Evolution and development of shape: integrating quantitative approaches

Multimodal in vivo Imaging of the Integrated Postnatal Development of Brain and Skull and Its Co-modulation With Neurodevelopment in a Down Syndrome Mouse Model

The brain and skeletal systems are intimately integrated during development through common molecular pathways. This is evidenced by genetic disorders where brain and skull dysmorphologies are associated. However, the mechanisms underlying neural and skeletal interactions are poorly understood. Using the Ts65Dn mouse model of Down syndrome (DS) as a case example, we performed the first longitudinal assessment of brain, skull and neurobehavioral development to determine alterations in the coordinated morphogenesis of brain and skull. We optimized a multimodal protocol combining in vivo micro-computed tomography (μCT) and magnetic resonance imaging (μMRI) with morphometric analyses and neurodevelopmental tests to longitudinally monitor the different systems' development trajectories during the first postnatal weeks. We also explored the impact of a perinatal treatment with green tea extracts enriched in epigallocatechin-3-gallate (GTE-EGCG), which can modulate cognition, brain and craniofacial development in DS. Our analyses quantified alterations associated with DS, with skull dysmorphologies appearing before brain anomalies, reduced integration and delayed acquisition of neurodevelopmental traits. Perinatal GTE-EGCG induced disparate effects and disrupted the magnitude of integration and covariation patterns between brain and skull. Our results exemplify how a longitudinal research approach evaluating the development of multiple systems can reveal the effect of morphological integration modulating the response of pathological phenotypes to treatment, furthering our understanding of complex genetic disorders.

Infirm effect of phylogeny on morphometric features in a cryptic Gobio species complex

Several recent notes prove that taxonomic relations of close relative animal groups (species complexes or cryptic species) can be revealed by the combined use of genetic and morphologic methodologies. At the same time scarce information can be found about how phylogeny, population origin, and sexual dimorphism affect the morphometric features of these species. In our present work, we performed simultaneous phylogenetic and morphological studies on the taxonomically still questionable Carpathian stream dwelling gudgeons (Cyprinidae, Gobio) by using two different methodologies (distance based and geometric morphometry). Our results were in correspondence with the previous findings, showing the presence of three phylogenetically more or less distinct groups in the area. The results of the whole-body geometric and the traditional, distance-based morphometry reflected the extent of phylogenetic differences. While the results of geometric scale morphometry did not correspond with the genetic subdivisions. Results of three way PERMANOVA analyses showed that the phylogenetic effects on morphometry is less considerable as the population origin or the sexual dimorphism at these cyprinid taxa. Our investigation contributed to the better understanding of the taxonomy of fish stocks in the Carpathian Basin, and to their conservation, but additional investigations will be needed to clarify the exact taxonomic position of the gudgeons (’Gobio sp1’) dominating the eastern part of the studied drainage.

Unraveling the heritage of lost traits

We synthesize ontogenetic work spanning the past century that show evolutionarily lost structures are rarely entirely absent from earlier developmental stages. We discuss morphological and genetic insights from developmental studies reveal about the evolution of trait loss and regain.

Functional random forests for curve response

The rapid advancement of functional data in various application fields has increased the demand for advanced statistical approaches that can incorporate complex structures and nonlinear associations. In this article, we propose a novel functional random forests (FunFor) approach to model the functional data response that is densely and regularly measured, as an extension of the landmark work of Breiman, who introduced traditional random forests for a univariate response. The FunFor approach is able to predict curve responses for new observations and selects important variables from a large set of scalar predictors. The FunFor approach inherits the efficiency of the traditional random forest approach in detecting complex relationships, including nonlinear and high-order interactions. Additionally, it is a non-parametric approach without the imposition of parametric and distributional assumptions. Eight simulation settings and one real-data analysis consistently demonstrate the excellent performance of the FunFor approach in various scenarios. In particular, FunFor successfully ranks the true predictors as the most important variables, while achieving the most robust variable sections and the smallest prediction errors when comparing it with three other relevant approaches. Although motivated by a biological leaf shape data analysis, the proposed FunFor approach has great potential to be widely applied in various fields due to its minimal requirement on tuning parameters and its distribution-free and model-free nature. An R package named 'FunFor', implementing the FunFor approach, is available at GitHub.

Three-Dimensional Geometric Morphometry of Facial Soft Tissue Changes After Bilateral Sagittal Split Ramus Osteotomy

ABSTRACT

This study aimed to evaluate the performance of geometric morphometry (GM) to assess the changes in facial soft tissue after orthognathic surgery. Subjects were 27 patients (skeletal class III) who underwent bilateral sagittal split ramus osteotomy and 27 volunteers as a control group. Computed tomography images of each patient were obtained before surgery (T0) and 6 months after surgery (T1). Computed tomography images of 27 volunteers (skeletal class I) were also obtained as a control group. Using a three-dimensional (3D) modeling software, 3D models were created and exported to a 3D surface analyzing software for geometric morphometry and principal component (PC) analysis. Significant differences in facial soft tissue were found in the first and second of 15 PC. The first PC represented variation in the lower facial height, and the second PC represented variation in the anterior-posterior position of the chin. Comparing the pre- and post-operative images, they illustrated that lower facial height was decreased, and the chin and lower lip moved posteriorly. Geometric morphometry showed to be a successful tool to isolate surgery-related changes from interindividual morphological variations.

