Controlling Hox gene expression and activity to build the vertebrate axial skeleton

Developmental Genetic Basis of Hoxd9 Homeobox Domain Deletion in Pampus argenteus Pelvic Fin Deficiency

Pampus argenteus is important for commercial fishery catch species and is an emerging target for aquaculture production. Notably, P. argenteus has a bizarre morphology and lacks pelvic fins. However, the reason for the lack of pelvic fins remains unclear, ultimately leading to frequent upside-down floating of P. argenteus during breeding and marked consumption of physical energy. Some lineages, including whales, fugu, snakes, and seahorse, independently lost the pelvic appendages over evolutionary time. Do different taxa employ the same molecular genetic pathways when they independently evolve similar developmental morphologies? Through analysis of the gene responsible for appendage localization, Hoxd9, it was discovered that the Hox domain was absent in the Hoxd9 gene of P. argenteus, and the Hoxd9b gene lacked the Hox9 activation region, a feature not observed in the Hoxd9 gene of other fish species. Interestingly, those distinctive characteristics are not observed in the Hoxd9 gene of other fish species. To determine the association between the Hoxd9 gene characteristics and the pelvic fin deletion in P. argenteus, the full-length cDNA of the Hoxd9a gene was cloned, and morphological observations of the species' juveniles were performed using stereomicroscopy and scanning electron microscopy. Thereafter, the tissue localization of Hoxd9a in the species was analyzed at the gene and protein levels. Based on the results, deletion of the Hoxd9a structural domain possibly leads to disruptions in the protein translation and the pelvic fin localization in P. argenteus during its early ontogenetic developmental stage, resulting in the absence of pelvic fins.

Evolution of vertebral numbers in primates, with a focus on hominoids and the last common ancestor of hominins and panins

The primate vertebral column has been extensively studied, with a particular focus on hominoid primates and the last common ancestor of humans and chimpanzees. The number of vertebrae in hominoids-up to and including the last common ancestor of humans and chimpanzees-is subject to considerable debate. However, few formal ancestral state reconstructions exist, and none include a broad sample of primates or account for the correlated evolution of the vertebral column. Here, we conduct an ancestral state reconstruction using a model of evolution that accounts for both homeotic (changes of one type of vertebra to another) and meristic (addition or loss of a vertebra) changes. Our results suggest that ancestral primates were characterized by 29 precaudal vertebrae, with the most common formula being seven cervical, 13 thoracic, six lumbar, and three sacral vertebrae. Extant hominoids evolved tail loss and a reduced lumbar column via sacralization (homeotic transition at the last lumbar vertebra). Our results also indicate that the ancestral hylobatid had seven cervical, 13 thoracic, five lumbar, and four sacral vertebrae, and the ancestral hominid had seven cervical, 13 thoracic, four lumbar, and five sacral vertebrae. The last common ancestor of humans and chimpanzees likely either retained this ancestral hominid formula or was characterized by an additional sacral vertebra, possibly acquired through a homeotic shift at the sacrococcygeal border. Our results support the 'short-back' model of hominin vertebral evolution, which postulates that hominins evolved from an ancestor with an African ape-like numerical composition of the vertebral column.

Natural selection and convergent evolution of the HOX gene family in Carnivora

HOX genes play a central role in the development and regulation of limb patterns. For mammals in the order Carnivora, limbs have evolved in different forms, and there are interesting cases of phenotypic convergence, such as the pseudothumb of the giant and red pandas, and the flippers or specialized limbs of the pinnipeds and sea otter. However, the molecular bases of limb development remain largely unclear. Here, we studied the molecular evolution of the HOX9 ~ 13 genes of 14 representative species in Carnivora and explored the molecular evolution of other HOX genes. We found that only one limb development gene, HOXC10, underwent convergent evolution between giant and red pandas and was thus an important candidate gene related to the development of pseudothumbs. No signals of amino acid convergence and natural selection were found in HOX9 ~ 13 genes between pinnipeds and sea otter, but there was evidence of positive selection and rapid evolution in four pinniped species. Overall, few HOX genes evolve via natural selection or convergent evolution, and these could be important candidate genes for further functional validation. Our findings provide insights into potential molecular mechanisms of the development of specialized pseudothumbs and flippers (or specialized limbs).

Hox genes in development and beyond

Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.

Investigating the effects of compound paralogous EPHB receptor mutations on mouse facial development

BACKGROUND

Variation in facial shape may arise from the combinatorial or overlapping actions of paralogous genes. Given its many members, and overlapping expression and functions, the EPH receptor family is a compelling candidate source of craniofacial morphological variation. We performed a detailed morphometric analysis of an allelic series of E14.5 Ephb1-3 receptor mutants to determine the effect of each paralogous receptor gene on craniofacial morphology.

