Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and physiology.One,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthetic capability.

Dendroclimatological study of Sabina saltuaria and Abies faxoniana in the mixed forests of the Qionglai Mountains,eastern Tibetan Plateau

Tree-ring chronologies were developed for Sabina saltuaria and Abies faxoniana in mixed forests in the Qionglai Mountains of the eastern Tibetan Plateau.Climate-growth relationship analysis indicated that the two co-exist-ing species reponded similarly to climate factors,although S.saltuaria was more sensitive than A.faxoniana.The strong-est correlation was between S.saltuaria chronology and regional mean temperatures from June to November.Based on this relationship,a regional mean temperature from June to November for the period 1605-2016 was constructed.Reconstruction explained 37.3%of the temperature variance during th period 1961-2016.Six major warm periods and five major cold periods were identified.Spectral analysis detected significant interannual and multi-decadal cycles.Reconstruction also revealed the influence of the Atlantic Multi-decadal Oscillation,confirming its importance on climate change on the eastern Tibetan Plateau.

A new species of Discostella guiyangensis sp.nov.(Bacillariophyta,Stephanodiscales)from Guiyang,China:morphology and phylogeny

We describe a new species of Discostella from Guiyang based on light and scanning electron microscopic observations,as well as molecular analysis.This species is morphologically distinguished from other species by a relatively smooth and slightly recessed central area with marginal striae of unequal lengths forked near the margin.Marginal fultoportulae and a single rimoportula are situated between every two costae or on the costae.Both morphological characters and the concatenated data of rbc L and SSU rDNA indicate that Discostella guiyangensis is a unique and new species.According to divergence time estimation analysis,Discostella guiyangensis is the oldest species among the Discostella species sequenced currently.In addition,we complement molecular data of Discostella asterocostata and Discostella stelligera.

Lineaperpetua gen.nov.:a new diatom genus in the Thalassiosirales supported by morphology and molecular data

Based on a combination of morphology and molecular data of ribosomal DNA genes,a new diatom genus Lineaperpetua gen.nov.Yu,You,Kociolek&Wang is described.The features that help define Lineaperpetua at the level of genus include:a tangentially undulated valve face;continuous cribra areolae on the valve interior consisting of pores arranged as strips;single rimoportula located inside the ring of marginal fultoportulae.Additionally,phylogenetic analysis based on nuclear small subunit(SSU)rDNA sequences and nuclear large subunit(LSU)rDNA gene placed the three strains of L.lacustris in a single,monophyletic clade at a considerable sequence distance from the other genera(Thalassiosira,Conticribra,Planktoniella,Shinodiscus,and other genera)belonging to Thalassiosirales.Despite the similarities with some species of Thalassiosira,Conticribra,and Spicaticribra,the suite of features found in Lineaperpetua differentiate it from these other genera.These molecular data and morphological characters suggest an affinity of the new genus to the Thalassiosiraceae.

A new diatom genus Spargeria gen.nov.(Bacillariophyceae)from Xizang,China,and the description of two new species

During our investigation of diatom biodiversity in Xizang,two species exhibited unique morphological features discriminative from all previously known genera.Herein we describe these two species and describe as new the genus,Spargeria gen.nov.The new genus features narrow to wide rectangular valves,narrow valve mantles,filiform raphe branches that occur on the valve face only,terminal raphe fissures straight or slightly deflected to same side,bow-tie shaped central areas,chambered striae present on the valve face only,being absent from the mantle,wider striae near the axial area and very narrow near the margin,multiseriate striae with small and round areolae that are occluded externally.Comparatively,Spargeria zhuii sp.nov.has larger and robust valves,radiate striae,with one divergent stria near the apices,while Spargeria chenia sp.nov.is smaller,with narrow valves,striae slightly radiate in the middle,becoming convergent or parallel near apices.This new genus belongs to the family Pinnulariaceae,and it was compared and contrasted with other genera of this family.Our work suggests the need for continued studies to document the biodiversity of diatoms in Xizang.

