多基因联合揭示海南鲌的遗传结构与遗传多样性

海南鲌(Culter recurviceps)是我国华南地区重要经济鱼类, 由于受到近些年水利开发、过度捕捞、环境污染等诸多因素的影响, 其资源量快速下降, 亟需得到更多的关注和保护。为保护和合理开发海南鲌种质资源, 本研究采集了华南地区23个地理群体207尾海南鲌样本, 测定了2个线粒体基因(Cytb和ND2)并从Barcode of Life Data System数据库获得相对应线粒体COI基因, 结合多种分析方法(系统发育分析、分化时间估算、单倍型网状图、群体遗传分析和Mantel检验)对海南鲌的遗传结构和遗传多样性展开研究。系统发育分析和单倍型网状图表明华南地区海南鲌群体被分成3个谱系(I、II和III), 其中谱系I和III由珠江的群体组成, 谱系II由海南岛的群体组成。分化时间估算发现3个谱系之间的分化时间介于0.028-0.251 Ma之间, 表明华南地区更新世气候变化可能是造成海南鲌谱系分化的重要原因。群体遗传分析发现海南鲌群体之间存在极显著的遗传分化(F_ST = 0.511, P < 0.001), 并且符合距离隔离模式(R = 0.348, P = 0.0010)。群体动态历史分析表明, 海南鲌群体可能在0.010-0.025 Ma经历了群体扩张, 表明更新世的气候波动也影响了海南鲌的群体大小和分布。综上所述, 海南鲌群体由3个谱系组成, 更新世气候变化是导致3个谱系分化和影响海南鲌群体动态历史的重要因素。此外, 海南鲌群体之间的遗传分化也可能受到了空间距离的影响。     

云南高黎贡山地区蝴蝶群落多样性

位于滇西北的高黎贡山是全球生物多样性研究和保护的热点地区之一, 然而该地区昆虫多样性缺乏系统调查和总结。本研究聚焦蝴蝶类群, 考虑该区域高山峡谷特点, 结合海拔梯度、生境类型和季节变化, 采用样线法调查、分析蝴蝶物种多样性及群落结构变化。结果显示: 共观测记录到蝴蝶2,055只, 隶属于5科85属151种, 在历史记录上新增27种, 使该地区已知蝴蝶种类达488种; 其中蛱蝶科物种多样性最高, 灰蝶科次之, 凤蝶科最低。蝴蝶群落多样性分析结果表明: 中海拔1,000-2,000 m区域种类丰富、多样性指数最高; 低海拔区蝴蝶分布明显聚集, 并且与高海拔地区空间上分离, 少有重叠。该地区不同生境中蝴蝶的种类及数量差异也较大, 物种数及多样性指数在自然保护区最高、边缘交错带居中及农业种植区最低。此外, 蝴蝶的种类和数量也存在季节差异, 春季调查到的个体数少, 夏季观察到的物种数少, 两年秋季调查到的物种丰富度、多样性均高, 但存在季节内变化。总之, 高黎贡山地区不同海拔、生境、季节间和季节内蝴蝶群落组成有自身特点, 共存物种有限, 蝴蝶群落相似性低。综合评估分布于该地区的蝴蝶保护种类, 包括易危种17种、近危种50种, 有国家二级保护蝴蝶3种。本研究弄清了高黎贡山地区蝴蝶的物种本底, 并调查获得其多样性随海拔、生境和季节变化的模式, 为加强区域物种多样性监测、保护生物多样性提供了科学依据。     

极小种群野生植物海南风吹楠的遗传多样性研究

为探讨海南风吹楠(Horsfieldiahainanensis)的濒危原因,利用限制性酶切位点相关的DNA测序技术(RAD-seq)开发单核苷酸多态性(SNPs),评估居群的遗传多样性和遗传结构。结果表明,海南风吹楠的遗传多样性较低(Ho=0.167),其中BWL居群表现出最高的遗传多样性;居群间存在中等程度的遗传分化(Fst=0.120)。Structure分析表明居群的最佳聚类值为2,但个别居群的遗传结构混杂,Mantel检测结果也表明遗传距离和地理距离没有相关性(r=0.733,P0.075)。自身更新能力低以及过度的人为活动干扰,可能是导致其濒危的主要原因。建议加强对遗传多样性高的居群(BWL和YGL)进行就地保护;对生境破坏严重的居群(EXL和DLS)进行近地或迁地保护,以增加居群间的基因交流,同时构建核心种质,防止遗传资源丢失加剧。     

In silico annotation of unreviewed acetylcholinesterase (AChE) in some lepidopteran insect pest species reveals the causes of insecticide resistance

Lepidoptera is the second most diverse insect order outnumbered only by the Coeleptera. Acetylcholinesterase (AChE) is the major target site for insecticides. Extensive use of insecticides, to inhibit the function of this enzyme, have resulted in the development of insecticide resistance. Complete knowledge of the target proteins is very important to know the cause of resistance. Computational annotation of insect acetylcholinesterase can be helpful for the characterization of this important protein. Acetylcholinesterase of fourteen lepidopteran insect pest species was annotated by using different bioinformatics tools. AChE in all the species was hydrophilic and thermostable. All the species showed lower values for instability index except L. orbonalis, S. exigua and T. absoluta. Highest percentage of Arg, Asp, Asn, Gln and Cys were recorded in P. rapae. High percentage of Cys and Gln might be reason for insecticide resistance development in P. rapae. Phylogenetic analysis revealed the AChE in T. absoluta, L. orbonalis and S. exigua are closely related and emerged from same primary branch. Three functional motifs were predicted in eleven species while only two were found in L. orbonalis, S. exigua and T. absoluta. AChE in eleven species followed secretory pathway and have signal peptides. No signal peptides were predicted for S. exigua, L. orbonalis and T. absoluta and follow non secretory pathway. Arginine methylation and cysteine palmotylation was found in all species except S. exigua, L. orbonalis and T. absoluta. Glycosylphosphatidylinositol (GPI) anchor was predicted in only nine species.     

