Independent Transitions Research Articles

Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade

Anaerobes have emerged in several major lineages of ciliates, but the number of independent transitions to anaerobiosis among ciliates is unknown. The APM clade (Armophorea, Muranotrichea, Parablepharismea) represents the largest clade of obligate anaerobes among ciliates and contains free-living marine and freshwater representatives as well as gut endobionts of animals. The evolution of APM group has only recently started getting attention, and our knowledge on its phylogeny and genetics is still limited to a fraction of taxa. While ciliates portray a wide array of alternatives to the standard genetic code across numerous classes, the APM ciliates were considered to be the largest group using exclusively standard nuclear genetic code. In this study, we present a pan-ciliate phylogenomic analysis with emphasis on the APM clade, bringing the first phylogenomic analysis of the family Tropidoatractidae (Armophorea) and confirming the position of Armophorida within Armophorea. We include five newly sequenced single cell transcriptomes from marine, freshwater, and endobiotic APM ciliates – Palmarella salina, Anteclevelandella constricta, Nyctotherus sp., Caenomorpha medusula, and Thigmothrix strigosa. We report the first discovery of an alternative nuclear genetic code among APM ciliates, used by Palmarella salina (Tropidoatractidae, Armophorea), but not by its close relative, Tropidoatractus sp., and provide a comparative analysis of stop codon identity and frequency indicating the precedency to the UAG codon loss/reassignment over the UAA codon reassignment in the specific ancestor of Palmarella. Comparative genomic and proteomic studies of this group may help explain the constraints that underlie UAR stop-to-sense reassignment, the most frequent type of alternative nuclear genetic code, not only in ciliates, but eukaryotes in general.

Genetic and Phenotypic Consequences of Local Transitions between Sexual and Parthenogenetic Reproduction in the Wild.

AbstractTransitions from sexual to asexual reproduction have occurred in numerous lineages, but it remains unclear why asexual populations rarely persist. In facultatively parthenogenetic animals, all-female populations can arise when males are absent or become extinct, and such populations could help to understand the genetic and phenotypic changes that occur in the initial stages of transitions to asexuality. We investigated a naturally occurring spatial mosaic of mixed-sex and all-female populations of the facultatively parthenogenetic Australian phasmid Megacrania batesii. Analysis of single-nucleotide polymorphisms indicated multiple independent transitions between reproductive modes. All-female populations had much lower heterozygosity and allelic diversity than mixed-sex populations, but we found few consistent differences in fitness-related traits between population types. All-female populations exhibited more frequent and severe deformities in their (flight-incapable) wings but did not show higher rates of appendage loss. All-female populations also harbored more ectoparasites in swamp (but not beach) habitats. Reproductive mode explained little variation in female body size, fecundity, or egg hatch rate. Our results suggest that transitions to parthenogenetic reproduction can lead to dramatic genetic changes with little immediate effect on performance. All-female M. batesii populations appear to consist of high-fitness genotypes that might be able to thrive for many generations in relatively constant and benign environments but could be vulnerable to environmental challenges, such as increased parasite abundance.

Zero-Order Markov Processes with Multiple Final Sequences of States

A zero-order Markov process with multiple final sequences of states represents a stochastic system with independent transitions that stops its evolution as soon as one of the given final sequences of states is reached. The transition time of the system is unitary and the transition probability depends only on the destination state. It is proved that the distribution of the evolution time is a homogeneous linear recurrent sequence and a polynomial algorithm to determine the initial state and the generating vector of this recurrence is developed. Using the generating function, the main probabilistic characteristics are determined.

Evolution of reproductive modes in sharks and rays.

The ecological and life history drivers of the diversification of reproductive modes in early vertebrates are not fully understood. Sharks, rays and chimaeras (group Chondrichthyes) have an unusually diverse variety of reproductive modes and are thus an ideal group to test the factors driving the evolution of reproductive complexity. Here, using 960 species representing all major Chondrichthyes taxa, we reconstruct the evolution of their reproduction modes and investigate the ecological and life history predictors of reproduction. We show that the ancestral Chondrichthyes state was egg-laying and find multiple independent transitions between egg-laying and live-bearing via an intermediate state of yolk-only live-bearing. Using phylogenetically informed analysis, we also show that live-bearing species have larger body size and larger offspring than egg-laying species. In addition, live-bearing species are distributed over shallow to intermediate depths, while egg-layers are typically found in deeper waters. This suggests that live-bearing is more closely associated with pelagic, rather than demersal habitats. Taken together, using a basal vertebrate group as a model, we demonstrat how reproductive mode co-evolves with environmental conditions and life-history traits.