High-resolution CT-scan data reveals the tooth replacement pattern of the Late Jurassic tyrannosauroid Guanlong wucaii (Dinosauria, Theropoda)

The Tyrannosauridae,which is characterized by specialized pachydont dentition and putative bone-cracking predatory strategies,is one of the most extensively studied theropod lineages.Although tooth replacement patterns,crucial for understanding feeding behaviors,have been thoroughly studied in this group,studies on non-tyrannosaurid tyrannosauroids are relatively scarce.This study utilizes high-resolution CT data to investigate the tooth replacement pattern in two specimens of Guanlong wucaii,a Late Jurassic tyrannosauroid,and provides insights into the evolution of tooth replacement across Tyrannosauroidea.Second-generation replacement teeth,a rarity observed mainly in giant predatory theropods(e.g.some tyrannosaurids),were detected in the dentary dentition of the juvenile Guanlong.Zahnreihen reconstructions display a consistent cephalad alternating tooth replacement pattern in the maxilla and the dentary of both of the examined individuals,with Z-spacing values exceeding 2.0.As Guanlong grows,the Z-spacing value in the maxillary dentition increases,resembling the ontogenetic changes documented in the Tyrannosauridae.Additionally,like Tarbosaurus,Guanlong also displays a discontinuity between the tooth replacement waves at the premaxilla-maxilla boundary.This study thus demonstrates that some tyrannosaurid-like tooth replacement patterns were acquired before the origin of the Tyrannosauridae.

April-September minimum temperature reconstruction based on Sabina tibetica ring-width chronology in the central eastern Tibetan Plateau,China

Minimum temperatures have remarkable impacts on tree growth at high-elevation sites on the Tibetan Plateau,but the shortage of long-term and high-resolution paleoclimate records inhibits understanding of recent minimum temperature anomalies.In this study,a warm season(April–September)reconstruction is presented for the past 467 years(1550–2016)based on Sabina tibetica ring-width chronology on the Lianbaoyeze Mountain of the central eastern Tibetan Plateau.Eight warm periods and eight cold periods were identified.Long-term minimum temperature variations revealed a high degree of coherence with nearby reconstructions.Spatial correlations between our reconstruction and global sea surface temperatures suggest that warm season minimum temperature anomalies in the central eastern Tibetan Plateau were strongly influenced by large-scale ocean atmospheric circulations,such as the El Ni?o-Southern Oscillation and the Atlantic Multidecadal Oscillation.

Comparison of Genomes of the Hepadnaviridae Family

Background: The Hepadnaviridae family is composed of small hepatotropic DNA viruses, divided into two main genera: Avihepadnavirus, which infects birds;and Orthohepadnavirus, which infects mammals. The human hepatitis B virus (HBV) is a member of the latter family and contains a relaxed circular double-stranded DNA genome of approximately 3 kb, and the objective of this study is to evaluate the genetic diversity of the genome of the Hepadnaviridae family. Materials and Methods: For this study, we evaluated the 26 NCBI reference sequences of the Hepadnaviridae family. Result: The two main genera, Avihepadnavirus and Orthohepadnavirus, show low similarity between them. The Orthohepadnavirus, to which HBV belongs, has two important hosts, monkeys and bats, while the genus, which infects humans, has greater diversity but is similar to the viruses that infect monkeys. The Paraepadnavirus isolated from the white sucker fish and the Herpetohepadnavirus from the Tibetan frog showed strong similarity with the Avihepadnavirus found in birds. The Metahepadnavirus isolated from the bluegill fish was the Hepadnaviridae which had the greatest difference, with less than 20% similarity using CLC Sequence Viewer. Conclusion: The Hepadnaviridae genomic replication cycle involves a late reverse transcriptase (RT) step. This polymerase, however, does not have proofreading activity, resulting in genetic variability in the Hepadnaviridae family.

