The influence of urban park characteristics on bird diversity in Nanjing, China

Background:Habitat loss,fragmentation and decrease of habitat quality caused by urbanization have led to a dramatic decline in biodiversity worldwide.For highly urbanized areas,parks have become“islands”or habitat fragments for wildlife.As an important indicator group of urban ecosystem health,the response of birds to urbanization has attracted the global attention of ecologists.Understanding the key factors affecting bird diversity in urbanized environment is crucial to the protection of biodiversity in urban ecosystems.Methods:We used the line-transect method to survey birds in 37 urban parks in Nanjing,China.We also measured a number of park characteristics(area,isolation,shape index,environmental noise,distance to city center,and habitat diversity)that are commonly assumed to influence bird diversity.We then used the information-theoretic multi-model inference approach to determine which park characteristics had significant impacts on bird species richness.Results:We found that park area,habitat diversity and the distance to city center were the best positive predictors of bird species richness in Nanjing urban parks.By contrast,park isolation,park shape and environmental noise had little or no influence on bird diversity.Conclusions:Our study highlights the importance of park area,habitat diversity and the distance to city center in determining bird diversity in Nanjing city parks.Therefore,from a conservation viewpoint,we recommend that large parks with complex and diverse habitats far away from the city center should be retained or constructed to increase bird diversity in urban design and planning.

Correlates of extinction risk in Chinese endemic birds

Background: China has a relative high degree of endemism of birds due to its large area, diversified topography, and varied climates and habitats. Among the 77 Chinese endemic birds, 29 species are classified as threatened according to the officially released China Biodiversity Red List in 2015. Chinese endemic birds should be the focus of conservation because their local extinction in China means complete global extinction. However, to date, no study has explicitly examined the patterns and processes of extinction and threat in Chinese endemic birds. Methods: We obtained eleven biological traits and four extrinsic factors that are commonly hypothesized to influence extinction risk. After phylogenetic correction, these factors were used separately and in combination to assess their associations with extinction risk. Results: We found that 37.7% of Chinese endemic birds were listed as threatened (Vulnerable, Endangered and Critically Endangered). Small range size, high hunting vulnerability, and high human population density were important predictors of high extinction risk in Chinese endemic birds. Conclusions: Our study is the first to systematically investigate the patterns and processes of extinction risk in Chinese endemic birds. We suggest that endemic species with small range size and living in area with high human densities require conservation priorities. Conservation efforts should also focus on the reduction of human threats, such as human hunting and habitat degradation, for the effective preservation of Chinese endemic birds.

Down regulated expression of S_(2)-RNase attenuates self-incompatibility in “Guiyou No.1”pummelo

Self-incompatibility(SI)substantially restricts the yield and quality of citrus.Therefore,breeding and analyzing selfcompatible germplasm is of great theoretical and practical signi ficance for citrus.Here,we focus on the mechanism of a self-compatibility mutation in‘Guiyou No.1'pummelo(Citrus maxima),which is a spontaneous mutant of‘Shatian’pummelo(Citrus maxima,self-incompatibility).The rate of fruit set and the growth of pollen tubes in the pistil con firmed that a spontaneous mutation in the pistil is responsible for the self-compatibility of‘Guiyou No.1'.Segregation ratios of the S genotype in progeny,expression analysis,and western blotting validated that the reduced levels of S_(2)-RNase mRNA contribute to the loss of SI in‘Guiyou No.1'.Furthermore,we report a phased assembly of the‘Guiyou No.1'pummelo genome and obtained two complete and well-annotated S haplotypes.Coupled with an analysis of SV variations,methylation levels,and gene expression,we identi fied a candidate gene(CgHB40),that may in fluence the regulation of the S/^RNase promoter.Our data provide evidence that a mutation that affects the pistilled to the loss of SI in‘Guiyou No.1'by in fluencing a poorly understood mechanism that affects transcriptional regulation.This work signi ficantly advances our understanding of the genetic basis of the SI system in citrus and provides information on the regulation of S-RNase genes.

