Averaging v. outlier removal. Decrypting variance among cryptic Lejeunea species (Lejeuneaceae: Jungermanniopsida) using geometric morphometrics

2013 ◽  
Vol 26 (1) ◽  
pp. 13 ◽  
Author(s):  
Matt A. M. Renner ◽  
Elizabeth A. Brown ◽  
Glenda M. Wardle
Keyword(s):  
Cryptic Species ◽  
Individual Variation ◽  
Species Difference ◽  
Molecular Data ◽  
Species Variation ◽  
Shape Variation ◽  
Outlier Removal ◽  
Geometric Morphometric ◽  
Size And Shape ◽  
Developmental Capacity

Molecular data have revealed many morphologically cryptic species. More surprising than lack of difference, however, is that morphological variation and complex patterns of overlapping features can mask cryptic species. We employ geometric morphometric methods (GMM) to explore patterns of variation within four liverwort species, three of which were previously attributed to Lejeunea tumida Mitt. Each species exhibited considerable variation within, and overlap among, species in size and shape, independent of degree of relatedness. Most variation was expressed within individuals, suggesting that the observed breadth of variation was within the developmental capacity of single genotypes. Size and shape variation within, and consequently overlap among, individuals resulted primarily from variance in growth of shoots. Inter-specific differences were swamped by intra- and inter-individual variation. We coupled GMM with multivariate methods for outlier removal, and simple averaging of individuals to explore whether intra-individual variation could be reconciled to maximise the inter-species difference, facilitating resolution of cryptic species despite extensive morphological continuity and overlap. Unfortunately, outlier removal did not achieve separation among species, because removing extremes failed to eliminate overlap resulting from within-species variation. Individual averaging was partially successful in extracting L. tumida as a discrete entity but did not segregate the remaining three species. Although the challenges for morphology-based identification of cryptic species are significant, GMM provide one of the best sets of methods for identifying and communicating any subtle morphological differences that may exist.

scholarly journals Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats

2019 ◽  
Author(s):  
Vera Weisbecker ◽  
Thomas Guillerme ◽  
Cruise Speck ◽  
Emma Sherratt ◽  
Hyab Mehari Abraha ◽  
...  
Keyword(s):  
Individual Variation ◽  
Principal Component ◽  
Individual Variability ◽  
Shape Variation ◽  
Mandibular Ramus ◽  
Geometric Morphometric ◽  
Skull Shape ◽  
Marsupial Species ◽  
Masticatory System ◽  
The Individual

AbstractBackgroundWithin-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, shape variation should not be dominated by allometry; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues.ResultsWe assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of thre species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus.DiscussionOur results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraint act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.

The Cheilosia canicularis group (Diptera: Syrphidae): species delimitation and evolutionary relationships based on wing geometric morphometrics

Zootaxa ◽  
2008 ◽  
Vol 1825 (1) ◽  
pp. 40 ◽  
Author(s):  
JASMINA LUDOŠKI ◽  
LJUBINKA FRANCUSKI ◽  
ANTE VUJIĆ ◽  
VESNA MILANKOV
Keyword(s):  
Sequence Data ◽  
Balkan Peninsula ◽  
Wing Shape ◽  
Canonical Variate ◽  
Wing Size ◽  
Shape Variation ◽  
Geometric Morphometric ◽  
Mahalanobis Distances ◽  
Size And Shape ◽  
Upgma Cluster Analysis

A landmark-based geometric morphometric approach was used to assess differences in the size and shape of wing among/within three species of the Cheilosia canicularis group (Diptera: Syrphidae): C. canicularis, C. himantopus and C. orthotricha. Wing size and shape variation was observed from 25, 176 and 41 specimens of C. canicularis, C. himantopus and C. orthotricha, respectively, collected from six localities on the Balkan Peninsula. Significant differences in wing size were obtained among the analysed species and canonical variate analysis showed that wing shape was sufficiently different to allow the correct classification of 73% individuals of C. canicularis, 80% of C. orthotricha and 94% of C. himantopus, and clear delimitation of the species pairs C. canicularis/C. orthotricha and C. himantopus/C. orthotricha. In all analysed species, the consistent sex dimorphism in wing shape was observed indicating that female specimens had shorter and broader wings than males. The UPGMA cluster analysis based on squared Mahalanobis distances revealed close accordance with previously published phylogenetic relationships of these species indicated by allozyme and DNA sequence data analysis. Our results suggested that wing parameters contain useful information in quantification phenotypic variation and identification of species in this challenging group for taxonomy and systematics.

