John S. S. Denton

A new phylogenetic test for comparing multiple high‐dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae)

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best‐fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high‐dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development‐informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best‐fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life‐history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.

Are characiform Fishes Gondwanan in Origin? Insights from a Time-Scaled Molecular Phylogeny of the Citharinoidei (Ostariophysi: Characiformes)

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.

Seven-locus molecular phylogeny of Myctophiformes (Teleostei; Scopelomorpha) highlights the utility of the order for studies of deep-sea evolution.

Fishes of the order Myctophiformes (Teleostei; Scopelomorpha) comprise over half of all deep-sea biomass, and are a critical component of marine ecosystems worldwide. Members of the family Myctophidae, within Myctophiformes, form the majority of species diversity within the order (∼250 species, 33 genera, 2 subfamilies), and are further known for their diverse bioluminescent traits, comprised of distinct cranial, postcranial, and caudal luminous systems that is perhaps the most elaborate among all vertebrates. These features make myctophids particularly compelling from both economic and scientific perspectives, yet no studies have sampled these fishes at a density appropriate for addressing any questions requiring a phylogenetic hypothesis as input. This study therefore presents a seven-locus molecular phylogeny of the order, sampling over 50% of all nominal myctophid species. This taxon sampling triples the representation of the next most comprehensive analysis, and reveals several new and well-supported hypotheses of relationships, in addition to supporting traditional hypotheses based on combined morphological data. This analysis shows that the slendertailed myctophids Gonichthys, Centrobranchus, Loweina, and Tarletonbeania are rendered non-monophyletic by a polyphyletic Myctophum; the enigmatic, monotypic genus Notolychnus valdiviae is nested within tribe Lampanyctini; the genus Diaphus is divided into at least two clades, with the suborbital (So) group recovered as monophyletic with strong support; and the genera Lampanyctus and Nannobrachium are recovered as non-monophyletic. These molecular results highlight the potential of myctophids as a premier model system for the application of modern comparative methods to studies of deep-sea evolution.

Indel information eliminates trivial sequence alignment in maximum likelihood phylogenetic analysis

Although there has been a recent proliferation in maximum‐likelihood (ML)‐based tree estimation methods based on a fixed sequence alignment (MSA), little research has been done on incorporating indel information in this traditional framework. We show, using a simple model on a single character example, that a trivial alignment of a different form than that previously identified for parsimony is optimal in ML under standard assumptions treating indels as “missing” data, but that it is not optimal when indels are incorporated into the character alphabet. We show that the optimality of the trivial alignment is not an artefact of simplified theory assumptions by demonstrating that trivial alignment likelihoods of five different multiple sequence alignment datasets exhibit this phenomenon. These results demonstrate the need for use of indel information in likelihood analysis on fixed MSAs, and suggest that caution must be exercised when drawing conclusions from software implementations claiming improvements in likelihood scores under an indels‐as‐missing assumption.

Pectoral Morphology in Doliodus: Bridging the ‘Acanthodian’-Chondrichthyan Divide

ABSTRACT Doliodus problematicus (NBMG 10127), from the Lower Devonian of New Brunswick, Canada (approx. 397–400 Mya) is the earliest sharklike jawed vertebrate (gnathostome) in which the pectoral girdle and fins are well preserved. Its pectoral endoskeleton included sharklike expanded paired coracoids, but Doliodus also possessed an “acanthodian-like” array of dermal spines, described here for the first time. Doliodus provides the strongest anatomical evidence to date that chondrichthyans arose from “acanthodian” fishes by exhibiting an anatomical mosaic of “acanthodian” and sharklike features.

Dermal denticle patterning in the Cretaceous hybodont shark Tribodus limae (Euselachii, Hybodontiformes), and its implications for the evolution of patterning in the chondrichthyan dermal skeleton

ABSTRACT As in modern elasmobranchs (sharks and rays), the shagreen of the hybodontiform shark Tribodus limae (Santana Formation, Aptian-Albian, Lower Cretaceous, northeastern Brazil) consists of non-growing (monodontode) dermal denticles that were shed, replaced, and supplemented by new ones during life. In modern elasmobranchs, these denticles are usually represented by a single size class (considered here to be the default arrangement), although larger denticles are sometimes present locally (e.g., thorn rows on the head and trunk in batomorphs). In Tribodus, however, the shagreen consists of two distinct morphological denticle types and size classes (two-size), both widely distributed over the body and fins, with smaller denticles overlying the bases of larger thorns as well as occupying areas between them. Using two conceptually distinct variants of a two-layer reaction-diffusion (R-D) simulation that is consistent with morphogen exchange across the basal lamina between the epidermal and dermal layers, we recovered two-size spatial arrangements similar to the Tribodus shagreen. Our results suggest that denticle patterning in the dermal skeleton of sharks can be replicated using R-D models with kinetics similar to those previously applied to a known mechanism of feather bud patterning in birds and to skin pigmentation patterning in modern teleost fishes. Reaction-diffusion simulations operationalize Reifs ‘odontode regulation theory,’ and so have an important conceptual place in the history of research on the dermal skeleton. Such a modeling framework may enable conceptual links to be drawn among seemingly disparate denticle arrays in Paleozoic and recent chondrichthyans, thereby guiding future work on the molecular and histological underpinnings of dermal skeleton development and evolution.