RESULTS

We found that Ephb1, Ephb2, and Ephb3 genotypes significantly influenced facial shape, but Ephb1 effects were weaker than Ephb2 and Ephb3 effects. Ephb2^-/- and Ephb3^-/- mutations affected similar aspects of facial morphology, but Ephb3^-/- mutants had additional facial shape effects. Craniofacial differences across the allelic series were largely consistent with predicted additive genetic effects. However, we identified a potentially important nonadditive effect where Ephb1 mutants displayed different morphologies depending on the combination of other Ephb paralogs present, where Ephb1^+/- , Ephb1^-/- , and Ephb1^-/- ; Ephb3^-/- mutants exhibited a consistent deviation from their predicted facial shapes.

CONCLUSIONS

This study provides a detailed assessment of the effects of Ephb receptor gene paralogs on E14.5 mouse facial morphology and demonstrates how the loss of specific receptors contributes to facial dysmorphology.

Body-axis organization in tetrapods: a model-system to disentangle the developmental origins of convergent evolution in deep time

Convergent evolution is a central concept in evolutionary theory but the underlying mechanism has been largely debated since On the Origin of Species. Previous hypotheses predict that developmental constraints make some morphologies more likely to arise than others and natural selection discards those of the lowest fitness. However, the quantification of the role and strength of natural selection and developmental constraint in shaping convergent phenotypes on macroevolutionary timescales is challenging because the information regarding performance and development is not directly available. Accordingly, current knowledge of how embryonic development and natural selection drive phenotypic evolution in vertebrates has been extended from studies performed at short temporal scales. We propose here the organization of the tetrapod body-axis as a model system to investigate the developmental origins of convergent evolution over hundreds of millions of years. The quantification of the primary developmental mechanisms driving body-axis organization (i.e. somitogenesis, homeotic effects and differential growth) can be inferred from vertebral counts, and recent techniques of three-dimensional computational biomechanics have the necessary potential to reveal organismal performance even in fossil forms. The combination of both approaches offers a novel and robust methodological framework to test competing hypotheses on the functional and developmental drivers of phenotypic evolution and evolutionary convergence.

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography

The characterization of developmental phenotypes often relies on the accurate linear measurement of structures that are small and require laborious preparation. This is tedious and prone to errors, especially when repeated for the multiple replicates that are required for statistical analysis, or when multiple distinct structures have to be analyzed. To address this issue, we have developed a pipeline for characterization of long-bone length using X-ray microtomography (XMT) scans. The pipeline involves semi-automated algorithms for automatic thresholding and fast interactive isolation and 3D-model generation of the main limb bones, using either the open-source ImageJ plugin BoneJ or the commercial Mimics Innovation Suite package. The tests showed the appropriate combination of scanning conditions and analysis parameters yields fast and comparable length results, highly correlated with the measurements obtained via ex vivo skeletal preparations. Moreover, since XMT is not destructive, the samples can be used afterward for histology or other applications. Our new pipelines will help developmental biologists and evolutionary researchers to achieve fast, reproducible and non-destructive length measurement of bone samples from multiple animal species.

Identification of Jmjd3 as an Essential Epigenetic Regulator of Hox Gene Temporal Collinear Activation for Body Axial Patterning in Mice

Body axial patterning develops via a rostral-to-caudal sequence and relies on the temporal colinear activation of Hox genes. However, the underlying mechanism of Hox gene temporal colinear activation remains largely elusive. Here, with small-molecule inhibitors and conditional gene knockout mice, we identified Jmjd3, a subunit of TrxG, as an essential regulator of temporal colinear activation of Hox genes with its H3K27me3 demethylase activity. We demonstrated that Jmjd3 not only initiates but also maintains the temporal collinear expression of Hox genes. However, we detected no antagonistic roles between Jmjd3 and Ezh2, a core subunit of PcG repressive complex 2, during the processes of axial skeletal patterning. Our findings provide new insights into the regulation of Hox gene temporal collinear activation for body axial patterning in mice.

Homeotic change in segment identity derives the human vertebral formula from a chimpanzee-like one

OBJECTIVES

One of the most contentious issues in paleoanthropology is the nature of the last common ancestor of humans and our closest living relatives, chimpanzees and bonobos (panins). The numerical composition of the vertebral column has featured prominently, with multiple models predicting distinct patterns of evolution and contexts from which bipedalism evolved. Here, we study total numbers of vertebrae from a large sample of hominoids to quantify variation in and patterns of regional and total numbers of vertebrae in hominoids.

