Phylogenetic Homogenization Research Articles

Impacts of the attributes of patches and the surrounding matrix on the phylogenetic diversity of tree species in urban remnant forests

AbstractUrbanization is a major cause of biotic homogenization and evolutionary poverty. Urban remnant forests are biodiversity hotspots in cities but are prone to phylogenetic homogenization. However, how urbanization‐driven changes in patch attributes and landscape heterogeneity levels of the surrounding matrix affect plant phylogenetic diversity in urban remnant forests remains unclear. We quantified tree phylogenetic diversity and structure in 30 remnant forest patches in Guiyang, China, using chloroplast genome data and analyzed the effects of patch attributes and the surrounding matrix on tree phylogenetic diversity and structure in the forests while considering tree species stage. The phylogenetic diversity of saplings/seedlings was lower than that of adult trees. Small patches contributed more than large patches to the overall phylogenetic diversity of remnant forest ecosystems. Additionally, tree phylogenetic diversity was positively associated with configurational heterogeneity of the surrounding matrix, while phylogenetic diversity and relatedness were negatively related to the percentage of surrounding impervious surfaces and patch size. Accordingly, we suggest maintaining configurational heterogeneity and controlling the speed of urban expansion in the surrounding matrix to better conserve urban remnant forests. Furthermore, the preservation of small forest remnants and tree species in the sapling/seedling stage should be prioritized.

Centromere plasticity with evolutionary conservation and divergence uncovered by wheat 10+ genomes.

Centromeres are the chromosomal regions that play a crucial role in maintaining genomic stability. The underling highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of centromeres in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat centromeres. We found that the most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core centromeres. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned centromeres. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize centromeres. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.

Anthropogenic activities and environmental filtering have reshaped freshwater fish biodiversity patterns in China over the past 120 years

Over the past centuries, freshwater fish introductions and extinctions have been the major environmental and ecological crises in various water bodies in China. However, consequences of such crises on freshwater fish biodiversity in China remain only partially or locally studied. Furthermore, identifications of relatively sensitive areas along with stressors (i.e., environmental and anthropogenic drivers) influencing freshwater fish biodiversity patterns are still pending. Taxonomic, functional, and phylogenetic facets of biodiversity can well describe and evaluate the underlying processes affecting freshwater fish biodiversity patterns under different dimensionalities. Here we thus evaluated temporal changes in these facets of freshwater fish biodiversity as well as a new developed biodiversity index, multifaceted changes in fish biodiversity, for over a century at the basin level throughout China using both alpha and beta diversity approaches. We also identified the drivers influencing the changes in fish biodiversity patterns using random forest models. The results showed that fish assemblages in Northwest and Southwest China (e.g., Ili River basin, Tarim basin, and Erhai Lake basin) experienced extreme temporal and multifaceted changes in the facets of biodiversity compared with other regions, and environmental factors (e.g., net primary productivity, average annual precipitation, and unit area) largely drove these changes. Since fish faunas in over 80% of China's water bodies covering more than 80% of China's surface were currently undergoing taxonomic, functional, and phylogenetic homogenization, targeted conservation and management strategies should be proposed and implemented, especially for the areas with relatively high changes in biodiversity.

Aridity and chronic anthropogenic disturbances cause a taxonomic, functional, and phylogenetic homogenization of ant communities in a Caatinga dry forest

Chronic anthropogenic disturbances (chronic disturbances) and climate change can eliminate sensitive species and support the proliferation of disturbance-adapted ones leading native communities to biotic homogenization. We investigate the individual and interactive effects of increasing chronic disturbances and aridity on the biotic homogenization of ant communities in a Caatinga dry forest in northeast Brazil. Ant communities were recorded across 20 forest stands covering gradients of annual rainfall and chronic disturbances (wood extraction, people pressure, and grazing pressure) intensity. Ant communities were described by adopting taxonomic, functional, and phylogenetic attributes. We collected 71 species (24 genera and 7 subfamilies). Aridity-driven reductions in beta diversity were stronger (about 73 %) than chronic disturbance-driven reductions (27 %) for all (but phylogenetic) biodiversity dimensions. Chronic disturbance-driven reduction in beta diversity was more evident via wood extraction than via people and grazing pressure. Intriguing interactive effects of chronic disturbance and aridity were observed for all biodiversity dimensions. Increased chronic disturbances led to slight increases in beta diversity in drier forest stands, probably due to spatial heterogeneity in aridity and chronic disturbance sources distribution. Results suggest that (1) aridity and chronic disturbance represent key drivers of community organization at the landscape scale, (2) chronic disturbance and aridity pose isolated and interactive effects, but aridity plays a major role, and (3) both community-level homogenization or divergence can emerge but in the extreme conditions ant communities converge taxonomically, functionally, and phylogenetically.

