Mammalia 2016; 80(3): 241–251 Bruce D. Patterson* and Ryan W. Norris Towards a uniform nomenclature for ground squirrels: the status of the Holarctic chipmunks Abstract: The chipmunks are a Holarctic group of ground Introduction squirrels currently allocated to the genus Tamias within the tribe Marmotini (Rodentia: Sciuridae). Cranial, post- The chipmunks represent a species-rich radiation of cranial, and genital morphology, cytogenetics, and ground squirrels that range over much of northern Eurasia genetics each separate them into three distinctive and and North America. At present, 25 species are recognized monophyletic lineages now treated as subgenera. These in a single genus, Tamias (Thorington and Hoffmann 2005, groups are found in eastern North America, western IUCN 2014). As a group, chipmunks represent almost 9% North America, and Asia, respectively. However, avail- of the 285 squirrel species recognized worldwide (Thoring- able genetic data (mainly from mitochondrial cytochrome ton et al. 2012). Their diurnal activity, conspicuousness, b) demonstrate that the chipmunk lineages diverged abundance, and distribution in areas accessible to scien- early in the evolution of the Marmotini, well before vari- tists in Europe, Asia, and North America all suggest that ous widely accepted genera of marmotine ground squir- chipmunks should be thoroughly studied and systemati- rels. Comparisons of genetic distances also indicate that cally well known. However, this is true neither concerning the chipmunk lineages are as or more distinctive from species limits nor their phylogenetic relationships. one another as are most ground squirrel genera. Chip- Chipmunks are typically both conservative and munk fossils were present in the late Oligocene of North variable in terms of cranial and external morphology America and shortly afterwards in Asia, prior to the main (Merriam 1886, Allen 1890, Pocock 1923, Patterson 1983), radiation of Holarctic ground squirrels. Because they are delaying appreciation of their true species richness coordinate in morphological, genetic, and chronologic (Howell 1929, Hall and Kelson 1959). The number of rec- terms with ground squirrel genera, the three chipmunk ognized chipmunk species grew with the realization that lineages should be recognized as three distinct genera, contiguously allopatric taxa were often strikingly diver- namely, Tamias Illiger, 1811, Eutamias Trouessart, 1880, gent in genital morphology (White 1953a, Callahan 1977, and Neotamias A. H. Howell, 1929. Each is unambiguously Sutton 1982, Patterson 1984). However, whereas prelimi- diagnosable on the basis of cranial, post-cranial, and nary studies at contact zones between chipmunk species external morphology. indicated congruence between genital morphology, vocalizations, and pelage (Sutton and Nadler 1974, Pat- Keywords: diagnosis; fossils; genetic distance; Holarctic; terson and Heaney 1987, Sutton 1987, Gannon and Lawlor nomenclature; phylogenetics; Sciuridae. 1989, Gannon and Stanley 1991), more sophisticated studies have documented complex cases of hybridiza- DOI 10.1515/mammalia-2015-0004 tion and introgression (Good and Sullivan 2001, Dem- Received January 7, 2015; accepted April 22, 2015; previously boski and Sullivan 2003, Good et al. 2003, 2008, Hird published online May 26, 2015 and Sullivan 2009, Hird et al. 2010). Regional studies based on both nuclear and mitochondrial sequences have shown varying degrees of past introgression among an array of chipmunk species in western North America (Reid et al. 2012, Sullivan et al. 2014). Assessing the lineages of chipmunks has been equally complicated. Currently, the 25 recognized species are allo- *Corresponding author: Bruce D. Patterson, Integrative Research cated to three subgenera within the genus Tamias: Tamias Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Illiger, 1811 for the lone species in eastern North America; Chicago, IL 60605, USA, e-mail: [email protected] Ryan W. Norris: Department of Evolution, Ecology and Organismal Eutamias Trouessart, 1880 for the one recognized Biology, Ohio State University, 4240 Campus Dr., Lima, OH 45804, Eurasian species (but see Obolenskaya et al. 2009); and USA Neotamias A. H. Howell, 1929 for 23 species from western 242 B.D. Patterson and R.W. Norris: Nomenclature of chipmunks North America. However, for much of the last century, Larson 2006), especially in situations where fast-evolving two genera of chipmunks were recognized (Howell 1929, genes have become saturated (Hugall et al. 2007, Dorn- 1938, Hall and Kelson 1959, Hall 1981): Tamias for chip- burg et al. 2014). If such systemic bias is present, it may munks lacking P3 (among other characters) and Eutamias affect both chipmunks and Holarctic ground