Phylogenetic Structure Of Plant Communities Research Articles

Seasonal Variations in Plant Species Diversity and Phylogenetic Diversity in Abandoned Farmland of China’s Huang–Huai Plain

Amidst urbanization and industrialization in China, abandoned farmland plays a crucial role in safeguarding plant diversity within agricultural landscapes. This study aimed to examine the patterns of seasonal variation in plant diversity within abandoned farmland habitats in the Huang–Huai Plain region. Nonparametric tests were employed to analyze plant species diversity and phylogenetic diversity across seasons. Redundancy analysis and linear regression were conducted to examine the associations between plant species composition, species diversity, phylogenetic diversity, and soil environmental factors. Our results showed that plant species diversity, richness, and phylogenetic diversity were highest in spring, followed by summer, and lowest in autumn. The phylogenetic structure of plant communities demonstrated a tendency to diverge in spring, become random in summer, and cluster in autumn. Soil available potassium and soil organic matter emerged as important factors influencing plant species composition. The content of soil organic matter and ammonium nitrogen level exhibited a significantly positive correlation with the species diversity and phylogenetic diversity of plants. This study underscores the significance of considering seasonal and temporal scales when investigating plant diversity and provides a theoretical basis for biodiversity conservation in agricultural landscapes.

Scale‐dependent shifts in functional and phylogenetic structure of Mediterranean island plant communities over two centuries

Abstract Since the Industrial Revolution, the rapid global population and economic expansion have had tremendous impacts on biodiversity across spatial scales, especially for islands. While changes in species richness are easily inferred, the impact of human activity on the underlying community assembly processes has been difficult to ascertain because of lack of long‐term community data. Here, we document how the manifestations of plant community assembly have changed over time and space in a Mediterranean archipelago, using a long‐term dataset of plant species composition on 16 Tuscan islands sampled across two centuries. The community structure of Mediterranean island plant communities was assessed by integrating species' trait and evolutionary distances. We found that, with increasing island area, the functional and phylogenetic structure of plant communities shifted from clustered early (1830–1950) to overdispersed more recently (1951–2015). On large islands, extirpated species were generally more phylogenetically or functionally similar to remaining residents than expected by chance, while colonists were generally more distantly related to residents. The extinction of similar species and the colonization of dissimilar species drove plant communities towards overdispersion. Synthesis. We provide evidence that plant community assembly on islands has dramatically changed following increased human impacts during the last two centuries, and that this change is shaped by the scale dependency of species extinctions and colonizations. Our results reveal accelerated species replacements of closely related residents by distant colonists on large islands over time, reflecting changes in community assembly and which could alter the functioning of island ecosystems in the future.

Phylogenetic structure of alpine steppe plant communities along a precipitation and temperature gradient on the Tibetan Plateau

Exploring plant community phylogenetic structure along precipitation and temperature gradients can facilitate the study of mechanisms governing community assembly. Herein, we assessed the phylogenetic structure of alpine steppe plant communities along a precipitation and temperature gradient in Xigaze, Naqu and Ali on the Tibetan Plateau. We found that alpine steppe plant communities were generally phylogenetically clustered on both small (3 m2) and intermediate (1000 m2) scales. We found that mean annual precipitation (MAP), rather than mean annual temperature (MAT), influenced plant species richness and phylogenetic diversity on an intermediate scale. In contrast, MAT, rather than MAP, influenced the phylogenetic structure of plant communities on an intermediate scale such that higher MAT was associated with greater plant community clustering. Additionally, no changes in phylogenetic structure were observed across scales (3 m2 vs 1000 m2). In summary, precipitation is an important regulator of plant diversity, whereas temperature is a key factor that influences the phylogenetic structure of plant communities on the Tibetan Plateau. Our data offer new insights that may better guide current understanding regarding community assembly mechanisms in alpine steppe ecosystems on the Tibetan Plateau faced with global climate change.

Modern Climate and Soil Properties Explain Functional Structure Better Than Phylogenetic Structure of Plant Communities in Northern China

Mechanisms of plant community assembly at geographical scale are an interesting topic in ecology and biogeography, which are of great significance for the understanding of species coexistence and biodiversity conservation. But so far, only a few studies have simultaneously assessed the relative roles of multiple-scale factors in shaping phylogenetic and functional structure of plant communities at a macroecological scale. In this study, we linked modern climate, glacial-interglacial climate change and soil properties with phylogenetic and functional structure of shrub and herbaceous plant communities in Inner Mongolia, China, an arid and semi-arid region. Our results showed that functional structure of plant communities was more associated with modern climate and soil properties than phylogenetic structure, especially for the soil properties. Modern precipitation was found in all the combinations of variables that were most closely related to the community structure in this arid and semi-arid region. These findings suggest that phylogenetic and functional structure of biotic communities may be affected by processes at divergent spatial-temporal scales. That is, functional structure is better linked with modern and local factors, while phylogenetic structure is more associated with historical and 2 regional processes. This study highlights the importance of the associations between different biodiversity dimensions and divergent drivers.

