Mean Phylogenetic Distance Research Articles

Phylogenetic trajectories during secondary succession in a Neotropical dry forest: Assembly processes, ENSO effects and the role of legumes

Phylogenetic analysis of plant communities is useful for inferring ecological mechanisms driving forest succession. However, such analysis has scarcely been undertaken in tropical dry environments, especially for the dynamics of demographic components (i.e., recruited, surviving and dead plants) affecting the successional process. Here, we combine chronosequence and dynamic data to study the role of habitat filtering and limiting similarity in the old-field succession of a seasonal tropical dry forest subjected to strong climatic events (e.g., the El Niño Southern Oscillation (ENSO) and heavy rains). We documented successional changes in the phylogenetic structure and phylodiversity of regenerative communities (shrubs and trees ≤ 1 m in height), assessed phylogenetic changes in demographic components during succession, and explored the effects of interannual rainfall variation on such changes. Over five years, we monitored the dynamics of regenerative plant communities in a chronosequence of nine abandoned pastures (fallow age of 0–12 years) and three old-growth sites. For each year and site, we quantified changes in the standardized mean phylogenetic distance (MPD.OBS.Z) and phylodiversity (PD) of entire regenerative communities and recruited, surviving and dead plants. For each phylogenetic metric and demographic component, we assessed the effect of successional age, time (years), and interannual rainfall variation. Large variation in MPD.OBS.Z and PD was observed among sites and years, especially in the recently abandoned pastures. Overall, the phylogenetic community structure was clustered early in succession and became more random as succession advanced. Species from the order Fabales made especially strong contributions to the phylogenetic clustering, especially during the first years of succession. In dead plants, the MPD.OBS.Z and PD increased in the drier year due to the high mortality of plants from several clades (orders). The high prevalence of clustered and random phylogenetic structure suggests that abiotic filtering and stochastic processes are major structuring mechanisms in this successional system. Due the strong contribution of Fabales in the phylogenetic structure of regenerative communities of tropical dry forest, the effects of strong climatic events (e.g., ENSO) on Fabales could influence the old-field succession of tropical dry forests.

Molecular Evolution of the Fusion Protein (F) Gene in Human Respirovirus 3.

To elucidate the evolution of human respirovirus 3 (HRV3), we performed detailed genetic analyses of the F gene (full-length) detected from hundreds of HRV3 strains obtained from various geographic regions. First, we performed time-scaled evolutionary analyses using the Bayesian Markov chain Monte Carlo method. Then, we performed analyses of phylodynamics, similarity, phylogenetic distance, selective pressure, and conformational B-cell epitope with the F-protein structural analyses. Time-scaled phylogenetic tree showed that the common ancestor of HRV3 and bovine respirovirus 3 diverged over 300 years ago and subdivided it into three major clusters and four subclusters during the most recent 100 years. The overall evolutionary rate was approximately 10–3 substitutions/site/year. Indigenous similarity was seen in the present strains, and the mean phylogenetic distance were 0.033. Many negative selection sites were seen in the ectodomain. The conformational epitopes did not correspond to the neutralizing antibody binding sites. These results suggest that the HRV3 F gene is relatively conserved and restricted in this diversity to preserve the protein function, although these strains form many branches on the phylogenetic tree. Furthermore, HRV3 reinfection may be responsible for discordances between the conformational epitopes and the neutralizing antibody binding sites of the F protein. These findings contribute to a better understanding of HRV3 virology.

Climate and evolutionary history define the phylogenetic diversity of vegetation types in the central region of South America.

In South America the biogeographic history has produced different biomes with different vegetation types and distinct floras. As these vegetation types may diverge in evolutionary histories, we analysed how alpha and beta phylogenetic diversity vary across them and determine the main drivers of variation in phylogenetic diversity. To this end, we compiled a list of 205 sites and 1222 tree species spread over four biomes and eight vegetation types in central South America. For each site we evaluated six measures of evolutionary alpha diversity (species richness, phylogenetic diversity sensu stricto and the standardized effect size of phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance) and beta diversity (phylogenetic Sorensen's similarity). We checked the influence of spatial and environmental variables using generalized least squares models. The greatest phylogenetic differentiation was found between west and east of central South America, mainly between the Chaco communities and the other vegetation types, suggesting that species found in this biome come from different lineages, comparing with the others vegetation types. Our results also showed a clustered phylogenetic structure for the Dry Chaco woodlands, which may be associated with harsh environmental conditions. In addition to historical process, climatic conditions are the main drivers shaping phylogenetic patterns among the distinct vegetation types. Understanding patterns of phylogenetic diversity and distribution can greatly improve conservation planning and management since it allows the conservation of unique biome characteristics.

