Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms

Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named “derivedness index” to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.

The first late cretaceous mawsoniid coelacanth (Sarcopterygii: Actinistia) from North America: Evidence of a lineage of extinct ‘living fossils’

Today, the only living genus of coelacanth, Latimeria is represented by two species along the eastern coast of Africa and in Indonesia. This sarcopterygian fish is nicknamed a "living fossil", in particular because of its slow evolution. The large geographical distribution of Latimeria may be a reason for the great resilience to extinction of this lineage, but the lack of fossil records for this genus prevents us from testing this hypothesis. Here we describe isolated bones (right angular, incomplete basisphenoid, fragments of parasphenoid and pterygoid) found in the Cenomanian Woodbine Formation in northeast Texas that are referred to the mawsoniid coelacanth Mawsonia sp. In order to assess the impact of this discovery on the alleged characteristic of "living fossils" in general and of coelacanths in particular: 1) we compared the average time duration of genera of ray-finned fish and coelacanth in the fossil record; 2) we compared the biogeographic signal from Mawsonia with the signal from the rest of the vertebrate assemblage of the Woodbine formation; and 3) we compared these life traits with those of Latimeria. The stratigraphical range of Mawsonia is at least 50 million years. Since Mawsonia was a fresh, brackish water fish with probably a low ability to cross large sea barriers and because most of the continental components of the Woodbine Fm vertebrate assemblage exhibit Laurasian affinities, it is proposed that the Mawsonia’s occurrence in North America is more likely the result of a vicariant event linked to the break-up of Pangea rather than the result of a dispersal from Gondwana. The link between a wide geographic distribution and the resilience to extinction demonstrated here for Mawsonia is a clue that a similar situation existed for Latimeria, which allowed this genus to live for tens of millions of years.

Living Fossils: Sturgeon of the San Francisco Estuary

Sturgeon are fish that are considered living fossils. Their ancestors date back over 200 million years, to the same time as dinosaurs. These fish can grow taller than humans (over 2 m), weigh over 160 kg, and live as long as humans. Sturgeon species have special adaptations, such as a vacuum-like mouth and body armor called scutes. There are 27 species of sturgeon worldwide. Two species, green and white sturgeon, are native to California, USA, and are some of the largest animals in San Francisco Bay. Sturgeon populations have declined due to habitat loss, water management, overfishing, poaching, pollution, and climate change. Sturgeon cannot jump over barriers like salmon can, so structures like dams that block water also block sturgeon from reaching their natural spawning habitat farther upstream in the river. Scientists are using new technologies to monitor sturgeon populations and discover the unique behaviors of these dinosaur-era fish in California’s rivers and estuaries.

Pleistocene Park, and other designs on deep time in the Interwar United States

Precisely how to reconstruct the planetary past is not predetermined. This article compares three contemporary plans, dreamed up in the United States during the Interwar and Depression years, that deploy diverse techniques to evoke extinct environments. Building on Martin Rudwick's historicization of ‘scenes from deep time’, this article develops the concept of designs on deep time to explain how public displays of the planetary past circulate anything-but-neutral ideas about past and present to awed audiences. By detailing three contemporary designs on deep time—Pleistocene Park at the La Brea Tar Pits, a sensational World's Fair exhibit called ‘The World a Million Years Ago’, and a dinosaur park where living fossils and ancient plants approximated a Mesozoic atmosphere—this article captures diverse philosophies about how to construct persuasive encounters with the prehistoric past. It also demonstrates how, despite disparate approaches, these designers of deep time displays all used the planetary past to legitimate present regimes and foster faith in human progress. During the 1920s and 1930s, when the wounds of war, changing demographics, and economic depression collaborated to dispute a prevailing myth of American progress, deep time by design buoyed faith in a better future.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Extension of M Dwarf Spectra Based on Adversarial AutoEncoder