Illuminating the cells:transient transformation of citrus to study gene functions and organelle activities related to fruit quality

Although multiple microscopic techniques have been applied to horticultural research,few studies of individual organelles in living fruit cells have been reported to date.In this paper,we established an efficient system for the transient transformation of citrus fruits using an Agrobacterium-mediated method.Kumquat(Fortunella crassifolia Swingle)was used;it exhibits higher transformation efficiency than all citrus fruits that have been tested and a prolonged-expression window.Fruits were transformed with fluorescent reporters,and confocal microscopy and live-cell imaging were used to study their localization and dynamics.Moreover,various pH sensors targeting different subcellular compartments were expressed,and the local pH environments in cells from different plant tissues were compared.The results indicated that vacuoles are most likely the main organelles that contribute to the low pH of citrus fruits.In summary,our method is effective for studying various membrane trafficking events,protein localization,and cell physiology in fruit and can provide new insight into fruit biology research.

A comprehensive proteomic analysis of elaioplasts from citrus fruits reveals insights into elaioplast biogenesis and function

Elaioplasts of citrus peel are colorless plastids which accumulate significant amounts of terpenes.However,other functions of elaioplasts have not been fully characterized to date.Here,a LC–MS/MS shotgun technology was applied to identify the proteins from elaioplasts that were highly purified from young fruit peel of kumquat.A total of 655 putative plastid proteins were identified from elaioplasts according to sequence homology in silico and manual curation.Based on functional classification via Mapman,~50%of the identified proteins fall into six categories,including protein metabolism,transport,and lipid metabolism.Of note,elaioplasts contained ATP synthase and ADP,ATP carrier proteins at high abundance,indicating important roles for ATP generation and transport in elaioplast biogenesis.Additionally,a comparison of proteins between citrus chromoplast and elaioplast proteomes suggest a high level of functional conservation.However,some distinctive protein profiles were also observed in both types of plastids notably for isoprene biosynthesis in elaioplasts,and carotenoid metabolism in chromoplasts.In conclusion,this comprehensive proteomic study provides new insights into the major metabolic pathways and unique characteristics of elaioplasts and chromoplasts in citrus fruit.

Spatiotemporal distribution of seasonal bird assemblages on land-bridge islands: linking dynamic and static views of metacommunities

Background: Although assessing temporal dynamics of populations is crucial for understanding metacommunities, empirical studies have primarily analyzed only static snapshots of communities. Here, we present a holistic view of how species traits and habitat characteristics relate to metacommunity dynamics and use it to test for differences in the spatiotemporal distribution of seasonal bird assemblages. Methods: We surveyed forest birds in breeding and winter seasons within 36 islands for 9 years. We then grouped birds into four landbird assemblages, selected on the basis of published differences in biology or ecology: winter residents, migratory winter visitors, breeding summer residents, and migratory summer visitors. We estimated dynamic species colonization and extirpation through the 9-year period, and evaluated the associations among island attributes, species attributes and community composition. Results: Overall, winter and summer residents showed strong associations between composition and habitat structure of the islands. In addition, winter and summer residents on large islands had lower extirpation and turnover than winter and summer visitors. Visitor assemblages showed no significant habitat associations, and in winter had high extirpation rates and small body sizes. By contrast, local extirpation of summer visitors was correlated with local species richness, indicating a likely effect of competition on extirpation. Conclusions: Our results demonstrated repeated patterns among species composition, bird traits, habitat/island characteristics and observed metacommunity dynamics. Winter and summer residents best matched species sorting and patch dynamics, respectively, due to differences in resource availability and requirements of overwinter survival versus breeding. Summer visitors were consistent with species sorting and winter visitors were randomly distributed, likely because of interactions with resident competitors. Our results highlight that coexisting seasonal migrant and resident assemblages differ in their spatial dynamics, with consequences for relevant conservation and management strategies.

A Rapid Identification Method for Germplasm Materials Resistant to Citrus Huanglongbing Disease

