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High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Ectocranial suture fusion patterns have been shown to contain biological and phylogenetic information. Previously the patterns of Homo, Pan, and Gorilla have been described. These data reflect the phylogenetic relationships among these species. In this study, we applied similar methodology to Pongo to determine the suture synostosis progression of this genus, and to allow comparison to previously reported data on other large-bodied hominoids. We hypothesized these data would strengthen the argument that suture synostosis patterns reflect the phylogeny of primate taxa. Results indicate that the synostosis of vault sutures in Pongo is similar to that reported for Gorilla (excluding Pan and Homo). However, the lateral-anterior pattern of fusion, in which there is a strong superior to inferior pattern, for Pongo is unique among these species, reflecting its phylogenetic distinctness among great ape taxa. Am J Phys Anthropol 143:473-477, 2010. [c] 2010 Wiley-Liss, Inc. KEY WORDS cranial suture; Pongo; synostosis; Guttman analysis DOI 10.1002/ajpa.21367

It has been suggested that the variability of the primate vomeronasal organ (VNO) may be greater than previously thought, especially among New World monkeys. It is not clear to what extent VNO variation reflects ontogenetic, functional, or phylogenetic differences among primates. The present study investigated VNO anatomy in an ontogenetic series of two genera of callitrichid primates, in order to assess recent attempts to develop VNO character states and to examine the evidence for VNO functionality at different life stages. A sample of six Leontopithecus rosalia, one L. chrysomelas, and six Saguinus geoffroyi was serially sectioned and stained using various methods. Two adult Callithrix jacchus were also sectioned for comparative purposes. The VNO of each primate was examined by light microscopy along its entire rostrocaudal extent. VNOs of the tamarins were described to determine whether they fit into 1 of 3 character states recently attributed to various New World monkeys. At birth, the two species of tamarins differed in the nature of communication between the VNO and nasopalatine duct (NPD). Two of 3 neonatal S. geoffroyi exhibited a fused VNO duct in a more dorsal position (adjacent to the nasal cavity) compared to that of L. rosalia. The VNO duct communicated with the NPD and was patent in neonatal L. rosalia. Both species appeared to have an age-related increase in the amount of sensory epithelium in the VNO. Subadult L. rosalia had caudal regions of the VNO that were exceptionally well-developed, similar to those of strepsirhine primates. Compared to subadults, all adult callitrichids appeared to have more ventral communications of the VNO duct directly into the NPD. Adult S. geoffroyi and L. chrysomelas both had VNO sensory epithelium separated by multiple patches of nonsensory epithelium. This contrasted with the VNOs of C. jacchus, which had a nearly continuous distribution of receptors on all surfaces of the VNO. The findings indicate that tamarins have delayed maturation of the VNO epithelium, and that some species have little or no perinatal function. These results also suggest that ontogenetic changes in craniofacial form may alter the position of the VNO in tamarins. The present study supports the use of at least two character states to categorize the VNO of various callitrichids, but it is suggested that one of these, previously called 'reduced sensory epithelium' should be instead termed 'interrupted sensory epithelium.' The distribution of VNO sensory epithelium does not appear to reflect phylogenetic influences; it is more likely a functional characteristic that varies throughout postnatal life. Therefore, this chemosensory system has a high degree of plasticity relating to age and function, which in some instances can confound the use of characteristics as phylogenetic traits. Further study is needed to quantify VNO receptors in various species to determine if functional differences exist and if some species have more precocious VNO function than others. KEY WORDS vomeronasal; nasopalatine; callitrichid; Saguinus geoffroyi; Leontopithecus