Medfly Phenotypic Plasticity as A Prerequisite for Invasiveness and Adaptation

The hypothesis of this study was that different plant hosts of the medfly Ceratitis capitata may cause variability as a prerequisite for its invasiveness. The main objective was to determine population variability based on medfly wing shape in three favorable medfly host plants (peach, fig and mandarin) from different agroecological growing areas with different pest management practices, and to evaluate phenotypic plasticity as a basis for future expansion into new areas and new hosts. Using geometric morphometric methods across 14 specific landmarks on the medfly wings, 10 populations were tested from infested peach, fig and mandarin fruits, as well as laboratory-grown sterile populations. The studies led to the following main findings: (1) all of the medfly populations that were studied exhibited sexual dimorphism in wing shape; (2) the hosts in which the medfly develops influence wing shape and condition its variability; (3) there is significant variability between laboratory mass-reared sterile and wild individuals in male and female populations; (4) a high phenotypic plasticity of medfly populations was observed along the study sites. Even the low but clearly detected variability between different agroecological conditions and localized variability indicate genotypic stability and high phenotypic plasticity, which can be considered as a prerequisite for medfly invasiveness and dispersal to new areas.

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes

Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

On Information Rank Deficiency in Phenotypic Covariance Matrices

This paper investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory, then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definitions of matrix rank, of which we define three: the full matrix rank (equal to the number of input variables), the mathematical rank (the number of non-zero eigenvalues), and the information rank or 'effective rank' (equal to the number of non-redundant eigenvalues). We demonstrate that effective rank deficiency arises from a combination of methodological factors - Generalized Procrustes analysis, use of the correlation matrix, and insufficient sample size - as well as phenotypic covariance. Secondly, we use dire wolf jaws to document how differences in effective rank deficiency bias two metrics used to measure phenotypic integration. The eigenvalue variance characterizes the integration change incorrectly, and the standardized generalized variance lacks the sensitivity needed to detect subtle changes in integration. Both metrics are impacted by the inclusion of many small, but non-zero, eigenvalues arising from a lack of information in the covariance matrix, a problem that usually becomes more pronounced as the number of landmarks increases. We propose a new metric for phenotypic integration that combines the standardized generalized variance with information entropy. This metric is equivalent to the standardized generalized variance, but calculated only from those eigenvalues that carry non-redundant information. It is the standardized generalized variance scaled to the effective rank of the eigenvalue spectrum. We demonstrate that this metric successfully detects the shift of integration in our dire wolf sample. Our third goal is to generalize the new metric to compare data sets with different sample sizes and numbers of variables. We develop a standardization for matrix information based on data permutation, then demonstrate that Smilodon jaws are more integrated than dire wolf jaws. Finally, we describe how our information entropy-based measure allows phenotypic integration to be compared in dense semilandmark data sets without bias, allowing characterization of the information content of any given shape, a quantity we term 'latent dispersion'.

Morphological integration of the head capsule in the millipede Megaphyllum unilineatum (C. L. Koch, 1838) (Diplopoda: Julida): can different modules be recognized?

Covariation of multiple morphological traits and modularity have been widely studied in the field of evolutionary developmental biology. Subunits of a morphological structure can evolve separately from each other in a modular fashion. The aims of our study therefore were: i) to test the hypothesis of modularity in the dorsal part of the head capsule and the gnathochilarium separately during late postembryogenesis in the julidan millipede Megaphyllum unilineatum (C. L. Koch, 1838) using geometric morphometrics; and ii) to investigate the influence of allometry on overall morphological integration in the dorsal part of the head capsule and the gnathochilarium in the mentioned species. Individuals from different ontogenetic stadia (stadium VI - stadium XI) were included in the analyses. Significant influence of fluctuating asymmetry on the dorsal part of the head capsule shape was detected by Procrustes ANOVA. Regressions were significant for the symmetric component of both analysed morphological traits, while non-significant regression was detected for the asymmetric component of the head capsule's dorsal part. Hypotheses of modularity for the dorsal part of the head capsule and the gnathochilarium are rejected because our results indicate that a small proportion of alternate partitions has higher covariation between subsets of structure than between the hypothesized modules. Contrary to our expectations, results of the present study show that allometry does not increase the level of morphological integration in the dorsal part of the head capsule and the gnathochilarium in M. unilineatum. Based on the obtained results, we conclude that the dorsal part of the head capsule and the gnathochilarium are not composed of independent modules and that in the case of the capsule's dorsal part, developmental processes affect morphological integration in different ways at different levels of shape variation.

The influence of divergent reproductive strategies in shaping modularity and morphological evolution in mammalian jaws

Marsupial neonates are born at an earlier developmental stage than placental mammals, but the rapid development of their forelimbs and cranial skeleton allows them to climb to the pouch, begin suckling and complete their development ex utero. The mechanical environment in which marsupial neonates develop is vastly different from that of placental neonates, which exhibit a more protracted development of oral muscles and bones. This difference in reproductive strategy has been theorized to constrain morphological evolution in the oral region of marsupials. Here, we use 3D morphometrics to characterize one of these oral bones, the lower jaw (dentary), and assess modularity (pattern of covariation among traits), morphological disparity and rates of morphological evolution in two clades of carnivorous mammals: the marsupial Dasyuromorphia and placental fissiped Carnivora. We find that dasyuromorph dentaries have fewer modules than carnivorans and exhibit tight covariation between the angular and coronoid processes, the primary attachment sites for jaw-closing muscles. This pattern of modularity may result from the uniform action of muscles on the developing mandible during suckling. Carnivorans are free from this constraint and exhibit a pattern of modularity that more strongly reflects genetic and developmental signals of trait covariation. Alongside differences in modularity, carnivorans exhibit greater disparity and faster rates of morphological evolution compared with dasyuromorphs. Taken together, this suggests dasyuromorphs have retained a signal of trait covariation that reflects the outsized influence of muscular force during early development, a feature that may have impacted the ability of marsupial carnivores to explore specialized regions of morphospace.

