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Plant Ecology and Evolution 152 (2): 131–141, 2019 https://doi.org/10.5091/plecevo.2019.1612 REVIEW Rampant homoplasy and adaptive radiation in pennate diatoms J. Patrick Kociolek1,2,*, David M. Williams3, Joshua Stepanek4, Qi Liu5, Yan Liu6, Qingmin You7, Balasubramanian Karthick8 & Maxim Kulikovskiy9 1Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80503, USA 2University of Michigan Biological Station, Pellston, MI 49769, USA 3Department of Life Sciences, the Natural History Museum, Cromwell Road, London, SW7 5BD, UK 4Department of Biology, St. Cloud State University, St. Cloud, MN 56301, USA 5School of Life Science, Shanxi University, Taiyuan 030006, China 6College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China. 7College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China 8Biodiversity and Palaeobiology Group, Agharkar Research Institute, GG Agarkar Road, Pune – 411004, Maharashtra, India 9Institute of Plant Physiology, Russian Academy of Sciences, 127276, Moscow, Russia *Author for correspondence: [email protected] Background and aims – We examine the possibility of the independent evolution of the same features multiple times across the pennate diatom tree of life. Methods and key results – Features we have studied include symmetry, raphe number and amphoroid symmetry. Phylogenetic analysis, with both morphological and molecular data suggest in each of these cases that the features evolved from 5 to 6 times independently. We also look at the possibility of certain features having evolved once and diagnosing large genera of diatoms, suggestive of an adaptive radiation in genera such as Mastogloia, Diploneis and Stauroneis. Conclusion – Formal phylogenetic analyses and recognition of monophyletic groups allow for the recognition of homoplasious or homologous features. Key words – Diatoms, homoplasy, phylogeny, characters, monophyly, molecular data, morphological data, species flocks. INTRODUCTION characterizing monophyletic groups and placing them within a natural classification (Lundholm et al. 2002a, 2002b). For some time now we have advocated basing diatom taxa, For some results, under some circumstances, there are and by extension, the discovery of a natural system of clas- inconsistencies between the evidence from morphology and sification, on monophyly alone (Kociolek & Williams 2015, the evidence from molecules. The reasons for inconsisten- Williams & Kociolek 2010). It is heartening to see that now cies, or incongruence, are many but in this paper, we will some who raised issues in opposition to this criterion (Mann discuss a few examples relating to the discrimination of ho- 1997, Medlin 2010, 2016, Medlin & Kaczmarska 2004) have mology from homoplasy, discriminating signal from noise. adopted this approach (Medlin 2018, Vanormelingen et al. We have focused on this aspect of inconsistency because it is 2007, 2008). In both morphological and (especially) mo- best rectified by reconsideration of the morphological char- lecular studies there has been a tremendous amount of work acters involved. © 2019 The Authors. This article is published and distributed in Open Access under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits use, distribution, and reproduction in any medium, provided the original work (author and source) is properly cited. Plant Ecology and Evolution is published by Meise Botanic Garden and Royal Botanical Society of Belgium ISSN: 2032-3913 (print) – 2032-3921 (online) Pl. Ecol. Evol. 152 (2), 2019 HOMOPLASIES AND HOMOLOGUES times contradictory, reasons (Schütt 1898, Karsten 1928, Pat- rick & Reimer 1975, Krammer & Lange-Bertalot 1986), that Diagnosing monophyletic groups with morphological fea- the canal raphe system, used to suggest close relationships tures that are synapomorphic for a lineage is an important between Bacillariales Hendey, Rhopalodiales D.G.Mann and part, if not the most important part, of systematic studies. Surirellales D.G.Mann, evolved twice: once in Bacillariales, This involves recognizing characters that might be under- positioned in the more basal part of the raphid diatom tree stood as homologues in different taxa. Whereas there have of life, and a second time in a clade uniting Rhopalodiales been methods (or tests) for determining whether features are and Surirellales (first shown in Medlin & Kaczmarska 2004). homologous (Patterson 1982), formal phylogenetic analyses Whereas the feature canal raphe can separately diagnose and the determination of most parsimonious hypotheses will Bacillariales and Rhopalodiales + Surirellales, a single group identify which character states are homologous and which (taxon) uniting all three is not recognized using molecular are