Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Human lineage mutations regulate RNA-protein binding of conserved genes NTRK2 and ITPR1 involved in human evolution

Background The role of human lineage mutations(HLMs)in human evolution through post-transcriptional modification is unclear.Aims To investigate the contribution of HLMs to human evolution through post-transcriptional modification.Methods We applied a deep learning model Seqweaver to predict how HLMs impact RNA-binding protein affinity.Results We found that only 0.27%of HLMs had significant impacts on RNA-binding proteins at the threshold of the top 1%of human common variations.These HLMs enriched in a set of conserved genes highly expressed in adult excitatory neurons and prenatal Purkinje neurons,and were involved in synapse organisation and the GTPase pathway.These genes also carried excess damaging coding mutations that caused neurodevelopmental disorders,ataxia and schizophrenia.Among these genes,NTRK2 and ITPR1 had the most aggregated evidence of functional importance,suggesting their essential roles in cognition and bipedalism.Conclusions Our findings suggest that a small subset of human-specific mutations have contributed to human speciation through impacts on post-transcriptional modification of critical brain-related genes.

Biogenesis of flavor-related linalool is diverged and genetically conserved in tree peony (Paeonia × suffruticosa)

Floral scent is an important and genetically complex trait in horticultural plants.Tree peony(Paeonia×suffruticosa)originates in the Pan-Himalaya and has nine wild species divided into two subsections,Delavayanae and Vaginatae.Their f lowers are beloved worldwide for their sweet f loral fragrance,yet the f lavor-related volatiles and underlying biosynthetic pathways remain unknown.Here,we characterized the volatile blends of all wild tree peony species and found that the flavor-related volatiles were highly divergent,but linalool was a unique monoterpene in subsect.Delavayanae.Further detection of volatiles in 97 cultivars with various genetic backgrounds showed that linalool was also the characteristic aroma component in Paeonia delavayi hybrid progenies,suggesting that linalool was conserved and dominant within subsect.Delavayanae and its hybrids,instead of species and cultivars from subsect.Vaginatae.Global transcriptome analysis of all wild tree peony species and 60 cultivars revealed five candidate genes that may be involved in key steps of linalool biosynthesis;especially the expressions of three TPS genes,PdTPS1,PdTPS2,and PdTPS4,were significantly positively correlated with linalool emissions across tree peony cultivars.Further biochemical evidence demonstrated that PdTPS1 and PdTPS4were the pivotal genes determining the species-specific and cultivar-specific emission of linalool.This study revealed a new insight into floral scent divergence in tree peony and would greatly facilitate our understanding of the phylogeny and evolution of Paeonia.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

Bird species composition and conservation challenges in the Gaoligong Mountains, one of the most diverse bird areas in the world

The Gaoligong Mountains(GLGM),located in southwestern China,extend north to south along the western border of the Hengduan Mountains,spanning approximately 600 km.In this study,we consolidated findings from 17 bird surveys conducted in the GLGM between 2010 and 2022.We found that the GLGM harbors tremendous bird diversity,with a total of 796 documented bird species in the region.Nearly a quarter(23.0%)of these species are listed as state key protected species or as Chinese and global threatened species.Analysis of species richness at the county level showed a decreasing trend with increasing latitude,with the greatest diversity in Yingjiang(661 species).Observations indicated that the GLGM belongs to the Oriental realm,primarily composed of bird species from southern and southwestern China.The GLGM plays an important role in avian conservation by sheltering exceptional bird diversity,providing corridors and flyways for bird migration and dispersal,and mitigating the effects of climate change.In response to the conservation needs of birds and other wildlife,the Chinese government has established numerous protected areas within the GLGM.Despite these efforts,avian conservation still faces considerable challenges in the GLGM due to limitations in the protected area network,transboundary nature of the regions,and existing gaps in monitoring and research.

