Application Of R In Studies Of Morphological And Genetic Variation Of Plant Populations

R is a free, open source programming language with large amount of packages. It is becoming second language for scientists. Currently R has included packages regarding plant taxonomy, morphological and genetic analysis. However, few reports have been found in those areas.Hypnum plumaeforme is a widely distributed moss, which bears great importance in systematics, evolution, and molecular ecology. Besides, it is also widely used in landscaping alteration, environmental indication, physiological studies and ecology. With its many morphotypes and wide distribution with various habitats, H. plumaeforme is an ideal material to study the relations between morphological, genetic variations and their relationships with environments.In this paper, a total of 105 H. plumaeforme samples from 14 locations has been collected and studied. In order to reveal the relations and patterns between morphological and genetic variations and their geological background, eight morphological characters and 12 ISSR markers were applied, then data were alayzed by R packages- clustering, principal component analysis and minimum spanning tree. The main results are listed below.(1) 105 samples of Hypnum plumaeforme could be clustered into nine groups based on 194 loci data by using Jaccard coefficient and UPGMA strategy(unweighted pair-group method with arithmetic means).(2) Eight morphological characteristics were studied- branch pattern, stem leaf tip pattern, stem leaf tip angularity, stem leave plication, stem leaf basal colour, pseudoparaphylia, stem leaf basal cell pattern, and branch leaf pattern. 105 samples could be clustered into five groups based on the eight morphological characters by using Bray-Curtis distance coefficient and UPGMA strategy.(3) Geological, genetic and morphological distances were calculated among the local objects. The relationships among these three types of distances were analyzed, and Shepard-like diagrams were also produced. The results showed that genetic differentiation among 14 populations of H. plumaeforme was influenced by their geographical background, their relationship coefficient being 0.369(n = 14, P < 0.2). However, their morphological data do not correspond with genetic data, their coefficient being only 0.11(n= 105, P < 0.5). Similarly, the morphological variation among these 14 populations has little relation with geological background either, and the coefficient in this regard is 0.107(n = 14, P > 0.5). That is to say, geological background has limited effect on morphological variation, maybe more to do with their local microhabitats.(4) Within all the 105 H. plumaeforme samples, the number of polymorphic loci is 192, which is 98.97% of all the 194 loci. Nei’s genetic diversity index is 0.1768, Shannon information index 0.2899, population overall genetic diversity(HT) 0.1736, intra-population genetic diversity(Hs) 0.0915, inter-population genetic differentiation coefficient is(Gst) 0.4728, 47.28% genetic variation existing among the populations, and 52.72 within populations.(5) Habitat diversity and geological insulation have effects on the genetic diversity of H. plumaeforme. The environments on Liujintan Garden of Shengsi main island and Jiangpianwan district of Gouqi Island are rather special. Gouqi, a small island, is the furthest east island among the Zhoushan archipelago, with distict geological insulation from the mainland. The terrain of Liujintan Garden of Shengsi main island is characterised with large boulders that do not offer nutritional value. It creates a singular habitat devoid of varied plant life. Polymorphism indices of these two populations are 22.28% and 19.69%, respectively, being lower than the average of 33.23%. Their gene diversity indices are, again, lower than average 0.0909, and their gene diversity indices are 0.0577 and 0.0609, respectively, and their Shannon diversity indices are 0.0918 and 0.0942, respectively, lower than the average of 1.444。The population that bears the highest genetic diversity was collected from Longtang Mt, whose percentage of polymorphic loci is as high as 58.03%, the genetic diversity index is 0.1379,Shannon information index 0.2264. Both indices are higher than average. Longtang Mt is located in the center of Sanqing Mt. National Natural Reserve where various habitats with high humidity are found.(6) In this study, cophenotype correlation analysis and fusion level values were firstly applied to decide on the clustering strategies and the clustering number of bryophyte taxa. The Silhoutte-optimal value was also used to reveal the validity of clustering analysis. For the present data of H. plumaeforme, UPGMA was found the most ideal clustering strategy based on cophenotype correlation coefficients, nine groups were suggested for the division of the 105 samples based the fusion level value, and all 105 samples were properly clustered into matching group.(7) Doubly ordered 105-sample and 194-loci table with dendrogram by using UPGMA strategy, heat map of distance matrix reorder according to the dendrogram of 105 samples based on ISSR data and eight morphological characters were produced, respectively. Transitional characteristic is more distinct among the different groups on morphological heat map of distance matrix than those based on ISSR data. The minimum spanning tree(MST), two-dimensional scatter plot with overlaid clustering results also show the differentiation status among the 105 samples, and which samples have special genetic background.(8) In order to analyze moprphological and genetic variation of H. plumaeforme and their relationship with geographical background, a total of 19 R programs was edited, which involve clustering analysis, cophenotype analysis, Shepard-like diagram, clustering fusion level value, Silhoutte-optimal value, cluster grouping, heat map of distance matrix reorder, doubly ordered 105-sample and 194-loci table with dendrogram, round clustering graph, principal component analysis, three-dimensional ordination graph, ordination scatter plot with overlaid clustering results, MST, and relation calculation among morphological, genetic and geographical background. The edited programs are supposed to be useful for data analysis of similar research in Bryology.