Since phylogenetic data provide the evolutionary history of the species and traits are the result of adaptation to the environmental conditions, joint analysis of these two aspects and ecological data may illuminate that how ecological processes affect the evolution of species and assembly of communities. In this study, we compared the community structure of sibling communities in order to illuminate the influence of environmental variability. We chose different Calligonum communities as research subjects which grow in active sand dunes and stabilized sand fields. Our results show that species which co-occurred in C. rubicundum community have greater phylogenetic evenness compared to species in other communities where co-occurring plants had similar traits. Soil variability might legitimately explain this result. Based on the similarity between the pattern of trait diversity and the pattern of phylogenetic
diversity, we inferred that the evolution of traits is conservative and species of all but C. rubicundum communities are under more intense selection pressure

Pan, Bo-Rong

Shi, Wei

Wang, Jian-Cheng

Wang, Xi-Yong

Yang, Hong-Lan

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EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   172 Original article: INFLUENCE OF ENVIRONMENTAL VARIABILITY ON  PHYLOGENETIC DIVERSITY AND TRAIT DIVERSITY WITHIN CALLIGONUM COMMUNITIES  Jian-Cheng Wang, Hong-Lan Yang, Xi-Yong Wang, Wei Shi, Bo-Rong Pan*  Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, P.R. China  * Corresponding author: Bo-rong Pan; E-mail: www-1256@ms.xjb.ac.cn  ABSTRACT Since phylogenetic data provide the evolutionary history of the species and traits are the result of adaptation to the environmental conditions, joint analysis of these two aspects and ecologi-cal data may illuminate that how ecological processes affect the evolution of species and as-sembly of communities. In this study, we compared the community structure of sibling com-munities in order to illuminate the influence of environmental variability. We chose different Calligonum communities as research subjects which grow in active sand dunes and stabilized sand fields. Our results show that species which co-occurred in C. rubicundum community have greater phylogenetic evenness compared to species in other communities where co-occurring plants had similar traits. Soil variability might legitimately explain this result. Based on the similarity between the pattern of trait diversity and the pattern of phylogenetic diversity, we inferred that the evolution of traits is conservative and species of all but C. rubi-cundum communities are under more intense selection pressure.  Keywords: Calligonum, community composition, ecological process, phylogenetic communi-ty structure, phylogenetic signal    INTRODUCTION An important goal of community ecolo-gy is to illuminate the processes governing the assembly and coexistence of species (Hardy, 2008). Because phenotypes are not randomly distributed with respect to phy-logeny, we should expect a direct link to exist between the evolutionary relatedness of organisms in a community, the charac-ters they possess, and the ecological pro-cesses that determine their distribution and abundance (Kraft et al., 2007). A phyloge-netic perspective that recognizes the dual role of evolutionary history in generating species diversity and in shaping phenotypes may provide insight into the relative im-portance of different processes affecting species coexistence and community assem-bly (Whitfeld et al., 2012). Nowadays, evo-lutionary ecologists are increasingly com-bining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecologi-cal relatedness (Emerson and Gillespie, 2008). Community composition at any point in time is the result of past immigration, spe-ciation and extinction, together with associ-ated interactions that vary according to the sequence of assembly and/or disturbance (Emerson and Gillespie, 2008). Patterns of community structure can be interpreted us-EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   173 ing a simple schematic (Figure 1). Numer-ous processes contribute to the assembly of communities (Kraft et al., 2007). Environ-mental filters can select for the species that possess phenotypes necessary for survival and successful reproduction resulting in a community of species that share a similar phenotype (Webb et al., 2002). By contrast, competition among different species leads to that related traits show evenness (Eiserhardt et al., 2013). The likelihood that a pathogen can infect two plant species de-creases continuously with the phylogenetic distance between the plants which tend to yield patterns of over-dispersion (Gilbert and Webb, 2007). Facilitation derived from related species sharing pollinators is pre-dicted to yield communities with phenotyp-ically similar species (Sargent and Ackerly, 2008). Nurse species facilitate distantly re-lated species and increase phylogenetic di-versity (Valiente-Banuet and Verdu, 2007).     Abiotic factors, which include high air temperature, low relative humidity, low wa-ter, low nutrient availability, act as envi-ronmental filters selecting for species with tolerant traits in arid areas (Rajaniemi et al., 2012). These have resulted in lower species diversity in community composition. How-ever, along with the variation in the type and gradient of limiting factor, community structure does not remain the same. On the contrary, similar communities, whose con-stituent species have a close genetic rela-tionship, may experience smaller differenti-ated ecological processes. Here, we chose different Calligonum communities as re-search subjects which grow in active sand dunes and stabilized sand fields. We ad-dress two critical questions: 1) whether dif-ferences exist in the community structure in terms of phylogeny and phenotype among sibling communities? 