Achievements and challenges of primate conservation in China

The dual impact of climate change and human activities has precipitated a sharp decline in primate biodiversity globally.China is home to the most diverse primate species in the Northern hemisphere,which face severe ecological threats due to the expansion of modern agriculture,extensive exploitation and consumption of natural resources,and excessive land development during its transition from an agricultural to a modern society.In response,China has implemented various ecological conservation measures,including habitat restoration and protection.These efforts have made substantial strides in biodiversity conservation,with certain regions witnessing an increase in primate populations.In the current study,we conducted a systematic review of historical documents and field research data related to Chinese primates,evaluating the endangered status of primate species in China.Despite improvements in the habitats of most primate species and some population growth,many species still face severe threats,including declining and small populations.Species such as the Myanmar snub-nosed monkey(Rhinopithecus strykeri),eastern black crested gibbon(Nomascus nasutus),and Hainan gibbon(N.hainanus)remain particularly vulnerable due to their limited distribution ranges and extremely small populations.Insufficient scientific data,fragmented information,and not enough studies in conservation biology further compound the challenges.Moreover,there is a notable lack of detailed population monitoring data for species such as the Bengal slow loris(Nycticebus bengalensis),pygmy slow loris(N.pygmaeus),Indochinese gray langur(Trachypithecus crepusculus),Shortridge’s langur(T.shortridgei),and capped langur(T.pileatus),which hinders the development of practical and targeted conservation management strategies.Therefore,for national biodiversity conservation,there is an urgent need for specialized primate surveys,enhancing habitat protection and restoration,and increasing focus on cross-border conservation strategies and regional cooperation.There is also a need to establish a comprehensive and systematic research database platform,conduct continuous and in-depth research in primate biology,and actively engage in the scientific assessment of ecotourism.Additionally,strengthening public awareness and education on wildlife conservation remains essential.Such integrated and systematic efforts will provide scientific support for the current and future conservation and management of primate species in China.

Mammals of Gaoligong Mountain in China:Diversity,distribution,and conservation

Gaoligong Mountain(hereafter,GLGM)is located at the intersection of Myanmar and China’s Yunnan Province and Xizang Zizhiqu,and spans three globally significant biodiversity hotspots:the Himalayas,Indo-Burma,and the Mountains of Southwest China.Although surveys of mammals in this ecologically important region have a long history,there is no comprehensive systematic checklist and distribution account of the mammals of GLGM.Here,we compiled a mammal species checklist of GLGM based on thorough field investigations and literature reviews.We also examined specimen collections and applied camera trapping surveys to explore the region’s mammal diversity and distribution patterns.We recorded 212 mammal species in nine orders,33 families,and 119 genera,which accounts for 30.5%of China’s mammal species,and a high proportion of nationally protected(50)and globally threatened(29)species.Mammal species richness showed a symmetrical unimodal curve along the elevation gradient,peaking at intermediate elevations(2000 to 2500 m above sea level(asl)),and increasing generally from south to north,slightly higher in the east slope than in the west.Cluster analysis and non-metric multidimensional scaling revealed three distinct elevational assemblages(<900 m asl.,900-3500 m asl.,and>3500 m asl)and significant south-to-north variation,but no substantial differences between the east and west slopes.The GLGM present a unique conservation value due to the high proportions of rare and endangered mammal species,complex faunal composition,high endemism,and being the distribution boundary for many species.This study is an important phased account of mammal diversity in GLGM and makes a prospect for future research.

