Phylogenetic Beta Diversity Research Articles

Spatial phylogenetics of the North American flora

AbstractNorth America is a large continent with extensive climatic, geological, soil, and biological diversity. As biota faces threat from habitat destruction and climate change, making a quantitative assessment of biodiversity becomes critically important. Rapid digitization of plant specimen records and accumulation of DNA sequence data enable a much‐needed broad synthesis of species occurrences with phylogenetic data. In this study, the first such synthesis of a flora from such a large and diverse part of the world is attempted, all seed plants from the North American continent (here defined to include Canada, United States, and Mexico), with a focus on examining phylogenetic diversity and endemism. We collected digitized plant specimen records and chose a coarse grain for analysis, recognizing that this grain is currently necessary for reasonable completeness per sampling unit. We found that raw richness and endemism patterns largely support previous hypotheses of biodiversity hotspots. The application of phylogenetic metrics and a randomization test revealed novel results, including a significant phylogenetic clustering across the continent, a striking east–west geographical difference in the distribution of branch lengths, and the discovery of centers of neo‐ and paleoendemism in Mexico, the southwestern USA, and the southeastern USA. Finally, our examination of phylogenetic beta diversity provides a new approach to compare centers of endemism. We discuss the empirical challenges of working at the continental scale and the need for more sampling across large parts of the continent, for both DNA data for terminal taxa and spatial data for poorly understood regions, to confirm and extend these results.

Global patterns and determinants of lake macrophyte taxonomic, functional and phylogenetic beta diversity

Documenting the patterns of biological diversity on Earth has always been a central challenge in macroecology and biogeography. However, for the diverse group of freshwater plants, such research program is still in its infancy. Here, we examined global variation in taxonomic, functional and phylogenetic beta diversity patterns of lake macrophytes using regional data from six continents. A data set of ca. 480 lake macrophyte community observations, together with climatic, geographical and environmental variables, was compiled across 16 regions worldwide. We (a) built the very first phylogeny comprising most freshwater plant lineages; (b) exploited a wide array of functional traits that are important to macrophyte autoecology or that relate to lake ecosystem functioning; (c) assessed if different large-scale beta diversity patterns show a clear latitudinal gradient from the equator to the poles using null models; and (d) employed evolutionary and regression models to first identify the degree to which the studied functional traits show a phylogenetic signal, and then to estimate community-environment relationships at multiple spatial scales. Our results supported the notion that ecological niches evolved independently of phylogeny in macrophyte lineages worldwide. We also showed that taxonomic and phylogenetic beta diversity followed the typical global trend with higher diversity in the tropics. In addition, we were able to confirm that species, multi-trait and lineage compositions were first and foremost structured by climatic conditions at relatively broad spatial scales. Perhaps more importantly, we showed that large-scale processes along latitudinal and elevational gradients have left a strong footprint in the current diversity patterns and community-environment relationships in lake macrophytes. Overall, our results stress the need for an integrative approach to macroecology, biogeography and conservation biology, combining multiple diversity facets at different spatial scales.

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.

Contrasting responses of beta diversity components to environmental and host‐associated factors in insect ectoparasites

1. The present study investigated whether different components (species replacement and species gains/losses) of compositional and phylogenetic beta diversity of insect ectoparasites responded similarly to environmental and host‐associated gradients using a large dataset on distribution of fleas and their rodent hosts in Mongolia.2. Generalised dissimilarity modelling was applied to investigate whether environmental variables or host dissimilarity was the best predictor of species/lineage replacement and species/lineage gains/losses (= richness difference) components of compositional and phylogenetic flea beta diversity.3. The total compositional beta diversity of fleas was influenced mainly by the gradient in air temperature and, to a lesser degree, by total host beta diversity, with the former effect being associated with the richness difference component and the latter effect being associated with species replacement component. The total phylogenetic beta diversity of fleas was best explained by the total phylogenetic beta diversity of hosts, with this effect being mainly associated with the lineage replacement component, whereas the lineage richness difference component responded mainly to the temperature gradient.4. The results of the present indicate that not only multiple beta diversity facets are driven by different factors, but also different components of the same beta diversity facet respond to different environmental (for parasites, including host‐associated) gradients. These patterns were masked when only total beta diversity was analysed.5. This emphasizes the importance of considering the components of insect beta diversity separately. Ignoring the separate components of beta diversity can lead to potentially erroneous inferences about the relative contribution of abiotic and biotic effects on beta diversity.

