Paralog dispensability shapes homozygous deletion patterns in tumor genomes.

Genomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer cell lines, paralogs have been shown to contribute substantially to genetic robustness-they are generally more dispensable for growth than singletons. Here, by analyzing copy number profiles of > 10,000 tumors, we test the hypothesis that the increased dispensability of paralogs shapes tumor genome evolution. We find that genes with paralogs are more likely to be homozygously deleted and that this cannot be explained by other factors known to influence copy number variation. Furthermore, features that influence paralog dispensability in cancer cell lines correlate with paralog deletion frequency in tumors. Finally, paralogs that are broadly essential in cancer cell lines are less frequently deleted in tumors than non-essential paralogs. Overall, our results suggest that homozygous deletions of paralogs are more frequently observed in tumor genomes because paralogs are more dispensable.

Comparative anatomy and functional implications of variation in the buccal mass in coleoid cephalopods.

In contrast to the well-studied articulated vertebrate jaws, the structure and function of cephalopod jaws remains poorly known. Cephalopod jaws are unique as the two jaw elements do not contact one another, are embedded in a muscular mass and connected through a muscle joint. Previous studies have described the anatomy of the buccal mass muscles in cephalopods and have proposed variation in muscle volume depending on beak shape. However, the general structure of the muscles has been suggested to be similar in octopuses, squids, and cuttlefish. Here we provide a quantitative analysis of the variation in the buccal mass of coleoids using traditional dissections, histological sections and contrast-enhanced computed tomography scans. Our results show that the buccal mass is composed of four main homologous muscles present in both decapodiforms and octopodiforms as suggested previously. However, we also report the presence of a muscle uniquely present in octopodiforms (the postero-lateral mandibular muscle). Our three dimensional reconstructions and quantitative analyses of the buccal mass muscles pave the way for future functional analyses allowing to better model jaw closing in coleoids. Finally, our results suggest differences in beak and muscle function that need to be validated using future in vivo functional analyses.

The anatomy of the head muscles in caecilians (Amphibia: Gymnophiona): Variation in relation to phylogeny and ecology?

In limbless fossorial vertebrates such as caecilians (Gymnophiona), head-first burrowing imposes severe constraints on the morphology and overall size of the head. As such, caecilians developed a unique jaw-closing system involving the large and well-developed m. interhyoideus posterior, which is positioned in such a way that it does not significantly increase head diameter. Caecilians also possess unique muscles among amphibians. Understanding the diversity in the architecture and size of the cranial muscles may provide insights into how a typical amphibian system was adapted for a head-first burrowing lifestyle. In this study, we use dissection and non-destructive contrast-enhanced micro-computed tomography (µCT) scanning to describe and compare the cranial musculature of 13 species of caecilians. Our results show that the general organization of the head musculature is rather constant across extant caecilians. However, the early-diverging Rhinatrema bivittatum mainly relies on the 'ancestral' amphibian jaw-closing mechanism dominated by the m. adductores mandibulae, whereas other caecilians switched to the use of the derived dual jaw-closing mechanism involving the additional recruitment of the m. interhyoideus posterior. Additionally, the aquatic Typhlonectes show a greater investment in hyoid musculature than terrestrial caecilians, which is likely related to greater demands for ventilating their large lungs, and perhaps also an increased use of suction feeding. In addition to three-dimensional interactive models, our study provides the required quantitative data to permit the generation of accurate biomechanical models allowing the testing of further functional hypotheses.

Is vertebral shape variability in caecilians (Amphibia: Gymnophiona) constrained by forces experienced during burrowing?

