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Figure 1 in Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

Figure 1. Measurements used as continuous characters in the phylogenetic analysis shown in an Alizarin Red-stained specimen of the apogonid Apogon maculatus (MZUSP 43155, 67.3 mm standard length): predorsal length (A), dorsal fin base length (B), pectoral fin length (C), prepelvic length (D), preanal length (E) and anal fin base length (F).

Figure 3 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)

Figure 3. Ventral view of hands showing the comparative size of discs on fingers I and II in frogs of genus Pristimantis. A, Pristimantis appendiculatus (Werner, 1894) (KU 165140). B, Pristimantis penelopus (Lynch & Rueda-Almonacid, 1999) (ICN

Figure 2 in Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

Figure 2. Left lateral view of dorsal fin and associated musculature of the apogonid Apogon maculatus (MZUSP 43155). Scale bar: 3 mm.

Figure 1 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)

Figure 1. Lateral view of pelvic and thigh musculature showing origins of the m. iliacus externus (ile) and m. tensor fasciae latae (tfl) from the iliac shaft (ish) in frogs of the superfamily Brachycephaloidea. A, Pristimantis kelephus (Lynch, 1998) (ICN 39671). B, Pristimantis cristinae (Lynch & Ruiz-Carranza, 1985) (ICN 3950). C, Craugastor longirostris (Boulenger, 1898) (ICN 42787). D, Ceuthomantis sp1 Colombia (JDL 32489). The red and green colours denote the portion anterior of the iliac shaft free of muscle fibres and the tensor fasciae latae (tfl), respectively. Scale bars = 2 mm.

Figure 4 in New phenotypic synapomorphies delimit three molecular-based clades of New World direct-developing frogs (Amphibia: Anura: Brachycephaloidea)

Figure 4. Distribution of unambiguously optimized phenotypic synapomorphies recovered in the current character analysis. The phylogenetic hypothesis for Brachycephaloidea is that of Padial et al. (2014) and relationships outside Brachycephaloidea follow Jetz & Pyron (2018). Genera and subgenera were collapsed, but the complete distribution of character states is shown in Table 1. Character numbers are given beneath each square, with primitive-derived character states inside each square (see text and Table 1 for character definitions). Colour coding: red = untransformed, homoplastic; blue = transformed, homoplastic.

opencc-zeroDec 2014View details →

Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails

The giant edible Placostylus snails of New Caledonia occur across a wide range of environmental conditions, from the dry southwest to the wetter central and northeastern regions. In large, slow-moving animals such as Placostylus, speciation could be assumed to be largely driven by allopatry and genetic drift as opposed to natural selection. We examined variation in shell morphology using geometric morphometrics and genetic structure within two species of Placostylus (P. fibratus, P. porphyrostomus), to determine the drivers of diversity in this group. Despite the current patchy distribution of snails on New Caledonia, both mtDNA and nuclear SNP data sets (>3000 loci) showed weak admixing between populations and species. Shell morphology was concordant with the genetic clusters we identified and had a strong relationship with local environment. The genetic data, in contrast to the morphological data, did not show concordance with climatic conditions, suggesting the snails are not limited in their ability to adapt to different environments. In sympatry, P. fibratus and P. porphyrostomus maintained genetic and morphological differences, suggesting a genetic basis of phenotypic variation. Convergence of shell shape was observed in two adjacent populations that are genetically isolated but experience similar habitat and climatic conditions. Conversely, some populations in contrasting environments were morphologically distinct although genetically indistinguishable. We infer that morphological divergence in the Placostylus snails of New Caledonia is mediated by adaptation to the local environment.

Figure 43 in Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

Figure 43. Left lateral view of an alcohol-preserved juvenile specimen of the stromateid Stromateus fiatola (68.7 mm standard length; USNM UNCAT). Arrow indicates the pelvic fin.

