Elliptic Fourier Coefficients Research Articles

Türkiye’den Salmo cinsine ait iki türün karşılaştırmalı otolit morfolojisi

In this study, the morphology of the sagittal otolith of Salmo coruhensis Turan, Kottelat & Engin, 2010 and Salmo fahrettini Turan, Kalayci, Bektaş, Kaya & Bayçelebi, 2020 from Çam Stream (Artvin) and Terme Stream (Samsun) was described by images of scanning electron microscopy. Its shape and contour were also analyzed with shape indices, elliptic Fourier coefficients and wavelet transforms. As the study material, a total of 30 S. coruhensis sample and 20 S. fahrettini sample were obtained. Interspecies differences in otolith shape and morphometry were evaluated by principal components analysis, canonical discrimination analysis, and permutational multivariate analysis of variance. The two salmonid species studied were distinguished by both morphometric and shape analysis methods. However, wavelet transform was found to be more effective than shape indices and elliptic Fourier coefficients in species discrimination, with an overall classification success rate of 80%. Our results showed that saccular otolith morphology could be an additional diagnostic character for trout species differentiation.

Classification of fragmented pottery with the use of Kohonen self‐organising maps (case study from the Hlyboke Ozero‐2 settlement in Eastern Ukraine)

AbstractThe paper is devoted to testing Kohonen self‐organising maps, with elliptic Fourier coefficients as quantitative variables, for the task of morphological classification of fragmented and non‐standardised ceramics. The advantage of the methodology used is its ability to account for the systematic statistical relationships inherent in the dataset, build models of varying degrees of generalisation and visualise multivariate data. The approbation of the method was carried out on materials from the Hlyboke Ozero‐2 settlement in Eastern Ukraine. The results are compared with the results obtained using principal component analysis + k‐means clustering.

Human identification: an investigation of 3D models of paranasal sinuses to establish a biological profile on a modern UK population.

Medical imaging is a valuable source for facilitating empirical research and provides an accessible gateway for developing novel forensic anthropological methods for analysis including 3D modelling. This is especially critical for the United Kingdom (UK), where methods developed from modern UK populations do not currently exist. This study introduces a new approach to assist in human identification using 3D models of the paranasal sinuses. The models were produced from a database of 500 modern CT scans provided by University College London Hospital. Linear measurements and elliptic Fourier coefficients taken from 1500 three-dimensional models across six ethnic groups assessed by one-way ANOVA and discriminant function analysis showed a range of classification rates with certain rates reaching 75-85.7% (p < 0.05) in correctly classifying age and sex according to size and shape. The findings offer insights into the potential for employing paranasal sinuses as an attribute for establishing the identification of unknown human remains in future crime reconstructions.

Effect of temperature and CO2 concentration on the morphogenesis of sagittal otoliths in Atlantic herring (Clupea harengus) larvae

Otoliths are very useful biomarkers especially for fish growth. Climate change with the associated global changes in warming and acidification could affect the calcification and the shape of otoliths during the crucial larval period in teleost fish. To evaluate this predicted combined effect of temperature and CO2, Atlantic herring (Clupea harengus) embryos and larvae were reared from hatching to respectively 47 and 60 days post-hatching (dph), under present day conditions and a scenario predicted for the year 2100 (IPCC RCP8.5). Otolith morphogenesis was tracked by analyzing area and normalized Elliptical Fourier coefficients. We found that otolith area for fish of similar size increased under the predicted 2100 climate change scenario compared to the present day. Climate change does not, however, seem to directly affect the otolith shape. Finally, the onset of otolith morphogenesis is hardwired, but the relationship between otolith and fish size is environment-dependent.

Sex-linked variations in the sagittal otolith biometry of Nemipterus randalli (Russell, 1986) from the eastern Mediterranean Sea.