Inflorescence preformation prior to winter: a surprisingly widespread strategy that drives phenology of temperate perennial herbs.

Organ preformation in overwintering buds of perennial plants has been known for almost two centuries. It is hypothesized to underlie fast growth and early flowering, but its frequency, phylogenetic distribution, and ecological relevance have never been systematically examined. We microscopically observed inflorescence preformation in overwintering buds (IPB) in the autumn. We studied a phylogenetically and ecologically representative set of 330 species of temperate perennial angiosperms and linked these observations with quantitative data on species' flowering phenology, genome size, and ecology. IPB was observed in 34% of species examined (in 14% species the stamens and/or pistils were already developed). IPB is fairly phylogenetically conserved and frequent in many genera (Alchemilla, Carex, Euphorbia, Geranium, Primula, Pulmonaria) or families (Ranunculaceae, Euphorbiaceae, Violaceae, Boraginaceae). It was found in species of any genome size, although it was almost universal in those with large genomes. Compared with non-IPB species, IPB species flowered 38d earlier on average and were more common in shaded and undisturbed habitats. IPB is a surprisingly widespread adaptation for early growth in predictable (undisturbed) conditions. It contributes to temporal niche differentiation and has important consequences for understanding plant phenology, genome size evolution, and phylogenetic structure of plant communities.

Climate, and not fire, drives the phylogenetic clustering of species with hard-coated seeds in Mediterranean Basin communities

Hardseededness is a common trait in Mediterranean plant communities, although the origin of its selection is controversial. It may be a mechanism of persistence to fire temperatures, but could also form part of a gap-detecting mechanism to provide germination cues under arid conditions. To disentangle this, we studied the phylogenetic structure of plant communities against fire frequency and aridity gradients. The phylogenetic structure in Mediterranean Basin ecosystems was analysed for the hardseededness trait as a whole and was separated by the families composing this trait (Fabaceae and Cistaceae). This study focused on woody perennial species. The phylogenetic structure was also contrasted against soil classes. Hardseededness on the whole, and for the Fabaceae family alone, showed phylogenetic clustering as aridity increased. Cistaceae displayed the opposite pattern with phylogenetic clustering in most humid areas, together with a significant soil effect. Surprisingly, fire frequency had no influence in any case. This climate-driven phylogenetic clustering indicates that the hardseededness trait could confer some fitness advantage under dry conditions. For this reason, coexisting species were more closely related in the community with increasing aridity. This effect was especially evident for the Fabaceae family. These results shed some light on the evolutionary selection of this adaptive trait under Mediterranean conditions. Our results question the role of fire in the selection of the hardseededness trait in Mediterranean Basin ecosystems and indicates that climate is the most important factor. Therefore, we should be cautious in assigning to fire a preponderant role in the selection of some plant traits.

Plant-plant interactions influence phylogenetic diversity at multiple spatial scales in a semi-arid mountain rangeland.

Molecular phylogenies are increasingly used to understand how biotic interactions and environment shape phylogenetic community structure (PCS). However, we do not understand the effects of plant-plant interactions and environment on PCS and phylogenetic diversity across spatial scales, particularly in rangelands. Here, we ask: (1) do plant-plant interactions and environment affect PCS and phylogenetic diversity differently across the three spatial scales of the patch, the community, and the habitat? (2) What are the impacts of dominant cushion-nurse plants on the phylogenetic structure of plant communities? We assessed the PCS of semi-arid plant communities along an elevation gradient at the patch, community and habitat scales. Then, we assessed co-occurrence patterns along two sample slopes. Our results indicated important roles for biotic interactions and environmental filtering in determining phylogenetic diversity, with biotic interactions, in particular, having a stronger tendency to increase phylogenetic diversity. This is most likely due to the asymmetrical effects of nurse plants across the three spatial scales on our two different slopes. The impact of biotic interactions caused non-random phylogenetic patterns in more severe environments. In conclusion, biotic interactions influence phylogenetic diversity by altering PCS across aspects and along elevation gradients.

