The complex traits of animals are the results of their long-term adaption to the evolution, and are the main basis for the existence of animal diversity. The imbalance of their regulation is the inherent reason of human major chronic diseases. The knowledge of the formation rule of animal complex traits is also significant to the improvement of economic traits of domestic animals and bionics of special functions of animals. Therefore, systemic analysis of the causes of animal complex traits is not noly a basic frontier scientific work to reveal the laws of nature, but also has significant application prospects.
According to the function, the complex traits of animals can be divided into two types, namely morphological and physiological functions. It has been debated for a long time whether the genetic mechanisms of the evolution of the two types are the same or not. In this research project, we select there traits:
(1) a morphological trait, namely animal cranial capacity, which is significant in the morphological evolution of vertebrates, and recently has been researched with breakthroughing progresses by CAS scientists;
(2) a physiological trait, the plateau adaptability of animals, which has significant Chinese characteristics and has our own research basis;

(3) a physiological trait, animal fat energy metabolism, which is closely related to the major chronic diseases in Chinese population, while CAS is at the international frontier on its research. The main line throughout the whole research understands the inherent law of the complex traits of animals, by gradually analyzing the origin of animal complex traits on three levels, including genetics, developmental regulation network evolution, and functional adaptability. On the genetics level, we mainly elucidate the genetic elements that determine the complex traits. On the level of developmental regulation network evolution, we try to find how these elements are assembled. On the functional adaptability level, we perform function-control experiments to verify the results of the above two levels, and try to understand the adaptive significance of the component of these elements and their interactions, as well as the mechanism resulting to the inadaptation when imbalance occurs.

1. Cranial capacity

One of the important characters of the morphological evolution of vertebrates, especially primates, is their increasing cranial capacity, with human beings at the peak. The increasing cranial capacity of primates usually is in accordance with higher cognitive competence, which is the basic reason for the complex cognitive behaviour of primates during evolution. In this project, we use eGPS formula and omics analysis methods to systematically compare the differences of large-scale cross-species animal brains on transcriptome, methylation and promote levels, carry out comprehensive analysis on the genes' functional modules and post-transcriptional regulation pathways, which are crucial for the origin and evolution of vertebrate brains, as well as elucidate the detailed dynamic profile of these modules during large-scale evolution of vertebrates. We are also aim to draw a comprehensive molecular map on the evolution of brain functions during the main evolving periods of higher primates and the important developmental stages after birth. The aim is also to find the genes, gene network and functional pathways that are playing important roles in the early origin of marmal brains, the increasing of cranial capacity, and the complex process of brain structure and neural network.

2. Plateau adaptability

The Tibetan Plateau has extreme environment, therefore different kinds of animals in this area have been evolving with plateau adaptability. Elucidating the physiological mechanism of animals adopting the extreme environment such as low oxygen, low atmospheric pressure and high ultraviolet radiation, is not only helpful to analyze the complex physiological traits of animals for plateau adaptability, but also provides important models for discussing the interaction mechanism between environment and genetic development.
The aim of this project on this area is as follows:
(1) To reveal the common features of native animal species that are adopting the plateau environment in long term, by comprehensively analyzing the convergence and divergence of genetic forces relating to the complex traits with plateau adaptability between poikilothermal animal and homothermal animal;
(2) To reveal the common features of animal species that are adopting the plateau environment in short term, by comprehensively analyzing the convergence and divergence of genetic forces relating to the complex traits with plateau adaptability between plateau human and domestic animal;
(3) To identify the molecular modules and developmental regulation networks that are commonly relating to the complex traits with plateau adaptability, comprehensively analyzing its genetic basis.

3. Fat energy metabolism

Fat energy metabolism is one of the basic and complex physiological functions in animal life activities, and is also closely related with serious human chronic diseases like diabetes and cardiovascular diseases. Overviewing the history of animal evolution, it is found that the fat storage and energy metabolism ways of different animal species have significant differences. For example, birds and marmals all have subcutaneous fat, but only marmals would have diabetes when fat is over accumulated. In human, with the improvement of living conditions, the "thrifty gene" that is benefit for saving fat efficiently, which is developed during human evolution, now has resulted in the increasing of metabolic diseases like diabetes. Therefore, analyzing the fat energy metabolism mechanism and its consequences on cross-species animals is not only helpful to understanding an important complex physiological trait, but also provides a new idea for comprehensively understanding the mechanism of metabolic diseases and its prevention.

4. Key theoretical model

The research on the analysis and regulation of the evolution of complex traits of animals will provide scientific basis for understanding the inherent causes of human major chronic diseases, improvement of economic traits of domestic animals, as well as bionics of special functions of annimals. This systems biology research requires comprehensive utilization of multi-level omics data on the whole genome as well as other derivated datasets, including genetic and epigenetic dataset, gene regulation dataset, proteomic dataset, metabolic dataset, biological image dataset, etc. These massive data of different species, different measuring technology platform, different levels and scales compose multivariate and heterogenenous data, which requires a unified mathematical tool to carry out integration at the system level in order to better understand the origin of complex traits of animals.
Meanwhile, we provide a platform for team members to publish information and share data, and a related system of non-model animals, with their omics data annotation, management and publication. We also provide integrated, open-sharing and one-stop data access service, including data publication, data submission and update, data retrieval, data download, visual preview, analysis tools integration, etc.