Patterns Of Phylogenetic Beta Diversity Research Articles

The Elevational Gradient of Bird Beta Diversity in the Meili Snow Mountains, Yunnan Province, China.

Understanding the elevational patterns of beta diversity in mountain regions is a long-standing problem in biogeography and ecology. Previous research has generally focused on the taxonomy facet on a large scale, but was limited with regard to multi-facet beta diversity. Accordingly, we constructed a multi-dimensional (taxonomic/phylogenetic/functional) framework to analyze the underlying mechanisms of beta diversity. Within an approximately 2000 m altitudinal range (from 2027 m to 3944 m) along the eastern slope of the Meili Snow Mountains in Deqin County, Yunnan Province, China, we performed field surveys of breeding and non-breeding birds in September/2011 and May/2012, respectively. In total, 132 bird species were recorded during the fieldwork. The results indicated that taxonomic beta diversity contributed 56% of the bird species diversity, and its turnover process dominated the altitudinal pattern of taxon beta diversity; beta phylogenetic diversity contributed 42% of the bird phylogenetic diversity, and its turnover process also appeared to be stronger than the nestedness. For both taxonomy and phylogeny, the null models standardized measures (SES.βsim/SES.βsne/SES.βsor) of paired dissimilarities between elevation zones all showed statistically significant differences (p ≤ 0.05) and were higher than expected (SES.β > 0). However, standardized functional beta diversity showed convergence along the elevational gradient with no significant change. Moreover, the functional beta diversity contributed 50% of the bird functional diversity; there was no significant difference between the turnover and the nestedness-resultant component. Based on these results, we discerned that taxonomic and phylogenetic beta diversity patterns among the elevational zone were overdispersed, which indicated that limiting similarity dominated the turnover process among the bird species and phylogenetic communities in the Meili Snow Mountains.

Patterns of phylogenetic beta diversity measured at deep evolutionary histories across geographical and ecological spaces for angiosperms in China

AbstractAimUnderstanding patterns and drivers of phylogenetic beta diversity in a region is important to understanding the origin and maintenance of the regional species diversity and variation in species diversity between local sites. Here we used a phylogenetic beta diversity metric quantifying deep evolutionary histories to explore geographical and ecological patterns of phylogenetic beta diversity in angiosperm assemblages across China.LocationChina.TaxonFlowering plants (angiosperms).MethodsChina was divided into 100 × 100 km grid cells. Species composition in each grid cell was documented. We used a basal‐weighted metric (Dpw) to quantify phylogenetic beta diversity among angiosperm assemblages with two sampling approaches (neighbourhood approach and pairwise approach). Dpw was related to latitude and climatic conditions of angiosperm assemblages and to geographical and climatic distances between angiosperm assemblages across China.ResultsWe found that the southeastern portion of China has much higher Dpw than the northwestern portion of China. The line of high versus low values of Dpw across China is generally consistent with the line of 500‐mm precipitation per year. Our study shows that precipitation is associated with Dpw more strongly than temperature, and Dpw decreases with latitude, particularly in the eastern part of China.Main conclusionsThe emergence of the observed pattern of basal‐weighted phylogenetic beta diversity is at least partly because the southeastern portion of China retains a large number of Tertiary relicts, making it a biogeographical museum, whereas many Tertiary relicts went extinct from the northwestern portion of China, particularly the Tibetan Plateau, due to the uplift of the plateau and the Himalayas, which makes the region a biogeographical grave for Tertiary relicts.

Taxonomic and phylogenetic diversity patterns in the Northern Sporades islets complex (West Aegean, Greece)

The Aegean archipelago has long been the main research area of numerous biogeographers, plant ecologists and taxonomists due to its intricate palaeogeography and high environmental and topographical heterogeneity. Nevertheless, some parts of this archipelago are essentially unexplored and the processes driving spatial variation in species composition remain unaddressed. Aiming to fill these gaps, we investigated the flora and plant diversity patterns of the Northern Sporades island group, as well as its biogeographical relationships. The study area lies in the biogeographical region of the West Aegean islands and comprises 23 islands and islets. The total flora of the study area consists of 1202 infrageneric taxa, belonging to 517 genera and 120 families, reflecting its geographical and bioclimatic characteristics. The endemic element consists of 41 taxa (3.4% of the flora), eight of which are restricted to the West Aegean islands and two are single island endemics. Area emerged as the most important variable in shaping plant species richness, while niche-based processes played a lesser role in driving these patterns. Regarding the taxonomic and phylogenetic beta-diversity patterns, environmental filtering and not dispersal limitation seems to shape the plant assemblages of the Northern Sporades islets. Biogeographically, the Northern Sporades island group seems to be closer connected to the Kiklades rather than to Evvia or the adjacent mainland, due to their longer isolation and separate palaeogeographical history during the Quaternary.

