Table_1_Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken.XLSX

In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions.

在进化生态学领域，生态型（ecotype）指的是在遗传层面适应特定环境条件的种群。对家畜生态型开展环境与遗传特征解析，在物种保护及育种改良中可发挥关键作用，尤其在提升气候韧性方面至关重要。然而当前家畜生态型的界定往往较为随意，未对其农业生态环境开展细致系统的解析。本研究采用一种将生态位模型（ENM）与基因组学相结合的新型整合分析方法，基于种群栖息地的环境特征划定生态型，并解析生态型基因组中的适应性选择信号。本研究将该方法应用于代表多样农业气候条件的25个埃塞俄比亚乡村鸡种群。通过生态位模型分析，本研究识别出6个关键的适应性环境驱动因子，并划定了12个生态型。通过生态型内的选择信号分析（采用Hp与iHS两种方法），本研究共鉴定出1056个与多种生物过程相关的候选选择清除区域（SRs）。尽管多数候选选择清除区域具有生态型特异性，但重叠基因所涉及的生物学通路在不同生态型间大体共享。部分生物学通路在多数生态型中均存在共享，所涉及的基因功能与散养鸡的生存适配高度相关，例如神经元发育/过程、免疫应答、视觉发育以及学习能力等。采用冗余分析（RDA）开展基因型-环境关联分析，可将约33%的候选选择清除区域与主要环境驱动因子建立关联。对选择信号分析与冗余分析筛选出的部分强候选基因进行功能注释，发现其功能与对应生态型的主要环境驱动因子高度相关。该整合分析方法为解析适应性进化的复杂过程（包括基因型×环境（G×E）互作）提供了强有力的研究工具。