Caecilians are predominantly burrowing, elongate, limbless amphibians that have been relatively poorly studied. Although it has been suggested that the sturdy and compact skulls of caecilians are an adaptation to their head-first burrowing habits, no clear relationship between skull shape and burrowing performance appears to exist. However, the external forces encountered during burrowing are transmitted by the skull to the vertebral column, and, as such, may impact vertebral shape. Additionally, the muscles that generate the burrowing forces attach onto the vertebral column and consequently may impact vertebral shape that way as well. Here, we explored the relationships between vertebral shape and maximal in vivo push forces in 13 species of caecilian amphibians. Our results show that the shape of the two most anterior vertebrae, as well as the shape of the vertebrae at 90% of the total body length, is not correlated with peak push forces. Conversely, the shape of the third vertebrae, and the vertebrae at 20% and 60% of the total body length, does show a relationship to push forces measured in vivo. Whether these relationships are indirect (external forces constraining shape variation) or direct (muscle forces constraining shape variation) remains unclear and will require quantitative studies of the axial musculature. Importantly, our data suggest that mid-body vertebrae may potentially be used as proxies to infer burrowing capacity in fossil representatives.

Regional differences in vertebral shape along the axial skeleton in caecilians (Amphibia: Gymnophiona).

Caecilians are elongate, limbless and annulated amphibians that, as far as is known, all have an at least partly fossorial lifestyle. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, relatively few studies have explored the axial skeleton in limbless tetrapods. In this study, we used µCT data and three-dimensional geometric morphometrics to explore regional differences in vertebral shape across a broad range of caecilian species. Our results highlight substantial differences in vertebral shape along the axial skeleton, with anterior vertebrae being short and bulky, whereas posterior vertebrae are more elongated. This study shows that despite being limbless, elongate tetrapods such as caecilians still show regional heterogeneity in the shape of individual vertebrae along the vertebral column. Further studies are needed, however, to understand the possible causes and functional consequences of the observed variation in vertebral shape in caecilians.

The evolutionary relationship between arm vertebrae shape and ecological lifestyle in brittle stars (Echinodermata: Ophiuroidea).

Ophiuroidea are one of the most diverse classes among extant echinoderms, characterized by their flexible arms composed of a series of ossicles called vertebrae, articulating with each other proximally and distally. Their arms show a wide range of motion, important for feeding and locomotion, associated with their epizoic and non-epizoic lifestyles. It remains to be explored to what degree the phenotypic variation in these ossicles also reflects adaptations to these lifestyles, rather than only their phylogenetic affinity. In this study, we analyzed the 3D shape variation of six arm vertebrae from the middle and distal parts of an arm in 12 species, belonging to the intertidal, subtidal and bathyal zones and showing epizoic and non-epizoic behaviors. A PERMANOVA indicated a significant difference in ossicle morphology between species and between lifestyles. A principal component analysis showed that the morphology of epizoic ophiuroids is distinct from non-epizoic ones; which may reflect variation in arm function related to these different lifestyles. The Phylogenetic MANOVA and phylogenetic signal analysis showed that shape variation in the vertebral articulation seems to reflect ecological and functional adaptations, whereas phylogeny controls more the lateral morphology of the vertebrae. This suggests a convergent evolution through ecological adaptation to some degree, indicating that some of these characters may have limited taxonomic value.

The relationship between head shape, head musculature and bite force in caecilians (Amphibia: Gymnophiona).

Caecilians are enigmatic limbless amphibians that, with a few exceptions, all have an at least partly burrowing lifestyle. Although it has been suggested that caecilian evolution resulted in sturdy and compact skulls as an adaptation to their head-first burrowing habits, no relationship between skull shape and burrowing performance has been demonstrated to date. However, the unique dual jaw-closing mechanism and the osteological variability of their temporal region suggest a potential relationship between skull shape and feeding mechanics. Here, we explored the relationships between skull shape, head musculature and in vivo bite forces. Although there is a correlation between bite force and external head shape, no relationship between bite force and skull shape could be detected. Whereas our data suggest that muscles are the principal drivers of variation in bite force, the shape of the skull is constrained by factors other than demands for bite force generation. However, a strong covariation between the cranium and mandible exists. Moreover, both cranium and mandible shape covary with jaw muscle architecture. Caecilians show a gradient between species with a long retroarticular process associated with a large and pennate-fibered m. interhyoideus posterior and species with a short process but long and parallel-fibered jaw adductors. Our results demonstrate the complexity of the relationship between form and function of this jaw system. Further studies that focus on factors such as gape distance or jaw velocity will be needed in order to fully understand the evolution of feeding mechanics in caecilians.

