Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships.

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Tooth and consequences: Heterodonty and dental replacement in piranhas and pacus (Serrasalmidae).

Tooth replacement in piranhas is unusual: all teeth on one side of the head are lost as a unit, then replaced simultaneously. We used histology and microCT to examine tooth-replacement modes across carnivorous piranhas and their herbivorous pacu cousins (Serrasalmidae) and then mapped replacement patterns onto a molecular phylogeny. Pacu teeth develop and are replaced in a manner like piranhas. For serrasalmids, unilateral tooth replacement is not an "all or nothing" phenomenon; we demonstrate that both sides of the jaws have developing tooth rows within them, albeit with one side more mineralized than the other. All serrasalmids (except one) share unilateral tooth replacement, so this is not an adaptation for carnivory. All serrasalmids have interlocking teeth; piranhas interdigitate lateral tooth cusps with adjacent teeth, forming a singular saw-like blade, whereas lateral cusps in pacus clasp together. For serrasalmids to have an interlocking dentition, their teeth need to develop and erupt at the same time. We propose that interlocking mechanisms prevent tooth loss and ensure continued functionality of the feeding apparatus. Serrasalmid dentitions are ubiquitously heterodont, having incisiform and molariform dentitions reminiscent of mammals. Finally, we propose that simultaneous tooth replacement be considered as a synapomorphy for the family.

The suction mechanism of the pipid frog, Pipa pipa (Linnaeus, 1758).

Most suction-feeding, aquatic vertebrates create suction by rapidly enlarging the oral cavity and pharynx. Forceful enlargement of the pharynx is powered by longitudinal muscles that retract skeletal elements of the hyoid, more caudal branchial arches, and, in many fish, the pectoral girdle. This arrangement was thought to characterize all suction-feeding vertebrates. However, it does not exist in the permanently aquatic, tongueless Pipa pipa, an Amazonian frog that can catch fish. Correlating high-speed (250 and 500 fps) video records with anatomical analysis and functional tests shows that fundamental features of tetrapod body design are altered to allow P. pipa to suction-feed. In P. pipa, the hyoid apparatus is not connected to the skull and is enclosed by the pectoral girdle. The major retractor of the hyoid apparatus arises not from the pectoral girdle but from the femur, which lies largely within the soft tissue boundaries of the trunk. Retraction of the hyoid is coupled with expansion of the anterior trunk, which occurs when the hypertrophied ventral pectoral elements are depressed and the urostyle and sacral vertebra are protracted and slide forward on the pelvic girdle, thereby elongating the entire trunk. We suggest that a single, robust pair of muscles adduct the cleithra to depress the ventral pectoral elements with force, while modified tail muscles slide the axial skeleton cranially on the pelvic girdle. Combined hyoid retraction, axial protraction, and pectoral depression expand the buccopharyngeal cavity to a volume potentially equal to that of the entire resting body of the frog. Pipa may be the only tetrapod vertebrate clade that enlarges its entire trunk during suction-feeding.

Interrogating genomic-scale data for squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families)

Interrogating genomic-scale data for squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families)

Scanning electron microscopy of changes in epidermal structure occurring during the shedding cycle in squamate reptiles.

Previous studies of squamate epidermal structure have focused on either histology and ultrastructure or oberhautchen surface texture as revealed by scanning electron microscopy (SEM). Using SEM data drawn from a variety of lizard taxa (primarily iguanids, but also agamids, chamaeleonids, and scincids), as well as amphisbaenians and colubrid snakes, we relate the surfaces encountered in gross dissection of squamate skin to histologically identifiable layers, and characterize their surface structure. Only the oberhautchen bears the repeating pattern of ornamentation noted by previous authors. Because the clear layer is a perfect template of the oberhautchen surface, it is the only layer with which the oberhautchen might be confused. However, the clear layer can be identified by its tendency to curl and crack during preparation. All other surfaces encountered were relatively featureless, except for impressions left by dermal "papillae" associated with mechanoreceptors. Using a method for examining preserved specimens to determine the stage in the shedding cycle, we assess two sources of variation in epidermal surface structure: stage in the shedding cycle and wear. Examination of immature renewal-phase epidermis suggests that the oberhautchen does not mature synchronously across a single scale or across body regions. Comparing inner- and outer-generation oberhautchen in sheddingphase epidermis, we conclude that changes in surface appearance caused by natural wear fall into two categories: discrete scratches and accumulation of debris. We see no evidence of overall "buffing" on a microscopic level, though surface structure may be obscured by scratches and gouges. Many squamate taxa show a gradient from low relief surface structure on elevated regions such as keels to high relief patterns at scale edges. This gradient is not due to wear; its significance is unknown.