[Objectives]This study was conducted to develop a rapid identification method for citrus germline materials resistant to Huanglongbing disease and lay a basis for accelerating citrus breeding for resistance to Huanglongbing and increasing the breeding efficiency.[Methods]Thirty-six citrus germplasms suspected to be resistant to citrus Huanglongbing disease were collected.The method of direct high grafting to citrus trees infected with Huanglongbing pathogen was adopted.The resistance of the test materials was identified and evaluated by field symptoms combined with quantitative PCR.It was defined as the top grafting identification method.[Results]The test materials that were grafted in spring started to germinate after one month,and three months late(June 5,2018)typical mottled yellowing on leaves was observed on KH-14 for the first time.After four months(July 5,2018)of top grafting,typical mottled yellowing occurred on 23 materials,and 11 materials showed no such symptom.After six months(September 4,2018)of top grafting,although the growth of KH-18,KH-12,KHY-4,KHY-5 and KHY-6 were normal,yellowing was observed on their leaves.Only KH-21 grew well,and showed no yellow shoots and yellowing leaves.It was identified as the material with resistance to Huanglongbing disease.Quantitative PCR tests on the above six materials showed that KH-21 was negative and other five were positive.Real-time fluorescence quantitative PCR test indicated that the average Huanglongbing bacteria amount in KH-21 was 1870.0 cell/μg DNA,and the average Huanglongbing bacteria amount in the control material was 372285.5 cell/μg DNA,indicating KH-21 was resistant to Huanglongbing bacteria.[Conclusions]The method for infecting bacteria by top grafting takes six months,can detect large amount of seedlings,and is time-saving,efficient,cost-saving and accurate.This method can quickly identify the resistance of citrus varieties to citrus Huanglongbing disease,and can be popularized and used in the identification of citrus Huanglongbing disease resistance.

Selective extinction and habitat nestedness are the main drivers of lizard nestedness in the Zhoushan Archipelago

Nested subset pattern(nestedness)is an important part of the theoretical framework of island biogeography and community ecology.However,most previous studies often used nestedness metrics or randomization algorithms that are vulnerable to type I error.In this study,we inves-tigated the nestedness of lizard assemblages on 37 islands in the Zhoushan Archipelago,China.We used the line-transect method to survey species occurrence,abundance,and habitat types of lizards on 37 islands during 2 breeding seasons in 2021 and 2022.We applied the nested metric WNODF and the conservative rc null model to control for type I error and quantify the significance of nestedness.Spearman rank cor relations were used to evaluate the role of 4 habitat variables(island area,2 isolation indices,and habitat diversity)and 4 ecological traits(body size,geographic range size,clutch size,and minimum area requirement)in generating nestedness.The results of WNODF analyses showed that lizard assemblages were significantly nested.The habitat-by-site matrix estimated by the program NODF was also significantly nested,support-ing the habitat nestedness hypothesis.The nestedness of lizard assemblages were significantly correlated with island area,habitat diversity.clutch size,and minimum area requirement.Overall,our results suggest that selective extinction and habitat nestedness were the main drivers of lizard nestedness in our system.In contrast,the nestedness of lizard assemblages was not due to passive sampling or selective colonization.To maximize the number of species preserved,our results indicate that we should protect both large islands with diverse habitats and species with largearea requirement and clutch size.

中国蛇类形态、生活史和生态学特征数据集

截至2023年1月,中国共记录312种蛇类,是世界上蛇类多样性最丰富的国家之一。物种特征决定其在环境中的生存能力,在进化生物学、生态学和保护生物学研究中具有重要作用。但是,目前还没有关于我国蛇类形态学、生活史和生态学等特征的完整数据库。本文通过系统查阅已出版的蛇类专业书籍、已发表的文献和爬行动物数据库,共收集整理了中国现有312种蛇类的41个特征数据。这些特征包括以下3个方面:形态特征(包括鳞片、牙齿等25个特征)、生活史特征(包括体长、食性、捕食方式、繁殖方式、活动时间、有无毒性等11个特征)和生态学特征(包括是否中国/岛屿特有种、成体生境、地理分布范围和海拔分布等5个特征)。在收集的41个特征中,除颏鳞、吻鳞和地理分布范围数据完整外(100%),其余特征数据都有不同程度的缺失(完整度为7.72%–99.70%)。本数据集是目前中国最新和最完整的蛇类特征数据集,可为我国蛇类的生态学、生物地理学和保护生物学等方面的研究提供基础数据支持。

中国鸟类的生活史和生态学特征数据集

中国现有1,445种鸟类,是世界上鸟类物种数最多的国家之一。物种特征反映了生物有机体的功能和适合度,在生态学、进化生物学和保护生物学研究中具有重要作用。但是,目前还没有关于我国鸟类生活史、生态学和地理分布等物种特征的完整数据库。通过系统查阅文献和各种数据资料,本文共收集整理出了中国1,445种鸟类17个功能特征数据:体重、体长、嘴峰长、翅长、尾长、跗蹠长、食性、窝卵数、卵大小、卵体积、巢址、巢的类型、集群状况、迁徙状况、是否特有种、地理分布范围和分布省份等。在这些特征中,除迁徙状况、是否特有种、地理分布范围和分布省份外,其余特征数据均存在不同程度的缺失,数据的完整度为60.83%‒100%。本数据库是目前关于中国鸟类最新和最全的物种特征数据库,期望能为我国鸟类生态学、进化生物学、生物地理学、保护生物学等研究提供支持。

Genome of Wild Mandarin and Domestication History of Mandarin

Mandarin （Citrus reticulata） is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins （MD1 and MD2） in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase （ACO） gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.

