Methods for Fish Biology, 2nd edition

Chapter 7: Phylogeography and the Fundamentals of Population Genetic Analyses

Michelle R. Gaither and Joseph D. DiBattista


Gaither, M. R., and J. D. DiBattista. 2022. Phylogeography and the fundamentals of population genetic analyses. Pages 207–245 in S. Midway, C. Hasler, and P. Chakrabarty, editors. Methods for fish biology, 2nd edition. American Fisheries Society, Bethesda, Maryland.


The term “phylogeography” was first coined just over three decades ago by Avise et al. (1987); since then the field, as indicated by the number of published articles (see Avise 2000: Figure 1.5), has grown exponentially. Phylogeography, as a subdiscipline of biogeography, is the study of the abiotic factors and evolutionary processes that affect the distribution of biodiversity through space and time. It is a dynamic and interdisciplinary field that involves geology, geography, evolution, and ecology. How it differs from the broader field of biogeography is its focus on patterns of genetic lineages and diversity at the intraspecific level (Avise 1998, 2000). At global and regional scales, comparative phylogeographic studies have offered important insights into the processes that shape patterns of biodiversity and separate populations (Bernatchez and Wilson 1998; Bowen et al. 2001, 2016; Gaither et al. 2010, 2016a; Gaither and Rocha 2013; Crandall et al. 2019). These approaches have been employed to identify genetically isolated populations in peripheral locations such as the Hawaiian Archipelago (Gaither et al. 2011b), the Tropical Eastern Pacific (Lessios and Robertson 2006), the Red Sea (DiBattista et al. 2016a, 2016b, 2017c), and the Sea of Cortez (Terry et al. 2000) and are often used to identify signatures of population structure that result from disjunct habitats (antitropical species; Bowen and Grant 1997; Grant et al. 2005; Box 7.1) or contrasting environmental conditions (von der Heyden et al. 2013; Gaither et al. 2015a, 2016b; Teske et al. 2019). Moreover, many studies have applied panels of microsatellite loci and SNPs (single nucleotide polymorphisms) to monitor stock composition and delineate conservation units (examples in salmonids include Seeb et al. 2011; Larson et al. 2014; Bradbury et al. 2015).