Sequence Evolution Research Articles

Magmatic–hydrothermal evolution of the Koktokay No. 3 pegmatite, Altai, northwestern China: Constraints from in situ boron isotope and chemical compositions of tourmaline

Lithium–Cs–Ta-enriched (LCT-type) pegmatites are characterized by zoning texture and extreme enrichment of rare-metals. The role of fluids in zonation development and rare-metal mineralization remains a topic of debate. The Koktokay No. 3 pegmatite in northwestern China represents a typical LCT-type pegmatite characterized by economically significant Li–Be–Nb–Ta–Cs mineralization. This pegmatite exhibits a complete evolutionary sequence from outer to inner zones, with diverse rare-metal mineralization. Tourmaline is ubiquitously present in all textural zones of LCT-type pegmatites. In the Koktokay No. 3 pegmatite, the tourmalines exhibit a range of compositions from dravite and schorl to elbaite and rossmanite. The tourmalines in this pegmatite are characterized by significantly enriched light B isotope compositions (δ11B = −14.8‰ to −8.1‰), similar to those typically observed in most pegmatites derived from continental crust sources. The tourmalines in the outer zones have less variable δ11B values (−13.8‰ to −11.5‰) and are interpreted to have crystallized in a viscous magma. The tourmalines in the inner zones exhibit larger variations in δ11B values (−14.8‰ to −8.1‰) than those from the outer zones. The decreasing δ11B values of tourmalines from the outer to inner zones are attributed to the separation of an immiscible fluid phase that preferentially incorporated heavy B isotopes. The occurrence of hydrothermal tourmaline as veinlets indicates the exsolution of fluids in inner zones, with high δ11B values ranging from −10.2‰ to −9.3‰. Therefore, the hydrothermal fluid can be saturated when the magma has been strongly evolved. In addition to fractional crystallization, exsolved fluids play a significant role in the formation of internal zones and rare-metal mineralization in LCT-type pegmatites. The rare-metals are gradually enriched through fractional crystallization of magma, and the fluid contains mobile elements such as Cs that facilitate precipitation of rare-metal minerals.

ProGen2: Exploring the boundaries of protein language models

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial-intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional fine-tuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. Our models and code are open sourced for widespread adoption in protein engineering. A record of this paper's Transparent Peer Review process is included in the supplemental information.

Asteroseismic age estimate of the open cluster NGC 6866 using Kepler and Gaia

Context. Asteroseismic investigations of solar-like oscillations in giant stars allow for the derivation of their masses and radii. For members of open clusters, this allows us to obtain an age estimate of the cluster that is expected to be identical to the age estimate given by the colour-magnitude diagram, but independent of the uncertainties that are present for that type of analysis. Thus, a more precise and accurate age estimate can be obtained. Aims. We aim to identify and measure the asteroseismic properties of oscillating giant members of the open cluster NGC 6866 and utilise them for a cluster age estimate. Model comparisons also allow constraints to be placed on the stellar physics. Here, we investigate the efficiency of convective-core overshoot during the main sequence evolution, which has a significant influence on the age estimations for these relatively massive giants. The effects of rotation and core overshoot are similar, but not identical, and so, we also investigated the potential of our measurements to distinguish between these effects. Methods. We identified six giant members of NGC 6866 via photometry, proper motions, and parallaxes from Gaia, and spectroscopic literature measurements. These were combined with asteroseismic measurements, which we derived using photometric data from the Kepler mission for five of the stars. Comparisons to stellar-model isochrones constrained the convective-core overshoot and enable a more precise and accurate age estimate than previously possible. Results. A significant amount of differential reddening is found for NGC 6866. Asteroseismology establishes the helium-core burning evolutionary phase for the giants, which have a mean mass of 2.8 M⊙. Their radii are significantly smaller than predicted by current 1D stellar models unless the amount of convective-core overshoot on the main sequence is reduced to αov ≤ 0.1 ⋅ Hp in the step-overshoot description. Our measurements also suggest that rotation has affected the evolution of the stars in NGC 6866 in a way that is consistent with 3D simulations, but not with current 1D stellar models. The age of NGC 6866 is estimated to be 0.43 ± 0.05 Gyr, which is significantly younger and more precise than most previous estimates. Conclusions. We derive a precise cluster age while constraining convective-core overshooting and the effects of rotation in the stellar models. A comparison to age estimates from machine learning methods of the same and similar giant stars uncovers potential biases for automated asteroseismic and non-asteroseismic age estimates of helium-core burning stars.

