Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

Turtle skull development unveils a molecular basis for amniote cranial diversity

Amniote skulls display diverse architectural patterns including remarkable variations in the number of temporal arches surrounding the upper and lower temporal fenestrae. However, the cellular and molecular basis underlying this diversification remains elusive. Turtles are a useful model to understand skull diversity due to the presence of secondarily closed temporal fenestrae and different extents of temporal emarginations (marginal reduction of dermal bones). Here, we analyzed embryos of three turtle species with varying degrees of temporal emargination and identified shared widespread coexpression of upstream osteogenic genes Msx2 and Runx2 and species-specific expression of more downstream osteogenic genes Sp7 and Sparc in the head. Further analysis of representative amniote embryos revealed differential expression patterns of osteogenic genes in the temporal region, suggesting that the spatiotemporal regulation of Msx2, Runx2, and Sp7 distinguishes the temporal skull morphology among amniotes. Moreover, the presence of Msx2- and/or Runx2-positive temporal mesenchyme with osteogenic potential may have contributed to their extremely diverse cranial morphology in reptiles.

Turtle Shell Kinesis Underscores Constraints and Opportunities in the Evolution of the Vertebrate Musculoskeletal System

Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or "hinges," which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.

An armoured marine reptile from the Early Triassic of South China and its phylogenetic and evolutionary implications

Sauropterygia was a taxonomically and ecomorphologically diverse clade of Mesozoic marine reptiles spanning the Early Triassic to the Late Cretaceous. Sauropterygians are traditionally divided into two groups representing two markedly different body plans - the short-necked, durophagous Placodontia and the long-necked Eosauropterygia - whereas Saurosphargidae, a small clade of armoured marine reptiles, is generally considered as the sauropterygian sister-group. However, the early evolutionary history of sauropterygians and their phylogenetic relationships with other groups within Diapsida are still incompletely understood. Here, we report a new saurosphargid from the Early Triassic (Olenekian) of South China - Prosaurosphargis yingzishanensis gen. et sp. nov. - representing the earliest known occurrence of the clade. An updated phylogenetic analysis focussing on the interrelationships among diapsid reptiles recovers saurosphargids as nested within sauropterygians, forming a clade with eosauropterygians to the exclusion of placodonts. Furthermore, a clade comprising Eusaurosphargis and Palatodonta is recovered as the sauropterygian sister-group within Sauropterygomorpha tax. nov. The phylogenetic position of several Early and Middle Triassic sauropterygians of previously uncertain phylogenetic affinity, such as Atopodentatus, Hanosaurus, Majiashanosaurus, and Corosaurus, is also clarified, elucidating the early evolutionary assembly of the sauropterygian body plan. Finally, our phylogenetic analysis supports the placement of Testudines and Archosauromorpha within Archelosauria, a result strongly corroborated by molecular data, but only recently recovered in a phylogenetic analysis using a morphology-only dataset. Our study provides evidence for the rapid diversification of sauropterygians in the aftermath of the Permo-Triassic mass extinction event and emphasises the importance of broad taxonomic sampling in reconstructing phylogenetic relationships among extinct taxa.

Electroretinography, Ocular Ultrasonography, and Phacoemulsification of Bilateral Cataracts in Two Juvenile Loggerhead Sea Turtles (Caretta caretta) of the Mediterranean Region

Bilateral cataracts were diagnosed in two rescued juvenile, immature loggerhead sea turtles (Caretta caretta), weighing 1.65 and 1.7 kg. Both animals showed vision impairment and difficulty in feeding without assistance. In fact, they did not notice the presence of the food in the tank unless it was brought close to touching the mouth. Ocular ultrasonography and electroretinography showed no lesions of the vitreal body and retinal layer, therefore, both animals were candidates for bilateral cataract surgery. Topical administration of tropicamide + phenylephrine alternating with rocuronium resulted in only minimal mydriasis. Administration of intracameral rocuronium did not improve mydriasis. Phacoemulsification using a one-handed technique was performed bilaterally with a phacoemulsification device (Sovereign, AMO (Abbott Medical Optics^®). After surgery, the systemic anti-inflammatory drug (dexamethasone 0.2 mg/kg, IM daily for one week) and antibiotics (enrofloxacin 10 mg/kg IM q 72 h, for 4 weeks; ceftazidime 20 mg/kg IM q 72 h for 3 weeks) were administered. Topical ofloxacin, flurbiprofen and tobramycin/dexamethasone were instilled TID for 4 weeks. Both turtles regained vision in both eyes. Results at a 10-month follow-up were satisfactory. This is the first report of cataracts in turtles rescued in the Mediterranean Sea and the first description of surgical treatment of cataracts in loggerhead turtles so young.