Evolutionary dynamics of whole-body regeneration across planarian flatworms

Regenerative abilities vary dramatically across animals. Even amongst planarian flatworms, well-known for complete regeneration from tiny body fragments, some species have restricted regeneration abilities while others are almost entirely regeneration incompetent. Here, we assemble a diverse live collection of 40 planarian species to probe the evolution of head regeneration in the group. Combining quantification of species-specific head-regeneration abilities with a comprehensive transcriptome-based phylogeny reconstruction, we show multiple independent transitions between robust whole-body regeneration and restricted regeneration in freshwater species. RNA-mediated genetic interference inhibition of canonical Wnt signalling in RNA-mediated genetic interference-sensitive species bypassed all head-regeneration defects, suggesting that the Wnt pathway is linked to the emergence of planarian regeneration defects. Our finding that Wnt signalling has multiple roles in the reproductive system of the model species Schmidtea mediterranea raises the possibility that a trade-off between egg-laying, asexual reproduction by fission/regeneration and Wnt signalling drives regenerative trait evolution. Although quantitative comparisons of Wnt signalling levels, yolk content and reproductive strategy across our species collection remained inconclusive, they revealed divergent Wnt signalling roles in the reproductive system of planarians. Altogether, our study establishes planarians as a model taxon for comparative regeneration research and presents a framework for the mechanistic evolution of regenerative abilities.

Genomic Insights into Mollusc terrestrialization: Parallel and Convergent Gene Family Expansions as Key Facilitators in out-of-the-sea transitions.

Animals abandoned their marine niche and successfully adapted to life on land multiple times throughout evolution, providing a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic factors underlying this process remain largely unknown. Here, we investigate the macroevolutionary dynamics of gene repertoire evolution during repeated transitions out of the sea in molluscs, a lineage that has transitioned to freshwater and terrestrial environments multiple independent times. Through phylogenomics and phylogenetic comparative methods, we examine approximately 100 genomic datasets encompassing all major molluscan lineages. We introduce a conceptual framework for identifying and analyzing parallel and convergent evolution at the orthogroup level (groups of genes derived from a single ancestral gene in the species in question), and explore the extent of these mechanisms. Despite deep temporal divergences, we found that parallel expansions of ancient gene families played a major role in facilitating adaptation to non-marine habitats, highlighting the relevance of the pre-existing genomic toolkit in facilitating adaptation to new environments. The expanded functions primarily involve metabolic, osmoregulatory, and defense-related systems. We further found functionally convergent lineage-exclusive gene gains, while family contractions appear to be driven by neutral processes. Also, genomic innovations likely contributed to fuel independent habitat transitions. Overall, our study reveals that various mechanisms of gene repertoire evolution -parallelism, convergence and innovation- can simultaneously contribute to major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of molluscan terrestrialization that pave the way towards further understanding the functional and evolutionary bases of this process.

Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes.

The transition from oviparity to viviparity has occurred independently over 150 times across vertebrates, presenting one of the most compelling cases of phenotypic convergence. However, whether the repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common signature in genomic divergence remains largely unknown. Although recent investigations into the evolution of viviparity have demonstrated striking similarity among the genes and molecular pathways involved across disparate vertebrate groups, quantitative tests for genome-wide convergent have provided ambivalent answers. Here, we investigate the potential role of molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo genomes and utilized publicly available genomes of viviparous and oviparous species to test for molecular convergence across both coding and noncoding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and in rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, both statistical power and biological confounds could constrain our ability to detect significant correlated evolution. We therefore identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. Motif enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development, and immunity occurred alongside the evolution of viviparity. Overall, however, our findings indicate that independent transitions to viviparity in these fish are not strongly associated with an excess of molecular convergence, but a few genes show convincing evidence of convergent evolution.

Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction

Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining (MAT) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By generating additional chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere-flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight toward the identification of a sexual cycle in Malassezia, with possible implications for pathogenicity.

When ecological transitions are not so infrequent: Independent colonizations of athalassohaline water bodies by Arcellidae (Arcellinida, Amoebozoa), with description of four new species.