Invariants for level-1 phylogenetic networks under the Cavendar-Farris-Neyman model

Phylogenetic networks model evolutionary phenomena that trees fail to capture such as horizontal gene transfer and hybridization. The same Markov models used for sequence evolution on trees can also be extended to networks and similar problems, such as determining if the network parameter is identifiable or finding the invariants of the model, can be studied. This paper focuses on finding the invariants of the Cavendar-Farris-Neyman (CFN) model on level-1 phylogenetic networks by reducing the problem to finding invariants of sunlet networks, which are level-1 networks consisting of a single cycle with leaves at each vertex. We determine all quadratic invariants for sunlet networks, and conjecture these generate the full sunlet ideal.

Sedimentary sequence and evolutionary characteristics of the rift system of Neoproterozoic Nanhua System and Doushantuo Formation: A case study from the northeastern margin of Sichuan Basin

Neoproterozoic strata are widely developed in the Upper Yangtze region of South China, among which the Sinian Dengying Formation has been discovered with numerous large gas fields in the Sichuan Basin, and hence they have become an essential domain for natural gas exploration and development. The early‐to‐middle Neoproterozoic Nanhua System and Doushantuo Formation are characterized by rifting deposits in the northeastern margin of Sichuan Basin, but their depositional succession and sequence architectures are still unclear, which has largely restricted our understanding of the resource potential of these strata. In this paper, based on the outcrops of the Neoproterozoic Nanhua System and Doushantuo Formation in the northeastern margin of Sichuan Basin, we describe the stratigraphic distribution and sedimentary evolutionary characteristics, and establish the regional stratigraphic framework, sedimentary cycle and evolutionary sequence of the Nanhua System and Doushantuo Formation. The results show that the lithology of the Nanhua System and Doushantuo Formation is primarily composed of conglomerate, conglomeratic sandstone, medium‐fine sandstone, siltstone, mudstone, shale and tillite; a variety of sedimentary facies including alluvial fan, river, delta, coastal shore, shelf, basin and tillite were developed; five third‐order sequences could be identified, representing multiple cycles of marine transgression and regression. The climate during the deposition of the Nanhua System and Doushantuo Formation underwent from a warm and humid pre‐glacial period through cold and arid multiple glacial periods to a warm and humid interglacial period, which consequently formed a sedimentary sequence of alluvial fan and fluvial delta to tillite during the early period, shelf basin to tillite during the middle period and slope basin to delta facies during the late period. In terms of a plan view, the depositional pattern is composed of alluvial fans and deltas at the proximal part of the rift, deep‐water shelf to slope at the middle part of the rift and slope to basin facies at the central part of the rift. Finally, we propose that large‐scale distribution of high‐quality source rocks developed in the interglacial Datangpo and Doushantuo formations, while fluvial‐deltaic reservoirs occurred in the Gucheng, Nantuo and Doushantuo formations, thus showing favourable resource potential and exploration prospects within the Sichuan Basin.

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences

BackgroundExploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences.ResultTherefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage.ConclusionOur study provides objective feature sets in constructing evolution relationships at the genomic level.

Is Over-parameterization a Problem for Profile Mixture Models?

Biochemical constraints on the admissible amino acids at specific sites in proteins lead to heterogeneity of the amino acid substitution process over sites in alignments. It is well known that phylogenetic models of protein sequence evolution that do not account for site heterogeneity are prone to long-branch attraction (LBA) artifacts. Profile mixture models were developed to model heterogeneity of preferred amino acids at sites via a finite distribution of site classes each with a distinct set of equilibrium amino acid frequencies. However, it is unknown whether the large number of parameters in such models associated with the many amino acid frequency vectors can adversely affect tree topology estimates because of over-parameterization. Here, we demonstrate theoretically that for long sequences, over-parameterization does not create problems for estimation with profile mixture models. Under mild conditions, tree, amino acid frequencies, and other model parameters converge to true values as sequence length increases, even when there are large numbers of components in the frequency profile distributions. Because large sample theory does not necessarily imply good behavior for shorter alignments we explore the performance of these models with short alignments simulated with tree topologies that are prone to LBA artifacts. We find that over-parameterization is not a problem for complex profile mixture models even when there are many amino acid frequency vectors. In fact, simple models with few site classes behave poorly. Interestingly, we also found that misspecification of the amino acid frequency vectors does not lead to increased LBA artifacts as long as the estimated cumulative distribution function of the amino acid frequencies at sites adequately approximates the true one. In contrast, misspecification of the amino acid exchangeability rates can severely negatively affect parameter estimation. Finally, we explore the effects of including in the profile mixture model an additional "F-class" representing the overall frequencies of amino acids in the data set. Surprisingly, the F-class does not help parameter estimation significantly and can decrease the probability of correct tree estimation, depending on the scenario, even though it tends to improve likelihood scores.