MATERIALS AND METHODS

We compile and study a large sample (N = 893) of hominoid vertebral formulae (numbers of cervical, thoracic, lumbar, sacral, caudal segments in each specimen) and analyze full vertebral formulae, total numbers of vertebrae, and super-regional numbers of vertebrae: presacral (cervical, thoracic, lumbar) vertebrae and sacrococcygeal vertebrae. We quantify within- and between-taxon variation using heterogeneity and similarity measures derived from population genetics.

RESULTS

We find that humans are most similar to African apes in total and super-regional numbers of vertebrae. Additionally, our analyses demonstrate that selection for bipedalism reduced variation in numbers of vertebrae relative to other hominoids.

DISCUSSION

The only proposed ancestral vertebral configuration for the last common ancestor of hominins and panins that is consistent with our results is the modal formula demonstrated by chimpanzees and bonobos (7 cervical-13 thoracic-4 lumbar-6 sacral-3 coccygeal). Hox gene expression boundaries suggest that a rostral shift in Hox10/Hox11-mediated complexes could produce the human modal formula from the proposal ancestral and panin modal formula.

Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

Relationship between sacral shape variation and phylogeny in Old World monkeys

The sacrum, an essential skeletal element in the trunk, articulates with the ilium and lumbar and caudal vertebrae. While there are known morphological differences between hominoids and cercopithecoids (Old World monkeys), sacral morphological variations among cercopithecoids have rarely been studied outside of research on tail length variation. Increased knowledge regarding sacral variations in extant primates, however, could help in understanding and reconstructing their evolutionary development. Therefore, this study aimed to explore phylogenetic sacral shape variations among cercopithecoids. Geometric morphometric analyses were performed on 221 sacra from 39 different cercopithecoid species. Clear shape differences were observed among Colobinae, Cercopithecini, and Papionini, particularly in the spinous processes and sacral lateral mass. These parts function as muscle attachment points or skeletal joints, and variations in them seemed to reflect their required functions. However, the significance of the relationship between shape and function was not so great as to explain all the observed variation. According to recent genetic/developmental biological studies, shape variations may also be caused by the pleiotropic effects of some genes, such as posterior Hox genes. Therefore, while skeletal morphology has previously been considered to be directly connected to skeletal function, this study's results suggest that other factors influencing sacral shape require further research.

How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World's Largest Rodent

Gigantism results when one lineage within a clade evolves extremely large body size relative to its small-bodied ancestors, a common phenomenon in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to increased mutational load. Second, gigantism is achieved through generating a higher number of cells along with higher rates of cell proliferation, thus increasing the likelihood of cancer. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we assembled a draft genome of the capybara (Hydrochoerus hydrochaeris), the world's largest living rodent. We found that the genome-wide ratio of nonsynonymous to synonymous mutations (ω) is elevated in the capybara relative to other rodents, likely caused by a generation-time effect and consistent with a nearly neutral model of molecular evolution. A genome-wide scan for adaptive protein evolution in the capybara highlighted several genes controlling postnatal bone growth regulation and musculoskeletal development, which are relevant to anatomical and developmental modifications for an increase in overall body size. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T-cell-mediated tumor suppression, offering a potential resolution to the increased cancer risk in this lineage. Our comparative genomic results uncovered the signature of an intragenomic conflict where the evolution of gigantism in the capybara involved selection on genes and pathways that are directly linked to cancer.

Sacral co-ossification in dinosaurs: The oldest record of fused sacral vertebrae in Dinosauria and the diversity of sacral co-ossification patterns in the group

The fusion of the sacrum occurs in the major dinosaur lineages, i.e. ornithischians, theropods, and sauropodomorphs, but it is unclear if this trait is a common ancestral condition, or if it evolved independently in each lineage, or even how or if it is related to ontogeny. In addition, the order in which the different structures of the sacrum are fused, as well as the causes that lead to this co-ossification, are poorly understood. Herein, we described the oldest record of fused sacral vertebrae within dinosaurs, based on two primordial sacral vertebrae from the Late Triassic of Candelária Sequence, southern Brazil. We used computed microtomography (micro-CT) to analyze the extent of vertebral fusion, which revealed that it occurred only between the centra. We also assessed the occurrence of sacral fusion in Dinosauria and close relatives. The degree of fusion observed in representatives of the major dinosaur lineages suggested that there may be a sequential pattern of fusion of the elements of the sacrum, more clearly observed in Sauropodomorpha. Our analyses suggest that primordial sacral vertebrae fuse earlier in the lineage (as seen in Norian sauropodomorphs). Intervertebral fusion is observed to encompass progressively more vertebral units as sauropodomorphs evolve, reaching up to five or more fully fused sacrals in Neosauropoda. Furthermore, the new specimen described here indicates that the fusion of sacral elements occurred early in the evolution of dinosaurs. Factors such as ontogeny and the increase in body size, combined with the incorporation of vertebrae to the sacrum may have a significant role in the process and in the variation of sacral fusion observed.