Few studies have been conducted on the sagittal otolith shape and morphometry of Nemipterus randalli, and none of these studies has examined the effect of sexual dimorphism on the otolith morphology of this species, therefore this study aimed to contribute to knowledge about the otolith morphology of N. randalli, an invasive fish species for the Mediterranean Sea. For this purpose, a total of 132 samples (51 female and 81 male) were obtained from İskenderun Bay with the help of commercial fishermen in November 2018. Relationships between otolith measurements and fish size were determined. Shape indices and elliptic Fourier coefficients were calculated. Significant differences were detected between males and females in all analysis. The sexes were separated from each other using both shape indices and elliptic Fourier coefficients. However, shape analysis was more effective in distinguishing sexes than traditional morphometric analysis. Asymmetry in the otolith morphology of sexes has been attributed to differences in the growth and sexual maturity of male and female fish. The results of this study indicated that sexual dimorphism in Nemipterus randalli was also reflected in the otolith morphology.

DNA Barcoding versus Morphological Variability of Pterostichus brevicornis brevicornis (Kirby, 1837) (Coleoptera, Carabidae) in the Arctic and Subarctic.

Simple SummaryTaxonomic studies on a polymorphic species inhabiting a region with relatively uniform environmental conditions (e.g., the Arctic) should involve an integrative approach. Ground beetles such as the subgenus Cryobius of the genus Pterostichus are a successful group in expansion in the tundra biome. The current taxonomy of Cryobius species is unclear and could be considered an obstacle to ecological studies; knowledge of their distribution patterns in the Arctic is rather limited. In this study, the first report on the phylogeography and phylogeny of the most abundant tundra subspecies, P. (Cryobius) brevicornis brevicornis (Kirby, 1837), within its continuous range throughout northern Eurasia and North America is presented. The results indicated that the male genitalia morphology of P. b. brevicornis from Eurasian populations shared a higher geographic variability compared with the pronotum shape and the mitochondrial DNA sequences.The geographic patterns of genetic and morphological variability in ground beetles were examined throughout Northern Eurasia and North America using the most abundant circumpolar tundra subspecies, Pterostichus (Cryobius) brevicornis brevicornis (Kirby, 1837), as a model. Phylogenetic structure was assessed on the basis of a Bayesian approach using two DNA markers (partial sequences of the COI and 28S rRNA genes), while phylogeographic patterns and population genetic diversity were estimated using the COI gene only. Morphological patterns were analysed using elliptical Fourier coefficients that were calculated based on the pronotum and male genitalia shape outlines. The subspecies shares 23 COI haplotypes throughout its entire circumpolar range, while eight haplotypes of 28S rRNA were detected in Northern Eurasia. Phylogenetic analysis did not reveal subdivided species lineages with strict geographical imprint. The network, FST and uncorrected pairwise divergence analyses showed that the genetic distances between populations increase by longitude from Northeastern Asia to Europe. The genetic variability among the five studied geographical population groups of P. b. brevicornis was relatively high. The MANOVA showed significant regional divergence between local populations in Northern Eurasia based on both morphological markers, but only male genitalia variability was geographically structured. Neither the pronotum shape nor the male genitalia shape aligned with the phylogeographic patterns discovered on the basis of COI sequences. The genetic (COI) marker had more variation within, rather than among, population groups in addition to morphology of pronotum but not male genitalia.

The effect of ontogenetic diet shifts on sagittal otolith shape of European perch, Perca fluviatilis (Actinopterygii: Percidae) from Lake Ladik, Turkey

European perch undergoes several ontogenetic dietary shifts during its lifetime. The present study focused on the variability in otolith shape caused by ontogenetic dietary changes in this species. A total of 172 specimens (7.5 to 27.5 cm TL) were caught by local fishermen in Lake Ladik from April to November 2019. Shape indices (SIs) and elliptic Fourier coefficients (EFCs) were calculated for each otolith. To detect ontogenetic changes in otolith shape, SIs and EFCs were compared among the three defined size classes (I, II, and III). Size-related groups were distinguished by both SIs and EFCs. Otolith shape analysis was more effective than morphometric analysis in distinguishing ontogenetic groups. Simultaneous use of both methods improved the classification success of each method alone. This study demonstrated that otolith shape of European perch is influenced by ontogenetic changes in diet. However, sexual maturity of the fish is also responsible for these variations in otolith shape.

