Becoming Different But Staying Alike: Patterns of Sexual Size and Shape Dimorphism in Bills of Hummingbirds

Hummingbirds are known for their distinctive patterns of sexual dimorphism, with many species exhibiting sex-related differences in various ecologically-relevant traits, including sex-specific differences in bill shape. It is generally assumed that such patterns are consistent across all hummingbird lineages, yet many taxa remain understudied. In this study we examined patterns of sexual size and sexual shape dimorphism in bills of 32 of 35 species in the monophyletic Mellisugini lineage. We also compared patterns of bill size dimorphism in this group to other hummingbird lineages, using data from 219 hummingbird species. Overall, the presence and degree of sexual size dimorphism was similar across all hummingbird lineages, with the majority of Mellisugini species displaying female-biased sexual size dimorphism, patterns that remain unchanged when analyzed in a phylogenetic context. Surprisingly however, we found that sexual dimorphism in bill shape was nearly absent in the Mellisugini clade, with only 3 of the 32 species examined displaying bill shape dimorphism. Based on observations in other hummingbird lineages, the lack of sexual shape dimorphism in Mellisugini is particularly unusual. We hypothesize that the patterns of sexual size dimorphism observed here may be the consequence of differential selective forces that result from competition for ecological resources. We further propose that an influential mechanism underlying shape dimorphism is competition and niche segregation. Taken together, the evolutionary changes in patterns of sexual shape dimorphism observed in Mellisugini suggest that the evolutionary trends of sexual dimorphism in the Trochilidae are far more dynamic than was previously believed.     

Natural Variation Identifies Multiple Loci Controlling Petal Shape and Size in Arabidopsis thaliana

Natural variation in organ morphologies can have adaptive significance and contribute to speciation. However, the underlying allelic differences responsible for variation in organ size and shape remain poorly understood. We have utilized natural phenotypic variation in three Arabidopsis thaliana ecotypes to examine the genetic basis for quantitative variation in petal length, width, area, and shape. We identified 23 loci responsible for such variation, many of which appear to correspond to genes not previously implicated in controlling organ morphology. These analyses also demonstrated that allelic differences at distinct loci can independently affect petal length, width, area or shape, suggesting that these traits behave as independent modules. We also showed that ERECTA (ER), encoding a leucine-rich repeat (LRR) receptor-like serine-threonine kinase, is a major effect locus determining petal shape. Allelic variation at the ER locus was associated with differences in petal cell proliferation and concomitant effects on petal shape. ER has been previously shown to be required for regulating cell division and expansion in other contexts; the ER receptor-like kinase functioning to also control organ-specific proliferation patterns suggests that allelic variation in common signaling components may nonetheless have been a key factor in morphological diversification.     

Wingless signaling and the control of cell shape in Drosophila wing imaginal discs

The control of cell morphology is important for shaping animals during development. Here we address the role of the Wnt/Wingless signal transduction pathway and two of its target genes, vestigial and shotgun (encoding E-cadherin), in controlling the columnar shape of Drosophila wing disc cells. We show that clones of cells mutant for arrow (encoding an essential component of the Wingless signal transduction pathway), vestigial or shotgun undergo profound cell shape changes and are extruded towards the basal side of the epithelium. Compartment-wide expression of a dominant-negative form of the Wingless transducer T-cell factor (TCF/Pangolin), or double-stranded RNA targeting vestigial or shotgun, leads to abnormally short cells throughout this region, indicating that these genes act cell autonomously to maintain normal columnar cell shape. Conversely, overexpression of Wingless, a constitutively-active form of the Wingless transducer β-catenin/Armadillo, or Vestigial, results in precocious cell elongation. Co-expression of Vestigial partially suppresses the abnormal cell shape induced by dominant-negative TCF. We conclude that Wingless signal transduction plays a cell-autonomous role in promoting and maintaining the columnar shape of wing disc cells. Furthermore, our data suggest that Wingless controls cell shape, in part, through maintaining vestigial expression.     

