ShapeR: an R package to study otolith shape variation among fish populations.
Ontology highlight
ABSTRACT:
SUBMITTER: Libungan LA
PROVIDER: S-EPMC4372608 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
ShapeR: an R package to study otolith shape variation among fish populations.
Libungan Lísa Anne LA Pálsson Snæbjörn S
PloS one 20150324 3
ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or Wavelet transform to the outlines and visualize the mean shape. The output ...[more]
Similar Datasets
Project description:The otoliths of teleost fishes exhibit a great deal of inter- and intra-species shape variation. The ecomorphology of the saccular otolith is often studied by comparing its shape across species and populations inhabiting a range of environments. However, formal tests are often lacking to examine how closely variation in otolith shape follows the genetic drift of a neutral trait. Here, we examine patterns of saccular otolith shape variation in four species of African cichlid fishes, each sampled from three field sites. All four species showed the greatest level of otolith shape variation along two principal component axes, one pertaining to otolith height and another to the prominence of an anterior notch. Fish collected from the same site possessed similarities in saccular otolith shape relative to fish from other sites, and these 'site-difference' signatures were consistent across species and observable in both sexes. Sex-differences in saccular otolith shape differed in magnitude from site to site. Population differences in saccular otolith shape did not covary with neutral genetic differentiation between those populations. Otolith height, in particular, displayed large site similarities across species, weak correlation with neutral genetic variation, and strong sex differences, collectively suggesting that otolith shape represents a selectively non-neutral trait.
| S-EPMC7393159 | biostudies-literature
Project description:Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50-km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.
| S-EPMC6912905 | biostudies-literature
Project description:Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment technique for providing information about RNA local flexibility. The local structural information contained in SHAPE reactivity data can be used as constraints in 2D/3D structure predictions. Here, we present SHAPE predictoR (SHAPER), a web server for fast and accurate SHAPE reactivity prediction. The main purpose of the SHAPER web server is to provide a portal that uses experimental SHAPE data to refine 2D/3D RNA structure selection. Input structures for the SHAPER server can be obtained through experimental or computational modeling. The SHAPER server can accept RNA structures with single or multiple conformations, and the predicted SHAPE profile and correlation with experimental SHAPE data (if provided) for each conformation can be freely downloaded through the web portal. The SHAPER web server is available at http://rna.physics.missouri.edu/shaper/.
| S-EPMC8355595 | biostudies-literature
Project description:BackgroundAlthough left ventricular cardiac geometric indices such as size and sphericity characterize adverse remodeling and have prognostic value in symptomatic patients, little is known of shape distributions in subclinical populations. We sought to quantify shape variation across a large number of asymptomatic volunteers, and examine differences among sub-cohorts.MethodsAn atlas was constructed comprising 1,991 cardiovascular magnetic resonance (CMR) cases contributed from the Multi-Ethnic Study of Atherosclerosis baseline examination. A mathematical model describing regional wall motion and shape was used to establish a coordinate map registered to the cardiac anatomy. The model was automatically customized to left ventricular contours and anatomical landmarks, corrected for breath-hold mis-registration between image slices. Mathematical techniques were used to characterize global shape distributions, after removal of translations, rotations, and scale due to height. Differences were quantified among ethnicity, sex, smoking, hypertension and diabetes sub-cohorts.ResultsThe atlas construction process yielded accurate representations of global shape (errors between manual and automatic surface points in 244 validation cases were less than the image pixel size). After correction for height, the dominant shape component was associated with heart size, explaining 32% of the total shape variance at end-diastole and 29% at end-systole. After size, the second dominant shape component was sphericity at end-diastole (13%), and concentricity at end-systole (10%). The resulting shape components distinguished differences due to ethnicity and risk factors with greater statistical power than traditional mass and volume indices.ConclusionsWe have quantified the dominant components of global shape variation in the adult asymptomatic population. The data and results are available at cardiacatlas.org. Shape distributions were principally explained by size, sphericity and concentricity, which are known correlates of adverse outcomes. Atlas-based global shape analysis provides a powerful method for quantifying left ventricular shape differences in asymptomatic populations.Trial registrationClinicalTrials.gov NCT00005487.