Diversity of Orchids in Terms of Their Distribution, Uses and Conservation in Annapurna Conservation Area of Nepal

The Annapurna Conservation Area (ACA), the first conservation area and the largest protected area (PA) in Nepal, is incredibly rich in biodiversity. Notwithstanding this, orchids in the ACA have not been explored enough yet thus making the need for ambitious research to be carried out. Previous study only included 81 species of orchids within ACA. This study aims to update the record of species and genera richness in the ACA. In total 198 species of orchids, belonging to 67 genera (40% and 62% of the total recorded orchid species and genera in Nepal) has been recorded in ACA. This represents an increase of 144% in species and 56% in genera over the previous data. Out of the 198 species, 99 were epiphytes, 6 were holomycotrophic and 93 were terrestrial. Among the 67 genera, Bulbophyllum (17) species were dominant, followed by Dendrobium (16), Herminium (10), Coelogyne, Plantanthera (9 each), Eria, Habenaria, Oberonia (8 each), Calanthe (7), and Liparis (6). Fifty-six species were found to be ornamentally significant and 85 species medicinally significant.

A Local Macroscopic Conservative(LoMaC)Low Rank Tensor Method with the Discontinuous Galerkin Method for the Vlasov Dynamics

In this paper,we propose a novel Local Macroscopic Conservative(LoMaC)low rank tensor method with discontinuous Galerkin(DG)discretization for the physical and phase spaces for simulating the Vlasov-Poisson(VP)system.The LoMaC property refers to the exact local conservation of macroscopic mass,momentum,and energy at the discrete level.The recently developed LoMaC low rank tensor algorithm(arXiv:2207.00518)simultaneously evolves the macroscopic conservation laws of mass,momentum,and energy using the kinetic flux vector splitting;then the LoMaC property is realized by projecting the low rank kinetic solution onto a subspace that shares the same macroscopic observables.This paper is a generalization of our previous work,but with DG discretization to take advantage of its compactness and flexibility in handling boundary conditions and its superior accuracy in the long term.The algorithm is developed in a similar fashion as that for a finite difference scheme,by observing that the DG method can be viewed equivalently in a nodal fashion.With the nodal DG method,assuming a tensorized computational grid,one will be able to(i)derive differentiation matrices for different nodal points based on a DG upwind discretization of transport terms,and(ii)define a weighted inner product space based on the nodal DG grid points.The algorithm can be extended to the high dimensional problems by hierarchical Tucker(HT)decomposition of solution tensors and a corresponding conservative projection algorithm.In a similar spirit,the algorithm can be extended to DG methods on nodal points of an unstructured mesh,or to other types of discretization,e.g.,the spectral method in velocity direction.Extensive numerical results are performed to showcase the efficacy of the method.

Nonuniform Dependence on the Initial Data for Solutions of Conservation Laws

In this paper,we study systems of conservation laws in one space dimension.We prove that for classical solutions in Sobolev spaces H^(s),with s>3/2,the data-to-solution map is not uniformly continuous.Our results apply to all nonlinear scalar conservation laws and to nonlinear hyperbolic systems of two equations.

A LOW-REGULARITY FOURIER INTEGRATOR FOR THE DAVEY-STEWARTSON II SYSTEM WITH ALMOST MASS CONSERVATION

In this work,we propose a low-regularity Fourier integrator with almost mass conservation to solve the Davey-StewartsonⅡsystem(hyperbolic-elliptic case).Arbitrary order mass convergence could be achieved by the suitable addition of correction terms,while keeping the first order accuracy in H~γ×H^(γ+1)for initial data in H^(γ+1)×H^(γ+1)withγ>1.The main theorem is that,up to some fixed time T,there exist constantsτ_(0)and C depending only on T and‖u‖_(L^(∞)((0,T);H^(γ+1)))such that,for any 0<τ≤τ_(0),we have that‖u(t_(n),·)-u^(n)‖H_γ≤C_(τ),‖v(t_(n),·)-v^(n)‖_(Hγ+1)≤C_(τ),where u^(n)and v^(n)denote the numerical solutions at t_(n)=nτ.Moreover,the mass of the numerical solution M(u^(n))satisfies that|M(u^(n))-M(u_0)|≤Cτ~5.