Arabidopsis SAUR63 seedling phenotypes and fluorescent fusion protein localization

In plants, regulated cell expansion determines organ size and shape. Several members of the family of redundantly acting Small Auxin Up RNA (SAUR) proteins can stimulate plasma membrane (PM) H+-ATPase proton pumping activity by inhibiting PM-associated PP2C.D phosphatases, thereby increasing the PM electrochemical potential, acidifying the apoplast, and stimulating cell expansion. Similarly, Arabidopsis thaliana SAUR63 was able to increase growth of various organs, antagonize PP2C.D5 phosphatase, and increase H+-ATPase activity. This dataset includes i) measurements of seedling growth in plants with altered activity of SAUR63 and PP2C.D5; ii) data from fluorescent images to measure extracellular pH; iii) analyses of subcellular localization of SAUR63:YFP fusion protein variants in roots; and iv) SAUR63:YFP localization after transient expression in Nicotiana benthamiana leaves with perturbed plasma membrane lipid composition. These data underlie figures presented in the linked manuscript. Using a gain-of-function approach to bypass genetic redundancy, we dissected structural requirements for SAUR63 growth-promoting activity. The divergent N-terminal domain of SAUR63 has a predicted basic amphipathic α-helix, and was able to drive partial PM association. Deletion of the N-terminal domain decreased PM association of a SAUR63 fusion protein, as well as decreasing protein level and eliminating growth-promoting activity. Conversely, forced PM association restored ability to promote H+-ATPase activity and cell expansion, indicating that SAUR63 is active when PM-associated. Lipid binding assays and perturbations of PM lipid composition indicate that the N-terminal domain can interact with PM anionic lipids. Mutations in the conserved SAUR domain also reduced PM association in root cells. Thus, both the N-terminal domain and the SAUR domain may cooperatively mediate the SAUR63 PM association required to promote growth. Data is licensed by the authors for use and distribution subject to citation of the original source in accordance with the Creative Commons Attribution (CC BY) license.

No evidence of predicted phenotypic changes after hurricane disturbance in a shade-specialist Caribbean anole

Extreme climatic events (ECE) such as hurricanes have been hypothesized to be a major driving force of natural selection. Recent studies argue that, following strong hurricane disturbance, Anolis lizards in the Caribbean undergo selection for traits such as longer forelimbs or smaller body sizes that improve their clinging ability to their substrates increasing their chances of surviving hurricane wind gusts. Some authors challenge the generalization of this hypothesis arguing that other mechanisms may explain these phenotypic changes or that they may not necessarily be generalizable due to system-specific idiosyncrasies. To address this issue, we compared body size and relative forelimb length of Anolis gundlachi, a trunk-ground anole living in closed canopy forests in Puerto Rico, before, four months after, and 15 months after Hurricanes Irma and Maria in 2017. Overall, our results show no clear evidence of a temporal decrease in body size or increase forelimb length (relative to body size) challenging the generalizability of the clinging ability hypothesis. Understanding how animals adapt to ECE is an emerging field. Still, we are quickly learning that this process is complex and nuanced.

opencc-by-4.0Jul 2021View details →

Cosegmentation for Plant Phenotyping+ (CosegPP+) Data Repository Collected Via a High-Throughput Imaging System

CosegPP+ is an extension of CosegPP (https://doi.org/10.5281/zenodo.5117176) with binary masks for a collection of cosegmentation and segmentation algorithms.  We thank Vincent Stoeger for acquiring the dataset using LemnaTec at the University of Nebraska-Lincoln. If you use this dataset, please cite this paper: <table> <tbody> <tr></tr> <tr> <td> <div>Quiñones, R., Samal, A., Das Choudhury, S., & Muñoz-Arriola, F. (2023). OSC-CO2: coattention and cosegmentation framework for plant state change with multiple features. Frontiers in Plant Science, 14, 1211409.</div> </td> </tr> <tr> <td> </td> </tr> </tbody> </table>

Evolutionary divergence in phenotypic plasticity shapes brain size variation between coexisting sunfish ecotypes

Mechanisms that generate brain size variation and the consequences of such variation on ecological performance are poorly understood in most natural animal populations. We use a reciprocal-transplant common garden experiment and foraging performance trials to test for brain size plasticity and the functional consequences of brain size variation in Pumpkinseed sunfish (Lepomis gibbosus) ecotypes that have diverged between nearshore littoral and offshore pelagic lake habitats. Different age-classes of wild-caught juveniles from both habitats were exposed for six months to treatments that mimicked littoral and pelagic foraging. Plastic responses in oral jaw size suggested that treatments mimicked natural habitat-specific foraging conditions. Plastic brain size responses to foraging manipulations differed between ecotypes, as only pelagic sourced fish showed brain size plasticity. Only pelagic juveniles under 1 year-old expressed this plastic response, suggesting that plastic brain size responses decline with age and so may be irreversible. Finally, larger brain size was associated with enhanced foraging performance on live benthic but not pelagic prey, providing the first experimental evidence of a relationship between brain size and prey-specific foraging performance in fishes. The recent post-glacial origin of these ecotypes suggests that brain size plasticity can rapidly evolve and diverge in fish under contrasting ecological conditions.

Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 12 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.

A single intronic SNP in splicing site of steroidogenic enzyme hsd17b1 is associated with phenotypic sex in oyster pompano, Trachinotus anak

Teleosts show varied master sex determining (MSD) genes and sex determination (SD) mechanisms, with frequent turnovers of sex chromosomes. Tracing the origins of MSD genes and turnovers of sex chromosomes in a taxonomic group is of particular interest in evolutionary biology. Oyster pompano (Trachinotus anak), a marine fish, belongs to the family Carangidae, in which 17b-hydroxysteroid dehydrogenase 1 (hsd17b1) has repeatedly evolved to a MSD gene. Using whole genome resequencing, a single SNP at Chromosome 24 was identified to be strictly associated with phenotypic sex, with females being the heterozygous sex. This SNP is located in a splicing site at the first exon/intron boundary of hsd17b1. The Z-linked SNP results in malfunction of all spliced isoforms, whereas the W-linked isoforms were predicted to have open reading frames (ORF) that are conserved among vertebrates, suggesting that hsd17b1 is a female determining gene. The differential alternative splicing patterns of ZZ and ZW genotypes were consistently observed both in undifferentiated stages and differentiated gonads. We observed elevated recombination around the SD locus and no differentiation between Z and W chromosomes. The extreme diversity of mutational mechanisms that hsd17b1 evolves to a MSD gene highlights frequent in situ turnovers between sex chromosomes in the Carangidae.

opencc-by-4.0Jul 2022View details →

Data files associated with the article entitled: "High-throughput behavioral phenotyping of tiny arthropods: chemosensory traits in a mesostigmatic hematophagous mite" (accepted in Journal of Experimental Zoology - part A))

Here are provided three groups of datasets, corresponding respectively to the data obtained from MiteMap bioassays (1) with the monomolecular reference substances (geraniol and NH3), (2) with the patented blend MIX1.0, (3) with the odors emitted by the mites' bodies. These datasets were analyzed using the script provided in RMarkdown format in the Zenodo repository DOI 10.5281/zenodo.6109388. A folder is also provided with the heatmaps associated with these data grouped in subfolders by farm x modality.

opencc-zeroAug 2022View details →

Temperature regime during embryogenesis alters subsequent behavioural phenotypes of juvenile brown trout

Climate warming imposes a serious threat, especially to freshwater ecosystems in temperate and (sub)polar regions, which are often dominated by cold-adapted ectotherms. Although relatively intense warming during winter is common across the climatic regions, comparably little focus has been put on the organismal impacts of winter warming. Embryonic development, which is exceptionally susceptible to ambient temperature, occurs during winter in various freshwater ectotherms. Yet, our knowledge of the effects of increased temperature during embryogenesis on later life stages is limited. Using brown trout (Salmo trutta), we examined how a 1.5°C temperature increase from fertilisation to hatching affects various traits at the onset of the free-swimming stage (i.e., a comparison between 3.5°C or 5.0°C treatments). Although all hatchlings were kept at the same temperature (7.0°C) from hatching to the onset of the free-swimming stage for about two months, the temperature increase during embryogenesis substantially reduced key ecological behaviours, i.e., activity and exploration levels, at the onset of the free-swimming stage despite only marginal temperature effects on morphological and physiological traits at this stage. Given the importance of behavioural traits in early growth and survival, our study suggests a likely pathway through which subtle changes in mean winter temperature affect early fitness.

opencc-zeroAug 2022View details →

Sexually mediated phenotypic variation within and between sexes as a continuum structured by ecology: The mosaic nature of skeletal variation across body regions in Threespine stickleback (Gasterosteus aculeatus L.)