Phylogenetically diverse native systems are more resistant to invasive plant species on Robben Island, South Africa 1.

Alien invasive species are problematic both economically and ecologically, particularly on islands. As such, understanding how they interact with their environment is necessary to inform invasive species management. Here, we ask the following questions: What are the main functional traits that correlate with invasion success of alien plants on Robben Island? How does phylogenetic structure shape biotic interactions on the island? Using multiple approaches to explore these questions, we found that alien invasive species flower later during the year and for longer period, although flowering phenology was sensitive to alternative starting date. Additionally, we observed that alien invasive species are mostly abiotically pollinated and are generally hermaphroditic whilst their native counterparts rely on biotic pollinators, flower earlier, and are generally dioecious, suggesting that alien invasive and native species use different ecological niches. Furthermore, we found a facilitative interaction between an alien invasive legume and other invasive plants as predicted by the invasional meltdown hypothesis, but this does not influence the phylogenetic structure of plant communities. Finally, phylogenetically diverse set of native species are less receptive to alien invasive species. Collectively, our findings reveal how biotic interactions and phylogenetic relatedness structure alien invasive - native co-existence.

Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids?

Polyploidy is widely acknowledged to have played an important role in the evolution and diversification of vascular plants. However, the influence of genome duplication on population-level dynamics and its cascading effects at the community level remain unclear. In part, this is due to persistent uncertainties over the extent of polyploid phenotypic variation, and the interactions between polyploids and co-occurring species, and highlights the need to integrate polyploid research at the population and community level. Here, we investigate how community-level patterns of phylogenetic relatedness might influence escape from minority cytotype exclusion, a classic population genetics hypothesis about polyploid establishment, and population-level species interactions. Focusing on two plant families in which polyploidy has evolved multiple times, Brassicaceae and Rosaceae, we build upon the hypothesis that the greater allelic and phenotypic diversity of polyploids allow them to successfully inhabit a different geographic range compared to their diploid progenitor and close relatives. Using a phylogenetic framework, we specifically test (1) whether polyploid species are more distantly related to diploids within the same community than co-occurring diploids are to one another, and (2) if polyploid species tend to exhibit greater ecological success than diploids, using species abundance in communities as an indicator of successful establishment. Overall, our results suggest that the effects of genome duplication on community structure are not clear-cut. We find that polyploid species tend to be more distantly related to co-occurring diploids than diploids are to each other. However, we do not find a consistent pattern of polyploid species being more abundant than diploid species, suggesting polyploids are not uniformly more ecologically successful than diploids. While polyploidy appears to have some important influences on species co-occurrence in Brassicaceae and Rosaceae communities, our study highlights the paucity of available geographically explicit data on intraspecific ploidal variation. The increased use of high-throughput methods to identify ploidal variation, such as flow cytometry and whole genome sequencing, will greatly aid our understanding of how such a widespread, radical genomic mutation influences the evolution of species and those around them.

Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia.

The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR) and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI) to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05); presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant communities on the Tianshan Mountains. This pattern of community phylogenetic structure could have resulted from shared ancestry and species pool among these sample plots.

Phylogenetic clustering found in lichen but not in plant communities in European heathlands

Species richness is a widespread measure to evaluate the effect of different management histories on plant communities and their biodiversity. However, analysing the phylogenetic structure of plant communities could provide new insights into the effects of different management methods on community assemblages and provide further guidance for conservation decisions. Heathlands require permanent management to ensure the existence of such a cultural landscape. While traditional management with grazing is time consuming, mechanical methods are often applied but their consequences on the phylogenetic community assemblages are still unclear. We sampled 60 vegetation plots in dry sandy heathlands (EU habitat type 2310) in northern Germany stratified by five different heathland management histories: fire, plaggen (turf cutting), mowing, deforestation and intensive grazing. Due to the distant relationship of vascular plants and lichens, we assembled two phylogenetic trees, one for vascular plants and one for lichens. We then calculated phylogenetic diversity (PD) and measures of phylogenetic community structure for vascular plant and lichen communities. Deforested areas supported significantly higher PD values for vascular plant communities. We found that PD was strongly correlated with species richness (SR) but the calculation of rarefied PD was uncorrelated to SR leading to a different ranking of management histories. We observed phylogenetic clustering in the lichen communities but not for vascular plants. Thus, management by mowing and intensive grazing promotes habitat filtering of lichens, while management histories that cause greater disturbance such as fire and plaggen do not seem to affect phylogenetic community structure. The set of management strategies fulfilled the goals of the managers in maintaining a healthy heathland community structure. However, management strategies that cause less disturbance can offer an additional range of habitat for other taxonomic groups such as lichen communities.

