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This study examines the impact of fire incidents on wildlife and habitats in the western oak forests of Iran (Zagros region). These forests are globally recognized for their exceptional biodiversity but are frequently threatened by wildfires. To achieve this, the study uses the space-time scan statistics permutation (STSSP) model to identify areas with a higher frequency of fires. The study also analyzes the effects of fires on the Zagros forests from 2000 to 2021 using remote-sensing MODIS data. Also, to understand the elements at risk of fire, burned areas were assessed based on the richness of vertebrate species, determined by the distribution of 88 vertebrate species. The results show that the annual fire rate in the Zagros forests is 76.2 (fire occurrences per year), calculated using the Poisson distribution. Findings show the highest fire rates are found in the northwest and a part of the south of the Zagros. The northwest of the Zagros also has the largest number of single fires and clusters, indicating a wide spatial distribution of fire in these regions. On the other side, it was unexpectedly found that these regions have the richest number of species and higher habitat value. The results demonstrate a significant correlation between the value of the habitat and the extent of burned areas (p < 0.05). The study also reveals that the greatest impact of fires is on small vertebrates. The overlap of frequent fire spots with the richest regions of Zagros oak forests in terms of vertebrate diversity emphasizes the need for strategic forest risk reduction planning, especially in these priority zones., (© 2024. The Author(s).)

The olfactory system is an ideal and tractable system for exploring how the brain transforms sensory inputs into behaviour. The basic tasks of any olfactory system include odour detection, discrimination and categorization. The challenge for the olfactory system is to transform the high-dimensional space of olfactory stimuli into the much smaller space of perceived objects and valence that endows odours with meaning. Our current understanding of how neural circuits address this challenge has come primarily from observations of the mechanisms of the brain for processing other sensory modalities, such as vision and hearing, in which optimized deep hierarchical circuits are used to extract sensory features that vary along continuous physical dimensions. The olfactory system, by contrast, contends with an ill-defined, high-dimensional stimulus space and discrete stimuli using a circuit architecture that is shallow and parallelized. Here, we present recent observations in vertebrate and invertebrate systems that relate the statistical structure and state-dependent modulation of olfactory codes to mechanisms of perception and odour-guided behaviour., (© 2024. Springer Nature Limited.)

The Living Planet Index (LPI) measures the average change in population size of vertebrate species over recent decades and has been repeatedly used to assess the changing state of nature. The LPI indicates that vertebrate populations have decreased by almost 70% over the last 50 years. This is in striking contrast with current studies based on the same population time series data that show that increasing and decreasing populations are balanced on average. Here, we examine the methodological pipeline of calculating the LPI to search for the source of this discrepancy. We find that the calculation of the LPI is biased by several mathematical issues which impose an imbalance between detected increasing and decreasing trends and overestimate population declines. Rather than indicating that vertebrate populations do not substantially change, our findings imply that we need better measures for providing a balanced picture of current biodiversity changes. We also show some modifications to improve the reliability of the LPI., (© 2024. The Author(s).)

Large predators have disproportionate effects on their underlying food webs. Thus, appropriately assigning trophic positions has important conservation implications both for the predators themselves and for their prey. Large-bodied predators are often referred to as apex predators, implying that they are many trophic levels above primary producers. However, theoretical considerations predict both higher and lower trophic position with increasing body size. Nitrogen stable isotope values (δ 15 N) are increasingly replacing stomach contents or behavioral observations to assess trophic position and it is often assumed that ontogenetic dietary shifts result in higher trophic positions. Intraspecific studies based on δ 15 N values found a positive relationship between size and inferred trophic position. Here, we use datasets of predatory vertebrate ectotherms (crocodilians, turtles, lizards and fishes) to show that, although there are positive intraspecific relationships between size and δ 15 N values, relationships between stomach-content-based trophic level (TP diet ) and size are undetectable or negative. As there is usually no single value for 15 N trophic discrimination factor (TDF) applicable to a predator species or its prey, estimates of trophic position based on δ 15 N in ectotherm vertebrates with large size ranges, may be inaccurate and biased. We urge a reconsideration of the sole use of δ 15 N values to assess trophic position and encourage the combined use of isotopes and stomach contents to assess diet and trophic level., (© 2024. The Author(s).)

Spexin (SPX, NPQ) is a 14-amino acid neuroactive peptide identified using bioinformatics. This amino acid sequence of the mature spexin peptide has been highly conserved during species evolution and is widely distributed in the central nervous system and peripheral tissues and organs. Therefore, spexin may play a role in various biological functions. Spexin, the cognate ligand for GALR2/3, acting as a neuromodulator or endocrine signaling factor, can inhibit reproductive performance. However, controversies and gaps in knowledge persist regarding spexin-mediated regulation of animal reproductive functions. This review focuses on the hypothalamic-pituitary-gonadal axis and provides a comprehensive overview of the impact of spexin on reproduction. Through this review, we aim to enhance understanding and obtain in-depth insights into the regulation of reproduction by spexin peptides, thereby providing a scientific basis for future investigations into the molecular mechanisms underlying the influence of spexin on reproductive function. Such investigations hold potential benefits for optimizing farming practices in livestock, poultry, and fish industries., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Chen, Feng, Dai, Guo, Yan, Liu and Zhu.)

Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family encodes phospholipases essential for the degradation of organelles in the lens of the eye. These phospholipases translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny and selection of plaat1 across bony fishes and tetrapods. We showed that plaat1 (probably ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual-acuity and blind mammals and fishes. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.