Woody plant taxonomic,functional,and phylogenetic diversity decrease along elevational gradients in Andean tropical montane forests:Environmental filtering and arrival of temperate taxa

Mountains are paramount for exploring biodiversity patterns due to the mosaic of topographies and climates encompassed over short distances.Biodiversity research has traditionally focused on taxonomic diversity when investigating changes along elevational gradients,but other facets should be considered.For first time,we simultaneously assessed elevational trends in taxonomic,functional,and phylogenetic diversity of woody plants in Andean tropical montane forests and explored their underlying ecological and evolutionary causes.This investigation covered four transects(traversing ca.2200 m a.s.l.) encompassing 114 plots of 0.1 ha across a broad latitudinal range(ca.10°).Using Hill numbers to quantify abundance-based diversity among 37,869 individuals we observed a consistent decrease in taxonomic,functional,and phylogenetic diversity as elevation increased,although the decrease was less pronounced for higher Hill orders.The exception was a slight increase in phylogenetic diversity when dominant species were over-weighted.The decrease in taxonomic and functional diversity might be attributed to an environmental filtering process towards highlands,where the increasingly harsher conditions exclude species and functional strategies.Besides,the differences in steepness decrease between Hill orders suggest that rare species disproportionately contribute to functional diversity.For phylogenetic diversity the shifting elevational trend between Hill orders indicates a greater than previously considered influence in central Andean highlands of tropical lowlands originated species with strong niche conservatism relative to distantly related temperate lineages.This could be explained by a decreasing presence and abundance of temperate,extratropical taxa towards the central Andes relative to northern or southern Andes,where they are more prevalent.

Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses

Although domestic ducks have been important poultry species throughout human history,their origin remains enigmatic,with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s)of domestic ducks.Here,we analyzed 118 whole genomes from mallard,Chinese spotbilled,and domestic ducks to reconstruct their evolutionary history.We found pervasive introgression patterns among these duck populations.Furthermore,we showed that domestic ducks separated from mallard and Chinese spotbilled ducks nearly 38 thousand years ago(kya)and 54 kya,respectively,which is considerably outside the time period of presumed duck domestication.Thus,our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled,rather than from present-day mallard and/or Chinese spot-billed ducks,as previously thought.Overall,this study provides new insight into the complex evolution of ducks.

Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics

The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.

Home Range and Habitat Use of the Moustached Warbler (Acrocephalus melanopogon) during the Reproductive Period in the Eastern Iberian Peninsula

Many populations of the Moustached Warbler (Acrocephalus melanopogon) have suffered a noticeable decrease over the last decades. This work has the aim of estimating the home range of the Moustached Warbler and its habitat use during the reproductive season. We captured 11 males during the reproductive period with mist nets and marked them with radio transmitters. We determined the home range by calculating minimum convex polygon and kernel areas at 95% (home range) and 50% (core area). Then, to study the habitat use, we registered the proportion of the different vegetation types within these areas and carried out a compositional analysis to investigate if there is a detectable habitat preference. The results seem to indicate that the marked individuals did not show territorial behavior, given that the overlaps between home ranges and also the core areas were over 70%. The compositional analysis showed that A. melanopogon prefers tall and short reeds and mixed vegetation with rushes and bulrushes. Thus, maintaining heterogeneous and stratified vegetation would favor this species.

Pre-and post-pollination barriers between two exotic and five native Sagittaria species:Implications for species conservation

Anthropogenic introduction of species has resulted in a breakdown of geographical barriers and hybridization in previously allopatric species.Thus,examining hybridization proneness of exotic species contributes to revealing its potential threat.Moreover,reproductive barriers may be strengthened or weakened due to long-term geographical isolation for these newly sympatric species.However,few studies have evaluated multiple barriers between alien and native species.In this study,we quantified the importance of four pre-pollination barriers(phenological,floral traits,pollen production,and floral constancy)and four post-pollination barriers(pollen-pistil incompatibility,seed set,seed viability,and seedling survival)between two introduced and five native Sagittaria species.Results showed that introduced S.platyphylla was cross-compatible with two native species,whereas introduced S.montevidensis was incapable of hybridizing with any native species.Different barriers were asymmetric within species pairs and multiple barriers acted in concert to maintain species boundaries.Postpollination barriers contributed more to total reproductive isolation in native species,whereas prepollination barriers played a stronger role in total reproductive isolation for two introduced species.Seed set was the only barrier that was positively correlated with genetic distance.Our results provide a perspective to better understand reproductive barriers for secondary contact species.We highlight the importance of monitoring hybridization events before human introduction and the possible conservation strategies to remove invasive species with hybridization proneness.