Nestedness and underlying processes of bird assemblages in Nanjing urban parks

Nestedness is an important pattern frequently reported for species assemblages on islands or fragmented systems.However,to date,there are few studies that comprehensively investigated faunal nestedness and underlying processes in urbanized landscapes.In this study,we examined the nestedness of bird assemblages and its underlying causal mechanisms in 37 urban parks in Nanjing,China.We used the line-transect method to survey birds from April 2019 to January 2020.We used the Weighted Nestedness metric based on Overlap and Decreasing Fill(WNODF)to estimate the nestedness of bird assemblages.We applied spearman partial correlation test to examine the relationships between nestedness ranks of sites and park characteristics(area,isolation,anthropogenic noise,number of habitat types,and building index),as well as between nestedness ranks of species and their ecological traits(body size,geographic range size,clutch size,minimum area requirement,dispersal ratio,and habitat specificity).We found that bird assemblages in urban parks were significantly nested.Park area,habitat diversity,building index,habitat specificity,and minimum area requirement of birds were significantly correlated with nestedness.Therefore,the nestedness of bird assemblages was caused by selective extinction,habitat nestedness,and urbanization.However,the nestedness of bird assemblages did not result from passive sampling,selective colonization,or human disturbance.Overall,to maximize the number of species preserved in our system,conservation priority should be given to parks with large area,rich habitat diversity,and less building index.From a species perspective,we should focus on species with large area requirement and high habitat specificity for their effective conservation.

CHH methylation of genes associated with fatty acid and jasmonate biosynthesis contributes to cold tolerance in autotetraploids of Poncirus trifoliata

Polyploids have elevated stress tolerance,but the underlying mechanisms remain largely elusive.In this study,we showed that naturally occurring tetraploid plants of trifoliate orange(Poncirus trifoliata(L.) Raf.) exhibited enhanced cold tolerance relative to their diploid progenitors.Transcriptome analysis revealed that whole-genome duplication was associated with higher expression levels of a range of well-characterized cold stress-responsive genes.Global DNA methylation profiling demonstrated that the tetraploids underwent more extensive DNA demethylation in comparison with the diploids under cold stress.CHH methylation in the promoters was associated with up-regulation of related genes,whereas CG,CHG,and CHH methylation in the 3’-regions was relevant to gene down-regulation.Of note,genes involved in unsaturated fatty acids(UFAs) and jasmonate(JA)biosynthesis in the tetraploids displayed different CHH methylation in the gene flanking regions and were prominently up-regulated,consistent with greater accumulation of UFAs and JA when exposed to the cold stress.Collectively,our findings explored the difference in cold stress response between diploids and tetraploids at both transcriptional and epigenetic levels,and gained new insight into the molecular mechanisms underlying enhanced cold tolerance of the tetraploid.These results contribute to uncovering a novel regulatory role of DNA methylation in better cold tolerance of polyploids.

中国蜥蜴类生活史和生态学特征数据集

截至2020年底,中国共有226种蜥蜴类(不包括外来入侵种),是世界上蜥蜴类多样性最丰富的国家之一。系统整理中国现有蜥蜴类的特征数据在物种起源与进化、形成与灭绝、保护生物学等研究中具有重要意义。但是,目前还没有关于我国蜥蜴类生活史、生态学和地理分布等物种特征的完整数据库。本文通过系统查阅文献和数据资料,共收集整理了中国现有226种本土蜥蜴类19个特征数据:描述年份、中国受威胁等级、全球受威胁等级、是否中国特有种、是否岛屿特有种、平均体长、平均体重、食性、窝卵数、繁殖模式、四肢发育、活动时间、栖息生境、栖息地类型、栖息地宽度、海拔分布范围、地理分布范围、动物地理界和分布省份。在上述特征中,除了四肢发育、描述年份、是否中国特有种、是否岛屿特有种和分布省份外,其余特征数据均存在不同程度的缺失,数据完整度为47.14%–100%。本数据集是目前关于中国蜥蜴类最新和最全的物种特征数据库,可为我国蜥蜴类生态学、进化生物学、生物地理学和保护生物学等研究领域提供数据支持。