The chronologically ordered generation of distinct cell types is essential for the establishment of neuronal diversity and the formation of neuronal circuits. Recently, single-cell transcriptomic analyses of various areas of the developing vertebrate nervous system have provided evidence for the existence of a shared temporal patterning program that partitions neurons based on the timing of neurogenesis. In this review, I summarize the findings that lead to the proposal of this shared temporal program before focusing on the developing spinal cord to discuss how temporal patterning in general and this program specifically contributes to the ordered formation of neuronal circuits., Competing Interests: Declaration of Competing Interest I hereby declare that I do not have any conflicts of interest. Work in the Sagner Lab is supported by funding from the Deutsche Forschungsgemeinschaft (German Research Foundation — Projektnummer 455354162) and the Interdisciplinary Centre for Clinical Research of the FAU Erlangen-Nürnberg (IZKF – E36). The funders had no role in preparation of the manuscript or the decision to publish., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Navigation requires a network of neurons processing inputs from internally generated cues and external landmarks. Most studies on the neuronal basis of navigation in vertebrates have focused on rats and mice and the canonical senses vision, hearing, olfaction, and somatosensation. Some animals have evolved the ability to sense the Earth's magnetic field and use it for orientation. It can be expected that in these animals magnetic cues are integrated with other sensory cues in the cognitive map. We provide an overview of the behavioral evidence and brain regions involved in magnetic sensing in support of this idea, hoping that this will guide future experiments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Neural-crest cells and neuromesodermal progenitors (NMPs) are multipotent cells that are important for development of vertebrate embryos. In embryos of ascidians, which are the closest invertebrate relatives of vertebrates, several cells located at the border between the neural plate and the epidermal region have neural-crest-like properties; hence, the last common ancestor of ascidians and vertebrates may have had ancestral cells similar to neural-crest cells. However, these ascidian neural-crest-like cells do not produce cells that are commonly of mesodermal origin. Here we showed that a cell population located in the lateral region of the neural plate has properties resembling those of vertebrate neural-crest cells and NMPs. Among them, cells with Tbx6-related expression contribute to muscle near the tip of the tail region and cells with Sox1/2/3 expression give rise to the nerve cord. These observations and cross-species transcriptome comparisons indicate that these cells have properties similar to those of NMPs. Meanwhile, transcription factor genes Dlx.b, Zic-r.b and Snai, which are reminiscent of a gene circuit in vertebrate neural-crest cells, are involved in activation of Tbx6-related.b. Thus, the last common ancestor of ascidians and vertebrates may have had cells with properties of neural-crest cells and NMPs and such ancestral cells may have produced cells commonly of ectodermal and mesodermal origins., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Transglutaminases (TGMs) cross-link proteins by introducing covalent bonds between glutamine and lysine residues. These cross-links are essential for epithelial cornification which enables tetrapods to live on land. Here, we investigated which evolutionary adaptations of vertebrates were associated with specific changes in the family of TGM genes. We determined the catalog of TGMs in the main clades of vertebrates, performed a comprehensive phylogenetic analysis of TGMs, and localized the distribution of selected TGMs in tissues. Our data suggest that TGM1 is the phylogenetically oldest epithelial TGM, with orthologs being expressed in the cornified teeth of the lamprey, a basal vertebrate. Gene duplications led to the origin of TGM10 in stem vertebrates, the origin of TGM2 in jawed vertebrates, and an increasing number of epithelium-associated TGM genes in the lineage leading to terrestrial vertebrates. TGM9 is expressed in the epithelial egg tooth, and its evolutionary origin in stem amniotes coincided with the evolution of embryonic development in eggs that are surrounded by a protective shell. Conversely, viviparous mammals have lost both the epithelial egg tooth and TGM9. TGM3 and TGM6 evolved as regulators of cornification in hair follicles and underwent pseudogenization upon the evolutionary loss of hair in cetaceans. Taken together, this study reveals the gain and loss of vertebrate TGM genes in association with the evolution of cornified skin appendages and suggests an important role of TGM9 in the evolution of amniotes., Competing Interests: Conflict of interest: The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data., (© 2024 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

The Kunming-Montreal Global Biodiversity Framework of the Convention on Biological Diversity calls for an expansion of the current protected areas (PAs) to cover at least 30% of global land and water areas by 2030 (i.e., the 30×30 target). Efficient spatial planning for PA expansion is an urgent need for global conservation practice. A spatial prioritization framework considering multiple dimensions of biodiversity is critical for improving the efficiency of the spatial planning of PAs, yet it remains a challenge. We developed an index for the identification of priority areas based on functionally rare, evolutionarily distinct, and globally endangered species (FREDGE) and applied it to 21,536 terrestrial vertebrates. We determined species distributions, conservation status (global endangerment), molecular phylogenies (evolutionary distinctiveness), and life-history traits (functional rarity). Madagascar, Central America, and the Andes were of high priority for the conservation of multiple dimensions of terrestrial vertebrate biodiversity. However, 68.8% of grid cells in these priority areas had <17% of their area covered by PAs, and these priority areas were under intense anthropogenic and climate change threats. These results highlight the difficulties of conserving multiple dimensions of biodiversity. Our global analyses of the geographical patterns of multiple dimensions of terrestrial vertebrate biodiversity demonstrate the insufficiency of the conservation of different biodiversity dimensions, and our index, based on multiple dimensions of biodiversity, provides a useful tool for guiding future spatial prioritization of PA expansion to achieve the 30×30 target under serious pressures., (© 2024 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Land-use and climate change are major pressures on terrestrial biodiversity. Species' extinction risk and responses to human pressures relate to ecological traits and other characteristics in some clades. However, large-scale comparative assessments of the associations between traits and responses to multiple human pressures across multiple clades are needed. We investigated whether a set of ecological characteristics that are commonly measured across terrestrial vertebrates (ecological traits and geographic range area) are associated with species' responses to different land-use types and species' likely sensitivity to climate change. We aimed to test whether generalizable patterns in response to these pressures arise across both pressures and across vertebrate clades, which could inform assessments of the global signature of human pressures on vertebrate biodiversity and guide conservation efforts. At the species level, we investigated associations between land-use responses and ecological characteristics with a space-for-time substitution approach, making use of the PREDICTS database. We investigated associations between ecological characteristics and expected climate-change sensitivity, estimated from properties of species realized climatic niches. Among the characteristics we considered, 3 were consistently associated with strong land-use responses and high climate-change sensitivity across terrestrial vertebrate classes: narrow geographic range, narrow habitat breadth, and specialization on natural habitats (which described whether a species occurs in artificial habitats or not). The associations of other traits with species' land-use responses and climate-change sensitivity often depended on species' class and land-use type, highlighting an important degree of context dependency. In all classes, invertebrate eaters and fruit and nectar eaters tended to be negatively affected in disturbed land-use types, whereas invertebrate-eating and plant- and seed-eating birds were estimated to be more sensitive to climate change, raising concerns about the continuation of ecological processes sustained by these species under global changes. Our results highlight a consistently higher sensitivity of narrowly distributed species and habitat specialists to land-use and climate change, which provides support for capturing such characteristics in large-scale vulnerability assessments., (© 2023 Society for Conservation Biology.)

