马门溪龙最早是在1952年于四川的公路修筑工地上发现。这个部分骨骸后来经研究,在1954年由著名的中国古生物学家杨锺健命名为建设马门溪龙(Mamenchisaurus constructus)。属名意为“马门溪的蜥蜴”,由汉语拼音mǎ“马”+mén“门”+chi(xi的改写)“溪”组成,意指化石最初发现地,位于四川宜宾金沙江的马鸣溪渡口旁的建设工地,但由于杨的口音而将马鸣溪龙误作为马门溪龙;[13]种名建设(constructus)则指第一具化石是在建筑工地出土。[2]正模标本(编号IVPP AS V.790)来自上沙溪庙组的汉通组层位,年代为侏罗纪晚期牛津阶。包含了14节不完整的颈椎。另外一个也是缺乏头颅的部分骨骼(编号IVPP V948)也被归入此种。[2]
在此之后,有其他多个物种陆续被命名。第二个有效种合川马门溪龙(Mamenchisaurus hochuanensis),它的模式标本编号为GCC V 20401,包含一个没有头骨的部分骨骼,保存了接近完整的19节颈椎。与模式种来自同一地层。最早于二战之前在合川太平地区被发现,直到1957年四月才被挖掘出来,并于1965年在北京清修完成,由杨锺健、赵喜进于1972年正式发表叙述。[3]文革期间,当时杨也担心着自己的安全,于是这个标本的复制模型被大量制作出来,并送往中国以外以便保护;这些模型后来成为象征着卡尔·马克思推崇的演化理论的印证。复制品的问题在于颈椎没有彼此分别开来,为了将其颈部弯曲,许多椎体中间被打断并出现原本不存在的关节位置。2001年标本编号ZDM 0126被归至合川马门溪龙,包含头骨、胸带及前肢,都是正模标本缺失的部分。[14]总共有至少五具以上的标本被归入此种。
葛瑞格利·保罗(英语:Gregory S. Paul)于2010年针对一些重要发现作了估计:他估计模式种建设马门溪龙长15米及重5吨,并认为此种的颈部并未极度加长;而合川马门溪龙的情况肯定不同,估计长20米及重14吨[10];1972年杨曾估计重达45吨。2016年的一份质量估计,根据21世纪北京制作的第二件骨架,由IVPP V456-V458三件标本组合而成,得出结论为最小估计值12063公斤。根据保罗于1988年的估计颈部长9.3米,在当时创下纪录,[16]直到超龙(颈长14米)及波塞东龙(颈长11.5至12米)发表才被超越。[17]相对于身体长度,颈部非常细长,且尾部也较短,使颈长相当于其余身体长度。后者观点也适用于杨氏种,保罗估计长17米及重7吨;而他估计井研种长20米及重12吨。保罗同意博物馆的模型并将其标示为中加种新标本的正确呈现,使其体长35米及重75吨,创下已发现的陆生骨骼的最大纪录;[10]其颈部长17米,超越波塞东龙、梁龙的地震种、超龙的数值成为新纪录;较小的模式标本颈长12米,颈肋长4.1米,也创下已叙述的最长蜥脚类颈肋记录,长于波塞东龙的3.42米。[18]保罗亦认为安岳种大型,长25米及重25吨,同样有极长颈部。[10][19]
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