Evidence for selectively constrained 3D flower shape evolution in a Late Miocene clade of Malagasy Bulbophyllum orchids

Questions concerning the evolution of complex biological structures are central to the field of evolutionary biology. Yet, still little information is known about the modes and temporal dynamics of three-dimensional (3D) flower shape evolution across the history of clades. Here, we combined high-resolution X-ray computed tomography with 3D geometric morphometrics and phylogenetic comparative methods to test models of whole-flower shape evolution in the orchid family, using an early Late Miocene clade (c. 50 spp.) of Malagasy Bulbophyllum as model system. Based on landmark data of 38 species, our high-dimensional model fitting decisively rejects a purely neutral mode of evolution, suggesting instead that flower shapes evolved towards a primary adaptive optimum. Only a small number of recently evolved species/lineages attained alternative shape optima, resulting in an increased rate of phenotypic evolution. Our findings provide evidence of constrained 3D flower shape evolution in a small-sized clade of tropical orchids, resulting in low rates of phenotypic evolution and uncoupled trait-diversification rates. We hypothesise that this deep imprint of evolutionary constraint on highly complex floral structures might reflect long-term (directional and/or stabilizing) selection exerted by the group's main pollinators (flies).

Effect of septal deviation on nasomaxillary shape: A geometric morphometric study

Nasal cavities in their primitive stage communicate with the oral cavity until the 8th week of intrauterine life where the posterior palate initiates its development. Hence, starting from the initial growth phases, a significant connection lays between the nasal structures and the maxillary bone and witnessing key functional roles, among which the respiration. Proper nasal breathing has been proven to be a crucial factor for the maturity of the craniofacial complex, and obstruction of the respiratory airway due to nasal septum deviation can generate clinically significant reduction of the nasal airflow. This situation will imply irreversible repercussions that hinders the harmonious development of the craniofacial complex. In order to understand such potential impacts of septal deviation, our first objective was to materialize the relation between septum deviation, and both nasal cavity and maxillary structures. For the second objective, we used Procrustes analysis to assess the shape variation of these two anatomical regions, the bivariate plots of Principal Components to evaluate their shape space, and a two-block Partial Least Square (PLS) to explore their covariation. We analysed, in this cross-sectional study, 62 posteroanterior cephalometric radiographs of adult subjects from both sexes (23 males, 39 females; mean age 25.3 years) collected from the database of the Department of Orthodontics at Lebanese University. Landmarks were plotted and variables were calculated and divided into nasal septum, nasal cavity and maxillary ones. The sample was further divided into two groups based on septal deviation severity (a septal deviation is considered minor if <6). The results suggested that nasal septum deviation was correlated to reduced nasal cavity area and a reduced maxillary area. Moreover, the comparison of the two groups concluded that the difference between all variables was statistically significant with higher scores in the minor septal deviation group. These findings were corroborated with the shape analysis where the mean centroid size of nasal cavity and that of the maxilla in the group of reduced septal deviation were significantly greater than those of the group with increased angle of deviation. Results of PLS analysis concluded to a strong covariation between nasal septum and nasomaxillary complex. These conclusions support the early septoplasty in growing patients as a solution to redirect the normal course of growth and re-establish a good function of the nasomaxillary complex.

The identification of grain size genes by RapMap reveals directional selection during rice domestication

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

The cichlid oral and pharyngeal jaws are evolutionarily and genetically coupled

Evolutionary constraints may significantly bias phenotypic change, while "breaking" from such constraints can lead to expanded ecological opportunity. Ray-finned fishes have broken functional constraints by developing two jaws (oral-pharyngeal), decoupling prey capture (oral jaw) from processing (pharyngeal jaw). It is hypothesized that the oral and pharyngeal jaws represent independent evolutionary modules and this facilitated diversification in feeding architectures. Here we test this hypothesis in African cichlids. Contrary to our expectation, we find integration between jaws at multiple evolutionary levels. Next, we document integration at the genetic level, and identify a candidate gene, smad7, within a pleiotropic locus for oral and pharyngeal jaw shape that exhibits correlated expression between the two tissues. Collectively, our data show that African cichlid evolutionary success has occurred within the context of a coupled jaw system, an attribute that may be driving adaptive evolution in this iconic group by facilitating rapid shifts between foraging habitats, providing an advantage in a stochastic environment such as the East African Rift-Valley.

Mechanobiology and Adaptive Plasticity Theory as a Potential Confounding Factor in Predicting Musculoskeletal Foot Function

There are many theoretical models that attempt to accurately and consistently link kinematic and kinetic information to musculoskeletal pain and deformity of the foot. Biomechanical theory of the foot lacks a consensual model: clinicians are enticed to draw from numerous paradigms, each having different levels of supportive evidence and contrasting methods of evaluation, in order to engage in clinical deduction and treatment planning. Contriving to find a link between form and function lies at the heart of most of these competing theories and the physical nature of the discipline has prompted an engineering approach. Physics is of great importance in biology and helps us to model the forces that the foot has to deal with in order for it to work effectively. However, the tissues of the body have complex processes that are in place to protect them and they are variable between individuals. Research is uncovering why these differences exist and how these processes are governed. The emerging explanations for adaptability of foot structure and musculoskeletal homeostasis offer new insights into how clinical variation in outcomes and treatment effects might arise. These biological processes underlie how variation in the performance and use of common traits, even within apparently similar subgroups, make anatomical distinction less meaningful and are likely to undermine the justification of a "foot type." Furthermore, mechanobiology introduces a probabilistic element to morphology based on genetic and epigenetic factors.

Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd

The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

Cranial skeletogenesis of one of the largest amphibians, Andrias japonicus, provides insight into ontogenetic adaptations for feeding in salamanders

Skeletal development in salamanders is greatly influenced by their complex life history. Although the relationship between skull development and life history has been investigated in a variety of salamander species, few studies have compared skull development among lineages. Here, we describe the cranial skeletogenesis of the Japanese giant salamander, Andrias japonicus (family Cryptobranchidae), for the first time. To conduct interspecific comparisons, we also describe the cranial skeletogenesis of Hynobius nebulosus (Hynobiidae), Pleurodeles waltl (Salamandridae) and Ambystoma mexicanum (Ambystomatidae). Our comparative analyses reveal interspecific differences in cranial skeletogenesis, particularly in the timing of the onset of ossification, the direction of ossification (e.g. from anterior to posterior) and the ossification pattern of the hyobranchial skeleton. The early onset of jaw ossification, posterior extension of the maxilla and posterolateral inclination of the squamosal in An. japonicus might be adaptations that allow An. japonicus to gulp feed, primarily using the suction force generated by opening the mouth wide, while also supplementing that force by depressing the hyobranchial skeleton. Multivariate regression of skull shape on log10-transformed centroid size revealed that the unique skull shape of adult and subadult An. japonicus forms through hypermorphosis.