The salinity and humidity barriers divide biodiversity and strongly influence the distribution of organisms. Crossing them opens the possibility for organisms to colonize new niches and diversify, but requires profound physiological adaptations and is supposed to happen rarely in evolutionary history. We tested the relative importance of each ecological barrier by building the phylogeny, based on mitochondrial cytochrome oxidase gene (COI) sequences, of a group of microorganisms common in freshwater and soils, the Arcellidae (Arcellinida; Amoebozoa). We explored the biodiversity of this family in the sediments of athalassohaline water bodies (i.e. of fluctuating salinity that have non-marine origins). We found three new aquatic species which represent, to our knowledge, the first reports of Arcellinida in these salt impacted ecosystems, plus a fourth terrestrial one in bryophytes. Culturing experiments performed on Arcella euryhalina sp. nov. showed similar growth curves in pure freshwater and under 20g/L salinity, and long term survival at 50g/L, displaying a halotolerant biology. Phylogenetic analyses showed that all three new athalassohaline species represent independent transition events through the salinity barrier by freshwater ancestor, in contrast to the terrestrial species, which are monophyletic and represent a unique ecological transition from freshwater to soil environments.

Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes.

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid Arabidopsis kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to ∼90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.

Independent and coherent transitions between antiferromagnetic states of few-molecule systems

Molecular spintronics is usually based on paramagnetic or ferromagnetic ($S$ \ensuremath{\ne} 0) species. Here, the authors study small ensembles of two molecular antiferromagnets, {Mn${}_{4}$} and {Co${}_{4}$}, bound to carbon nanotube quantum dots. The current through the quantum dots shows a random telegraph signal caused by transitions between nondegenerate ${S}_{t\phantom{\rule{0}{0ex}}o\phantom{\rule{0}{0ex}}t}$ = 0 states of individual molecular antiferromagnets. Statistical analysis shows that transitions between those states are independent in the case of {Co${}_{4}$} ensembles, while {Mn${}_{4}$} ensembles display long-lived coherent superposition involving multiple complexes.

Experimentally mapping the oriented-to-misoriented transition in laser powder bed fusion Ti-10%Mo alloys

Understanding the oriented-to-misoriented transition (OMT) and its origins is critical to additive manufacturing design processes. The Ti – 10 wt.% Mo alloy was printed at laser scan speeds ranging from 500 mm/s to 2500 mm/s and volumetric energy densities (VED) ranging from 50 J/mm3 to 150 J/mm3. A technique for rapidly mapping the OMT over the design space using X-ray diffraction was developed with electron backscattered diffraction verification. Mapping of the OMT revealed two independent transitions as functions of scan speed and VED respectively. Cross sections of in-situ single track scans at constant VED revealed the scan speed based OMT to be caused by a decrease in penetration depth and larger equiaxed grain zones during weld pool solidification.

Tentative detection of titanium oxide in the atmosphere of WASP-69 b with a 4m ground-based telescope

ABSTRACT Transiting planets provide unique opportunities for the atmospheric characterization of exoplanets as they can reveal composition and the temperature structures at the day–night terminator regions in planetary atmospheres, and help understand the atmospheric process and formation environments of exoplanets. Here, we present the optical transmission spectroscopic study of an inflated Saturn-mass planet WASP-69 b, obtained by the 4m ground-based telescope Southern Astrophysical Research Telescope (SOAR). We obtain spectroscopic transit light curves in 20 passbands from 502 to 890 nm, and fit them using Gaussian processes and an analytical transit model to obtain independent transit depths for each. The derived transmission spectrum of WASP-69 b shows a slope with absorption depth increasing towards blue wavelengths, indicating a Rayleigh scattering in the atmosphere consistent with previous works. The retrieval analysis yields a tentative detection of TiO absorption feature in the transmission spectrum. We present the first results from the SOAR telescope to characterize exoplanetary atmospheres proving its capability and precision for hot Jupiters around bright stars in an area dominated by results from large ground-based telescopes or space telescopes.

