The Evolutionary History of Ore-forming Processes of Metallic Ore Deposits in Northern Guangxi

The northern Guangxi region is an important rare metal, rare earth metal and polymetallic metallogenic province. In the region there exist five metallogenic series and two metallogenic subseries, whose metallogenesis shows features of polycyclic spiral evolution throughout the geological history. As far as various cycles are concerned, mantle-derived ore substances were reduced while crust-derived ore substances increased from early to late timesfin the whole geological evolutionary history, mantle-derived substances decreased gradually while crust-derived ones increased. Meanwhile ore element associations became more and more varied. In terms of space, mineralization migrated from the old basement outwards, i.e. from west to east during the Precambrian, and from north to south during the Phanerozoic, and again from east to west during the Yanshanian.

The Janus of macrophysiology： stronger effects of evolutionary history, but weaker effects of climate on upper thermal limits are reversed for lower thermal limits in ants

Species may exhibit similar traits via different mechanisms： environmental filtering and local adaptation （geography） and shared evolutionary history （phylogeny） can each contribute to the resemblance of traits among species. Parsing trait variation into geographic and phylogenetic sources is important, as each suggests different constraints on trait evolution. Here, we explore how phylogenetic distance, geographic distance, and geographic variation in climate shape physiological tolerance of high and low temperatures using a global dataset of ant thermal tolerances. We found generally strong roles for evolutionary history and geographic variation in temperature, but essen- tially no detectable effects of spatial proximity per se on either upper or lower thermal tolerance. When we compared the relative importance of the factors shaping upper and lower tolerances, we found a much stronger role for evolutionary history in shaping upper versus lower tolerance, and a moderately weaker role for geographic variation in temperature in shaping upper tolerance when compared with lower tolerance. Our results demonstrate how geographic variation in climate and evolutionary history may have differential effects on the upper and lower endpoints of physiological tolerance. This Janus effect, where the relative contributions of geographic variation in climate and evolutionary history are reversed for lower versus upper physiological tolerances, has gained some support in the literature, and our results for ant physiological tolerances provide further evidence of this pa^ern. As the climate continues to change, the high phylogenetic conservatism of upper tolerance may suggest potential constraints on the evolution of tolerance of high temperatures.

Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle,and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments.However,neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood.Here,we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains.We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene.Ancestral character state reconstructions and phylogenetic analyses showed that narG,nirS,and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically.In contrast,nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis.This study expands our understanding of the genomic potential for incomplete denitrification in Thermus,revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae,and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.

Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history.Herein,we estimated the de novo mutation rate of pigs as 3.6×10-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation.Using this mutation rate,we re-investigated the evolutionary history of pigs.The estimated divergence time of~10 kiloyears ago(KYA)between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence.However,other divergence events inferred here were not as ancient as previously described.Our estimates suggest that Sus speciation occurred~1.36 million years ago(MYA);European wild pigs split from Asian wild pigs only~219 KYA;and south and north Chinese wild pigs split~25 KYA.Meanwhile,our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain,northern China,approximately 20 KYA,supporting the possibly independent domestication in northern China along the middle Yellow River.We also found that the maximum effective population size of pigs was~6 times larger than estimated before.An archaic migration from other Sus species originating~2 MYA to European pigs was detected during western colonization of pigs,which may affect the accuracy of previous demographic inference.Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway

Plants, as primary producers, have been playing an indispensable role in other organisms’ survival and the balance of whole ecosystem on Earth. Especially, they provide the main source of energy, food, and medicine for human beings, some of which are derived from the primary or secondary metabolites

Impacts of Early Pleistocene glacial vicariance among refugial lineages and Mid-Late Pleistocene interglacial dispersal and expansion on forging population genetic structure of the giant clam Tridacna squamosa(Bivalvia:Cardiidae:Tridacninae)across the Red Sea and Indo-West Pacific oceans

This study aims at identifying the microevolutionary processes responsible for the onset of the remarkable phylogeographic structure already recorded for the endangered giant clam Tridacna squamosa across its distribution range.For this purpose,the evolutionary,biogeographic and demographic histories of the species were comprehensively reconstructed in a mitochondrial dataset comprising nearly the whole available published cytochrome c oxidase 1 gene sequences of T.squamosa.Relatively higher level of genetic diversification was unveiled within T.squamosa,in comparison to earlier macro-geographic investigations,whereby five mitochondrial clusters were delineated.The resulting divergent gene pools in the Red Sea,western Indian Ocean,Indo-Malay Archipelago and western Pacific were found to be driven by Early Pleistocene glacial vicariance events among refugial lineages.Accentuated genetic diversification of the species across the Indo-Malay Archipelago was successively triggered by historical dispersal event during the Mid-Pleistocene MIS19c interglacial.This latter historical event might have also enabled genetically distinct giant clams from the Indo-Malay Archipelago to subsequently colonize the western Pacific,accounting for the genetic diversity hotspot detected within this region(comprising three divergent mitochondrial clusters).Late Pleistocene demographic expansion of T.squamosa,during the Last Interglacial period,could have contributed to forging spatial distribution of the so far delineated genetic entities across the Indo-Western Pacific.Overall,being resilient to major climate shifts during the Pleistocene through adaptation and consequent diversification,T.squamosa could be used as a model species to track the impact of climate change on genetic variability and structure of marine species.In particular,the new information,provided in this investigation,may help with understanding and/or predicting the consequences of ongoing global warming on genetic polymorphism of endangered coral reef species among which Tridacna sp.are listed as ecologically important.

Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

In pig-to-human xenotransplantation,the transmission risk of porcine endogenous retroviruses(PERVs)is of great concern.However,the distribution of PERVs in pig genomes,their genetic variation among Eurasian pigs,and their evolutionary history remain unclear.We scanned PERVs in the current pig reference genome(assembly Build 11.1),and identified 36 long complete or near-complete PERVs(lc PERVs)and 23 short incomplete PERVs(si PERVs).Besides three known PERVs(PERV-A,-B,and-C),four novel types(PERV-JX1,-JX2,-JX3,and-JX4)were detected in this study.According to evolutionary analyses,the newly discovered PERVs were more ancient,and PERV-Bs probably experienced a bottleneck~0.5 million years ago(Ma).By analyzing63 high-quality porcine whole-genome resequencing data,we found that the PERV copy numbers in Chinese pigs were lower(32.0±4.0)than in Western pigs(49.1±6.5).Additionally,the PERV sequence diversity was lower in Chinese pigs than in Western pigs.Regarding the lc PERV copy numbers,PERV-A and-JX2 in Western pigs were higher than in Chinese pigs.Notably,Bama Xiang(BMX)pigs had the lowest PERV copy number(27.8±5.1),and a BMX individual had no PERV-C and the lowest PERV copy number(23),suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors.Furthermore,we identified 451 PERV transposon insertion polymorphisms(TIPs),of which 86 were shared by all 10 Chinese and Western pig breeds.Our findings provide systematic insights into the genomic distribution,variation,evolution,and possible biological function of PERVs.

Detection of biosignatures in Terrestrial analogs of Martian regions:Strategical and technical assessments

For decades, the search for potential signs of Martian life has attracted strong international interest and has led to significant planning and scientific implementation. Clearly, in order to detect potential life signals beyond Earth, fundamental questions, such as how to define such terms as “life” and “biosignature”, have been given considerable attention. Due to the high costs of direct exploration of Mars, Mars-like regions on Earth have been invaluable targets for astrobiological research, places where scientists could practice the search for “biosignatures” and refine ways to detect them. This review summarizes scientific instrumental techniques that have resulted from this work. Instruments must necessarily be our “eyes” and “hands” as we attempt to identify and quantify biosignatures on Mars.Scientific devices that can be applied in astrobiology include mass spectrometers and electromagnetic-spectrum-based spectrometers,redox potential indicators, circular dichroism polarimeters, in situ nucleic acid sequencers, life isolation/cultivation systems, and imagers.These devices and how to interpret the data they collect have been tested in Mars-analog extreme environments on Earth to validate their practicality on Mars. To anticipate the challenges of instrumental detection of biosignatures through the full evolutionary history of Mars, Terrestrial Mars analogs are divided into four major categories according to their similarities to different Martian geological periods(the Early-Middle Noachian Period, the Late Noachian-Early Hesperian Period, the Late Hesperian-Early Amazonian Period, and the Middle-Late Amazonian Period). Future missions are suggested that would focus more intensively on Mars’ Southern Hemisphere, once landing issues there are solved by advances in spacecraft engineering, since exploration of these early terrains will permit investigations covering a wider continuum of the shifting habitability of Mars through its geological history. Finally, this paper reviews practical applications of the range of scientific instruments listed above, based on the four categories of Mars analogs here on Earth. We review the selection of instruments suitable for autonomous robotic rover tests in these Mars analogs. From considerations of engineering efficiency,a Mars rover ought to be equipped with as few instrument assemblies as possible. Therefore, once candidate landing regions on Mars are defined, portable suites of instruments should be smartly devised on the basis of the known geological, geochemical, geomorphological,and chronological characteristics of each Martian landing region. Of course, if Mars sample-return missions are successful, such samples will allow experiments in laboratories on Earth that can be far more comprehensive and affordable than is likely to be practicable on Mars.To exclude false positive and false negative conclusions in the search for extraterrestrial life, multiple diverse and complementary analytical techniques must be combined, replicated, and carefully interpreted. The question of whether signatures of life can be detected on Mars is of the greatest importance. Answering that question is extremely challenging but appears to have become manageable.