Exploring copy number variants in deceased fetuses and neonates with abnormal vertebral patterns and cervical ribs

Background

Cervical patterning abnormalities are rare in the general population, but one variant, cervical ribs, is particularly common in deceased fetuses and neonates. The discrepancy between the incidence in the general population and early mortality is likely due to indirect selection against cervical ribs. The cause for the co‐occurrence of cervical ribs and adverse outcome remains unidentified. Copy number variations resulting in gain or loss of specific genes involved in development and patterning could play a causative role.

Methods

Radiographs of 374 deceased fetuses and infants, including terminations of pregnancies, stillbirths and neonatal deaths, were assessed. Copy number profiles of 265 patients were determined using single nucleotide polymorphism array.

Results

274/374 patients (73.3%) had an abnormal vertebral pattern, which was associated with congenital abnormalities. Cervical ribs were present in 188/374 (50.3%) and were more common in stillbirths (69/128 [53.9%]) and terminations of pregnancies (101/188 [53.7%]), compared to live births (18/58, 31.0%). Large (likely) deleterious copy number variants and aneuploidies were prevalent in these patients. None of the rare copy number variants were recurrent or overlapped with candidate genes for vertebral patterning.

Conclusions

The large variety of copy number variants in deceased fetuses and neonates with similar abnormalities of the vertebral pattern probably reflects the etiological heterogeneity of vertebral patterning abnormalities. This genetic heterogeneity corresponds with the hypothesis that cervical ribs can be regarded as a sign of disruption of critical, highly interactive stages of embryogenesis. The vertebral pattern can probably provide valuable information regarding fetal and neonatal outcome.

Giant extinct caiman breaks constraint on the axial skeleton of extant crocodylians

The number of precaudal vertebrae in all extant crocodylians is remarkably conservative, with nine cervicals, 15 dorsals and two sacrals, a pattern present also in their closest extinct relatives. The consistent vertebral count indicates a tight control of axial patterning by Hox genes during development. Here we report on a deviation from this pattern based on an associated skeleton of the giant caimanine Purussaurus, a member of crown Crocodylia, and several other specimens from the Neogene of the northern neotropics. P. mirandai is the first crown-crocodylian to have three sacrals, two true sacral vertebrae and one non-pathological and functional dorsosacral, to articulate with the ilium (pelvis). The giant body size of this caiman relates to locomotory and postural changes. The iliosacral configuration, a more vertically oriented pectoral girdle, and low torsion of the femoral head relative to the condyles are hypothesized specializations for more upright limb orientation or weight support.

GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures

Bone area is one measure of bone size that is easily derived from dual-energy X-ray absorptiometry (DXA) scans. In a GWA study of DXA bone area of the hip and lumbar spine (N ≥ 28,954), we find thirteen independent association signals at twelve loci that replicate in samples of European and East Asian descent (N = 13,608 - 21,277). Eight DXA area loci associate with osteoarthritis, including rs143384 in GDF5 and a missense variant in COL11A1 (rs3753841). The strongest DXA area association is with rs11614913[T] in the microRNA MIR196A2 gene that associates with lumbar spine area (P = 2.3 × 10-42, β = -0.090) and confers risk of hip fracture (P = 1.0 × 10-8, OR = 1.11). We demonstrate that the risk allele is less efficient in repressing miR-196a-5p target genes. We also show that the DXA area measure contributes to the risk of hip fracture independent of bone density.

