生態形態學的起源可追溯至19世紀後期[3],當時形態學的重點是描述與比較不同物種的外形特徵,主要用於鳥類分類。但在20世紀30年代和40年代,生態形態學因為新分類技術的興起而出現學科衰落,但在50年代因為演化形態學的興起又使得學科復興[4]。高速攝影和X光攝影可以對身體部位的活動進行觀察,而肌電圖則可以監測肌肉活動,這使得形態學家可以更好的研究生物的行為細節。在50年代和60年代,生態學家也開始使用形態學測量來研究演化和生態問題,之後由華盛頓大學的詹姆斯·卡爾(James R. Karr)和佛羅里達州立大學的弗朗西斯·詹姆斯(Frances Crews James)兩人在1975年首次使用了「生態形態學」一詞[5]。隨後脊椎動物形態和生態條件之間的聯繫被現代生態形態學的概念確定[6][7]。
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