The emergence of new structures can often be linked to the evolution of novel cell types that follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are characterized by a complex body plan compared to the other chordate clades and the question remains of whether and how the emergence of vertebrate morphological innovations can be related to the appearance of new embryonic cell populations. We previously proposed, by studying mesoderm development in the cephalochordate amphioxus, a scenario for the evolution of the vertebrate head mesoderm. To further test this scenario at the cell population level, we used scRNA-seq to construct a cell atlas of the amphioxus neurula, stage at which the main mesodermal compartments are specified. Our data allowed us to validate the presence of a prechordal-plate like territory in amphioxus. Additionally, the transcriptomic profile of somite cell populations supports the homology between specific territories of amphioxus somites and vertebrate cranial/pharyngeal and lateral plate mesoderm. Finally, our work provides evidence that the appearance of the specific mesodermal structures of the vertebrate head was associated to both segregation of pre-existing cell populations, and co-option of new genes for the control of myogenesis., (© 2024. The Author(s).)

Background: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes., Results: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses., Conclusions: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome., (© 2024. The Author(s).)

DSCAM (Down syndrome cell adhesion molecule) is a unique neuronal adhesion protein with extensively documented multifaceted functionalities. DSCAM also has interesting properties in vertebrates and invertebrates, respectively. In Drosophila species, particularly, Dscam exhibits remarkable genetic diversity, with tens of thousands of splicing isoforms that modulate the specificity of neuronal wiring. Interestingly, this splice variant diversity of Dscam is absent in vertebrates. DSCAM plays a pivotal role in mitigating excessive adhesion between identical cell types, thereby maintaining the structural and functional coherence of neural networks. DSCAM contributes to the oversight of selective intercellular interactions such as synaptogenesis; however, the precise regulatory mechanisms underlying the promotion and inhibition of cell adhesion involved remain unclear. In this review, we aim to delineate the distinct molecules that interact with DSCAM and their specific roles within the biological landscapes of Drosophila and vertebrates. By integrating these comparative insights, we aim to elucidate the multifunctional nature of DSCAM, particularly its capacity to facilitate or deter intercellular adhesion., Competing Interests: Declaration of interests None. The authors declare that this study was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest. The figures were created using Biorender. com., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

This review examines the possible role of mitochondria in maintaining calcium and phosphate ion homeostasis and participating in the mineralization of bone, cartilage and other vertebrate hard tissues. The paper builds on the known structural features of mitochondria and the documented observations in these tissues that the organelles contain calcium phosphate granules. Such deposits in mitochondria putatively form to buffer excessively high cytosolic calcium ion concentrations and prevent metabolic deficits and even cell death. While mitochondria protect cytosolic enzyme systems through this buffering capacity, the accumulation of calcium ions by mitochondria promotes the activity of enzymes of the tricarboxylic acid (TCA/Krebs) cycle, increases oxidative phosphorylation and ATP synthesis, and leads to changes in intramitochondrial pH. These pH alterations influence ion solubility and possibly the transitions and composition in the mineral phase structure of the granules. Based on these considerations, mitochondria are proposed to support the mineralization process by providing a mobile store of calcium and phosphate ions, in smaller cluster or larger granule form, while maintaining critical cellular activities. The rise in the mitochondrial calcium level also increases the generation of citrate and other TCA cycle intermediates that contribute to cell function and the development of extracellular mineral. This paper suggests that another key role of the mitochondrion, along with the effects just noted, is to supply phosphate ions, derived from the breakdown of ATP, to endolysosomes and autophagic vesicles originating in the endoplasmic reticulum and Golgi and at the plasma membrane. These many separate but interdependent mitochondrial functions emphasize the critical importance of this organelle in the cellular control of vertebrate mineralization., Competing Interests: Declaration of competing interest All authors have no conflicts to declare., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Vertebrate mineralized tissues, present in bones, teeth and scales, have complex 3D hierarchical structures. As more of these tissues are characterized in 3D using mainly FIB SEM at a resolution that reveals the mineralized collagen fibrils and their organization into collagen fibril bundles, highly complex and diverse structures are being revealed. In this perspective we propose an approach to analyzing these tissues based on the presence of modular structures: material textures, pore shapes and sizes, as well as extents of mineralization. This modular approach is complimentary to the widely used hierarchical approach for describing these mineralized tissues. We present a series of case studies that show how some of the same structural modules can be found in different mineralized tissues, including in bone, dentin and scales. The organizations in 3D of the various structural modules in different tissues may differ. This approach facilitates the framing of basic questions such as: are the spatial relations between modular structures the same or similar in different mineralized tissues? Do tissues with similar sets of modules carry out similar functions or can similar functions be carried out using a different set of modular structures? Do mineralized tissues with similar sets of modules have a common developmental or evolutionary pathway? STATEMENT OF SIGNIFICANCE: 3D organization studies of diverse vertebrate mineralized tissues are revealing detailed, but often confusing details about the material textures, the arrangements of pores and differences in the extent of mineralization within a tissue. The widely used hierarchical scheme for describing such organizations does not adequately provide a basis for comparing these tissues, or addressing issues such as structural components thought to be characteristic of bone, being present in dermal tissues and so on. The classification scheme we present is based on identifying structural components within a tissue that can then be systematically compared to other vertebrate mineralized tissues. We anticipate that this classification approach will provide insights into structure-function relations, as well as the evolution of these tissues., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.)

Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial roles in embryonic development. To further our knowledge of CNEs in other parts of the animal tree, we conducted a large-scale characterization of CNEs in more than 50 genomes from three of the main branches of the metazoan tree: Cnidaria, Mollusca, and Arthropoda. We identified hundreds of thousands of CNEs and reconstructed the temporal dynamics of their appearance in each lineage, as well as determining their spatial distribution across genomes. We show that CNEs evolve repeatedly around the same genes across the Metazoa, including around homeodomain genes and other transcription factors; they also evolve repeatedly around genes involved in neural development. We also show that transposons are a major source of CNEs, confirming previous observations from vertebrates and suggesting that they have played a major role in wiring developmental gene regulatory mechanisms since the dawn of animal evolution., (Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution 2024.)

Prestosuchus chiniquensis is the best represented pseudosuchian archosaur from the Pinheiros-Chiniquá Sequence, Middle-Late Triassic (Ladinian/Carnian) of the Santa Maria Supersequence, Southern Brazil. Several incomplete specimens attributed to this species have been described, but the morphology of the postcranial skeleton of P. chiniquensis is poorly known. In this contribution we present the postcranial material of the UFRGS-PV-0629-T specimen, concluding its description, as its skull and endocast have already been described. Additionally, histological data provided new information on the poorly known ontogenetic series of P. chiniquensis, and on its growth patterns suggesting a longer period of slow growth when compared to other basal Loricata species. A phylogenetic analysis placed UFRGS-PV-0629-T in a group composed by the lectotype, paralectotype, and other described P. chiniquensis specimens, further corroborating our taxonomic hypothesis, that specimens of basal Loricata collected in Brazil are closely related to each other. Due to the association of characters found in the phylogenetic analysis, the specimen UFRGS-PV-0629-T is attributed as the most complete material ever found for P. chiniquensis. As such, it is clear that the material presented here provides important new information on P. chiniquensis. Based on the results presented here, we revised the diagnosis for P. chiniquensis. However, it also evidences the need for new discoveries and studies of other specimens seeking to understand this and other closely related species, which were important components of worldwide trophic webs of the Triassic biotas., (© 2024 American Association for Anatomy.)

During gastrulation, Hox genes are activated in a time-sequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated with changes in the chromatin structure and epigenetic profiles of Hox clusters, suggesting a process at least partly based on sequential gene accessibility. Here, we discuss recent work on this issue, as well as a possible mechanism based on the surprising conservation in both the distribution and orientation of CTCF sites inside vertebrate Hox clusters., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing financial interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Our knowledge of the diversity and evolution of South American Triassic pseudosuchians has greatly improved in the past 15 years, due to new discoveries, but also to the revision of several historically important specimens. One of the earliest descriptions of pseudosuchians from the Triassic of Brazil stems from the classic work of Huene from the first half of the 20th century, who described several species, including such influential taxa as Rauisuchus tiradentes or Prestosuchus chiniquensis, which have recently been reviewed. The more poorly known proposed second species of Prestosuchus, P. loricatus, is the focus of the present work. The original material included some elements of the axial skeleton (cervical and caudal vertebrae, ribs, osteoderms) and the hindlimb (ischia, calcaneum, metatarsus), collected from the Dinodontosaurus Assemblage Zone of the Chiniquá area, west of São Pedro do Sul. "Prestosuchus" loricatus shows numerous differences to P. chiniquensis, including the shape of cervical neural spines, presence of epipophyses on the cervical vertebrae, presence of a pit in the iliac articulation of the ischium, lack of longitudinal furrows in the dorsolateral surface of the ischial shafts, the more slender calcaneal tuber and a less pronounced ventral pit in the calcaneum, and is thus referred to a new genus, Schultzsuchus gen. nov. Phylogenetic analysis indicates an early branching position within Poposauroidea for Schultzsuchus, making it the oldest known member of this clade in South America., (© 2024 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences., (© The Author(s) 2024. Published by Oxford University Press.)

