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Barley AJ, Ho DV, Baumann P, Wang IJ, Shaffer HB, Fisher RN, Gray LN, Krabbenhoft TJ, Espinosa RE, Escalona M, Toffelmier E, Sahasrabudhe R, Nguyen O, Fairbairn CW, Beraut E, Thomson RC. Speciation genomics in the tiger whiptail lizards (Aspidoscelis tigris complex). Genome Biology and Evolution 17:evaf218, https://doi.org/10.1093/gbe/evaf218
Schwarz P, Krabbenhoft TJ, Near TJ, MacGuigan DJ. (2025) Mosaic tri-lineage secondary contact shapes diverse genomic outcomes in darters, Evolution qpaf260, https://doi.org/10.1093/evolut/qpaf260
Pelosi JA, Davenport R, Kuo L-Y, Gray LN, Dant AJ, Kim EH, Li F-W, Dlugosch KM, Krabbenhoft TJ, Barbazuk WB, Sessa EB (2025) The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant. Proceedings of the National Academy of Sciences 122:e2504773122. https://doi.org/10.1073/pnas.2504773122.
Turner TF, Dearmon ES, Osborne MJ, Caeiro-Dias G, Dowling TE, Wicks AJ, Krabbenhoft TJ, Mussmann SM, Wilson WD (2025) Building a tissue archive to support conservation genomics of Colorado River fishes. Miscellaneous Publications Museum of Zoology, University of Michigan 209(6):1-19
Backenstose NJC, MacGuigan DJ, Osborne CA, Bernal MA, Thomas EK, Normandeau E, Yule DL, Stott W, Ackiss AS, Albert VA, Bernatchez L, Krabbenhoft TJ (2024) Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum. Communications Biology. doi.org/10.1038/s42003-024-06503-z.
Eaton KM, Krabbenhoft TJ, Backenstose NJC, Bernal MA (2024) The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history. G3 Genes|Genomes|Genetics: jkae096. doi.org/10.1093/g3journal/jkae096.
Salojärvi J, A Rambani, Z Yu, R Guyot, S Strickler, M Lepelley, S Rajaraman, P Rastas, C Zheng, D Santos Muñoz, J Meidanis, AR Paschoal, Y Bawin, TJ Krabbenhoft, ZQ Wang, S Fleck, R Aussel, L Bellanger, A Charpagne, C Fournier, M Kassam, G Lefebvre, S Métairon, D Moine, M Rigoreau, J Stolte, P Hamon, E Couturon, C Tranchant-Dubreuil, M Mukherjee, T Lan, M Pietrella, J Engelhardt, P Stadler, SM Correia De Lemos, SI Suzuki, U Sumirat, W Ching Man, N Dauchot, S Orozco-Arias, A Garavito, C Kiwuka, P Musoli, A Nalukenge, E Guichoux, H Reinout, M Smit, L Carretero-Paulet, O Guerreiro Filho, MT Braghini, L Padilha, GH Sera, T Ruttink, R Henry, P Marraccini, Y Van de Peer, A Andrade, D Domingues, G Giuliano, L Mueller, L Filipe Pereira, S Plaisance, V Poncet, S Rombauts, D Sankoff, VA Albert, D Crouzillat, A de Kochko, P Descombes (2024) The genome and population genomics of allopolyploid Coffea arabica reveals the diversification history of modern coffee cultivars. Nature Genetics 56:721–731. doi.org/10.1038/s41588-024-01695-w.
Miles LS, Waterman H, Ayoub NA, Garb JE, Haney RA, Rosenberg MS, Krabbenhoft TJ, Verrelli B (2024) Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. Journal of Heredity 115:241–252. Selected as “Editor’s Choice” article. https://doi.org/10.1093/jhered/esae018.
Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA (2024) High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Communications Biology 7, 54. https://doi.org/10.1038/s42003-023-05748-4
Lynch AJ, DiSanto A, Olden JD, Chu C, Paukert CP, Gundermann D, Lang M, Zhang R, Krabbenhoft TJ (2023) Climate impacts to inland fishes: shifting research topics over time. PLoS Climate 2:e0000326. doi.org/10.1371/journal.pclm.0000326
MacGuigan DJ, Porto-Hannes I, Foote B, Backenstose NJC, Osborne CA, Louisor K, Waterman H, Chang SL, Cochran J, Krabbenhoft TJ (2023) Spotty distributions: spotted gar (Lepisosteus oculatus) and spotted sucker (Minytrema melanops) range expansions in eastern Lake Erie. Journal of Great Lakes Research 4:931-940. doi.org/10.1016/j.jglr.2023.05.009
Caeiro-Dias G, Osborne M, Waterman H, Krabbenhoft TJ, Turner TF (2023) Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae). Journal of Heredity. doi.org/10.1093/jhered/esad039
MacGuigan DJ, Krabbenhoft TJ, Harrington RC, Wainwright DK, Backenstose NJC, Near TJ (2023) Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes. Evolution 77:1505-1521. doi.org/10.1093/evolut/qpad067
Albert VA, Krabbenhoft TJ (2023) Navigating the CoGe online software suite for polyploidy research. Pp 19-45, in Van de Peer et al, Polyploidy: Methods and Protocols.