scholarly journals Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)

2017 ◽  
Author(s):  
Lionel Hautier ◽  
Guillaume Billet ◽  
Benoit De Thoisy ◽  
Frédéric Delsuc
Keyword(s):  
Morphological Variation ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Guiana Shield ◽  
Shape Variation ◽  
Skull Morphology ◽  
Geometric Morphometric ◽  
Skull Shape ◽  
Shape And Size

Background. The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (D. novemcinctus). Methods. We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on µCT-scans. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results. We show that the shape and size of the skull vary greatly between Dasypus species, with D. pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in D. novemcinctus evidences clear links to the geographic distribution and argue in favour of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillo, especially a very distinctive unit circumscribed to the Guiana Shield. Discussion. As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that D. novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.

scholarly journals Size and shape variation in the calcareous nannoplankton genus Braarudosphaera following the Cretaceous/Paleogene (K/Pg) mass extinction: clues as to its evolutionary success

Paleobiology ◽  
2021 ◽  
pp. 1-24
Author(s):  
Heather L. Jones ◽  
Zachary Scrobola ◽  
Timothy J. Bralower
Keyword(s):  
Cryptic Species ◽  
Mass Extinction ◽  
Evolutionary History ◽  
Late Triassic ◽  
Shape Variation ◽  
Calcareous Nannoplankton ◽  
Size And Shape ◽  
Water Column Stratification ◽  
Early Paleocene ◽  
Tethys Ocean

Abstract Calcareous nannoplankton have been one of the dominant primary producers in the surface oceans since the late Triassic. The bolide impact at the Cretaceous/Paleogene (K/Pg) boundary ~66.0 Ma, led to the elimination of >90% of nannoplankton species: the largest extinction event in their evolutionary history. One of the few nannoplankton genera to survive the K/Pg mass extinction and even thrive in its aftermath was Braarudosphaera, which precipitates pentagonal calcite plates (pentaliths). The only Braarudosphaera species to span the K/Pg boundary (B. bigelowii) is extant and has formed geographically and temporally restricted “blooms” throughout geologic time. Four morphologically and genetically distinct cryptic species of B. bigelowii have been identified in the modern ocean. However, it is uncertain whether these cryptic species have disparate ecophysiological tolerances that have allowed them to adapt to varying environmental conditions. For the first time, we assess changes in the size and shape of Braarudosphaera pentaliths following the K/Pg mass extinction at three geographically and environmentally disparate sites that have early Paleocene Braarudosphaera blooms. Our results show that different Braarudosphaera morphotypes were dominant in the Gulf of Mexico compared with the Tethys Ocean, likely due to regional environmental differences. In addition, we provide evidence that the dominant Braarudosphaera morphotypes shifted in response to changes in upper water column stratification. This ability to rapidly adapt to unstable environments likely helped Braarudosphaera thrive in the aftermath of the K/Pg extinction and explains why this lineage has enjoyed such a long evolutionary history.

scholarly journals The First Insight into the Patterns of Size and Shape Variation of a Microcerberid Isopod

Water ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 515
Author(s):  
Jeongho Kim ◽  
Jaehyun Kim ◽  
Wonchoel Lee ◽  
Ivana Karanovic
Keyword(s):  
Cryptic Species ◽  
Size Variation ◽  
Shape Variation ◽  
Morphological Pattern ◽  
Size And Shape ◽  
Taxonomic Methods ◽  
Morphological Differences ◽  
High Degree ◽  
Insight Into ◽  
Genetic Species