A highly conserved ontogenetic limb allometry and its evolutionary significance in the adaptive radiation of Anolis lizards

Diversifications often proceed along highly conserved, evolutionary trajectories. These patterns of covariation arise in ontogeny, which raises the possibility that adaptive morphologies are biased towards trait covariations that resemble growth trajectories. Here, we test this prediction in the diverse clade of Anolis lizards by investigating the covariation of embryonic growth of 13 fore- and hindlimb bones in 15 species, and compare these to the evolutionary covariation of these limb bones across 267 Anolis species. Our results demonstrate that species differences in relative limb length are established already at hatching, and are resulting from both differential growth and differential sizes of cartilaginous anlagen. Multivariate analysis revealed that Antillean Anolis share a common ontogenetic allometry that is characterized by positive allometric growth of the long bones relative to metapodial and phalangeal bones. This major axis of ontogenetic allometry in limb bones deviated from the major axis of evolutionary allometry of the Antillean Anolis and the two clades of mainland Anolis lizards. These results demonstrate that the remarkable diversification of locomotor specialists in Anolis lizards are accessible through changes that are largely independent from ontogenetic growth trajectories, and therefore likely to be the result of modifications that manifest at the earliest stages of limb development.

Evidence of Wing Shape Sexual Dimorphism in Aedes (Stegomyia) albopictus in Mallorca, Spain

The Asian tiger mosquito Aedes albopictus (Skuse, 1894) is a highly invasive species widely distributed on the Spanish Mediterranean coast and the Balearic archipelago. Most studies involving this species in Spain have been focused on surveillance and control methods. However, micro-evolutionary studies for Ae. albopictus in Spain have been traditionally neglected. Morphological diversity could be the result of long-term evolutionary diversification in responses to selective pressures such as temperature, precipitation, food availability, predation, or competition that may influence flight activity, host-seeking, and blood-feeding behavior. Wing geometric morphometric have been used not only to study micro- and macro-evolution in mosquitoes but also in studies of population structuring and sexual dimorphism. Therefore, the main goal of this study was to investigate the wing shape patterns of Ae. albopictus populations to unveil sexual dimorphism that could provide information about their ecology and behavior. Mosquito eggs were collected using oviposition traps at the main campus of the University of the Balearic Islands (Palma de Mallorca, Spain) and reared under laboratory conditions. In order to study wing shape variation patterns in Ae. albopictus males and females, the left wing of each adult mosquito was removed and analyzed based on 18 landmarks. Our results indicated strong levels of sexual dimorphism between Ae. albopictus males and females. Furthermore, according to the cross-validated reclassification test, males were correctly distinguished from females with an accuracy of 84% and females from males 75%. We observed a significant sexual dimorphism in the wing shape patterns of Ae. albopictus when considering different seasonal patterns (spring vs. autumn). Our results suggested that selective pressures may affect males differently to females. Host-seeking, blood-feeding, and oviposition behavior of females may act as a major driver for wing shape sexual dimorphism. These results should be considered for the development of more effective and targeted mosquito control strategies.

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.

Population genetics and geometric morphometrics of the freshwater snail Segmentina nitida reveal cryptic sympatric species of conservation value in Europe

Segmentina nitida Müller 1774 is a rare European freshwater snail of drainage ditches and marshland, which has seen a marked decrease in range (~ 80%) over the last 100 years in the UK. This has been attributed to over-dredging of drainage ditches for land management, conversion of grazing marshes to arable farmland, as well as eutrophication. Segmentina nitida is identified as a priority species in the UK Biodiversity Action Plan (UKBAP) that recommends further research to inform reintroduction and translocation for its conservation. We used nuclear markers (microsatellites and ITS2) and a mitochondrial (COI) marker to investigate population structure in S. nitida individuals sampled from Poland, Germany, Sweden, and the UK to identify differences within and between populations. Data based on 2D landmark-based geometric morphometrics of S. nitida shells was used to determine if phenotypic variation followed genetic differentiation. Two distinct genetic lineages of S. nitida were identified in ITS and COI phylogenies as well as cluster analysis of microsatellite markers, one of these lineages was present in eastern Europe (Poland, Sweden- Lineage 2), and one in western Europe (UK, Germany- Lineage 1), with lineages co-occurring in German populations. No genetic admixture was observed in German populations containing both lineages. These two lineages were also distinct in shape, with lineage 2 individuals having significantly wider shells and taller and wider apertures than those in Lineage 1. ~ 85% of shells assigned to the predicted lineage in a discriminant analysis of Procrustes shape coordinates. We infer that S. nitida includes at least one sympatric cryptic species. We discuss the implications of these findings on the conservation status of S. nitida in the UK and Europe.

Automatic Fruit Morphology Phenome and Genetic Analysis: An Application in the Octoploid Strawberry

Automatizing phenotype measurement will decisively contribute to increase plant breeding efficiency. Among phenotypes, morphological traits are relevant in many fruit breeding programs, as appearance influences consumer preference. Often, these traits are manually or semiautomatically obtained. Yet, fruit morphology evaluation can be enhanced using fully automatized procedures and digital images provide a cost-effective opportunity for this purpose. Here, we present an automatized pipeline for comprehensive phenomic and genetic analysis of morphology traits extracted from internal and external strawberry (Fragaria x ananassa) images. The pipeline segments, classifies, and labels the images and extracts conformation features, including linear (area, perimeter, height, width, circularity, shape descriptor, ratio between height and width) and multivariate (Fourier elliptical components and Generalized Procrustes) statistics. Internal color patterns are obtained using an autoencoder to smooth out the image. In addition, we develop a variational autoencoder to automatically detect the most likely number of underlying shapes. Bayesian modeling is employed to estimate both additive and dominance effects for all traits. As expected, conformational traits are clearly heritable. Interestingly, dominance variance is higher than the additive component for most of the traits. Overall, we show that fruit shape and color can be quickly and automatically evaluated and are moderately heritable. Although we study strawberry images, the algorithm can be applied to other fruits, as shown in the GitHub repository.

