Genome-wide parallelism underlies contemporary adaptation in urban lizards.

Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated "natural experiments" in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus, a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions.

Seed color patterns in domesticated common bean are regulated by MYB-bHLH-WD40 transcription factors and temperature.

Seed colors and color patterns are critical for the survival of wild plants and the consumer appeal of crops. In common bean, a major global staple, these patterns are also essential in determining market classes, yet the genetic and environmental control of many pigmentation patterns remains unresolved. In this study, we genetically mapped variation for several important seed pattern loci, including T, Bip, phbw, and Z, which co-segregated with candidate genes PvTTG1, PvMYC1, PvTT8, and PvTT2, respectively. Proteins encoded by these genes are predicted to work together in MYB-bHLH-WD40 (MBW) complexes, propagating flavonoid biosynthesis across the seed coat as observed in Arabidopsis. Whole-genome sequencing of 37 accessions identified mutations, including seven unique parallel mutations in T (PvTTG1) and non-synonymous SNPs in highly conserved residues in bipana (PvMYC1) and z (PvTT2). A 612 bp intron deletion in phbw (PvTT8) eliminated motifs conserved since the Papilionoideae origin and corresponded to a 20-fold reduction in transcript abundance. In multi-location field trials of seven varieties with partial seed coat pigmentation patterning, the pigmented seed coat area correlated positively with ambient temperature, with up to 11-fold increases in the pigmented area from the coolest to the warmest environments. In controlled growth chamber conditions, an increase of 4°C was sufficient to cause pigmentation on an average additional 21% of the seed coat area. Our results shed light on key steps of flavonoid biosynthesis in common bean. They will inform breeding efforts for seed coat color/patterning to improve consumer appeal in this nutritious staple crop.

Molecular parallelism in signaling function across different sexually selected ornaments in a warbler.

Extravagant ornaments are thought to signal male quality to females choosing mates, but the evidence linking ornament size to male quality is controversial, particularly in cases in which females prefer different ornaments in different populations. Here, we use whole-genome sequencing and transcriptomics to determine the genetic basis of ornament size in two populations of a widespread warbler, the common yellowthroat (Geothlypis trichas). Within a single subspecies, females in a Wisconsin population prefer males with larger black masks as mates, while females in a New York population prefer males with larger yellow bibs. Despite being produced by different pigments in different patches on the body, the size of the ornament preferred by females in each population was linked to numerous genes that function in many of the same core aspects of male quality (e.g., immunity and oxidative balance). These relationships confirm recent hypotheses linking the signaling function of ornaments to male quality. Furthermore, the parallelism in signaling function provides the flexibility for different types of ornaments to be used as signals of similar aspects of male quality. This could facilitate switches in female preference for different ornaments, a potentially important step in the early stages of divergence among populations.

HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.

BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure. RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software. CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.

Prevalent Introgression Underlies Convergent Evolution in the Diversification of Pungitius Sticklebacks.

New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analyzed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures-important diagnostic traits in Pungitius systematics-and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the long-standing challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish.

Non-constant mean relative potency for antibody-dependent cellular cytotoxicity assays.

Bioassays are regulated, analytical methods used to ensure proper activity (potency) of biological products at release and during long-term storage. Potency is commonly reported on a relative basis by comparing and calibrating a concentration-response curve from the test material to that of a reference standard material. The relative potency approach depends on an assumption that the two concentration-response curves exhibit similar (equivalent) shapes, except for a potency shift. In certain circumstances, however, biological factors preclude the similarity assumption, and the traditional approach becomes unworkable. The antibody-mediated cytotoxicity assay is one example where the similarity assumption does not always hold. Other examples also arise in the fields of toxicology and pharmacology. In this work, we present a non-constant mean relative potency approach which averages the relative potency across a common range of the concentration-response curves. The proposed method captures the changing nature of the relative potency into a summary statistic that can be reported for batch calibration and quality control purposes. We provide inferential methods for this statistic and summarize the results of a simulation comparing these methods across a number of non-constant relative potency scenarios and assay conditions.

Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with model-based approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning ∼0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution.

Researching the CNN Collaborative Inference Mechanism for Heterogeneous Edge Devices.

