation.
The dissertation ends with a short (one and a half page) chapter entitled Key results and Conclusions, where the author properly summarises her results and suggests other methods for analysing diatom morphology.
General questions for the Ph.D. candidate
1. In the Introduction section of your first article, your “aim was to describe and quantify the general patterns of the shape dynamics connected to the diatom life cycle” (p. 31). Considering the fact that for your studies you selected four strains characterized by similar size, valve shape and symmetry, please explain to what extent your results on the morphological variability (circularity, disparity, asymmetry) can be extrapolated on the whole diatom group? Do your results apply to diatoms having various morphology, including large (e.g. some Pinnularia) and small (e.g. some Navicula) taxa, and taxa with various shapes and types of asymmetry (vertical – heteropolar, e.g.
in Gomphonema, horizontal – dorsiventral, e.g. in Halamphora, transversal – sigmoid, e.g. in Gyrosigma)?
2. In the Discussion section of your second article on two diatom strains of Luticola poulickovae, you pointed to relatively high measurement error (ME) estimates and the possibility of significant limitation of ME levels by using high-precision microphotographs (pp. 64–65). Do you think that using scanning electron microphotographs which are commonly used in taxonomic works on diatoms instead of microphotographs obtained with a light microscope in your study could reduce the ME levels in your dataset?
3. In the Discussion section of your third article, you concluded that “the strong allometric relationship of the asymmetric deformations in Eunotia bilunaris, contrasting with the absence of similar patterns in the subtle shape fluctuation asymmetry in the generaNavicula, Luticola, and Sellaphora grown under optimal conditions, provides indirect evidence that the observed variation represented a teratogenic response at the population level that was accentuated in the course of the vegetation cycle” (p. 81). What kind of analysis would you perform to obtain direct evidence of the teratogenic response? How would laboratory experiments on a monoclonal strain of Eunotia bilunaris in controlled conditions instead of a sample from environment be suitable for that?
4. In the submitted book chapter, your analysis of allometric trajectories in the genus Eunotia is based on published microphotographs of specimens from various environmental conditions. How, in your opinion, the results of the trajectories could differ if the analysis was based on cultured strains in the same laboratory conditions?
5. In the Discussion section of your submitted book chapter, you stated that “species typical by divergent allometric trajectories often had complex/elaborate shapes” and that these species “in general, (...) were characterized by more heterogeneous shape changes during the size reduction phase”. Your observation was that “the complexity of the outlines and the heterogeneity are not necessarily related and testing this hypothesis may be a future area of research” (p. 102). How would you plan an experiment, as well as data collection and analysis to test this hypothesis?
Other remarks and suggestions on the Ph.D. dissertation
1. In the first article,a) light or scanning electron microphotographs of all four studied strains should be shown pointing on the types of symmetries they have (vertical, horizontal, and transversal),
b) the mistake in Fig. 5 (percentages of the first and second relative warps are replaced with each other) should be removed.
2. In the second article,
a) Tables 1 and 2 would be more related to the description of the results if the abbreviations of directional asymmetry (DA), fluctuating asymmetry (FA) and measurement error (ME) were added to the tables,
b) it would be helpful to show positions of the stigma and the raphe in Figs 7 and 8.
3 3. In the submitted book chapter,
a) examples of groups of organisms in which species with more divergent allometric trajectories are morphologically and evolutionary more diverse could be given, if they exist (p. 103), b) item numbers should be added to Table 1,
c) drawings of species, which were described in the text (p. 97), for extreme values of both relative warps (RW1 and RW2), should be added to Figs 2 and 3,
d) description of morphology (p. 99) should only consider species presented in Fig. 4,
e) a specific location of the species showing various allometric shape changes should be added to the morphospace in Fig. 4.
4. In the Introduction of the dissertation,
a) the title of the paragraph “Diatom morphology, morphogenesis and allometry” should be changed into a title like “Diatom systematics” (p. 11), which would better reflect its content;
the present title is split and repeated later (p. 13 “Frustule morphology”, p. 14 “Valve morphogenesis”, p. 15 “Diatom life cycle and morphological allometry”),
b) more figures should be added, especially those presenting the pores and the raphe in the studied taxa (p. 13), explaining the cis, trans and cis/trans frustules (p. 14), presenting examples of diatom taxa having various types of asymmetry (p. 19) and presenting diatom taxa the author studied in the frames of the dissertation (p. 21),
c) explanation of the abbreviations LM (p. 13) and SA:V (p. 17) should be given,
d) explanation of what is presented in Fig. 2 should be made more clearly using terminology given on p. 14, e.g. sternum, nodule (p. 15),
e) the letters in the caption of Fig. 4 should be made in accordance with the letters in this figure (p. 20),
f) an order in the cited articles should be made (pp. 22–28), including addition of numerous items to the References (Williams & Kociolek 2007; Mann 1988; Falasco 2021; Falasco et al.
2009a, b; Lavoie et al. 2012; Cooper et al. 2003; Cattaneo 2004; Olenici et al. 2017;
Klingenberg et al. 2002) and removal of a few items from the References (Adams et al. 2013;
Cattaneo et al. 2004; Klingenberg 2002; Lavoie et al. 2017; Mann & Round 1988; Pappas et al. 2014).
5. I wonder if the title of the submitted chapter is correctly written in the dissertation; should the number of the symposium be added (p. 5)?
6. The text of the Abstract, the Introduction, the Key results and Conclusions, and the References should be justified.
7. Minor punctuation errors should be removed from the dissertation.
I have no comments to the linguistic preparation of the dissertation.
I declare neither bias nor conflict of interest in relation to the author of the dissertation.
Conclusion
The Ph.D. dissertation presents novel results which broaden our understanding of patterns of morphological variability in diatom taxa during life cycle and the new possibilities which geometric morphometrics offers for assessing this variability. The dissertation shows that Ph.D. candidate Kateřina Woodard performed sufficient research and has predisposition for scientific work, including designing original studies, her patience while conducting long-term laboratory experiments and collecting data, skills in applying complex geometric morphometric methods, as well as ability to publish articles in recognized peer-reviewed journals. Judging by the dissertation, the candidate Kateřina Woodard merits the Ph.D. degree. Therefore, I recommend the dissertation for the defence.
In Kraków on 10th March 2023
Dr. hab. Joanna LENARCZYK, Ph.D.