Bernal MA, Yule DL, Stott W, Evrard L, Dowling TE, Krabbenhoft TJ (2022) Concordant patterns of morphological, stable isotope, and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.). Molecular Ecology 31:4495-4509. https://doi.org/10.1111/mec.16596.
Lynch AJ, Myers BJE, Wong JP, Chu C, Tingley III RW, Falke JA, Kwak TJ, Paukert CP, Krabbenhoft TJ (2022) Reducing uncertainty in climate change responses for inland fisheries management: a decision-path approach. Conservation Science and Practice. https://doi.org/10.1111/csp2.12724
Pelosi JA, Bernal MA, Krabbenhoft TJ, Galbo S, Prada C, Coffroth MA, Lasker HR (2022) Fine-scale morphological, genomic, reproductive, and symbiont differences delimit the Caribbean octocorals Plexaura homomalla and P. kükenthali. Coral Reefs 41:635-653. https://doi.org/10.1007/s00338-021-02175-x.
Krabbenhoft TJ, MacGuigan DJ, Backenstose NJC, Waterman H, Lan T, Pelosi JA, Tan M, Sandve SR (2021) Chromosome-level genome assembly of Chinese sucker (Myxocyprinus asiaticus) reveals strongly-conserved synteny following a catostomid-specific whole genome duplication. Genome Biology and Evolution, evab1900, https://doi.org/10.1093/gbe/evab190.
Lynch AJ, Thompson LM, Beever EA, Coe DN, Engman AC, Hawkins Hoffman C, Jackson ST, Krabbenhoft TJ, Lawrence DJ, Limpinsel D, Magill RT, Melvin TA, Morton JM, Newman RA, Peterson JO, Porath MT, Rahel FJ, Schurman GW, Sethi SA, Wilkening JL (2021) Guiding principles for managing ecosystem transformation. Frontiers in Ecology and the Environment, https://doi.org/10.1002/fee.2377.
Eaton KM, Bernal MA, Backenstose NJC, Yule DL, Krabbenhoft TJ (2021) Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes. Genome Biology and Evolution, https://doi.org/10.1093/gbe/evaa237
Code for nanopore genotyping available at: github.com/KrabbenhoftLab/rhodopsin
Wetlab protocol for nanopore amplicon sequencing available at: biorxiv.org/content/10.1101/2020.06.13.150334v1.supplementary-material
See news coverage at: AAAS EurekAlert! "This Great Lakes fish may have evolved to see like its marine ancestors did."
See news coverage at: WBFO NPR: "UB research looking at freshwater fish with deep sea eyes."
Thompson LM, Lynch AJ, Beever EA, Engman AC, Falke JA, Jackson ST, Krabbenhoft TJ, Lawrence DJ, Limpinsel D, Magill RT, Melvin TA, Morton JM, Newman RA, Peterson JO, Porath MT, Rahel FJ, Sethi SA, Wilkening JL (2021) Responding to ecosystem transformation: resist, accept, or direct? Fisheries, doi.org/10.1002/fsh.10506
Turner TF, Dowling TE, Krabbenhoft TJ, Osborne MJ, Pilger TJ (2020) Conservation genetics of desert fishes in the genomics age. Chapter 14, Pg. 207-224 in Standing Between Life and Extinction. Eds. Propst DL, Williams JE, Bestgen KR, Hoagstrom CW. University of Chicago Press.
Krabbenhoft, TJ*, Myers BJE*, Wong J, Chu C, Tingley III, R, Falke JA, Kwak TJ, Paukert CP, Lynch AJ (2020) FiCli, the Fish and Climate Change Database, informs climate adaptation and management for freshwater fishes. Scientific Data 7, 124. DOI: 10.1038/s41597-020-0465-z *Contributed equally.
See news coverage at: AAAS EurekAlert: (https://www.eurekalert.org/pub_releases/2020-04/uab-cct042220.php)
Olson K, Krabbenhoft TJ, Hrabik T, Mendsaikhan B, Jensen OP (2019) Pelagic-littoral resource polymorphism in Hovsgol grayling Thymallus nigrescens from Lake Hovsgol, Mongolia. Ecology of Freshwater Fish 28:411-423.
Smith GR, Zaroban DW, High B, Sigler JW, Krabbenhoft TJ, Dowling TE (2018) Introgressive mtDNA transfer in hybrid lake suckers (Teleostei, Catostomidae) in western United States. Pp. 84-117 In: Fishes of the Mio-Pliocene Western Snake River Plain and Vicinity, Miscellaneous Publications of the Museum of Zoology, University of Michigan, No. 204, No. 3.