New and interesting diatoms from the Shimen Wetwalls,Yunnan Province,China.Ⅱ.The diatom genus Nupela Vyverman&Compère(Bacillariophyceae)

We detailed the valve morphology of five new species of diatom genus Nupela from wetwall communities in Yunnan Province,China,with light and scanning electron microscope.The five new species demonstrate great variability within the genus,as three of them are biraphid and two are monoraphid.In addition,variation was noted in the structure of internal proximal raphe ends,with some species having anchor-shaped ends and other species have hooked ends.The genus Nupela has grown considerably in 30years since it was first proposed,going from a monotypic genus to over 85 taxa.Diagnosis of the genus is based on the presence of an external covering over the areolae.We discussed the systematic placement of Nupela within the naviculoid diatoms.Yunnan Province appears to harbor many endemic diatom taxa,and many regions of the province have yet to be studied.

Qinia gen.nov.(Bacillariophyceae:Cymbellales)from Yunnan Province,China

An interesting group of cymbelloid diatoms was collected from lakes in Yunnan Province,China,and observations on their valve morphology made using light and scanning electron microscopy.These cymbelloid species all have apical pore fields,slit-like areolae,and areolar occlusions,and they all lack of stigmata.In this paper we propose the new genus Qinia gen.nov.for these taxa and describe them as new:Q.lashii sp.nov.,Q.aequalis sp.nov.,and Q.daliensis sp.nov.The genus Qinia gen.nov.has lanceolate valves asymmetrical about their apical axes,raphe located in the middle of valve,distal raphe ends bent to the dorsal margin that bisects the apical pore fields(APFs),no stigmata,areolae with slit-like external openings and projections occluding the areolar openings internally.This genus resembles the genus Cymbella in the presence of APFs,but differs from Cymbella by a lack of stigmata,and by having external distal raphe ends that bisect the apical pore fields.Like Reimeria,the external distal raphe ends bisect the lobes of the APF,but Qinia species differ from Reimeria in that they have no stigmata and the distal raphe ends are deflected dorsally,not ventrally.Comparisons were made between Qinia and other cymbelloid genera whose members possess apical pore fields.Features that distinguish each species of the new genus are also discussed.

Developmental environment contributes to rapid trait shifts among newly colonized subterranean habitats

Recent colonization of extreme environments provides unique opportunities to study the early steps of adaptation and the potential for rapid convergent evolution.However,phenotypic shifts during recent colonization may also be due to plasticity in response to changes in the rearing environment.Here,we analyzed a suite of morphological and behavioral traits in paired surface,subterranean,and facultatively subterranean Mexican tetras(Astyanax mexicanus)from recent introductions in two separate watersheds outside of their native range.We found a variety of phenotypic and behavioral shifts between subterranean and surface populations that are similar to those observed in relatively ancient populations in Mexico.Despite this rapid morphological divergence,we found that most of these trait differences were due to plasticity in response to rearing environments.While most trait assays in common-garden,lab-raised fish indicated that phenotypic shifts in wild fish were the result of plasticity,we also found evidence of genetic control in several traits present in subterranean populations.Interestingly,wall-following behavior,an important subterranean foraging behavior,was greater in lab-born subterranean fish than in lab-born surface fish,suggesting rapid divergence of this trait between subterranean and surface populations.Thus,this study sheds light on the early steps of subterranean evolution,identifies potential rapid behavioral evolution,and suggests that plasticity in traits involving exploratory behavior may facilitate subterranean colonization.

Interannual dynamics of stemwood nonstructural carbohydrates in temperate forest trees surrounding drought