Under pressure: the relationship between cranial shape and burrowing force in caecilians (Gymnophiona).

Caecilians are elongate, limbless and annulated amphibians that, with the exception of one aquatic family, all have an at least partly fossorial lifestyle. It has been suggested that caecilian evolution resulted in sturdy and compact skulls with fused bones and tight sutures, as an adaptation to their head-first burrowing habits. However, although their cranial osteology is well described, relationships between form and function remain poorly understood. In the present study, we explored the relationship between cranial shape and in vivo burrowing forces. Using micro-computed tomography (µCT) data, we performed 3D geometric morphometrics to explore whether cranial and mandibular shapes reflected patterns that might be associated with maximal push forces. The results highlight important differences in maximal push forces, with the aquatic Typhlonectes producing a lower force for a given size compared with other species. Despite substantial differences in head morphology across species, no relationship between overall skull shape and push force could be detected. Although a strong phylogenetic signal may partly obscure the results, our conclusions confirm previous studies using biomechanical models and suggest that differences in the degree of fossoriality do not appear to be driving the evolution of head shape.

Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines.

Pairs of paralogs may share common functionality and, hence, display synthetic lethal interactions. As the majority of human genes have an identifiable paralog, exploiting synthetic lethality between paralogs may be a broadly applicable approach for targeting gene loss in cancer. However, only a biased subset of human paralog pairs has been tested for synthetic lethality to date. Here, by analyzing genome-wide CRISPR screens and molecular profiles of over 700 cancer cell lines, we identify features predictive of synthetic lethality between paralogs, including shared protein-protein interactions and evolutionary conservation. We develop a machine-learning classifier based on these features to predict which paralog pairs are most likely to be synthetic lethal and to explain why. We show that our classifier accurately predicts the results of combinatorial CRISPR screens in cancer cell lines and furthermore can distinguish pairs that are synthetic lethal in multiple cell lines from those that are cell-line specific. A record of this paper's transparent peer review process is included in the supplemental information.

KBoost: a new method to infer gene regulatory networks from gene expression data.

Reconstructing gene regulatory networks is crucial to understand biological processes and holds potential for developing personalized treatment. Yet, it is still an open problem as state-of-the-art algorithms are often not able to process large amounts of data within reasonable time. Furthermore, many of the existing methods predict numerous false positives and have limited capabilities to integrate other sources of information, such as previously known interactions. Here we introduce KBoost, an algorithm that uses kernel PCA regression, boosting and Bayesian model averaging for fast and accurate reconstruction of gene regulatory networks. We have benchmarked KBoost against other high performing algorithms using three different datasets. The results show that our method compares favorably to other methods across datasets. We have also applied KBoost to a large cohort of close to 2000 breast cancer patients and 24,000 genes in less than 2 h on standard hardware. Our results show that molecularly defined breast cancer subtypes also feature differences in their GRNs. An implementation of KBoost in the form of an R package is available at: https://github.com/Luisiglm/KBoost and as a Bioconductor software package.

Body size miniaturization in a lineage of colubrid snakes: Implications for cranial anatomy.

As body size strongly determines the biology of an organism at all levels, it can be expected that miniaturization comes with substantial structural and functional constraints. Dwarf snakes of the genus Eirenis are derived from big, surface-dwelling ancestors, considered to be similar to those of the sister genus Dolichophis. To better understand the structural implications of miniaturization on the feeding apparatus in Eirenis, the morphology of the cranial musculoskeletal system of Dolichophis schmidti was compared with that of the miniature Eirenis punctatolineatus and E. persicus using high-resolution µCT data. The gape index was compared between D. schmidti and 14 Eirenis species. Our results show a relatively increased neurocranium size and decreased maximal jaw muscle force in E. persicus, compared with the D. schmidti, and an intermediate situation in E. punctatolineatus. A significant negative allometry in gape index relative to body size is observed across the transition from the Dolichophis to Pediophis and Eirenis subgenera. However, the gape index relative to head size showed a significant negative allometry only across the transition from the Dolichophis to Pseudocyclophis subgenus. In Dolichophis-Eirenis dwarfing lineages, different structural patterns are observed through miniaturization, indicating that overcoming the challenge of miniaturization has achieved via different adaptations.