Hox gene expression profiles during embryonic development of common sole

Common sole (Solea solea) aquaculture production is based mostly on wild-caught breeders. Recently, the successful reproduction of first-generation fish that were reared in captivity was accomplished. A consistent good quality and quantity of produced eggs throughout the year, and of next-generation broodstock, is important for reducing the overall cost of production. Hox genes play a pivotal role in normal embryonic development and alterations of their temporal expression level may be important for egg viability. Expression profile analysis of five hox genes (hoxa1a, hoxa2a, hoxa2b, hoxb1a and hoxb1b) involved in early embryonic development and of hoxa13a, which is involved in late stages, was carried out. Results revealed a premature and/or maternal expression of hoxa13a in sole embryos, and the detection of hoxa2a and hoxa2b genes as members of paralog group 2. Principal Component Analysis of hox gene expression in 54 ± 6 hours post fertilization embryos coming from wild-caught broodstock and a first-generation one reared in the hatchery, unveiled that these broodstocks are clearly distinct. In addition, their pairwise comparison revealed significant differences in the expression levels of hoxb1a and hoxb1b genes. Hox gene regulation during embryonic development could give valuable insight into rearing sole broodstocks with different origin in concert, and also into gaining a steady mass production of eggs, either in quality or quantity, all year round.

Is NF2 a Key Player of the Differentially Expressed Gene Between Spinal Cord Ependymoma and Intracranial Ependymoma?

BACKGROUND

Although intracranial and spinal ependymomas are histopathologically similar, the molecular landscape is heterogeneous. An urgent need exists to identify differences in the genomic profiles to tailor treatment strategies. In the present study, we delineated differential gene expression patterns between intracranial and spinal ependymomas.

METHODS

We searched the Gene Expression Omnibus database using the term "ependymoma" and analyzed the raw gene expression profiles of 292 ependymomas (31 spinal and 261 intracranial). The gene expression data were analyzed to find differentially expressed genes (DEGs) between 2 regions. The fold change (FC) and false discovery rate (FDR) were used to assess DEGs after gene integration (|log₂FC|>2; FDR P < 0.01). Enrichment and pathway analysis was also performed.

RESULTS

A total of 201 genes (105 upregulated and 96 downregulated) were significant DEGs in the data sets. The underexpression of NF2 in spinal ependymomas was statistically significant (FDR P = 7.91 × 10^-9). However, the FC of NF2 did not exceed the cutoff value (log₂FC, -1.2). The top 5 ranked upregulated genes were ARX, HOXC6, HOXA9, HOXA5, and HOXA3, which indicated that spinal ependymomas frequently demonstrate overexpression of HOX family genes, which play fundamental roles in specifying anterior/posterior body patterning. Moreover, the gene ontology enrichment analysis specified "anterior/posterior pattern specification" and "neuron migration" in spinal and intracranial ependymomas, respectively.

CONCLUSIONS

The most substantial magnitude of DEGs in ependymoma might be HOX genes. However, whether the differential expression of these genes is the cause or consequence of the disease remains to be elucidated in a larger prospective study.

Evolutionary changes of Hox genes and relevant regulatory factors provide novel insights into mammalian morphological modifications

The diversity of body plans of mammals accelerates the innovation of lifestyles and the extensive adaptation to different habitats, including terrestrial, aerial and aquatic habitats. However, the genetic basis of those phenotypic modifications, which have occurred during mammalian evolution, remains poorly explored. In the present study, we synthetically surveyed the evolutionary pattern of Hox clusters that played a powerful role in the morphogenesis along the head–tail axis of animal embryos and the main regulatory factors (Mll, Bmi1 and E2f6) that control the expression of Hox genes. A deflected density of repetitive elements and lineage‐specific radical mutations of Mll have been determined in marine mammals with morphological changes, suggesting that evolutionary changes may alter Hox gene expression in these lineages, leading to the morphological modification of these lineages. Although no positive selection was detected at certain ancestor nodes of lineages, the increased ω values of Hox genes implied the relaxation of functional constraints of these genes during the mammalian evolutionary process. More importantly, 49 positively‐selected sites were identified in mammalian lineages with phenotypic modifications, indicating adaptive evolution acting on Hox genes and regulatory factors. In addition, 3 parallel amino acid substitutions in some Hox genes were examined in marine mammals, which might be responsible for their streamlined body.

Heterochronic evolution explains novel body shape in a Triassic coelacanth from Switzerland

A bizarre latimeriid coelacanth fish from the Middle Triassic of Switzerland shows skeletal features deviating from the uniform anatomy of coelacanths. The new form is closely related to a modern-looking coelacanth found in the same locality and differences between both are attributed to heterochronic evolution. Most of the modified osteological structures in the new coelacanth have their developmental origin in the skull/trunk interface region in the embryo. Change in the expression of developmental patterning genes, specifically the Pax1/9 genes, may explain a rapid evolution at the origin of the new coelacanth. This species broadens the morphological disparity range within the lineage of these ‘living fossils’ and exemplifies a case of rapid heterochronic evolution likely trigged by minor changes in gene expression.

