Kirk Fitzhugh's research while affiliated with Natural History Museum of Los Angeles County and other places
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Publications (44)
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 nom...
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 s...
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...
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...
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 Whit...
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 t...
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 bo...
Ernst Mayr suggested that understanding the features of organisms involves the study of what he called “proximate” and “ultimate” causes. Proximate causes of characters occur during the life of the organism; ultimate causes occur prior to the life of the organism, as part of the evolutionary history leading to organisms in the present. Mayr also po...
Crother and Murray (Cladistics 31: 573–574, 2015) criticize the statement by Assis (Cladistics 30: 240–242, 2014) that phylogenetic hypotheses are amenable to testing but not falsification. The claims by both sets of authors are based on long-standing misconceptions about testing developed within systematics. Testing phylogenetic hypotheses confuse...
The emphasis on testing phylogenetic hypotheses has been prominent since the English language introductions of Willi Hennig’s Phylogenetic Systematics (1966) and Karl Popper’s (1959) Logic of Scientific Discovery. While the mechanics of hypothesis and theory testing are well established in other fields of science, adherence to those prescriptions i...
Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Becaus...
The serpulid annelid Ficopomatus enigmaticus is found as a non-indigenous species in many subtropical and temperate habitats, where it often has major effects on the physical structure and community ecology of invaded habitats. In the northeastern Pacific, it has been present in northern California since about 1920, but clearly established populati...
A phylogenetic analysis was performed to determine the monophyly of non-monotypic genera of the terebelliform family Polycirridae, i.e. Polycirrus, Amaeana, Lysilla, and Hauchiella, and the evolution of characters among members of this clade. The monotypic genera, Enoplobranchus and Biremis, were also included, together with members of both known s...
A comprehensive phylogenetic analysis of the Terebellidae and related families was undertaken. Type material of all genera of Terebellinae was examined, together with representatives of nearly all genera of remaining Terebellidae subfamilies, and representatives of the families that have been traditionally regarded as being closely related, compris...
Ernst Mayr's (1961, Science 131: 1501–1506) distinction between proximate and ultimate causation in biology is examined with regard to the acquisition of understanding in biological systematics. Rather than a two-part distinction, understanding in systematics is characterized by relations between three explanatory components: descriptive (observati...
The Fabriciinae genus Fabricia Blainville is revised. In the past, the type species designation for the genus has been confused; explicit designations have included Tubularia fabricia Müller and Amphicora sabella Ehrenberg. The type species is actually T. stellaris {SCMüller}, by monotypy. Based on this latter designation, most species previously p...
Cladistic relationships among fabriciids have to date been explored in the context of adult morphology, but resolution has been declining as more species are described. In this study, we incorporated data on the reproductive system, including features related to the male sperm and sperm storage by females, to supplement existing data on adult morph...
A new species of Fabricinuda Fitzhugh, F. longilabrum, is described from 60 to 70 m depth from the Gulf of Thailand, increasing the number of described species to six. Fabricinuda longilabrum most closely resembles F. pseudopalpa Fitzhugh in that both have well-developed branchial crown dorsal lips, but lack vascularized, ventral filamentous append...
Previous descriptions of members of Fabricia oregonica Banse, 1956, have distinguished it by the presence of only narrowly hooded inferior thoracic notochaetae, in contrast to the presence of pseudospatulate chaetae in median chaetigers of the type species, F. stellaris (Müller, 1774). In other respects, past descriptions of specimens to which F. o...
Members of Parasabella minuta Treadwell, 1941, subsequently moved to Perkinsiana, were collected during a survey of rocky intertidal polychaetes along the state of São Paulo, Brazil. Additional specimens, which are referred to two new species, were also found in similar habitats from the Bocas del Toro Archipelago, Caribbean Panama, and Oahu Island...
The popular defense of intelligent design/creationism (ID) theories, as well as theories in evolutionary biology, especially
from the perspective that both are worthy of scientific consideration, is that empirical evidence has been presented that
supports both. Both schools of thought have had a tendency to rely on the same class of evidence, namel...
The formal definition of species as explanatory hypotheses presented by Fitzhugh (Marine Biol 26:155-165, 2005a, b) is emended. A species is an explanatory account of the occurrences of the same character(s) among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In add...
Cladistic relationships of the sabellid subfamilies Fabriciinae and Sabellinae are examined in light of recent revisions of fabriciin taxa. The potential placement of Caobangia in the Sabellinae is suggested from an initial analysis of selected fabriciin species and genera. Subsequent cladistic analyses at the family level produced over 1800 cladog...
Two species of Pseudofabriciola Fitzhugh from the the Mediterranean Sea, P. analis sp. nov. and P. longipyga sp. nov., are described. These species most closely resemble P. australiensis (Hartmann-Schroder) and P. incisura Fitzhugh in that all have a membranous, anterior peristomial ring collar which is distally flared. Cladistic relationships amon...
Character loss, as opposed to absence, in the Annelida is regarded by Bleidorn (2007, Journal of Zoological Systematics and Evolutionary Research, 45, 299–307) as a problem for phylogenetic inference. Bleidorn's concern is derived from two misconceptions. First, from an epistemic standpoint, objects are perceived by way of their properties. ‘Absenc...
A common claim among advocates of the ‘phylogenetic’ system of nomenclature (PN) is that the ‘Linnean’ system (LN) is defective
because it fails to promote stability, universality, and unambiguous meaning in the naming of phylogenetic hypotheses. This
claim rests on the premise that biological systematization should be phylogenetic. The foundation...
Fitzhugh, K. (2007). Fact, theory, test and evolution. — Zoologica Scripta, 37, 109–113.