Discrimination of red porgy Pagrus pagrus (Sparidae) potential stocks in the south-western Atlantic by otolith shape analysis.

Otolith shape analysis is a powerful method for fish stock identification. We compared the otolith shape of Pagrus pagrus (Linnaeus 1758) along with its distribution in four south-western Atlantic regions where it is commercially fished: Rio de Janeiro, Rio Grande do Sul in southern Brazil, the Argentine-Uruguayan Common Fishing Zone (UA) and the Argentinian Exclusive Fishing Zone (AR). Otolith shapes were compared by Elliptical Fourier and Wavelet coefficients among specimens in a size range with similar otoliths, morphometric parameters and ages. Four potential stocks were identified: one in the AR, a second along the UA which included specimens from southern Brazil with well-marked opaque bands in its otoliths (MRS), the third in southern Brazil with faint or absent opaque bands in its otoliths (FRS) and the fourth along Rio de Janeiro. The difference in the otolith shape among regions followed differences reported using other stock identification techniques. The similarity between otoliths from UA and MRS (ANOVA-like, P > 0.01) can be explained by seasonal short-range migrations. Otoliths shape differences between MRS and FRS (ANOVA-like, P < 0.01) suggest that P. pagrus does not form a homogeneous group in southern Brazil.

Do environmental conditions (temperature and food composition) affect otolith shape during fish early-juvenile phase? An experimental approach applied to European Seabass (Dicentrarchus labrax)

Otolith shape is an efficient tool for fish stock discrimination. Therefore, it is crucial to identify the environmental parameters that could influence otolith morphogenesis and growth. Current global ocean warming negatively affects the production of polyunsaturated fatty acids (EPA and DHA) by phytoplankton and thus their availability in marine food webs. As EPA and DHA are essential nutrients for most fish species, their deficiency could affect many aspects of fish physiology, notably otolith morphogenesis. The goal of this study was to assess experimentally the combined influences of temperature (T) and dietary polyunsaturated fatty acid (PUFA) content on European seabass (Dicentrarchus labrax) otolith morphogenesis during early life stages. 300 individuals were reared from 94 to 200 days post hatch (dph) at 15 or 20 °C and fed a high (1.65% PUFA) or low (0.73% PUFA) nutrient diet. To analyze the temperature effect, Growing Degree Days (GDD) were used. Otolith morphometric measurements, shape factors and normalized Elliptical Fourier coefficients describing outline shape were extracted using image analysis. The directional asymmetry (DA) between left and right otolith shapes was not significantly correlated to the GDD or food nutrient level. The effects of T and PUFA on otolith shape were estimated using four linear mixed effects models and, for all descriptors of otolith outline, the best model included GDD, PUFA and T and their interaction as predictors. This temperature effect was described by GDD value and the interaction between GDD and T. Consequently, temperature has an effect on the speed but also on the morphogenesis trajectory of the otolith. Conversely, the concentration of PUFA in the diet had no significant effect on otolith shape. The otolith shape was first modified by a decrease in the width/length ratio during the first period of experiment and by the distance between rostrum and antirostrum during the second period of experiment. Our results indicate that otolith shape is very sensitive to environmental temperature and, as such, can be an effective tool for identifying fish stocks that have experienced different temperature regimes.

An objective method of shape descriptor state establishment using elliptic Fourier analysis (EFA)

AbstractThis research attempts to systematically establish shape descriptor states through elliptic Fourier analysis (EFA) using pili (Canarium ovatum Engl.) kernel as a model. Kernel images of 53 pili accessions from the National Plant Genetic Resources Laboratory (NPGRL), University of the Philippines Los Baños were acquired using VideometerLab 3. Shape features, such as roundness, compactness and elongation, were extracted from the images. Shapes outlines were characterized using elliptic Fourier coefficients calculated from SHAPE version 1.3 software. Principal component analysis and cluster analysis were used to elucidate clusters representing the shape descriptor states. The first principal component accounts for the variation in length to width ratio; whereas, the second and third principal components explain the variation in the location of the widest portion and the truncation of the apex and base of the kernel, respectively. Cluster analysis separated the different accessions into six distinct clusters at 0.04 Euclidian distance. Six descriptor states, narrowly elliptic, elliptic, widely elliptic, ovate, obovate and lance-ovate, were characterized from the shape outlines and visualized through R's shape on r package. The discrimination between clusters was validated through MANOVA and LDA with 95% correct classification. The Fourier coefficients were also able to represent the variation observed from the physical properties of shape. The method may be used in establishing shape descriptors of all plant parts of all crop species.