The mitochondrial genomes of Macrocheraia grandis grandis and Myrmoplasta mira(Hemiptera:Heteroptera:Pentatomomorpha) and the unique mitogenome rearrangement in Pyrrhocoroidea

Sequencing technology has developed rapidly in recent years. Complete or nearly complete mitochondrial genomes(mitogenomes) of 155 species from 47 families in Heteroptera have been sequenced. However, the amounts of mitogenomes between those families are unbalanced, which makes it difficult to correctly discern the patterns of mitogenome rearrangement in Heteroptera. Among 21 species from ten families, ten variations in mitogenome rearrangement had been previously reported, among which the translocation between tRNA-Thr and tRNA-Pro was considered as a synapomorphy of Pyrrhocoroidea based on two mitogenomes. As only one mitogenome in each of Largidae and Pyrrhocoridae had been sequenced to conclude the synapomorphy, more mitogenomes of Pyrrhocoroidea need to be explored. In this study, additional two mitogenomes of Pyrrhocoroidea(Macrocheraia grandis grandis(Gray, 1832) and Myrmoplasta mira Gerst-cker, 1892) were sequenced. Both of them also possess the same translocation between tRNA-Thr and tRNA-Pro, which reaffirms that this kind of rearrangement is a molecular synapomorphy of Pyrrhocoroidea. Moreover, we discovered a more complex rearrangement in Myrmoplasta mira, in which six nearly identical duplications of tRNA-Thr were found located downstream of tRNA-Pro. Considering the high biodiversity of Heteroptera, more mitogenomic studies are needed to improve our knowledge about mitogenome rearrangements and the potential synapomorphies.

Mitochondrial phylogenomics reveal the origin and adaptive evolution of the deep-sea caridean shrimps(Decapoda:Caridea)

The deep-sea is considered as the most extensive ecosystem on the Earth.It is meaningful for elucidating the life origins by exploring the origin and adaptive genetic mechanisms of the large deepsea organisms.Caridean shrimps have colonized and successfully adapted to deep-sea environments.They provide an ideal model to analyze the origin and adaptive evolution of modern deep-sea fauna.Here,we conducted the phylogenetic analyses of mitocho ndrial genomes(mitogenomes)from carideans,including 11 newly sequences reported in this investigation to explore the habitat origins,divergence times,and adaptive evolution of deep-sea(seamounts and hydrothermal vents)caridean shrimps.The results showed that the species of deep-sea Caridea formed a monophyletic group.Phylogenetic analysis supported that the deepsea caridean shrimps may originated from shallow sea.The hydrothermal vents alvinocaridid shrimps and Lebbeus shinkaiae from Thoridae underwent a second range expansion from seamounts to vent ecosystems.Estimates of divergence time showed that the caridean shrimps invaded into deep-sea at 147.75 Ma.The divergence of most of the modern seamount and hydrothermal vent species are in the late Cretaceous/early Tertiary.This may associate with the geological events of the Western Pacific,the climate change,and the global deep-water anoxic/dysoxic events during this period.Twenty-two potentially important adaptive residues were detected in the deep-sea shrimp lineage,which were located in atp6,atp8,cox1,cox3,cytb,nad2,nad4 l,and nad5.This investigation adds our understanding of the evolutionary history of deep-sea caridean shrimps,and provides insights into the mitochondrial genetic basis of deep-sea adaptation in this group.

Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens

Understanding the genetic basis of adaptive evolution following habitat expan-sion can have important implications for pest management.The pink rice borer(PRB),Sesamia inferens(Walker),is a destructive pest of rice that was historically restricted to regions south of 34o N latitude in China.However,with changes in global climate and farming practices,the distribution of this moth has progressively expanded,en-compassing most regions in North China.Here,3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural vari-ant datasets across China,corresponding to northern,southern China regions,and the Yunnan-Guizhou Plateau,with significant patterns of isolation by geographic and envi-ronmental distances.Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations.Selective sweep analyses esti-mated strong selection at insect cuticle glycine-rich cuticular protein genes which are as-sociated with enhanced desiccation adaptability in the northern group,and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population.Our findings have significant implications for the development of effective strategies to control this pest.