Ecological character displacement between the sexes, and sexual selection, integrate into a convergent set of factors that produce sexual variation. Ecologically-modulated, sexually mediated variation within and between sexes may be a major contributor to the amount of total variation that selection can act on in species. Threespine stickleback (Gasterosteus aculeatus) display rapid adaptive responses and sexual variation in many phenotypic traits. We examined phenotypic variation in the skull, pectoral and pelvic girdles of threespine stickleback from two freshwater and two coastal marine sites on the Sunshine Coast of British Columbia, Canada, using an approach that avoids a priori assumptions about bimodal patterns of variation. We quantified shape and size of the cranial, pectoral and pelvic regions of sticklebacks in marine and freshwater habitats using 3D geometric morphometrics and an index of sexually mediated variation. We show that the expression of phenotypic variation is structured in part by the effects of both habitat marine vs freshwater and the effects of individual sites within each habitat. Relative size exerts variable influence, and patterns of phenotypic variation associated with sex vary among body regions. This fine-grained quantification of sexually mediated variation in the context of habitat difference and different anatomical structures indicates a complex relationship between genetically inferred sex and environmental factors, demonstrating that the interplay between shared genetic background and sexually mediated, ecologically-based selective pressures structures the phenotypic expression of complex traits.

opencc-zeroSep 2022View details →

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

To predict how widely distributed species will perform under future climate change it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate-change scenario for central Europe and revealed the population structure through whole genome sequencing. Plants were grown under two temperature (18°C, 21°C) and three precipitation regimes (65 mm, 75 mm, 90 mm) to measure their response in biomass and fecundity related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations and another cluster containing Central European populations. Population genetic diversity decreased with increasing latitude and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.

opencc-zeroSep 2022View details →

Data from: A camera trap based assessment of climate-driven phenotypic plasticity of seasonal moulting in an endangered carnivore

For many species, the ability to rapidly adapt to changes in seasonality is essential for long-term survival. In the Arctic, seasonal moulting is a key life history event that provides year-round camouflage and thermal protection. However, increased seasonal variability can lead to phenological mismatch. In this study, we investigated whether winter-white (white morph) and winter-brown (blue morph) Arctic foxes (Vulpes lagopus) could adjust their winter-to-summer moult to match local environmental conditions. We used camera trap images spanning an eight-year period to quantify the timing and rate of fur change in a polymorphic subpopulation in south-central Norway. Seasonal snow cover duration and temperature governed the phenology of the spring moult. We observed a later onset and longer moulting duration with decreasing temperature and longer snow season. Additionally, white foxes moulted earlier than blue in years with shorter periods of snow cover and warmer temperatures. These results suggest that phenotypic plasticity allows Arctic foxes to modulate the timing and rate of their spring moult as snow conditions and temperatures fluctuate. With the Arctic warming at an unprecedented rate, understanding the capacity of polar species to physiologically adapt to a changing environment is urgently needed in order to develop adaptive conservation efforts. Moreover, we provide the first evidence for variations in the moulting phenology of blue and white Arctic foxes. Our study underlines the different intraspecific selective pressures that can exist in populations where several morphs co-occur, and illustrates the importance of integrating morph-based differences in future management strategies of such polymorphic species.

opencc-by-4.0Oct 2022View details →

Dataset with values of morphological parameters and phenotypes of cells and colonies from three human pluripotent stem cell lines

The dataset is a part of the following manuscript submitted for publication in International Journal of Molecular Sciences (MDPI): "Prognostic Analysis of Human Pluripotent Stem Cells Based on their Morphological Portrait and Expression of Pluripotent Markers" by Olga A. Krasnova, Vitaly V. Gursky, Alina S. Chabina, K. A. Kulakova, L. L. Alekseenko, Alexandra V. Panova, Sergey L. Kiselev and Irina E. Neganova The files contain values of several morphological parameters and phenotypes obtained for cells and colonies from hESC line H9, hiPSC line AD3, and hiPSC line CaSR. The phenotypic information is presented in three forms: four possible classes of colonies according to the visually assessed phenotype ('bad', 'average', 'good', and 'excellent'), three possible classes (previous 'good' and 'excellent' combined in one 'good' class), and two possible classes (previous 'bad' and 'average' combined in one 'bad' class, and previous 'good' and 'excellent' combined in one 'good' class).