Evidence for heterothermic endothermy and reptile-like eggshell mineralization in Troodon, a non-avian maniraptoran theropod

The dinosaur-bird transition involved several anatomical, biomechanical, and physiological modifications of the theropod bauplan. Non-avian maniraptoran theropods, such as Troodon, are key to better understand changes in thermophysiology and reproduction occurring during this transition. Here, we applied dual clumped isotope (Δ47 and Δ48) thermometry, a technique that resolves mineralization temperature and other nonthermal information recorded in carbonates, to eggshells from Troodon, modern reptiles, and modern birds. Troodon eggshells show variable temperatures, namely 42 and 29 ± 2 °C, supporting the hypothesis of an endothermic thermophysiology with a heterothermic strategy for this extinct taxon. Dual clumped isotope data also reveal physiological differences in the reproductive systems between Troodon, reptiles, and birds. Troodon and modern reptiles mineralize their eggshells indistinguishable from dual clumped isotope equilibrium, while birds precipitate eggshells characterized by a positive disequilibrium offset in Δ48. Analyses of inorganic calcites suggest that the observed disequilibrium pattern in birds is linked to an amorphous calcium carbonate (ACC) precursor, a carbonate phase known to accelerate eggshell formation in birds. Lack of disequilibrium patterns in reptile and Troodon eggshells implies these vertebrates had not acquired the fast, ACC-based eggshell calcification process characteristic of birds. Observation that Troodon retained a slow reptile-like calcification suggests that it possessed two functional ovaries and was limited in the number of eggs it could produce; thus its large clutches would have been laid by several females. Dual clumped isotope analysis of eggshells of extinct vertebrates sheds light on physiological information otherwise inaccessible in the fossil record.

Creating morphological diversity in reptilian temporal skull region: A review of potential developmental mechanisms

Reptilian skull morphology is highly diverse and broadly categorized into three categories based on the number and position of the temporal fenestrations: anapsid, synapsid, and diapsid. According to recent phylogenetic analysis, temporal fenestrations evolved twice independently in amniotes, once in Synapsida and once in Diapsida. Although functional aspects underlying the evolution of tetrapod temporal fenestrations have been well investigated, few studies have investigated the developmental mechanisms responsible for differences in the pattern of temporal skull region. To determine what these mechanisms might be, we first examined how the five temporal bones develop by comparing embryonic cranial osteogenesis between representative extant reptilian species. The pattern of temporal skull region may depend on differences in temporal bone growth rate and growth direction during ontogeny. Next, we compared the histogenesis patterns and the expression of two key osteogenic genes, Runx2 and Msx2, in the temporal region of the representative reptilian embryos. Our comparative analyses suggest that the embryonic histological condition of the domain where temporal fenestrations would form predicts temporal skull morphology in adults and regulatory modifications of Runx2 and Msx2 expression in osteogenic mesenchymal precursor cells are likely involved in generating morphological diversity in the temporal skull region of reptiles.

Africa's oldest dinosaurs reveal early suppression of dinosaur distribution

The vertebrate lineages that would shape Mesozoic and Cenozoic terrestrial ecosystems originated across Triassic Pangaea^1-11. By the Late Triassic (Carnian stage, ~235 million years ago), cosmopolitan 'disaster faunas' (refs. ^12-14) had given way to highly endemic assemblages^12,13 on the supercontinent. Testing the tempo and mode of the establishment of this endemism is challenging-there were few geographic barriers to dispersal across Pangaea during the Late Triassic. Instead, palaeolatitudinal climate belts, and not continental boundaries, are proposed to have controlled distribution^15-18. During this time of high endemism, dinosaurs began to disperse and thus offer an opportunity to test the timing and drivers of this biogeographic pattern. Increased sampling can test this prediction: if dinosaurs initially dispersed under palaeolatitudinal-driven endemism, then an assemblage similar to those of South America^4,19-21 and India^19,22-including the earliest dinosaurs-should be present in Carnian deposits in south-central Africa. Here we report a new Carnian assemblage from Zimbabwe that includes Africa's oldest definitive dinosaurs, including a nearly complete skeleton of the sauropodomorph Mbiresaurus raathi gen. et sp. nov. This assemblage resembles other dinosaur-bearing Carnian assemblages, suggesting that a similar vertebrate fauna ranged high-latitude austral Pangaea. The distribution of the first dinosaurs is correlated with palaeolatitude-linked climatic barriers, and dinosaurian dispersal to the rest of the supercontinent was delayed until these barriers relaxed, suggesting that climatic controls influenced the initial composition of the terrestrial faunas that persist to this day.

Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

Structural and physiological changes in the female reproductive system underlie the origins of pregnancy in multiple vertebrate lineages. In mammals, the glandular portion of the lower reproductive tract has transformed into a structure specialized for supporting fetal development. These specializations range from relatively simple maternal nutrient provisioning in egg-laying monotremes to an elaborate suite of traits that support intimate maternal-fetal interactions in Eutherians. Among these traits are the maternal decidua and fetal component of the placenta, but there is considerable uncertainty about how these structures evolved. Previously, we showed that changes in uterine gene expression contributes to several evolutionary innovations during the origins of pregnancy (Mika et al., 2021b). Here, we reconstruct the evolution of entire transcriptomes ('ancestral transcriptome reconstruction') and show that maternal gene expression profiles are correlated with degree of placental invasion. These results indicate that an epitheliochorial-like placenta evolved early in the mammalian stem-lineage and that the ancestor of Eutherians had a hemochorial placenta, and suggest maternal control of placental invasiveness. These data resolve major transitions in the evolution of pregnancy and indicate that ancestral transcriptome reconstruction can be used to study the function of ancestral cell, tissue, and organ systems.

Distinguishing Evolutionary Conservation from Derivedness

While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.

Reduction, reorganization and stasis in the evolution of turtle shell elements

Novel phenotypic configurations can profoundly alter the evolutionary trajectories of species. Although innovation can precede lengthy periods of evolutionary stasis, the potential for species to diversify further can be realized via modular changes across distinct levels of hierarchical organization. To test this expectation, we undertook anatomical network analyses to model the organization and composition of the turtle’s shell. Our results suggest that stem turtles featured the greatest diversity in the number of skeletal (bones) and epidermal (scutes) shell elements. The shell subsequently underwent numerical simplification. Thus, the sum of potential connections (links) in shell networks has diminished in modern turtles. Some network system descriptors of complexity, integration and modularity covaried with the number of network components (nodes), which has remained evolutionarily stable since the Jurassic. We also demonstrated that shell reorganization might be feasible within modular subdivisions, particularly in modern turtles with simplified and less integrated network structures. We discuss how these findings align with previous studies on numerical simplification with enhanced skeletal specialization in the tetrapod skull. Altogether, our analyses expose the evolvability of the turtle’s shell and bolster the foundation for further macroevolutionary comparisons of ancient and modern species.

The menisci are not shock absorbers: A biomechanical and comparative perspective

The lateral and medial menisci are fibrocartilaginous structures in the knee that play a crucial role in normal knee biomechanics. However, one commonly cited role of the menisci is that they function as "shock absorbers." Here we provide a critique of this notion, drawing upon a review of comparative anatomical and biomechanical data from humans and other tetrapods. We first review those commonly, and often exclusively, cited studies in support of a shock absorption function and show that evidence for a shock absorptive function is dubious. We then review the evolutionary and comparative evidence to show that (1) the human menisci are unremarkable in morphology compared with most other tetrapods, and (2) "shock" during locomotion is uncommon, with humans standing out as one of the only tetrapods that regularly experiences high levels of shock during locomotion. A shock-absorption function does not explain the origin of menisci, nor are human menisci specialized in any way that would explain a unique shock-absorbing function during human gait. Finally, we show that (3) the material properties of menisci are distinctly poorly suited for energy dissipation and that (4) estimations of meniscal energy absorption based on published data are negligible, both in their absolute amount and in comparison to other well-accepted structures which mitigate shock during locomotion. The menisci are evolutionarily ancient structures crucial for joint congruity, load distribution, and stress reduction, among a number of other functions. However, the menisci are not meaningful shock absorbers, neither in tetrapods broadly, nor in humans.

A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins

Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the turtle tree is characterized by relatively constant diversification (speciation minus extinction) punctuated by a single threefold increase. We also found that this shift is temporally and geographically associated with newly emerged continental margins that appeared during the Eocene-Oligocene transition about 30 million years before present. In apparent contrast, the fossil record from this time period contains evidence for a major, but regional, extinction event. These seemingly discordant findings appear to be driven by a common global process: global cooling and drying at the time of the Eocene-Oligocene transition. This climatic shift led to aridification that drove extinctions in important fossil-bearing areas, while simultaneously exposing new continental margin habitat that subsequently allowed for a burst of speciation associated with these newly exploitable ecological opportunities.

First evidence of convergent lifestyle signal in reptile skull roof microanatomy

BACKGROUND

The study of convergently acquired adaptations allows fundamental insight into life's evolutionary history. Within lepidosaur reptiles-i.e. lizards, tuatara, and snakes-a fully fossorial ('burrowing') lifestyle has independently evolved in most major clades. However, despite their consistent use of the skull as a digging tool, cranial modifications common to all these lineages are yet to be found. In particular, bone microanatomy, although highly diagnostic for lifestyle, remains unexplored in the lepidosaur cranium. This constitutes a key gap in our understanding of their complexly interwoven ecology, morphology, and evolution. In order to bridge this gap, we reconstructed the acquisition of a fossorial lifestyle in 2813 lepidosaurs and assessed the skull roof compactness from microCT cross-sections in a representative subset (n = 99). We tested this and five macroscopic morphological traits for their convergent evolution.

RESULTS

We found that fossoriality evolved independently in 54 lepidosaur lineages. Furthermore, a highly compact skull roof, small skull diameter, elongate cranium, and low length ratio of frontal and parietal were repeatedly acquired in concert with a fossorial lifestyle.

CONCLUSIONS

We report a novel case of convergence that concerns lepidosaur diversity as a whole. Our findings further indicate an early evolution of fossorial modifications in the amphisbaenian 'worm-lizards' and support a fossorial origin for snakes. Nonetheless, our results suggest distinct evolutionary pathways between fossorial lizards and snakes through different contingencies. We thus provide novel insights into the evolutionary mechanisms and constraints underlying amniote diversity and a powerful tool for the reconstruction of extinct reptile ecology.