New tendencies in the digital transformation of the world economy

Main problem: processes of economic modernization in practical solution should reveal common understanding between institutional, legislative and industrial relations, essence of organizational transformations, formulation of basic provisions for instrumental support of independent transition of technological processes to new round of socio‑economic relations. Processes should be based on new characteristics of standardization, methodology of system functioning, technical conditions, norms, rules, instructions and regulations, which provides for institutional changes. Purpose: to explore new trends in digital transformation of the world economy, as well as to show that tasks and settings of vector of technological processes of digital economy go far beyond known principles of economic development, joining the mainstream of global trends. Methods: theoretical and methodological basis was concepts, hypotheses and theories presented in works of domestic and foreign researchers. The methodology is based on systematic approach, in which methods of comparative, factorial, subject-object, structural-functional, statistical, correlation analysis and extrapolation were applied. Results and their significance: analytical review of theoretical approaches of foreign economists on this problem was carried out, which allowed author to identify theoretical, methodological and applied foundations for determining directions within framework of state strategy for planning socio-economic development. Scientific discussion on conditions for changing model of economic development, modernization of economy with transition to first and second generation platforms, hereinafter referred to as ecosystems, is evaluated. The fundamental differences between theoretical argumentation of proponents of promoted digital technologies and their opponents are determined. Positions of argumentation of impact on change of driving factors are analyzed in order to adjust methods of state policy and choice of vector of technological processes. The question of correlation of macroeconomic theory in evolutionary sense, which goes beyond known principles of economic thought of digital transformation, is considered.

Multiple transitions between realms shape relict lineages of Proteus cave salamanders.

In comparison to biodiversity on Earth's surface, subterranean biodiversity has largely remained concealed. The olm (Proteus anguinus) is one of the most enigmatic extant cave inhabitants, and until now little was known regarding its genetic structure and evolutionary history. Olms inhabit subterranean waters throughout the Dinaric Karst of the western Balkans, with a seemingly uniform phenotypic appearance of cave-specialized traits: an elongate body, snout and limbs, degenerated eyes and loss of pigmentation ("white olm"). Only a single small region in southeastern Slovenia harbours olms with a phenotype typical of surface animals: pigmented skin, eyes, a blunt snout and short limbs ("black olm"). We used a combination of mitochondrial DNA and genome-wide single nucleotide polymorphism data to investigate the molecular diversity, evolutionary history and biogeography of olms along the Dinaric Karst. We found nine deeply divergent species-level lineages that separated between 17 and 4 million years ago, while molecular diversity within lineages was low. We detected no signal of recent admixture between lineages and only limited historical gene flow. Biogeographically, the contemporaneous distribution of lineages mostly mirrors hydrologically separated subterranean environments, while the historical separation of olm lineages follows microtectonic and climatic changes in the area. The reconstructed phylogeny suggests at least four independent transitions to the cave phenotype. Two of the species-level lineages have miniscule ranges and may represent Europe's rarest amphibians. Their rarity and the decline in other lineages call for protection of their subterranean habitats.

Synthesis and properties of semicrystalline non‐isocyanate polyurethane with tunable triple shape memory properties

AbstractNowadays, polyurethanes with multifunctional and multiple shape memory effects, especially those without the use of toxic phosgene and isocyanate, have attracted significant attention. In this work, to prepare a kind of non‐isocyanate polyurethane (NIPU) with triple shape memory effect, we introduced the behenic acid (BA) with good crystallinity into the NIPUs network, which combines glass transition of the cross‐linked network and crystallization‐melting of behenic acid, endowing the NIPUs with two independent transition temperatures: the glass transition temperature (Tg) and crystallization melting temperature (Tm). Specifically, the NIPUs were synthesized by the addition reaction of bi‐functional cyclic carbonate and semi‐crystalline curing agent. The bi‐functional cyclic carbonate was prepared by thiol‐ene click reaction, and the BA was grafted onto polyethyleneimine to prepare semi‐crystalline curing agent. By adjusting the ratio of BA to PEI and curing temperature, the crystallinity of NIPU can be tuned in a wide range, so that the NIPUs has tunable and superior triple shape memory performance, and the shape recovery rate is almost 100%.

PredRNN: A Recurrent Neural Network for Spatiotemporal Predictive Learning.

The predictive learning of spatiotemporal sequences aims to generate future images by learning from the historical context, where the visual dynamics are believed to have modular structures that can be learned with compositional subsystems. This paper models these structures by presenting PredRNN, a new recurrent network, in which a pair of memory cells are explicitly decoupled, operate in nearly independent transition manners, and finally form unified representations of the complex environment. Concretely, besides the original memory cell of LSTM, this network is featured by a zigzag memory flow that propagates in both bottom-up and top-down directions across all layers, enabling the learned visual dynamics at different levels of RNNs to communicate. It also leverages a memory decoupling loss to keep the memory cells from learning redundant features. We further propose a new curriculum learning strategy to force PredRNN to learn long-term dynamics from context frames, which can be generalized to most sequence-to-sequence models. We provide detailed ablation studies to verify the effectiveness of each component. Our approach is shown to obtain highly competitive results on five datasets for both action-free and action-conditioned predictive learning scenarios.

