Kirk Fitzhugh’s research while affiliated with Natural History Museum of Los Angeles County and other places

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Publications (49)


The monophyly of Magelona F. Müller, 1858 (Polychaeta, Magelonidae): Comments on Meißner et al.'s (2023) reinstatement of Octomagelona Aguirrezabalaga, Ceberio & Fiege, 2001
  • Article

August 2024

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60 Reads

Zootaxa

Kirk Fitzhugh

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The first published phylogenetic hypotheses involving members of the polychaete taxon Magelonidae Cunningham & Ramage, 1888, were reported by Mortimer et al. (2021), wherein results showed that for the two genera in the family, Magelona F. Müller, 1858, was paraphyletic relative to Octomagelona Aguirrezabalaga, Ceberio & Fiege, 2001. The only option to formally name at least some of the resultant phylogenetic hypotheses was to place Octomagelona into synonymy with Magelona, leaving the definition of Magelonidae redundant with that of a monophyletic Magelona. Meißner et al. (2023) subsequently described specimens as members of new species, Octomagelona borowskii Fiege, Knebelsberger & Meißner, 2023, and O. sp. cf. O. borowskii, with the view that Octomagelona should be maintained as distinct from Magelona. We present reasons why reestablishing the paraphyly of Magelona is scientifically unwarranted.


Putting the cart before the horse: SeqCode’s attempt to solve systematics issues with changes to nomenclature

December 2022

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141 Reads

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2 Citations

Bionomina

This opinion paper examines the recent proposal for a new nomenclatural code for prokaryotes (SeqCode). It addresses four problematic issues: (1) epistemological—failure of the SeqCode to acknowledge taxa as explanatory hypotheses, (2) conceptual—designating as a name-bearer a coded section of the genome of an organism, (3) operational—changing nomenclatural procedure as a means of resolving systematic challenges, and (4) political (policy)—SeqCode developed independent in opposition to the International Committee on Systematics of Prokaryotes (ICSP). Each of these matters should be alarms to the scientific community as the SeqCode proposal embodies many potentially negative consequences that would dramatically hinder systematics (science) and nomenclature (a tool in science) in other groups of organisms, e.g., animals, plants, fungi, if analogous proposals were sought.


Figure 1. Map of distribution of Euclymene species, including the new species described in this paper. (1) E. vidali sp. nov., (2) E. coronata, (3) E. dispar, (4) E. luderitziana, (5) E. natalensis, (6) E. mossambica, (7) E. lindrothi, (8) E. droebachiensis, (9) E. palermitana, (10) E. collaris, (11) E. lombricoides, (12) E. oerstedii, (13) E. annandalei, (14) E. uncinata, (15) E. trinalis, (16) E. aucklandica, (17) E. insecta, (18) E. delineata.
Figure 2. Euclymene vidali sp. nov. (a), Anterior end showing the first four chaetigers and mouth; (b) anterior end showing first achaetigerous segment, and peristomium; (c) Cephalic plate showing nuchal grooves and length of prostomium (Modified from De Assis & Christoffersen 2011); (d) Parapodium showing acicular spine and capillary chaetae (Modified from De Assis & Christoffersen 2011); (e) Parapodium from chaetiger 9, showing modified serrate capillary chaetae, and limbate capillary chaetae; (f) Parapodium from chaetiger 15 showing spinose, and limbate capillaries chaetae. Abbreviations: acha, achaetiger head; as, acicular spine; cha, chaetigers; cp, cephalic plate; sec, serrate capillary chaetae; lic, limbate capillary chaetae; spc, spinose capillary chaetae chaetae; m, mouth; nc, notochaetae; ng, nuchal groove; pe, peristomium; pr, prostomium; sc, spinose capillary. Scales bars: (a) = 1 mm; (b) = 300 µm, (c, d, e, f) = 100 µm.
Figure 3. (a) Tufts of modified serrate capillary chaetae from chaetiger 9; (b-c) spinose and limbate capillaries chaetae from chaetiger of segment 15; (d) acicular spine of first chaetigerous segment, with denticulate tip; (e) Row of rostrate uncini from chaetigerous segment 15; (f) Rostrate uncini from chaetigerous segment 15 showing capitium, rostrum and barbules. Abbreviations: as, acicular spine; b, barbules; c, capitium, d, denticules; sec, serrate capillary chaetae; lic, limbate capillary chaetae; r, rostrum, ru, rostrate uncini; sc, spinose capillary chaetae. Scales bars: (a-f) = 10 µm.
Figure 4. (a) Posterior end of Euclymene vidali sp. nov. Showing the pre-pygidial achaetous segment and pygidium (Modified from De Assis & Christoffersen 2011); (b) Anal funnel with sub-triangular cirri showing a long midventral cirrus (Modified from De Assis & Christoffersen 2011). Abbreviations: ac, anal cirri; ppa, pre-pygidial achaetiger; ch, chaetigers; cr, callus ring; mvc, medioventral cirrus; ne, neuropodium; nt, notopodium; p, pygidium. Scales bars: (a) = 1 mm, (b) = 200 µm.
Figure 5. (a) anterior end of Euclymene vidali sp. nov. showing the first chaetigerous segment and prostomium with ocelli; (b) Median segments of Euclymene vidali sp. nov. showing longitudinal glandular strips; (c) Nephridial papillae from chaetigerous segment 6; (d) Posterior end of Euclymene vidali sp. nov. with one preanal achaetigerous segment and pygidium. Abbreviation: Np, nephridial papillae. Scales bars: (a and d) = 1 mm, (b and c) = 300 µm. -Ten chaetigers; cephalic plate with slight lateral notches; posterior edge slightly crenulated ……………………..E. delineata* Moore, 1923