Beyond species loss: How anthropogenic disturbances drive functional and phylogenetic homogenization of Neotropical dung beetles

Anthropogenic activities drive tropical forest loss and biodiversity decay. However, few studies have addressed how the biodiversity response varies between disturbance-adapted species (i.e., winners) and those highly susceptible to disturbance (i.e., losers), or whether such responses differ between the taxonomic, functional, or phylogenetic dimensions of diversity. Understanding these dynamics can help prevent or buffer biotic homogenization processes. Using a meta-analytical approach with dung beetles as model organisms, we evaluated how anthropogenic habitat disturbances influence the multiple diversity dimensions of winner and loser species relative to conserved forest sites in the Neotropics. Habitats were organized according to a disturbance gradient ranging from second-growth forests, shaded agroforestry, lowly-shaded agroforestry, living fences, and pastures. Our database included 30 studies, from which we calculated nine metrics divided into three alfa diversity aspects: richness, evenness, and divergence. We also evaluated the beta-diversity response to disturbance and forest protection. All dimensions of dung beetle diversity decreased significantly with increasing disturbance levels, with phylogenetic diversity showing the highest losses, whereas evenness metrics increased in second-growth forests and agroforestry systems. Loser dung beetles showed high diversity loss as well as functional and phylogenetic clustering, reflecting a pervasive biotic homogenization in the most severely disturbed habitats, whereas winner species were insensitive to anthropogenic disturbances. Beta diversity increased significantly with disturbance and forest protection. Our study showed that heavy disturbances erode and homogenized all diversity dimensions of loser dung beetles. However, second-growth forests and agroforestry systems mitigated diversity loss and homogenization processes by favoring the coexistence between functional and phylogenetically distant species and maintaining assemblages compositionally similar to those in conserved forests, highlighting their importance for conservation. We encourage natural resource managers to consider protection of disturbed off-reserve forests in management schemes as these are essential for maintaining biodiversity in an increasingly anthropized world.

Assessing the effect of roads on mountain plant diversity beyond species richness.

A comprehensive understanding of the effects of mountain roads on plant diversity is critical to finding the most effective solutions for managing this particular driver. Little is known, however, about the simultaneous effects that road have on the multiple facets of biodiversity, although roads are considered to be one of the major disturbances in the Qionglai mountain range. In this study, we analyzed the impact of roads on the multiple facets of plant diversity (taxonomic, functional and phylogenetic diversity) in the study area using Hill numbers by comparing plant diversity between roadside and interior plots at the landscape scale, then, we used linear mixed models to analyze the effect of mountain roads on the multiple facets of plant diversity along an elevational gradient. The results showed that the roadside plots lacked 29.45% of the total number of species with particular functional traits (such as a relatively high specific leaf area (SLA), a relatively low leaf dry matter content (LDMC) and relatively old clades) and exclusively contained 14.62% of the total number of species. Compared with the interior community, the taxonomic, functional and phylogenetic diversity of roadside community decreased by no more than 26.78%, 24.90% and 16.62%, respectively. Taxonomic and functional diversity of dominant and common species showed greater changes to road disturbances, while rare species showed the greatest change in phylogenetic diversity. Taxonomic homogenization of roadside communities was accompanied by functional and phylogenetic homogenization. Additionally, the impact of roads on these three facets of plant diversity showed the characteristics of peak clipping along the elevation gradient. Our findings highlight the negative impact of roads on the taxonomic, functional and phylogenetic diversity of the Qionglai mountain range, as roads promote communities that are more similar in taxonomic, functional, and phylogenetic composition, and to a greater extent contributed to compositional evenness. These effects tend to be functionally and phylogenetically non-random, and species in some clades or with some functional traits are at higher risk of loss. Our results are important for the conservation and management of nature reserves, especially for local governments aiming to create new infrastructure to connect natural mountainous areas.