Convolutional Neural Networks (CNNs) have been widely applied in various edge computing devices based on intelligent sensors. However, due to the high computational demands of CNN tasks, the limited computing resources of edge intelligent terminal devices, and significant architectural differences among these devices, it is challenging for edge devices to independently execute inference tasks locally. Collaborative inference among edge terminal devices can effectively utilize idle computing and storage resources and optimize latency characteristics, thus significantly addressing the challenges posed by the computational intensity of CNNs. This paper targets efficient collaborative execution of CNN inference tasks among heterogeneous and resource-constrained edge terminal devices. We propose a pre-partitioning deployment method for CNNs based on critical operator layers, and optimize the system bottleneck latency during pipeline parallelism using data compression, queuing, and "micro-shifting" techniques. Experimental results demonstrate that our method achieves significant acceleration in CNN inference within heterogeneous environments, improving performance by 71.6% compared to existing popular frameworks.

Iterative Reconstruction of Micro Computed Tomography Scans Using Multiple Heterogeneous GPUs.

Graphics processing units (GPUs) facilitate massive parallelism and high-capacity storage, and thus are suitable for the iterative reconstruction of ultrahigh-resolution micro computed tomography (CT) scans by on-the-fly system matrix (OTFSM) calculation using ordered subsets expectation maximization (OSEM). We propose a finite state automaton (FSA) method that facilitates iterative reconstruction using a heterogeneous multi-GPU platform through parallelizing the matrix calculations derived from a ray tracing system of ordered subsets. The FSAs perform flow control for parallel threading of the heterogeneous GPUs, which minimizes the latency of launching ordered-subsets tasks, reduces the data transfer between the main system memory and local GPU memory, and solves the memory-bound of a single GPU. In the experiments, we compared the operation efficiency of OS-MLTR for three reconstruction environments. The heterogeneous multiple GPUs with job queues for high throughput calculation speed is up to five times faster than the single GPU environment, and that speed up is nine times faster than the heterogeneous multiple GPUs with the FIFO queues of the device scheduling control. Eventually, we proposed an event-triggered FSA method for iterative reconstruction using multiple heterogeneous GPUs that solves the memory-bound issue of a single GPU at ultrahigh resolutions, and the routines of the proposed method were successfully executed on each GPU simultaneously.

Optimization of Automated Dimethylmethylene Blue Assay for Quantification of Pediatric Urine Samples.

The metachromatic dye dimethylmethylene blue is used to quantify total glycosaminoglycans in urine. Understanding the interaction of dimethylmethylene blue with glycosaminoglycans is pertinent to optimize the assay procedure depending on the type of sample and interpret the findings meaningfully. The present spectrophotometric study determined the optimum sample-to-dye ratio, primary wavelength for measuring absorbance, after studying the interaction of two different chondroitin sulfate species (unfractionated chondroitin sulfate from bovine trachea vs. chondroitin sulfate oligosaccharide with degree of polymerization of 12, from shark cartilage) with dimethylmethylene blue. Respective dye-glycosaminoglycan complexes of the two chondroitin sulfate species showed significantly different absorbance maxima, while that of the chondroitin sulfate oligosaccharide was closer to absorbance maxima of urine glycosaminoglycans. The chondroitin sulfate oligosaccharide showed relatively less stable absorbance readings at higher concentrations in the reaction volume. Furthermore, the chondroitin sulfate reference materials exhibited differences in the linearity of standard curves and hence parallelism. Based on the findings, the method was semiautomated on Beckman Coulter D✕C 700 biochemistry analyzer using the chondroitin sulfate oligosaccharide as the standard. The urine glycosaminoglycan concentration obtained was slightly lower but reasonably close to that obtained through the External Quality Assurance (EQA) scheme administrated by ERNDIM (European Research Network, Inherited Disorders of Metabolism). The findings of the present study can be used to guide the dimethylmethylene blue assay optimization, redevelopment efforts, and harmonization across laboratories. The chondroitin sulfate oligosaccharide is better than the unfractionated chondroitin sulfate from bovine trachea due to its absorbance maxima closer to urine glycosaminoglycans. On the other hand, unfractionated chondroitin sulfate exhibit poor parallelism leading to falsely lower urine glycosaminoglycan levels.

The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.

Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation.

Pollination syndromes and the origins of floral traits.

BACKGROUND: A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. SCOPE: The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. CONCLUSIONS: The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.

A universal surrogate matrix assay for urea measurement in clinical pharmacokinetic studies of respiratory diseases.