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A new species of Euclymene (Maldanidae, Annelida) from Brazil, with new combinations, and phylogenetic implications for Euclymeninae
  • Article
  • Full-text available

December 2022

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360 Reads

Anais da Academia Brasileira de Ciências

Abstract Maldanids are tube-building polychaetes, known as bamboo-worms; inhabit diverse marine regions throughout the world. The subfamily Euclymeninae was proposed to include forms with anal and cephalic plates, a funnel-shaped pygidium, and a terminal anus. Euclymene, the type genus of Euclymeninae, has about 18 valid species. Euclymene vidali sp. nov. is defined and members of the species described from Northeastern Brazil. Members of this species have 23 chaetigers, and one pre-pygidial achaetous segment; nuchal grooves extend through three quarters of the cephalic plate, and there is one acicular spine with a denticulate tip. Euclymene africana, and E. watsoni, are here recognized, respectively, as Isocirrus africana comb. nov., and I. watsoni comb. nov. Three monotypic genera are invalid: Macroclymenella, Eupraxillella, and Pseudoclyemene; their species should be recognized as Clymenella stewartensis com. nov., Praxillella antarctica com. nov., and Praxillela quadrilobata com. nov., respectively. An identification key and a comparative table for all species of Euclymene are provided. A comparative table for all genera of Euclymeninae is also furnished. The paraphyletic status of Euclymene and Euclymeninae is discussed. The taxon Maldanoplaca is not code compliant and should only be regarded as an informal name.

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Who’s who in Magelona: phylogenetic hypotheses under Magelonidae Cunningham & Ramage, 1888 (Annelida: Polychaeta)

September 2021

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559 Reads

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13 Citations

Known as shovel head worms, members of Magelonidae comprise a group of polychaetes readily recognised by the uniquely shaped, dorso-ventrally flattened prostomium and paired ventro-laterally inserted papillated palps. The present study is the first published account of inferences of phylogenetic hypotheses within Magelonidae. Members of 72 species of Magelona and two species of Octomagelona were included, with outgroups including members of one species of Chaetopteridae and four of Spionidae. The phylogenetic inferences were performed to causally account for 176 characters distributed among 79 subjects, and produced 2,417,600 cladograms, each with 404 steps. A formal definition of Magelonidae is provided, represented by a composite phylogenetic hypothesis explaining seven synapomorphies: shovel-shaped prostomium, prostomial ridges, absence of nuchal organs, ventral insertion of palps and their papillation, presence of a burrowing organ, and unique body regionation. Octomagelona is synonymised with Magelona due to the latter being paraphyletic relative to the former. The consequence is that Magelonidae is monotypic, such that Magelona cannot be formally defined as associated with any phylogenetic hypotheses. As such, the latter name is an empirically empty placeholder, but because of the binomial name requirement mandated by the International Code of Zoological Nomenclature, the definition is identical to that of Magelonidae. Several key features for future descriptions are suggested: prostomial dimensions, presence/absence of prostomial horns, morphology of anterior lamellae, presence/absence of specialised chaetae, and lateral abdominal pouches. Additionally, great care must be taken to fully describe and illustrate all thoracic chaetigers in descriptions.