Ontogenetic and sexual patterns in the cranial system of the brown rat (Rattus norvegicus Berkenhout, 1769) from Hai'l region, Kingdom of Saudi Arabia

The brown rat, Rattus norvegicus, is a model system in ecological and systematic science, but little is known about its skull morphology and developmental patterns. Our objective was to investigate the cranial ontogenetic patterns in the brown rats, from Hai'l, Kingdom of Saudi Arabia. Quantitative analysis of sexual shape dimorphisms (SShD) and age-classes were investigated using 28 landmarks plotted on two-dimensional images for dorsal and ventral views. Our results detected statistically significant sexual dimorphism (P-value <0.0001) in cranial shape and size for R. norvegicus. Nevertheless, males are much larger than females and display variation around the brain-case, while females tend to show greater variation around the occipital bone. In addition, there are subtle age-classes during ontogeny in the skull. However, the older age classes (i.e. age classes 3 and 4) represent well-built crania with an extended case of the brain and shortest nasal, while youngest specimens represent an elongated snout of minimum crania. Future GMM research should therefore examine the pre-defined age-classes and sex-related individuals in brown rat skulls in relation to genotype to characterize trends in skull shape variation that may affect teeth, zygomatic arches, brain case, and compartments of muscle attachments through its ecological patterns.

Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

Background

The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks.

Results

We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus.

Conclusion

This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01787-9.

WingBank: A Wing Image Database of Mosquitoes

Mosquito-borne diseases affect millions of people and cause thousands of deaths yearly. Vaccines have been hitherto insufficient to mitigate them, which makes mosquito control the most viable approach. But vector control depends on correct species identification and geographical assignment, and the taxonomic characters of mosquitoes are often inconspicuous to non-taxonomists, which are restricted to a life stage and/or even damaged. Thus, geometric morphometry, a low cost and precise technique that has proven to be efficient for identifying subtle morphological dissimilarities, may contribute to the resolution of these types of problems. We have been applying this technique for more than 10 years and have accumulated thousands of wing images with their metadata. Therefore, the aims of this work were to develop a prototype of a platform for the storage of biological data related to wing morphometry, by means of a relational database and a web system named “WingBank.” In order to build the WingBank prototype, a multidisciplinary team performed a gathering of requirements, modeled and designed the relational database, and implemented a web platform. WingBank was designed to enforce data completeness, to ease data query, to leverage meta-studies, and to support applications of automatic identification of mosquitoes. Currently, the database of the WingBank contains data referring to 77 species belonging to 15 genera of Culicidae. From the 13,287 wing records currently cataloged in the database, 2,138 were already made available for use by third parties. As far as we know, this is the largest database of Culicidae wings of the world.

Developmental plasticity reveals hidden fish phenotypes and enables morphospace diversification

The establishment of a given phenotype is only one expression from a range of hidden developmental possibilities. Developmental plasticity at hidden reaction norms might elicit phenotypic diversification under new developmental environments. Current discussion benefits from empirical analyses that integrate multiple environmental stimuli to evaluate how plastic responses may shape phenotypic variation. We raised Megaleporinus macrocephalus fish in different environmental settings to address contributions of developmental plasticity for emergence of new phenotypes and subsequent morphospace diversification. Plastic morphotypes were evaluated at two complementary scales, the M. macrocephalus morphospace and the higher taxonomic level of Anostomidae family. Morphospace analyses demonstrated that developmental plasticity quickly releases distinct head morphotypes that were hidden in the parental monomorphic population. Plastic morphotypes occupied discrete and previously unfilled morphospace regions, a result obtained from comparisons with a control population and in analyses including several Anostomidae species. Plastic responses involved adjustments in shape and relative position of head bonesets, and fish raised under specific environmental combinations rescued phenotypic patterns described for different genera. Therefore, developmental plasticity possibly contributes to adaptive radiation in Anostomidae. Results illustrate how plastic responses enable morphospace diversification and contribute to evolution.

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

Simple Summary

The seed beetle Acanthoscelides obtectus used in this study is a worldwide pest species that inhabits storage facilities and fields of beans. Knowing that sexual dimorphism is very common among insects, we investigated the level of morphological differences between the sexes. Such an approach allowed us to look into the modular organization of this organism. As expected, the females were larger than the males. The observed two modular organization (thorax and abdomen) was sex specific, indicating that reproductive function has the central role in forming the patterns of modularity. It seems that natural selection is driving force for females, while males are influenced more by sexual selection.

Abstract

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

Ontogeny of cranial base during the first two years of life

The integration of the growth of the brain and the cranial base suggests that each system may influence the other, notably during the first three years of life, although this influence has never been proven to be exclusive. The aim of our work was to analyse the dynamics of normal growth on the one hand, and the development and ontogenetic allometry of the cranial base in the infant on the other hand.

MATERIAL AND METHOD

A total of 32 infants (17 males/15 femeles) having been included in the unexpected infant death french protocol were analyzed. Three-dimensional reconstructions of the cranial base were performed from CT scans. The technique combined manual segmentation of regions of interest, contour extraction and surface reconstruction. Nineteen landmarks were positioned on each of the bone surfaces.

