Research Article |
Corresponding author: Natália Lima Boroni ( natalia_boroni@hotmail.com ) Academic editor: Diego Astúa
© 2017 Natália Lima Boroni, Leonardo Souza Lobo, Pedro Seyferth R. Romano, Gisele Lessa.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Boroni NL, Lobo LS, Romano PSR, Lessa G (2017) Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia). Zoologia 34: 1-11. https://doi.org/10.3897/zoologia.34.e19864
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The taxonomic identification of micromammals might be complicated when the study material is fragmented, as it is the case with pellets and fossil material. On the other hand, tooth morphology generally provides accurate information for species identification. Teeth preserve notably well, retaining their original morphology, unlike skulls and mandibles, which can get crushed or have missing parts. Here, we explored a geometric morphometrics approach (GM) to identify fragmented specimens of two sympatric Calomys Waterhouse, 1837 species – Calomys tener (Winge, 1888) and Calomys expulsus (Lund, 1841) – using the morphology of intact molars as the basis for identification. Furthermore, we included some specimens of uncertain taxonomic identification to test their affinities and the utility of the shape of the molar to identify incomplete specimens. We evaluated the variations in the shape of the first upper molar (M1) among 46 owl pellets specimens of Calomys, including C. expulsus (n = 15), C. tener (n = 15), and unidentified specimens treated as Calomys sp. (n = 16) through GM analysis using 17 landmarks. The data was explored using PCA, PERMANOVA, and Discriminant analyses over the Procrustes residuals matrix were applied to evaluate inter- and intraspecific shape differences. Also, we evaluated whether allometric shape differences could impact the data, but found no evidence of a correlation between size and shape. Our results support that shape differences in the M1 are effective for discriminating between C. tener and C. expulsus. Moreover, the unidentified specimens do not represent a third shape but could be identified with confidence either as C. tener or C. expulsus. Our results show that even with fragmentary materials, GM is a feasible and useful tool for exploring inter-specific shape differences and assisting in taxonomic identification as a complement to traditional qualitative description of diagnostic features in poorly preserved specimens.
Landmarks, morphology, owl pellets, Sigmodontinae , taxonomy
The complex morphology of the molars (with the cones, flexes, and lophs) is a source of information for the study of cricetid rodent taxonomy, as these structures provide diagnostic characteristics for subfamilies (
Among the genera with complicated taxonomy and great morphological similarity between some species is Calomys Waterhouse, 1837 (
In Brazil, C. tener and C. expulsus are both widely distributed (
Although karyotypes and gene sequences may be useful for discriminating among Calomys species (
Calomys and other members of the tribe Phyllotini generally share simplified molars and complete loss of the mesoloph and mesolophid (
The aim of present study is to explore geometric morphometric analysis to identify fragmented materials (modern and fossil) of small vertebrates based on molars; and to assess whether this method allows for accurate identifications. For this we applied this technique in one area: species-level identification of Calomys (C. expulsus and C. tener) based on their upper molars.
The Calomys specimens analyzed were from owl pellets collected in the Natural Monument Peter Lund, Cordisburgo, in the central karst region of Minas Gerais, the Bambuí group, Brazil (Fig.
In the Köppen climate classification system, the regional climate is Aw tropical humid, characterized by hot, rainy summers and dry winters (
For species identification, we analyzed complete and fragmented skulls, maxillae and mandibles, examining the cranial sutures and morphology of the teeth. However, some fragments did not allow a consistent identification to the species level, thus restricting classification to the level of genus. The nomenclature of the species was based on that described by
With the fragmented skull, the best characteristics used to differentiate C. tener from C. expulsus was the presence of alisphenoid strut, which is observed only in C. tener (
A total of 124 skulls were analyzed and separated into classes of dental wear, including 32 of C. tener, 57 of C. expulsus, and 35 of Calomys sp. (Suppl. material
The wear category class 2 showed the most numerically balanced sample between C. tener, C. expulsus, and Calomys sp. (Table
The landmarks were digitalized using TpsDig v.2.17 (
The multivariate analyses were performed using the MorphoJ v. 1.05f (
Specimens examined and the respective sample sizes by dental wear category.