Among cradles and museums: seasonally dry forest promotes lineage exchanges between rain forest and savanna

ABSTRACTBackground: Cerrado comprises heterogeneous vegetation types. The flora of the vegetation types has distinct biogeographic origins and thus can be hypothesised to have distinct evolutionary imprints.Aims: We hypothesised that the flora of riparian forest was phylogenetically overdispersed, whereas those of more open habitats were phylogenetically clustered.Methods: We built a species-level phylogeny for 1,663 species of trees, shrubs and palms and analysed the pattern of lineage distribution, alpha and beta phylogenetic diversity among Cerrado vegetation types (riparian forest, rocky savana, savana and seasonally dry forest - SDTF).Results: We found a gradient of high phylogenetic diversity and overdispersion from riparian forests towards phylogenetic clustering in vegetation in more open and drier habitats. Habitat shifts were common along the evolutionary history of all families analysed and most families showed a high frequency of shifts from SDTF to riparian forest and savanna.Conclusions: SDTF seems to be a transitional habitat in evolutionary terms, promoting lineage exchanges between stands of riparian forest and savanna. While riparian forest can be seen as a ‘museum’, that harbours ancient lineages, savanna and rocky savanna are a ‘cradle’ of derived lineages. Habitat shifts are an important underlying drive of high present-day Cerrado flora diversity.

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.

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.

Latitudinal gradient of cyanobacterial diversity in tidal flats.

Latitudinal diversity gradients are well-known for plants and animals, but only recently similar patterns have been described for some specific microbial communities in distinct habitats. Although microbial diversity is well-investigated worldwide, most of the studies are spatially too restricted to allow general statements about global diversity patterns. Additionally, methodological differences make it hard and often impossible to compare several studies. This study investigated the cyanobacterial diversity in tidal flats along geographical and ecological gradients based on high-throughput sequencing of 16S rRNA gene fragments (Illumina MiSeq) and environmental data on a large spatial scale from the subtropics to the Arctic. Latitude and strongly correlated environmental parameters (e.g. temperature) were identified as important drivers of cyanobacterial diversity on global scale resulting in a latitudinal diversity gradient similar to that known from plants and animals. Other non-correlated parameters (e.g. grain size) were shown to be more important on local scales, although no consistent pattern occurred across different locations. Among a total number of 989 operational taxonomic units (OTUs) only one cosmopolitan (classified as Coleofasciculus chthonoplastes), but many location-specific and putative endemic ones (78%) were detected. High proportions of rare members of the community (up to 86%) were found in all samples. Phylogenetic beta diversity was shown to be influenced by the developmental stage of the mat community becoming increasingly similar with increasing stabilization.

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.

Erosion of phylogenetic diversity in Neotropical bat assemblages: findings from a whole-ecosystem fragmentation experiment

The traditional focus on taxonomic diversity metrics for investigating species responses to habitat loss and fragmentation has limited our understanding of how biodiversity is impacted by habitat modification. This is particularly true for taxonomic groups such as bats which exhibit species-specific responses. Here, we investigate phylogenetic alpha and beta diversity of Neotropical bat assemblages across two environmental gradients, one in habitat quality and one in habitat amount. We surveyed bats in 39 sites located across a whole-ecosystem fragmentation experiment in the Brazilian Amazon, representing a gradient of habitat quality (interior-edge-matrix, hereafter IEM) in both continuous forest and forest fragments of different sizes (1, 10, and 100 ha; forest size gradient). For each habitat category, we quantified alpha and beta phylogenetic diversity, then used linear mixed-effects models and cluster analysis to explore how forest area and IEM gradient affect phylogenetic diversity. We found that the secondary forest matrix harboured significantly lower total evolutionary history compared to the fragment interiors, especially the matrix near the 1 ha fragments, containing bat assemblages with more closely related species. Forest fragments ≥ 10 ha had levels of phylogenetic richness similar to continuous forest, suggesting that large fragments retain considerable levels of evolutionary history. The edge and matrix adjacent to large fragments tend to have closely related lineages nonetheless, suggesting phylogenetic homogenization in these IEM gradient categories. Thus, despite the high mobility of bats, fragmentation still induces considerable levels of erosion of phylogenetic diversity, suggesting that the full amount of evolutionary history might not be able to persist in present-day human-modified landscapes.

