Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds

The patella (kneecap) exhibits multiple evolutionary origins in birds, mammals, and lizards, and is thought to increase the mechanical advantage of the knee extensor muscles. Despite appreciable interest in the specialized anatomy and locomotion of palaeognathous birds (ratites and relatives), the structure, ontogeny and evolution of the patella in these species remains poorly characterized. Within Palaeognathae, the patella has been reported to be either present, absent, or fused with other bones, but it is unclear how much of this variation is real, erroneous or ontogenetic. Clarification of the patella’s form in palaeognaths would provide insight into the early evolution of the patella in birds, in addition to the specialized locomotion of these species. Findings would also provide new character data of use in resolving the controversial evolutionary relationships of palaeognaths. In this study, we examined the gross and histological anatomy of the emu patellar tendon across several age groups from five weeks to 18 months. We combined these results with our observations and those of others regarding the patella in palaeognaths and their outgroups (both extant and extinct), to reconstruct the evolution of the patella in birds. We found no evidence of an ossified patella in emus, but noted its tendon to have a highly unusual morphology comprising large volumes of adipose tissue contained within a collagenous meshwork. The emu patellar tendon also included increasing amounts of a cartilage-like tissue throughout ontogeny. We speculate that the unusual morphology of the patellar tendon in emus results from assimilation of a peri-articular fat pad, and metaplastic formation of cartilage, both potentially as adaptations to increasing tendon load. We corroborate previous observations of a ‘double patella’ in ostriches, but in contrast to some assertions, we find independent (i.e., unfused) ossified patellae in kiwis and tinamous. Our reconstructions suggest a single evolutionary origin of the patella in birds and that the ancestral patella is likely to have been a composite structure comprising a small ossified portion, lost by some species (e.g., emus, moa) but expanded in others (e.g., ostriches)

Identification of widely conserved biosynthetic gene cluster involved in pigment production of Bacillus subtilis

Bacillus subtilis is widely studied in the microbial secondary metabolite (SM) field due to its rich variety of important natural products and genetic tractability. We report a pigment observed in B. subtilis soil isolate MB9_B4 on certain media. We characterize the conditions where this pigment is produced and identify the corresponding biosynthetic gene cluster (BGC) using a comparative genomic approach exploiting our strain collection containing other isolates with pigment production ability. The responsible BGC carried several genes, which were annotated as parts of the tryptophan biosynthesis pathway, possibly originating from duplication and divergence of originally primary metabolism. Identification of the pigment gene cluster additionally led to the discovery of additional pigment BGC carrier B. subtilis isolates, some of which were described at the earliest in 1896 under the name Bacillus aterrimus, referring to a characteristic dark pigmentation (the Latin “aterrimus” meaning very black). In addition, we employed solid-state nuclear magnetic resonance and Fourier transform infrared spectroscopies to characterize the chemical groups of the pigment. This study describes the chemical and biological features of a new class of SM BGC, which we hope will serve to improve the current BGC discovery pipelines in Bacilli.Microbial Biotechnolog

Data S3: Phylogenetic matrix

Diplodocids are among the best known sauropod dinosaurs. Numerous specimens of currently 15 accepted species belonging to ten genera have been reported from the Late Jurassic to Early Cretaceous of North and South America, Europe, and Africa. The highest diversity is known from the Upper Jurassic Morrison Formation of the western United States: a recent review recognized 12 valid, named species, and possibly three additional, yet unnamed ones. One of these is herein described in detail and referred to the genus Galeamopus. The holotype specimen of Galeamopus pabsti sp. nov., SMA 0011, is represented by material from all body parts but the tail, and was found at the Howe-Scott Quarry in the northern Bighorn Basin in Wyoming, USA. Autapomorphic features of the new species include a horizontal canal on the maxilla that connects the posterior margin of the preantorbital and the ventral margin of the antorbital fenestrae, a vertical midline groove marking the sagittal nuchal crest, the presence of a large foramen connecting the postzygapophyseal centrodiapophyseal fossa and the spinopostzygapophyseal fossa of mid- and posterior cervical vertebrae, a very robust humerus, a laterally placed, rugose tubercle on the concave proximal portion of the anterior surface of the humerus, a relatively stout radius, the absence of a distinct ambiens process on the pubis, and a distinctly concave posteroventral margin of the ascending process of the astragalus. In addition to the holotype specimen SMA 0011, the skull USNM 2673 can also be referred to Galeamopus pabsti. Histology shows that the type specimen SMA 0011 is sexually mature, although neurocentral closure was not completed at the time of death. Because SMA 0011 has highly pneumatized cervical vertebrae, the development of the lamination appears a more important indicator for individual age than neurocentral fusion patterns. SMA 0011 is one of very few sauropod specimens that preserves the cervico-dorsal transition in both vertebrae and ribs. The association of ribs with their respective vertebrae shows that the transition between cervical and dorsal vertebrae is significantly different in Galeamopus pabsti than in Diplodocus carnegii or Apatosaurus louisae, being represented by a considerable shortening of the centra from the last cervical to the first dorsal vertebra. Diplodocids show a surprisingly high diversity in the Morrison Formation. This can possibly be explained by a combination of geographical and temporal segregation, and niche partitioning