Sacral anatomy of the phytosaur Smilosuchus adamanensis, with implications for pelvic girdle evolution among Archosauriformes

The sacrum - consisting of those vertebrae that articulate with the ilia - is the exclusive skeletal connection between the hindlimbs and axial skeleton in tetrapods. Therefore, the morphology of this portion of the vertebral column plays a major role in the evolution of terrestrial locomotion. Whereas most extant reptiles only possess the two plesiomorphic sacral vertebrae, additional vertebrae have been incorporated into the sacrum multiple times independently among early-diverging archosaurian (crocodylians + birds) clades. Phytosauria was a diverse, abundant, and cosmopolitan clade of archosauriforms throughout the Late Triassic, but postcrania of this clade are rarely described and few species-level taxonomic placements of phytosaurian postcranial material are available, potentially hampering knowledge of morphological disparity in the postcranial skeleton among phytosaurs. Here, we describe the sacrum of Smilosuchus adamanensis, a phytosaur recovered from the Upper Triassic Chinle Formation of Arizona. This sacrum consists of the two primordial sacral vertebrae, but has a vertebra incorporated from the trunk into the sacrum (= a dorsosacral) and is therefore the first Late Triassic phytosaur and one of the first non-archosaurian archosauromorphs to be described with more than two sacral vertebrae. Our interpretation of this element as a dorsosacral is justified by the lateral extent of the dorsosacral ribs, clear surfaces of articulation between the distal ends of the dorsosacral ribs and the first primordial sacral ribs, and the scar on the medial surface of each ilium for articulation with each dorsosacral rib. Additionally, we provide the first detailed description of the vertebral junction formed by two anteriorly projecting flanges on the first primordial sacral ribs and their corresponding facets on the centrum of the dorsosacral. Computed tomographic (CT) imaging reveals that the two primordial sacrals are not co-ossified and that the dorsosacral morphology of this specimen is not the result of obvious pathology. We place this incorporation of a trunk vertebra into the phytosaurian sacrum in a broader evolutionary context, with this shift in vertebral identity occurring at least seven times independently among Triassic archosauriforms, including at least three times in early crocodylian-line archosaurs and at least four times among bird-line archosaurs. Additionally, anteriorly projecting flanges of sacral ribs which articulate with the anterior-adjacent centrum have evolved several times in archosauriforms, and we interpret 'shared' sacral ribs (= a sacral rib that articulates with two adjacent sacral centra more or less equally) present in some archosaurian clades as a more extreme example of this morphology. In extant taxa the highly conserved Hox gene family plays a central role in the patterning of the axial skeleton, especially vertebral identity; therefore, the independent incorporation of a trunk vertebra into the sacrum across multiple archosauriform lineages may suggest a homologous underlying developmental mechanism for this evolutionary trend.

A Hox complex activates and potentiates the Epidermal Growth Factor signaling pathway to specify Drosophila oenocytes

Hox transcription factors specify distinct cell types along the anterior-posterior axis of metazoans by regulating target genes that modulate signaling pathways. A well-established example is the induction of Epidermal Growth Factor (EGF) signaling by an Abdominal-A (Abd-A) Hox complex during the specification of Drosophila hepatocyte-like cells (oenocytes). Previous studies revealed that Abd-A is non-cell autonomously required to promote oenocyte fate by directly activating a gene (rhomboid) that triggers EGF secretion from sensory organ precursor (SOP) cells. Neighboring cells that receive the EGF signal initiate a largely unknown pathway to promote oenocyte fate. Here, we show that Abd-A also plays a cell autonomous role in inducing oenocyte fate by activating the expression of the Pointed-P1 (PntP1) ETS transcription factor downstream of EGF signaling. Genetic studies demonstrate that both PntP1 and PntP2 are required for oenocyte specification. Moreover, we found that PntP1 contains a conserved enhancer (PntP1OE) that is activated in oenocyte precursor cells by EGF signaling via direct regulation by the Pnt transcription factors as well as a transcription factor complex consisting of Abd-A, Extradenticle, and Homothorax. Our findings demonstrate that the same Abd-A Hox complex required for sending the EGF signal from SOP cells, enhances the competency of receiving cells to select oenocyte cell fate by up-regulating PntP1. Since PntP1 is a downstream effector of EGF signaling, these findings provide insight into how a Hox factor can both trigger and potentiate the EGF signal to promote an essential cell fate along the body plan.

Applying evolutionary genetics to developmental toxicology and risk assessment

Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.