Identificación de stocks de &lt;i&gt;Engraulis ringens&lt;/i&gt; en Chile utilizando morfometría de otolitos

Anchovy (Engraulis ringens) population units were analyzed in three zones off the coast of Chile: 1: Arica-Iquique, 2: Coquimbo and 3: Talcahuano-Valdivia from samples obtaineds during the 2012 spawning season. We used 50 left sagittae otoliths from each zone to perform a morphometric analysis, which included basic measurements, shape indexes and contour analysis (elliptical Fourier analysis). A MANOVA and Tukey multiple comparison analyses, applied on basic measures and shape indexes showed significant differences between zone 3 and zones 1 and 2. A classification by Canonical Discriminant analysis of elliptical Fourier harmonics, indicated significant differences among zones. It is concluded, therefore, that otolith shape analysis could be used to discriminate population units of Engraulis ringens. Better results were achieved using elliptic Fourier coefficients than using only shape indices.

Geometric morphometry of pupae to identify four medically important flies (Order: Diptera) in Thailand

Abstract. Chaiphongpachara T, Tubsamut P. 2019. Geometric morphometry of pupae to identify four medically important flies (Order: Diptera) in Thailand. Biodiversitas 20: 1504-1509. In this study, we evaluated an outline-based geometric morphometric (GM) approach for species identification from pupae of four common flies medically important in Thailand, Chrysomya megacephala, Lucilia cuprina, Musca domestica, and Boettcherisca nathani. For size estimation, mean perimeter length was used. For shape analysis, Elliptic Fourier Analysis was performed to produce the contour shape variables, which was calculated as Normalised Elliptic Fourier coefficients. Then, principal component analysis was performed on the Normalized Fourier coefficients for discriminant analysis, and used to estimate pupal shape variation among the species. The difference in size and shape between the fly species was analyzed using a non-parametric test based on 1000 permutations after Bonferroni correction for the significance level (p &lt; 0.05). In the size analysis, the mean perimeter length for pupae of B. nathani was the largest (20.35 mm) followed by C. megacephala (14.73 mm), while that for M. domestica was the smallest (11.82 mm). The size differences were statistically significant between all species (p &lt; 0.05). The contour shapes of all pupae were significantly different among all species. The results of this study can be used as a basis for the future application of GM to identify other types of flies via their pupae.

Comparative study of otolith and sulcus morphology for stock discrimination of yellow drum along the Chinese coast

Otolith morphology is widely used for fish stock identification. The sulcus, a structure on the medial side of the otolith, is an important feature in morphological analysis. This study was conducted to evaluate the feasibility of using sulcus morphology for stock identification and to compare its performance with commonly used otolith morphology analysis. Otoliths were collected and analyzed from three geographical groups (the Huanghe (Yellow) River estuary, HHE; the Jiaozhou Bay, JZB; and the Changjiang (Yangtze) River estuary, CJE) of yellow drum Nibea albiflora. The results show that the analysis of sulcus morphology based on shape indices (SIs), elliptic Fourier coefficients (EFc), and a combination of the two parameters identified stocks at overall classification rates of 51.0%, 72.5%, and 73.2%, respectively. These classification rates are similar to those obtained using otolith morphology analysis (57.0%, 73.8%, and 76.5% by SIs, EFc, and their combination, respectively). The findings suggest that sulcus morphology is comparable to the commonly used otolith morphology for identifying stocks of sciaenids, such as the yellow drum. For both otolith and sulcus morphology, EFc could identify the stocks more efficiently than SIs, while the combination of SIs and EFc was even better.