Summary: This study describes the myosin composition of extrafusal and intrafusal muscle fibers found in the human thyroarytenoid (TA) and sternohyoid (control) muscles. We sought to determine the presence of [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/S0892-1997(03)00027-4 Byline: Carla A Brandon (a), Clark Rosen (a ), George Georgelis (a), Michael J Horton (a), Mark P Mooney (a)(a ), James J Sciote (a) Abbreviations: Posterior cricoarytenoid muscle compartments; Vocal fold immobilization; Myosin heavy chain Abstract: Summary: The human posterior cricoarytenoid (PCA) muscle is divided into two compartments, the vertical and horizontal bellies, which contain differences in their myosin heavy chain (MyHC) composition. Using immunohistochemical techniques on whole PCA samples, this study provides a more thorough description of the fiber type composition of entire bellies of the PCA. Four patients provided complete PCA samples containing both compartments of their right and left sides; two with unilaterally immobilized vocal folds. The horizontal belly had 80% slow (type I) fibers and 20% fast (type II) fibers. The vertical belly contained equal amounts of slow and fast fibers ([approximately equal to]55%:45%); clearly distinguishing between two compartments. Atrophy of muscle fibers and fiber type grouping were also present in both normal and affected subjects; providing no clear confirmation of the clinical findings of vocal fold immobilization. Further study of the PCA muscle from patients with unilaterally immobilized vocal folds is needed. Author Affiliation: (a) Department of Orthodontics, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania, USA (a ) Department of Otolaryngology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA (a ) Department of Oral Medicine and Pathology, Anthropology, Plastic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA Article History: Accepted 28 March 2002

Reconstruction of life history variables of fossil hominids on the basis of dental development requires understanding of and comparison with the pattern and timing of dental development among both living humans and pongids. Whether dental development among living apes or humans provides a better model for comparison with that of Plio-Pleistocene hominids of the genus Australopithecus remains a contentious point. This paper presents new data on chimpanzees documenting developmental differences in the dentitions of modern humans and apes and discusses their significance in light of recent controversies over the human or pongid nature of australopithecine dental development. Longitudinal analysis of 299 lateral head radiographs from 33 lab-reared chimpanzees (Pan troglodytes) of known chronological age allows estimation of means and standard deviations for the age at first appearance of 8 developmental stages in the mandibular molar dentition. Results are compared with published studies of dental development among apes and with published standards for humans. Chimpanzees are distinctly different from humans in two important aspects of dental development. Relative to humans, chimpanzees show advanced molar development visa vis anterior tooth development, and chimpanzees are characterized by temporal overlap in the calcification of adjacent molar crowns, while humans show moderate to long temporal gaps between the calcification of adjacent molar crowns. In combination with recent work on enamel incremental markers and CAT scans of developing dentitions of Plio-Pleistocene hominids, this evidence supports an interpretation of a rapid, essentially 'apelike' ontogeny among australopithecines. KEY WORDS Longitudinal analysis, Molar development, Pan troglodytes, Australopithecines, Plio-Pleistocene, Ontogeny, Hominids, Pongids

To better understand the contribution of congenital dysmorphogenesis to postnatal midfacial dysplasia in individuals with complete cleft lip and palate (CLP), a series of studies were undertaken to investigate age related changes in a number of midfacial components for a sample of 20 normal and 9 complete CLP second trimester fetal specimens. Using data from this sample, the present study assessed the complex multivariate relationships among these variables which represent the fetal normal and CLP midface. Ten variables were standardized relative to crown-rump length and used in Canonical Discriminant Function Analysis (CDFA). CDF analysis revealed that five variables best described the midface and accounted for 72% of the overall variance. These included nasal capsule length, nasal airway volume, premaxillary length, premaxillary volume, and tongue volume. Classification using the CDFA coefficients resulted in correct group membership assignment for 26 of 29 total specimens 89.66%), 8 of 9 cleft 88.9%), and 18 of 20 normal specimens (90.0%). These results suggest that by as early as the second trimester CLP fetuses have a significantly distinct set of midfacial morphological relationships. Some or all of these factors may be responsible for postnatal growth dysplasias noted in CLP individuals.

The anterior nasal spine (ANS) is considered by some to be a unique characteristic of modern humans; however, it has been reported to occur in chimpanzees. Among human populations, ANS size correlates with facial prognathism and timing of premaxillary-maxillary sutural fusion, which may have implications for models of midfacial growth. To investigate these questions, skulls from 55 chimpanzees (Pan troglodytes) 29 male, 26 female), ranging in age from infants to adults, were examined. None of the 55 specimens examined had a true ANS, but a number of specimens exhibited raised anterior nasal prominences or tubercles (ANT) on the nasal surface of the premaxilla. Female specimens had significantly (P < .05) more ANTs and more extensive fusion of both the palatal and facial components of the suture than did the male specimens. Results from the present study document the presence of an ANT in a sample of chimpanzee crania and are consonant with associations predicted by a septal-traction model of midfacial growth.