From yellow to silver: Transforming cranial morphology in European eel (Anguilla anguilla).

The European eel (Anguilla anguilla) has been extensively studied, especially because of its highly specialized migratory behaviour associated with substantial phenotypic transformations. During this migration, one of those transformations the eel undergoes is from yellow to silver eel, a process known as silvering. Although the cranial morphology during the earlier glass, elver and yellow eel stages are well studied, little is known about actual morphological changes during the transformation process from the yellow to the silver eel stage. Yet, literature suggests drastic changes in musculoskeletal anatomy. Here, we investigated the cranial musculoskeletal morphology of 11 male European eels at different stages during silvering, resulting both from natural and artificial maturation. Using 3D-reconstructed µCT data of the head, the skull and cranial muscles associated with jaw closing and respiration were studied. Eye size was used as a proxy for the silvering stage. Size-adjusted jaw muscle volumes increased during silvering, although insignificantly. Accordingly, a near-significant increase in bite force was observed. Respiratory muscles size did increase significantly during silvering, however. Considering the eel's long migration, which often includes deep and thus potentially oxygen-poor environments, having a better performing respiratory system may facilitate efficient migration. Both overall skull dimensions and specifically orbit size increased with eye index, suggesting they play a role in accommodating the enlarging eyes during silvering. Finally, artificially matured eels had a wider and taller skull, as well as larger jaw muscles than wild silver eels. This could be caused (a) by different conditions experienced during the yellow eel stage, which are maintained in the silver eel stage, (b) by side effects of hormonal injections or (c) be part of the maturation process as artificially induced silver eels had a higher eye index than the wild silver eels.

Is variation in tail vertebral morphology linked to habitat use in chameleons?

Chameleons (Chamaeleonidae) are known for their arboreal lifestyle, in which they make use of their prehensile tail. Yet, some species have a more terrestrial lifestyle, such as Brookesia and Rieppeleon species, as well as some chameleons of the genera Chamaeleo and Bradypodion. The main goal of this study was to identify the key anatomical features of the tail vertebral morphology associated with prehensile capacity. Both interspecific and intra-individual variation in skeletal tail morphology was investigated. For this, a 3D-shape analysis was performed on vertebral morphology using µCT-images of different species of prehensile and nonprehensile tailed chameleons. A difference in overall tail size and caudal vertebral morphology does exist between prehensile and nonprehensile taxa. Nonprehensile tailed species have a shorter tail with fewer vertebrae, a generally shorter neural spine and shorter transverse processes that are positioned more anteriorly (with respect to the vertebral center). The longer tails of prehensile species have more vertebrae as well as an increased length of the processes, likely providing a greater area for muscle attachment. At the intra-individual level, regional variation is observed with more robust proximal tail vertebrae having longer processes. The distal part has relatively longer vertebrae with shorter processes. Although longer, the small size and high number of the distal vertebrae allows the tail to coil around perches.

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines.

What makes a gene essential for cellular survival? In model organisms, such as budding yeast, systematic gene deletion studies have revealed that paralog genes are less likely to be essential than singleton genes and that this can partially be attributed to the ability of paralogs to buffer each other's loss. However, the essentiality of a gene is not a fixed property and can vary significantly across different genetic backgrounds. It is unclear to what extent paralogs contribute to this variation, as most studies have analyzed genes identified as essential in a single genetic background. Here, using gene essentiality profiles of 558 genetically heterogeneous tumor cell lines, we analyze the contribution of paralogy to variable essentiality. We find that, compared to singleton genes, paralogs are less frequently essential and that this is more evident when considering genes with multiple paralogs or with highly sequence-similar paralogs. In addition, we find that paralogs derived from whole genome duplication exhibit more variable essentiality than those derived from small-scale duplications. We provide evidence that in 13-17% of cases the variable essentiality of paralogs can be attributed to buffering relationships between paralog pairs, as evidenced by synthetic lethality. Paralog pairs derived from whole genome duplication and pairs that function in protein complexes are significantly more likely to display such synthetic lethal relationships. Overall we find that many of the observations made using a single strain of budding yeast can be extended to understand patterns of essentiality in genetically heterogeneous cancer cell lines.