Differentiation of Environmental Conditions Promotes Variation of Two Quercus wutaishanica Community Assembly Patterns

Two contradictory niche-based processes, environmental filtering and competitive exclusion, are important ecological processes in community assembly. Quercus wutaishanica forests are the climax communities in the Qinling Mountains and the Loess Plateau, China. Since these areas are characterized by different climate and evolutionary histories, these forests could be a suitable study system to test the phylogenetic niche conservatism hypothesis. We compared variation in community assembly of two distinct Q. wutaishanica forest communities and analyzed how the variations are formed. Quercus wutaishanica forest communities had significantly different species pool, phylogenetic structure and phylogenetic diversity between the two regions that were driven by inconsistency in environment conditions and evolutionary history at the local scale. Soil ammonium nitrogen, soil water content, and nitrate nitrogen play a major role in phylogenetic beta diversity patterns. The effect of environmental filtering on community assembly was more significant on the Loess Plateau than in the Qinling Mountains. Our study also found that local environment is important in mediating the patterns of phylogenetic structure. These findings provide insights into the mechanisms of local community assembly.

Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang

Thallium (Tl) is a toxic element, but little is known about microbial communities’ response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.

Untangling the assembly of macrophyte metacommunities by means of taxonomic, functional and phylogenetic beta diversity patterns

Metacommunity ecology has broadened considerably with the recognition that measuring beta diversity beyond the purely taxonomic viewpoint may improve our understanding of the dispersal- and niche-based mechanisms across biological communities. In that perspective, we applied a novel multidimensional approach including taxonomic, functional and phylogenetic data to enhance our basic understanding of macrophyte metacommunity dynamics. For each beta diversity metric, we calculated the mean overall value and tested whether the mean value was different from that expected by chance using null models. We also employed evolutionary and spatially constrained models to first identify the degree to which the studied functional traits showed a phylogenetic signal, and then to estimate the relative importance of spatial and environmental effects on metacommunity structure. We first found that most individual ponds were inhabited by species that were merely random draws from the taxonomic and phylogenetic species pool available in the study region. Contrary to our expectations, not all measured traits were conserved along the phylogeny. We also showed that trait and phylogenetic dimensions strongly increased the amount of variation in beta diversity that can be explained by degree of environmental filtering and dispersal limitation. This suggests that accounting for functional traits and phylogeny in metacommunity ecology helps to explain idiosyncratic patterns of variation in macrophyte species distribution. Importantly, phylogenetic and functional analyses identified the influence of underlying mechanisms that would otherwise be missed in an analysis of taxonomic turnover. Together, these results let us conclude that macrophyte species have labile functional traits adapted to dispersal-based processes and some evolutionary trade-offs that drive community assembly via species sorting. Overall, our exploration of different facets of beta diversity showed how functional and phylogenetic information may be used with species-level data to test community assembly hypotheses that are more ecologically meaningful than assessments of environmental patterns based on the purely taxonomic viewpoint.

Geographical patterns of phylogenetic beta‐diversity components in terrestrial mammals