Inhibitory control (IC) plays a central role in behaviour control allowing an individual to resist external lures and internal predispositions. While IC has been consistently investigated in humans, other mammals, and birds, research has only recently begun to explore IC in other vertebrates. This review examines current literature on teleost fish, focusing on both methodological and conceptual aspects. I describe the main paradigms adopted to study IC in fish, identifying well-established tasks that fit various research applications and highlighting their advantages and limitations. In the conceptual analysis, I identify two well-developed lines of research with fish examining IC. The first line focuses on a comparative approach aimed to describe IC at the level of species and to understand the evolution of interspecific differences in relation to ecological specialisation, brain size, and factors affecting cognitive performance. Findings suggest several similarities between fish and previously studied vertebrates. The second line of research focuses on intraspecific variability of IC. Available results indicate substantial variation in fish IC related to sex, personality, genetic, age, and phenotypic plasticity, aligning with what is observed with other vertebrates. Overall, this review suggests that although data on teleosts are still scarce compared to mammals, the contribution of this group to IC research is already substantial and can further increase in various disciplines including comparative psychology, cognitive ecology, and neurosciences, and even in applied fields such as psychiatry research., (© 2024. The Author(s).)

Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources of raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute to the evolution of morphological complexity during the course of vertebrate evolution, such as the evolution from two heart chambers (fishes) to four heart chambers (mammals and birds). We addressed this issue by our heart RNA-Seq experiments combined with published data, using 13 vertebrates and one invertebrate (sea squirt, as an outgroup). Our evolutionary transcriptome analysis showed that number of ancient paralogous genes expressed in heart tends to increase with the increase of heart chamber number along the vertebrate phylogeny, in spite that most of them were duplicated at the time near to the origin of vertebrates or even more ancient. Moreover, those paralogs expressed in heart exert considerably different functions from heart-expressed singletons: the former are functionally enriched in cardiac muscle and muscle contraction-related categories, whereas the latter play more basic functions of energy generation like aerobic respiration. These findings together support the notion that recruiting anciently paralogous genes that are expressed in heart is associated with the increase of chamber number in vertebrate evolution., (© 2024 Wiley Periodicals LLC.)

Vertebrate species worldwide are currently facing significant declines in many populations. Although we have gained substantial knowledge about the direct threats that affect individual species, these threats only represent a fraction of the broader vertebrate threat profile, which is also shaped by species interactions. For example, threats faced by prey species can jeopardize the survival of their predators due to food resource scarcity. Yet, indirect threats arising from species interactions have received limited investigation thus far. In this study, we investigate the indirect consequences of anthropogenic threats on biodiversity in the context of European vertebrate food webs. We integrated data on trophic interactions among over 800 terrestrial vertebrates, along with their associated human-induced threats. We quantified and mapped the vulnerability of various components of the food web, including species, interactions, and trophic groups to six major threats: pollution, agricultural intensification, climate change, direct exploitation, urbanization, and invasive alien species and diseases. Direct exploitation and agricultural intensification were two major threats for terrestrial vertebrate food webs: affecting 34% and 31% of species, respectively, they threaten 85% and 69% of interactions in Europe. By integrating network ecology with threat impact assessments, our study contributes to a better understanding of the magnitude of anthropogenic impacts on biodiversity., (© 2024 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

RNA Binding Proteins regulate, in part, alternative pre-mRNA splicing and, in turn, gene expression patterns. Polypyrimidine tract binding proteins PTBP1 and PTBP2 are paralogous RNA binding proteins sharing 74% amino acid sequence identity. Both proteins contain four structured RNA-recognition motifs (RRMs) connected by linker regions and an N-terminal region. Despite their similarities, the paralogs have distinct tissue-specific expression patterns and can regulate discrete sets of target exons. How two highly structurally similar proteins can exert different splicing outcomes is not well understood. Previous studies revealed that PTBP2 is post-translationally phosphorylated in the unstructured N-terminal, Linker 1, and Linker 2 regions that share less sequence identity with PTBP1 signifying a role for these regions in dictating the paralog's distinct splicing activities. To this end, we conducted bioinformatics analysis to determine the evolutionary conservation of RRMs versus linker regions in PTBP1 and PTBP2 across species. To determine the role of PTBP2 unstructured regions in splicing activity, we created hybrid PTBP1-PTBP2 constructs that had counterpart PTBP1 regions swapped to an otherwise PTBP2 protein and assayed on differentially regulated exons. We also conducted molecular dynamics studies to investigate how negative charges introduced by phosphorylation in PTBP2 unstructured regions can alter their physical properties. Collectively, results from our studies reveal an important role for PTBP2 unstructured regions and suggest a role for phosphorylation in the differential splicing activities of the paralogs on certain regulated exons., Competing Interests: Conflict of interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The mechanisms by which the vertebrate stomach undergoes its evolutionarily conserved leftward bending remain incompletely understood. Although the left and right sides of the organ are known to possess different gene expression patterns and undergo distinct morphogenetic events, the physical mechanisms by which these differences generate morphological asymmetry remain unclear. Here, we develop a continuum model of asymmetric stomach morphogenesis. Using a morphoelastic framework, we investigate the morphogenetic implications of a variety of hypothetical, tissue-level growth differences between the left and right sides of a simplified tubular organ. Simulations reveal that, of the various differential growth mechanisms tested, only one category is consistent with the leftward stomach curvature observed in wild-type embryos: equal left and right volumetric growth rates, coupled with transversely isotropic tissue thinning on the left side. Simulating this mechanism in a defined region of the model over a longer period of growth leads to mature stomach-like curvatures., (Copyright © 2024. Published by Elsevier B.V.)