Dimension by Dimension Finite Volume HWENO Method for Hyperbolic Conservation Laws

In this paper,we propose a finite volume Hermite weighted essentially non-oscillatory(HWENO)method based on the dimension by dimension framework to solve hyperbolic conservation laws.It can maintain the high accuracy in the smooth region and obtain the high resolution solution when the discontinuity appears,and it is compact which will be good for giving the numerical boundary conditions.Furthermore,it avoids complicated least square procedure when we implement the genuine two dimensional(2D)finite volume HWENO reconstruction,and it can be regarded as a generalization of the one dimensional(1D)HWENO method.Extensive numerical tests are performed to verify the high resolution and high accuracy of the scheme.

The Current Conservation Efforts and Future Prospects for the Endangered Nubian Ibex (Capra nubiana ibex) in Sudan

A comprehensive action plan for the conservation of the endangered species, the Nubian ibex in Sudan, can be developed by gaining a thorough understanding of their current status, conservation strategy, and relevant laws and regulations, as well as raising awareness about the importance of protecting endangered species. The Nubian ibex is listed as an endangered species on The International Union for Conservation of Nature (IUCN) Red List, highlighting the need for further research on population conservation efforts due to insufficient population data. To address this knowledge gap, a questionnaire was conducted with various stakeholders, including police officers, researchers, and lecturers, representing a diverse range of organizations and universities. The findings revealed that hunting is the primary factor contributing to endangerment. Mammals account for 80% of endangered species, while reptiles comprise less than one-tenth. Research centers are recognized as the main governing body, and 85% of participants are concerned about the declining population. Hunting accounted for less than half of the threats to the ibex population in Sudan, while habitat loss made up a quarter. Mining, climate change, human activity, and agriculture were also identified as risks. However, there were no plans, strategies, procedures, or measures in place to conserve the Nubian ibex. There were also no initiatives to preserve its biodiversity, and awareness about endangered species was lacking. Although participants believed that laws were effective in protecting the ibex, no licenses were issued for its conservation, and annual surveys were not conducted. Additionally, there were no recorded instances of Mukhalfat related to the Nubian ibex. In light of these findings, we propose various conservation measures to address these challenges. These measures include the implementation of laws and regulations, conducting annual surveys to monitor population trends, protecting habitats, establishing breeding and releasing programs, launching awareness campaigns, undertaking rehabilitation efforts, enhancing research efforts, and developing comprehensive conservation strategies. Additionally, it is crucial to foster cooperation among wildlife institutes to ensure the effective implementation of these conservation measures.

Bilateral Congenital Upper Eyelid Eversion (Ectropion): A Rare Presentation Responded Well to Conservative Treatment at Temeke Regional Referral Hospital-Tanzania

Congenital eversion of the upper eyelids is a rare condition, the exact cause of which remains unknown. It is more frequently associated with Down’s syndrome and black babies. If diagnosed early and treated properly, the condition can be managed without surgery. We report a case of non syndromic congenital bilateral severe upper eyelid eversion in otherwise normal 3 days old neonate of African descent (Tanzanian), born by vaginal delivery. The case was conservatively managed by lubricants, antibiotics and eyelid patching. We report this case because from the best of our knowledge it has never been documented here at our hospital and Tanzania before.

Characteristic analysis of 5D symmetric Hamiltonian conservative hyperchaotic system with hidden multiple stability

Conservative chaotic systems have unique advantages over dissipative chaotic systems in the fields of secure communication and pseudo-random number generator because they do not have attractors but possess good traversal and pseudorandomness. In this work, a novel five-dimensional(5D) Hamiltonian conservative hyperchaotic system is proposed based on the 5D Euler equation. The proposed system can have different types of coordinate transformations and time reversal symmetries. In this work, Hamilton energy and Casimir energy are analyzed firstly, and it is proved that the new system satisfies Hamilton energy conservation and can generate chaos. Then, the complex dynamic characteristics of the system are demonstrated and the conservatism and chaos characteristics of the system are verified through the correlation analysis methods such as phase diagram, equilibrium point, Lyapunov exponent, bifurcation diagram, and SE complexity. In addition, a detailed analysis of the multistable characteristics of the system reveals that many energy-related coexisting orbits exist. Based on the infinite number of center-type and saddle-type equilibrium points, the dynamic characteristics of the hidden multistability of the system are revealed. Then, the National Institute of Standards and Technology(NIST)test of the new system shows that the chaotic sequence generated by the system has strong pseudo-random. Finally, the circuit simulation and hardware circuit experiment of the system are carried out with Multisim simulation software and digital signal processor(DSP) respectively. The experimental results confirm that the new system has good ergodicity and realizability.