Whole Genome Sequencing Identifies a Missense Mutation in HES7 Associated with Short Tails in Asian Domestic Cats

Domestic cats exhibit abundant variations in tail morphology and serve as an excellent model to study the development and evolution of vertebrate tails. Cats with shortened and kinked tails were first recorded in the Malayan archipelago by Charles Darwin in 1868 and remain quite common today in Southeast and East Asia. To elucidate the genetic basis of short tails in Asian cats, we built a pedigree of 13 cats segregating at the trait with a founder from southern China and performed linkage mapping based on whole genome sequencing data from the pedigree. The short-tailed trait was mapped to a 5.6 Mb region of Chr E1, within which the substitution c. 5T > C in the somite segmentation-related gene HES7 was identified as the causal mutation resulting in a missense change (p.V2A). Validation in 245 unrelated cats confirmed the correlation between HES7-c. 5T > C and Chinese short-tailed feral cats as well as the Japanese Bobtail breed, indicating a common genetic basis of the two. In addition, some of our sampled kinked-tailed cats could not be explained by either HES7 or the Manx-related T-box, suggesting at least three independent events in the evolution of domestic cats giving rise to short-tailed traits.

New insights into the vertebral Hox code of archosaurs

Variation in axial formulae (i.e., number and identity of vertebrae) is an important feature in the evolution of vertebrates. Vertebrae at different axial positions exhibit a region-specific morphology. Key determinants for the establishment of particular vertebral shapes are the highly conserved Hox genes. Here, we analyzed Hox gene expression in the presacral vertebral column in the Nile crocodile in order to complement and extend a previous examination in the alligator and thus establish a Hox code for the axial skeleton of crocodilians in general. The newly determined expression of HoxA-4, C-5, B-7, and B-8 all revealed a crocodilian-specific pattern. HoxA-4 and HoxC-5 characterize cervical morphologies and the latter furthermore is associated with the position of the forelimb relative to the axial skeleton. HoxB-7 and HoxB-8 map exclusively to the dorsal vertebral region. The resulting expression patterns of these two Hox genes is the first description of their exact expression in the archosaurian embryo. Our comparative analyses of the Hox code in several amniote taxa provide new evidence that evolutionary differences in the axial skeleton correspond to changes in Hox gene expression domains. We detect two general processes: (i) expansion of a Hox gene's expression domain as well as (ii) a shift of gene expression. We infer that the ancestral archosaur Hox code may have resembled that of the crocodile. In association with the evolution of morphological traits, it may have been modified to patterns that can be observed in birds.

Why are there race/ethnic differences in adult body mass index-adiposity relationships? A quantitative critical review

Body mass index (BMI) is now the most widely used measure of adiposity on a global scale. Nevertheless, intense discussion centers on the appropriateness of BMI as a phenotypic marker of adiposity across populations differing in race and ethnicity. BMI-adiposity relations appear to vary significantly across race/ethnic groups, but a collective critical analysis of these effects establishing their magnitude and underlying body shape/composition basis is lacking. Accordingly, we systematically review the magnitude of these race-ethnic differences across non-Hispanic (NH) white, NH black and Mexican American adults, their anatomic body composition basis and potential biologically linked mechanisms, using both earlier publications and new analyses from the US National Health and Nutrition Examination Survey. Our collective observations provide a new framework for critically evaluating the quantitative relations between BMI and adiposity across groups differing in race and ethnicity; reveal new insights into BMI as a measure of adiposity across the adult age-span; identify knowledge gaps that can form the basis of future research and create a quantitative foundation for developing BMI-related public health recommendations.

Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan.

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A transgenic mouse line expressing fish Hox genes has anterior homeotic transformations.

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Fish Hox genes are capable of inducing tetrapod specific vertebral characters.

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A sacral Hox-code influences adult hindlimb position, yet not the position of limb budding.

Targeted Deletion of Btg1 and Btg2 Results in Homeotic Transformation of the Axial Skeleton