Altitudinal Patterns of Species Diversity and Phylogenetic Diversity across Temperate Mountain Forests of Northern China.

The spatial patterns of biodiversity and their underlying mechanisms have been an active area of research for a long time. In this study, a total of 63 samples (20m × 30m) were systematically established along elevation gradients on Mount Tai and Mount Lao, China. We explored altitudinal patterns of plant diversity in the two mountain systems. In order to understand the mechanisms driving current diversity patterns, we used phylogenetic approaches to detect the spatial patterns of phylogenetic diversity and phylogenetic structure along two elevation gradients. We found that total species richness had a monotonically decreasing pattern and tree richness had a unimodal pattern along the elevation gradients in the two study areas. However, altitudinal patterns in shrub richness and herbs richness were not consistent on the two mountains. At low elevation, anthropogenic disturbances contributed to the increase of plant diversity, especially for shrubs and herbs in understory layers, which are more sensitive to changes in microenvironment. The phylogenetic structure of plant communities exhibited an inverted hump-shaped pattern along the elevation gradient on Mount Tai, which demonstrates that environmental filtering is the main driver of plant community assembly at high and low elevations and inter-specific competition may be the main driver of plant community assembly in the middle elevations. However, the phylogenetic structure of plant communities did not display a clear pattern on Mount Lao where the climate is milder. Phylogenetic beta diversity and species beta diversity consistently increased with increasing altitudinal divergence in the two study areas. However, the altitudinal patterns of species richness did not completely mirror phylogenetic diversity patterns. Conservation areas should be selected taking into consideration the preservation of high species richness, while maximizing phylogenetic diversity to improve the potential for diversification in the future.

The effect of environmental and phylogenetic drivers on community assembly in an alpine meadow community

To predict the consequences of environmental change on plant communities at local scales, one needs to understand the regional drivers structuring these communities. Here, we used a formal analytical framework incorporating functional traits and evolutionary histories to understand the importance of environmental filtering and species interactions in the assembly of alpine plant communities. The study was conducted in the Tibetan Plateau using field plots experiencing changes in land use (fertilization and grazing). We observed evidence for both trait-based convergence (associated with plant height and tissue nitrogen) and divergence (associated with specific leaf area) within alpine plant communities, suggesting that environmental filtering and limiting similarity are acting simultaneously during assembly processes. Although we did not observe evidence of phylogenetic niche conservatism in relation to intensified land use, we did observe support for the phylogenetic structure of plant communities influencing community-weighted mean trait values, suggesting that evolutionary constraints represent a significant driver of community assembly in this system. Therefore, evolutionary and ecological processes may have independent effects on alpine plant communities facing land use intensification.

Do niche‐structured plant communities exhibit phylogenetic conservatism? A test case in an endemic clade

Summary The growing literature on the phylogenetic structure of plant communities places great emphasis on the role of phylogenetic niche conservatism (PNC) in community assembly. However, the patterns revealed by such analyses are difficult to interpret in the absence of independent data on niche structure. While there is increasing evidence that plant coexistence does depend upon niche differences, it is still not clear in most cases what the relevant niche axes are. We address this problem by testing for PNC within the African Restionaceae (‘restios’), a clade endemic to the Western Cape where we have shown niche segregation along soil moisture gradients to be common. Significant niche segregation on soil moisture gradients occurred among restios in 7 of 10 communities sampled, but PNC was detectable in only one of these and then only by one of three methods used. Phylogenetic analysis of the evolution of hydrological niche traits for the species pool of 37 Restionaceae in the study showed tolerance of drought to be convergent rather than conserved. Synthesis. The demonstration that clear niche segregation may occur among related species without PNC being detectable supports the hypothesis that hydrological niche responses are evolutionarily labile. More generally, the results demonstrate that phylogenetic analysis can be a poor guide to the process of community assembly. We argue that it may in future be better to apply ecological data to the interpretation of phylogenies, rather than to follow the current preoccupation with the application of phylogenies to ecology.

Environmental conditions and biotic interactions acting together promote phylogenetic randomness in semi-arid plant communities: new methods help to avoid misleading conclusions.