Morphological and histological characterization of an ectopically mineralized structure in a gilthead sea bream Sparus aurata with opercular deformation.

In this study, we describe an abnormal ectopically mineralized structure (EMS) that was found inside the skull of a juvenile Sparus aurata that also showed a bilateral opercular deformation. The overall phenotype and tissue composition were studied using micro-CT scanning and histological analyses. The ectopic structure occupies a large volume of the brain cavity, partially extruding into the gill cavity. It shows a dense mineralization and an extracellular matrix-rich phenotype, with variation in both the morphology and size of the cell lacunae, combined with an irregular fibre organization inside the matrix. This study is the first to report such an EMS in a juvenile teleost fish, where the tissue does not resemble any other connective tissue type described in bony fish so far. The tissue phenotype seems to rule out that the EMS corresponds to a tumorous cartilage. Yet, it is rather reminiscent of a highly mineralized structure found in cartilaginous fish, where it is suggested to be associated with damage repair.

Head shape disparity impacts pollutant accumulation in European eel.

Several aspects of the life cycle of the critically endangered European eel (Anguilla anguilla) remain poorly understood. One such aspect is the broad-versus narrow-head dimorphism, and how this impacts their overall performance at different stages of their life cycle. At the yellow eel stage, the phenotypes show a trophic divergence. We investigated whether pollutant accumulation is affected by this disparity. We show that broad-headed eels contained higher concentrations of mercury and several lipophilic organic pollutants, compared to narrow-headed ones, irrespective of their fat content. The hereby confirmed link between the phenotypic disparity, its associated feeding ecology and its impact on pollutant accumulation thus raises further concerns about their migratory and reproductive success. Considering that pollution is an important contributor to the European eel's decline, our results demonstrate that broad-headed eels are more vulnerable to detrimental pollutant accumulation. This compromises their successful contribution to their population's reproduction and its restoration.

Musculoskeletal anatomy and feeding performance of pre-feeding engyodontic larvae of the European eel (Anguilla anguilla).

Being part of the elopomorph group of fishes, Anguillidae species show a leptocephalus larval stage. However, due to largely unknown spawning locations and habitats of their earliest life stages, as well as their transparency, these Anguilla larvae are rarely encountered in nature. Therefore, information regarding the early life history of these larvae, including their exogenous feeding strategy and feeding performance, is rather scarce. To better understand the structural basis and functional performance of larval feeding in captivity, the functional morphology of the cranial musculoskeletal system in pre- and first-feeding engyodontic leptocephali of the European eel (Anguilla anguilla) was studied. A 3D reconstruction of the feeding apparatus (head of the leptocephali < 1 mm) was used to visualize and describe the musculoskeletal changes throughout these stages. To analyze the ontogenetic changes in the functionality of the feeding apparatus towards the active feeding phase, 3D data of joints, levers and muscles derived from the reconstructions were used to estimate bite and joint reaction forces (JRFs). Observing a maximum estimated bite force of about 65 µN (and corresponding JRFs of 260 µN), it can be hypothesized that leptocephalus larvae are functionally constrained to feed only on soft food particles. Additionally, potential prey items are size delimited, based on the theoretically estimated average gape of these larvae of about 100 µm. This hypothesis appears to be in line with recent observations of a diet consisting of small and/or gelatinous prey items (Hydrozoa, Thaliacea, Ctenophora, Polycystenia) found in the guts of euryodontic leptocephalus larvae.

Functional and evolutionary anatomy of the African suckermouth catfishes (Siluriformes: Mochokidae): convergent evolution in Afrotropical and Neotropical faunas.