Cryptic species are a biological phenomenon only recently recognized due to progress in molecular studies. They pose a significant challenge to conventional taxonomic work since these species manifest low morphological differences, but considerable genetic disparity. New taxonomic methods are in development but have yet to be tested for many animal groups. Isopods belonging to the suborder Microcerberidea are one such group. The Asian microcerberid isopod, Coxicerberus fukudai (Ito, 1974), is a major component of marine interstitial fauna with suspected cryptic species inhabiting Japan and Korea. We chose six Korean populations with high molecular interpopulations divergence and applied 2D landmark-based geometric morphometrics to cephalic sensilla, pleonal points, and male pleopod II. This quantitative approach allowed us to study interpopulation size and shape variations, morphospace structure, and whether the morphological pattern mirrored the genetic species. We determined that a high degree of interpopulation size variation significantly influences shape changes. Once we removed the allometric effect, the size-corrected male pleopod II shape variations yielded a new species, C. jangsaensis sp. nov. At the same time, we were able to resolve the C. fukadai species complex.

scholarly journals Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Vera Weisbecker ◽  
Thomas Guillerme ◽  
Cruise Speck ◽  
Emma Sherratt ◽  
Hyab Mehari Abraha ◽  
...  
Keyword(s):  
Individual Variation ◽  
Principal Component ◽  
Individual Variability ◽  
Shape Variation ◽  
Mandibular Ramus ◽  
Geometric Morphometric ◽  
Skull Shape ◽  
Marsupial Species ◽  
Masticatory System ◽  
The Individual

Abstract Background Within-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, allometry may not dominate within-species shape variation, even if it is a driver of evolutionary shape divergence; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues. Results We assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of three species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus. Discussion Our results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraints act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.

A three-dimensional geometric morphometric analysis of variation in cranial size and shape in tammar wallaby (Macropus eugenii) populations

2009 ◽  
Vol 57 (5) ◽  
pp. 337 ◽  
Author(s):  
Claire Hadley ◽  
Nick Milne ◽  
Lincoln H. Schmitt
Keyword(s):  
Three Dimensional ◽  
Tammar Wallaby ◽  
Shape Variation ◽  
Isolated Populations ◽  
Geometric Morphometric ◽  
Island Populations ◽  
Macropus Eugenii ◽  
Size And Shape ◽  
Geographic Separation ◽  
Analysis Of Variation

This study uses geometric morphometric techniques to examine cranial size and shape variation in nine isolated populations of the tammar wallaby (Macropus eugenii). A set of 36 three-dimensional landmarks were digitised on 143 tammar crania from two mainland and seven island populations. While there was no evidence of island dwarfism or gigantism, cranial size increased with both increasing island size and increasing latitude. As latitude increased, the palate narrowed relative to the nasal bones, cranial flexion and nasal height increased, and the zygomatic arches spread out laterally from the cranium. Overall, the anterior nasal aperture (nares) narrowed with increasing latitude. Mean shapes were calculated for each population, and pair-wise comparisons were made; most of these were significantly different. There was a clear tendency for island populations and those with greater geographic separation to show greater shape differentiation. Thus, regional and population differences in the cranial size and shape of tammar wallabies provide examples of selection, founder effect and random genetic drift.

scholarly journals Sexual Dimorphism and Morphological Modularity in Acanthoscelides obtectus (Say, 1831) (Coleoptera: Chrysomelidae): A Geometric Morphometric Approach

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 350
Author(s):  
Sanja Budečević ◽  
Uroš Savković ◽  
Mirko Đorđević ◽  
Lea Vlajnić ◽  
Biljana Stojković
Keyword(s):  
Sexual Dimorphism ◽  
Reproductive Function ◽  
Morphological Integration ◽  
Stabilizing Selection ◽  
Shape Variation ◽  
Acanthoscelides Obtectus ◽  
Geometric Morphometric ◽  
Size And Shape ◽  
Acanthoscelides Obtectus Say ◽  
Functional Hypothesis