The subgingival microbial community of feline periodontitis and gingivostomatitis: characterization and comparison between diseased and healthy cats

Periodontitis is a common and important health problem in domestic cats. The subgingival microbiota of cats diagnosed with chronic periodontitis (CP), aggressive periodontitis (AP), and feline chronic gingivostomatitis (FCGS) are not well characterized. Thus, the aim of the present study was to characterize and compare the periodontal microbiota of periodontally healthy cats versus cats diagnosed with CP, AP, and FCGS by using next-generation sequencing. In total, 44 domestic cats were enrolled, and 139 subgingival samples were subjected to 16S rRNA gene sequencing to investigate the microbiota composition of each periodontal group evaluated. Our results identified several key genera previously described in periodontal disease (e.g. Treponema and Filifactor) and in the oral microbiota (e.g. Moraxella and Capnocytophaga) of healthy cats. Phylogenetic beta diversity analysis showed that the microbiota of periodontally healthy cats were distinguishable from diseased cats. Even though most of the genera known to be associated with periodontal disease were also identified in healthy cats, they were present at significantly lower relative abundance. Remarkably, alpha diversity was found to be higher in the disease groups compared to healthy animals. These results suggest a pathological mechanism involving opportunistic behavior. Our findings corroborate those in the current literature regarding the complexity of the subgingival microbiota of the domestic cat and reveal both differences and similarities among periodontally healthy and diseased cats.

Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms

Despite important progress, uncertainty persists regarding the ecological forces driving microbial community assembly. Here, we present the first study to use phylogenetic information to interpret the structure and diversity of diatom communities. We examined local phylogenetic divergence and beta- phylogenetic diversity in a large dataset of 595 freshwater benthic diatom communities and we investigated how this diversity is influenced by gradients in nutrients, pH, organic matter and catchment size. Overall, we found that diatom communities were phylogenetically clustered, i.e. species within communities were more closely related than expected by chance. Phylogenetic clustering was stronger in nutrient-poor environments and in sites with a small catchment area. The variation of the phylogenetic beta-diversity index was much better explained by space and environment than the variation of the taxonomic index was. Both approaches detected a significant effect of environment and space on diatom community turnover. Our results support the view that diatom communities are primarily shaped by environmental filtering, in particular by nutrient availability. Moreover, they highlight the importance of considering dispersal-related processes and the depth of phylogenetic signal in functional traits when interpreting patterns of diversity.

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.

Spatial variation in phylogenetic diversity of communities of Atlantic Forest harvestmen (Opiliones, Arachnida)

Abstract The study of diversity has become increasingly sophisticated, including the use of measures of phylogenetic diversity. We calculate the spatial variation in species richness, taxonomic beta diversity, and alpha and beta phylogenetic diversity (PDα and PDβ, respectively) of Atlantic Forest harvestman communities using a data set containing 556 species from 68 sites, distributed in 12 Brazilian states. We compare the congruence of phylogenetic and taxonomic diversity patterns, and also compare PDα with null model expectations, to check for phylogenetic clustering or overdispersion in communities. Species richness and PDα are correlated, peaking in southern and south‐eastern coastal sites and decreasing towards the interior and towards the north‐east. PDα in north‐eastern sites was higher than expected, while a clustered phylogenetic pattern characterised most other sites. Communities in the southern and south‐eastern regions were dominated by species from the large family Gonyleptidae, presenting a high richness and a low PDα. As the dominance of Gonyleptidae decreased towards the north, where local communities have fewer species, but a higher PDα, they contain representatives of other families. The beta diversity was more sensitive to the compositional changes involving closely related Gonyleptidae species, while PDβ is more influenced by deeper phylogenetic compositional changes, between more distant lineages. Phylogenetic diversity may be of special importance to assess the conservation value of distantly related lineages. These species‐poor groups are less likely to influence taxonomic‐based diversity analyses, but their importance for conservation arises from their phylogenetic distinctiveness, captured by PDα and PDβ measures.

Relative roles of the replacement and richness difference components of beta diversity following the ecological restoration of a mountain meadow, north China

Replacement and richness difference are two main components in generating beta diversity patterns. This study we explored the effects of ecological restoration on the relative roles of replacement (βrepl) and richness difference (βrich) components in terms of taxon (Tβtotal), phylogenetic (Pβtotal), and functional (Fβtotal) beta diversity in the Lishan mountain meadow, north China. The results reflected the relatively high values of beta diversity in the severely disturbed areas. Following restoration, the compositions of disturbed areas were closer to that of non-disturbed areas than that pre-restoration. In addition, we found the changes in Tβtotal were similar to those of Pβtotal and Fβtotal. However, when βtotal was partitioned into βrepl and βrich components, the processes generating the beta diversity patterns appeared to be different in the different disturbance areas. The patterns of taxon and phylogenetic beta diversity resulted equally from the replacement and richness difference components, whereas the functional richness difference was higher than the functional replacement for functional beta diversity in the severely disturbed subarea. When the community was subjected to slight anthropogenic activity, only the replacement component had an important role in generating beta diversity patterns. With an increase in anthropogenic activity, both replacement and richness difference components played the important role. The relative roles of replacement and richness difference highlighted the anthropogenic effects on the community composition pre- and post-restoration. Disintegrating the relative roles of these two components was beneficial to understand the status of vegetation restoration and for taking appropriate measures in the different stages of restoration.

Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits

This study aimed to evaluate how the feeding strategy of rabbit kits at the onset of solid feed intake could affect ecological diversity and co-occurrence patterns of the cecal bacterial community. From birth to 18 days of age kits were exclusively milk-fed, and between 18 and 35 days the young rabbits also had access to solid feed. After weaning at (35 days), young rabbits were exclusively fed solid feed. Three experimental feeds were used: a high concentrate diet [H: 10.16 MJ digestible energy (DE)/kg and 15.3% crude protein (CP)], a low concentrate diet (L: 9.33 MJ DE/kg and 14.7% CP) and a reproductive female diet (R: 10.57 MJ DE/kg and 17.3% CP). The rabbit kits (n = 357) were divided into three groups, differing by the diet received during two periods: from 18 to 28 and from 28 to 49 days of age. In the groups LL and HH, rabbit kits were fed L or H diets, respectively, during both periods. Kits in the group RL received feeds R and L from 18 to 28 and 28 to 49 days of age, respectively. Cecal bacterial communities of 10 rabbits per group were carried out at 18, 28, 35, 43 and 49 days of age by MiSeq Illumina sequencing 16S rRNA encoding genes. Between 18 and 28 days of age, solid feed intake was higher in the group RL compared to the other two groups (+24%; P < 0.01). Overall, 13.4% of the OTUs detected were present in the cecal ecosystem from 18 to 49 days old, whereas 17.4% were acquired with the onset of solid feeding and kept from 28 days on. Exclusive milk consumption constrains the bacterial community toward a similar structure but high phylogenetic beta-diversity. Introduction of solid feed induced a sharp change of microbial community structure and decreased phylogenetic diversity. A strong relationship in bacterial community network occurred only from 43 days on. Our feeding strategy at the onset of solid feed ingestion exhibited only a moderate effect on the microbial community structure (P = 0.072), although the LL group seemed to reach faster maturity compared to the two other groups.

Adjacency and Area Explain Species Bioregional Shifts in Neotropical Palms.

Environmental and geographical variables are known drivers of community assembly, however their influence on phylogenetic structure and phylogenetic beta diversity of lineages within different bioregions is not well-understood. Using Neotropical palms as a model, we investigate how environmental and geographical variables affect the assembly of lineages into bioregions across an evolutionary time scale. We also determine lineage shifts between tropical (TRF) and non-tropical (non-TRF) forests. Our results identify that distance and area explain phylogenetic dissimilarity among bioregions. Lineages in smaller bioregions are a subset of larger bioregions and contribute significantly to the nestedness component of phylogenetic dissimilarity, here interpreted as evidence for a bioregional shift. We found a significant tendency of habitat shifts occurring preferentially between TRF and non-TRF bioregions (31 shifts) than from non-TRF to TRF (24) or from TRF to TRF (11) and non-TRF to non-TRF (9). Our results also present cases where low dissimilarity is found between TRF and non-TRF bioregions. Most bioregions showed phylogenetic clustering and larger bioregions tended to be more clustered than smaller ones, with a higher species turnover component of phylogenetic dissimilarity. However, phylogenetic structure did not differ between TRF and non-TRF bioregions and diversification rates were higher in only two lineages, Attaleinae and Bactridinae, which are widespread and overabundant in both TRF and non-TRF bioregions. Area and distance significantly affected Neotropical palm community assembly and contributed more than environmental variables. Despite palms being emblematic humid forest elements, we found multiple shifts from humid to dry bioregions, showing that palms are also important components of these environments.

