DOI: 10.5061/dryad.g1jwstqv9
title: Data from: Potentials of closed contour analysis in species differentiation and holotype designation: a case study on lower Norian (Upper Triassic) conodonts

description: Geometric morphometric approaches become increasingly applied in the
 fields of biology and paleontology. Taxonomy is a good example, where a
 long-standing intention of scientists is to eliminate subjectivity as much
 as possible. In the case of biostratigraphically important conodont
 elements, the application of such methods is not widespread. Indeed, only
 a handful of studies attempted to deal with the morphological variance of
 conodont elements from this aspect. The detailed description of five lower
 Norian (Upper Triassic) taxa (Ancyrogondolella quadrata, A. rigoi, A.
 triangularis, A. uniformis and Metapolygnathus mazzai) is presented here
 based on landmarks and Fourier analysis of the P1 element and keel
 outlines. Both methods led to similar outcomes regarding taxonomic
 differentiation and exposing shape variability. Consensus shapes were
 generated to objectively reveal the typical contour shape of each taxon,
 which allowed their comparison with each other, and with the members of
 their respective sample population including the holotypes. The results
 pointed out that the holotype of a taxon is generally not an average
 representative, but rather a peripheral form with well-separable
 morphological characteristics. Ancyrogondolella quadrata and A. rigoi
 turned out to represent a morphological continuum with ample transitional
 forms between these two end-members that may cause bias in their
 biostratigraphic applicability; however, their combined shape variance
 seems to be too large for uniting them into a single species. Given the
 results that may be too subtle to realize based solely on qualitative
 observations, future taxonomic studies and type material designation could
 greatly benefit from the application of similar methodologies.
description: Material The
 analysis involved a total of 136 lower Norian conodont P1 elements. The
 material originates from various localities of the western Tethys and
 western North America. Eighty percent of the specimens were unambiguously
 assigned to the taxa <em>Ancyrogondolella quadrata, A. rigoi, A.
 triangularis, A. uniformis</em> and <em>Metapolygnathus
 mazzai</em>. For specimens bearing morphological characters not
 fully fitting in the original diagnoses of these species, the open
 nomenclatural term “ex gr.” (of the group) was used. Holotypes of the
 listed species were also included in the study based on the best
 illustrations from the literature. Only non-deformed, complete, adult
 (GS4-GS6; based on the ontogenetic series defined in Mazza &
 Martínez-Pérez 2015) specimens were involved in the present
 study. Shape descriptors For the
 shape description, we chose to analyse the element and the keel outlines.
 To avoid bias induced by bilaterality, all dextral elements were mirrored
 into their sinistral counterpart. Outline digitization was carried out
 manually (as in Sinitsa et al. 2019) using the multi-point tool of the
 open-access ImageJ software (v1.53; Abramoff et al. 2004; Schneider et al.
 2012). Uniform point allocation was achieved by the equidistantCurve
 function of the <em>Morpho</em> package within the R
 programming environment (v4.1.2; R Core Team 2013; Schlager 2017). In
 total, the coordinates of 100 shape descriptors were recorded to describe
 the element and the keel outlines, separately. In addition, the position
 of the pit was marked in aboral view. To be able to record the position of
 the tip of the cusp, which is not visible in this view, images made in
 oral view were mirrored and projected on the corresponding aboral views.
 The more posteriorly inclined the cusp is, the further behind the pit its
 projection falls.  Landmark analysis
 The points related to the location of the cusp and the pit were
 recognized as type I landmarks (i.e. homologous anatomical points). Type
 II or geometrical landmarks (sensu Bookstein 1992) were selected on the
 outlines using automated algorithms that searched for the sharpest inward
 facing angle between neighbouring equidistant shape descriptors of a
 specific region. On the element outline the anterior end and the
 posterolateral corners were marked. On the keel outline the anterior end
 and the two posterior tips if the keel was bifid or the posterolateral
 corners if the keel was non-bifid were selected. The sections between the
 type II landmarks were resampled by a pre-defined number of equidistantly
 placed non-sliding semilandmarks (6 on the posterior margin and 12 on each
 lateral margin) to retain finer details of the shape (see Gunz and
 Mitteroecker 2013). To eliminate variability induced by size and
 orientational differences a generalized Procrustes superimposition was
 used: the landmark (LM) configurations were centred, scaled to the same
 centroid size, and rotated until the minimum sum of squared distances
 between the LMs and their corresponding average position was reached
 (Gower 1975). To extract the primary patterns of variation, a principal
 component analysis (PCA) was performed on the resulting aligned
 coordinates with the prcomp function of the built-in
 <em>stats</em> package of R. Fourier
 analysis Fourier descriptors (FDs) were calculated
 using equation 31.6 of Smith (2002) by a provided custom function (dft)
 written in the R programming language (v4.1.2; R Core Team 2013). The
 previously produced coordinate sets containing 100 equidistant shape
 descriptors were used as the basis of these calculations. Contrary to the
 LM-based approach, the positions of the pit and the cusp were ignored, and
 all contour points (including the ones selected before as type II LMs)
 were treated equally during the Fourier analysis. Following the steps
 described by Kuhl & Giardina (1981) and Godefroy et al. (2012),
 the FDs were rescaled so that the major axis of the first ellipse (i.e.
 the sum of the amplitudes of the first two epicycles) became equal to 1.
 The centred outlines were rotated until the minor and major axes coincided
 with the horizontal and vertical axes of the underlying Cartesian
 coordinate system. The FDs were also corrected so that the starting phase
 angle of the first two epicycles became 0. These steps were achieved by
 another provided custom R function (normDft). Similar to the LM
 configurations, the resulting Fourier coefficients were used as variables
 in a PCA implemented by the prcomp function of the built-in
 <em>stats</em> package of R. Only the first 20 pairs of FDs
 were considered for this analysis to provide a good balance between a
 satisfying description of the element shape, and an efficient filtering of
 measurement noise without using excessive epicycles.
description: To run the provided scripts, the open-access R programming
 environment (v4.1.2) and the RStudio desktop application (build 353) is
 recommended. To begin, "Virag_Karadi_2023_CONODONTS_script.R"
 should be opened with RStudio, and if run step by step, it will load the
 necessary packages (<em>Morpho</em>), custom functions
 ("Virag_Karadi_2023_CONODONTS_functions.R") and data files (all
 provided .csv files), automatically during the session.