Calomys tener | Calomys expulsus | Calomys sp. | |
---|---|---|---|
Class 1 | 7 | 10 | 8 |
Class 2 | 15 | 15 | 16 |
Class 3 | 9 | 20 | 8 |
Class 4 | – | 11 | 2 |
Total | 32 | 57 | 35 |
For increased reliability of data, an analysis of error in digitization of anatomical landmarks was performed following the protocol of
From this experimental design, a preliminary principal component analysis (PCA) was performed using only species anatomically distinguishable, namely, 15 specimens of C. tener and 15 specimens of C. expulsus. This PCA was conducted to visualize the projection of individuals from the two axes of greatest variation, thereby detecting the distribution pattern in the graph. Then, we included the 16 specimens that could not be definitively identified as C. tener or may be C. expulsus. This addition aimed to increase the sample, totaling to 46 specimens, and explore the projection of Calomys sp. in the two axes of the PCA in the presence of distinguishable specimens. The second goal of adding specimens of Calomys sp. was to classify the unidentified specimens to one or another expected species (C. tener or C. expulsus). The wireframe, which helps in comparing the shapes of the specimens plotted in the PCA, was used whenever necessary to describe and discuss the shape of the specimens.
After each Calomys spp. was assigned to C. tener or C. expulsus through the pattern observed in the PCA, a Discriminant analysis (DA) was performed using MorphoJ v. 1.05f (
Lastly, a pooled regression within each species (multivariate regression) was performed to evaluate whether the differences in the size of the tooth were correlated to the pattern of differentiation of the PCA projection. For this analysis, we used the centroid size of specimens as the independent variable and Procrustes coordinates as the dependent variable. Also, we performed a permutation test with 10,000 rounds to evaluate whether the dependence of shape (Procrustes distances) on the size (centroid size) of the tooth is significant.
The first PCA was performed only with C. expulsus and C. tener together. The PC1 and PC2 totaled 29.5% and 13.8% of the total variance, respectively, explaining 43.3% of the shape variation within the sample. It was possible to visualize either species separated in PC1 vs PC2 individual projections (Suppl. material
The variation expressed by PC1 showed differences in shape of the occlusal between both species. These differences are illustrated based on the wireframe view of mean shape (Fig.
CT 02 (C. tener) can be distinguished from the other individuals by observing the shape differences explained by PC2 and illustrated in Fig.
To evaluate whether tooth size influences the patterns of variation in oclusal surface, we performed a multivariate regression with the Procrustes coordinates residual (shape) on the centroid size (size measurement). This regression showed a weak relationship that accounted for just 5.3% of the shape variation predicted by the size (Fig.
Discriminant analysis results (classification/misclassification table) for Calomys expulsus and Calomys tener.
Discriminant function – Allocated to | Total | Percentage | ||
Calomys expulsus | Calomys tener | |||
Calomys expulsus | 22 | 0 | 22 | 100 |
Calomys tener | 0 | 24 | 24 | 100 |
Cross-validation – Allocated to | ||||
Calomys expulsus | Calomys tener | |||
Calomys expulsus | 19 | 3 | 22 | 86.4 |
Calomys tener | 5 | 19 | 24 | 79.2 |
PCA showing the individual projections of Calomys sp., C. expulsus and C. tener in the two major axis (PC1 28.7%, PC2 12.3% of the variance). The wireframes illustrate shape differences between most different specimens: CE 09, CT 05, CT 02, and SP 11. Black circles: C. expulsus; Gray triangle: C. tener; Black square: Calomys sp. identified as C. expulsus; Gray square: Calomys sp. identified as C. tener; Gray triangle with black edge: specimen CT 02; Stars: mean shape for each species.