Of those fishes scraping food off substrates and using head parts in substrate attachment for station-holding, the catfish families Loricariidae, Astroblepidae and Mochokidae display the most dramatically adapted morphologies. Loricariidae and Astroblepidae, living in the Neotropical freshwaters, exclusively contain suckermouth catfish species, and their anatomy and head kinematics have already been studied into detail. Among Mochokidae, living in the tropical freshwaters of Africa, only the chiloglanidine subfamily has a sucker mouth, and occupies similar niches in Africa as both Neotropical families do in South America. Having derived from relatively unrelated catfish ancestors, their anatomy is poorly known, and the nature of their scraping and station-holding capabilities is not known at all. This paper provides details on the chiloglanidine head anatomy and function (relating their anatomy to that of the non-suckermouth Mochokidae), and compares this Afrotropical suckermouth taxon with both Neotropical suckermouth families. It identifies both convergences and differing anatomical and kinematic solutions to the same key needs of food-scraping and station-holding suckermouth fishes. Chiloglanidine mochokids differ from both Neotropical families in having less mobile jaws, with an upper jaw assisting more in station-holding than in feeding. They share the highly mobile lower lip with both Neotropical taxa, although the configuration of the intermandibular/protractor hyoidei muscle system, changing the volume of the sucker-disc cavity, differs in all three taxa. Chiloglanidines have a single, posterior inflow opening into this cavity, whereas Loricariidae have two lateral openings, and Astroblepidae have none, using an opercular incurrent opening instead. The chiloglanidine buccal valve system consists of two passive valves, as in Astroblepidae. Although less diverse in number of genera and species, this Afrotropical suckermouth taxon possesses the anatomical and kinematic key elements allowing a successful occupation of a niche similar to the one found in the Loricariidae + Astroblepidae clade.

Structural tissue organization in the beak of Java and Darwin's finches.

Birds are well known for occupying diverse feeding niches, and for having evolved diverse beak morphologies associated with dietary specialization. Birds that feed on hard seeds typically possess beaks that are both deep and wide, presumably because of selection for fracture avoidance, as suggested by prior studies. It follows then that birds that eat seeds of different size and hardness should vary in one or more aspects of beak morphology, including the histological organization of the rhamphotheca, the cellular interface that binds the rhamphotheca to the bone, and the organization of trabeculae in the beak. To explore this expectation we here investigate tissue organization in the rhamphotheca of the Java finch, a large granivorous bird, and describe interspecific differences in the trabecular organization of the beak across 11 species of Darwin's finches. We identify specializations in multiple layers of the horny beak, with the dermis anchored to the bone by Sharpey's fibers in those regions that are subjected to high stresses during biting. Moreover, the rhamphotheca is characterized by a tight dermo-epidermal junction through interdigitations of these two tissues. Herbst corpuscles are observed in high density in the dermis of the lateral aspect of the beak as observed in other birds. Finally, the trabecular organization of the beak in Darwin's finches appears most variable in regions involved most in food manipulation, with the density of trabeculae in the beak generally mirroring loading regimes imposed by different feeding habits and beak use in this clade.

Soft dentin results in unique flexible teeth in scraping catfishes.

Teeth are generally used for actions in which they experience mainly compressive forces acting toward the base. The ordered tooth enamel(oid) and dentin structures contribute to the high compressive strength but also to the minor shear and tensile strengths. Some vertebrates, however, use their teeth for scraping, with teeth experiencing forces directed mostly normal to their long axis. Some scraping suckermouth catfishes (Loricariidae) even appear to have flexible teeth, which have not been found in any other vertebrate taxon. Considering the mineralized nature of tooth tissues, the notion of flexible teeth seems paradoxical. We studied teeth of five species, testing and measuring tooth flexibility, and investigating tooth (micro)structure using transmission electron microscopy, staining, computed tomography scanning, and scanning electron microscopy-energy-dispersive spectrometry. We quantified the extreme bending capacity of single teeth (up to 180°) and show that reorganizations of the tooth (micro)structure and extreme hypomineralization of the dentin are adaptations preventing breaking by allowing flexibility. Tooth shape and internal structure appear to be optimized for bending in one direction, which is expected to occur frequently when feeding (scraping) under natural conditions. Not all loricariid catfishes possess flexible teeth, with the trait potentially having evolved more than once. Flexible teeth surely rank among the most extreme evolutionary novelties in known mineralized biological materials and might yield a better understanding of the processes of dentin formation and (hypo)mineralization in vertebrates, including humans.