Exploring the effects of gene dosage on mandible shape in mice as a model for studying the genetic basis of natural variation

Mandible shape in the mouse is a complex trait that is influenced by many genetic factors. However, little is known about the action of single genes on adult mandible shape so far, since most developmentally relevant genes are already required during embryogenesis, i.e., knockouts lead to embryonic death or severe deformations, before the mandible is fully formed. We employ here a geometric morphometric approach to identify subtle phenotypic differences caused by dosage effects of candidate genes. We use mouse strains with specific gene modifications (knockouts and knockins) to compare heterozygous animals with controls from the same stock, which is expected to be equivalent to a change of gene expression of the respective locus. Such differences in expression level are also likely to occur as part of the natural variation. We focus on Bmp pathway genes (Bmp4, its antagonist Noggin, and combinations of Bmp5-7 genotypes), but include also two other developmental control genes suspected to affect mandible development in some way (Egfr and Irf6). In addition, we study the effects of Hoxd13, as well as an extracellular matrix constituent (Col2a1). We find that subtle but significant shape differences are caused by differences in gene dosage of several of these genes. The changes seen for Bmp4 and Noggin are partially compatible with the action of these genes known from birds and fish. We find significant shape changes also for Hoxd13, although this gene has so far only been implicated in skeletal patterning processes of the limbs. Comparing the effect sizes of gene dosage changes to the variation found in natural populations of mice as well as quantitative trait loci (QTL) effects on mandible shape, we find that the effect sizes caused by gene dosage changes are at the lower end of the spectrum of natural variation, but larger than the average additive effects found in QTL studies. We conclude that studying gene dosage effects have the potential to provide new insights into aspects of craniofacial development, variation, and evolution.     

Dynamics of Cell Shape Inheritance in Fission Yeast

Every cell has a characteristic shape key to its fate and function. That shape is not only the product of genetic design and of the physical and biochemical environment, but it is also subject to inheritance. However, the nature and contribution of cell shape inheritance to morphogenetic control is mostly ignored. Here, we investigate morphogenetic inheritance in the cylindrically-shaped fission yeast Schizosaccharomyces pombe. Focusing on sixteen different ‘curved’ mutants - a class of mutants which often fail to grow axially straight – we quantitatively characterize their dynamics of cell shape inheritance throughout generations. We show that mutants of similar machineries display similar dynamics of cell shape inheritance, and exploit this feature to show that persistent axial cell growth in S. pombe is secured by multiple, separable molecular pathways. Finally, we find that one of those pathways corresponds to the swc2-swr1-vps71 SWR1/SRCAP chromatin remodelling complex, which acts additively to the known mal3-tip1-mto1-mto2 microtubule and tea1-tea2-tea4-pom1 polarity machineries.     

Butterfly species identification by branch length similarity entropy

We previously developed a shape recognition methodology that uses “branch length similarity” (BLS) entropy, which is defined as a simple branching network consisting of a single node and branches. The simple network is referred to as a “unit branching network” (UBN). Our approach involves obtaining BLS entropy profiles from UBNs created by joining each pixel in the outline of a shape with every other pixel in the shape's border. The profiles successfully characterize the shapes by comparing their BLS entropy profiles. Presently, we modified this approach to facilitate its application to butterfly species identification by partitioning and weighting the entropy profile. As a test, we identified the butterfly species Colias erate, Parnassius bremeri, Eurema hecabe, Gonepteryx rhamni, and Papilio maackii. Each species group consisted of 10 specimens. We used wing shape to identify a species. We extracted evenly spaced x–y coordinates of boundary pixels for the wing shapes in a counter counterclockwise direction. The number of the pixels was 749. We then sequentially partitioned 749 x–y pairs into 15 groups, calculated entropy profiles for the groups, and weighted the profiles. The profiles were combined in order, resulting in a single weighted BLS entropy profile for a wing's shape. Subsequently, we statistically compared the correlation coefficient among the weighted BLS profiles. Our experimental results showed that this method was statistically successful for butterfly species identification. The advantage of the partitioning and weighting process in shape recognition is also discussed.     