Interactions between water and carbon dynamics underlie drought-related tree mortality.While whole-tree water relations have been shown to play a key role in the response to and recovery from drought,the role of nonstructural carbohydrates(NSC) and how their storage and allocation changes surrounding drought events deserves further attention and is critical for understanding tree survival.Here,we quantified in situ NSC responses of temperate forest trees to the 2016 drought in the northeastern United States.Sugar and starch concentrations were measured in the stemwood of five tree species from 2014 to 2019,which allowed us to monitor NSCs in relation to climatic conditions before,during,and after the natural drought.We found that immediately following the drought,measured stemwood NSC concentrations decreased.However,NSC concentrations rebounded quickly within three years.Notably,trees allocated proportionally more to starch than to sugars following the 2016 drought.In winter 2017,starch comprised 45% of total stemwood stores,whereas starch made up only 1-2% in other years.Further,we modeled and assessed the climatic drivers of total NSC concentrations in the stem.Variation in total NSC concentrations was significantly predicted by the previous year’s temperature,precipitation,and standardized precipitation-evapotranspiration index(SPEI),with stemwood concentrations decreasing following hotter,drier periods and increasing following cooler,wetter periods.Overall,our work provides insight into the climatic drivers of NSC storage and highlights the important role that a tree’s carbon economy may play in its response and recovery to environmental stress.

A review on protein based nanocarriers for polyphenols:interaction and stabilization mechanisms

Protein has been used as the carrier for protecting and targeting polyphenols and increasing their shelf-life.Interactions of a protein molecule with polyphenols are important,which change functions and physiochemical properties of the complex and provide protection to polyphenols.Interactions between proteins and polyphenols are largely non-covalent.Factors that affect such interactions include pH,temperature,and the structure of both proteins and polyphenols.Moreover,excellent stability of polyphenols can be achieved by using nanoencapsulation techniques such as emulsion,nanohydrogel,and nanocomplex formation.The use of protein combined with other compounds such as lipids and carbohydrates was found to be the most suitable carrier for polyphenols encapsulation.This review aims to describe the interaction between proteins and polyphenols,focusing on applying nanoencapsulation for increasing stability and targeted delivery of phenolic compounds.

Climate change impacts the distribution of Quercus section Cyclobalanopsis(Fagaceae),a keystone lineage in East Asian evergreen broadleaved forests

East Asian evergreen broadleaved forests(EBFLs) harbor high species richness,but these ecosystems are severely impacted by global climate change and deforestation.Conserving and managing EBLFs requires understanding dominant tree distribution dynamics.In this study,we used 29 species in Quercus section Cyclobalanopsis-a keystone lineage in East Asian EBLFs-as proxies to predict EBLF distribution dynamics using species distribution models(SDMs).We examined climatic niche overlap,similarity,and equivalency among seven biogeographical regions’ species using’ecospat’.We also estimated the effectiveness of protected areas in the predicted range to elucidate priority conservation regions.Our results showed that the climatic niches of most geographical groups differ.The western species under the Indian summer monsoon regime were mainly impacted by temperature factors,whereas precipitation impacted the eastern species under the East Asian summer monsoon regime.Our simulation predicted a northward range expansion of section Cyclobalanopsis between 2081 and 2100,except for the ranges of the three Himalayan species analyzed,which might shrink significantly.The greatest shift of highly suitable areas was predicted for the species in the South Pacific,with a centroid shift of over 300 km.Remarkably,only 7.56% of suitable habitat is currently inside protected areas,and the percentage is predicted to continue declining in the future.To better conserve Asian EBLFs,establishing nature reserves in their northern distribution ranges,and transplanting the populations with predicted decreasing numbers and degraded habitats to their future highly suitable areas,should be high-priority objectives.

Historical relationships of the Mesoamerican highlands,with emphasis on tropical montane cloud forests:a temporal cladistic biogeographical analysis

The historical relationships of nine areas of endemism of the tropical montane cloud forests(TMCFs)were analysed based on a temporal cladistic biogeographical approach.Three cladistic biogeographical analyses were conducted based on 29cladograms of terrestrial taxa by partitioning them into three time-slices,namely,Miocene,Pliocene,and Pleistocene.The results showed different area relationships over time.For the Miocene and Pliocene time slices,the Isthmus of Tehuantepec acted as a geographic barrier that fragmented the TMCFs into two portions:west of the Isthmus and east of the Isthmus.In the case of the Pleistocene,the TMCFs were broken into two portions,one related to the Neotropical region and the other to the Nearctic region.Furthermore,the analyses allowed us to detect the influences of different geological and paleoclimatological events on the distribution of the TMCFs over time.Therefore,the TMCFs current distribution might have been driven by geological events during the Miocene-Pliocene,whereas climatic fluctuations have the highest impact during the Pleistocene.