Krabbenhoft TJ, Turner TF (2018) Comparative transcriptomics of cyprinid minnows and carp in a common wild setting: a resource for ecological genomics in freshwater communities. DNA Research 25:11-23.
Myers BJE, Lynch AJ, Bunnell DB, Chu C, Falke JA, Kovach R, Krabbenhoft TJ, Kwak TJ, Paukert CP (2017) *Authors 3-9 listed alphabetically. Global synthesis of the projected and documented climate change effects on inland fishes. Reviews in Fish Biology and Fisheries 27:339-361. Invited contribution for special issue: Impacts of climate change on marine and inland fishes and fisheries.
Lynch AJ, Myers BJE, Chu C, Eby LA, Falke JA, Kovach RP, Krabbenhoft TJ, Kwak TJ, Lyons J, Paukert CP, Whitney JE (2016) Climate change effects on North American inland fish populations and assemblages. Authors 3-9 listed alphabetically by last name. Fisheries 41:346-361. Invited contribution for a special issue on effects of climate change on inland fishes of North America.
Turner TF, Krabbenhoft TJ, Collyer ML, Krabbenhoft CA, Edwards MS, Sharp ZD (2015) Retrospective stable isotope analysis reveals ecosystem responses to river regulation over the last century. Ecology 96:3213-3226.
Mercado-Silva N, Lyons J, Moncayo-Estrada R, Gesundheit P, Krabbenhoft TJ, Powell DL, Piller KR (2015) Stable isotope evidence for trophic overlap of sympatric Mexican Lake Chapala silversides (Teleostei: Atherinopsidae: Chirostoma spp.). Neotropical Ichthyology 13:389-400.
Krabbenhoft TJ, Platania SP, Turner TF (2014) Interannual variation in reproductive phenology in a riverine fish assemblage: implications for predicting the effects of climate change and alteration of flow regimes. Freshwater Biology 59:1744-1754.
Krabbenhoft TJ, Turner TF (2014) Clock gene evolution: seasonal timing, phylogenetic inertia, or functional constraint? Journal of Heredity 105(3):407-415.
Turner TF, Collyer ML, Krabbenhoft TJ (2010) A general hypothesis-testing framework for stable isotope ratios in ecological studies. Ecology 91:2227-2233.
Munroe TA, Krabbenhoft TJ (2010) Two unusually large pre-transitional tonguefish larvae (Pleuronectiformes: Cynoglossidae: Symphurus) collected in Oceanic waters near the Galapagos Islands. Bulletin of Marine Science 86:13-31.
Turner TF, Krabbenhoft TJ, Burdett AS (2010) Reproductive phenology and fish community structure in an arid-land river system. In: Gido K & Jackson D (Eds.): Community Ecology of Stream Fishes. American Fisheries Society Symposium 73:427-446.
Renshaw MA, Carson EW, Hanna A, Rexroad CE, III, Krabbenhoft TJ, Gold JR (2009) Microsatellite markers for species of the genus Dionda (Cyprinidae) from the American southwest. Conservation Genetics 10(5):1569-1575.
Krabbenhoft TJ, Collyer ML, Quattro JM (2009) Differing evolutionary patterns underlie convergence on elongate morphology in endemic fishes of Lake Waccamaw, North Carolina. Biological Journal of the Linnean Society 98:636-645.
Krabbenhoft TJ, Rohde FC, Quattro JM (2009) Threatened Fishes of the World: Fundulus waccamensis Hubbs and Raney, 1946 (Fundulidae). Environmental Biology of Fishes 84:173-174.
Snelson FF, Krabbenhoft TJ, Quattro JM (2009) Elassoma gilberti: A new species of pygmy sunfish (Elassomatidae) from Florida and Georgia. Bulletin of the Florida Museum of Natural History 48(4):119-144.
Krabbenhoft TJ, Rohde FC, Leibman AN, Quattro JM (2008) Concordant nuclear and mitochondrial DNA partitions define evolutionarily significant units in the imperiled pinewoods darter, Etheostoma mariae (Pisces:Percidae). Copeia 2008:909-915.
Krabbenhoft TJ, Rohde FC, Quattro JM (2006) Threatened Fishes of the World: Etheostoma perlongum (Hubbs and Raney 1946) (Percidae). Environmental Biology of Fishes 76:411-412.
Krabbenhoft TJ, Rohde FC, Quattro JM (2005) Threatened Fishes of the World: Menidia extensa (Hubbs and Raney 1946) (Atherinopsidae). Environmental Biology of Fishes 73:48.
Krabbenhoft TJ, Munroe TA (2003) Symphurus bathyspilus: a new species of cynoglossid flatfish (Pleuronectiformes:Cynoglossidae) from deepwaters of the Indo-West Pacific. Copeia 2003:810-817.