中国两栖类生活史和生态学特征数据集

截至2021年底,中国共记载591种两栖类(不包括外来入侵种),是世界上两栖类物种数最多的国家之一。物种特征影响和决定了物种在环境中的生存能力,在进化生物学、生态学和保护生物学研究中具有重要作用。目前,中国两栖类在线数据库(https://www.amphibiachina.org)已经整理了我国两栖类的形态特征、生物学信息和地理分布等部分物种特征,但仍缺乏一个完整的、可自由检索的数据集。通过系统查阅文献和数据检索,本文收集整理了中国全部591种本土两栖类的22个特征数据,包括物种发现时间(最早发现和描述新物种文章的发表时间)、模式产地、中国受威胁等级、全球受威胁等级、致危因子、是否中国特有种、是否岛屿特有种、雄性体长、雌性体长、窝卵数、卵径、产卵地点、幼体主要生境、成体微生境、活动模式、生殖周期、繁殖时间、是否有亲本照顾、受精方式、海拔范围、分布地区、分布省份数。除了物种发现时间、是否岛屿特有种、分布地区、分布省份数外,其余特征数据都有不同程度的缺失,数据完整度为27.92%-100%,平均完整度为71.72%,标准差为24%。本数据集是目前我国两栖类最新和最全的物种特征数据库,希望可以为我国两栖类生态学、保护生物学、生物地理学等研究提供数据支持。

Biological and extrinsic correlates of extinction risk in Chinese lizards

China is a country with one of the most species-rich reptile faunas in the world.However,nearly a quarter of Chinese lizard species assessed by the China Biodiversity Red List are threatened.Nevertheless,to date,no study has explicitly examined the pattern and processes of extinction and threat in Chinese lizards.In this study,we conducted the first comparative phylogenetic analysis of extinction risk in Chinese lizards.We addressed the following 3 questions:(1)What is the pattern of extinction and threat in Chinese lizards?(2)Which species traits and extrinsic factors are related to their extinction risk?(3)How can we protect Chinese lizards based on our results?We collected data on 10 species traits(body size[BS],clutch size,geographic range size,activity time,reproductive mode,habitat specialization[HS],habitat use,leg development,maximum elevation,and elevation range)and 7 extrinsic factors(mean annual precipitation(MAP),mean annual temperature,mean annual solar insolation,normalized difference vegetation index(NDVI),human footprint,human population density,and human exploitation).After phylogenetic correction,these variables were used separately and in combination to assess their associations with extinction risk.We found that Chinese lizards with a small geographic range,large BS,high HS,and living in high MAP areas were vulnerable to extinction.Conservation priority should thus be given to species with the above extinction-prone traits so as to effectively protect Chinese lizards.Preventing future habitat destruction should also be a primary focus of management efforts because species with small range size and high HS are particularly vulnerable to habitat loss.

NEW INSIGHTS INTO THE PHYLOGENY AND SPECIATION OF KUMQUAT (FORTUNELLA SPP.) BASED ON CHLOROPLAST SNP, NUCLEAR SSR AND WHOLE-GENOME SEQUENCING

Kumquat(Fortunella spp.)is a fruit and ornamental crop worldwide due to the palatable taste and high ornamental value of its fruit.Although Fortunella is classified into the economically important true citrus fruit tree group together with Citrus and Poncirus,few studies have been focused on its evolutionary scenario.In this study,analysis of five chloroplast loci and 47 nuclear microsatellites(nSSR)loci from 38 kumquat and 10 citrus accessions revealed the independent phylogeny of Fortunella among citrus taxa,and that Fortunella mainly comprises two populations:CUL,cultivated Fortunella spp.(F.margarita,F.crassifolia and F.japonica);and HK,wild Hong Kong kumquat(Fortunella hindsii).Genomic analysis based on whole-genome SNPs indicated that the allele frequency of both pupations deviated from the neutral selection model,suggesting directional selection was a force driving their evolutions.CUL exhibited lower genomic diversity and higher linkage strength than HK,suggesting artificial selection involved in its origin.A high level of genetic differentiation(Fst=0.364)was detected and obviously asynchronous demographic changes were observed between CUL and HK.Based on these results,a new hypothesis for the speciation of Fortunella is proposed.