| S-EPMC4145340 | biostudies-literature
Project description:Otoliths are biocalcified bodies connected to the sensory system in the inner ears of fish. Their layered, biorhythm-following formation provides individual records of the age, the individual history and the natural environment of extinct and living fish species. Such data are critical for ecosystem and fisheries monitoring. They however often lack validation and the poor understanding of biomineralization mechanisms has led to striking examples of misinterpretations and subsequent erroneous conclusions in fish ecology and fisheries management. Here we develop and validate a numerical model of otolith biomineralization. Based on a general bioenergetic theory, it disentangles the complex interplay between metabolic and temperature effects on biomineralization. This model resolves controversial issues and explains poorly understood observations of otolith formation. It represents a unique simulation tool to improve otolith interpretation and applications, and, beyond, to address the effects of both climate change and ocean acidification on other biomineralizing organisms such as corals and bivalves.
| S-EPMC3215717 | biostudies-literature
Project description:Ocean acidification (OA) may have varied effects on fish eco-physiological responses. Most OA studies have been carried out in laboratory conditions without considering the in situ pCO2/pH variability documented for many marine coastal ecosystems. Using a standard otolith ageing technique, we assessed how in situ ocean acidification (ambient, versus end-of-century CO2 levels) can affect somatic and otolith growth, and their relationship in a coastal fish. Somatic and otolith growth rates of juveniles of the ocellated wrasse Symphodus ocellatus living off a Mediterranean CO2 seep increased at the high- pCO2 site. Also, we detected that slower-growing individuals living at ambient pCO2 levels tend to have larger otoliths at the same somatic length (i.e. higher relative size of otoliths to fish body length) than faster-growing conspecifics living under high pCO2 conditions, with this being attributable to the so-called 'growth effect'. Our findings suggest the possibility of contrasting OA effects on fish fitness, with higher somatic growth rate and possibly higher survival associated with smaller relative size of otoliths that could impair fish auditory and vestibular sensitivity.
| S-EPMC6405470 | biostudies-literature
Project description:The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species' local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.
| S-EPMC8065892 | biostudies-literature
Project description:BackgroundDescribing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe.ResultsThe genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude.ConclusionOur results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.
| S-EPMC10838002 | biostudies-literature
Project description:Aedes albopictus and Aedes scapularis are vectors of several arboviruses, including the dengue, chikungunya, and Rocio virus infection. While Ae. albopictus is a highly invasive species native to Asia and has been dispersed by humans to most parts of the world, Ae. scapularis is native to Brazil and is widely distributed in the southeast of the country. Both species are highly anthropophilic and are often abundant in places with high human population densities. Because of the great epidemiological importance of these two mosquitoes and the paucity of knowledge on how they have adapted to different urban built environments, we investigated the microgeographic population structure of these vector species in the city of São Paulo, Brazil, using wing geometric morphometrics. Females of Ae. albopictus and Ae. scapularis were collected in seven urban parks in the city. The right wings of the specimens were removed and digitized, and eighteen landmarks based on vein intersections in the wing venation patterns were used to assess cross-sectional variation in wing shape and size. The analyses revealed distinct results for Ae. albopictus and Ae. scapularis populations. While the former had less wing shape variation, the latter had more heterogeneity, indicating a higher degree of intraspecific variation. Our results indicate that microgeographic selective pressures exerted by different urban built environments have a distinct effect on wing shape patterns in the populations of these two mosquito species studied here.
| S-EPMC7761735 | biostudies-literature
Project description:Fish stocks can be defined by differences in their distribution, life history, and genetics. Managing fish based on stock structure is integral to successful management of a species because fishing may affect stocks disproportionately. Genetic and environmental differences can affect the shape and growth of otoliths and these differences may be indicative of stock structure. To investigate the potential for speciation or stock structure in giant grenadier, Albatrossia pectoralis, we quantified the shape of female giant grenadier otoliths and compared body growth rates for fish with three otolith shapes; shape types were classified visually by an experienced giant grenadier age reader, and were not defined by known distribution or life history differences. We found extreme variation in otolith shape among individuals; however, the shapes were a gradation and not clearly defined into three groups. The two more extreme shapes, visually defined as "hatchet" and "comb", were discernable based on principal component analyses of elliptical Fourier descriptors, and the "mixed" shape overlapped both of the extreme shapes. Fish with hatchet-shaped otoliths grew faster than fish with comb-shaped otoliths. A genetic test (cytochrome c oxidase 1 used by the Fish Barcode of Life Initiative) showed almost no variability among samples, indicating that the samples were all from one species. The lack of young specimens makes it difficult to link otolith shape and growth difference to life history. In addition, shape could not be correlated with adult movement patterns because giant grenadiers experience 100% mortality after capture and, therefore, cannot be tagged and released. Despite these limitations, the link between body growth and otolith shape indicates measurable differences that deserve more study.
| S-EPMC5489205 | biostudies-literature