RESULTS

No correlation was observed between sex assigned at birth and shape, weight, crown-heel length, or head circumference. Principal component analysis showed that 85.5% of the variance observed on the first component was secondary to growth. After Procrustes superimposition, 25% of the shape variance observed was explained by the first principal component. It showed anteroposterior lengthening of the cranial base. In addition, the height, width and length of the posterior fossa increased and the relative position of the basion was displaced inferiorly and anteriorly with flexion of the sphenoid angle. Negative allometry was also observed.

CONCLUSION

Our study, carried out in a rigorously selected population of infants, presents a fundamental approach to ontogeny through study of shape, growth and ontogenetic allometry.

Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?

Pathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr Salvelinus namaycush ecotypes in Rush Lake, USA. A rapid phenotypic shift in body and head shape was found within a decade. The magnitude and direction of the observed phenotypic change were consistent in both ecotypes, which suggests similar pathways caused the variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early-stage (ages 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing changes in growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.

Constraints associated with captivity alter craniomandibular integration in wild boar

The domestication process is associated with substantial phenotypic changes through time. However, although morphological integration between biological structures is purported to have a major influence on the evolution of new morphologies, little attention has been paid to the influence of domestication on the magnitude of integration. Here, we assessed the influence of constraints associated with captivity, considered as one of the crucial first steps in the domestication process, on the integration of cranial and mandibular structures. We investigated the craniomandibular integration in Western European Sus scrofa using three-dimensional (3D) landmark-based geometric morphometrics. Our results suggest that captivity is associated with a lower level of integration between the cranium and the mandible. Plastic responses to captivity can thus affect the magnitude of integration of key functional structures. These findings underline the critical need to develop integration studies in the context of animal domestication to better understand the processes accountable for the set-up of domestic phenotypes through time.

Ontogenetic allometry and scaling in catarrhine crania

In studies of ontogenetic allometry, ontogenetic scaling has often been invoked to explain cranial morphological differences between smaller and larger forms of closely related taxa. These scaled variants in shape have been hypothesized to be the result of the extension or truncation of common growth allometries. In this scenario, change in size is the determining factor, perhaps under direct selection, and changes in cranial shapes are byproducts, not under direct selection themselves. However, many of these conclusions are based on studies that used bivariate generalizations of shape. Even among multivariate analyses of growth allometries, there are discrepancies as to the prevalence of ontogenetic scaling among primates, how shared the trajectories need to be, and which taxa evince properties of scaled variants. In this investigation, we use a large, comparative ontogenetic sample, geometric morphometric methods, and multivariate statistical tests to examine ontogenetic allometry and evaluate if differences in cranial shape among closely related catarrhines of varying sizes are primarily driven by size divergence, that is, ontogenetic scaling. We then evaluate the hypothesis of size as a line of least evolutionary resistance in catarrhine cranial evolution. We found that patterns of ontogenetic allometry vary among taxa, indicating that ontogenetic scaling sensu stricto does not often account for most morphological differences and that large and small taxa within clades are generally not scaled variants. The presence of a variety of ontogenetic pathways for the evolution of cranial shapes provides indirect evidence for selection acting directly on the cranial shape, rather than on size alone.

Anatomical comparison across heads, fore- and hindlimbs in mammals using network models

Animal body parts evolve with variable degrees of integration that nonetheless yield functional adult phenotypes: but, how? The analysis of modularity with Anatomical Network Analysis (AnNA) is used to quantitatively determine phenotypic modules based on the physical connection among anatomical elements, an approach that is valuable to understand developmental and evolutionary constraints. We created anatomical network models of the head, forelimb, and hindlimb of two taxa considered to represent a 'generalized' eutherian (placental: mouse) and metatherian (marsupial: opossum) anatomical configuration and compared them with our species, which has a derived eutherian configuration. In these models, nodes represent anatomical units and links represent their physical connection. Here, we aimed to identify: (1) the commonalities and differences in modularity between species, (2) whether modules present a potential phylogenetic character, and (3) whether modules preferentially reflect either developmental or functional aspects of anatomy, or a mix of both. We predicted differences between networks of metatherian and eutherian mammals that would best be explained by functional constraints, versus by constraints of development and/or phylogeny. The topology of contacts between bones, muscles, and bones + muscles showed that, among all three species, skeletal networks were more similar than musculoskeletal networks. There was no clear indication that humans and mice are more alike when compared to the opossum overall, even though their musculoskeletal and skeletal networks of fore- and hindlimbs are slightly more similar. Differences were greatest among musculoskeletal networks of heads and next of forelimbs, which showed more variation than hindlimbs, supporting previous anatomical studies indicating that in general the configuration of the hindlimbs changes less across evolutionary history. Most observations regarding the anatomical networks seem to be best explained by function, but an exception is the adult opossum ear ossicles. These ear bones might form an independent module because the incus and malleus are involved in forming a functional primary jaw that enables the neonate to attach to the teat, where this newborn will complete its development. Additionally, the human data show a specialized digit 1 module (thumb/big toe) in both limb types, likely the result of functional and evolutionary pressures, as our ape ancestors had highly movable big toes and thumbs.

Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales

Phylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these “constructional details” are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the relative extent of bones independently of differences in overall shape. We also show how to decompose total shape variation into small-scale and large-scale shape variation. We apply both methods to the midsagittal cranial morphology of papionin monkeys, which are well known for the discrepancy between morphological similarities and phylogenetic relationships. We study phylogenetic signal and functional adaptation using a molecular phylogeny and contextual data on feeding ecology and locomotor behavior. As expected, total cranial shape, bone outline shape, and large-scale shape features were only weakly associated with phylogenetic distance. But the relative bone contributions and small-scale shape features were both highly correlated with phylogenetic distances. By contrast, the association with ecological and behavioral variables was strongest for the outline shape and large-scale shape features. Studies of morphological adaptation and phylogenetic history thus profit from a decomposition of shape variation into different spatial scales. [Adaptation; canalization; cranial shape; geometric morphometrics; papionini; partial warps; phylogeny.]

