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AIM: To define biome‐scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them with ‘classical’ hotspots based on species richness (SR) alone. LOCATION: Global. METHODS: SR, PD and FD were computed for 782 terrestrial ecoregions using the distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework incorporating the relative species coverage in each ecoregion. We built large‐scale multifaceted diversity–area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each facet of diversity. Finally we defined hotspots as the top‐ranked ecoregions. RESULTS: While ignoring relative species coverage led to a fairly good congruence between biome‐scale top ranked SR, PD and FD hotspots, ecoregions harbouring a rich and abundantly represented evolutionary history and FD did not match with the top‐ranked ecoregions defined by SR. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than SR as a function of area. MAIN CONCLUSIONS: The fact that PD/FD reach their maximum value faster than SR could suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it has been quantified at a global scale and should have important consequences for conservation. Incorporating relative species coverage into the delineation of multifaceted hotspots of diversity led to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail to preserve those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at a global scale.

Aim: Characterizing macroecological patterns in biodiversity is key to improve our understanding of community assembly. Global biodiversity for many taxa follows a latitudinal gradient, with increased diversity in tropical latitudes. Less is known about global parasite biodiversity, inhibiting our ability to predict how global change will impact parasitic disease emergence. Using distribution and phylogenetic data for 2,386 avian haemosporidian blood parasites (genera Plasmodium, Haemoproteus and Leucocytozoon), I assessed how contemporary and historical drivers influence the composition of parasite communities worldwide. Location: Global. Time period: Current. Major taxa studied: Haemosporidian blood parasites. Methods: Parasite distribution and cytochrome b sequence data were accessed from an opensource database. Bayesian phylogenetic tree distributions were constructed for each parasite genus using two substitution models to capture uncertainty. Hierarchical regressions assessed effects of environmental variation, latitude and phylogenetic β-diversity (βdiv; a proxy for phylogenetic uniqueness) on the diversity and asymmetry of parasite communities around the globe. Results: I uncovered biodiversity hotspots and identified broad variation in global diversity patterns among parasite genera. Community diversity increased with increasing phylogenetic uniqueness for all three parasite genera; however, these diverse and unique regions did not consistently occur in the tropics. I found no evidence of a latitudinal diversity gradient, and support for a latitudinal gradient in community phylogenetic asymmetry was weak. Main conclusions: Global variation in avian haemosporidian phylogenetic diversity does not reflect a latitudinal gradient. Instead, parasite biogeography may reflect fundamental differences in hostswitching tendencies or the timing of avian evolutionary radiations. Examining the interplay between shared evolutionary history and phylogenetic diversity can provide important insights into the drivers of parasite biodiversity at global scales.

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thorn, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.

AIM: To propose a unified framework for quantifying taxon (Tβ), phylogenetic (Pβ) and functional (Fβ) beta diversity via pairwise comparisons of communities, which allows these types of beta diversity to be partitioned into ecologically meaningful additive components. LOCATION: Global, with case studies in Europe and the Azores archipelago. METHODS: Using trees as a common representation for taxon, phylogenetic and functional diversity, we partition total beta diversity (βₜₒₜₐₗ) into its replacement (turnover, βᵣₑₚₗ) and richness difference (βᵣᵢcₕ) components according to which part of a global tree was shared by or unique to communities that were being compared. We demonstrate the application of this framework using artificial and empirical examples (mammals in Europe and epigean arthropods in the Azores). RESULTS: Our empirical examples show that comparing Pβ and Fβ with the most commonly used Tβ revealed previously hidden patterns of beta diversity. More importantly, we demonstrate that partitioning Pβₜₒₜₐₗ and Fβₜₒₜₐₗ into their respective βᵣₑₚₗ and βᵣᵢcₕ components facilitates the detection of more complex patterns than using the overall coefficients alone, further elucidating the different forces operating in community assembly. MAIN CONCLUSIONS: The methods presented here allow the integration and full comparison of Tβ, Pβ and Fβ. They provide a tool for effectively disentangling the replacement (turnover) and richness difference components of the different biodiversity facets within the same methodological framework.