Breast-Shape Classification and Implant Construction Method for Unilateral Breast Reconstruction

Unilateral breast reconstruction is different from bilateral breast reconstruction and breast augmentation, as it requires more consideration of the symmetry between the reconstructed breast and the contralateral breast. However, there are currently no implants specifically targeted to unilateral breast reconstruction, nor is there is objective classification criteria for breast appearance type. A total of 212 breasts from 153 patients were measured. Breast measurements, breast surface curvature distributions, and elliptic Fourier coefficients were used to describe breast features. We objectively classified the appearance of breasts using machine learning and used the resulting cluster centers to construct the most adaptive implants for each type of breast. All of the breasts clustered into 4 types. The implants corresponding to each type of breast were constructed using cluster centers. The resulting cluster centers were then used to choose a suitable implant for patients requiring unilateral breast reconstruction. Contour coefficients were used to evaluate the clustering results, with an average score of 0.53. The two breasts that develop normally in the same person were treated as the same class. The score obtained after statistical classification was 0.47. These results demonstrate that our proposed method can improve the classification of breasts of different shapes. This method provides a foundation for improving the symmetry of unilateral breast reconstruction and the construction and selection of implants.

Otolith shape analysis for stock discrimination of two Collichthys genus croaker (Pieces: Sciaenidae,) from the northern Chinese coast

The otolith morphology of two croaker species (Collichthys lucidus and Collichthys niveatus) from three areas (Liaodong Bay, LD; Huanghe (Yellow) River estuary, HRE; Jiaozhou Bay, JZ) along the northern Chinese coast were investigated for species identification and stock discrimination. The otolith contour shape described by elliptic Fourier coefficients (EFC) were analysed using principal components analysis (PCA) and stepwise canonical discriminant analysis (CDA) to identify species and stocks. The two species were well differentiated, with an overall classification success rate of 97.8%. And variations in the otolith shapes were significant enough to discriminate among the three geographical samples of C. lucidus (67.7%) or C. niveatus (65.2%). Relatively high mis-assignment occurred between the geographically adjacent LD and HRE samples, which implied that individual mixing may exist between the two samples. This study yielded information complementary to that derived from genetic studies and provided information for assessing the stock structure of C. lucidus and C. niveatus in the Bohai Sea and the Yellow Sea.

Geometrical Characterization of Sediment Deposits at the Confluence of Mountain Streams

Debris flow injections from tributaries into a main mountain stream generate deposits of sediments which, in turn, result in obstruction and eventual damming of the river section. This contribution presents the results of a series of flume experiments on the dynamics of these deposits, with reference to three different types of blockage: no blockage, partial blockage, and full blockage. Results show that the shape of the deposit is mainly controlled by the ratio between the debris flow discharge and the main river discharge. The experimental dataset is used to develop a deposit resilience stability index based on the shape of the deposit contour retrieved from photos taken from above. The proposed index is based on the invariant elliptic Fourier coefficients and the dimensionless transverse obstruction parameter. The elliptic Fourier coefficients give information on the symmetry of the deposit contour. High symmetry indicates more stable and resilient deposits. The proposed index is calibrated on the basis of the flume experiments and tested with field data. The results are quite promising and suggest that the index can be appropriate for a fast hazard assessment of multiple debris flow deposits at a regional scale.

Use of otolith shape to inform stock structure in Patagonian toothfish (Dissostichus eleginoides) in the south-western Atlantic

An analysis of patterns in otolith shape is an effective tool for discriminating among fish stocks. Otolith shapes of Patagonian toothfish (Dissostichus eleginoides) and Antarctic toothfish (D. mawsoni) were investigated for geographic variability within seven regions across the Patagonian Shelf, and South Georgia and the South Sandwich Islands (SGSSI). Otolith shape was characterised by its elliptical Fourier coefficients (EFCs), corrected for fish length before being analysed, using multivariate methods. Non-metric multidimensional scaling analysis suggested the following three main groupings: Patagonian Shelf, SGSSI, and the third for Antarctic toothfish. This result was supported by ANOVA-like permutation tests, indicating significant (P&lt;0.001) differences in otolith shape among these three groupings. Linear discriminant analysis (LDA) cross-validation analyses of the EFCs resulted in otoliths being correctly classified to the sampling region from which they came, with an accuracy ranging from 78.95 to 100%. LDA cross-validation analyses on sampling regions within SGSSI and the Patagonian Shelf were able to classify individuals back to their sampling region with an accuracy of greater than 89.74 and 78.95% respectively. These results have provided some alternative insights into the stock structure of Patagonian toothfish across southern South America, South Atlantic and SGSSI.