Size and shape regulation during larval growth in the lepidopteran Pieris brassicae

By adopting a longitudinal study design and through geometric morphometrics methods, we investigated size and shape regulation in the head capsule during the larval development of the cabbage butterfly Pieris brassicae under laboratory conditions. We found evidence of size regulation by compensatory growth, although not equally effective in all larval stages. Size compensation is not attained through the regulation of developmental timing, but rather through the modulation of per-time growth rate. As for the shape, neither the variance of the symmetric component of shape, nor the level of fluctuating asymmetry show any evidence of increase across stages, either at the population or individual level, which is interpreted as a mark of ontogenetic shape regulation. In addition, also the geometry of individual asymmetry is basically conserved across stages. While providing specific documentation on the ontogeny of size and shape variation in this insect, this study may contribute to a more general understanding of developmental regulation and its influence on phenotypic evolution.

Does divergence from normal patterns of integration increase as chromosomal fusions increase in number? A test on a house mouse hybrid zone

Chromosomal evolution is widely considered an important driver of speciation because it can promote the establishment of reproductive barriers. Karyotypic reorganization is also expected to affect the mean phenotype, as well as its development and patterns of phenotypic integration, through processes such as variation in genetic linkage between quantitative trait loci or between regulatory regions and their targets. Here we explore the relationship between chromosomal evolution and phenotypic integration by analyzing a well-known house mouse parapatric contact zone between a highly derived Robertsonian (Rb) race (2n = 22) and populations with standard karyotype (2n = 40). Populations with hybrid karyotypes are scattered throughout the hybrid zone connecting the two parental races. Using mandible shape data and geometric morphometrics, we test the hypothesis that patterns of integration progressively diverge from the “normal” integration pattern observed in the standard race as they accumulate Rb fusions. We find that the main pattern of integration observed between the posterior and anterior part of the mandible can be largely attributed to allometry. We find no support for a gradual increase in divergence from normal patterns of integration as fusions accumulate. Surprisingly, however, we find that the derived Rb race (2n = 22) has a distinct allometric trajectory compared with the standard race. Our results suggest that either individual fusions disproportionately affect patterns of integration or that there are mechanisms which “purge” extreme variants in hybrids (e.g. reduced fitness of hybrid shape).

Effects of Reduced Connexin43 Function on Mandibular Morphology and Osteogenesis in Mutant Mouse Models of Oculodentodigital Dysplasia

Mutations in the gene encoding the gap-junctional protein connexin43 (Cx43) are the cause of the human disease oculodentodigital dysplasia (ODDD). The mandible is often affected in this disease, with clinical reports describing both mandibular overgrowth and conversely, retrognathia. These seemingly opposing observations underscore our relative lack of understanding of how ODDD affects mandibular morphology. Using two mutant mouse models that mimic the ODDD phenotype (I130T/+ and G60S/+), we sought to uncover how altered Cx43 function may affect mandibular development. Specifically, mandibles of newborn mice were imaged using micro-CT, to enable statistical comparisons of shape. Tissue-level comparisons of key regions of the mandible were conducted using histomorphology, and we quantified the mRNA expression of several cartilage and bone cell differentiation markers. Both G60S/+ and I130T/+ mutant mice had altered mandibular morphology compared to their wildtype counterparts, and the morphological effects were similarly localized for both mutants. Specifically, the biggest phenotypic differences in mutant mice were focused in regions exposed to mechanical forces, such as alveolar bone, muscular attachment sites, and articular surfaces. Histological analyses revealed differences in ossification of the intramembranous bone of the mandibles of both mutant mice compared to their wildtype littermates. However, chondrocyte organization within the secondary cartilages of the mandible was unaffected in the mutant mice. Overall, our results suggest that the morphological differences seen in G60S/+ and I130T/+ mouse mandibles are due to delayed ossification and suggest that mechanical forces may exacerbate the effects of ODDD on the skeleton.

Phenotypic integration in feliform carnivores: Covariation patterns and disparity in hypercarnivores versus generalists

The skeleton is a complex arrangement of anatomical structures that covary to various degrees depending on both intrinsic and extrinsic factors. Among the Feliformia, many species are characterized by predator lifestyles providing a unique opportunity to investigate the impact of highly specialized hypercarnivorous diet on phenotypic integration and shape diversity. To do so, we compared the shape of the skull, mandible, humerus, and femur of species in relation to their feeding strategies (hypercarnivorous vs. generalist species) and prey preference (predators of small vs. large prey) using three-dimensional geometric morphometric techniques. Our results highlight different degrees of morphological integration in the Feliformia depending on the functional implication of the anatomical structure, with an overall higher covariation of structures in hypercarnivorous species. The skull and the forelimb are not integrated in generalist species, whereas they are integrated in hypercarnivores. These results can potentially be explained by the different feeding strategies of these species. Contrary to our expectations, hypercarnivores display a higher disparity for the skull than generalist species. This is probably due to the fact that a specialization toward high-meat diet could be achieved through various phenotypes. Finally, humeri and femora display shape variations depending on relative prey size preference. Large species feeding on large prey tend to have robust long bones due to higher biomechanical constraints.

Morphometric analysis of the palatal shape and arch dimension in subjects with buccally displaced canine

OBJECTIVES

To analyse morphological variations of the palate shape and maxillary arch dimension between a group of subjects with unilaterally or bilaterally buccally impacted maxillary canines and a control group (CG) by means of 3D geometric morphometric (GMM).

MATERIALS

Pre-treatment records of 50 subjects (16 males and 34 females; mean age 13.9 years ± 1.8) with one or both canines buccally displaced were collected retrospectively. A CG of 50 subjects was selected from a list of orthodontic patients at the same dental hospital. The experimental group, buccally displaced canine (BDC) was divided in two groups: unilateral buccally displaced canine (UBDC) and bilateral buccally displaced canine (BBDC). To analyse the palate's shape and maxillary arch dimension, study casts were scanned. To study the entirety of the palatal shape, 3D GMM analysis was used. To analyse the maxillary arch dimension, the virtual three-dimensional models were measured with a specific software (VAM, Vectra, Canfield Scientific, Fairfield, New Jersey, USA).

