REVIEWS Stable isotope analysis in deep-sea chondrichthyans: recent challenges, ecological insights, and future directions Oliver. N. Shipley . Edward J. Brooks . Daniel J. Madigan . Christopher J. Sweeting . R. Dean Grubbs Received: 21 May 2016 / Accepted: 10 January 2017 Ó Springer International Publishing Switzerland 2017 Abstract Deep-sea chondrichthyans are cryptic species subject to increasing anthropogenic exploita- tion. Defining their role in deep-water ecosystems is therefore crucial for predicting the ecosystem-wide effects of their removal. Stable isotope analyses (SIA) of carbon and nitrogen have been increasingly used in chondrichthyan studies as a non-lethal method to investigate aspects of their ecology. In recent years these methods have been applied to deep-sea chon- dricthyans to investigate their trophic structure, niche width, and describe energy flow in the deep sea. Despite the increasing popularity of SIA in deep-sea chondrichthyan studies, methods rely on a multitude of assumptions, such as the need to determine accurate trophic discrimination and tissue turnover rates, which are currently lacking for most species. These uncer- tainties may preclude the reliability of isotope-based approaches, and as a result inferences from isotopic data must be viewed with relative caution. Due to the growing use of isotopic-based approaches in deep-sea chondrichthyans, we review the literature in the context of current methodological challenges and ecological inferences. We provide recommendations and novel approaches that may help develop and refine a rapidly growing field of study. Keywords Vulnerable Á Deep-water Á Food web Á Chemical tracer Á Carbon Á Nitrogen Introduction In recent decades, stable isotope analysis (SIA) has emerged as a useful tool to perform quantitative ecological assessments of food web structure and wider community interactions across all major marine biomes (Boecklen et al. 2011). SIA relies on deter- mining the ratio of heavy to light isotopes present within animal tissues (reported in %) as these are transferred in a relatively predictable manner from primary producers or prey to consumer (defined as trophic discrimination; DeNiro and Epstein 1978, 1981). The isotope ratios of carbon (d 13 C), Oliver. N. Shipley (&) School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11780, USA e-mail: oliver.shipley@stonybrook.edu Oliver. N. Shipley Á E. J. Brooks Shark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, Bahamas D. J. Madigan Harvard University Centre for the Environment, Harvard University, Cambridge, MA 02138, USA C. J. Sweeting School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne NE17RU, UK R. Dean Grubbs Florida State University Coastal and Marine Laboratory, 3618 Coastal Highway 98, St.Teresa, FL 32358, USA 123 Rev Fish Biol Fisheries DOI 10.1007/s11160-017-9466-1