Btg1 and Btg2 encode highly homologous proteins that are broadly expressed in different cell lineages, and have been implicated in different types of cancer. Btg1 and Btg2 have been shown to modulate the function of different transcriptional regulators, including Hox and Smad transcription factors. In this study, we examined the in vivo role of the mouse Btg1 and Btg2 genes in specifying the regional identity of the axial skeleton. Therefore, we examined the phenotype of Btg1 and Btg2 single knockout mice, as well as novel generated Btg1^-/-;Btg2^-/- double knockout mice, which were viable, but displayed a non-mendelian inheritance and smaller litter size. We observed both unique and overlapping phenotypes reminiscent of homeotic transformation along the anterior-posterior axis in the single and combined Btg1 and Btg2 knockout animals. Both Btg1^-/- and Btg2^-/- mice displayed partial posterior transformation of the seventh cervical vertebra, which was more pronounced in Btg1^-/-;Btg2^-/- mice, demonstrating that Btg1 and Btg2 act in synergy. Loss of Btg2, but not Btg1, was sufficient for complete posterior transformation of the thirteenth thoracic vertebra to the first lumbar vertebra. Moreover, Btg2^-/- animals displayed complete posterior transformation of the sixth lumbar vertebra to the first sacral vertebra, which was only partially present at a low frequency in Btg1^-/- mice. The Btg1^-/-;Btg2^-/- animals showed an even stronger phenotype, with L5 to S1 transformation. Together, these data show that both Btg1 and Btg2 are required for normal vertebral patterning of the axial skeleton, but each gene contributes differently in specifying the identity along the anterior-posterior axis of the skeleton.

Correlation between Hox code and vertebral morphology in archosaurs

The relationship between developmental genes and phenotypic variation is of central interest in evolutionary biology. An excellent example is the role of Hox genes in the anteroposterior regionalization of the vertebral column in vertebrates. Archosaurs (crocodiles, dinosaurs including birds) are highly variable both in vertebral morphology and number. Nevertheless, functionally equivalent Hox genes are active in the axial skeleton during embryonic development, indicating that the morphological variation across taxa is likely owing to modifications in the pattern of Hox gene expression. By using geometric morphometrics, we demonstrate a correlation between vertebral Hox code and quantifiable vertebral morphology in modern archosaurs, in which the boundaries between morphological subgroups of vertebrae can be linked to anterior Hox gene expression boundaries. Our findings reveal homologous units of cervical vertebrae in modern archosaurs, each with their specific Hox gene pattern, enabling us to trace these homologies in the extinct sauropodomorph dinosaurs, a group with highly variable vertebral counts. Based on the quantifiable vertebral morphology, this allows us to infer the underlying genetic mechanisms in vertebral evolution in fossils, which represents not only an important case study, but will lead to a better understanding of the origin of morphological disparity in recent archosaur vertebral columns.

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

Hox genes underlie the specification of body segment identity in the anterior-posterior axis. They are activated during gastrulation and undergo a dynamic shift from a transcriptionally repressed to an active chromatin state in a sequence that reflects their chromosomal location. Nevertheless, the precise role of chromatin modifying complexes during the initial activation phase remains unclear. In the current study, we examined the role of chromatin regulators during Hox gene activation. Using embryonic stem cell lines lacking the transcriptional activator MOZ and the polycomb-family repressor BMI1, we showed that MOZ and BMI1, respectively, promoted and repressed Hox genes during the shift from the transcriptionally repressed to the active state. Strikingly however, MOZ but not BMI1 was required to regulate Hox mRNA levels after the initial activation phase. To determine the interaction of MOZ and BMI1 in vivo, we interrogated their role in regulating Hox genes and body segment identity using Moz;Bmi1 double deficient mice. We found that the homeotic transformations and shifts in Hox gene expression boundaries observed in single Moz and Bmi1 mutant mice were rescued to a wild type identity in Moz;Bmi1 double knockout animals. Together, our findings establish that MOZ and BMI1 play opposing roles during the onset of Hox gene expression in the ES cell model and during body segment identity specification in vivo. We propose that chromatin-modifying complexes have a previously unappreciated role during the initiation phase of Hox gene expression, which is critical for the correct specification of body segment identity.

Hoxb6 can interfere with somitogenesis in the posterior embryo through a mechanism independent of its rib-promoting activity

Formation of the vertebrate axial skeleton requires coordinated Hox gene activity. Hox group 6 genes are involved in the formation of the thoracic area due to their unique rib-promoting properties. We show here that the linker region (LR) connecting the homeodomain and the hexapeptide is essential for Hoxb6 rib-promoting activity. The LR-defective Hoxb6 protein was still able to bind a target enhancer together with Pax3 producing a dominant negative effect, indicating that the LR brings additional regulatory factors to target DNA elements. We also found an unexpected association between Hoxb6 and segmentation in the paraxial mesoderm. In particular, Hoxb6 can disturb somitogenesis and anterior-posterior somite patterning by deregulating Lfng expression. Interestingly, this interaction occurred differently in thoracic and more caudal embryonic areas, indicating functional differences in somitogenesis before and after the trunk to tail transition. Our results suggest the requirement of precisely regulated Hoxb6 expression for proper segmentation at tailbud stages.