One-Dimensional Cellular Automaton Transitions and Integral Value Transformations Representing Deoxyribonucleic Acid Sequence Evolutions

The cellular automaton (CA) and an integral value transformation (IVT) evolving in discrete time steps are two mathematical models that are well established. Theoretically, it can be suggested that a CA possesses the capacity to produce varieties of evolutionary patterns. However, computing a CA in higher dimensions or computing a nonlinear CA may be complex. In such cases, an IVT can be conveniently used. This paper presents the relation between the transition functions of a one-dimensional CA and an IVT. It also highlights the algebraic structures on the basis of binary operations for a set of transition functions of a one-dimensional CA and for a set of IVTs. The suitability of using an IVT over a CA is discussed. Also, we present the evolutionary models of two deoxyribonucleic acid (DNA) sequences through IVTs and their spacetime diagrams. This can eventually bring out some characteristic features of the evolutionary sequences.

Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements.

Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.

Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus.

Histone proteins bind DNA and organize the genomes of eukaryotes and most archaea, whereas bacteria rely on different nucleoid-associated proteins. Homology searches have detected putative histone-fold domains in a few bacteria, but whether these function like archaeal/eukaryotic histones is unknown. Here we report that histones are major chromatin components in the bacteria Bdellovibrio bacteriovorus and Leptospira interrogans. Patterns of sequence evolution suggest important roles for histones in additional bacterial clades. Crystal structures (<2.0 Å) of the B. bacteriovorus histone (Bd0055) dimer and the histone-DNA complex confirm conserved histone-fold topology but indicate a distinct DNA-binding mode. Unlike known histones in eukaryotes, archaea and viruses, Bd0055 binds DNA end-on, forming a sheath of dimers encasing straight DNA rather than wrapping DNA around their outer surface. Our results demonstrate that histones are present across the tree of life and highlight potential evolutionary innovation in how they associate with DNA.

Insights into the Evolution of Ohnologous Sequences and Their Epigenetic Marks Post-WGD in Malus Domestica.

A Whole Genome Duplication (WGD) event occurred several Ma in a Rosaceae ancestor, giving rise to the Maloideae subfamily which includes today many pome fruits such as pear (Pyrus communis) and apple (Malus domestica). This complete and well-conserved genome duplication makes the apple an organism of choice to study the early evolutionary events occurring to ohnologous chromosome fragments. In this study, we investigated gene sequence evolution and expression, transposable elements (TE) density, and DNA methylation level. Overall, we identified 16,779 ohnologous gene pairs in the apple genome, confirming the relatively recent WGD. We identified several imbalances in QTL localization among duplicated chromosomal fragments and characterized various biases in genome fractionation, gene transcription, TE densities, and DNA methylation. Our results suggest a particular chromosome dominance in this autopolyploid species, a phenomenon that displays similarities with subgenome dominance that has only been described so far in allopolyploids.

IS26 mediated blaCTX-M-65 amplification in Escherichia coli increase the antibiotic resistance to cephalosporin in vivo

To characterize two Escherichia coli strains isolated from a patient pre- and post-treatment, using β-lactams and β-lactam/β-lactamase inhibitor combinations (BLBLIs). A combination of antibiotic susceptibility testing (AST) with whole genome sequencing using Illumina and Oxford Nanopore platforms. Long-read sequencing and reverse transcription-quantitative PCR were performed to determine the copy numbers and expression levels of antibiotic resistance genes (ARGs), respectively. Effect on fitness costs were assessed by growth rate determination. The strain obtained from the patient after the antibiotic treatment (XH989) exhibited higher resistance to cefepime, BLBLIs and quinolones compared with the pre-treatment strain (XH987). Sequencing revealed IS26-mediated duplications of a IS26-fosA3-blaCTX-M-65 plasmid-embedded element in strain XH989. Long-read sequencing (7.4 G data volume) indicated a variation in copy numbers of blaCTX-M-65 within one single culture of strain XH989. Increased copy numbers of the IS26-fosA3-blaCTX-M-65 element were correlated with higher CTX-M-65 expression level and did not impose fitness costs, while facilitating faster growth under high antibiotic concentrations. Our study is an example from the clinic how BLBLIs and β-lactams exposure in vivo possibly promoted the amplification of an IS26-multiple drug resistance (MDR) region. The observation of a copy number variation seen with the blaCTX-M-65 gene in the plasmid of the post-treatment strain expands our knowledge of insertion sequence dynamics and evolution during treatment.

