Deep time perspective on turtle neck evolution: chasing the Hox code by vertebral morphology

Extreme neck elongation evolved despite strong developmental constraints in bizarre Triassic reptiles-implications for neck modularity in archosaurs

The Triassic radiation of vertebrates saw the emergence of the modern vertebrate groups, as well as numerous extinct animals exhibiting conspicuous, unique anatomical characteristics. Among these, members of Tanystropheidae (Reptilia: Archosauromorpha) displayed cervical vertebral elongation to an extent unparalleled in any other vertebrate. Tanystropheids were exceptionally ecologically diverse and had a wide spatial and temporal distribution. This may have been related to their neck anatomy, yet its evolution and functional properties remain poorly understood. We used geometric morphometrics to capture the intraspecific variation between the vertebrae comprising the cervical column among early archosauromorphs, to trace the evolutionary history of neck elongation in these animals. Our results show that the cervical series of these reptiles can be divided into modules corresponding to those of extant animals. Tanystropheids achieved neck elongation through somite elongation and a shift between cervical and thoracic regions, without presacral vertebrae count increase-contrary to crown archosaurs. This suggests a peculiar developmental constraint that strongly affected the evolution of tanystropheids. The data obtained just at the base of the archosauromorph phylogenetic tree are crucial for further studies on the modularity of vertebral columns of not only Triassic reptile groups but extant and other extinct animals as well.

Whole genome sequencing of Luxi Black Head sheep for screening selection signatures associated with important traits

Objective

Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH.

Methods

We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (θ_π) ratio.

Results

The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected.

Conclusion

The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

Limb reduction in squamate reptiles correlates with the reduction of the chondrocranium: A case study on serpentiform anguids

BACKGROUND

In vertebrates, the skull evolves from a complex network of dermal bones and cartilage-the latter forming the pharyngeal apparatus and the chondrocranium. Squamates are particularly important in this regard as they maintain at least part of the chondrocranium throughout their whole ontogeny until adulthood. Anguid lizards represent a unique group of squamates, which contains limbed and limbless forms and show conspicuous variation of the adult skull.

RESULTS

Based on several emboadryonic stages of the limbless lizards Pseudopus apodus and Anguis fragilis, and by comparing with other squamates, we identified and interpreted major differences in chondrocranial anatomy. Among others, the most important differences are in the orbitotemporal region. P. apodus shows a strikingly similar development of this region to other squamates. Unexpectedly, however, A. fragilis differs considerably in the composition of the orbitotemporal region. In addition, A. fragilis retains a paedomorphic state of the nasal region.

CONCLUSIONS

Taxonomic comparisons indicate that even closely related species with reduced limbs show significant differences in chondrocranial anatomy. The Pearson correlation coefficient suggests strong correlation between chondrocranial reduction and limb reduction. We pose the hypothesis that limb reduction could be associated with the reduction in chondrocrania by means of genetic mechanisms.

Evolution of the Mammalian Neck from Developmental, Morpho-Functional, and Paleontological Perspectives

The mammalian neck adopts a variety of postures during daily life and generates numerous head trajectories. Despite its functional diversity, the neck is constrained to seven cervical vertebrae in (almost) all mammals. Given this low number, an unexpectedly high degree of modularity of the mammalian neck has more recently been uncovered. This work aims to review neck modularity in mammals from a developmental, morpho-functional, and paleontological perspective and how high functional diversity evolved in the mammalian neck after the occurrence of meristic limitations. The fixed number of cervical vertebrae and the developmental modularity of the mammalian neck are closely linked to anterior Hox genes expression and strong developmental integration between the neck and other body regions. In addition, basic neck biomechanics promote morpho-functional modularity due to preferred motion axes in the cranio-cervical and cervico-thoracic junction. These developmental and biomechanical determinants result in the characteristic and highly conserved shape variation among the vertebrae that delimits morphological modules. The step-wise acquisition of these unique cervical traits can be traced in the fossil record. The increasing functional specialization of neck modules, however, did not evolve all at once but started much earlier in the upper than in the lower neck. Overall, the strongly conserved modularity in the mammalian neck represents an evolutionary trade-off between the meristic constraints and functional diversity. Although a morpho-functional partition of the neck is common among amniotes, the degree of modularity and the way neck disparity is realized is unique in mammals.

Deep Genome Resequencing Reveals Artificial and Natural Selection for Visual Deterioration, Plateau Adaptability and High Prolificacy in Chinese Domestic Sheep

Sheep were one of the earliest domesticated animals. Both artificial and natural selection during domestication has resulted in remarkable changes in behavioral, physiological, and morphological phenotypes; however, the genetic mechanisms underpinning these changes remain unclear, particularly for indigenous Chinese sheep. In the present study, we performed pooled whole-genome resequencing of 338 sheep from five breeds representative of indigenous Chinese breeds and compared them to the wild ancestors of domestic sheep (Asian mouflon, Ovis orientalis) for detection of genome-wide selective sweeps. Comparative genomic analysis between domestic sheep and Asian mouflon showed that selected regions were enriched for genes involved in bone morphogenesis, growth regulation, and embryonic and neural development in domestic sheep. Moreover, we identified several vision-associated genes with funtional mutations, such as PDE6B (c.G2994C/p.A982P and c.C2284A/p.L762M mutations), PANK2, and FOXC1/GMSD in all five Chinese native breeds. Breed-specific selected regions were determined including genes such as CYP17 for hypoxia adaptability in Tibetan sheep and DNAJB5 for heat tolerance in Duolang sheep. Our findings provide insights into the genetic mechanisms underlying important phenotypic changes that have occurred during sheep domestication and subsequent selection.

High HOXD4 protein expression in gastric adenocarcinoma tissues indicates unfavorable clinical outcomes

BACKGROUND/AIM

Homeobox D4 (HOXD4) belongs to the homeobox (HOX) family, which plays a crucial role in the early embryo development and cell differentiation. The role of HOXD4 in human gastric adenocarcinoma has not been elucidated. In the present study, we aimed to examine the expression levels of HOXD4 and dissect whether the HOXD4 expression is associated with aggressive clinicopathological outcomes of patients with gastric adenocarcinoma.

PATIENTS AND METHODS

Clinicopathological analyses were performed in 127 patients with gastric adenocarcinoma. Expression of HOXD4 was tested by immunohistochemistry staining and quantitative RT-PCR. Clinical outcomes were evaluated by the Kaplan-Meier method and log-rank test. The prognostic role of HOXD4 in gastric adenocarcinoma patients was assessed by univariate and multivariate analyses. The effects and mechanisms of HOXD4 on cell proliferation, migration and invasion were explored through cellular experiments.

RESULTS

HOXD4 expression was elevated in gastric adenocarcinoma tissues compared to non-tumorous gastric tissues (P = 0.018). High expression of HOXD4 was significantly associated with larger tumor size (P = 0.008), advanced tumor invasion depth (P = 0.014), and positive lymph node metastasis (P < 0.001). Moreover, patients with high HOXD4 expression had poorer overall survival (P = 0.001), and HOXD4 was identified as an independent prognosis factor according to multivariate analysis [hazard ratio (HR) =2.253, 95% confident interval (CI) 1.028-4.979, P = 0.044]. Cellular results revealed that HOXD4 can promote tumor cell proliferation by upregulating c-Myc and cyclin D1.

CONCLUSIONS

Our study demonstrated that overexpression of HOXD4 was significantly correlated with poorer prognosis of gastric adenocarcinoma patients, indicating the potential of HOXD4 as a novel clinical predictive biomarker and drug target.