Local rise of phylogenetic diversity due to invasions and extirpations leads to a regional phylogenetic homogenization of fish fauna from Chinese isolated plateau lakes

Human-mediated introductions of exotic species and extirpations of native species have modified the composition of biotic communities throughout the world, but the consequences of introductions and extirpations on local phylogenetic diversity (alpha-diversity) and on phylogenetic distinctiveness between sites (beta-diversity) remains poorly investigated. Here we analyze the long-term impacts of extirpations and invasions on both phylogenetic and taxonomic alpha and beta diversity of fish assemblages in Chinese isolated lakes. Data of fish assemblages in 15 lakes were grouped into three periods spanning the last 75 years: historical, intermediate and current periods. We partitioned phylogenetic beta diversity into turnover and nestedness component, and examined how introductions and extirpations led to temporal changes in alpha and beta diversity using linear regression and multiple regression models on distance matrices, respectively. Introductions and extirpations caused an increase of phylogenetic diversity (Δ+) and phylogenetic unevenness (Λ+) within the lakes, but the phylogenetic dissimilarity between lakes declined. Such trend, resulting from 60 years introductions and extirpations, was mainly due to a decline of the phylogenetic turnover, indicating that the replacement of native endemic species by widespread exotic species was the main driver of the observed phylogenetic homogenization. Temporal changes in phylogenetic and taxonomic dissimilarities were positively correlated, and taxonomic homogenization causes phylogenetic homogenization in ca. 60% of the lake pairs. Nevertheless, taxonomic homogenization turns to phylogenetic differentiation in one third of lake pairs due to the extirpation of the closely-related species and the introduction of distinct exotic species belonging to different lineages among lakes. Therefore, measuring phylogenetic diversity changes provides complementary information to taxonomy, and gives support to the Darwin’s naturalization hypothesis stipulating that species distantly related to natives easily establish in their introduction range. Our results demonstrate that half a century of anthropogenic disturbance was sufficient to blur the phylogenetic distinctiveness among lakes that resulted from the last 5 million years evolutionary history of the Yun-Gui plateau.

A comparison of phylogenetic and species beta diversity measures describing vegetation assemblages along an elevation gradient

AbstractQuestionEcologists have long been interested in the delineation and description of plant communities but have only recently included phylogenetic data into these analyses. Here, we assess whether species‐based dissimilarities (beta diversity, BD) and more recent phylogenetic beta diversity (PhBD) measures are correlated with dissimilarities among sites based on abiotic variables. Additionally, we examine whether BD and PhBD measures aggregate sites into clusters that reflect their environmental attributes. Assuming phylogenetic conservatism in abiotic niche preferences, we predict PhBD dissimilarity matrices will correlate to those based on abiotic site variables, and that clusters determined by PhBD will more closely match to assemblages clustered by abiotic environment than will clusters determined by species BD.LocationMount Irony, Labrador in the Eastern Canadian subarctic.MethodsWe combine vascular plant co‐occurrence data collected from an elevation gradient on Mount Irony with information on phylogenetic relatedness to compare site dissimilarities based on abiotic variables with those estimated on measures of BD and PhBD. We also examine whether clusters based on BD and PhBD resemble clusters based on abiotic variables, and investigate whether similarly clustered sites are composed of species with similar evolutionary histories.ResultsWe found significant correlations among the dissimilarity matrices and ordinations for the abiotic variables, BD and PhBD; however, neither BD nor PhBD aggregated assemblages into clusters that reflected their environmental differences. Further, we found no evidence that species within clusters were any more closely related than expected by chance. We observed similar patterns when communities were defined by all vascular plants and only angiosperms.ConclusionsThe correlations among site dissimilarities based on abiotic variables, BD and PhBD suggest environmental filtering; however, sites clustered by BD and PhBD did not resemble those clustered by abiotic variables, indicating that the added value of phylogenetic data for local scale analyses might be limited.

Historical biogeography of fishes from coastal basins of Maranhão State, northeastern Brazil

ABSTRACT The Amazonian ichthyofauna is one of the most diverse in the world, yet fishes from the adjacent coastal basins of Maranhão State in Northeastern Brazil remain poorly known. We use phylogeographic, community phylogenetic and phylogenetic beta diversity methods to study the biogeographic history of fishes from the coastal basins of Maranhão State. We report a total of 160 fish species from the basins of the Maranhão region, representing a 93% increase over results of previous studies. All the fish species assemblages from Maranhão are polyphyletic, with only a few putative sister species pairs inhabiting the region. The modern watershed divides among Maranhão basins do not form substantial barriers to dispersal for freshwater fish species, and are more effectively modelled as biogeographic islands than as biogeographic provinces. In combination these results suggest that the Maranhão ichthyofauna was assembled under the influence of several macroevolutionary (extinction, dispersal) and landscape evolution processes, during the Miocene and Pliocene, as well as by the modern ecological characteristics of the region. The results indicate that the distinctive geological and climatic conditions and history of Northeastern Brazil strongly constrained the formation of aquatic faunas in coastal basins of Maranhão State.