The homogenization of avian morphological and phylogenetic diversity under the global extinction crisis

Biodiversity is facing a global extinction crisis that will reduce ecological trait diversity, evolutionary history, and ultimately ecosystem functioning and services.1-4 A key challenge is understanding how species losses will impact morphological and phylogenetic diversity at global scales.5,6 Here, we test whether the loss of species threatened with extinction according to the International Union for Conservation of Nature (IUCN) leads to morphological and phylogenetic homogenization7,8 across both the whole avian class and within each biome and ecoregion globally. We use a comprehensive set of continuous morphological traits extracted from museum collections of 8,455 bird species, including geometric morphometric beak shape data,9 and sequentially remove species from those at most to least threat of extinction. We find evidence of morphological, but not phylogenetic, homogenization across the avian class, with species becoming more alike in terms of their morphology. We find that most biome and ecoregions are expected to lose morphological diversity at a greater rate than predicted by species loss alone, with the most imperiled regions found in East Asia and the Himalayan uplands and foothills. Only a small proportion of assemblages are threatened with phylogenetic homogenization, in particular parts of Indochina. Species extinctions will lead to a major loss of avian ecological strategies, but not a comparable loss of phylogenetic diversity. As the decline of species with unique traits and their replacement with more widespread generalist species continues, the protection of assemblages at most risk of morphological and phylogenetic homogenization should be a key conservation priority.

Traits and phylogenies modulate the environmental responses of wood‐inhabiting fungal communities across spatial scales

Abstract Identifying the spatial scales at which community assembly processes operate is fundamental for gaining a mechanistic understanding of the drivers shaping ecological communities. In this study, we examined whether and how traits and phylogenetic relationships structure fungal community assembly across spatial scales. We applied joint species distribution modelling to a European‐scale dataset on 215 wood‐inhabiting fungal species, which includes data on traits, phylogeny and environmental variables measured at the local (log‐level) and regional (site‐level) scales. At the local scale, wood‐inhabiting fungal communities were mostly structured by deadwood decay stage, and the trait and phylogenetic patterns along this environmental gradient suggested the lack of diversifying selection. At regional scales, fungal communities and their trait distributions were influenced by climatic and connectivity‐related variables. The fungal climatic niches were not phylogenetically structured, suggesting that diversifying selection or stabilizing selection for climatic niches has played a strong role in wood‐inhabiting communities. In contrast, we found a strong phylogenetic signal in the responses to connectivity‐related variables, revealing phylogenetic homogenization in small and isolated forests. Synthesis. Altogether, our results show that species‐level traits and phylogenies modulate the responses of wood‐inhabiting fungi to environmental processes acting at different scales. This result suggests that the evolutionary histories of fungal traits diverge along different environmental axes.

Phylogenetic homogenization of Amazonian tree assemblages in forest islands after 26 years of isolation

AbstractQuestionLosses in species richness and functional diversity of tree assemblages have often been observed in Neotropical fragmented landscapes, but the way in which tree phylogenetic diversity responds to forest insularization over decadal timescales remains unclear. Here, we examine how tree phylogenetic diversity and structure have responded to profound landscape alteration and subsequent non‐random species losses within forest islands created within a vast hydroelectric reservoir.LocationBalbina Hydroelectric Dam Reservoir, Central Brazilian Amazonia.MethodsWe used a large tree data set including 435 subplots of 0.05 ha each in 34 forest islands of variable sizes and three continuous forest sites in the Balbina Hydroelectric Dam, which contained 11,000 stems representing 365 species and 188 genera. In each subplot we quantified tree phylogenetic diversity and structure and investigated their relationship with landscape structure metrics and the proportion of species within specific functional groups.ResultsWe uncovered a reduction in phylogenetic diversity in small (<10 ha) isolated islands, particularly in more fire‐prone areas near forest edges and surrounded by low amounts of forest cover. Additionally, assemblage‐wide phylogenetic decay was a result of non‐random species losses, given that tree assemblages dominated by small‐seeded, soft‐wooded pioneer species exhibited lower values of phylogenetic diversity and structure. We also uncovered a phylogenetic signal in traits associated with disturbance‐adapted species within this major man‐made forest archipelago.ConclusionWe uncovered pronounced phylogenetic diversity decay that was mostly driven by the proliferation of disturbance‐adapted species, such as small‐seeded pioneer species exhibiting fast life histories. Our results undermine more optimistic views based on studies in fragmented landscapes dominated by terrestrial matrix habitats, and indicate that true land‐bridge forest islands experience more detrimental effects on different components of tree diversity. Our study contributes to elucidate a growing underestimation of the pervasive threats posed by mega‐dams to tropical forest biodiversity and ecosystem functioning.