Sexual dimorphism and specific patterns of development contribute in a great manner to the direction and degree of the sexual differences in body size and shape in many insects. Using a landmark-based geometric morpohometrics approach, we investigated sex-specific morphological size and shape variation in the seed beetle, Acanthoscelides obtectus. We also tested the functional hypothesis of the two morphological modules—thorax and abdomen in both sexes. Female-biased sexual dimorphism in size was shown, while differences in shape were reflected in the wider thorax and abdomen and shorter abdomen in females in comparison to males. The functional hypothesis of a two-module body was confirmed only in females before correction for size, and in both sexes after the allometry correction. Our results indicate that reproductive function has the central role in forming the patterns of modularity. We hypothesize that high morphological integration of the abdomen in females results from intense stabilizing selection, while the more relaxed integration in males is driven by the higher intensity of sexual selection.

Body shape evolution of Chromis and Azurina species (Percifomes, Pomacentridae) of the eastern Pacific

2013 ◽  
Vol 63 (2) ◽  
pp. 217-232 ◽  
Author(s):  
Rosalía Aguilar-Medrano
Keyword(s):  
Body Shape ◽  
Phylogenetic Signal ◽  
Molecular Data ◽  
The Body ◽  
Eastern Pacific ◽  
Morphological Pattern ◽  
Geometric Morphometric ◽  
Morphometric Variation ◽  
Size And Shape ◽  
Morphometric Analyses

Chromis is a circumglobal tropical and temperate genus with over 84 species of damselfishes. Studies based in osteological and molecular data have cited the relationship between Azurina and Chromis in the eastern Pacific. The main objectives of the study are: (1) to characterize size and shape in all Chromis and Azurina species of the eastern Pacific, (2) explore the phylogenetic signal of external morphology, and (3) present a hypothesis of the diversification process of this group. According to the results, there is no significant relationship between size and shape. The variation in body shape among all species is related to the height of the trunk, position of the snout and eye, and length of the caudal peduncle. The main morphologic variation between Azurina and Chromis is the degree of elongation of the body. Both Azurina species are closely related to C. punctipinnis and C. atrilobata. The morphological pattern of Azurina integrated it into Chromis. The phylogenetic pattern found by geometric morphometric analyses presented a high similarity with previous results based on molecular data. Phylogeny recovered two main clades, slender-bodied and deep-bodied species. This pattern of morphometric variation is closely related to exploitation of two different reef environments.

scholarly journals Beyond the carapace: skull shape variation and morphological systematics of long-nosed armadillos (genus Dasypus)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3650 ◽  
Author(s):  
Lionel Hautier ◽  
Guillaume Billet ◽  
Benoit de Thoisy ◽  
Frédéric Delsuc
Keyword(s):  
Morphological Variation ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Shape Variation ◽  
Micro Computed Tomography ◽  
Dasypus Novemcinctus ◽  
Skull Morphology ◽  
Geometric Morphometric ◽  
Skull Shape

Background The systematics of long-nosed armadillos (genus Dasypus) has been mainly based on a handful of external morphological characters and classical measurements. Here, we studied the pattern of morphological variation in the skull of long-nosed armadillos species, with a focus on the systematics of the widely distributed nine-banded armadillo (Dasypus novemcinctus). Methods We present the first exhaustive 3D comparison of the skull morphology within the genus Dasypus, based on micro-computed tomography. We used geometric morphometric approaches to explore the patterns of the intra- and interspecific morphological variation of the skull with regard to several factors such as taxonomy, geography, allometry, and sexual dimorphism. Results We show that the shape and size of the skull vary greatly among Dasypus species, with Dasypus pilosus representing a clear outlier compared to other long-nosed armadillos. The study of the cranial intraspecific variation in Dasypus novemcinctus evidences clear links to the geographic distribution and argues in favor of a revision of past taxonomic delimitations. Our detailed morphometric comparisons detected previously overlooked morphotypes of nine-banded armadillos, especially a very distinctive unit restricted to the Guiana Shield. Discussion As our results are congruent with recent molecular data and analyses of the structure of paranasal sinuses, we propose that Dasypus novemcinctus should be regarded either as a polytypic species (with three to four subspecies) or as a complex of several distinct species.

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