Fire is a key disturbance affecting plant biodiversity patterns and evolution. Although a wide range of studies have shown important impacts of fire on vegetation, most have focused on taxonomic diversity, with less emphasis on other aspects of biodiversity, such as functional and phylogenetic diversity. Therefore, we assessed the recovery of biodiversity facets across different times since the last fire in semiarid shrublands in Northeast Iran. We quantified changes in plant biodiversity facets, including taxonomic, functional, and phylogenetic diversity, and the diversity of seven functional traits in five ecologically comparable sites that have experienced wildfire disturbances at short-term (1 and 4 year sites) and long-term (10 and 20 year sites) intervals, in com- parison to an unburnt site. Our results showed significant changes in all biodiversity facets related to the year since the last fire, with a significant increase in biodiversity and diversity of functional traits under long-term rather than short-term conditions, and in comparison to the unburned site. We conclude that wildfire influences the presence of plant species with distant functional and evolutionary relatedness and causes an increase in plant species and diversity of functional traits de- pending on time intervals. Therefore, wildfire can promote positive effects on the recovery of bio- diversity aspects and the evolution of vegetation in semiarid shrublands.

Abstract Among the factors influencing the animal gastrointestinal tract microbiome (AGM) diversity, diet and phylogeny have been extensively studied. However, what made the studies particularly challenging is that diet characteristics per se are product of evolution, and hence totally disentangling both effects is unrealistic, likely explaining the lack of consensus in existing literatures. To further explore microbial diversity and host-phylogeny–diet relationships, we performed a big-data meta-analysis with 4903 16S rRNA AGM samples from 318 animal species covering all six vertebrate and four major invertebrate classes. We discovered that the relationship between AGM-diversity and phylogenetic timeline (PT) follows a power-law or log-linear model, including diet specific power-law relationships. The log-linear nature predicts a generally rising trend of AGM diversity along the evolutionary tree starting from the root, which explains the observation why Mammalia exhibited the highest AGM-diversity. The power-law property suggests that a handful of taxa carry disproportionally large weights to the evolution of diversity patterns than the majority of taxa, which explains why the species richness of Insecta was significant different than those from the other nine classes. Finally, we hypothesize that the diversity—PT power-law relationship explains why species-abundance distributions generally follow highly skewed probability distributions. Based on 4903 gastrointestinal-microbiome samples of 318 animal species covering six major invertebrate and all vertebrate classes, we found that power-law patterns seem to govern microbiome-diversity and host-phylogeny–diet relationships.

Aim: To test whether native and non-native species have similar diversity-area relationships (species-area relationships [SARs] and phylogenetic diversity-area relationships [PDARs]) and whether they respond similarly to environmental variables. Location: United States. Methods: Using lists of native and non-native species as well as environmental variables for >250 US national parks, we compared SARs and PDARs of native and nonnative species to test whether they respond similarly to environmental conditions. We then used multiple regressions involving climate, land cover and anthropogenic variables to further explore underlying predictors of diversity for plants and birds in US national parks. Results: Native and non-native species had different slopes for SARs and PDARs, with significantly higher slopes for native species. Corroborating this pattern, multiple regressions showed that native and non-native diversity of plants and birds responded differently to a greater number of environmental variables than expected by chance. For native species richness, park area and longitude were the most important variables while the number of park visitors, temperature and the percentage of natural area were among the most important ones for non-native species richness. Interestingly, the most important predictor of native and non-native plant phylogenetic diversity, temperature, had positive effects on non-native plants but negative effects on natives. Main conclusions: SARs, PDARs and multiple regressions all suggest that native and non-native plants and birds responded differently to environmental factors that influence their diversity. The agreement between diversity-area relationships and multiple regressions with environmental variables suggests that SARs and PDARs can be both used as quick proxies of overall responses of species to environmental conditions. However, more importantly, our results suggest that global change will have different effects on native and non-native species, making it inappropriate to apply the large body of knowledge on native species to understand patterns of community assembly of non-native species.

