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Comparing the brains of related species faces the challenges of establishing homologies whilst accommodating evolutionary specializations. Here we propose a general framework for understanding similarities and differences between the brains of primates. The approach uses white matter blueprints of the whole cortex based on a set of white matter tracts that can be anatomically matched across species. The blueprints provide a common reference space that allows us to navigate between brains of different species, identify homologous cortical areas, or to transform whole cortical maps from one species to the other. Specializations are cast within this framework as deviations between the species' blueprints. We illustrate how this approach can be used to compare human and macaque brains.
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annotating characters with community ontology terms, links between novel species anatomy and the genes that may underlie them can be made. But given the enormity of the legacy literature, how can this largely unexploited wealth of descriptive data be rendered amenable to large-scale computation? To identify the bottlenecks, we quantified the time involved in the major aspects of phenotype curation as we annotated characters from the vertebrate phylogenetic systematics literature. This involves attaching fully computable logical expressions consisting of ontology terms to the descriptions in character-by-taxon matrices. The workflow consists of: (i) data preparation, (ii) phenotype annotation, (iii) ontology development and (iv) curation team discussions and software development feedback. Our results showed that the completion of this work required two person-years by a team of two post-docs, a lead data curator, and students. Manual data preparation required close to 13% of the effort. This part in particular could be reduced substantially with better community data practices, such as depositing fully populated matrices in public repositories. Phenotype annotation required ∼40% of the effort. We are working to make this more efficient with Natural Language Processing tools. Ontology development (40%), however, remains a highly manual task requiring domain (anatomical) expertise and use of specialized software. The large overhead required for data preparation and ontology development contributed to a low annotation rate of approximately two characters per hour, compared with 14 characters per hour when activity was restricted to character annotation. Unlocking the potential of the vast stores of morphological descriptions requires better tools for efficiently processing natural language, and better community practices towards a born-digital morphology. Database URL: http://kb.phenoscape.org
Previous descriptive work on deciduous dentition of primates has focused disproportionately on great apes and humans. To address this bias in the literature, we studied 131 subadult nonhominoid specimens (including 110 newborns) describing deciduous tooth morphology and assessing maximum hydroxyapatite density (MHD). All specimens were CT scanned at 70 kVp and reconstructed at 20.5-39 μm voxels. Grayscale intensity from scans was converted to hydroxyapatite (HA) density (mg HA/cm3 ) using a linear conversion of grayscale values to calibration standards of known HA density (R2 = .99). Using Amira software, mineralized dental tissues were captured by segmenting the tooth cusps first and then capturing the remainder of the teeth at descending thresholds of gray levels. We assessed the relationship of MHD of selected teeth to cranial length using Pearson correlation coefficients. In monkeys, anterior teeth are more mineralized than postcanine teeth. In tarsiers and most lemurs and lorises, postcanine teeth are the most highly mineralized. This suggests that monkeys have a more prolonged process of dental mineralization that begins with incisors and canines, while mineralization of postcanine teeth is delayed. This may in part be a result of relatively late weaning in most anthropoid primates. Results also reveal that in lemurs and lorises, MHD of the mandibular first permanent molar (M1 ) negatively correlates with cranial length. In contrast, the MHD of M1 positively correlates with cranial length in monkeys. This supports the hypothesis that natural selection acts independently on dental growth as opposed to mineralization and indicates clear phylogenetic differences among primates.
The subbasal nerve plexus (SNP) is the densest and most recognizable component of the mammalian corneal innervation; however, the anatomical configuration of the SNP in most animal models remains incompletely described. The purpose of the current study is to describe in detail the SNP architecture in eight different mammals, including several popular animal models used in cornea research.