Ecogeographical variation in skull morphometry of howler monkeys (Primates: Atelidae)

Our aim is to identify ecomorphological adaptations in the skull shape of the South American howler monkeys (species of the genus Alouatta, Lacépède, 1799, Primates, Atelidae). Since Alouatta is relatively homogenous in feeding ecology, we expect skull shape variation to be relatively conservative across species. We used geometric morphometrics to quantify craniodental morphology in six species of Alouatta. Multivariate regression, two-block Partial Least Squares, and variation partitioning were used to test for the impact of taxonomy, sexual dimorphism, allometry, geography and climate on skull shape. We found morphological overlap among species and sexes, although some discrimination occurs between species living in seasonal environments as opposed to rain forest species. There was a negative latitudinal gradient in skull size across species, with size explaining 34% of total shape variance. Latitude and climate, though important, were secondary in explaining shape variance. Amazonian Alouatta are larger, have thinner molars, wide incisors, and proportionally larger neurocranium. Overall, the shape of southern species seem well adapted to cope with proportionally tougher food items, whereas Amazonian species seem better equipped to deal with a diet richer in fruits, as confirmed by independent field observations. The small size of Alouatta in the South is possibly linked to the effect of competition with the larger folivorous atelid Brachyteles.     

A Targeted Gain-of-Function Screen Identifies Genes Affecting Salivary Gland Morphogenesis/Tubulogenesis in Drosophila

During development individual cells in tissues undergo complex cell-shape changes to drive the morphogenetic movements required to form tissues. Cell shape is determined by the cytoskeleton and cell-shape changes critically depend on a tight spatial and temporal control of cytoskeletal behavior. We have used the formation of the salivary glands in the Drosophila embryo, a process of tubulogenesis, as an assay for identifying factors that impinge on cell shape and the cytoskeleton. To this end we have performed a gain-of-function screen in the salivary glands, using a collection of fly lines carrying EP-element insertions that allow the overexpression of downstream-located genes using the UAS-Gal4 system. We used a salivary-gland-specific fork head-Gal4 line to restrict expression to the salivary glands, in combination with reporters of cell shape and the cytoskeleton. We identified a number of genes known to affect salivary gland formation, confirming the effectiveness of the screen. In addition, we found many genes not implicated previously in this process, some having known functions in other tissues. We report the initial characterization of a subset of genes, including chickadee, rhomboid1, egalitarian, bitesize, and capricious, through comparison of gain- and loss-of-function phenotypes.     

Mapping of two suppressors of OVATE (sov) loci in tomato

Tomato fruit shape varies significantly in the cultivated germplasm. To a large extent, this variation can be explained by four genes including OVATE. While most varieties with the OVATE mutation bear elongated fruits, some accessions carry round fruit, suggesting the existence of suppressors of OVATE in the germplasm. We developed three intraspecific F₂ populations with parents that carried the OVATE mutation but differed in fruit shape. We used a bulk segregant analysis approach and genotyped the extreme classes using a high-throughput genotyping platform, the SolCAP Infinium Assay. The analyses revealed segregation at two quantitative trait loci (QTLs), sov1 and sov2. These loci were confirmed by genotyping and QTL analyses of the entire population. More precise location of those loci using progeny testing confirmed that sov1 on chromosome 10 controlled obovoid and elongated shape, whereas sov2 on chromosome 11 controlled mainly elongated fruit shape. Both loci were located in intervals of <2.4 Mb on their respective chromosomes.     

An osmoregulatory basis for shape oscillations in regenerating hydra

The freshwater polyp Hydra has considerable regeneration capabilities. A small fragment of tissue excised from an adult animal is sufficient to regenerate an entire Hydra in the course of a few days. During the initial stages of the regeneration process, the tissue forms a hollow sphere. Then the sphere exhibits shape oscillations in the form of repeated cycles of swelling and collapse. We propose a biophysical model for the swelling mechanism. Our model takes the osmotic pressure difference between Hydra's inner and outer media and the elastic forces of the Hydra shell into account. We validate the model by a comprehensive experimental study including variations in initial medium concentrations, Hydra sphere sizes and temperatures. Numerical simulations of the model provide values for the swelling rates that are in agreement with the ones measured experimentally. Based on our results we argue that the shape oscillations are a consequence of Hydra's osmoregulation.     