Phylogenetic Inference and the Misplaced Premise of Substitution Rates

May 2021

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46 Reads

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4 Citations

Acta Biotheoretica

Three competing 'methods' have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.


13th International Polychaete Conference (IPC13) Editorial

December 2020

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40 Reads

Zoosymposia

BRUNO PERNET

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KIRK FITZHUGH

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[...]

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CHRISTINE WHITCRAFT

In 1989, Donald Reish hosted the 3rd International Polychaete Conference (IPC3) in Long Beach, on the campus of California State University Long Beach. In 2015 he asked one of us (Bruno Pernet) if it might be possible to bring IPC13 back to Long Beach, thirty years later. Bruno assembled a planning committee consisting of himself and Christine Whitcraft (CSU Long Beach), Kirk Fitzhugh and Leslie Harris (Natural History Museum of Los Angeles County), and Larry Lovell (Dancing Coyote Environmental). The committee’s proposal was accepted at the International Polychaetology Association (IPA) general meeting in Wales in 2016, and the planning committee morphed into an organizational committee!


Taking a closer look: an SEM review of Levinsenia species (Polychaeta: Paraonidae) reported from California

March 2020

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531 Reads

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5 Citations

Zootaxa

Scanning electron (SEM) and light microscope examinations of members of Levinsenia Mesnil, 1897, species from California yielded a new species, new characters, emended name and range extension for L. kirbyorum Lovell, 2002. Specimens of L. gracilis (Tauber, 1879) from Sweden, Iceland, and California were compared and could not be distinguished on the basis of morphology. Two other Californian species, L. multibranchiata (Hartman, 1957) and L. oculata (Hartman, 1957), were also examined. SEM revealed features previously undescribed for the genus. Additional prostomial ciliary bundles, dorsal transverse ciliary branchial connections, notopodial sensory pores, and neurochaetal fascicle configurations. Levinsenia barwicki n.sp. possessing a terminal sensory organ, 4-8 leaf-like ciliate branchiae, and recurved neurochaete with distal hood is described More SEM work is necessary to confirm if these features are present among other members of Levinsenia and other Paraonidae genera. The status of Levinsenia according to the phylogenetic analysis performed by Langeneck et al. (2019, Molecular Phylogenetics and Evolution, 136, 1-13) is discussed.



Phylogenetic analysis of the family Telothelepodidae Nogueira, Fitzhugh & Hutchings, 2013 (Annelida: Terebelliformia)

May 2017

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803 Reads

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6 Citations

Marine Biology Research

Members of the 12 known species of the family Telothelepodidae, plus individuals of three additional undescribed species, were examined to infer phylogenetic relationships within the family and evaluate the status of genera. The outgroups include members of three species of Polycirridae and three of Thelepodidae. Members of 21 species, including both in- and outgroups, were coded for 47 subjects (‘characters’) and 109 characters sensu stricto (subject-predicate relations or ‘states’). The results, based on 15 minimum-length trees, each 103 steps long, suggest that telothelepodids should be divided into four genera, according to the morphology of the lower lip, presence or absence of eyespots, and visibility of segment 1. By necessity two of these genera are monotypic and plesiomorphic to two monophyletic genera; the latter two genera with five and eight species, respectively. Telothelepus, Parathelepus and Rhinothelepus are redefined, and the new genus Mesopothelepus gen. nov. is erected, all to accommodate the phylogenetic hypotheses presented. The problem of properly defining monotypic supraspecific taxon names as representative of phylogenetic hypotheses is discussed in relation to the inherent limitations of Article 13.1.1 of the International Code of Zoological Nomenclature. http://zoobank.org/urn:lsid:zoobank.org:pub:8C05DBD2-8226-4738-BF4A-E623A97ACB75


Citations (41)


... Naturally enough, the SeqCode makes no specific provisions for eukaryotes (or viruses, for that matter; Simmonds et al. 2017) at this stage, although we suppose that there is nothing -at least in principle -that would rule out such an expansion of target groups and inclusiveness over time. While the ultimate fate of SeqCode remains to be seen (Marinov et al. 2022), it does set an example of what the future may hold in store for ICN should DFT continue to be ignored. The present authors feel that it would be much better to modify the ICN than to consider more drastic actions. ...