The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial.
Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against
the RTE has not be...
The coding of observations of organisms into a data matrix for the inference of phylogenetic hypotheses has suffered from a variety of problems that have precluded development of a uniform approach to the issue. Probably the most notable consequence is that the philosophical basis for coding has been prominently ignored in lieu of emphasis placed o...
The formal structure of the inference of a phylogenetic hypothesis is analyzed in the context of the different classes of reasoning applied in all fields of science. Rather than making the traditional distinction between deductive and inductive reasoning, it is shown that phylogenetic hypotheses are derived from a form of non-deductive inference co...
A formal definition of the term ‘species’ is presented that is logically consistent with the inferential structures that lead to other taxonomic categories in biological systematics. A species name denotes an explanatory hypothesis that accounts for specified intrinsic or relational properties of organisms that can be accounted for by way of past t...
The phylogenetic position of Echiura and Pogonophora was recently reconsidered using 346 bp of elongation factor 1-alpha (EF-1α). On the basis of these results alone it was suggested that the relationships of Anne lida be reconsidered and that the systematics of the group changed accordingly. An examination of these data, however, reveals difficult...
Traditionally, broadcast spawning and planktonic larvae have been considered the plesiomorphic ‘ground plan’ for the Polychaeta and other metazoan groups. To assess whether this reproductive mode is in fact ‘primitive’, the study of monophyletic groups with various reproductive modes should be informative. A large range of body sizes would allow te...
fecal groove, forming dorsolateral pockets. Megalomma cinctum is distinct from these species by the presence of a narrow, white, transverse band on setiger 2, and sometimes also on setiger 3. The number of pairs of radi- olar eyes in M. cinctum is much more variable than has been reported in other species, and is strongly correlat- ed with body siz...
A new genus and species of South African sabellid polychaete, Terebrasabella heterouncinata, is described. The species lives in burrows in living gastropod shells and was first discovered in 1993 in red abalone aquaculture facilities in southern California. Shell abnormalities in cultured abalones, caused by heavy sabellid infestations, raised conc...
Five new species are described from among the genera Fabriciola Friedrich, 1939 (one species from Okinawa), Novafabricia Fitzhugh, 1990 (two species from Australia and Papua New Guinea, respectively), and two new monotypic genera, Brifacia gen. n. (Australia), and Pseudoaugeneriella gen. n. (Okinawa). All species are known only from the intertidal....
Citations
... 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. ...
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... Additionally, SEM and LM studies of thoracic chaetae in O. borowskii sp. nov., as well as the paratype of O. bizkaiensis, revealed that thoracic capillary chaetae are, in fact, unilimbate in O. bizkaiensis (Fig. 12L) as stated in the original description (Aguirrezabalaga et al. 2001) and not bilimbate as coded by Mortimer et al. (2021: table S1, coding matrix character 31). In specimens of Octomagelona borowskii sp. ...
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... 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. ...
... 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]). ...
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... 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). ...
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... 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. ...
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... The reason is because the act of 'optimizing' characters on a previously inferred tree topology, i.e. a set of explanatory hypotheses for a set of characters used to infer those hypotheses, is not an action that can be interpreted as an epistemically meaningful inference. Inferring phylogenetic hypotheses involves a form of non-deductive reasoning known as abduction (Peirce 1931, 1932, 1933ab, 1934, 1935, 1958a-b, Hanson 1958, Fann 1970, Reilly 1970, Thagard 1988, Josephson & Josephson 1994, Magnani 2001, Psillos 2002, Walton 2004, Gabbay & Woods 2005, Aliseda 2006, Schurz 2008, Park 2017, for considerations of abduction in relation to systematics see Fitzhugh 2006aFitzhugh -2006bFitzhugh , 2008Fitzhugh , 2009Fitzhugh , 2010aFitzhugh , 2012Fitzhugh , 2013Fitzhugh , 2014Fitzhugh , 2015Fitzhugh , 2016a. At a minimum, the premises of an abductive inference involve the conjunction of some causal theory(ies) and effect(s) to be explained. ...
... A partir desta perspectiva, há uma importação do monismo peirciano(VIANA, 2014, p. 61), que quando realizada, evidencia uma manobra epistemológica acriteriosa (se o objetivo for conservar a fundação ontológica hennigiana), pois, tendo em vista a sua concepção de realidade enquanto possibilidade, que é compatível com uma epistemologia encerrada na agência do sujeito no mundo, a ontologia filogenética levantada por Willi Hennig, por outro lado, importa o realismo crítico de Nicolai Hartmann, consolidando uma base ontológica apriorística para toda fundação teórica sobre a qual a metodologia e lógica inferencial está acoplada. O caso mais concreto de tal "reducionismo pragmático" é o da concepção dos táxons somente enquanto hipóteses explicativas(FITZHUGH, 2009;2015;2016b). A deixa de Hennig, onde ele infere que "a mutabilidade dos organismos não é a questão primária da sistemática... ...
... 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. ...
... This is in line with him citing Geoffroy St. Hillaire's adoption of the term referring to the same underlying principle (although Owen objected to his claim of identical development as necessary criterion for parts to be homologues; Owen, 1847: 173). In fact, Owen's frequent use of homology and homologue in the same context contradicts the assumption of a substantial conceptual distinctness (as has been interpreted e.g. by Fitzhugh, 2016) of homologue and homology. Owen aims at "proposing a definite name for each distinct bone, declaratory of its special homology" (Owen, 1847: 173) and discusses the search for the "true homologue" (Owen, 1847: 182). ...