Three-dimensional reconstruction of Late Miocene Trapa from eastern Zhejiang Province,China:Insights into its phytogeography and evolution

Abundant plant fossils were found in the Upper Miocene Shengxian Formation,eastern Zhejiang Province,China,among which Trapa belongs to a dominant population.The fossil fruits of Trapa were well preserved with abundant details.However,due to compaction during fossilization,Trapa fruits were often flattened,leading to the loss of some characteristic features.Thereby,a bias in taxonomic and phylogenetic studies would occur when such studies were based on these fruit fossils.In this study,we present the first quantitative three-dimensional reconstruction of compressed Trapa fruit fossils to restore their original morphology prior to burial.This approach provides a novel perspective for the identification and classification of compressed fruit fossils.The three-dimensional reconstruction of Trapa fruit fossils enabled accurate comparisons with extant species.We subsequently identified it as a new species,named Trapa radiatiformis L.Xiao sp.nov.,revealing differences from previously known taxa of Trapa.Importantly,our comparison suggests that the long lower horns and residual stalk may represent inherent characteristics of early Trapa fruits.However,these traits gradually degenerated during fruit evolution,resulting in morphological simplification during geological time.T.radiatiformis with primitive features exhibits good resemblance to Trapa natans fruit characteristics,which means it may be an ancestor of T.natans.We summarize the palaeogeographic distribution of fossil Trapa using previously published literature and demonstrate that the genus was mostprosperous in the Miocene and exhibited the same distribution as that at present.Additionally,through detailed morphological comparisons between Trapa and Hemitrapa fruits,along with phylogenetic analysis within the Primotrapa genus itself,we propose a homology between Trapa and Hemitrapa,suggesting that they could have a common ancestor.

Distinct evolution process among type I interferon in mammals

Interferon (IFN) is thought to play an important role in the vertebrate immune system, but systemic knowledge of IFN evolution has yet to be elucidated. To evaluate the phylogenic distribution and evolutionary history of type I IFNs, 13genomes were searched using BLASTn program, and a phylogenetic tree of vertebrate type I IFNs was constructed. In the present study, an IFNδ-like gene in the human genome was identified, refuting the concept that humans have no IFNδ genes, and other mammalian IFN genes were also identified. In the phylogenetic tree, the mammalian IFNβ, IFNɛ, and IFNκ formed a clade separate from the other mammalian type I IFNs, while piscine and avian IFNs formed distinct clades. Based on this phylogenetic analysis and the various characteristics of type I IFNs, the evolutionary history of type I IFNs was further evaluated. Our data indicate that an ancestral IFNα-like gene forms a core from which new IFNs divided during vertebrate evolution. In addition, the data suggest how the other type I IFNs evolved from IFNα and shaped the complex type I IFN system. The promoters of type I IFNs were conserved among different mammals, as well as their genic regions. However, the intergenic regions of type I IFN clusters were not conserved among different mammals, demonstrating a high selection pressure upon type I IFNs during their evolution.

Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution

Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic interest.Despite numerous studies,the mechanisms underlying its adaptation and evolution remain enigmatic.Here,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically.We complete a chromosome-level assembly and annotation of the E.onukii genome,showing notable expansions of gene families associated with adaptation to chemoreception and detoxification.Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions.Patterns of genetic variations among 54 E.onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China.Our results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of E.onukii.This work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustainable pest management.

Conservation priority of global Galliformes species based on phylogenetic diversity

In this study,based on phylogenetic diversity(PD),I develop a conservation strategy for Galliformes species around the world.A cladogram of 197 Galliformes species derived from a previous study was used for calculat­ing PD metrics.Branch length is an important aspect of the phylogenetic information a tree can convey,but 2 traditionally-used metrics,the number of phylogenetic groups to which a taxon belongs(I)and the proportion that each taxon contributes to the total diversity of the group(W),are fully node-based and do not take branch length into account.Therefore,to measure PD more appropriately,I combined a branch-related metric,pen­dant edge(P),in addition to I and W.A final combined rank for Galliformes species was obtained by summing the ranks of the 3 metrics.My results showed that the 5%top priority species for conserving evolutionary po­tential were Galloperdix lunulata,Haematortyx sanguiniceps,Margaroperdix madagarensis,Syrmaticus soem­merringii,Coturnix pectoralis,Polyplectron napoleonis,Alectoris melanocephala,Xenoperdix udzungwensis,Afropavo congensis and Syrmaticus reevesii.The current species priority ranking based on pylogenetic diversi­ty and the official International Union for Conservation of Nature(IUCN)ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN(critical endangered,endangered,vulnera­ble,near threatened and least concern).This indicated the feasibility of introducing the PD index into the net­work of IUCN regional Red List assessment.The 5%top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China,Indonesia,Mexico,India,Colombia,Australia,Brazil,Angola,Congo and Japan(in descending order).China,Indonesia,Mexico,Brazil,India and Colombia are consistently selected among the 4 top priority sets of richness,rarity,endemicity and PD.This re­sult indicated that the priority result from PD is highly congruent with conventional measures.Along with oth­er conventional ecological attributes,the alternative conservation scenario based on PD is reasonable and can be adopted in systematic conservation planning.