Phylogenetic Dissimilarity Research Articles

Coexisting orchid species have distinct mycorrhizal communities and display strong spatial segregation

Because orchids are dependent on mycorrhizal fungi for germination and establishment of seedlings, differences in the mycorrhizal communities associating with orchids can be expected to mediate the abundance, spatial distribution and coexistence of terrestrial orchids in natural communities. We assessed the small-scale spatial distribution of seven orchid species co-occurring in 25×25m plots in two Mediterranean grasslands. In order to characterize the mycorrhizal community associating with each orchid species, 454 pyrosequencing was used. The extent of spatial clustering was assessed using techniques of spatial point pattern analysis. The community of mycorrhizal fungi consisted mainly of members of the Tulasnellaceae, Thelephoraceae and Ceratobasidiaceae, although sporadically members of the Sebacinaceae, Russulaceae and Cortinariaceae were observed. Pronounced differences in mycorrhizal communities were observed between species, whereas strong clustering and significant segregation characterized the spatial distribution of orchid species. However, spatial segregation was not significantly related to phylogenetic dissimilarity of fungal communities. Our results indicate that co-occurring orchid species have distinctive mycorrhizal communities and show strong spatial segregation, suggesting that mycorrhizal fungi are important factors driving niche partitioning in terrestrial orchids and may therefore contribute to orchid coexistence.

Highly diverse and spatially heterogeneous mycorrhizal symbiosis in a rare epiphyte is unrelated to broad biogeographic or environmental features

Symbiotic interactions are common in nature. In dynamic or degraded environments, the ability to associate with multiple partners (i.e. broad specificity) may enable species to persist through fluctuations in the availability of any particular partner. Understanding how species interactions vary across landscapes is necessary to anticipate direct and indirect consequences of environmental degradation on species conservation. We asked whether mycorrhizal symbiosis by populations of a rare epiphytic orchid (Epidendrum firmum) is related to geographic or environmental heterogeneity. The latter would suggest that interactions are governed by environmental conditions rather than historic isolation of populations and/or mycorrhizal fungi. We used DNA-based methods to identify mycorrhizal fungi from eleven E.firmum populations in Costa Rica. We used molecular and phylogenetic analyses to compare associations. Epidendrum firmum exhibited broad specificity, associating with diverse mycorrhizal fungi, including six Tulasnellaceae molecular operational taxonomic units (MOTUs), five Sebacinales MOTUs and others. Notably, diverse mycorrhizal symbioses formed in disturbed pasture and roadside habitats. Mycorrhizal fungi exhibited significant similarity within populations (spatial and phylogenetic autocorrelation) and significant differences among populations (phylogenetic community dissimilarity). However, mycorrhizal symbioses were not significantly associated with biogeographic or environmental features. Such unexpected heterogeneity among populations may result from complex combinations of fine-scale environmental factors and macro-evolutionary patterns of change in mycorrhizal specificity. Thus, E.firmum exhibits broad specificity and the potential for opportunistic associations with diverse fungi. We suggest that these characteristics could confer symbiotic assurance when mycorrhizal fungi are stochastically available, which may be crucial in dynamic or disturbed habitats such as tropical forest canopies.

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes.

Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Partitioning phylogenetic and functional diversity into alpha and beta components along an environmental gradient in aMediterranean rangeland

AbstractQuestionsTo what extent is the functional structure of plant communities captured by phylogenetic structure? Are some functional dimensions better represented by phylogenetic relationships? In an empirical study, we propose to test the congruence between phylogenetic and functional structure at the alpha and the beta scale along an environmental gradient.LocationCausse duLarzac, southernFrance.MethodsWe measured species abundances and eight key functional traits in 12 plant communities distributed along a gradient of soil depth and resource availability in aMediterranean rangeland. A phylogenetic super‐tree of the species was assembled, and after quantifying the degree of phylogenetic signal present in each trait, we quantified taxonomic (TD), phylogenetic (PD) and functional (FD) diversity both within (alpha scale) and among (beta scale) communities, taking species abundances into account. We tested for trends in diversity along the environmental gradient, and looked for congruence among different facets of diversity, both at the alpha and the beta scale.ResultsWe found a significant phylogenetic signal for seven out of eight traits. However, when accounting for trends in taxonomic diversity (i.e. richness and evenness),PDdid not capture the strong functional structure observed within and among the communities. At the alpha scale, we found an overall pattern of phylogenetic convergence of abundant species, which did not reflect the observed functional divergence. At the beta scale, despite some congruence between betaPDand betaFDfor three individual traits, phylogenetic dissimilarities did not capture the overall environmental and functional sorting of species according to habitats.ConclusionsWe show that even when traits display a significant phylogenetic signal,PDdoes not capture the complex functional structure of communities in response to environmental gradients. Nevertheless, results suggest that phylogenetic relationships may partially capture differences in the beta niche of species and provide additional insights on assembly processes not captured by the set of measured functional traits. Only by accounting for patterns in taxonomic diversity were we able to disentangle the functional and evolutionary determinants of species assembly along the gradient.