squirrels (including Neotamias as a subgenus) for forms retaining equally, but the bias would be corrected only for the Hol- this tooth (but see Ellerman 1940 and Bryant 1945, who arctic ground squirrels, thanks to the presence of a cali- treated them as one). Allocating all chipmunks to a single brating fossil. A similar analysis without age constraints is genus became generally accepted following Nadler et al. needed to confirm whether the apparent age of chipmunk (1977), Corbet (1978), and Ellis and Maxson (1979) and lineages results from their underlying genetics. was codified by global checklists (Corbet and Hill 1980 Assigning ranks to supraspecific groups is ultimately a and later editions, Honacki et al. 1982 and later editions). subjective exercise, although some have argued that higher Although several analyses of mitochondrial and nuclear taxa are real natural entities (Humphreys and Barraclough gene sequences have clarified the interspecific relation- 2014). Group names are referents for sets of taxa, and ships of chipmunks (Piaggio and Spicer 2000, 2001, Reid extended arguments have been made for adopting a rank- et al. 2012) and made nomenclatural recommendations less system (e.g., de Queiroz 2006). However, most biolo- to separate them as distinct genera (Piaggio and Spicer gists regard the taxonomic ranks as a nested system for 2001), little attention has focused on their higher-level information storage and retrieval (Mayr 1969, Hawksworth relationships. 2010). The value of any hierarchical system depends on Collectively, chipmunks belong either in their own coordinate rankings for coordinate entities, and this value tribe Tamiini (Black 1963, McKenna and Bell 1997) or as is particularly great for sister taxa, where biological com- the sister group to all other Holarctic ground squirrels and parisons are most meaningful (Benton 2007). Relative to marmots within the tribe Marmotini (Thorington et al. other squirrel genera, how different are the three chip- 2012) of the squirrel subfamily Xerinae. The remarkable munk lineages currently regarded as subgenera? In partic- diversity of social systems among ground squirrels and ular, how do evolutionary differences among chipmunks marmots has invited phylogenetic analyses to document compare to those among the ground squirrels that com- their historical relationships (e.g., Harrison et al. 2003), prise their sister group? The taxonomic rank accorded to inadvertently uncovering paraphyly in some widely rec- the chipmunk lineages should be comparable to the ranks ognized groups (Herron et al. 2004). Recently, the ground separating other equivalent groups of Marmotini. squirrel genus Spermophilus was revised to eliminate its To address these questions, we compiled available paraphyly with respect to both prairie dogs (Cynomys) and evidence from morphology, paleontology, and genetics. marmots (Marmota). Eight former subgenera of Spermo- We analyzed genetic sequence data generated in previ- philus were thereby elevated to generic rank on the basis ously published studies across the Marmotini using both of diagnostic morphology, distinctive craniometrics, and distance metrics and a Bayesian approach to estimate reciprocal monophyly in molecular phylogenetic studies relative divergence times. We also compared these relative (Helgen et al. 2009). This revised taxonomy of ground estimates to calibrated estimates of divergence times and squirrels and marmots has since been widely adopted to the fossil record itself. (Thorington et al. 2012, Bradley et al. 2005, Ge et al. 2014, Roskov et al. 2014). Recently, Ge et al. (2014) produced a timetree of Sci- Materials and methods uridae suggesting that the earliest divergences among chipmunks are as old as or older than splits among the Genetic data were obtained from already-generated Holarctic ground squirrels. However, their analysis was sequences deposited in GenBank (http://www.ncbi.nlm. calibrated at multiple nodes within the Xerinae, and the nih.gov/genbank/). Cytochrome b (Cytb) is the only gene constraints on these nodes could have contributed to their where sequence data are currently available for repre- result. Specifically, Ge and colleagues constrained the sentatives of the three subgenera of chipmunks. Although earliest divergence among Holarctic ground squirrels to sequences have been generated for exon 1 of the interpho- be 16 Mya but imposed no constraints on the age of chip- toreceptor binding protein (IRBP) in sciurids (DeBry and munks. Systemic bias in molecular age estimates has been Sagel 2001, Mercer and Roth 2003, Roth and Mercer 2008), demonstrated in numerous studies (Ho and Jermiin 2004, they are available for only two of the chipmunk lineages Jansa et al. 2006, Norris et al. 2015).