The mouse is the most important animal model within neuroscientific research, a position strengthened by the wide-spread use of transgenic mouse models. Discoveries in animals are followed by corroboration in humans, and the interchange between these fields of research is essential to our understanding of the human brain. With the advent of advanced technologies such as single-cell transcriptomics, epigenetic profiling and diffusion MRI, many prominent research institutes and collaborations have emerged, aiming to construct complete human or mouse brain atlases with data on gene expression, connectivity and cell types. These initiatives are indispensable resources, but frequently require extensive, time-consuming development, and rely on updates by the provider. They often come in the shape of applications which require practice or prior technical know-how. Importantly, none of them place the human and the mouse brain next to each other to allow for immediate comparison. We present BrainWiki, a user-friendly, web-based atlas that links the human and the mouse brain together, side-by-side. The platform gives the user a simple overview of brain anatomy along with published articles relating to each brain region that allows the user to delve deeper into the current state of research concerning circuitry, brain functions and pathology. The website relies on interactivity and supports user contributions resulting in a dynamic website that evolves at the pace of neuroscience. It is designed to allow for constant updates and new features in the future which will contain data such as gene expression and neuronal cell types.
In vivo neuroimaging studies have established several reproducible volumetric sex differences in the human brain, but the causes of such differences are hard to parse. While mouse models are useful for understanding the cellular and mechanistic bases of sex-biased brain development in mammals, there have been no attempts to formally compare mouse and human sex differences across the whole brain to ascertain how well they translate. Addressing this question would shed critical light on use of the mouse as a translational model for sex differences in the human brain and provide insights into the degree to which sex differences in brain volume are conserved across mammals. Here, we use cross-species structural magnetic resonance imaging to carry out the first comparative neuroimaging study of sex-biased neuroanatomical organization of the human and mouse brain. In line with previous findings, we observe that in humans, males have significantly larger and more variable total brain volume; these sex differences are not mirrored in mice. After controlling for total brain volume, we observe modest cross-species congruence in the volumetric effect size of sex across 60 homologous brain regions (r=0.30; e.g.: M>F amygdala, hippocampus, bed nucleus of the stria terminalis, and hypothalamus and F>M anterior cingulate, somatosensory, and primary auditory cortices). This cross-species congruence is greater in the cortex (r=0.33) than non-cortex (r=0.16). By incorporating regional measures of gene expression in both species, we reveal that cortical regions with greater cross-species congruence in volumetric sex differences also show greater cross-species congruence in the expression profile of 2835 homologous genes. This phenomenon differentiates primary sensory regions with high congruence of sex effects and gene expression from limbic cortices where congruence in both these features was weaker between species. These findings help identify aspects of sex-biased brain anatomy present in mice that are retained, lost, or inverted in humans. More broadly, our work provides an empirical basis for targeting mechanistic studies of sex-biased brain development in mice to brain regions that best echo sex-biased brain development in humans.
The locus coeruleus (LC) is a dense cluster of neurons that projects axons throughout the neuroaxis and is located in the rostral pontine tegmentum extending from the level of the inferior colliculus to the motor nucleus of the trigeminal nerve. LC neurons are lost in the course of several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. In this study we used Nissl staining and tyrosine hydroxylase (TH) immunoreactivity to compare the human LC with that of closely related primate species, including great and lesser apes, and macaque monkeys. TH catalyzes the initial and rate-limiting step in catecholamine biosynthesis. The number of TH-immunoreactive (TH-ir) neurons was estimated in each species using stereologic methods. In the LC of humans the mean total number of TH-ir neurons was significantly higher compared to the other primates. Because the total number of TH-ir neurons in the LC was highly correlated with the species mean volume of the medulla oblongata, cerebellum, and neocortical gray matter, we conclude that much of the observed phylogenetic variation can be explained by anatomical scaling. Notably, the total number of LC neurons in humans was most closely predicted by the nonhuman allometric scaling relationship relative to medulla size, whereas the number of LC neurons in humans was considerably lower than predicted according to neocortex and cerebellum volume.