A new technique for analysing interacting factors affecting biodiversity patterns: crossed-DPCoA.

We developed an approach for analysing the effects of two crossed factors A and B on the functional, taxonomic or phylogenetic composition of communities. The methodology, known as crossed-DPCoA, defines a space where species, communities and the levels of the two factors are organised as a set of points. In this space, the Euclidean distance between two species-specific points is a measure of the (functional, taxonomic or phylogenetic) dissimilarity. The communities are positioned at the centroid of their constitutive species; and the levels of two factors at the centroid of the communities associated with them. We develop two versions for crossed-DPCoA, the first one moves the levels of factor B to the centre of the space and analyses the axes of highest variance in the coordinates of the levels of factor A. It is related to previous ordination approaches such as partial canonical correspondence analysis and partial non-symmetrical correspondence analysis. The second version projects all points on the orthogonal complement of the space generated by the principal axes of factor B. This second version should be preferred when there is an a priori suspicion that factor A and B are associated. We apply the two versions of crossed-DPCoA to analyse the phylogenetic composition of Central European and Mediterranean bird communities. Applying crossed-DPCoA on bird communities supports the hypothesis that allopatric speciation processes during the Quaternary occurred in open and patchily distributed landscapes, while the lack of geographic barriers to dispersal among forest habitats may explain the homogeneity of forest bird communities over the whole western Palaearctic. Generalizing several ordination analyses commonly used in ecology, crossed-DPCoA provides an approach for analysing the effects of crossed factors on functional, taxonomic and phylogenetic diversity, environmental and geographic structure of species niches, and more broadly the role of genetics on population structures.

Phylogenetic beta diversity in tropical forests: Implications for the roles of geographical and environmental distance

AbstractVarious mechanistic theories of community assembly have been proposed ranging from niche‐based theory to neutral theory. Analyses of beta diversity in a phylogenetic context could provide an excellent opportunity for testing many of these hypotheses. We analyzed the patterns of phylogenetic beta diversity in tropical tree communities in Panama to test several community assembly hypotheses. In particular, the degree to which the phylogenetic dissimilarity between communities can be explained by geographical or environmental distance can yield support for stochastic or deterministic assembly processes, respectively. Therefore, we examined: (i) the existence of distance decay of phylogenetic similarity among communities and its degree of departure from that expected under a null model; and (ii) the relative importance of geographical versus environmental distance in predicting the phylogenetic dissimilarity of communities. We found evidence that the similarity in the phylogenetic composition of communities decayed with geographical distance and environmental gradients. Null model evidence showed that beta diversity in the study system was phylogenetically non‐random. Our results highlighted not only the role of local ecological mechanisms, including environmental filtering and competitive exclusion, but also biogeographical processes such as speciation, dispersal limitation, and niche evolution in structuring phylogenetic turnover. These results also highlight the importance of niche conservatism in structuring species diversity patterns.

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

The study of biodiversity has tended to focus primarily on relatively information‐poor measures of species diversity. Recently, many studies of local diversity (alpha diversity) have begun to use measures of functional and phylogenetic alpha diversity. Investigations into the phylogenetic and functional dissimilarity (beta diversity) of communities have been far less numerous, but these dissimilarity measures have the potential to infer the mechanisms underlying community assembly and dynamics. Here, we relate levels of phylogenetic and functional alpha diversity to levels of phylogenetic and functional beta diversity to infer the mechanism or mechanisms responsible for the assembly of tree communities in six forests located in tropical and temperate latitudes. The results show that abiotic filtering plays a role in structuring local assemblages and governing spatial turnover in community composition and that phylogenetic measures of alpha and beta diversity are not strong predictors of functional alpha and beta diversity in the forests studied.