M dwarfs are main sequence stars and they exist in all stages of galaxy evolution. As the living fossils of cosmic evolution, the study of M dwarfs is of great significance to the understanding of stars and the stellar populations of the Milky Way. Previously, M dwarf research was limited due to insufficient spectroscopic spectra. Recently, the data volume of M dwarfs was greatly increased with the launch of large sky survey telescopes such as Sloan Digital Sky Survey and Large Sky Area Multi-Object Fiber Spectroscopy Telescope. However, the spectra of M dwarfs mainly concentrate in the subtypes of M0–M4, and the number of M5–M9 is still relatively limited. With the continuous development of machine learning, the generative model was improved and provides methods to solve the shortage of specified training samples. In this paper, the Adversarial AutoEncoder is proposed and implemented to solve this problem. Adversarial AutoEncoder is a probabilistic AutoEncoder that uses the Generative Adversarial Nets to generate data by matching the posterior of the hidden code vector of the original data extracted by the AutoEncoder with a prior distribution. Matching the posterior to the prior ensures each part of prior space generated results in meaningful data. To verify the quality of the generated spectra data, we performed qualitative and quantitative verification. The experimental results indicate the generation spectra data enhance the measured spectra data and have scientific applicability.

The adaptation front equation explains diversification hotspots and living-fossilization

Taxonomic turnovers are common in the evolutionary histories of biological communities. Such turnovers are often associated with the emergence and diversification of groups that have achieved fundamental innovations beneficial in various ecological niches. In the present study, we show that such innovation-driven turnovers could be analyzed using an equation that describes the dynamics of zero-fitness isoclines in a two-dimensional trait space comprising a "fundamental trait" (describing fundamental innovation) and a "niche trait" (describing niche position) or with its higher-dimensional extensions. Our equation allows analytical prediction of evolutionary source-sink dynamics along the niche axis for an arbitrary unimodal (or multimodal with weak separation) carrying capacity distribution. The prediction was confirmed by numerical simulation under different assumptions for resource competition, reproduction, and mutation. In the simulated evolution, biodiversity sources are the central niches having higher carrying capacities than the outer niches, allowing species there the faster evolutionary advancement in fundamental traits and their repeated diversification into outer niches, which outcompete the indigenous less advanced species. The outcompeted species go extinct or evolve directionally toward the far outer niches of the far slower advancement because of the far lower carrying capacities. In consequence of this globally acting process over niches, species occupying peripheral (i.e., the outermost) niches can have significantly primitive fundamental traits and deep divergence times from their closest relatives, and thus, they correspond to living fossils. The extension of this analysis for multiple geographic regions showed that living fossils are also expected in geographically peripheral regions for the focal species group.

Stringy-running-vacuum-model inflation: from primordial gravitational waves and stiff axion matter to dynamical dark energy

In previous works, we have derived a Running Vacuum Model (RVM) for a string Universe, which provides an effective description of the evolution of 4-dimensional string-inspired cosmologies from inflation till the present epoch. In the context of this “stringy RVM” version, it is assumed that the early Universe is characterised by purely gravitational degrees of freedom, from the massless gravitational string multiplet, including the antisymmetric tensor field. The latter plays an important role, since its dual gives rise to a ‘stiff’ gravitational axion “matter”, which in turn couples to the gravitational anomaly terms, assumed to be non-trivial at early epochs. In the presence of primordial gravitational wave (GW) perturbations, such anomalous couplings lead to an RVM-like dynamical inflation, without external inflatons. We review here this framework and discuss potential scenarios for the generation of such primordial GW, among which the formation of unstable domain walls, which eventually collapse in a non-spherical-symmetric manner, giving rise to GW. We also remark that the same type of “stiff” axionic matter could provide, upon the generation of appropriate potentials during the post-inflationary eras, (part of) the Dark Matter (DM) in the Universe, which could well be ultralight, depending on the parameters of the string-inspired model. All in all, the new (stringy) mechanism for RVM inflation preserves the basic structure of the original (and more phenomenological) RVM, as well as its main advantages: namely, a mechanism for graceful exit and for generating a huge amount of entropy capable of explaining the horizon problem. It also predicts axionic DM and the existence of mild dynamical Dark Energy (DE) of quintessence type in the present universe, both being “living fossils” of the inflationary stages of the cosmic evolution. Altogether the modern RVM appears to be a theoretically sound (string-based) approach to cosmology with a variety of phenomenologically testable consequences.