Animal colour vision is based on comparing signals from different photoreceptors. It is generally assumed that processing different spectral types of photoreceptor mainly serves colour vision. Here I propose instead that photoreceptors are parallel feature channels that differentially support visual-motor programmes like motion vision behaviours, prey capture and predator evasion. Colour vision may have emerged as a secondary benefit of these circuits, which originally helped aquatic vertebrates to visually navigate and segment their underwater world. Specifically, I suggest that ancestral vertebrate vision was built around three main systems, including a high-resolution general purpose greyscale system based on ancestral red cones and rods to mediate visual body stabilization and navigation, a high-sensitivity specialized foreground system based on ancestral ultraviolet cones to mediate threat detection and prey capture, and a net-suppressive system based on ancestral green and blue cones for regulating red/rod and ultraviolet circuits. This ancestral strategy probably still underpins vision today, and different vertebrate lineages have since adapted their original photoreceptor circuits to suit their diverse visual ecologies., (© 2024. Springer Nature Limited.)

Detecting declines and quantifying extinction risk of long-lived, highly fecund vertebrates, including fishes, reptiles, and amphibians, can be challenging. In addition to the false notion that large clutches always buffer against population declines, the imperiled status of long-lived species can often be masked by extinction debt, wherein adults persist on the landscape for several years after populations cease to be viable. Here we develop a demographic model for the eastern hellbender (Cryptobranchus alleganiensis), an imperiled aquatic salamander with paternal care. We examined the individual and interactive effects of three of the leading threats hypothesized to contribute to the species' demise: habitat loss due to siltation, high rates of nest failure, and excess adult mortality caused by fishing and harvest. We parameterized the model using data on their life history and reproductive ecology to model the fates of individual nests and address multiple sources of density-dependent mortality under both deterministic and stochastic environmental conditions. Our model suggests that high rates of nest failure observed in the field are sufficient to drive hellbender populations toward a geriatric age distribution and eventually to localized extinction but that this process takes decades. Moreover, the combination of limited nest site availability due to siltation, nest failure, and stochastic adult mortality can interact to increase the likelihood and pace of extinction, which was particularly evident under stochastic scenarios. Density dependence in larval survival and recruitment can severely hamper a population's ability to recover from declines. Our model helps to identify tipping points beyond which extinction becomes certain and management interventions become necessary. Our approach can be generalized to understand the interactive effects of various threats to the extinction risk of other long-lived vertebrates. As we face unprecedented rates of environmental change, holistic approaches incorporating multiple concurrent threats and their impacts on different aspects of life history will be necessary to proactively conserve long-lived species., (© 2024 The Ecological Society of America.)

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution 1-3 . Here we investigate the complex history, timing and functional role of genome-wide duplications 4-7 and programmed DNA elimination 8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1R V ) that predates the early Cambrian cyclostome-gnathostome split, followed by a mid-late Cambrian allo-tetraploidization (2R JV ) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidization (2R CY ) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan 1,2 . Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys 10,11 . Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates., (© 2024. The Author(s).)

The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism., (© 2024 Cold Spring Harbor Laboratory Press.)

Background: Recent studies in the field of molecular identification have described 16S rRNA gene as a highly informative fragment of mitochondrial DNA for species discrimination. This study presents a newly developed universal primer pair yielding an approximately 350 bp fragment of mitochondrial 16S rRNA, variable enough to encompass and identify all vertebrate classes., Methods and Results: The primers were designed by aligning and analyzing over 1500 16S rRNA sequences downloaded from the NCBI nucleotide database. A total of 93 vertebrate species, spanning 27 orders and 55 families, were PCR-amplified to validate the primers. All the target species were successfully amplified and identified when aligned with reference sequences from the NCBI nucleotide database. Using the Kimura 2-parameter model, low intra-species genetic divergence of the target region was observed - from 0 to 4.63%, whereas relatively higher inter-species genetic divergence was observed, ranging from 4.88% to 69.81%. Moreover, the newly developed primers were successfully applied to a direct PCR protocol, making the workflow very cost-effective, time-saving and less laborious in comparison to conventional PCR., Conclusions: The short length, high variability and conserved priming sites of the target fragment across all vertebrate species make it a highly desirable marker for species identification and discrimination., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Ionotropic glutamate receptors (iGluRs) mediate excitatory signals between cells by binding neurotransmitters and conducting cations across the cell membrane. In the mammalian brain, most of these signals are mediated by two types of iGluRs: AMPA and NMDA (i.e. iGluRs sensitive to 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl)propanoic acid and N-methyl-D-aspartic acid, respectively). Delta-type iGluRs of mammals also form neurotransmitter-binding channels in the cell membrane, but in contrast, their channel is not activated by neurotransmitter binding, raising biophysical questions about iGluR activation and biological questions about the role of delta iGluRs. We therefore investigated the divergence of delta iGluRs from their iGluR cousins using molecular phylogenetics, electrophysiology, and site-directed mutagenesis. We find that delta iGluRs are found in numerous bilaterian animals (e.g., worms, starfish, and vertebrates) and are closely related to AMPA receptors, both genetically and functionally. Surprisingly, we observe that many iGluRs of the delta family are activated by the classical inhibitory neurotransmitter, γ-aminobutyric acid (GABA). Finally, we identify nine amino acid substitutions that likely gave rise to the inactivity of today's mammalian delta iGluRs, and these mutations abolish activity when engineered into active invertebrate delta iGluRs, partly by inducing receptor desensitization. These results offer biophysical insight into iGluR activity and point to a role for GABA in excitatory signaling in invertebrates., Competing Interests: Competing interests statement:The authors declare no competing interest.