Shape differences wireframes in PC1. Gray solid lines indicate C. tener (positive PC1 values) and black dotted lines indicate C. expulsus (negative PC1 values), see Fig.
Calomys tener and C. expulsus are grouped into different clades (
The overlap areas in morphometric cranial analyses using orthogonal matrix transformation techniques as PCA, irrespective of whether traditional or geometric, have also been identified in other species of other genera and in Calomys (
The main criterion for distinguishing C. tener from C. expulsus by traditional morphometrics is the size of the body (
As mentioned earlier, C. expulsus and C. tener occur in sympatry, and were differentiated in the present study through the presence of alisphenoid strut and length of maxillary molars. We observed a high similarity between our analysis and previous identification based on both characteristics, with more than 80% accuracy in DA. However, our results indicate that tooth size characters are not useful to diagnose either species. Thus, we suggest that the use of size characters (e.g.,
In our results, CT02 deserves mention. This specimen was identified as C. tener because it had alisphenoid strut and a 3.7 mm long molar. However, the shape of this specimen, at least observing the differences explained by PC1, reveals more similarity with C. expulsus. Since CT 02 is a fragmentary specimen, our conclusion regarding its identification is limited. This specimen could be C. tener with larger molars or perhaps C. expulsus with alisphenoid strut and small molars. On the other hand, another possibility is that CT02 is a C. cerqueirai, a species described from near the investigation area of the present study (see
We observed a pattern of differentiation in the oclusal shape of class 2, among sympatric specimens of C. expulsus and C. tener. In this class, the cusps of C. tener (as protocone and hipocone) were more retracted, whereas the cusps of C. expulsus are expanded in the lingual-labial axis (when compared with C. tener); the flexus (as paraflexus and protoflexus) are expanded and the aperture angles are larger in C. tener than in C. expulsus. Different molar morphologies in rodents can represent adaptations to different diets and can be relevant to avoid intraspecific competition (
The possibility to perform taxonomic identifications based on molar shape, principally in rodents, is a very useful, especially when working with fossil materials (
Many studies using small mammal fossils or owl pellets for taxonomic identification are restricted to the level of genus (e.g.
This is the first study using molars found in owl pellets for taxonomic identification through geometric morphometrics in South America. Our results were effective for the identification of dubious Calomys sp. specimens. All of them were identified either as C. tener or C. expulsus based on the individual projections of the PC1. The use of size as a diagnostic character is not effective for molar differentiation of C. tener and C. expulsus, as the regression test showed no evidence of correlation between size and shape. These results demonstrated the huge potential of geometric morphometric analysis as a tool in the rodent taxonomic identification using molars, especially in works with fragmented material (modern or fossil). This technique can be extensively useful principally by paleontologists, who have to identify isolated morphological elements, as molars of small vertebrates. This method can be also applied to other genera (e.g. Oligoryzomys Bangs, 1900 and Akodon Meyen, 1833) and to other groups such as bats and marsupials, wherever accurate taxonomic identifications of morphologically similarity and sympatric species are needed.
We are grateful to Ulyses Pardiñas for the initial support in the identification of the owl pellets. Rodolfo Stumpp and the reviewers for all relevant comments. We thank the staff of Peter Lund National Monument for allowing us to use their facilities for the collection of samples. We are also grateful to Prof. Weyder Santana for permitting us to use the stereoscopic microscope and camera. The Federal Forest Institute (IEF) granted permits for the collection of specimens. We also thank Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for the student scholarship. This study was supported by Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG APQ-02262-12), grants to Gisele Lessa and was developed during 2013 at the Graduation Program in Animal Biology of the Federal University of Viçosa.
Alisphenoid strut
Data type: multimedia
Wear categories
Data type: measurement
Specimens of the wear category class 2
Data type: species data
Protocol for testing error in the digitalization
Data type: statistical data
Tests for normality, hornoscedasticity and homogeneity
Data type: statistical data
PCA with Calomys terrer and C. expulsus
Data type: statistical data