Dr. Annie Lindgren

Contact Information


     Email: arl3@pdx.edu

     Phone: (503) 725-8712

     Office: SRTC 428

     Mailing address:

     Portland State University, Department of Biology

     PO Box 751

     Portland, OR 97207-0751



I joined PSU in 2011 as the cordinator for the Center for Life in Extreme Environments.  When not overseeing the day-to-day activities of the Center, I train and mentors students, coordinate outreach activities, teach several courses in the Biology department and conduct independent research.

My research focuses on systematics and taxonomy of the molluscan class Cephalopoda (squids, octopuses and cuttlefish). I use molecular and morphological approaches to identify new species of deep sea squid, trace biogeographic patterns of distribution and work to identify barriers to dispersal in the open ocean. I also use phylotranscriptomics and bioinformatic tools to continue to improve our understanding of how the major groups of cephalopods are related.  Recently, I have become more involved in understanding how cephalopods will respond to climate change, particularly in areas where oxygen minimum zones are expanding.  Cephalopods are one of the rare groups with members that can live in oxygen-limited/absent waters for a prolonged period of time; understanding the mechanisms behind this process may shed light on how or if other large predators will adjust.



I work extensively with CLEE faculty and the PSU Museum of Natural History to increase informal STEM opportunities for the public via several avenues including: training PSU students in informal STEM education via coursework (BI 410/510: Museum Curation and Outreach), providing local schools access to research and collections through field trips to PSU Biology (elementary through high school), and yearly open house events.  As an OMSI Communication Fellow, I regularly also participate in “Meet a Scientist” events and works to engage school aged children in STEM activities. If you are interested in scheduling tours, having visitors come to speak, or simply want to know more about STEM resources available through CLEE, please don’t hesitate to email me or use the contact form.



Lindgren AR and Anderson FE. 2018. Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods. Mol. Phylogen. Evol. 118:330-342.

Shea EK, Judkins H, Staudinger MD, Dimkovikj VH, Lindgren AR, Vecchione M. 2017.  Cephalopod biodiversity in the vicinity of Bear Seamount, western North Atlantic based on exploratory trawling from 2000 to 2014.  Marine Biodiversity (DOI: 10.1007/s12526-017-0633-3).

Lindgren AR, Buckley BA, Eppley S, Reysenbach A-L, Stedman KM, Wagner J.  2016.   Life on the Edge – the Biology of Organisms Inhabiting Extreme Environments: An Introduction to the Symposium.  Integrative and Comparative Biology. Online early (DOI: 10.1093/icb/icw094)

Allcock AL, Lindgren A, Strugnell JM.  2014.  The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review.  Journal of Natural History. doi: 10.1080/00222933.2013.825342

Spieser DI, Pankey MS, Zaharoff AK, Batelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren, AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH.  2014.  Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms.  BMC Bioinformatics 15: 350.

Reysenbach A-L, LiuY, Lindgren AR, Wagner ID, Sislak CD, Mets A, Schouten S.  2013. Mesoaciditoga lauensis gen. nov., sp. nov., a moderate thermoacidophilic Thermatogales from a deep-sea hydrothermal vent.  Int. J. Syst. Evol. Micro. 63: 4724-4729.

Oakley, TH, Wolfe, JM, Lindgren, AR, Zaharoff, AK.  2013.  Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny.  Mol. Biol. Evol. 30(1): 175-188 (DOI:10.1093/molbev/mss216).

DeSilva-Davila R, Hochberg FG, Lindgren AR, Franco-Gordo C.  2013.  Paralarval development, abundance, and distribution of Pterygioteuthis hoylei (Cephalopoda: Oegopsida:Pyroteuthidae) in the Gulf of California, Mexico.  Molluscan Res. 33(1): 50-64.

Lindgren AR, Pankey MS, Hochberg FG, Oakley TH.  2012.  A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment.  BMC Evol. Biol. 12: 129.  (DOI:10.1186/1471-2148-12-129)

Albertin C, et al. 2012.  Cephalopod Genomics: A plan of strategies and organization.  St. Gen. Sci. 7:1. (DOI:10.4056/sigs.3136559)

Lindgren AR. 2010.  Systematics and distribution of the genus Pterygioteuthis (Cephalopoda: Oegopsida) in the eastern tropical Pacific with the elevation of Pterygioteuthis giardi hoylei to species status.  Journal of Molluscan Studies 76(4): 389-398.

Lindgren AR.  2010.  A molecular phylogeny of Decapodiformes (Mollusca: Cephalopoda) with special focus on the squid Order Oegopsida.  Molecular Phylogenetics and Evolution 56: 77-90.

Strugnell JA, Lindgren AR, Allcock L.  2009.  Evolution of Cephalopoda.  In: TimeTree of Life S.B. Hedges and S. Kumar (eds.), Oxford University Press.  Pp. 242-246.

Young RE, Lindgren AR, Vecchione MV.  2008.  Mastigoteuthis microlucens: a new species of the squid family Mastigoteuthidae (Mollusca: Cephalopoda).  Proceedings of the Biological Society of Washington 121(2): 276-282.

Lindgren AR. and Daly M.  2007.  The impact of length-variable data and alignment criterion on the phylogeny of Decapodiformes (Mollusca: Cephalopoda).  Cladistics. 23: 464-476.

Strugnell JA. and Lindgren AR.  2007.  A barcode of life database for the Cephalopoda:  Considerations and Concerns.  CIAC Special Edition of Reviews in Fish Biology and Fisheries 17(2-3): 337-344.

Giribet G, Okusu A, Lindgren AR, Huff SW, Schrodl M, Nishiguchi MK.  2006.  Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons.  Proceedings of the National Academy of Science of the USA 103(20): 7723-7728.

Lindgren AR, Katugin O, Amezquita E, Nishiguchi MK.  2005.  A molecular phylogeny of Gonatidae (Mollusca: Cephalopoda).  Molecular Phylogenetics and Evolution 36:101-111.

Lindgren AR, Giribet G, Nishiguchi MK.  2004.  A combined approach to the phylogeny of Cephalopoda (Mollusca).  Cladistics 20: 454-486.