Molecular phylogenies are being increasingly used to better understand the mechanisms structuring natural communities. The prevalent theory is that environmental factors and biotic interactions promote the phylogenetic clustering and overdispersion of plant communities, respectively. However, both environmental filtering and biotic interactions are very likely to interact in most natural communities, jointly affecting community phylogenetic structure. We asked the following question: How do environmental filters and biotic interactions jointly affect the phylogenetic structure of plant communities across environmental gradients? Eleven Stipa tenacissima L. grasslands located along an environmental gradient from central to south-east Spain, which covers the core of the distribution area of this vegetation type in Europe. We jointly evaluated the effects of environmental conditions and plant-plant interactions on the phylogenetic structure -measured with the mean phylogenetic distance index- of the studied communities. As an indicator of environmental conditions, we used a PCA ordination including eight climatic variables. Different metrics were used to measure the following processes: i) competition/facilitation shifts at the entire community level (Species Combination index), and ii) the effect of the microclimatic amelioration provided by the two most important nurses on neighbours composition (similarity indices and comparison of the phylogenetic pattern between canopy patches and bare ground areas). Biotic interactions and, to a less extent, environmental conditions, affected the phylogenetic pattern of the studied communities. While positive plant-plant interactions (both at the community and the scale of individual nurses) increased phylogenetic overdispersion, higher rainfall increased phylogenetic clustering. The opposed effects of environmental conditions and biotic interactions could be the main cause of the overall random phylogenetic structure found in most of these communities. Our results illustrate, for the first time, how an overall random phylogenetic pattern may not be promoted only by the lack of influence of either environmental filtering or biotic interactions, but rather by their joint and opposing effects. They caution about making inferences about the underlying mechanisms shaping plant communities from the sole use of their phylogenetic pattern. We also provide a comprehensive set of easy-to-measure tools to avoid misleading conclusions when interpreting phylogenetic structure data obtained from observational studies.

The impact of ecological differentiation and dispersal limitation on species turnover and phylogenetic structure of inselberg's plant communities

Phylogenetic structure analysis is a novel way to address the relative importance of stochastic and deterministic processes governing species assemblages. Here we investigate the phylogenetic structure of the vegetation of inselbergs located in the African rain forest. Inselbergs combine strong ecological gradients at the local scale due to soil depth variation and insular properties at the regional scale. They are therefore ideal models to assess the influence of ecological sorting and dispersal limitation on the phylogenetic structure of plant communities. On 21 inselbergs separated by up to 200 km where five microhabitat‐types were recognized, 311 vegetation plots were inventoried. We found that floristic similarity between plots depended on both microhabitat differentiation and spatial distance, while phylogenetic clustering (i.e. excess of phylogenetic similarity between species from a same plot) only appeared between plots from differentiated microhabitats and increased with ecological distance. Within a microhabitat‐type, the absence of phylogenetic structure between inselbergs indicates that species turnover is probably due to dispersal limitation rather than to regional‐scale variations in environmental factors. Hence, phylogenetic structure analysis can help disentangle the effects of ecological sorting and dispersal limitation on species assemblages. To estimate the time‐scale of the processes generating the phylogenetic structure, we investigated how lineage similarity changes with increasing age in the phylogenetic tree. High lineage similarity levels between ecologically very differentiated plots were only reached at the proximity of the root of the phylogenetic tree. This was observed even when considering only plots sharing no species and indicates that phylogenetic niche conservatism has been important for generating the observed phylogenetic structure. Hence, ancient diversification exerts an impact on the assembly of current plant communities.

Phylogenetic overdispersion of plant species in southern Brazilian savannas

Ecological communities are the result of not only present ecological processes, such as competition among species and environmental filtering, but also past and continuing evolutionary processes. Based on these assumptions, we may infer mechanisms of contemporary coexistence from the phylogenetic relationships of the species in a community. We studied the phylogenetic structure of plant communities in four cerrado sites, in southeastern Brazil. We calculated two raw phylogenetic distances among the species sampled. We estimated the phylogenetic structure by comparing the observed phylogenetic distances to the distribution of phylogenetic distances in null communities. We obtained null communities by randomizing the phylogenetic relationships of the regional pool of species. We found a phylogenetic overdispersion of the cerrado species. Phylogenetic overdispersion has several explanations, depending on the phylogenetic history of traits and contemporary ecological interactions. However, based on coexistence models between grasses and trees, density-dependent ecological forces, and the evolutionary history of the cerrado flora, we argue that the phylogenetic overdispersion of cerrado species is predominantly due to competitive interactions, herbivores and pathogen attacks, and ecological speciation. Future studies will need to include information on the phylogenetic history of plant traits.