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Geometric morphometrics (GM) is a powerful analytical approach for evaluating phenotypic variation relevant to taxonomy and systematics, and as with any statistical methodology, requires adherence to fundamental assumptions for inferences to be strictly valid. An important consideration for GM is how landmark configurations, which represent sets of anatomical loci for evaluating shape variation through Cartesian coordinates, relate to underlying homology (Zelditch et al. 1995; Polly 2008). Perhaps more so than with traditional morphometrics, anatomical homology is a crucial assumption for GM because of the mathematical and biological interpretations associated with shape change depicted by deformation grids, such as the thin plate spline (Klingenberg 2008; Zelditch et al. 2012). GM approaches are often used to analyze shapes or outlines of structures, which are not necessarily related to common ancestry, and in this respect GM approaches that use linear semi-landmarks and related methods are particularly amenable to evaluating primary homology, or raw similarity between structures (De Pinna 1991; Palci & Lee 2019). This relaxed interpretation of homology that focuses more on recognizable and repeatable landmarks is defensible so long as authors are clear regarding the purpose of the analyses and in defining their landmark configurations (Palci & Lee 2019). Secondary homology, or similarity due to common ancestry, can also be represented with GM methods and is often assumed to be reflected in fixed Type 1 (juxtaposition of tissues) or Type 2 (self-evident geometry) landmarks (Bookstein 1991). 

The Mohave Rattlesnake (Crotalus scutulatus) is a highly venomous pitviper inhabiting the arid interior deserts, grasslands, and savannas of western North America. Currently two subspecies are recognized: the Northern Mohave Rattlesnake (C. s. scutulatus) ranging from southern California to the southern Central Mexican Plateau, and the Huamantla Rattlesnake (C. s. salvini) from the region of Tlaxcala, Veracruz, and Puebla in south-central Mexico. Although recent studies have demonstrated extensive geographic variation in venom composition and cryptic genetic diversity in this species, no modern studies have focused on geographic variation in morphology. Here we analyzed a series of qualitative, meristic, and morphometric traits from 347 specimens of C. scutulatus and show that this species is phenotypically cohesive without discrete subgroups, and that morphology follows a continuous cline in primarily color pattern and meristic traits across the major axis of its expansive distribution. Interpreted in the context of previously published molecular evidence, our morphological analyses suggest that multiple episodes of isolation and secondary contact among metapopulations during the Pleistocene were sufficient to produce distinctive genetic populations, which have since experienced gene flow to produce clinal variation in phenotypes without discrete or diagnosable distinctions among these original populations. For taxonomic purposes, we recommend that C. scutulatus be retained as a single species, although it is possible that C. s. salvini, which is morphologically the most distinctive population, could represent a peripheral isolate in the initial stages of speciation.