Phylogenetic diversity patterns in forests of a putative refugial area in Greece: A community level analysis

Patterns of phylogenetic diversity and structure of flora in refugial areas may be very complex due to habitat heterogeneity and legacies of various historical processes. Revealing these patterns can help understand the nature of the refugia. Here we study phylogenetic patterns of the flora in one of the main putative Pleistocene refugia of temperate forest biota in Europe through a community-level analysis for the main types of forests. For this purpose, a database of vegetation plots from deciduous and mountain coniferous forests of northern and central Greece was created. The plots were classified into floristically and ecologically interpretable community types. Faith’s phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance, as well as their standardized equivalents, were used to characterize the mean phylogenetic diversity and structure of each community type. All analyses were applied both for all the vascular plant taxa and for angiosperm taxa only. We related the measures of phylogenetic diversity and structure to ecological factors and compared them among community types. The 25 identified community types differed in their phylogenetic diversity and structure. The observed patterns were significantly different when old evolutionary lineages, such as gymnosperms and ferns, were taken into account. A random or overdispersed phylogenetic structure was observed for most of the community types, while only two oak-dominated community types were clustered. The highest phylogenetic diversity and a notably high proportion of plots with an overdispersed phylogenetic structure were observed in two mesic ravine forest community types (one of these transitional to beech forests). Phylogenetic metrics correlated with ecological conditions, in particular, overdispersion was more common in shaded, cool and moist forests. The high phylogenetic diversity and overdispersed structure of the two ravine community types can be related to the putative refugial role of these forest habitats.

Species sorting and mass effect along forest succession: Evidence from taxonomic, functional, and phylogenetic diversity of amphibian communities.

Species recovery after forest disturbance is a highly studied topic in the tropics, but considerable debate remains on the role of secondary forests as biodiversity repositories, especially regarding the functional and phylogenetic dimensions of biodiversity. Also, studies generally overlook how alpha and beta diversities interact to produce gamma diversity along successional gradients.We used a metacommunity approach to assess how species sorting (i.e., environmental filtering) and mass effect (i.e., source‐sink dynamics) affect 14 complementary metrics of amphibian taxonomic, functional, and phylogenetic diversity along a successional gradient in southern Mexico. As amphibians have narrow environmental tolerances and low dispersal capabilities, we expected that species sorting may be relatively more important than mass effect in structuring amphibian communities.Between 2010 and 2012, we sampled frogs, salamanders, and caecilians in 23 communities distributed in four successional stages: young (2–5 years old) and intermediate (13–28 years old) secondary forests, old‐growth forest fragments, and old‐growth continuous forest. We assessed 15 ecologically relevant functional traits per species and used a time‐calibrated molecular phylogeny.We recorded 1,672 individuals belonging to 30 species and 11 families. Supporting our expectations from the species sorting perspective, from the poorest (younger forests) to the best quality (continuous forest) scenarios, we observed (a) an increase in alpha diversity regardless of species abundances; (b) a clear taxonomic segregation across successional stages; (c) an increase in functional richness and dispersion; (d) an increase in mean phylogenetic distance and nearest taxon index; and (e) a reduction in mean nearest taxon distance. However, 10 species occurred in all successional stages, resulting in relatively low beta diversity. This supports a mass effect, where interpatch migrations contribute to prevent local extinctions and increase compositional similarity at the regional scale.Our findings indicate that amphibian metacommunities along forest successional gradients are mainly structured by species sorting, but mass effects may also play a role if high levels of forest cover are conserved in the region. In fact, secondary forests and forest fragments can potentially safeguard different aspects of amphibian diversity, but their long‐term conservation value requires preventing additional deforestation.

Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities.