Metabolism underpins all life-sustaining processes and varies profoundly with body size, temperature and locomotor activity. A current theory explains some of the size-dependence of metabolic rate (its mass exponent, b) through changes in metabolic level (L). We propose two predictive advances that: (a) combine the above theory with the evolved avoidance of oxygen limitation in water-breathers experiencing warming, and (b) quantify the overall magnitude of combined temperatures and degrees of locomotion on metabolic scaling across air- and water-breathers. We use intraspecific metabolic scaling responses to temperature (523 regressions) and activity (281 regressions) in diverse ectothermic vertebrates (fish, reptiles and amphibians) to show that b decreases with temperature-increased L in water-breathers, supporting surface area-related avoidance of oxygen limitation, whereas b increases with activity-increased L in air-breathers, following volume-related influences. This new theoretical integration quantitatively incorporates different influences (warming, locomotion) and respiration modes (aquatic, terrestrial) on animal energetics., (© 2024 The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

Here, we review recent developments in the literature that provide insight into self-organization at supracellular scales in vertebrate organ morphogenesis. We briefly present a historical and conceptual analysis of the term "self-organization." Based on this analysis, we suggest that self-organizing processes, at their root, possess a form of causal relationship, reciprocal causality, that is markedly distinct from linear causal chains. We survey the extent to which reciprocal causality can be used to interpret or clarify supracellular studies in development and disease. Finally, we explore how reciprocal causality can exist across length-scales, identifying situations where multiple scales require simultaneous analysis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Carrion decomposition is fundamental to nutrient cycling in terrestrial ecosystems because it provides a high-quality resource to diverse organisms. A conceptual framework incorporating all phases of carrion decomposition with the full community of scavengers is needed to predict the effects of global change on core ecosystem processes. Because global change can differentially impact scavenger guilds and rates of carrion decomposition, our framework explicitly incorporates complex interactions among microbial, invertebrate, and vertebrate scavenger communities across three distinct phases of carcass decomposition. We hypothesize that carrion decomposition rates will be the most impacted when global change affects carcass discovery rates and the foraging behavior of competing scavenger guilds., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Telomeres are short repetitive DNA sequences capping the ends of chromosomes. Telomere shortening occurs during cell division and may be accelerated by oxidative damage or ameliorated by telomere maintenance mechanisms. Consequently, telomere length changes with age, which was recently confirmed in a large meta-analysis across vertebrates. However, based on the correlation between telomere length and age, it was concluded that telomere length can be used as a tool for chronological age estimation in animals. Correlation should not be confused with predictability, and the current data and studies suggest that telomeres cannot be used to reliably predict individual chronological age. There are biological reasons for why there is large individual variation in telomere dynamics, which is mainly due to high susceptibility to a wide range of environmental, but also genetic factors, rendering telomeres unfeasible as a tool for age estimation. The use of telomeres for chronological age estimation is largely a misguided effort, but its occasional reappearance in the literature raises concerns that it will mislead resources in wildlife conservation., (© 2023 Wiley Periodicals LLC.)

Cross-border neighboring areas could be particularly vulnerable to biological invasions due to short geographic distances and frequent interactions, although the invasion risk remains unevaluated worldwide. Here, based on global datasets of distributions of established alien vertebrates as well as vectors of introduction and establishment, we show that more than one-third of the world's transboundary neighboring areas are facing high invasion risk of alien vertebrates, especially in Europe, North America, South Asia, and Southeast Asia. The most important predictors of high introduction and establishment risk are bilateral trade, habitat disturbance and the richness of established alien vertebrates. Interestingly, we found that border fences may have limited effects in reducing the risk, as only 7.9% of border fences spatially overlap with hotspots of biological invasion even in the Eurasia areas (13.7% overlap) where physical border barriers are mainly located. We therefore recommend the implementation of immediate and proactive prevention and control measures to cope with cross-border invasions in response to continued globalization., (© 2024. The Author(s).)

The richest and most diverse assemblage of early terrestrial tetrapods is preserved within the infilled cave system of Richards Spur, Oklahoma (289-286 Mya 1 ). Some of the oldest-known terrestrial amniotes 2 , This phenomenon has also afforded the preservation of exceedingly rare integumentary soft tissues, reported here, providing critical first evidence into the anatomical changes marking the transition from the aquatic and semiaquatic lifestyles of anamniotes to the fully terrestrial lifestyles of early amniotes. This is the first record of a skin-cast fossil (3D carbonization of the skin proper) from the Paleozoic Era and the earliest known occurrence of epidermal integumentary structures. We also report on several compression fossils (carbonized skin impressions), all demonstrating similar external morphologies to extant crocodiles. A variety of previously unknown ossifications, as well as what are likely palpebral ossifications of the deeper dermis layer of the skin, are also documented. These fossils also serve as invaluable references for paleontological reconstructions. Chromatographic analysis of extractable hydrocarbons from bone and cave samples indicates that the source rock is the Devonian age Woodford Shale. Hydrocarbons derived from ancient marine organisms interacting with geologically younger terrestrial vertebrates have therefore resulted in the oldest-known preservation of amniote skin proper.3 are exquisitely preserved here because of early impregnation and encasement of organic material by oil-seep hydrocarbons within rapidly deposited clay-rich cave sediments under toxic anoxic conditions. 4 This phenomenon has also afforded the preservation of exceedingly rare integumentary soft tissues, reported here, providing critical first evidence into the anatomical changes marking the transition from the aquatic and semiaquatic lifestyles of anamniotes to the fully terrestrial lifestyles of early amniotes. This is the first record of a skin-cast fossil (3D carbonization of the skin proper) from the Paleozoic Era and the earliest known occurrence of epidermal integumentary structures. We also report on several compression fossils (carbonized skin impressions), all demonstrating similar external morphologies to extant crocodiles. A variety of previously unknown ossifications, as well as what are likely palpebral ossifications of the deeper dermis layer of the skin, are also documented. These fossils also serve as invaluable references for paleontological reconstructions. Chromatographic analysis of extractable hydrocarbons from bone and cave samples indicates that the source rock is the Devonian age Woodford Shale. Hydrocarbons derived from ancient marine organisms interacting with geologically younger terrestrial vertebrates have therefore resulted in the oldest-known preservation of amniote skin proper., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Chemokine signalling performs key functions in cell migration via chemoattraction, such as attracting leukocytes to the site of infection during host defence. The system consists of a ligand, the chemokine, usually secreted outside the cell, and a chemokine receptor on the surface of a target cell that recognises the ligand. Several noncanonical components interact with the system. These include a variety of molecules that usually share some degree of sequence similarity with canonical components and, in some cases, are known to bind to canonical components and/or to modulate cell migration. Whereas canonical components have been described in vertebrate lineages, the distribution of the noncanonical components is less clear. Uncertainty over the relationships between canonical and noncanonical components hampers our understanding of the evolution of the system. We used phylogenetic methods, including gene-tree to species-tree reconciliation, to untangle the relationships between canonical and noncanonical components, identify gene duplication events, and clarify the origin of the system. We found that unrelated ligand groups independently evolved chemokine-like functions. We found noncanonical ligands outside vertebrates, such as TAFA "chemokines" found in urochordates. In contrast, all receptor groups are vertebrate-specific and all-except ACKR1-originated from a common ancestor in early vertebrates. Both ligand and receptor copy numbers expanded through gene duplication events at the base of jawed vertebrates, with subsequent waves of innovation occurring in bony fish and mammals., (© 2024 Aleotti et al.)