Phylogenetic tools have increasingly been used in community ecology to describe the evolutionary relationships among co‐occurring species. In studies of succession, such tools may allow us to identify the evolutionary lineages most suited for particular stages of succession and habitat rehabilitation. However, to date, these two applications have been largely separate. Here, we suggest that information on phylogenetic community structure might help to inform community restoration strategies following major disturbance. Our study examined phylogenetic patterns of succession based on a chronosequence of three abandoned subarctic mine spoil heaps (waste piles) dating from the early 1970s, mid‐1970s and early 1980s. The vegetation at each mine site was compared to the surrounding vegetation, and community structure on mines was explored assuming species pools at nested spatial scales. We found that the adjacent vegetation was more phylogenetically clustered than the vegetation on the mines, with mines demonstrating weaker phylogenetic community structure. Using simulation models, we showed that phylogenetic dissimilarity between mine sites did not depart from null expectations. However, we found evidence for species sorting along abiotic gradients (slope and aspect) on the mine sites that had been abandoned for the longest. Synthesis and applications. Understanding the trajectory of succession is critical for restoration efforts. Our results suggest that early colonizers represent a phylogenetically random subset of species from the local species pool. Over time, there appears to be selection for particular lineages that come to be filtered across space and environment. The species most appropriate for mine site restoration might, therefore, depend on the successional stage of the community and the local species composition. For example, in later succession, it could be more beneficial to facilitate establishment of more distant relatives. Our findings can improve management practices by providing relatedness information for known successful colonizers and by informing seeding decisions with knowledge of the surrounding and regional species pools. The application of phylogenetics to restoration ecology and succession is relatively new, but it has the potential to provide novel insight into the dynamics of changing community structures during succession.

The species-area relationship (SAR) is a well-established, globally recognized ecological pattern, and research on SAR has expanded to include the phylogenetic diversity-area relationship (PDAR). However, this research has generally been limited to terrestrial systems. Using data on freshwater macroinvertebrates, the log–log form of the SAR and PDAR power models were compared between the Lhasa River and the Niyang River on the Tibetan Plateau in China. The study reveals that there is a significant difference in the slopes of SAR and PDAR between the two rivers, with the Lhasa River having a considerably higher slope. The beta diversity calculations in these two basins support this pattern, with the Lhasa River exhibiting significantly higher numbers of species and greater total phylogenetic beta diversity than the Niyang River. Regarding species replacement, the turnover component was the primary driver of both species and phylogenetic beta diversity in both rivers. These differences in the beta diversity components were mainly driven by dispersal constraints because spatial distance had a large effect on total beta diversity and turnover fractions. In addition, the nestedness component was more affected by climate and land cover, indicating that highland rivers are subject to the threats of anthropogenic disturbance and climate change. Therefore, spatial factors play a crucial role in determining the distribution of passively dispersed benthic organisms as the scale of change in rivers increases from local to regional effects.

Biodiversity is an important determinant of primary productivity in experimental ecosystems. We combine two streams of research on understanding the effects of biodiversity on ecosystem function: quantifying phylogenetic diversity as a predictor of biodiversity effects in species-rich systems and the contribution of pairwise interspecific interactions to ecosystem function. We developed a statistical model that partitions the effect of biodiversity into effects due to community phylogenetic diversity and other community properties (e.g., average pairwise interaction, between- and within-functional-group effects, and so forth). The model provides phylogenetically based species-level explanations of differences in ecosystem response for communities with differing species composition. In two well-known grassland experiments, the model approach provides a parsimonious description of the effects of diversity as being due to the joint effect of the average pairwise statistical interaction and to community phylogenetic diversity. Effects associated with functional groupings of species in communities are largely explained by community phylogenetic diversity. The model approach quantifies a direct link between a measure of the evolutionary diversity of species and their interactive contribution to ecosystem function. It proves a useful tool in developing a mechanistic understanding of variation in ecosystem function.