Identifying the processes that generate and maintain biodiversity requires understanding of how evolutionary processes interact with abiotic conditions to structure communities. Edaphic gradients are strongly associated with floristic patterns but, compared with climatic gradients, have received relatively little attention. We asked (1) How does the phylogenetic composition of palm communities vary along edaphic gradients within major habitat types? and (2) To what extent are phylogenetic patterns determined by (a) habitat specialists, (b) small versus large palms, and (c) hyperdiverse genera? We paired data on palm community composition from 501 transects of 0.25 ha located in two main habitat types (non-inundated uplands and seasonally inundated floodplains) in western Amazonian rain forests with information on soil chemistry, climate, phylogeny and metrics of plant size. We focused on exchangeable base concentration (cmol+ kg-1) as a metric of soil fertility and a floristic index of inundation intensity. We used a null model approach to quantify the standard effect size of mean phylogenetic distance for each transect (a metric of phylogenetic community composition) and related this value to edaphic variables using generalized linear mixed models, including a term for spatial autocorrelation. Overall, we recorded 112 008 individuals belonging to 110 species. Palm communities in non-inundated upland transects (but not floodplain transects) were more phylogenetically clustered in areas of low soil fertility, measured as exchangeable base concentration. In contrast, floodplain transects with more severe flood regimes (as inferred from floristic structure) tended to be phylogenetically clustered. Nearly half of the species recorded (44 %) were upland specialists while 18 % were floodplain specialists. In both habitat types, phylogenetic clustering was largely due to the co-occurrence of small-sized habitat specialists belonging to two hyperdiverse genera (Bactris and Geonoma). Edaphic conditions are associated with the phylogenetic community structure of palms across western Amazonia, and different factors (specifically, soil fertility and inundation intensity) appear to underlie diversity patterns in non-inundated upland versus floodplain habitats. By linking edaphic gradients with palm community phylogenetic structure, our study reinforces the need to integrate edaphic conditions in eco-evolutionary studies in order to better understand the processes that generate and maintain tropical forest diversity. Our results suggest a role for edaphic niche conservatism in the evolution and distribution of Amazonian palms, a finding with potential relevance for other clades.

Tracing the diversification history of a Neogene rodent invasion into South America

We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co‐occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more slowly diversifying include Central America, northern South America, and the Atlantic forest. In southern South America, recent species turnover appears to have been higher. Ancestral locations for the main tribes of sigmodontines were also estimated, suggesting eastern South America and the Amazonian lowlands were colonized before some central Andean regions, even though the latter are now centers of species richness for these rodents. Moreover, a past connection between the tropical Andes and the Atlantic Forest is suggested by our results, highlighting a role for a hypothetical arc connecting the two biomes, which would have impacted many other groups of organisms. Whether rapid, recent speciation in some regions is related to Quaternary climatic fluctuations and the young age of sigmodontines (~12.7 Ma crown age) or instead to intrinsic traits of these rodents remains an open question. If the former is true, we hypothesize that contrasting trends will characterize older Neotropical clades.

Patterns of phylogenetic community structure of sand dune plant communities in the Yucatan Peninsula: the role of deterministic and stochastic processes in community assembly

ABSTRACTBackground: Tropical sand dunes are ideal systems for understanding drivers of community assembly as dunes are subject to both deterministic and stochastic processes. However, studies that evaluate the factors that mediate plant community assembly in these ecosystems are few.Aims: We evaluated phylogenetic community structure to elucidate the role of deterministic and stochastic processes in mediating the assembly of plant communities along the north of the Yucatan Peninsula, Mexico.Methods: We used plastid genetic markers to evaluate phylogenetic relationships in 16 sand-dune communities. To evaluate the role of climate in shaping plant community structure we carried out linear regressions between climatic variables and mean phylogenetic distance. We estimated the Net Relatedness Index and Nearest Taxon Index to identify ecological processes mediating community assembly.Results: Observed phylogenetic structure was not different from random, suggesting that stochastic processes are the major determinants of community assembly. Climate was slightly correlated with phylogenetic diversity suggesting that abiotic environment plays a minimal role in community assembly.Conclusions: Random assembly appears to be the primary factor structuring the studied sand dune plant communities. Environmental filters may represent a secondary factor contributing to the observed phylogenetic structure. Thus, both processes may act simultaneously to mediate the assembly of sand-dune plant communities.