not; those that are not are usually called homoplasies. For data (Medlin & Kaczmarska 2004, Ruck & Theriot 2011). example, the valve process first called a strutted process but Similarly, Witkowski et al. (2015) elegantly demonstrated now better known by its Latin name, fultoportula, was de- that the systematic position of the enigmatic genus Simon- fined as: “[…] a tube through the valve surrounded by 2–5 senia Lange-Bert., and the homoplastic nature of some of its chambers or pores […] through the valve wall separated in- features. When the genus was first proposed (Lange-Bertalot ternally by arched supports, often with threads extruded from 1979), prior to the arrival of large-scale (in terms of taxa and/ the exterior part” (Anonymous 1975: 328, Ross et al. 1979: or genes) molecular studies, Simonsenia was thought to be an 522). Thalassiosiraceae Lebour was given as an example, intermediate between groups that possess canals and keels on where it was later noted of that family that the “[…] fultopor- only the side of the valve (Bacillariales) and the Surirellales, tulae […] are confined to the centric order Thalassiosirales” which have canals, keels and fenestrae and portulae around (Round et al. 1990: 35) and, later, “all having strutted process the periphery. Simonsenia has keels, fenestrae and portulae [fultoportula] as the main morphological, taxonomic charac- on one side of the valve. Witkowski et al. (2015) showed that ter” (Hasle & Syvertsen 1996: 29 – they go on to define the keels, fenestrae and portulae are homoplastic between the fultoportula more precisely than in the two terminology pa- Bacillariales and Surirellales. As Witkowski et al. (2015: 1) pers). The processes where first formally recognised by Ha- noted “Lack of homology between the surirelloid and simon- sle (1972), who used the term ‘strutted tubuli’, and Ross & senioid keels is reflected in subtle differences in the morphol- Sims (1972: 160), who used the term fultoportula – that is, ogy and ontogeny of the portulae and fenestrae”, thus, there the structure, and its limited distribution in diatoms, was rec- is no single group (taxon) of that has all of these features. ognized by morphologists once the structure was examined Recognition of homology and homoplasy is a natural out- using the scanning electron microscope (“Under the light mi- come of any formal phylogenetic study. Our attention in this croscope it is often impossible to distinguish between spines, paper focuses on situations where features that have been rimoportules and fultoportules”, Ross & Sims 1972: 160). used to support classification schemes have not only turned Hasle used the feature to diagnose the Thalassiosiraceae out to be homoplasious, but also the degree of homoplasy is (1973) and Hasle & Syvertsen refer to the “main morpho- substantial, which we term here, “rampant” homoplasy, be- logical, taxonomic character” of the family (Hasle & Syvert- cause the apparent same features is identified in several line- sen 1996: 29), which, adopting a more modern terminology, ages. We suggest these features have been used to classify means fultoportulae are recognized as homologous and as a diatoms for a number of reasons: their ease of recognition synapomorphy for Thalassiosiraceae (-ales). Further, recent (features that are “Convenient”); those thought to be fun- summaries of molecular data and their results, support the damental because of their function and importance (“Con- view that fultoportulae evolved only once, that they are syna- servative” features); and those features that are, because of pomorphic for Thalassiosiraceae (-ales) (Sims et al. 2006, their structural organization, so complex that it could have Theriot et al. 2015). Fultoportulae are homologous for all evolved once (“Complex” features). taxa that possess it; it diagnoses a monophyletic group and Identifying rampant homoplasy in morphology for pen- we recognize this group in our classification system. nate diatoms is based on the recent accumulation of molecu- Similarly, it appears that the raphe system evolved once lar studies that facilitate the interpretation (or re- interpre- and it is homologous for all taxa that have it (or used to tation) of character state evolution. It is quite possible that have it, because some taxa do not have a raphe caused by similar outcomes will be elsewhere in other groups of dia- secondary loss). The presence of a raphe system diagnoses toms as well. For each example, we cite one or more anal- a monophyletic group that we recognize in our classifica- ysis that supports the notion of rampant homoplasy within tion system as raphid diatoms (Bacillariophyceae Haeckel). pennate diatoms. Our examples
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