Opening the door to understanding fish collagen

Matthew J Collins

University of York, Department of Archaeology, BioArCh

Fish collagen, while still highly conserved, is much more variable than mammal collagen and poses a number of unique problems for ZooMS. First, fish collagen has a slightly different set of biochemical constraints than mammal collagen. In general the structural constraints on collagen in fish are relaxed due to a lower body temperature and lack of weight baring. This increases the mutation rate compared to mammals. Instead of the typical (a1)2a2 structure, fish can have (a1)3, (a1)2a2, or a1a2a3 and several groups of fish are actually expressing two copies of each collagen gene due to whole genome duplications. Second, the database of different species of fish is much larger than the corresponding database of mammals at any given location. Frequently the number of fish species available locally is higher than the number of mammals. In addition, many elements of the fish skeleton are not morphologically distinguishable to species or even family. This necessitates a large ZooMS database for fish. Finally, the reality of a large database is complicated by the lack of available collagen sequence data for many archaeologically relevant fish species. The authors will describe the ways in which we can overcome these problems including working closely with ichthyologists, mining transcriptome databases for collagen sequence data, and working to understand the biochemistry of fish collagen to predict ZooMS markers. We will then describe several examples of identification of fish to species for archaeologically or ecologically relevant questions in several fish families: salmonids, cyprinids, and scombrids (tuna).