The greater expansion of the frontal lobes along the phylogeny scale has been interpreted as the signature of evolutionary changes underlying higher cognitive abilities in humans functions in humans. However, it is unknown how an increase in number of gyri, sulci and cortical areas in the frontal lobe have coincided with a parallel increase in connectivity. Here, using advanced tractography based on spherical deconvolution, we produced an atlas of human frontal association connections that we compared with axonal tracing studies of the monkey brain. We report several similarities between human and monkey in the cingulum, uncinate, superior longitudinal fasciculus, frontal aslant tract and orbito-polar tract. These similarities suggest to preserved functions across anthropoids. In addition, we found major differences in the arcuate fasciculus and the inferior fronto-occipital fasciculus. These differences indicate possible evolutionary changes in the connectional anatomy of the frontal lobes underlying unique human abilities.
Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported.
Triploids are rare in nature because of difficulties in meiotic and gametogenic processes, especially in vertebrates. The Carassius complex of cyprinid teleosts contains sexual tetraploid crucian carp/goldfish (C. auratus) and unisexual hexaploid gibel carp/Prussian carp (C. gibelio) lineages, providing a valuable model for studying the evolution and maintenance mechanism of unisexual polyploids in vertebrates. Here we sequence the genomes of the two species and assemble their haplotypes, which contain two subgenomes (A and B), to the chromosome level. Sequencing coverage analysis reveals that C. gibelio is an amphitriploid (AAABBB) with two triploid sets of chromosomes; each set is derived from a different ancestor. Resequencing data from different strains of C. gibelio show that unisexual reproduction has been maintained for over 0.82 million years. Comparative genomics show intensive expansion and alterations of meiotic cell cycle-related genes and an oocyte-specific histone variant. Cytological assays indicate that C. gibelio produces unreduced oocytes by an alternative ameiotic pathway; however, sporadic homologous recombination and a high rate of gene conversion also exist in C. gibelio. These genomic changes might have facilitated purging deleterious mutations and maintaining genome stability in this unisexual amphitriploid fish. Overall, the current results provide novel insights into the evolutionary mechanisms of the reproductive success in unisexual polyploid vertebrates.
Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent 'natural' phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.
The Rubiaceae are ideal for studying the diversity of fruits that develop from flowers with inferior ovary. We aimed to identify morpho-anatomical changes during fruit development that distinguish those derived from the carpel versus the extra-carpellary tissues. In addition, we present the fruit genetic core regulatory network in selected Rubiaceae species and compare it in terms of copy number and expression patterns to model core eudicots in the Brassicaceae and the Solanaceae.
Development and validation of an animal model of labral healing would facilitate translation of novel surgical and biological strategies to improve glenolabral healing. The purpose of this study was to characterize the anatomic and histological properties of the shoulder labrum in rat, rabbit, dog, pig, goat, and humans. Given the demonstrated similarities in size and structural morphology in other joints, it was hypothesized that the goat glenoid with surrounding capsulolabral complex would most closely resemble that of humans in terms of dimensions and structure, as observed grossly and histologically.
Comparative wood anatomy of Viburnum was carried out to understand the differences in wood features amongst the species which might be useful for taxonomic discrimination in the genus. Altogether, nine taxa belonging to five clades were investigated using a sliding microtome and light microscopy. The growth rings are well represented and earlywood and latewood are distinguishable in cross-section. Some of the important wood features include angular, oval and rounded vessels with scalariform perforation plates, opposite to scalariform inter-vessel pitting, rounded pits with slit-like apertures, thick-walled xylem tracheids with simple, rounded bordered pits, diffuse axial parenchyma, uni- and multiseriate rays, 2-4 cells wide. In general, there is a remarkable uniformity in the qualitative wood features in Viburnum species, although quantitative measurement showed some disparities. The most significant quantitative wood variables which might be useful for taxonomic groupings of the species comprise a frequency of vessels and rays, the diameter of the vessels and tracheids in the radial and tangential planes and height and width of rays in the tangential plane.
