Are geometric morphometric analyses replicable? Evaluating landmark measurement error and its impact on extant and fossil Microtus classification

Abstract

Geometric morphometric analyses are frequently employed to quantify biological shape and shape variation. Despite the popularity of this technique, quantification of measurement error in geometric morphometric datasets and its impact on statistical results is seldom assessed in the literature. Here, we evaluate error on 2D landmark coordinate configurations of the lower first molar of five North American Microtus (vole) species. We acquired data from the same specimens several times to quantify error from four data acquisition sources: specimen presentation, imaging devices, interobserver variation, and intraobserver variation. We then evaluated the impact of those errors on linear discriminant analysis‐based classifications of the five species using recent specimens of known species affinity and fossil specimens of unknown species affinity. Results indicate that data acquisition error can be substantial, sometimes explaining >30% of the total variation among datasets. Comparisons of datasets digitized by different individuals exhibit the greatest discrepancies in landmark precision, and comparison of datasets photographed from different presentation angles yields the greatest discrepancies in species classification results. All error sources impact statistical classification to some extent. For example, no two landmark dataset replicates exhibit the same predicted group memberships of recent or fossil specimens. Our findings emphasize the need to mitigate error as much as possible during geometric morphometric data collection. Though the impact of measurement error on statistical fidelity is likely analysis‐specific, we recommend that all geometric morphometric studies standardize specimen imaging equipment, specimen presentations (if analyses are 2D), and landmark digitizers to reduce error and subsequent analytical misinterpretations.

Optimizing digitalization effort in morphometrics

“…If possible, tests should be performed using the exact same set of reference specimens. That being said, error should always be interpreted in the context of the biological question explored [ 14 , 21 , 37 ]. The amount of acceptable error will indeed depend on the data used and the comparisons being made [ 17 , 21 , 38 , 39 ].…”

“…Several approaches have been proposed to assess error in morphometrics based on replicated measurements [ 12 , 20 , 21 ]. Less studies have addressed the problem of pooling data from various sources [ 13 , 14 , 16 ].…”

“…Yezerinac et al [ 20 ] identified multiple sources of imprecision in morphometric measurements including: not well-defined measurements, structure flexibility, operator experience, IO and repeatability variation, non-human sources precision, and lightning conditions. These can be summarized into the three categories of methodological, instrumental, and personal sources of error [ 14 ]. Unfortunately, MEs, both within and among operators, are rarely evaluated and even more rarely quantified and published.…”

Insect morphometry is reproducible under average investigation standards

“…Understanding of the degree to which measurement errors may affect the transferability of findings is urgently needed. During the last few decades, reproducibility issues have been studied in vertebrate systematics (e.g., Oxnard, 1983; Corrucini, 1988; Yezerinac et al., 1992; Helm & Albrecht, 2000; Takacs et al., 2016; Fox et al., 2020), clinical research (e.g., Bland & Altman, 1986; Ridgway et al., 2008; Phexell et al., 2019), social science (e.g., Salganik et al., 2020), molecular phylogeny and genetic clustering (e.g., Huelsenbeck, 1998; Jones et al., 1998; DeBiasse & Ryan, 2019), and morphometric data generally (Andrew et al., 2015). However, to date, reproducibility assessments of morphometric data in entomology are extremely limited (Johnson et al., 2013; Mutanen & Pretorius, 2007).…”

Linking patterns of intraspecific morphology to changing climates

“…We analysed 101 fossil m1s, 307 modern m1s and 361 modern upper Table S2). Specimens were photographed using a Nikon D70s and AF Micro-NIKKOR 60 mm f/2.8D macro lens ensuring, and best practices for small-specimen photographing were followed (Fox, Veneracion, & Blois, 2020).…”