Planar polarity and short-range polarization in Drosophila embryos

Planar cell polarity is a common and probably universal feature of epithelial cells throughout their life. It is not only visible in the external parts of adult animals and plants, but also present in newborn cells such as in the primary Drosophila epithelium. It controls not only cell shape and differentiation, but also cell motility, cell shape changes and it directs how animals are shaped. In this review, we report how planar cell polarity arises in Drosophila embryos and thereby illustrate how general and extensive planar polarity is during development, from the very beginning to the end. We present the main features of planar cell polarization in Drosophila embryos, in particular the fact that it occurs over a short range of just a few cell diameters, and within a very short time window. We contrast these with other systems, such as the adult Drosophila wing where planar cell polarity occurs at longer range.     

Exploration into natural variation for genes associated with fruit shape and size among Capsicum chinense collections

Phenotype diversity within cultivated Capsicum chinense is particularly evident for fruit shape and size. We used this diversity in C. chinense to further unravel the genetic mechanisms underlying fruit shape variation in pepper and related Solanaceous species. We identified candidate genes for C. chinense fruit shape, explored their contribution to population structure, and characterized their potential function in pepper fruit shape. Using genotyping by sequencing, we identified 43,081 single nucleotide polymorphisms (SNPs) from diverse collections of C. chinense. Principal component, neighbor-joining tree, and population structure analyses resolved 3 phylogenetically robust clusters associated with fruit shapes. Genome-wide association study (GWAS) was used to identify associated genomic regions with various fruit shape traits obtained from image analysis with Tomato Analyzer software. In our GWAS, we selected 12 SNPs associated with locule number trait and 8 SNP markers associated with other fruit shape traits such as perimeter, area, obovoid, ellipsoid and morphometrics (5y, 6y and 7y). The SNPs in CLAVATA1, WD-40, Auxin receptor, AAA type ATPase family protein, and RNA polymerase III genes were the major markers identified for fruit locule number from our GWAS results. Furthermore, we found SNPs in tetratricopeptide-repeat thioredoxin-like 3, enhancer of ABA co-receptor 1, subunit of exocyst complex 8 and pleiotropic drug resistance proteins associated with various fruit shape traits. CLAVATA1, WD-40 and Auxin receptor genes are known genes that affect tomato fruit shape. In this study, we used Arabidopsis thaliana T-DNA insertion knockout mutants and expression profiles for functional characterization of newly identified genes and to understand their role in fruit shape.     

Geometric shape as a trait to study phytoplankton distributions in aquatic ecosystems

The geometric shape is traditionally used to calculate phytoplankton cell measurements (e.g. biovolume), but it can also play an important role in determining community distributions. Little is known about how geometric shapes relate to other morphological traits or to the environment. We explored whether shapes and related morphological traits are selected by environmental forcing. For this, samples were collected seasonally at 21 stations in coastal-marine waters of the Salento Peninsula (Italy). Phytoplankton taxa were classified in terms of geometric shape, biovolume (organism size) and surface-to-volume ratio (S:V). The relationship between greatest axial linear dimension (GALD) and S:V was assessed for each shape. A Canonical Correspondence Analysis (CCA) was performed to evaluate phytoplankton shape distribution on temporal and spatial scales. Phytoplankton community was characterized by high morphological diversity. GALD and S:V were inversely related in most of the shapes. CCA showed that phytoplankton shape distribution was influenced more by seasonal than by spatial variation: elongated shapes characterized the cold period; rounded and combined shapes the warmer period. Most of the shapes showed conservatism of the S:V and trade-off with the size. Geometric shapes represent an interesting feature to be considered in trait-based approaches to study phytoplankton distributions in aquatic ecosystems.     