Secondary Hyperparathyroidism in Dialysis Patients: Short- and Long-Term Outcomes of Conservative Parathyroidectomy

Secondary hyperparathyroidism (HPT) is frequent in dialysis patients. Parathyroidectomy (PTX) is indicated for patients who failed medical therapy. We reviewed the data from 184 dialysis patients who underwent PTX between January 2015 and January 2023. We aimed to evaluate the short and long term outcomes of PTX in dialysis patients, comparing the conservative 3/4 versus 7/8 techniques in this population.166 dialysis patients with secondary HPT were included. A conservative subtotal PTX (sPTX) 7/8 was performed in 72% of patients and sPTX 3/4 in 28% of them. Severe postoperative hypocalcaemiaocurred in 45 patients (27%). Hypocalcaemia was significantly more frequent in the sPTX 7/8 group (p = 0.012). One case of persistent HPT (0.6%) and 20 cases of recurrence (12%) were diagnosed. Recurrence was more frequent in the sPTX 3/4 group (15%). No deaths were reported during the perioperative period.

ENERGY CONSERVATION FOR THE WEAK SOLUTIONS TO THE 3D COMPRESSIBLE NEMATIC LIQUID CRYSTAL FLOW

In this paper,we establish some regularity conditions on the density and velocity fields to guarantee the energy conservation of the weak solutions for the three-dimensional compressible nematic liquid crystal flow in the periodic domain.

Fertilization and Soil Ploughing Practices under Changing Physical Environment Lead to Soil Organic Carbon Dynamics under Conservation Agriculture in Rice-Wheat Cropping System: A Scoping Review

Ploughing and fertilization practices in rice-wheat system have deteriorated the soil carbon (C) pools. Conservation agriculture (CA) based management approaches have proven to enhance C sequestration and reverse the loss of soil-organic-carbon (SOC), which further enhances soil fertility. Different fractions of SOC pools react to the alterations in management practices and indicate changes in SOC dynamics as compared to total C in the soil. Higher SOC levels in soil have been observed in case of reduced/no-till (NT) practices than conventional tillage (CT). However, between CT and zero tillage/NT, total SOC stocks diminished with an increase in soil depth, which demonstrated that the benefits of SOC are more pronounced in the topsoil under NT. Soil aggregation provides physical protection to C associated with different-sized particles, thus, the improvement in soil aggregation through CA is an effective way to mitigate soil C loss. Along with less soil disturbance, residual management, suitable crop rotation, rational application of manures and fertilizers, and integrated nutrient management have been found to be effective in not only improving soil C stock but also enhancing the soil health and productivity. Thus, CA can be considered as a potential method in the build-up of SOC of soil in rice-wheat system.

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss.However,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative introgression.Here we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread C.kwechowensis-C yunnanensis complex.We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation.Population genomics revealed that both C.chinensis and the C.kwechowensis-C.yunnanensis complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern differentiation.Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(C.chinensis) or have even recovered from population bottlenecks(C.kwechowensis-C.yunnanensis complex) during the Quaternary.Compared with C.kwechowensis-C. yunnanensis complex,C.chinensis showed significantly lower genomic diversity and higher inbreeding level.However,C.chinensis carried significantly fewer deleterious mutations than C.kwechowensis-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous variants.We also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local adaptation.Hence,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C.chinensis.Overall,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.