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上述代谢的主要途径，如糖酵解和柠檬酸循环，存在于生物的全部三个领域中，并存在于最后的普遍共同祖先中。这种普遍的祖先细胞是原核生物<ref name="SmithE" /><ref>{{cite journal | vauthors = Romano AH, Conway T | title = Evolution of carbohydrate metabolic pathways | journal = Research in Microbiology | volume = 147 | issue = 6–7 | pages = 448–55 | year = 1996 | pmid = 9084754 | doi = 10.1016/0923-2508(96)83998-2 }}</ref>，也许是一种具有广泛的氨基酸、核苷酸、碳水化合物和脂质代谢的产烷菌<ref>{{cite book |author=Koch A |title=How did bacteria come to be? |journal=Adv Microb Physiol |volume=40 |pages=353–99 |year=1998 |pmid=9889982 |doi=10.1016/S0065-2911(08)60135-6 |series=Advances in Microbial Physiology |isbn=978-0-12-027740-7}}</ref><ref>{{cite journal | vauthors = Ouzounis C, Kyrpides N | title = The emergence of major cellular processes in evolution | journal = FEBS Letters | volume = 390 | issue = 2 | pages = 119–23 | date = July 1996 | pmid = 8706840 | doi = 10.1016/0014-5793(96)00631-X}}</ref>。在后来的进化过程中，这些古老的途径之所以得以保留，可能是因为这些反应为它们特定的代谢问题提供了最佳解决方案，这些途径（如糖酵解和三羧酸循环）以最少的步骤高效地产生它们的最终产物。最初的基于酶的代谢途径可能是嘌呤核苷酸代谢的一部分<ref name="Ebenhoh" /><ref name="Cascante" />，而之前的代谢途径是远古RNA界的一部分<ref>{{cite journal | vauthors = Caetano-Anollés G, Kim HS, Mittenthal JE | title = The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 22 | pages = 9358–63 | date = May 2007 | pmid = 17517598 | pmc = 1890499 | doi = 10.1073/pnas.0701214104 | bibcode = 2007PNAS..104.9358C }}</ref>。
上述代谢的主要途径，如糖酵解和柠檬酸循环，存在于生物的全部三个领域中，并存在于最后的普遍共同祖先中。这种普遍的祖先细胞是原核生物<ref name="SmithE" /><ref>{{cite journal | vauthors = Romano AH, Conway T | title = Evolution of carbohydrate metabolic pathways | journal = Research in Microbiology | volume = 147 | issue = 6–7 | pages = 448–55 | year = 1996 | pmid = 9084754 | doi = 10.1016/0923-2508(96)83998-2 }}</ref>，也许是一种具有广泛的氨基酸、核苷酸、碳水化合物和脂质代谢的产烷菌<ref>{{cite book |author=Koch A |title=How did bacteria come to be? |journal=Adv Microb Physiol |volume=40 |pages=353–99 |year=1998 |series=Advances in Microbial Physiology |isbn=978-0-12-027740-7}}</ref><ref>{{cite journal | vauthors = Ouzounis C, Kyrpides N | title = The emergence of major cellular processes in evolution | journal = FEBS Letters | volume = 390 | issue = 2 | pages = 119–23 | date = July 1996 | pmid = 8706840 | doi = 10.1016/0014-5793(96)00631-X}}</ref>。在后来的进化过程中，这些古老的途径之所以得以保留，可能是因为这些反应为它们特定的代谢问题提供了最佳解决方案，这些途径（如糖酵解和三羧酸循环）以最少的步骤高效地产生它们的最终产物。最初的基于酶的代谢途径可能是嘌呤核苷酸代谢的一部分<ref name="Ebenhoh" /><ref name="Cascante" />，而之前的代谢途径是远古RNA界的一部分<ref>{{cite journal | vauthors = Caetano-Anollés G, Kim HS, Mittenthal JE | title = The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 22 | pages = 9358–63 | date = May 2007 | pmid = 17517598 | pmc = 1890499 | doi = 10.1073/pnas.0701214104 | bibcode = 2007PNAS..104.9358C }}</ref>。
人们提出了许多模型来描述新代谢途径的演变机制。其中包括将新的酶顺序添加到一个短的祖传途径，整个途径的复制和分化，吸纳原有的酶或者把这些机制组装成新的反应途径。这些机制的相对重要性尚不清楚<ref>{{cite journal | vauthors = Schmidt S, Sunyaev S, Bork P, Dandekar T | title = Metabolites: a helping hand for pathway evolution? | journal = Trends in Biochemical Sciences | volume = 28 | issue = 6 | pages = 336–41 | date = June 2003 | pmid = 12826406 | doi = 10.1016/S0968-0004(03)00114-2 }}</ref>，但基因组研究表明，一条途径中的酶很可能有共同的祖先，这意味着许多途径是逐步进化而来的，途径中预先存在的步骤创造出了新的功能。