Reference:

How, not if, is the question mycologists should be asking about DNA-based typification
Putting the cart before the horse: SeqCode’s attempt to solve systematics issues with changes to nomenclature
  • Citing Article
  • December 2022

Bionomina

... We agree with these authors that the 'magelonid-like body regionation' FIGURE. 1. Strict consensus tree, modified from Mortimer et al. (2021: fig. 17 is an important synapomorphy for Magelonidae (Mortimer et al. 2021: 67 and abstract) but we regard the two different character states for the thoracic body region, i.e. the presence of eight versus nine thoracic chaetigers, as an easy to observe and taxonomically sufficient character to distinguish between the two genera. ...

Who’s who in Magelona: phylogenetic hypotheses under Magelonidae Cunningham & Ramage, 1888 (Annelida: Polychaeta)

... We will not argue the traditional defences that monophyly is preferred because it defines supraspecific taxa by way of synapomorphies, refers to all descendants derived from a common ancestor, or favours natural groups (e.g., Oosterbroek 1987, Schmidt-Lebuhn 2012, Zachos 2014. Rather, Mortimer et al. (2021) emphasize the importance of recognizing formal names of phylogenetic hypotheses as referring to explanatory accounts of specified characters of organisms, as mentioned in the previous section, which by default necessitates monophyly (Fitzhugh 2005, Fitzhugh 2006a, Fitzhugh 2006b, Fitzhugh 2008, Fitzhugh 2009, Fitzhugh 2012, Fitzhugh 2013, Fitzhugh 2014, Fitzhugh 2016a, Fitzhugh 2016b, Fitzhugh 2016c, Fitzhugh 2021. Too often discussions of mono-and paraphyly lay emphasis on groups of organisms rather than phylogenetic hypotheses qua past causal conditions of character origin/fixation and subsequent population splitting events. ...

Phylogenetic Inference and the Misplaced Premise of Substitution Rates
  • Citing Article
  • May 2021

Acta Biotheoretica

... Optical microscopy is the most common technique for this process; however, SEM and micro-CT are also used either for better results or due to their specific imaging features. In the literature, the majority of studies describing new species is using a combination of OM and SEM (e.g., [85,86]). ...

Taking a closer look: an SEM review of Levinsenia species (Polychaeta: Paraonidae) reported from California

Zootaxa

... The question of whether or not the stratigraphic ages of fossils should be taken into account when estimating phylogeny was a major debate within paleontology in the 1990s and early 2000s (Wagner 1995;Lockwood 1998;Siddall 1998;Smith 1998;Fox et al. 1999;Heyning and Thacker 1999;Smith 2000;Geiger et al. 2001;Alroy 2002). Those advocating the incorporation of stratigraphic data into phylogenetic analysis assert that the age of fossils can be informative about the plausibility of competing phylogenetic hypotheses and can therefore be used to improve estimates of phylogenetic relationships (Fisher 2008). ...

Timeless characters: A response to Vermeij (1999)

Paleobiology

... Our study included only one member of Telothelepodidae, a group that is currently viewed as separate from Thelepodinae because of their elongate, narrow upper lip [13,66]. Although transcriptomic data is not yet available for any member of Telothelepodidae, the total evidence analysis confidently placed Rhinothelepus lobatus inside Thelepodinae. ...

Phylogenetic analysis of the family Telothelepodidae Nogueira, Fitzhugh & Hutchings, 2013 (Annelida: Terebelliformia)

Marine Biology Research

... We will not argue the traditional defences that monophyly is preferred because it defines supraspecific taxa by way of synapomorphies, refers to all descendants derived from a common ancestor, or favours natural groups (e.g., Oosterbroek 1987, Schmidt-Lebuhn 2012, Zachos 2014. Rather, Mortimer et al. (2021) emphasize the importance of recognizing formal names of phylogenetic hypotheses as referring to explanatory accounts of specified characters of organisms, as mentioned in the previous section, which by default necessitates monophyly (Fitzhugh 2005, Fitzhugh 2006a, Fitzhugh 2006b, Fitzhugh 2008, Fitzhugh 2009, Fitzhugh 2012, Fitzhugh 2013, Fitzhugh 2014, Fitzhugh 2016a, Fitzhugh 2016b, Fitzhugh 2016c, Fitzhugh 2021. Too often discussions of mono-and paraphyly lay emphasis on groups of organisms rather than phylogenetic hypotheses qua past causal conditions of character origin/fixation and subsequent population splitting events. ...