Underdispersion of anti‐herbivore defence traits and phylogenetic structure of cerrado tree species at fine spatial scale

AbstractQuestionDo species phylogeny and herbivory‐related defence traits influence species co‐occurrence in the cerrado? Are anti‐herbivory defence traits under‐ or overdispersed in the quadrats? Do soil features mediate these patterns?LocationA cerrado site in SE Brazil (21°58′05.3″ S, 47°52′10.1″ W).MethodsWe analysed 100 quadrats of 5 m × 5 m each, and sampled all woody individuals. For each species, we measured nine defence traits against herbivory and tested against null models whether (1) phylogenetic dissimilarities were under‐ or overdispersed, (2) trait species dissimilarities were under‐ or overdispersed, and (3) these spatial patterns were associated with soil nutrient content, considering the variation of sum of bases, organic matter, and aluminium.ResultsWe found phylogenetic signals in two traits, and conservatism of traits as a whole was significant. Phylogenetic structure of communities was in general clustered. We found trait underdispersion for specific leaf area, water content, leaf toughness, and leaf nutritional quality. Specific leaf area was also overdispersed in quadrats. We did not find either under‐ or overdispersion related to soil features.ConclusionsAs phylogenetic and trait underdispersion were not associated with soil features, and fire and drought are not expected to change at study scale, some biotic interaction may be responsible for underdispersion. We postulated that insect herbivory, when representing a large constraint to trees in this environment, could lead to functional and phylogenetic underdispersion.

Compositional and phylogenetic dissimilarity of host communities drives dissimilarity of ectoparasite assemblages: geographical variation and scale-dependence

We tested the hypothesis that compositional and/or phylogenetic dissimilarity of host assemblages affect compositional and/or phylogenetic dissimilarity of parasite assemblages, to different extents depending on scale, using regional surveys of fleas parasitic on small mammals from 4 biogeographical realms. Using phylogenetic community dissimilarity metric, we calculated the compositional and phylogenetic dissimilarity components between all pairs of host and parasite communities within realms and hemispheres. We then quantified the effect of compositional or phylogenetic dissimilarity in host regional assemblages, and geographical distance between assemblages, on the compositional or phylogenetic dissimilarity of flea regional assemblages within a realm, respectively. The compositional dissimilarity in host assemblages strongly affected compositional dissimilarity in flea assemblages within all realms and within both hemispheres. However, the effect of phylogenetic dissimilarity of host assemblages on that of flea assemblages was mostly confined to the Neotropics and Nearctic, but was detected in both the Old and New World at the higher scale, possibly because of phylogenetic heterogeneity in flea and host faunas between realms. The clearer effect of the compositional rather than the phylogenetic component of host community dissimilarity on flea community dissimilarity suggests important roles for host switching and ecological fitting during the assembly history of flea communities.

Phylogenetic beta diversity of native and alien species in European urban floras

ABSTRACTAim Human activities have weakened biogeographical barriers to dispersal, increasing the rate of introduction of alien plants. However, their impact on beta diversity and floristic homogenization is poorly understood. Our goal is to compare the phylogenetic beta diversity of native species with that of two groups of alien species, archaeophytes and neophytes (introduced before and after ad 1500, respectively), across European urban floras to explore how biological invasions affect phylogenetic turnover at a continental scale.Location Twenty European cities located in six countries between 49 and 53° N latitude in continental Europe and the British Isles.Methods To compare the phylogenetic beta diversity of native and alien species we use the average phylogenetic dissimilarity of individual floras from their group centroid in multivariate space. Differences in phylogenetic beta diversity among different species groups are then assessed using a randomization test for homogeneity of multivariate dispersions.Results Across European urban floras, and when contrasted with natives, archaeophytes are usually associated with lower levels of phylogenetic beta diversity while neophytes tend to increase phylogenetic differentiation.Main conclusions While archaeophytes tend to promote limited homogenization in phylogenetic beta diversity, because of their diverse geographical origin together with short residence times in the invaded regions, neophytes are not promoting biotic homogenization of urban floras across Europe. Therefore, in spite of the increasing rate of alien invasion, an intense phylogenetic homogenization of urban cities is not to be expected soon.

Phylogenetic Beta Diversity Metrics, Trait Evolution and Inferring the Functional Beta Diversity of Communities

The beta diversity of communities along gradients has fascinated ecologists for decades. Traditionally such studies have focused on the species composition of communities, but researchers are becoming increasingly interested in analyzing the phylogenetic composition in the hope of achieving mechanistic insights into community structure. To date many metrics of phylogenetic beta diversity have been published, but few empirical studies have been published. Further inferences made from such phylogenetic studies critically rely on the pattern of trait evolution. The present work provides a study of the phylogenetic dissimilarity of 96 tree communities in India. The work compares and contrasts eight metrics of phylogenetic dissimilarity, considers the role of phylogenetic signal in trait data and shows that environmental distance rather than spatial distance is the best correlate of phylogenetic dissimilarity in the study system.