RESULTS

When comparing the groups with the GMM analysis, patients with BDC showed a statistically significant narrower and higher palatal vault. About the analysis of linear measurements, the intercanine width, the anterior and posterior segment length were significantly smaller in BDC, UBDC, and BBDC subjects when compared with the controls and there were no differences between UBDC versus BBDC groups.

CONCLUSIONS

Patients with buccally displaced permanent canine tended to have maxillary transverse constriction and variation in palatal vault morphology. The morphometric variation of the palatine vault and arch dimensions can be considered a clinical factor associated with the presence of BDC.

Allometric Biomass Models for European Beech and Silver Fir: Testing Approaches to Minimize the Demand for Site-Specific Biomass Observations

In this paper, site-specific allometric biomass models were developed for European beech (Fagus sylvatica L.) and silver fir (Abies alba Mill.) to estimate the aboveground biomass in Șinca virgin forest, Romania. Several approaches to minimize the demand for site-specific observations in allometric biomass model development were also investigated. Developing site-specific allometric biomass models requires new measurements of biomass for a sample of trees from that specific site. Yet, measuring biomass is laborious, time consuming, and requires extensive logistics, especially for very large trees. The allometric biomass models were developed for a wide range of diameters at breast height, D (6–86 cm for European beech and 6–93 cm for silver fir) using a logarithmic transformation approach. Two alternative approaches were applied, i.e., random intercept model (RIM) and a Bayesian model with strong informative priors, to enhance the information of the site-specific sample (of biomass observations) by supplementing with a generic biomass sample. The appropriateness of each model was evaluated based on the aboveground biomass prediction of a 1 ha sample plot in Șinca forest. The results showed that models based on both D and tree height (H) to predict tree aboveground biomass (AGB) were more accurate predictors of AGB and produced plot-level estimates with better precision, than models based on D only. Furthermore, both RIM and Bayesian approach performed similarly well when a small local sample (of seven smallest trees) was used to calibrate the allometric model. Therefore, the generic biomass observations may effectively be combined with a small local sample (of just a few small trees) to calibrate an allometric model to a certain site and to minimize the demand for site-specific biomass measurements. However, special attention should be given to the H-D ratio, since it can affect the allometry and the performance of the reduced local sample approach.

The development of body and organ shape

Background

Organisms show an incredibly diverse array of body and organ shapes that are both unique to their taxon and important for adapting to their environment. Achieving these specific shapes involves coordinating the many processes that transform single cells into complex organs, and regulating their growth so that they can function within a fully-formed body.

Main text

Conceptually, body and organ shape can be separated in two categories, although in practice these categories need not be mutually exclusive. Body shape results from the extent to which organs, or parts of organs, grow relative to each other. The patterns of relative organ size are characterized using allometry. Organ shape, on the other hand, is defined as the geometric features of an organ’s component parts excluding its size. Characterization of organ shape is frequently described by the relative position of homologous features, known as landmarks, distributed throughout the organ. These descriptions fall into the domain of geometric morphometrics.

Conclusion

In this review, we discuss the methods of characterizing body and organ shape, the developmental programs thought to underlie each, highlight when and how the mechanisms regulating body and organ shape might overlap, and provide our perspective on future avenues of research.

Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany

Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of Aedes species: Aedes annulipes vs. Aedes cantans, Aedes cinereus vs. Aedes rossicus and Aedes communis vs. Aedes punctor. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three Aedes-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.

Symmetric and Asymmetric Components of Shape Variation in the Diatom Genus Frustulia (Bacillariophyta)

Irregularities in cell division can produce asymmetry in symmetric structures, such as outlines of diatom cells, which can reflect genetic, environmental, or random variability in developmental processes. This study examined 12 phylogenetic lineages of the diatom genus Frustulia using landmark-based geometric morphometrics to assess the variation between cell segments separated by apical and transapical axes. Although asymmetric variation within cells differed in some lineages, these irregularities most likely did not reflect the evolutionary history of the lineages. The intraclonal phenotypic plasticity of diatom frustules was induced rather by nongenetic factors, i.e., inherited valve abnormalities, constraints of siliceous cell walls, and random developmental instability during morphogenesis. The positive correlations between the symmetric and asymmetric components of shape variation indicated that the morphogenesis of diatom cell walls affected irregularities within cells and variability among the symmetrized cells to a similar extent.

Walking on Kendall’s Shape Space: Understanding Shape Spaces and Their Coordinate Systems

More and more analyses of biological shapes are using the techniques of geometric morphometrics based on configurations of landmarks in two or three dimensions. A fundamental concept at the core of these analyses is Kendall’s shape space and local approximations to it by shape tangent spaces. Kendall’s shape space is complex because it is a curved surface and, for configurations with more than three landmarks, multidimensional. This paper uses the shape space for triangles, which is the surface of a sphere, to explore and visualize some properties of shape spaces and the respective tangent spaces. Considerations about the dimensionality of shape spaces are an important step in understanding them, and can offer a coordinate system that can translate between positions in the shape space and the corresponding landmark configurations and vice versa. By simulation studies “walking” along that are great circles around the shape space, each of them corresponding to the repeated application of a particular shape change, it is possible to grasp intuitively why shape spaces are curved and closed surfaces. From these considerations and the available information on shape spaces for configurations with more than three landmarks, the conclusion emerges that the approach using a tangent space approximation in general is valid for biological datasets. The quality of approximation depends on the scale of variation in the data, but existing analyses suggest this should be satisfactory to excellent in most empirical datasets.

The role of core and variable Gene Regulatory Network modules in tooth development and evolution

Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, e.g., during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.