Lanternfish (Teleostei, Myctophiformes, Myctophidae) Body Fossils from the Modelo Formation (Upper Miocene) of Los Angeles County, California

ABSTRACT Representative fossils of three extant lanternfish (Myctophidae) genera (Bolinichthys, Lampanyctus, and Myctophum) from the collections of Natural History Museum of Los Angeles County were identified, based on a combination of osteological and photophore characters. These specimens come from the upper Miocene Modelo Formation (Mohnian-Delmontian) of California, and represent the first skeletal records of Bolinichthys (otherwise identified as otoliths from the Late Miocene of Italy) and Myctophum body fossils in North America, and confirm that both modern myctophid subfamilies exhibited a cosmopolitan distribution by the late Miocene.

Cranial morphology in Mollisquama sp. (Squaliformes; Dalatiidae) and patterns of cranial evolution in dalatiid sharks

Dalatiid sharks are members of a family of predominantly small, midwater meso‐ and bathypelagic chondrichthyans. The family is notable for both its number of monotypic genera and high morphological disparity. Three of the seven dalatiid genera are known only from holotype specimens (Mollisquama parini) or from only a handful of specimens (Euprotomicroides zantedeschia, Heteroscymnoides marleyi), with the only detailed anatomical work consistent across all taxa being studies of dentition. Here, we present detailed anatomical description of the second‐ever specimen of Mollisquama (Mollisquama sp.) covering chondrocranial, jaw, dental, and muscular anatomy, derived from a phase‐contrast synchrotron microtomographic scan. Mollisquama sp. is unique among dalatiids in possessing a deep carinal process, extending ventrally from the bar between the subethmoid region and basal angle in squaloid sharks, containing a large fenestra infiltrated by the suborbitalis muscle. Mollisquama sp. also exhibits additional possibly diagnostic features, including a planar configuration of the labial cartilages and the absence of labial folds; a pad‐like orbital process on the palatoquadrate; and the origination of the suborbitalis muscle solely on the carina, rather than the intraorbital wall. Character optimization of anatomical data onto a phylogeny of dalatiid sharks suggests Mollisquama sp. to be among the most specialized in the family, expanding the existing dalatiid morphospace. However, the functional significance of such transformations remains unclear. Synchrotron‐derived data, which do not require chemical pretreatment of specimens, may elucidate soft‐tissue functional correlates in future studies of undersampled taxa, such as dalatiids.

Measuring inferential importance of taxa using taxon influence indices

Abstract Assessing the importance of different taxa for inferring evolutionary history is a critical, but underutilized, aspect of systematics. Quantifying the importance of all taxa within a dataset provides an empirical measurement that can establish a ranking of extant taxa for ecological study and/or quantify the relative importance of newly announced or redescribed specimens to enable the disentangling of novelty and inferential influence. Here, we illustrate the use of taxon influence indices through analysis of both molecular and morphological datasets, introducing a modified Bayesian approach to the taxon influence index that accounts for model and topological uncertainty. Quantification of taxon influence using the Bayesian approach produced clear rankings for both dataset types. Bayesian taxon rankings differed from maximum likelihood (ML)‐derived rankings from a mitogenomic dataset, and the highest ranking taxa exhibited the largest interquartile range in influence estimate, suggesting variance in the estimate must be taken into account when the ranking of taxa is the feature of interest. Application of the Bayesian taxon influence index to a recent morphological analysis of the Tully Monster (Tullimonstrum) reveals that it exhibits consistently low inferential importance across two recent treatments of the taxon with alternative character codings. These results lend support to the idea that taxon influence indices may be robust to character coding and therefore effective for morphological analyses. These results underscore a need for the development of approaches to, and application of, taxon influence analyses both for the purpose of establishing robust rankings for future inquiry and for explicitly quantifying the importance of individual taxa. Quantifying the importance of individual taxa refocuses debates in morphological studies from questions of character choice/significance and taxon sampling to explicitly analytical techniques, and guides discussion of the context of new discoveries.