How the Activity Schedules Impact the Children with Autism Spectrum Disorder? A Meta-analysis

: The main purpose of this study was to meta-analyse the single-case studies on the use of activity schedules with individuals with autism spectrum disorders. The other purposes were to assess the design standards of activity schedule studies, estimate the treatment effect of activity schedule, describe the characteristics of activity schedule studies, and determine whether activity schedule is an evidence-based practice for children with autism spectrum disorders in improving appropriate behaviours. The nonoverlap of all pairs (NAP) was used to analyse the treatment effect measure. According to results, seven out of 32 activity schedule studies met the design standards with and without reservation. Twenty-four children with autism spectrum disorders whose age ranged between 3 and 17 years participated in the studies. The target behaviours were on task, independent transition, appropriate peer-play, and following schedule. The photographs and texts were used in both traditional and innovative activity schedules. The overall NAP score shows that the activity schedule has a strong effect for those participants with autism spectrum disorders. Finally, this meta-analysis indicates that an activity schedule can be recommended as an evidence-based practice to improve the appropriate behaviours of children with autism spectrum disorders.

Coupling of [Formula: see text] and [Formula: see text] kinetics: insights from multiple exercise transitions below the estimated lactate threshold.

During a step-change in exercise power output (PO), ventilation ([Formula: see text]) increases with a similar time course to the rate of carbon dioxide delivery to the lungs ([Formula: see text]). To test the strength of this coupling, we compared [Formula: see text] and [Formula: see text] kinetics from ten independent exercise transitions performed within the moderate-intensity domain. Thirteen males completed 3-5 repetitions of ∆40W step transitions initiated from 20, 40, 60, 80, 100, and 120W on a cycle ergometer. Preceding the ∆40W step transitions from 60, 80, 100, and 120W was a 6min bout of 20W cycling from which the transitions of variable ∆PO were examined. Gas exchange ([Formula: see text] and oxygen uptake, [Formula: see text]) and [Formula: see text] were measured by mass spectrometry and volume turbine. The kinetics of the responses were characterized by the time constant (τ) and amplitude (Δ[Formula: see text]/Δ[Formula: see text]). Overall, [Formula: see text] kinetics were consistently slower than [Formula: see text] kinetics (by ~ 45%) and τ[Formula: see text] rose progressively with increasing baseline PO and with heightened ∆PO from a common baseline. Compared to τ[Formula: see text], τ[Formula: see text] was on average slightly greater (by ~ 4s). Repeated-measures analysis of variance revealed that there was no interaction between τ[Formula: see text] and τ[Formula: see text] in either the variable baseline (p = 0.49) and constant baseline (p = 0.56) conditions indicating that each changed in unison. Additionally, for Δ[Formula: see text]/Δ[Formula: see text], there was no effect of either variable baseline PO (p = 0.05) or increasing ΔPO (p = 0.16). These data provide further evidence that, within the moderate-intensity domain, both the temporal- and amplitude-based characteristics of V̇E kinetics are inextricably linked to those of [Formula: see text].

Clamping effect on temperature-induced valence transition in epitaxial EuPd2Si2 thin films grown on MgO(001)

Bulk ${\mathrm{EuPd}}_{2}{\mathrm{Si}}_{2}$ show a temperature-driven valence transition of europium from $\ensuremath{\sim}+2$ above 200 K to $\ensuremath{\sim}+3$ below 100 K, which is correlated with a shrinking by approximately 2% of the tetragonal crystal lattice along the two $a$-axes. Due to this interconnection between lattice and electronic degrees of freedom the influence of strain in epitaxial thin films is particularly interesting. Ambient x-ray diffraction (XRD) confirms an epitaxial relationship of tetragonal ${\mathrm{EuPd}}_{2}{\mathrm{Si}}_{2}$ on MgO(001) with an out-of plane $c$-axis orientation for the thin film, whereby the $a$-axes of both lattices align. XRD at low temperatures reveals a strong coupling of the thin film lattice to the substrate, showing no abrupt compression over the temperature range from 300 to 10 K. Hard x-ray photoelectron spectroscopy at 300 and 20 K reveals a temperature-independent valence of $+2.0$ for Eu. The evolving biaxial tensile strain upon cooling is suggested to suppress the valence transition. Instead temperature-dependent transport measurements of the resistivity and the Hall effect in a magnetic field up to 5 T point to a film thickness independent phase transition at 16 to 20 K, indicating magnetic ordering.