Real-time fish animation generation by monocular camera

Fish animation generation is an interesting topic since it plays an important role in building virtual underwater worlds. Accurate motion capture and flexible retargeting of fish is difficult, in particular with the challenges of underwater marker attachment and feature description for soft bodies. Little research into this problem has been published and real-time fish motion retargeting with a desirable motion pattern remains elusive. Motivated by our goal of achieving high-quality data-driven fish animation with a light-weight, mobile device, this paper develops a novel framework of motion capturing, retargeting, and fine tuning for a fish. We demonstrate a markerless technique for the motion capture of an actual fish using a monocular camera. The elliptical Fourier coefficients are then integrated into the contour-based feature extraction process to analyze fish swimming patterns. This novel approach can obtain motion information in a robust way, utilizing the smooth medial axis as the descriptor for a soft fish body. For motion retargeting, we propose a two-level scheme to transfer the captured motion into new models, such as 2D meshes (with texture) generated from pictures or 3D models designed by artists, regardless of the body geometry and fin proportions amongst various species of fish. Both the motion capture and retargeting processes operate in real time. Hence, the system can obtain video sequences of real fish using a monocular camera and simultaneously create fish animation with variation. In addition, a motion fine tuning method is provided for animators to efficiently refine the retargeted frames in an interactive manner. It can enhance the final output animation to an appropriate level of fidelity.

Statolith morphometrics as a tool to distinguish among populations of three cubozoan species

Little is known on cubomedusae population structure, and what is known for many species is mostly from rare occurrences or from a metapopulation perspective. Knowledge on population units is critical for understanding population dynamics as well as predicting potential risk to swimmers. Otolith shape analysis is a proven stock identification technique in fishes; here, we applied shape analysis to cubomedusae statoliths. Medusae of three species were collected from three distinct populations around the coastline and nearshore islands of northern Queensland, Australia. Canonical discriminant analysis was performed on normalised elliptical fourier coefficients for statolith proximal, oral and lateral faces and combinations of statolith faces for each species. Significant discrimination of sampling populations was achieved in two species (Copula sivickisi statolith proximal face and Chironex fleckeri oral + lateral faces). Differences in statolith shape, therefore, were capable of successful discrimination among sampling locations but was not capable for one species. The ecological niche, and associated ecological pressures, of some cubozoan species (e.g. Carukia barnesi) may not vary enough for differences in statolith shape among locations to occur. Statolith shape in combination with other stock identification techniques, such as genetics and/or elemental chemistry, will help to discriminate the spatial scales of cubozoan populations.

Statolith Morphometrics Can Discriminate among Taxa of Cubozoan Jellyfishes

Identification of potentially harmful cubomedusae is difficult due to their gelatinous nature. The only hard structure of medusae, the statolith, has the potential to provide robust measurements for morphometric analysis. Traditional morphometric length to width ratios (L: W) and modern morphometric Elliptical Fourier Analysis (EFA) were applied to proximal, oral and lateral statolith faces of 12 cubozoan species. EFA outperformed L: W as L: W did not account for the curvature of the statolith. Best discrimination was achieved with Canonical Discriminant Analysis (CDA) when analysing proximal + oral + lateral statolith faces in combination. Normalised Elliptical Fourier (NEF) coefficients classified 98% of samples to their correct species and 94% to family group. Statolith shape agreed with currently accepted cubozoan taxonomy. This has potential to assist in identifying levels of risk and stock structure of populations in areas where box jellyfish envenomations are a concern as the severity of envenomation is family dependent. We have only studied 12 (27%) of the 45 currently accepted cubomedusae, but analyses demonstrated that statolith shape is an effective taxonomic discriminator within the Class.