A Novel System of Cytoskeletal Elements in the Human Pathogen Helicobacter pylori

Pathogenicity of the human pathogen Helicobacter pylori relies upon its capacity to adapt to a hostile environment and to escape from the host response. Therefore, cell shape, motility, and pH homeostasis of these bacteria are specifically adapted to the gastric mucus. We have found that the helical shape of H. pylori depends on coiled coil rich proteins (Ccrp), which form extended filamentous structures in vitro and in vivo, and are differentially required for the maintenance of cell morphology. We have developed an in vivo localization system for this pathogen. Consistent with a cytoskeleton-like structure, Ccrp proteins localized in a regular punctuate and static pattern within H. pylori cells. Ccrp genes show a high degree of sequence variation, which could be the reason for the morphological diversity between H. pylori strains. In contrast to other bacteria, the actin-like MreB protein is dispensable for viability in H. pylori, and does not affect cell shape, but cell length and chromosome segregation. In addition, mreB mutant cells displayed significantly reduced urease activity, and thus compromise a major pathogenicity factor of H. pylori. Our findings reveal that Ccrp proteins, but not MreB, affect cell morphology, while both cytoskeletal components affect the development of pathogenicity factors and/or cell cycle progression.     

Plasticity of epithelial cell shape in response to upstream signals: A whole-organism study using transgenic Hydra

Multicellular organisms consist of a variety of cells of distinctive morphology, with the cell shapes often reproduced with astonishing accuracy between individuals and across species. The morphology of cells varies with tissues, and cell shape changes are of profound importance in many occasions of morphogenesis. To elucidate the mechanisms of cell shape determination and regulation is therefore an important issue. One of the simplest multicellular organisms is the freshwater polyp Hydra. Although much is known about patterning in this early branching metazoan, there is currently little understanding of how cells in Hydra regulate their shape in response to upstream signals. We previously reported generation of transgenic Hydra to trace cells and to study cell behavior in vivo in an animal at the basis of animal evolution. Here, we use a novel transgenic line which expresses enhanced green fluorescent protein (eGFP) specifically in the ectodermal epithelial cells to analyze the structure and shape of epithelial cells as they are recruited into specific regions along the body column and respond to upstream signals such as components of the canonical Wnt signaling pathway. As a general theme, in contrast to epithelial cells in more complex animals, ectodermal epithelial cells in Hydra are capable of drastic changes in structure, shape, and cell contact along the body column. The remarkable phenotypic plasticity of epithelial cells in response to positional signals allows Hydra to build its body with only a limited number of different cell types.     

The Rap GTPase activator Drosophila PDZ-GEF regulates cell shape in epithelial migration and morphogenesis

Epithelial morphogenesis is characterized by an exquisite control of cell shape and position. Progression through dorsal closure in Drosophila gastrulation depends on the ability of Rap1 GTPase to signal through the adherens junctional multidomain protein Canoe. Here, we provide genetic evidence that epithelial Rap activation and Canoe effector usage are conferred by the Drosophila PDZ-GEF (dPDZ-GEF) exchange factor. We demonstrate that dPDZ-GEF/Rap/Canoe signaling modulates cell shape and apicolateral cell constriction in embryonic and wing disc epithelia. In dPDZ-GEF mutant embryos with strong dorsal closure defects, cells in the lateral ectoderm fail to properly elongate. Postembryonic dPDZ-GEF mutant cells generated in mosaic tissue display a striking extension of lateral cell perimeters in the proximity of junctional complexes, suggesting a loss of normal cell contractility. Furthermore, our data indicate that dPDZ-GEF signaling is linked to myosin II function. Both dPDZ-GEF and cno show strong genetic interactions with the myosin II-encoding gene, and myosin II distribution is severely perturbed in epithelia of both mutants. These findings provide the first insight into the molecular machinery targeted by Rap signaling to modulate epithelial plasticity. We propose that dPDZ-GEF-dependent signaling functions as a rheostat linking Rap activity to the regulation of cell shape in epithelial morphogenesis at different developmental stages.     

A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature

Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and Drosophila yakuba. We designed a semi‐automatic measurement machine learning pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches in D. yakuba but that in D. santomea ventral branches tend to morph into a D. yakuba‐like shape at lower temperature. We found that male genitalia structures involved in reproductive isolation can be relatively variable within one species and can resemble the shape of closely related species’ genitalia through plasticity to temperature. Our results suggest that reproductive isolation mechanisms can be dependent on the environmental context.     

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes—PRDM16, PAX3, TP63, C5orf50, and COL17A1—in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facial features. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facial morphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications.