Relaxed Substrate Specificity in Qβ Replicase through Long-Term In Vitro Evolution

A change from RNA- to DNA-based genetic systems is hypothesized as a major transition in the evolution of early life forms. One of the possible requirements for this transition is a change in the substrate specificity of the replication enzyme. It is largely unknown how such changes would have occurred during early evolutionary history. In this study, we present evidence that an RNA replication enzyme that has evolved in the absence of deoxyribonucleotide triphosphates (dNTPs) relaxes its substrate specificity and incorporates labeled dNTPs. This result implies that ancient replication enzymes, which probably evolved in the absence of dNTPs, could have incorporated dNTPs to synthesize DNA soon after dNTPs became available. The transition from RNA to DNA, therefore, might have been easier than previously thought.

Hemolymph Ecdysteroid Titer Affects Maternal mRNAs during Bombyx mori Oogenesis

Silkworm larval–pupal metamorphosis and the first half of pupal–adult development occur during oogenesis from previtellogenesis to vitellogenesis and include two peaks of the hemolymph ecdysteroid titer. Moreover, a rise in 20-hydroxyecdysone titer in early pupae can trigger the first major transition from previtellogenesis to vitellogenesis in silkworm oogenesis. In this study, we first investigated the expression patterns of 66 maternal genes in the ovary at the wandering stage. We then examined the developmental expression profiles in six time-series samples of ovaries or ovarioles by reverse transcription–quantitative PCR. We found that the transcripts of 22 maternal genes were regulated by 20-hydroxyecdysone in the isolated abdomens of the pupae following a single injection of 20-hydroxyecdysone. This study is the first to determine the relationship between 20-hydroxyecdysone and maternal genes during silkworm oogenesis. These findings provide a basis for further research into the embryonic development of Bombyx mori.

Transitions to asexuality and evolution of gene expression in Artemia brine shrimp

While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia , neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.

Differentiated appendages in Isoxys illuminate origin of arthropodization

The Cambrian fossil record has produced remarkable insights into the origin of euarthropods, particularly the evolution of their versatile body plan of segments bearing specialized, jointed appendages for different functions including feeding and locomotion [01, 02]. Early euarthropod evolution involved a major transition from lobopodian-like taxa [03, 04, 05] to organisms featuring a fully sclerotized trunk (arthrodization) and limbs (arthropodization) [02, 06, 07, 08]. However, the precise origin of arthropodization remains controversial because some of the earliest branching euarthropods possess a broad dorsal carapace that obscures critical details of the trunk and appendage organization [09, 10, 11, 12, 13, 14, 15]. Here, we demonstrate the presence of fully arthropodized ventral appendages in the upper stem-group euarthropod Isoxys curvirostratus from the early Cambrian Chengjiang biota in South China. Micro-computed tomography reveals the detailed three-dimensional structure of the biramous appendages in I. curvirostratus for the first time. In addition to the raptorial frontal appendages I. curvirostratus also possesses two batches of morphologically distinct biramous limbs, with the first batch consisting of four pairs of short cephalic appendages bearing prominent endites with a feeding function, followed by a second batch of elongate trunk appendages for locomotion. Each biramous limb bears an endopod with more than 12 well-defined podomeres, and an exopod consisting of a slender shaft carrying approximately a dozen paddle-shaped lamellae. Our findings clarify the enigmatic appendicular organization of Isoxys, one of the most ubiquitous euarthropods in Cambrian Burgess Shale-type deposits worldwide [01, 10, 11, 12, 14, 15, 16, 17, 18]. Critically, our new material shows that the trunk of I. curvirostratus was not arthrodized. The phylogenetic position of isoxyiids as possibly the earliest branching members of Deuteropoda [01, 02, 07, 15, 19], suggests that arthropodized biramous appendages evolved before the pattern of full trunk arthrodization that characterizes most extant and extinct members of this successful animal phylum.

Social complexity, life-history and lineage influence the molecular basis of caste in a major transition in evolution

Major evolutionary transitions describe how biological complexity arises; e.g. in the evolution of complex multicellular bodies, and superorganismal insect societies. Such transitions involve the evolution of division of labour, e.g. as queen and worker castes in insect societies. A key mechanistic hypothesis for the evolution of division of labour is that a shared set of genes co-opted from a common solitary ancestral ground plan - a so-called genetic toolkit for sociality - regulate insect castes across different levels of social complexity. The vespid wasps represent an excellent system in which to test this. Here, using conventional and machine learning analyses of brain transcriptome data from nine species of vespid wasps, we find evidence of a shared genetic toolkit across species representing different levels of social complexity, with a large suite of genes classifying castes correctly across species. However, we also found evidence of additional fine-scale differences in predictive gene sets, functional enrichment and rates of gene evolution that were related to level of social complexity, but also life-history traits (e.g. mode of colony founding). Thus, there appear to be shifts in the gene networks regulating social behaviour and rates of gene evolution that are influenced by innovations in both social complexity and life-history. These results suggest that the concept of a shared genetic toolkit for sociality may be too simplistic to fully describe the process of the major transition to sociality, even within a single lineage. Diversity in lineage, social complexity and life-history traits must be taken into account in the quest to uncover the molecular bases of the major transition to sociality.

Mutualists construct the ecological conditions that trigger the transition from parasitism

The evolution of mutualism between hosts and initially parasitic symbionts represents a major transition in evolution. Although vertical transmission of symbionts during host reproduction and partner control both favour the stability of mutualism, these mechanisms require specifically evolved features that may be absent during the transition. Therefore, the first steps of the transition from parasitism to mutualism are not fully understood. Spatial structure might be the key to this transition. We explore this hypothesis using a spatially explicit agent-based model. We demonstrate that, starting from a parasitic system with global dispersal, the coevolution between mutualistic effort and local dispersal of hosts and symbionts leads to a stable coexistence between parasites and mutualists. The local dispersal evolution mimics vertical transmission and triggers the formation of mutualistic clusters, counteracting the individual selection level of parasites that maintain global dispersal. However, the transition also requires competition between hosts in order to occur. Indeed, the transition occurs when mutualistic symbionts increase the density of hosts, which strengthens competition between hosts and disfavours parasitic host/symbiont pairs: mutualists create ecological conditions that allow their own spread. Therefore, the transition to mutualism may come from an eco-evolutionary feedback loop involving spatially structured population dynamics.

Changes in Attachment and Commitment in Couples Transitioning to Parenthood

This study examined whether attachment predicts changes in commitment and whether commitment predicts changes in attachment in both partners during the transition to parenthood. Both partners of 93 couples completed online questionnaires individually at the second trimester of pregnancy and at 4 months postpartum. Autoregressive cross-lagged path analyses based on the Actor–Partner Interdependence Model tested the bidirectional associations between attachment dimensions (anxiety and avoidance) and three modes of commitment (optimal, over-commitment, and under-commitment). Results revealed that for both partners, prenatal attachment avoidance was associated with a decrease in optimal commitment and an increase in under-commitment from pre- to postpartum. Fathers’ attachment anxiety was associated with a decrease in mothers’ under-commitment. Furthermore, prenatal optimal commitment was associated with a decrease in attachment avoidance, whereas under-commitment was associated with an increase in attachment avoidance. Fathers’ prenatal over-commitment was associated with an increase in their own attachment anxiety and avoidance. These results highlight how attachment insecurities and relationship commitment interrelate during this major transition.

Musculoskeletal modelling of sprawling and parasagittal forelimbs provides insight into synapsid postural transition

The sprawling-parasagittal postural shift was a major transition during synapsid evolution and is considered key to mammalian ecological diversity. Despite a good fossil record, debate remains over when the shift to parasagittal posture occurred, primarily due to limited comparative biomechanical data on extant species. Here, we built forelimb musculoskeletal models of three extant taxa that bracket the sprawling-parasagittal transition: a tegu lizard, an echidna, and an opossum. We measured shoulder joint range of motion (ROM) about all three degrees of rotational freedom and characterized shoulder muscle moment arms (MMAs) across the entire pose space. Our results show that both the opossum and the tegu had high shoulder joint ROM, and both were substantially higher than the echidna. However, the opossum occupied a distinct region of pose space characterized by high humeral retraction angles. There are clear interspecific differences in MMAs related to posture, with the sprawling tegu and echidna emphasizing humeral depression, and the parasagittal opossum emphasizing humeral elevation. There are also notable differences between our sprawling taxa, with the echidna possessing much greater moment arms for humeral pronation than the tegu. We demonstrate clear functional variation between locomotor grades and use these data to hypothesize major shifts in forelimb function and posture along the mammalian stem.

Vertebrate whole genome duplications shaped the current 3D genome architecture

Topologically associated domains (TADs) are interaction sub-networks of 3D genomes. TAD boundaries frequently coincide with genome breaks while their deletion is under negative selection, suggesting that TADs act as modules facilitating genome rearrangements and metazoan evolution. However, the role of TADs in the evolution of gene regulation and essentiality is not well understood. Here, we show that TADs play a role organising ancestral functions and evolutionary novelty. We discovered that genes co-localise by evolutionary age in the human and mouse genomes, resulting in TADs that have different proportions of younger and older genes. A major transition in the TAD age co-localisation patterns is observed between the genes born as a result of the vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also found that primate- and rodent-specific genes are more frequently essential when they are located in 'aged' TADs and connected to genes that have not duplicated since the WGD. Our data suggests that evolutionary success of recent genes may increase when located in functionally relevant TADs with established regulatory networks.

Patients with PMD who are thoroughly screened by Genomic medicine have a considerable chance of benefiting greatly from whole-genome sequencing

It appears that the role of genetics in neurology is undergoing a major transition in the present. The scope of genomic medicine has advanced from the only realm of academic investigation to the well-established and widely accepted instrument for genetic labs. Previously, this test was reserved for the most challenging patients, but today it is being utilized as a first step in looking at rare inherited neurological disorders. Researchers and clinicians working in the field of mitochondrial medicine will need to employ new laboratory techniques and DNA sequencing technology in order to move forward with future diagnosis methods and cut down on research time. Patients with PMD who are thoroughly screened have a considerable chance of benefiting greatly from whole-genome sequencing (WGS) at the beginning of their diagnostic process. Using long-read sequencing, there is the potential to help in the discovery of new genetic causes of PMD, the resolution of phasing issues, and the advancement of RNA and mtDNA investigations by way of direct sequencing. With the use of a great number of tissue samples from patients with PMD, there are significant advantages which can greatly promote the quick implementation of this technique into diagnostic laboratories. As RNA-seq technology is introduced into diagnostic laboratories, it will serve as an accurate means to examine the entire spectrum of disease while providing support for difficult cases. The plentiful supply of tissue samples from patients with PMD further enhances the ability of RNA-seq to rapidly be adopted in these laboratories. Finally, more validation of innovative tRNA approaches will be required in order to determine the pathogenicity of this common group of mtDNA-related PMDs.