Automated Uterine Fibroids Detection in Ultrasound Images Using Deep Convolutional Neural Networks.

Fibroids of the uterus are a common benign tumor affecting women of childbearing age. Uterine fibroids (UF) can be effectively treated with earlier identification and diagnosis. Its automated diagnosis from medical images is an area where deep learning (DL)-based algorithms have demonstrated promising results. In this research, we evaluated state-of-the-art DL architectures VGG16, ResNet50, InceptionV3, and our proposed innovative dual-path deep convolutional neural network (DPCNN) architecture for UF detection tasks. Using preprocessing methods including scaling, normalization, and data augmentation, an ultrasound image dataset from Kaggle is prepared for use. After the images are used to train and validate the DL models, the model performance is evaluated using different measures. When compared to existing DL models, our suggested DPCNN architecture achieved the highest accuracy of 99.8 percent. Findings show that pre-trained deep-learning model performance for UF diagnosis from medical images may significantly improve with the application of fine-tuning strategies. In particular, the InceptionV3 model achieved 90% accuracy, with the ResNet50 model achieving 89% accuracy. It should be noted that the VGG16 model was found to have a lower accuracy level of 85%. Our findings show that DL-based methods can be effectively utilized to facilitate automated UF detection from medical images. Further research in this area holds great potential and could lead to the creation of cutting-edge computer-aided diagnosis systems. To further advance the state-of-the-art in medical imaging analysis, the DL community is invited to investigate these lines of research. Although our proposed innovative DPCNN architecture performed best, fine-tuned versions of pre-trained models like InceptionV3 and ResNet50 also delivered strong results. This work lays the foundation for future studies and has the potential to enhance the precision and suitability with which UF is detected.

Driving drowsiness detection using spectral signatures of EEG-based neurophysiology.

Introduction: Drowsy driving is a significant factor causing dire road crashes and casualties around the world. Detecting it earlier and more effectively can significantly reduce the lethal aftereffects and increase road safety. As physiological conditions originate from the human brain, so neurophysiological signatures in drowsy and alert states may be investigated for this purpose. In this preface, A passive brain-computer interface (pBCI) scheme using multichannel electroencephalography (EEG) brain signals is developed for spatially localized and accurate detection of human drowsiness during driving tasks. Methods: This pBCI modality acquired electrophysiological patterns of 12 healthy subjects from the prefrontal (PFC), frontal (FC), and occipital cortices (OC) of the brain. Neurological states are recorded using six EEG channels spread over the right and left hemispheres in the PFC, FC, and OC of the sleep-deprived subjects during simulated driving tasks. In post-hoc analysis, spectral signatures of the δ, θ, α, and ß rhythms are extracted in terms of spectral band powers and their ratios with a temporal correlation over the complete span of the experiment. Minimum redundancy maximum relevance, Chi-square, and ReliefF feature selection methods are used and aggregated with a Z-score based approach for global feature ranking. The extracted drowsiness attributes are classified using decision trees, discriminant analysis, logistic regression, naïve Bayes, support vector machines, k-nearest neighbors, and ensemble classifiers. The binary classification results are reported with confusion matrix-based performance assessment metrics. Results: In inter-classifier comparison, the optimized ensemble model achieved the best results of drowsiness classification with 85.6% accuracy and precision, 89.7% recall, 87.6% F1-score, 80% specificity, 70.3% Matthews correlation coefficient, 70.2% Cohen's kappa score, and 91% area under the receiver operating characteristic curve with 76-ms execution time. In inter-channel comparison, the best results were obtained at the F8 electrode position in the right FC of the brain. The significance of all the results was validated with a p-value of less than 0.05 using statistical hypothesis testing methods. Conclusions: The proposed scheme has achieved better results for driving drowsiness detection with the accomplishment of multiple objectives. The predictor importance approach has reduced the feature extraction cost and computational complexity is minimized with the use of conventional machine learning classifiers resulting in low-cost hardware and software requirements. The channel selection approach has spatially localized the most promising brain region for drowsiness detection with only a single EEG channel (F8) which reduces the physical intrusiveness in normal driving operation. This pBCI scheme has a good potential for practical applications requiring earlier, more accurate, and less disruptive drowsiness detection using the spectral information of EEG biosignals.

Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates.

Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles.

The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.

Vector Phase Analysis Approach for Sleep Stage Classification: A Functional Near-Infrared Spectroscopy-Based Passive Brain-Computer Interface.