Marine vertebrate biodiversity is fundamental to ocean ecosystem health but is threatened by climate change, overharvesting, and habitat degradation. High-quality reference genomes are valuable foundational scientific resources that can inform conservation efforts. Consequently, global consortia are striving to produce reference genomes for representatives of all life. Here, we summarize the current landscape of available marine vertebrate reference genomes, including their phylogenetic diversity and geographic hotspots of production. We discuss key logistical and technical challenges that remain to be overcome if we are to realize the vision of a comprehensive reference genome library of all marine vertebrates., (© The Author(s) 2024. Published by Oxford University Press GigaScience.)

Morphogenesis is a physical process that sculpts the final functional forms of tissues and organs. Remarkably, the lungs of terrestrial vertebrates vary dramatically in form across species, despite providing the same function of transporting oxygen and carbon dioxide. These divergent forms arise from distinct physical processes through which the epithelium of the embryonic lung responds to the mechanical properties of its surrounding mesenchymal microenvironment. Here we compare the physical processes that guide folding of the lung epithelium in mammals, birds, and reptiles, and suggest a conceptual framework that reconciles how conserved molecular signaling generates divergent mechanical forces across these species., (Copyright © 2024. Published by Elsevier Inc.)

Morphogenesis from cells to tissue gives rise to the complex architectures that make our organs. How cells and their dynamic behavior are translated into functional spatial patterns is only starting to be understood. Recent advances in quantitative imaging revealed that, although highly heterogeneous, cellular behaviors make reproducible tissue patterns. Emerging evidence suggests that mechanisms of cellular coordination, intrinsic variability and plasticity are critical for robust pattern formation. While pattern development shows a high level of fidelity, tissue organization has undergone drastic changes throughout the course of evolution. In addition, alterations in cell behavior, if unregulated, can cause developmental malformations that disrupt function. Therefore, comparative studies of different species and of disease models offer a powerful approach for understanding how novel spatial configurations arise from variations in cell behavior and the fundamentals of successful pattern formation. In this chapter, I dive into the development of the vertebrate nervous system to explore efforts to dissect pattern formation beyond molecules, the emerging core principles and open questions., (Copyright © 2024. Published by Elsevier Inc.)

Background: The phylotypic or intermediate stages are thought to be the most evolutionary conserved stages throughout embryonic development. The contrast with divergent early and later stages derived from the concept of the evo-devo hourglass model. Nonetheless, this developmental constraint has been studied as a whole embryo process, not at organ level. In this review, we explore brain development to assess the existence of an equivalent brain developmental hourglass. In the specific case of vertebrates, we propose to split the brain developmental stages into: (1) Early: Neurulation, when the neural tube arises after gastrulation. (2) Intermediate: Brain patterning and segmentation, when the neuromere identities are established. (3) Late: Neurogenesis and maturation, the stages when the neurons acquire their functionality. Moreover, we extend this analysis to other chordates brain development to unravel the evolutionary origin of this evo-devo constraint., Summary: Based on the existing literature, we hypothesise that a major conservation of the phylotypic brain might be due to the pleiotropy of the inductive regulatory networks, which are predominantly expressed at this stage. In turn, earlier stages such as neurulation are rather mechanical processes, whose regulatory networks seem to adapt to environment or maternal geometries. The later stages are also controlled by inductive regulatory networks, but their effector genes are mostly tissue-specific and functional, allowing diverse developmental programs to generate current brain diversity. Nonetheless, all stages of the hourglass are highly interconnected: divergent neurulation must have a vertebrate shared end product to reproduce the vertebrate phylotypic brain, and the boundaries and transcription factor code established during the highly conserved patterning will set the bauplan for the specialised and diversified adult brain., Key Messages: The vertebrate brain is conserved at phylotypic stages, but the highly conserved mechanisms that occur during these brain mid-development stages (Inducing Regulatory Networks) are also present during other stages. Oppositely, other processes as cell interactions and functional neuronal genes are more diverse and majoritarian in early and late stages of development, respectively. These phenomena create an hourglass of transcriptomic diversity during embryonic development and evolution, with a really conserved bottleneck that set the bauplan for the adult brain around the phylotypic stage., (© 2024 S. Karger AG, Basel.)