In pharmacokinetic studies for respiratory diseases, urea is a commonly used dilution marker for volume normalization of various biological matrices, owing to the fact that urea diffuses freely throughout the body and is minimally affected by disease states. In this study, we developed a convenient liquid chromatography-tandem mass spectrometry (LC-MS/MS) surrogate matrix assay for accurate urea quantitation in plasma, serum and epithelial lining fluid. Different mass spectrometer platforms and ionization modes were compared in parallel. The LC method and mass spectrometer parameters were comprehensively optimized to reduce interferences, to smooth the baseline and to maximize the signal-to-noise ratio. Saline was selected as the surrogate matrix, and its suitability was confirmed by good parallelism and accurate quality control sample measurements. Reliable and robust assay performance was demonstrated by precision and accuracy, dilution integrity, sensitivity, recovery and stability, all of which met bioanalysis requirements to support clinical studies. The assay performance was also verified and better understood by comparing it with a colorimetric assay and to a surrogate analyte assay. The newly developed surrogate matrix assay has the potential to be further expanded for urea quantitation in numerous physiological matrices.

A Hardware-Friendly High-Precision CNN Pruning Method and Its FPGA Implementation.

To address the problems of large storage requirements, computational pressure, untimely data supply of off-chip memory, and low computational efficiency during hardware deployment due to the large number of convolutional neural network (CNN) parameters, we developed an innovative hardware-friendly CNN pruning method called KRP, which prunes the convolutional kernel on a row scale. A new retraining method based on LR tracking was used to obtain a CNN model with both a high pruning rate and accuracy. Furthermore, we designed a high-performance convolutional computation module on the FPGA platform to help deploy KRP pruning models. The results of comparative experiments on CNNs such as VGG and ResNet showed that KRP has higher accuracy than most pruning methods. At the same time, the KRP method, together with the GSNQ quantization method developed in our previous study, forms a high-precision hardware-friendly network compression framework that can achieve "lossless" CNN compression with a 27× reduction in network model storage. The results of the comparative experiments on the FPGA showed that the KRP pruning method not only requires much less storage space, but also helps to reduce the on-chip hardware resource consumption by more than half and effectively improves the parallelism of the model in FPGAs with a strong hardware-friendly feature. This study provides more ideas for the application of CNNs in the field of edge computing.

Predictive structure building in language comprehension: a large sample study on incremental licensing and parallelism.

In online language comprehension, the parser incrementally builds hierarchical syntactic structures. The predictive nature of this structure-building process has been the subject of extensive debate. A previous study observed that when a wh-phrase indicates parallelism between the upcoming wh-clause and a preceding clause (e.g., John told some stories, but we couldn't remember which stories…), the parser predictively constructs the wh-clause. This observation demonstrates predictive structure building. However, the study also suggests that the parser does not make a prediction when the wh-phrase indicates that parallelism does not hold (e.g., John told some stories … with which stories…), a potential limit to the prediction of syntactic structures. Crucially, these findings are controversial because the study did not observe processing difficulty when disambiguating input indicated that the predicted continuation was inconsistent with the globally grammatical structure (garden-path effects). The controversial results may be due to a lack of statistical power. Therefore, the present study conducted a large-scale replication study (324 participants and 24 sets of materials). The results revealed that the parser predicts the clausal structure, irrespective of the type of wh-phrase. There was also evidence of garden-path effects, supporting the finding that the parser makes a prediction. These observations suggest that the prediction algorithm inherent in the human parser is more powerful than assumed by the previous study and that the parser attempts to construct globally grammatical structures during revision.

A Hybrid Parallel Balanced Phasmatodea Population Evolution Algorithm and Its Application in Workshop Material Scheduling.

The phasmatodea population evolution algorithm (PPE) is a recently proposed meta-heuristic algorithm based on the evolutionary characteristics of the stick insect population. The algorithm simulates the features of convergent evolution, population competition, and population growth in the evolution process of the stick insect population in nature and realizes the above process through the population competition and growth model. Since the algorithm has a slow convergence speed and falls easily into local optimality, in this paper, it is mixed with the equilibrium optimization algorithm to make it easier to avoid the local optimum. Based on the hybrid algorithm, the population is grouped and processed in parallel to accelerate the algorithm's convergence speed and achieve better convergence accuracy. On this basis, we propose the hybrid parallel balanced phasmatodea population evolution algorithm (HP_PPE), and this algorithm is compared and tested on the CEC2017, a novel benchmark function suite. The results show that the performance of HP_PPE is better than that of similar algorithms. Finally, this paper applies HP_PPE to solve the AGV workshop material scheduling problem. Experimental results show that HP_PPE can achieve better scheduling results than other algorithms.

Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations.

How biodiversity arises and can be maintained in asexual microbial populations growing on a single resource remains unclear. Many models presume that beneficial genotypes will outgrow others and purge variation via selective sweeps. Environmental structure like that found in biofilms, which are associated with persistence during infection and other stressful conditions, may oppose this process and preserve variation. We tested this hypothesis by evolving Pseudomonas aeruginosa populations in biofilm-promoting arginine media for 3 months, using both a bead model of the biofilm life cycle and planktonic serial transfer. Surprisingly, adaptation and diversification were mostly uninterrupted by fixation events that eliminate diversity, with hundreds of mutations maintained at intermediate frequencies. The exceptions included genotypes with mutator alleles that also accelerated genetic diversification. Despite the rarity of hard sweeps, a remarkable 40 genes acquired parallel mutations in both treatments and often among competing genotypes within a population. These incomplete soft sweeps include several transporters (including pitA, pntB, nosD, and pchF) suggesting adaptation to the growth media that becomes highly alkaline during growth. Further, genes involved in signal transduction (including gacS, aer2, bdlA, and PA14_71750) reflect likely adaptations to biofilm-inducing conditions. Contrary to evolution experiments that select mutations in a few genes, these results suggest that some environments may expose a larger fraction of the genome and select for many adaptations at once. Thus, even growth on a sole carbon source can lead to persistent genetic and phenotypic variation despite strong selection that would normally purge diversity.

The Genomic Consistency of the Loss of Anadromy in an Arctic Fish (Salvelinus alpinus).

AbstractThe potentially significant genetic consequences associated with the loss of migratory capacity of diadromous fishes that have become landlocked in freshwater are poorly understood. Consistent selective pressures associated with freshwater residency may drive repeated differentiation both between allopatric landlocked and anadromous populations and within landlocked populations (resulting in sympatric morphs). Alternatively, the strong genetic drift anticipated in isolated landlocked populations could hinder consistent adaptation, limiting genetic parallelism. Understanding the degree of genetic parallelism underlying differentiation has implications for both the predictability of evolution and management practices. We employed an 87k single-nucleotide polymorphism (SNP) array to examine the genetic characteristics of landlocked and anadromous Arctic char (Salvelinus alpinus) populations from five drainages within Labrador, Canada. One gene was detected as an outlier between sympatric, size-differentiated morphs in each of two landlocked lakes. While no single locus differentiated all replicate pairs of landlocked and anadromous populations, several SNPs, genes, and paralogs were consistently detected as outliers in at least 70% of these pairwise comparisons. A significant C-score suggested that the amount of shared outlier SNPs across all paired landlocked and anadromous populations was greater than expected by chance. Our results indicate that despite their isolation, selection due to the loss of diadromy may drive consistent genetic responses in landlocked populations.

Inconsistent evolution and growth-survival tradeoffs in Gambusia affinis.

Growth-survival tradeoffs may be a generalizable mechanism influencing trajectories of prey evolution. Here, we investigate evolutionary contributions to growth and survival in western mosquitofish (Gambusia affinis) from 10 populations from high- and low-predation ancestral environments. We assess (i) the degree to which evolutionary components of growth and survival are consistent or inconsistent across populations within ancestral predation environments, and (ii) whether growth and survival trade off at the population level. We measure growth and survival on groups of common-reared mosquitofish in pond mesocosms. We find that evolution of growth is consistent, with fish from low-predation ancestral environments showing higher growth, while the evolution of survival is inconsistent, with significant population-level divergence unrelated to ancestral predation environment. Such inconsistency prevents a growth-survival tradeoff across populations. Thus, the generalizability of contemporary evolution probably depends on local context of evolutionary tradeoffs, and a continued focus on singular selective agents (e.g. predators) without such local context will impede insights into generalizable evolutionary patterns.

The developmental hourglass model and recapitulation: An attempt to integrate the two models.

Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome-based studies, on the other hand, have reported that mid-embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid-embryonic period. In accordance with this, recapitulation-like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility-based study provided molecular evidence for recapitulation in the mid-to-late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular-based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass-like evolutionary conservation in vertebrate embryogenesis.