Novel artificial intelligence machine learning approaches to precisely predict survival and site-specific recurrence in cervical cancer: A multi-institutional study

BackgroundMachine learning (ML) has been gradually integrated into oncologic research but seldom applied to predict cervical cancer (CC), and no model has been reported to predict survival and site-specific recurrence simultaneously. Thus, we aimed to develop ML models to predict survival and site-specific recurrence in CC and to guide individual surveillance.MethodsWe retrospectively collected data on CC patients from 2006 to 2017 in four hospitals. The survival or recurrence predictive value of the variables was analyzed using multivariate Cox, principal component, and K-means clustering analyses. The predictive performances of eight ML models were compared with logistic or Cox models. A novel web-based predictive calculator was developed based on the ML algorithms.ResultsThis study included 5112 women for analysis (268 deaths, 343 recurrences): (1) For site-specific recurrence, larger tumor size was associated with local recurrence, while positive lymph nodes were associated with distant recurrence. (2) The ML models exhibited better prognostic predictive performance than traditional models. (3) The ML models were superior to traditional models when multiple variables were used. (4) A novel predictive web-based calculator was developed and externally validated to predict survival and site-specific recurrence.ConclusionML models might be a better analytic approach in CC prognostic prediction than traditional models as they can predict survival and site-specific recurrence simultaneously, especially when using multiple variables. Moreover, our novel web-based calculator may provide clinicians with useful information and help them make individual postoperative follow-up plans and further treatment strategies.     

花苜蓿小尺度空间遗传结构研究

以花苜蓿（Medicago ruthenica Trautv.）为材料,在内蒙古克什克腾旗建立两个25 m×50 m的样方（山谷YF1和山坡YF2）,采集该范围内的所有个体,利用8对SSR分子标记对其遗传变异特性进行分析。结果显示,克什克腾旗花苜蓿居群遗传多样性较高。两个居群个体的空间自相关分析结果表明,9 m内的个体间为非随机邻近交配,且在同距离范围内,山谷居群的个体间遗传相似性更低,推测此区域可能是历史和地理因素塑造了花苜蓿丰富的遗传多样性,两个小尺度空间格局的个体间基因流模式主要受地形影响。     

Mitochondrial DNA Sequence Analyses and Phylogenetic Relationships Among Two Nigerian Goat Breeds and the South African Kalahari Red

The first hypervariable (HV1) region of mitochondrial DNA (mtDNA) of two popular Nigerian goat breeds: West African Dwarf (WAD) (n = 35) and Red Sokoto (RS) (n = 37) and one exotic breed: Kalahari Red (KR) (n = 38) imported from South Africa were sequenced to investigate sequence diversity, genetic structure, origin, and demographic history of the populations. A total of 68 polymorphic sites were found in 110 sequences that grouped into 68 haplotypes. Average haplotype and nucleotide diversities for all breeds were 0.982 ± 0.005 and 0.02350 ± 0.00213, respectively. Phylogenetic analysis revealed two mtDNA lineages (A and B). Lineage A was predominant and included all haplotypes from WAD and RS and 5 out of 11 haplotypes of KR goats. The remaining haplotypes (6 Amills M, Ramírez O, Tomàs A, et al. Mitochondrial DNA diversity and origins of South and Central American goats. Animal Genetics 2009; 40(3): 315–322.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) of KR belong to lineage B. The analysis of molecular variance revealed a high-within breed genetic variance of 82.4% and a low-between breed genetic variance of 17.6%. The three breeds clustered with Capra aegagrus as their wild ancestor. Mismatch distribution analysis showed that WAD, RS and haplogroup A have experienced population expansion events. The study has revealed very high diversity within the three breeds which are not strongly separated from each other based on mtDNA analysis. The information obtained on the genetic structure of the breeds will be useful in planning improvement and conservation programs for the local populations.     

Microsatellite Analysis of Genetic Population Structure of Zebu Cattle (Bos indicus) Breeds from North-Western Region of India

The present study aims to understand the existing genetic diversity and structure of six native cattle breeds (Rathi, Tharparkar, Nagori, Mewati, Gir, and Kankrej) adapted to the north-western arid and semi-arid region of India based on microsatellite loci. Various diversity estimates, mean number of alleles (12.84); effective number of alleles (5.02); gene diversity (0.769), and observed heterozygosity (0.667) reflected the existence of substantial within-breed diversity in all the investigated cattle breeds. Mean estimates of F-statistics: F_IT = 0.144 ± 0.023, F_IS = 0.071 ± 0.021, and F_ST = 0.078 ± 0.014 were significantly different from zero (P < 0.05). The interbreed relationships indicated moderate level of breed differentiation between the six cattle breeds with least differentiation between Kankrej-Mewati pair. The phylogeny structuring further supported close grouping of Kankrej and Mewati breeds. Correspondence analysis plotted Rathi, Tharparkar, and Gir individuals into three separate areas of multivariate space; whereas, Kankrej, Mewati, and Nagori cattle showed low breed specific clustering. This reflected the existence of discrete genetic structure for Tharparkar, Rathi, and Gir, the prominent dairy breeds of the region; whereas, admixture was observed for Kankrej, Mewati, and Nagori individuals.     

Genetic Diversity and Population Structure Analysis Between Indian Red Jungle Fowl and Domestic Chicken Using Microsatellite Markers

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ?K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.