2) what kind of link exists among traits, phylogenetic relation-ships and environmental conditions of these communities?  Figure 1: Patterns of community structure predicted to be produced by various community assembly processes   Source species Difficulty in arriving High LowHabitat limitationsPhylogenetic clustering Trait variation Phenotypic clustering Phenotypic evenness Phenotypic clustering HighTrait variationPhylogenetic clustering Phylogenetic evenness Phenotypic evenness Trait variationPhylogenetic evenness Random Limiting similarity of traits associated with competition High High High Low Low Low Low EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   174 MATERIAL AND METHODS Data Calligonum Linnaeus is a genus in the family Polygonaceae with 35 species across the Mediterranean Sea region, Asia and North Africa (Wu et al., 2003). Based pri-marily on fruit morphology and anatomy, Calligonum species were divided into four sections, including Sect. Calliphysa, Sect. Calligonum, Sect. Medusa and Sect. Ptero-coccus (Mao and Pan, 1986). A representa-tive of each section was selected as the comparison target, including C. calliphysa, C. ebi-nuricum, C. klementzii, and C. rubi-cundum. We consulted the plant specimens collected in several units of Chinese Acad-emy of Sciences including Institute of Botany, Cold and Arid Regions Environ-mental and Engineering Research Institute, Xinjiang Institute of Ecology and Geogra-phy, Kunming Institute of Botany, Jiangsu Institute of Botany, The Northwest Institute of Plateau Biology, and Northwest A&F University, Lanzhou University, Inner Mongolia University, Inner Mongolia Agri-cultural University, Xinjiang University, Xinjiang Agricultural University. Accord-ing to the distribution of each species, we identified 22 plots. In July 2007, we ran-domly placed three quadrats in each plot and computed the number of each species in each quadrat. Plant voucher specimens were deposited in the specimen museum of Xinjiang Institute of Ecology and Geogra-phy. We obtained the state of relatively sta-ble traits (smaller intraspecific variation) from Flora of China and Flora Xinjiangen-sis. Plant traits are encoded according to supplementary Table 1, which shows the characters and character states scored for plant morphology. In total 16 characters were taken into consideration. 9 characters were scored as binary and the remaining characters were scored as multi-state char-acters. We used Phylomatic version 3 web ser-vice (http://phylodiversity.net/phylomatic/) to construct a phylogeny for the species list, using the stored tree R20120829 (Phylo-matic tree R20120829 for plants). Phyloge-netic distance between species should ideal-ly be proportional to divergence time (Blomberg and Garland, 2002). We approx-imated divergence times in phylocom 4.2 using the branch length adjustment (BLADJ) function.   Analyses When conducting analysis of phyloge-netic community composition, communities with fewer species can cause large errors. Therefore, community collection in accord-ance with the constructive species was used as analysis objects. We used the function pcd in the R package “picante” to calculate phylogenetic community dissimilarity (PCD) that is partitioned into a nonphylo-genetic component that reflects shared spe-cies between communities and a phyloge-netic component that reflects the evolution-ary relationships among nonshared species (Ives and Helmus, 2010), and subsequently used the function hclust in the R package “stats” to implement hierarchical cluster analysis.  Phylogenetic community structure was quantified as the net relatedness index (NRI), which is based on the mean phylo-genetic distance (MPD) between taxa in an observed sample compared to random draws from the species pool (Webb et al., 2002). NRI expresses the deviation of the mean pairwise distance from random in a given community, and positive NRI indi-cates phylogenetic clustering, while nega-tive NRI indicates evenness. We used the abundance-based construct algorithm in Phylocom to calculate NRI. Significance of the NRI values is assessed by comparing the observed MPD value with the expected MPD value based on the null distribution of the 999 random assemblages. The species pool was all species found in the 22 plots. In this study, we calculated measures of trait diversity within communities in a manner analogous to the methods we used to calculate phylogenetic diversity by sub-EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   175 stituting a trait distance matrix for the phy-logenetic distance matrix. Its statistics Trait SES (MPD) is equivalent to -1 times NRI. Negative values indicate relatively similar traits, while positive value indicates even-ness.   RESULTS We sampled 67 species from 16 fami-lies and 51 genera in 22 plots. The largest plant families in Calligonum communities are Amaranthaceae (24 species) and Aster-aceae (11 species). The number of taxa in C. rubicundum community was highest among 4 kinds of communities at different levels of family, genera and species. Phylo-genetic relationships of co-occurring spe-cies in Calligonum community were shown in Figure 2.   Figure 2: Phylogenetic relationships of seed plants occurring in Calligonum community. Graphic located in front of species name shows the community that the species may occur. The distance among communities is in-consistent in terms of phylogenetic relation-ship. According to the results returned by pairwise dissimilarity in phylogenetic community composition, hierarchical clus-ter analysis was carried out and shown by Figure 3. C. rubicundum community showed a larger dissimilarity in phylogenet-ic community composition with other communities. C. calliphysa and C. klementzii showed the highest similarity, due to a larger number of shared species between communities (10 species).   