Survival of fossil fields during the pre-main sequence evolution of intermediate-mass stars

Context. Chemically peculiar Ap and Bp stars host strong large-scale magnetic fields in the range of 200 G up to 30 kG, which are often considered to be the origin of fossil magnetic fields. Aims. We assess the evolution of such fossil fields during the star formation process and the pre-main sequence evolution of intermediate stars based on: fully convective models, models including a transition to a radiative protostar, and models with a radiative core. We also examine the implications of the interaction between the fossil field and the core dynamo. Methods. We employed analytic and semi-analytic calculations, combined with current observational constraints. Results. For fully convective models, we show that magnetic field decay via convection can be expected to be very efficient for realistic parameters of turbulent resistivities. Based on the observed magnetic field strength-density relation, as well as the expected amount of flux loss due to ambipolar diffusion, it appears unlikely that convection could be suppressed via strong enough magnetic fields. On the other hand, a transition from a convective to a radiative core could very naturally explain the survival of a significant amount of flux, along with the presence of a critical mass. We show that in some cases, the interaction of a fossil field with a core dynamo may further lead to changes in the surface magnetic field structure. Conclusions. In the future, it will be important to understand in more detail how the accretion rate evolves as a function of time during the formation of intermediate-mass protostars, including its impact on the protostellar structure. The latter may even allow us to derive quantitative predictions concerning the expected population of large scale magnetic fields in radiative stars.

Research on the path of high-quality development of tourism in Hainan based on international comparison

Abstract This paper analyzes the current situation of the development of tourism in Hainan and provides a new reference for the high-quality development of Hainan tourism. Firstly, the evaluation model and evaluation indexes of Hainan tourism high quality development based on a comprehensive evaluation method are constructed, the comprehensive index method is used to dimensionless process the data, and the entropy value method is used to conduct a comprehensive analysis of the quantitative relationship of selected indexes and the degree of variation to determine the index weights. Then the multi-objective linear weighting method is used to calculate the comprehensive level of Hainan tourism quality development. Then the regional difference characteristics of Hainan tourism quality development and the trend of tourism development time sequence evolution were analyzed, and finally, the path of Hainan tourism quality development was analyzed from multiple factors. On the regional difference characteristics, the northern and southern regions of Hainan have obvious advantages in terms of quality tourism development, with a comprehensive development index of 0.498 and 0.482 respectively, while the central region is relatively backward, with a development index of 0.364. The dynamics of industrial development in Hainan are relatively low, with slow and unstable growth, rising only from 0.0048 in 2013 to 0.0059 in 2018 and also showing a small downward trend in 2015 and 2016. This study has important implications for the high-quality development of tourism in Hainan.

Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand.

A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2-7 agar media. Strain GXMU-J15T grew at 20-50 °C (optimum, 35 °C), at pH 5.0-8.0 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces. Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA-DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces. The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).

Detection of transcriptome-wide microRNA–target interactions in single cells with agoTRIBE

MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.

Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables.

Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species

Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.

Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution.

Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of 5 statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, greater among-lineage rate variation in the data led to improved performance of all 5 methods, particularly for Bayesian relaxed-clock analysis when the rate model was mismatched. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

Multidimensional Feature-Based Graph Attention Networks and Dynamic Learning for Electricity Load Forecasting

Electricity load forecasting is of great significance for the overall operation of the power system and the orderly use of electricity at a later stage. However, traditional load forecasting does not consider the change in load quantity at each time point, while the information on the time difference of the load data can reflect the dynamic evolution information of the load data, which is a very important factor for load forecasting. In addition, the research topics in recent years mainly focus on the learning of the complex relationships of load sequences in time latitude by graph neural networks. The relationships between different variables of load sequences are not explicitly captured. In this paper, we propose a model that combines a differential learning network and a multidimensional feature graph attention layer, it can model the time dependence and dynamic evolution of load sequences by learning the amount of load variation at different time points, while representing the correlation of different variable features of load sequences through the graph attention layer. Comparative experiments show that the prediction errors of the proposed model have decreased by 5–26% compared to other advanced methods in the UC Irvine Machine Learning Repository Electricity Load Chart public dataset.