Phylogenetic distance can predict susceptibility to attack by natural enemies

If related species share enemies, variation in the damage experienced by species within a community may be predictable based on phylogeny. We examined the hypothesis that plant species more closely related to other community members experience greater herbivory by assessing leaf damage to native and exotic plants in two North American communities: an Eastern hardwood forest and a Rocky Mountain montane community. Pairwise phylogenetic distances between focal species and the hundreds of other native species in each community were calculated. We examined the influence of four measures of relatedness within each community: NND (phylogenetic distance to the nearest native neighbor), MPD (mean phylogenetic distance to the native species in the community), and two new metrics, MIPD (mean inverse phylogenetic distance) and INND (inverse nearest neighbor distance). These new metrics assume a nonlinear increase in interaction strength with relatedness; in the context of natural enemies, they posit that the sharing of enemies between any two species increases nonlinearly with their relatedness. Using regression models, we found that herbivore damage decreased with decreasing phylogenetic similarity of focal species to native species (as measured by MIPD) in both sites, although the pattern was significant only for native focal species in the montane community and exotic focal species in the hardwood forest. Similar decreases in herbivory with decreasing relatedness were detected using INND (montane natives) and MPD (hardwood forest exotics). There was no significant relationship between NND and herbivory for any of the four site by focal plant origin combinations. Our results are the first to support the hypothesis that native species can escape attack as a function of their phylogenetic dissimilarity to the larger community of native species, and to demonstrate that exotic species show these patterns in the wild (as opposed to in common gardens). We suggest that phylogenetic distance metrics assuming a nonlinear increase in interaction strength with relatedness show promise for broader application.

Phylogenetic Metrics of Community Similarity

We derive a new metric of community similarity that takes into account the phylogenetic relatedness among species. This metric, phylogenetic community dissimilarity (PCD), can be partitioned into two components, a nonphylogenetic component that reflects shared species between communities (analogous to Sørensen' s similarity metric) and a phylogenetic component that reflects the evolutionary relationships among nonshared species. Therefore, even if a species is not shared between two communities, it will increase the similarity of the two communities if it is phylogenetically related to species in the other community. We illustrate PCD with data on fish and aquatic macrophyte communities from 59 temperate lakes. Dissimilarity between fish communities associated with environmental differences between lakes often has a phylogenetic component, whereas this is not the case for macrophyte communities. With simulations, we then compare PCD with two other metrics of phylogenetic community similarity, II(ST) and UniFrac. Of the three metrics, PCD was best at identifying environmental drivers of community dissimilarity, showing lower variability and greater statistical power. Thus, PCD is a statistically powerful metric that separates the effects of environmental drivers on compositional versus phylogenetic components of community structure.

Evolutionary history and distance dependence control survival of dipterocarp seedlings

One important hypothesis to explain tree-species coexistence in tropical forests suggests that increased attack by natural enemies near conspecific trees gives locally rare species a competitive advantage. Host ranges of natural enemies generally encompass several closely related plant taxa suggesting that seedlings should also do poorly around adults of closely related species. We investigated the effects of adult Parashorea malaanonan on seedling survival in a Bornean rain forest. Survival of P. malaanonan seedlings was highest at intermediate distances from parent trees while heterospecific seedlings were unaffected by distance. Leaf herbivores did not drive this relationship. Survival of seedlings was lowest for P. malaanonan, and increased with phylogenetic dissimilarity from this species, suggesting that survival of close relatives of common species is reduced. This study suggests that distance dependence contributes to species coexistence and highlights the need for further investigation into the role of shared plant enemies in community dynamics.

Concurrent invaders—four exotic species of Monogenea now established on exotic freshwater fishes in Australia

Four species of exotic monogeneans are reported from five species of exotic freshwater fish in Australia: Gyrodactylus bullatarudis from Poecilia reticulata and Xiphophorus helleri in Queensland; Gyrodactylus macracanthus from Misgurnus anguillicaudatus in the Australian Capital Territory; Dactylogyrus extensus from Cyprinus carpio in the Australian Capital Territory; and Dactylogyrusanchoratus from Carassius auratus in the Australian Capital Territory. This is the first published record of described species of monogeneans of the genus Dactylogyrus or Gyrodactylus from Australia and the first report of parasites of M. anguillicaudatus in Australia. The establishment of exotic monogenean populations on Australian native fishes via host-switching is considered less likely than for other parasitic groups due to the generally high host-specificity of monogeneans, combined with the phylogenetic dissimilarity of native and exotic fishes. Similar establishments have occurred elsewhere, however, and the risk of these events increases with each new fish species introduction.