AbstractAimTo inve stigate geographical patterns of phylogenetic beta diversity (PBD) and its turnover and nestedness‐resultant components for terrestrial mammals. We expect an increase in the importance of the nestedness‐resultant component towards temperate regions given the historical loss of lineages caused by environmental and spatial constraints. Analogously, we expect to find a similar increase in the contribution of the nestedness‐resultant component towards higher elevations. We expect these patterns to be stronger for Rodentia because they have poor dispersal ability and may have been less efficient in recolonizing areas after glaciations.LocationWorld‐wide.MethodsWe generated the species composition of terrestrial Mammalia for 200 km × 200 km cells to calculate PBD and its turnover and nestedness‐resultant components. All measures were computed for each cell and the cells in the surrounding radius of one, two or three adjacent layers. We calculated the relative importance of the nestedness‐resultant component as the proportion of the total PBD (PBDratio) and also PBD deviation given taxonomic beta diversity (PBDdev). PBDdev measures the importance of phylogenetic beta diversity after factoring out taxonomic beta diversity. We used simple linear regressions and piecewise regressions to investigate relationships between PBDratio and mean annual temperature and elevation.ResultsWe found a major contribution of the nestedness‐resultant component linked to temperate climate, especially for groups with better dispersal capacity. Higher elevations were associated with a major contribution of the turnover‐resultant component, particularly for Rodentia.Main conclusionsWe provide the first global representation of PBD in terrestrial mammals and demonstrate that at higher latitudes PBD is mostly a result of lineage loss, whereas in highlands it is linked to lineage turnover. By analysing global patterns of the contribution of PBD components, we demonstrate that dispersal capacity is essential in determining the response of different lineages to geographical and environmental barriers.

Phylogenetic turnover along local environmental gradients in tropical forest communities.

While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3% and 0.4-8.8% of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved.

A novel phylogenetic regionalization of phytogeographical zones of southern Africa reveals their hidden evolutionary affinities

AbstractAimAlthough existing bioregional classification schemes often consider the compositional affinities within regional biotas, they do not typically incorporate phylogenetic information explicitly. Because phylogeny captures information on the evolutionary history of taxa, it provides a powerful tool for delineating biogeographical boundaries and for establishing relationships among them. Here, we present the first vegetation delineation of the woody flora of southern Africa based upon evolutionary relationships.LocationSouthern Africa.MethodsWe used a published time‐calibrated phylogenetic tree for 1400 woody plant species along with their geographical distributions and a metric of phylogenetic beta diversity to generate a phylogenetic delineation of the woody vegetation of southern Africa. We then explored environmental correlates of phylogenetic turnover between them, and the evolutionary distinctiveness of the taxa within them.ResultsWe identified 15 phylogenetically distinct biogeographical units, here referred to as phyloregions. The largest phyloregion broadly overlaps with Savanna vegetation, while the phyloregion overlapping with the south‐western portion of the Fynbos biome is the most evolutionarily distinct. Potential evapotranspiration and mean annual temperature differ significantly among phyloregions and correlate with patterns of phylogenetic beta diversity between them. Our phylogeny‐based delimitation of southern Africa's woody vegetation broadly matches currently recognized phytogeographical classifications, but also highlights parts of the Namib Karoo and Greater Limpopo Transfrontier Park as distinct, but previously under‐recognized biogeographical units.Main conclusionsOur analysis provides new insights into the structure and phylogenetic relationships among the woody flora of southern Africa. We show that evolutionary affinities differentiate phyloregions closely resembling existing vegetation classifications, yet also identify ‘cryptic’ phyloregions that are as evolutionarily distinct as some of the recognized African vegetation types.

Patterns of phylogenetic beta diversity in China's grasslands in relation to geographical and environmental distance

Patterns and determinants of beta (β-) diversity can be used to explore the underlying mechanisms regulating community assembly. Despite being the most commonly used measure of β-diversity, species turnover does not consider the evolutionary differences among species, treating all species equally. Incorporating information on phylogenetic non-independence or relatedness among species in the calculation of β-diversity may substantially advance our understanding of the ecological and evolutionary mechanisms structuring communities. Here, we investigate the relative influence of geographical distance and differences in environmental conditions (environmental distance) on the phylogenetic β-diversity between grassland communities expanding 4000km across the Tibetan Plateau, the Inner Mongolia Plateau and the Xinjiang Autonomous Region in China. Both observed and standardized effect size of phylogenetic β-diversity were significantly correlated with geographical and environmental distance across all regions. However, the effect of geographical distance on the standardized effect size of phylogenetic β-diversity disappeared when environmental distance was controlled. We also found that within different regions, the effect of environmental distance on both observed and standardized effect size of phylogenetic β-diversity was more significant than geographical distance. Among environmental variables, climate played a more important role in shaping observed phylogenetic β-diversity across and within regions, and standardized effect size of phylogenetic β-diversity across regions. Soil properties played a more important role in shaping standardized effect size of phylogenetic β-diversity within regions. The phylogenetic β-diversity of species from dicot and monocot clades exhibited similar patterns along environmental and geographical distance. The results suggest that at the study scale, phylogeny of grassland communities in China is predominantly structured by environmental filtering, and the dominant environmental factors may be scale-dependent.