Figure 3: Phylogenetic community dissimilarity (PCD) of communities. Distance reflects the degree of dissimilarity among different commu-nities.  Each community had different perfor-mance in phylogenetic community structure (Figure 4). The NRI was significant nega-tive value in C. rubicundum community, and became positive values in the other three communities. The results indicated that species that co-occurred in C. rubicun-dum community have greater phylogenetic evenness compared to species in other communities. That is to say, co-occurring plants were more distantly related than ex-pected by chance in C. rubicundum com-munity (NRI < 0). EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   176  Figure 4: Comparison of phylogenetic commu-nity structure among different communities. Positive NRI indicates phylogenetic clustering, while negative NRI indicates evenness.   Trait SES (MPD) represents the stand-ardized effect size of trait diversity by measuring trait dissimilarity among co-occurring species. These metrics of all communities but C. rubicundum communi-ty were below 0, and trait diversity was lower than expected (Figure 5). The statisti-cal test demonstrated that trait diversities within C. ebi-nuricum and C. Klementzii communities were significantly different from randomization. The results indicated that co-occurring plants had similar traits, and this pattern of trait clustering was stronger in C. ebi-nuricum and C. Klementzii communities. The pattern of trait diversity was similar to the pattern we saw for phylogenetic diversity.   Figure 5: Comparison of trait diversity among different communities. Negative Trait SES (MPD) indicates relatively similar traits, while positive value indicates evenness. DISCUSSION Phylogenetic data provide a historical framework to quantify evolutionary and ecological patterns and infer evolutionary and ecological processes (Emerson and Gillespie, 2008). For example, pattern of phylogenetic clustering was generally con-sidered to result from (1) difficulty in dis-persing to some habitats or, (2) environ-mental filtering for a conserved niche. In this study, C. rubicundum community was distinguished from other three communities in phylogenetic community composition, and the latter in community structure dis-played as phylogenetic clustering. In addi-tion, to test for community assembly pro-cesses we need to quantify both the trait evolution and the phylogenetic structure of the community (Pausas and Verdu, 2010). Our results showed that phenotypic pattern of these traits are identical with phylogenet-ic community structure among different communities. Thus, there were differences in the community structure in terms of phy-logeny and phenotype among sibling com-munities and gives an affirmative answer to question 1. When species enter a community, spe-cies possessing the necessary traits to com-plete their life cycle within that habitat are retained by ecological processes controlling community assembly. In other words, envi-ronmental conditions impose absolute bounds on the phenotype space (Lovette and Hochachka, 2006). Thenceforth, the competition as an important factor drives competitive exclusion or niche differentia-tion of similar traits related to competition. Other literature reports that total salt con-tent and pH values of soil are significantly different among communities, and all but C. rubicundum communities have distinct degrees of salinization and alkalization (Tan et al., 2009). Compared with the C. rubicundum community, trait diversity was lower than expected in the other three communities and similar to the pattern we saw for phylogenetic diversity. Therefore, we can infer that species of these communi-EXCLI Journal 2014;13:172-177 – ISSN 1611-2156 Received: October 07, 2013, accepted: February 16, 2014, published: February 24, 2014   177 ties are under more intense selection pres-sure and evolution of traits is conservative. There were more than expected annuals in C. ebi-nuricum and C. klementzii communi-ty, and we guessed that it is an environmen-tal filtering to directional selection under stressful conditions. There was a definite relationship that environmental conditions limit phylogenetic diversity and trait diver-sity within communities. In order to potentially restore the eco-system functioning of desert plant commu-nities, understanding how ecological pro-cess affects community composition is an essential prerequisite. In this study, we compared the community structure of simi-lar communities in order to illuminate the influence of environmental variability gov-erning the assembly and coexistence of species. Based on the similarity between the pattern of trait diversity and the pattern of phylogenetic diversity, we inferred that the evolution of traits is conservative and spe-cies of all but C. rubicundum communities are under more intense selection pressure.  ACKNOWLEDGMENTS This work was supported by the Nation-al Natural Science Foundation of China (Grant No 31100150) and the West Light Talents Cultivation Program of Chinese Academy of Sciences (XBBS 201202).  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Influence of environmental variability on phylogenetic diversity and trait diversity within Calligonum communities

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Influence of environmental variability on phylogenetic diversity and trait diversity within Calligonum communities

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