A passive brain-computer interface (BCI) based upon functional near-infrared spectroscopy (fNIRS) brain signals is used for earlier detection of human drowsiness during driving tasks. This BCI modality acquired hemodynamic signals of 13 healthy subjects from the right dorsolateral prefrontal cortex (DPFC) of the brain. Drowsiness activity is recorded using a continuous-wave fNIRS system and eight channels over the right DPFC. During the experiment, sleep-deprived subjects drove a vehicle in a driving simulator while their cerebral oxygen regulation (CORE) state was continuously measured. Vector phase analysis (VPA) was used as a classifier to detect drowsiness state along with sleep stage-based threshold criteria. Extensive training and testing with various feature sets and classifiers are done to justify the adaptation of threshold criteria for any subject without requiring recalibration. Three statistical features (mean oxyhemoglobin, signal peak, and the sum of peaks) along with six VPA features (trajectory slopes of VPA indices) were used. The average accuracies for the five classifiers are 90.9% for discriminant analysis, 92.5% for support vector machines, 92.3% for nearest neighbors, 92.4% for both decision trees, and ensembles over all subjects' data. Trajectory slopes of CORE vector magnitude and angle: m(|R|) and m(∠R) are the best-performing features, along with ensemble classifier with the highest accuracy of 95.3% and minimum computation time of 40 ms. The statistical significance of the results is validated with a p-value of less than 0.05. The proposed passive BCI scheme demonstrates a promising technique for online drowsiness detection using VPA along with sleep stage classification.

The Evolution of Sox Gene Repertoires and Regulation of Segmentation in Arachnids.

The Sox family of transcription factors regulates many processes during metazoan development, including stem cell maintenance and nervous system specification. Characterizing the repertoires and roles of these genes can therefore provide important insights into animal evolution and development. We further characterized the Sox repertoires of several arachnid species with and without an ancestral whole-genome duplication and compared their expression between the spider Parasteatoda tepidariorum and the harvestman Phalangium opilio. We found that most Sox families have been retained as ohnologs after whole-genome duplication and evidence for potential subfunctionalization and/or neofunctionalization events. Our results also suggest that Sox21b-1 likely regulated segmentation ancestrally in arachnids, playing a similar role to the closely related SoxB gene, Dichaete, in insects. We previously showed that Sox21b-1 is required for the simultaneous formation of prosomal segments and sequential addition of opisthosomal segments in P. tepidariorum. We studied the expression and function of Sox21b-1 further in this spider and found that although this gene regulates the generation of both prosomal and opisthosomal segments, it plays different roles in the formation of these tagmata reflecting their contrasting modes of segmentation and deployment of gene regulatory networks with different architectures.

Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species.

In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These appendages are used for grasping the female during mating and so their divergence is most likely driven by sexual selection. Mapping studies indicate a highly polygenic and generally additive genetic basis for these morphological differences. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used new D. simulans/D. mauritiana introgression lines on chromosome arm 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the expressed genes and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development in D. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulates tartan (trn), a gene known to contribute to divergence in clasper morphology. Taken together, our results provide new insights into the regulation of genital development and how this has evolved between species.

Characterization of the Genetic Architecture Underlying Eye Size Variation Within Drosophila melanogaster and Drosophila simulans.

The compound eyes of insects exhibit striking variation in size, reflecting adaptation to different lifestyles and habitats. However, the genetic and developmental bases of variation in insect eye size is poorly understood, which limits our understanding of how these important morphological differences evolve. To address this, we further explored natural variation in eye size within and between four species of the Drosophila melanogaster species subgroup. We found extensive variation in eye size among these species, and flies with larger eyes generally had a shorter inter-ocular distance and vice versa We then carried out quantitative trait loci (QTL) mapping of intra-specific variation in eye size and inter-ocular distance in both D. melanogaster and D. simulans This revealed that different genomic regions underlie variation in eye size and inter-ocular distance in both species, which we corroborated by introgression mapping in D. simulans This suggests that although there is a trade-off between eye size and inter-ocular distance, variation in these two traits is likely to be caused by different genes and so can be genetically decoupled. Finally, although we detected QTL for intra-specific variation in eye size at similar positions in D. melanogaster and D. simulans, we observed differences in eye fate commitment between strains of these two species. This indicates that different developmental mechanisms and therefore, most likely, different genes contribute to eye size variation in these species. Taken together with the results of previous studies, our findings suggest that the gene regulatory network that specifies eye size has evolved at multiple genetic nodes to give rise to natural variation in this trait within and among species.

Three Quantitative Trait Loci Explain More than 60% of Variation for Chill Coma Recovery Time in a Natural Population of Drosophila ananassae.

Ectothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) in Drosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions. We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with diverging CCRT phenotypes. The RIAILs were phenotyped for their CCRT and, together with the founder strains, genotyped for polymorphic markers with double-digest restriction site-associated DNA (ddRAD) sequencing. Using a hierarchical mapping approach that combined standard interval mapping and a multiple-QTL model, we mapped three QTL which altogether explained 64% of the phenotypic variance. For two of the identified QTL, we found evidence of epistasis. To narrow down the list of cold tolerance candidate genes, we cross-referenced the QTL intervals with genes that we previously identified as differentially expressed in response to cold in D. ananassae, and with thermotolerance candidate genes of D. melanogaster Among the 58 differentially expressed genes that were contained within the QTL, GF15058 showed a significant interaction of the CCRT phenotype and gene expression. Further, we identified the orthologs of four D. melanogaster thermotolerance candidate genes, MtnA, klarsicht, CG5246 (D.ana/GF17132) and CG10383 (D.ana/GF14829) as candidates for cold tolerance in D. ananassae.

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution.

Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary 'hotspots' are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is understood in sufficient detail, the path of evolution may be predictable. The repeated evolutionary loss of larval trichomes among Drosophila species is caused by the loss of shavenbaby (svb) expression. svb is also required for development of leg trichomes, but the evolutionary gain of trichomes in the 'naked valley' on T2 femurs in Drosophila melanogaster is caused by reduced microRNA-92a (miR-92a) expression rather than changes in svb. We compared the expression and function of components between the larval and leg trichome GRNs to investigate why the genetic basis of trichome pattern evolution differs in these developmental contexts. We found key differences between the two networks in both the genes employed, and in the regulation and function of common genes. These differences in the GRNs reveal why mutations in svb are unlikely to contribute to leg trichome evolution and how instead miR-92a represents the key evolutionary switch in this context. Our work shows that variability in GRNs across different developmental contexts, as well as whether a morphological feature is lost versus gained, influence the nodes at which a GRN evolves to cause morphological change. Therefore, our findings have important implications for understanding the pathways and predictability of evolution.

Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum.

MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.

From shavenbaby to the naked valley: trichome formation as a model for evolutionary developmental biology.

Microtrichia or trichomes are non-sensory actin protrusions produced by the epidermal cells of many insects. Studies of trichome formation in Drosophila have over the last 30 years provided key insights towards our understanding of gene regulation, gene regulatory networks (GRNs), development, the genotype to phenotype map, and the evolution of these processes. Here we review classic studies that have used trichome formation as a model to shed light on Drosophila development as well as recent research on the architecture of the GRN underlying trichome formation. This includes the findings that both small peptides and microRNAs play important roles in the regulation and evolution of this network. In addition, we review research on the evolution of trichome patterns that has provided novel insights into the function and architecture of cis-regulatory modules, and into the genetic basis of morphological change. We conclude that further research on these apparently simple and often functionally enigmatic structures will continue to provide new and important knowledge about development and evolution.

A perspective on micro-evo-devo: progress and potential.

The term "micro-evo-devo" refers to the combined study of the genetic and developmental bases of natural variation in populations and the evolutionary forces that have shaped this variation. It thus represents a synthesis of the fields of evolutionary developmental biology and population genetics. As has been pointed out by several others, this synthesis can provide insights into the evolution of organismal form and function that have not been possible within these individual disciplines separately. Despite a number of important successes in micro-evo-devo, however, it appears that evo devo and population genetics remain largely separate spheres of research, limiting their ability to address evolutionary questions. This also risks pushing contemporary evo devo to the fringes of evolutionary biology because it does not describe the causative molecular changes underlying evolution or the evolutionary forces involved. Here we reemphasize the theoretical and practical importance of micro-evo-devo as a strategy for understanding phenotypic evolution, review the key recent insights that it has provided, and present a perspective on both the potential and the remaining challenges of this exciting interdisciplinary field.

Genetic and developmental analysis of differences in eye and face morphology between Drosophila simulans and Drosophila mauritiana.