The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
Comparative anatomy and physiology are disciplines related to structures and mechanisms in three-dimensional (3D) space. For the past centuries, scientific reports in these fields have relied on written descriptions and two-dimensional (2D) illustrations, but in recent years 3D virtual modelling has entered the scene. However, comprehending complex anatomical structures is hampered by reproduction on flat inherently 2D screens. One way to circumvent this problem is in the production of 3D-printed scale models. We have applied computed tomography and magnetic resonance imaging to produce digital models of animal anatomy well suited to be printed on low-cost 3D printers. In this communication, we report how to apply such technology in comparative anatomy and physiology to aid discovery, description, comprehension and communication, and we seek to inspire fellow researchers in these fields to embrace this emerging technology.
The histaminergic system and its relationships to the other aminergic transmitter systems in the brain of the zebrafish were studied by using confocal microscopy and immunohistochemistry on brain whole-mounts and sections. All monoaminergic systems displayed extensive, widespread fiber systems that innervated all major brain areas, often in a complementary manner. The ventrocaudal hypothalamus contained all monoamine neurons except noradrenaline cells. Histamine (HA), tyrosine hydroxylase (TH), and serotonin (5-HT) -containing neurons were all found around the posterior recess (PR) of the caudal hypothalamus. TH- and 5-HT-containing neurons were found in the periventricular cell layer of PR, whereas the HA-containing neurons were in the surrounding cell layer as a distinct boundary. Histaminergic neurons, which send widespread ascending and descending fibers, were all confined to the ventrocaudal hypothalamus. Histaminergic neurons were medium in size (approximately 12 microm) with varicose ascending and descending ipsilateral and contralateral fiber projections. Histamine was stored in vesicles in two types of neurons and fibers. A close relationship between HA fibers and serotonergic raphe neurons and noradrenergic locus coeruleus neurons was evident. Putative synaptic contacts were occasionally detected between HA and TH or 5-HT neurons. These results indicate that reciprocal contacts between monoaminergic systems are abundant and complex. The results also provide evidence of homologies to mammalian systems and allow identification of several previously uncharacterized systems in zebrafish mutants.
Damage-repair is particularly important for the maintenance of the water-storing abilities of succulent plants such as cacti. Comparative morphological, anatomical, and biomechanical analyses of self-repair were performed on artificially wounded branches of Opuntia ficus-indica and Cylindropuntia bigelovii. Macroscopic observations, contrast staining, and lignin-proof staining were used to investigate morphological and anatomical responses after wounding at various time intervals. Two-point bending tests were repeatedly performed on the same branches under unwounded, freshly wounded, and healed conditions by using customized 3D-printed clamping jaws. Morphologically, both species showed a rolling-in of the wound edges, but no mucilage discharge. Anatomically, ligno-suberized peridermal layers developed that covered the wound region, and new parenchyma cells formed, especially in O. ficus-indica. In all samples, the wounding effect directly after damage caused a decrease between 18% and 37% in all the tested mechanical parameters, whereas a positive healing effect after 21 days was only found for C. bigelovii. Based on our data, we hypothesize a high selection pressure on the restoration of structural integrity in the wound area, with a focus on the development of efficient water-retaining mechanisms, whereas the concept of "sufficient is good enough" seems to apply for the restoration of the mechanical properties.
Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.
The hyper-diverse clade Passeriformes (crown group passerines) comprises over half of extant bird diversity, yet disproportionately few studies have targeted passerine comparative anatomy on a broad phylogenetic scale. This general lack of research attention hinders efforts to interpret the passerine fossil record and obscures patterns of morphological evolution across one of the most diverse clades of extant vertebrates. Numerous potentially important crown passeriform fossils have proven challenging to place phylogenetically, due in part to a paucity of phylogenetically informative characters from across the passerine skeleton. Here, we present a detailed analysis of the morphology of extant passerine carpometacarpi, which are relatively abundant components of the passerine fossil record. We sampled >70% of extant family-level passerine clades (132 extant species) as well as several fossils from the Oligocene of Europe and scored them for 54 phylogenetically informative carpometacarpus characters optimised on a recently published phylogenomic scaffold. We document a considerable amount of previously undescribed morphological variation among passerine carpometacarpi, and, despite high levels of homoplasy, our results support the presence of representatives of both crown Passeri and crown Tyranni in Europe during the Oligocene.
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