另一种模型来自于追踪代谢网络中蛋白质结构演化的研究<ref>{{cite journal | vauthors = Light S, Kraulis P | title = Network analysis of metabolic enzyme evolution in Escherichia coli | journal = BMC Bioinformatics | volume = 5 | pages = 15 | date = February 2004 | pmid = 15113413 | pmc = 394313 | doi = 10.1186/1471-2105-5-15 }} {{cite journal | vauthors = Alves R, Chaleil RA, Sternberg MJ | title = Evolution of enzymes in metabolism: a network perspective | journal = Journal of Molecular Biology | volume = 320 | issue = 4 | pages = 751–70 | date = July 2002 | pmid = 12095253 | doi = 10.1016/S0022-2836(02)00546-6 }}</ref>，它指出酶被普遍利用，生物体借用酶在不同的代谢途径中执行相似的功能(在 MANET 数据库中显而易见)<ref>{{cite journal | vauthors = Kim HS, Mittenthal JE, Caetano-Anollés G | title = MANET: tracing evolution of protein architecture in metabolic networks | journal = BMC Bioinformatics | volume = 7 | pages = 351 | date = July 2006 | pmid = 16854231 | pmc = 1559654 | doi = 10.1186/1471-2105-7-351 }}</ref>。这些征用过程导致了进化酶的嵌合<ref>{{cite journal | vauthors = Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C | title = Small-molecule metabolism: an enzyme mosaic | journal = Trends in Biotechnology | volume = 19 | issue = 12 | pages = 482–6 | date = December 2001 | pmid = 11711174 | doi = 10.1016/S0167-7799(01)01813-3 }}</ref>。第三种可能性是，新陈代谢的某些部分可能作为“模块”存在，可以在不同的途径中重复使用，并对不同的分子执行类似的功能<ref>{{cite journal | vauthors = Spirin V, Gelfand MS, Mironov AA, Mirny LA | title = A metabolic network in the evolutionary context: multiscale structure and modularity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 23 | pages = 8774–9 | date = June 2006 | pmid = 16731630 | pmc = 1482654 | doi = 10.1073/pnas.0510258103 | bibcode = 2006PNAS..103.8774S }}</ref>。
人们提出了许多模型来描述新代谢途径的演变机制。其中包括将新的酶顺序添加到一个短的祖传途径，整个途径的复制和分化，吸纳原有的酶或者把这些机制组装成新的反应途径。这些机制的相对重要性尚不清楚<ref>{{cite journal | vauthors = Schmidt S, Sunyaev S, Bork P, Dandekar T | title = Metabolites: a helping hand for pathway evolution? | journal = Trends in Biochemical Sciences | volume = 28 | issue = 6 | pages = 336–41 | date = June 2003 | pmid = 12826406 | doi = 10.1016/S0968-0004(03)00114-2 }}</ref>，但基因组研究表明，一条途径中的酶很可能有共同的祖先，这意味着许多途径是逐步进化而来的，途径中预先存在的步骤创造出了新的功能。另一种模型来自于追踪代谢网络中蛋白质结构演化的研究<ref>{{cite journal | vauthors = Light S, Kraulis P | title = Network analysis of metabolic enzyme evolution in Escherichia coli | journal = BMC Bioinformatics | volume = 5 | pages = 15 | date = February 2004 | pmid = 15113413 | pmc = 394313 | doi = 10.1186/1471-2105-5-15 }} {{cite journal | vauthors = Alves R, Chaleil RA, Sternberg MJ | title = Evolution of enzymes in metabolism: a network perspective | journal = Journal of Molecular Biology | volume = 320 | issue = 4 | pages = 751–70 | date = July 2002 | pmid = 12095253 | doi = 10.1016/S0022-2836(02)00546-6 }}</ref>，它指出酶被普遍利用，生物体借用酶在不同的代谢途径中执行相似的功能(在 MANET 数据库中显而易见)<ref>{{cite journal | vauthors = Kim HS, Mittenthal JE, Caetano-Anollés G | title = MANET: tracing evolution of protein architecture in metabolic networks | journal = BMC Bioinformatics | volume = 7 | pages = 351 | date = July 2006 | pmid = 16854231 | pmc = 1559654 | doi = 10.1186/1471-2105-7-351 }}</ref>。这些征用过程导致了进化酶的嵌合<ref>{{cite journal | vauthors = Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C | title = Small-molecule metabolism: an enzyme mosaic | journal = Trends in Biotechnology | volume = 19 | issue = 12 | pages = 482–6 | date = December 2001 | pmid = 11711174 | doi = 10.1016/S0167-7799(01)01813-3 }}</ref>。第三种可能性是，新陈代谢的某些部分可能作为“模块”存在，可以在不同的途径中重复使用，并对不同的分子执行类似的功能<ref>{{cite journal | vauthors = Spirin V, Gelfand MS, Mironov AA, Mirny LA | title = A metabolic network in the evolutionary context: multiscale structure and modularity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 23 | pages = 8774–9 | date = June 2006 | pmid = 16731630 | pmc = 1482654 | doi = 10.1073/pnas.0510258103 | bibcode = 2006PNAS..103.8774S }}</ref>。