Beta diversity of woody plants in the Japanese archipelago: the roles of geohistorical and ecological processes

AbstractAimWe addressed the roles of geohistorical and ecological factors on beta diversity patterns of woody plants in the Japanese archipelago. We scrutinized the contribution of recent diversification in shaping the woody plant diversity of insular areas in East Asia.LocationThe Japanese archipelago.MethodsThe distribution data of 1030 woody plant species were compiled for 65 localities in the archipelago. First, the relationships between geohistorical (straits, distance and area) and ecological (topographical heterogeneity, minimum temperature and annual precipitation) variables and taxonomic and phylogenetic beta diversity were tested using regression models. Second, geographical patterns of phylogenetic beta diversity were compared with those of taxonomic beta diversity using ordination and randomization tests. These analyses were applied to the woody plants overall and their functional groups defined by life‐form (coniferous, deciduous broad‐leaved and evergreen broad‐leaved groups).ResultsDistance and minimum temperature showed significant positive relationships with both measures of beta diversity across the woody plants overall and the functional groups. The contributions of geographical barriers, topographical heterogeneity and annual precipitation varied among groups. Ordinations by phylogenetic beta diversity produced patterns that were consistent with those generated by taxonomic beta diversity, showing three clusters of localities in relation to geographical barriers, except in the coniferous group. The regression slopes of phylogenetic beta diversity versus distance were significantly smaller than those of taxonomic beta diversity versus distance across all groups.Main conclusionsIn the Japanese archipelago, the combination of geographical isolation and environmental filtering in response to geohistorical perturbations and environmental gradients has configured the beta diversity patterns of woody plants. The recent diversification of phylogenetically close relatives probably caused the spatial variations that exist in woody plant diversity. The archipelago functions as a refugium for relict taxa and as a hotspot for neoendemics, contributing to the broad‐scale diversity bias favouring East Asia.

Global patterns of phylogenetic beta diversity components in bats

AbstractAimTo investigate global patterns of phylogenetic beta diversity (phylobetadiversity, PBD) components in bats (Chiroptera), testing whether the strong dispersal barriers among realms led to lineage differentiation between them and whether the flight capability of the study group created distance‐decay patterns in PBD, with lower turnover rates between the closest biogeographical regions.LocationGlobal, delimited by biogeographical regions.MethodsUsing the global distribution of bats and a supertree available for most species, we calculated PBD using the complement of the PhyloSor index. In addition, to distinguish the relative roles of local (e.g. lineage filtering) and regional processes (e.g. speciation) in shaping broad‐scale patterns of PBD, we partitioned PBD into two components: the turnover component (PBDTurn) and the phylogenetic diversity (PD) component (PBDPD). We used a null model to test whether assemblages were more or less phylogenetically dissimilar than expected by chance. We also performed a Mantel analysis to analyse the distance‐decay patterns of PBD and its two components.ResultsThe most striking difference in PBD was found between the Old World and the New World. In general, the PBD pattern was determined by PBDTurn. For some adjacent regions we noticed the PBDPD component was more important, indicating that the dissimilarity was mostly due to differences in phylogenetic diversity. On the other hand, for other adjacent regions, the observed PBDTurn was higher than expected by chance and the PBDPD was lower. This demonstrates that, although these regions are relatively close in space, there are other factors driving phylogenetic differences between them (i.e. ecological factors).Main conclusionsOur results suggest that at broad scales, the PBD of bats is determined by PBDTurn. We postulate that the flight ability of bats led to low turnover rates between adjacent regions in the absence of other factors that can drive differences between them (e.g. strong environmental barriers).

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.

A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds

1. Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. 2. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. 3. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. 4. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. 5. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. 6. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co-existence.