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

Related plant species respond similarly to chronic anthropogenic disturbance: Implications for conservation decision‐making

Abstract Many developing countries harbour large numbers of species that face little‐understood, gradual changes in their environment, including chronic anthropogenic disturbance (CAD), a high frequency but low intensity form of disturbance. These countries also lack the resources to study each species, so conservation practices have been generalized, assuming that complete taxonomic groups may be managed in the same ways. This approach could be justified if closely related species respond similarly to threats. We assessed if related species respond similarly to CAD, whether this affects phylogenetic diversity and if such patterns occur in different systems. Species’ identity and abundance was recorded in 59 sites differing in CAD intensity in a semi‐arid grassland and a tropical dry forest in Mexico. Disturbance response indices were calculated for each species. Nested analysis of variance coupled with null models were applied to determine if generalizations within taxa are justified and which taxonomic level explained the most variation in disturbance response among species. We obtained phylogenetic trees using molecular data for the grassland and published data for the tropical forest. Phylogenetic signal was measured with Pagel's λ. Community mean phylogenetic distance was regressed on CAD. Higher taxonomic levels explained more variation than expected by chance, indicating that related species respond similarly to CAD. However, only species in the same genus behaved similarly enough to make generalizations reliable. This is the result of an underlying, if modest, phylogenetic signal in CAD responses. Mean phylogenetic distance decreased with CAD in the grassland but not the tropical dry forest. This suggests that CAD was a stronger environmental filter in the grassland but weak in the tropical dry forest, where it was less intense. Policy implications. Species inform us how their relatives respond to chronic anthropogenic disturbance (CAD), supporting the idea that generalizations in management are possible. However, this procedure is seemingly reliable only within genera, which explain over 80% of the accumulated variance in species’ CAD responses, and not within orders or families. CAD may reduce phylogenetic diversity, perhaps leading to ecosystem function loss.

Variation in the phylogenetic diversity of wild bees at produce farms and prairies

Declines in pollinators, particularly wild bees, along with rising demands for their services has intensified efforts to examine bee communities in different types of habitats. In this study we use a phylogenetic approach to compare and contrast bee communities associated with six small produce farms, eight large prairies, and five naturally small hill prairies in Iowa. We compare the mean phylogenetic distance (MPD) and the mean nearest taxon distance (MNTD) of bees in each community to expected mean MPD and MNTD values generated from 1000 random permutations of a tree composed of 144 species found across all sites. Standardized effect size scores for MPD using presence-absence data showed significant clustering of bee communities at five of six farms and two of the five hill prairies. Clustering at the farms and hill prairies was due primarily to the significantly lower number of species in the Andrenidae (0–5 species per site), especially species of Andrena, as well as significantly greater number of species in the Halictidae (9–22 species/site), particularly Lasioglossum (Dialictus). Lack of Andrenidae spp. may be related to a lack of appropriate floral resources, indicating that enriched prairie plantings for pollinators at farms could enhance the abundance of Andrena species and hence pollinator services at these sites. The higher richness of the ground-nesting Lasioglossum likely results from soil disturbance regimes at produce farms and the naturally shallow, rocky soil with exposed surface at hill prairies, respectively. Analyses of MNTD using either abundance weighted or presence-absence data and analyses of MPD using abundance data did not indicate consistent differences between the three site types, but do point to important differences between sites in phylogenetic composition of bee communities. Our results show that phylogenetic analyses of wild bee community diversity may be a useful tool for measuring how bee communities differ in composition as a result of natural variation and human-related changes in landscapes.

The impact of phylogenetic uncertainty on the metrics of community phylogenetic structure

Phylogeny has been widely used to quantify community phylogenetic structure and to infer the underlying mechanism. Many studies, however, neglected phylogeny uncertainty and its potential impact on community phylogenetic structure. In this study, we explored the potential impact of phylogenetic uncertainty among 150 species in a 20 hm2 plot in Tiantong, Zhejiang. One consensus tree and 999 phylogenetic trees representing the phylogenetic uncertainty were estimated based on two cpDNA fragments (rbcL and matK). Combined with the species distribution data, community phylogenetic structure was quantified by two common indices (NRI and NTI) and their significances were tested by the independent swap null model. Our results showed that tree topology and node age showed a large uncertainty. The uncertainty was larger for young species and significantly increased with mean phylogenetic distance. Phylogenetic uncertainty increased the variation of both standardized NRI and NTI in each quadrat. These impacts were independent between both indices in either spatial pattern or the degree of impact. NRI was more sensitive than NTI to the uncertainty. At community scale, phylogenetic uncertainty also affected the variation of the mean standardized NRI and NTI of all quadrats, with mean standard deviation of 0.37 and 0.077, respectively. Such a result suggests that mean standardized NRI at community level was more vulnerable to the phylogenetic uncertainty, which is consistent with the result at the sample level. Our findings showed that phylogenetic uncertainty could add different variation into the NRI and NTI series indices and might increase biases in the quantification of community phylogenetic structure and its underlying ecological processes. Our results implied that non-random community phylogenetic structure was probably overestimated in the previous studies which ignored phylogenetic uncertainty.