Eye and head morphology vary considerably among insects and even between closely related species of Drosophila. Species of the D. melanogaster subgroup, and other Drosophila species, exhibit a negative correlation between eye size and face width (FW); for example, D. mauritiana generally has bigger eyes composed of larger ommatidia and conversely a narrower face than its sibling species. To better understand the evolution of eye and head morphology, we investigated the genetic and developmental basis of differences in eye size and FW between male D. mauritiana and D. simulans. QTL mapping of eye size and FW showed that the major loci responsible for the interspecific variation in these traits are localized to different genomic regions. Introgression of the largest effect QTL underlying the difference in eye size resulted in flies with larger eyes but no significant difference in FW. Moreover,introgression of a QTL region on the third chromosome that contributes to the FW difference between these species affected FW, but not eye size. We also observed that this difference in FW is detectable earlier in the development of the eye­antennal disc than the difference in the size of the retinal field. Our results suggest that different loci that act at different developmental stages underlie changes in eye size and FW. Therefore, while there is a negative correlation between these traits in Drosophila, we show genetically that they also have the potential to evolve independently and this may help to explain the evolution of these traits in other insects.

Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster.

Identifying the genetic mechanisms underlying phenotypic change is essential to understanding how gene regulatory networks and ultimately the genotype-to-phenotype map evolve. It is recognized that microRNAs (miRNAs) have the potential to facilitate evolutionary change [1-3]; however, there are no known examples of natural morphological variation caused by evolutionary changes in miRNA expression. Therefore, the contribution of miRNAs to evolutionary change remains unknown [1, 4]. Drosophila melanogaster subgroup species display a portion of trichome-free cuticle on the femur of the second leg called the "naked valley." It was previously shown that Ultrabithorax (Ubx) is involved in naked valley variation between D. melanogaster and D. simulans [5, 6]. However, naked valley size also varies among populations of D. melanogaster, ranging from 1,000 up to 30,000 µm(2). We investigated the genetic basis of intraspecific differences in the naked valley in D. melanogaster and found that neither Ubx nor shavenbaby (svb) [7, 8] contributes to this morphological difference. Instead, we show that changes in mir-92a expression underlie the evolution of naked valley size in D. melanogaster through repression of shavenoid (sha) [9]. Therefore, our results reveal a novel mechanism for morphological evolution and suggest that modulation of the expression of miRNAs potentially plays a prominent role in generating organismal diversity.

Evolution of eye morphology and rhodopsin expression in the Drosophila melanogaster species subgroup.

A striking diversity of compound eye size and shape has evolved among insects. The number of ommatidia and their size are major determinants of the visual sensitivity and acuity of the compound eye. Each ommatidium is composed of eight photoreceptor cells that facilitate the discrimination of different colours via the expression of various light sensitive Rhodopsin proteins. It follows that variation in eye size, shape, and opsin composition is likely to directly influence vision. We analyzed variation in these three traits in D. melanogaster, D. simulans and D. mauritiana. We show that D. mauritiana generally has larger eyes than its sibling species, which is due to a combination of larger ommatidia and more ommatidia. In addition, intra- and inter-specific differences in eye size among D. simulans and D. melanogaster strains are mainly caused by variation in ommatidia number. By applying a geometric morphometrics approach to assess whether the formation of larger eyes influences other parts of the head capsule, we found that an increase in eye size is associated with a reduction in the adjacent face cuticle. Our shape analysis also demonstrates that D. mauritiana eyes are specifically enlarged in the dorsal region. Intriguingly, this dorsal enlargement is associated with enhanced expression of rhodopsin 3 in D. mauritiana. In summary, our data suggests that the morphology and functional properties of the compound eyes vary considerably within and among these closely related Drosophila species and may be part of coordinated morphological changes affecting the head capsule.

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus.

Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a "species tree" (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.

A phylogenetic hot spot for evolutionary novelty in Middle American treefrogs.

Among the various types of evolutionary changes in morphology, the origin of novel structures may be the most rare and intriguing. Here we show statistically that the origins of different novel structures may be correlated and phylogenetically clustered into "hot spots" of evolutionary novelty, in a case study involving skull elements in treefrogs. We reconstruct phylogenetic relationships within a clade of Middle American treefrogs based on data from 10 nuclear and four mitochondrial genes and then analyze morphological evolution across this tree. New cranial elements are rare among anurans and tetrapods in general, but three novel elements have evolved within this clade, with a 40% increase in the number of skull roof elements in some species. Two of these elements also evolved in a related clade of treefrogs, and these two novel elements may have each evolved repeatedly within one or both clades. The molecular phylogeny suggests striking homoplasy in cranial morphology and shows that parsimony and Bayesian analyses of the morphological data have produced misleading results with strong statistical support. The origins of the novel elements are associated with an overall increase in the ossification of dermal skull roof elements (suggesting peramorphosis) and with the evolution of a novel adaptive behavior. Our study may be the first to statistically document significant phylogenetic clustering and correlation in the origins of novel structures, and to demonstrate the strongly misleading effects of peramorphosis on phylogenetic analysis.