Character mapping and cladogram comparison versus the requirement of total evidence: does it matter for polychaete systematics?
  • Citing Article
  • January 2014

Memoirs of Museum Victoria

... We will not argue the traditional defences that monophyly is preferred because it defines supraspecific taxa by way of synapomorphies, refers to all descendants derived from a common ancestor, or favours natural groups (e.g., Oosterbroek 1987, Schmidt-Lebuhn 2012, Zachos 2014. Rather, Mortimer et al. (2021) emphasize the importance of recognizing formal names of phylogenetic hypotheses as referring to explanatory accounts of specified characters of organisms, as mentioned in the previous section, which by default necessitates monophyly (Fitzhugh 2005, Fitzhugh 2006a, Fitzhugh 2006b, Fitzhugh 2008, Fitzhugh 2009, Fitzhugh 2012, Fitzhugh 2013, Fitzhugh 2014, Fitzhugh 2016a, Fitzhugh 2016b, Fitzhugh 2016c, Fitzhugh 2021. Too often discussions of mono-and paraphyly lay emphasis on groups of organisms rather than phylogenetic hypotheses qua past causal conditions of character origin/fixation and subsequent population splitting events. ...

Ernst Mayr, causal understanding, and systematics: an example using sabelliform polychaetes
  • Citing Article
  • August 2016

Invertebrate Biology

... Operationally each form of reasoning plays a respective role in different stages of inquiry, where those stages include at a minimum the inferences of theories and hypotheses, and the subsequent empirical testing of those propositions. The stage of inquiry most associated with systematics is abduction (Peirce, 1878;Peirce, 1931;Peirce, 1932;Peirce, 1933a;Peirce, 1933b;Peirce, 1934;Peirce, 1935;Peirce, 1958a;Peirce, 1958b;Hanson, 1958;Achinstein, 1970;Fann, 1970;Reilly, 1970;Curd, 1980;Nickles, 1980;Thagard, 1988;Josephson & Josephson, 1994;Baker, 1996;Hacking, 2001;Magnani, 2001;Magnani, 2009;Magnani, 2017;Psillos, 2002;Psillos, 2007;Psillos, 2011;Godfrey-Smith, 2003;Norton, 2003;Walton, 2004;Gabbay & Woods, 2005;Aliseda, 2006;Schurz, 2008;Park, 2017), i.e., the inferences of hypotheses as the means of causally accounting for the various differentially shared characters observed among organisms (Fitzhugh, 2005a;Fitzhugh, 2005b;Fitzhugh, 2006a;Fitzhugh, 2006b;Fitzhugh, 2008a;Fitzhugh, 2008b;Fitzhugh, 2008c;Fitzhugh, 2009;Fitzhugh, 2010a;Fitzhugh, 2013;Fitzhugh, 2014;Fitzhugh, 2015;Fitzhugh, 2016a;Fitzhugh, 2016b;Fitzhugh, 2016c;Fitzhugh, 2016d;Fitzhugh, 2021). Subsequent empirical assessments of explanatory hypotheses rely on deducing predictions of expected consequences-potential test evidence-if the causal claims in hypotheses are true. ...

Phylogenetic Hypotheses: Neither Testable Nor Falsifiable

... We will not argue the traditional defences that monophyly is preferred because it defines supraspecific taxa by way of synapomorphies, refers to all descendants derived from a common ancestor, or favours natural groups (e.g., Oosterbroek 1987, Schmidt-Lebuhn 2012, Zachos 2014. Rather, Mortimer et al. (2021) emphasize the importance of recognizing formal names of phylogenetic hypotheses as referring to explanatory accounts of specified characters of organisms, as mentioned in the previous section, which by default necessitates monophyly (Fitzhugh 2005, Fitzhugh 2006a, Fitzhugh 2006b, Fitzhugh 2008, Fitzhugh 2009, Fitzhugh 2012, Fitzhugh 2013, Fitzhugh 2014, Fitzhugh 2016a, Fitzhugh 2016b, Fitzhugh 2016c, Fitzhugh 2021. Too often discussions of mono-and paraphyly lay emphasis on groups of organisms rather than phylogenetic hypotheses qua past causal conditions of character origin/fixation and subsequent population splitting events. ...

Dispelling five myths about hypothesis testing in biological systematics
  • Citing Article
  • March 2016

Organisms Diversity & Evolution