No Effect of Variations in Overstory Diversity and Phylogenetic Distance on Early Performance of Enrichment Planted Seedlings in Restoration Plantations

Enrichment planting is a strategy to increase tree diversity and reintroduce desirable species in restored forests, mainly in fragmented landscapes. However, the conditions that improve the performance of enrichment planted seedlings are not yet fully known. Here, we evaluate the role that overstory taxonomic diversity and mean overstory to seedling phylogenetic distance have as predictors of early performance of native tree seedlings planted beneath mixed-species restoration plantations in the Brazilian Atlantic Forest. By applying a phylogenetic approach, our study responds to recent calls for testing the application of such tools in restoration. We planted 12 mid- to late-successional species beneath a mixed-species restoration plantation with three nested tree diversity levels of 19, 58, and 107 species and estimated the mean phylogenetic distance between each seedling species and the overstory community. Seedling performance was not significantly affected by overstory diversity or mean phylogenetic distance. Overall good performance of the seedlings shows that enrichment planting beneath a mixed-species overstory can be successful even under variations in overstory species number and phylogenetic distance. However, significant species-specific differences in performance highlight the importance of an informed selection of which species to enrich plant.

不同时间和空间尺度上台湾水青冈群落谱系结构动态变化

PDF HTML阅读 XML下载 导出引用 引用提醒 不同时间和空间尺度上台湾水青冈群落谱系结构动态变化 DOI: 10.5846/stxb201612302712 作者: 作者单位: 浙江理工大学,浙江理工大学,浙江大学,浙江清凉峰国家级自然保护区管理局,浙江清凉峰国家级自然保护区管理局,浙江大学,浙江理工大学 作者简介: 通讯作者: 中图分类号: 基金项目: 浙江理工大学科研启动项目（13052168-Y）；浙江理工大学"521"人才项目 Dynamics of phylogenetic structure in Fagus hayatae communities vary across temporal and spatial scales Author: Affiliation: Zhejiang Sci-Tech University,Zhejiang Sci-Tech University,,,,,Zhejiang Sci-Tech University Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:群落谱系结构是了解群落聚群过程的一个基础研究内容。但是现有大部分研究内容集中在群落组成和结构的时空差异，对谱系结构的动态变化研究较少。以浙江省清凉峰国家级自然保护区的国家二级保护植物台湾水青冈（Fagus hayatae）林为研究对象，利用2006年、2011年、2016年3次群落动态调查数据，从10、20、50m的3个空间尺度上研究该群落在10a间的谱系结构动态变化，分析时空尺度对台湾水青冈群落谱系结构的影响，探究调控台湾水青冈群落动态变化的主要因子，为后期台湾水青冈林的保护提供理论基础。研究发现（1）在10a森林动态变化过程中，群落的MPD指数下降，MNTD指数增加。NRI和NTI指数在大尺度上随时间显著增加，但在小尺度上无显著变化。（2）随着空间尺度的增加，上述指数的动态变化趋势均不断增强。以上结果表明，2006-2016年间台湾水青冈群落总体谱系结构表现出不断聚集的趋势，而近缘种的谱系关系则不断疏远；群落谱系结构的聚集趋势随空间尺度的增加而增强。大尺度上的环境过滤和小尺度上的随机过程和种间竞争作用可能是导致该地区台湾水青冈群落谱系结构动态变化的主要生态学过程。 Abstract:The phylogenetic structure of communities is a fundamental component in our ability to understand community assembly processes and species coexistence. However, although there have been many studies of the spatial and temporal variation in community structure, few have applied these observations to the dynamics of phylogenetic structure. Here, we performed such an analysis to study temporal and spatial variations in the phylogenetic structure of Fagus hayatae communities, Class Ⅱ protected plant, in China. In 2006, all free-standing woody stems with a diameter at breast height (DBH) ≥ 1cm were tagged, mapped, identified, and measured for DBH, and height in a 1 hm2 forest dynamic plot in Qingliangfeng National Nature Reserve, China. This was followed by re-censuses in 2011 and 2016, in which we recorded the survival status and DBH for previously recorded stems and documented new stems with DBH ≥ 1cm. On the basis of these three censuses spread across a decade (2006, 2011, 2016), we measured the dynamics of the phylogenetic structure at three spatial scales (10m, 20m, and 50m). We used global seed plant phylogenetic data to construct a phylogenetic tree of F. hayatae communities, and selected the mean phylogenetic distance (MPD), mean nearest taxon distance (MNTD), net relatedness index (NRI), and nearest taxon index (NTI) to describe the phylogenetic structure of F. hayatae communities. Additionally, we randomly resampled 999 plots at 10m, 20m, 50m scales using a moving split-window technique to create plots at different spatial scales. Analysis across spatial and temporal scales produced the following results. (1) On decadal time scales, the species richness and abundance of F. hayatae communities both decreased. MPD decreased, whereas MNTD increased. NRI and NTI both significantly positively increased at large scales, but did not change at small scales. (2) As the spatial extent of analyses increased, so did the strength of the trends observed. Thus, the phylogenetic structure of F. hayatae communities showed a clustering pattern and was spatial scale dependent. The largest variation in the phylogenetic structure across time was found at the 50m scale. We concluded that from 2006 to 2016, the phylogenetic structure of F. hayatae communities was clustering, whereas the phylogenetic relationships between nearest species became more distant. Moreover, the effects of environmental filtering dominated the phylogenetic structure dynamics of F. hayatae communities at large scales. This is in contrast to the effects of stochastic processes and interspecific competition, which dominated at small scales. Against a background of global climate change and forest degradation, further studies on scale dependence are needed to gain a better understanding of the mechanisms of community assembly, and to protect these endangered species. 参考文献 相似文献 引证文献

Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones.

Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (D pw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant–arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.

Spatial analysis of phylogenetic community structure: New version of a classical method

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

Intraspecific and phylogenetic density-dependent seedling recruitment in a subtropical evergreen forest.

Recent evidence suggests that plant performance can be influenced by the phylogenetic diversity of neighboring plants. However, no study to date has examined the effect of such phylogenetic density dependence on the transition from seed to seedling. Using 6years of data on seedling recruitment and seed rain of 13 species from 130 stations (one 0.5m2 seed trap and three adjacent 1m2 seedling plots) in a subtropical evergreen forest, we asked: (1) Does negative density dependence act across seed to seedling stages? (2) Is there evidence for phylogenetic density dependence during the seed to seedling transition? (3) Does the strength of density dependence vary among years? Generalized linear mixed-effects models were used to model seed to seedling transition as a function of conspecific seed and seedling densities, heterospecific seed and seedling densities, and mean phylogenetic distance of heterospecific seeds and seedling. Conspecific seed density had a significant negative effect on seedling transition rates for 12 of 13 focal species. In contrast, conspecific seedling density had a positive effect for 7 species, suggesting species-specific habitat preferences. Few species were significantly affected by the density or phylogenetic relatedness of heterospecific seeds and seedlings. Only conspecific seed density effects varied among years for most focal species. Overall, our results reveal that conspecific seed and seedling densities play a more important role than the density or relatedness of heterospecific seeds and seedlings during the seed to seedling stage, suggesting that species-specific seed predators, along with habitat preferences, may contribute to diversity maintenance in this forest.

Parallel Evolution of Metazoan Mitochondrial Proteins.

Amino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared with a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure.

Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus , measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel's lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated.

Environmental quality of a stream can be better predicted by phylogenetic than by taxonomic diversity

Different indices of taxonomic diversity (TD) and phylogenetic diversity (PD) of the macrobenthos were compared to determine the efficient predictors of environmental quality (EQ) in different types of watercourses in Poland. Archived data of 864 samples of benthic invertebrates identified to the family level were analysed on the basis of linear and non-linear multiply regression. The strengths of the correlations between two measures of EQ:BMWPpl (British Monitoring Working Party score system, Polish modification) and MMI (Multimetric Macroinvertebrate Index) and the values of taxonomic richness and three well-known TD indices: Shannon, Margalef and J' Evenness were compared to those for values of three PD indices, based on taxonomic distinctness. Taxonomic richness and all PD indices correlated more strongly with both measures of EQ than all TD indices. Correlations with both types of diversity indices were visibly stronger for BMWPpl when compared with MMI. We suggest that analysed indices of PD, especially MDis (mean phylogenetic distance between families in a sample), are related with EQ strongly enough to be taken into account as potential metrics in selection procedures of biological assessment.