Multidimensional diversity of bird communities across spatial variation of land cover in Zoige on the eastern Qinghai-Tibetan Plateau

BackgroundSpatial variation of land cover can result in the changes of community similarities and biotic homogenization, whereby the increasing similarity would reduce the adaptive capacity of biotic assemblages to further disturbance, and degenerate ecosystem services they offer. However, it remains scarce to integrate multidimensional diversity for unveiling how variations in land cover may influence the patterns and processes of biotic homogenization in the Anthropocene. In this study, we examined how spatial variation of land cover could alter taxonomic, phylogenetic and functional homogenization of bird communities simultaneously in a compound ecosystem of Zoige Marsh on the eastern Qinghai-Tibetan Plateau. Acting as the largest alpine marsh and peatland in the world, Zoige Marsh has undergone great changes in the land cover pattern due to climate change and anthropogenic activities.MethodsWe conducted transect surveys for bird communities over six years (2014‒2019) during breeding seasons in four main land cover types (meadow, woodland, village and marsh), representing the spatial variation of land covers in the study area. We compared multidimensional diversity (taxonomic, phylogenetic and functional diversity) among land covers to assess the effects of spatial variation in land cover type on bird communities, particularly whether this variation has homogenized biotic communities.ResultsBird communities during breeding seasons were different and complementary in the four land covers. Taxonomic, phylogenetic and functional similarities were significantly lower in meadow than in the other three types, i.e. woodland, village and marsh. However, when we controlled for the effects of taxonomic similarities, the pattern of phylogenetic similarities almost reversed, with the highest standardized effect size (SES) phylogenetic similarity in meadow; and we found no significant difference in SES functional similarity among land covers.ConclusionsOur results suggest that spatial variation of land cover can play a crucial role in regulating multiple dimensions of bird diversity in Zoige Marsh. The findings indicate that taxonomic, phylogenetic and functional homogenization of bird communities may differently response to the variation of land covers. It thus highlights not only the relative roles of different land covers in maintaining biodiversity and community structures of birds, but also the urgency of retarding ecosystem degradations on the eastern Qinghai-Tibetan Plateau.

Something is not quite right: Effects of two land uses on anuran diversity in subtropical grasslands

AbstractAlthough habitat modification is considered one of the main causes of biodiversity loss, the relative contribution of different rural land uses to biodiversity conservation is far less known. Additionally, the realization of the multidimensionality of biodiversity demands studies integrating variation of functional traits and phylogenetic information as complements to address the effects of land use on the structure of animal communities. Herein, we investigated the effects of land use (i.e., intensive agricultural and extensive livestock rearing) on functional and phylogenetic diversity of anuran communities in farmland ponds from the Uruguayan savanna ecoregion, while considering the effects of local factors (i.e., water depth) on species composition. We surveyed adults and tadpoles in 22 ponds and quantified five traits related to tadpole feeding, habitat use, and predator avoidance. Tadpole identification was corroborated by DNA barcoding based on a fragment of the mitochondrial 16S rRNA gene. We observed a decline in phylogenetic mean nearest taxon distance associated with increase of surrounding agricultural land use. While land use intensification did not affect richness (functional or phylogenetic), ponds in livestock ranches hosted about four times more tadpoles than agricultural ponds. Functional evenness decreased with water depth, although such relationship disappeared when considering phylogenetic non‐independence. Our results indicated that specific anuran clades were more sensitive to intensification in land use, reinforcing a recent view of phylogenetic homogenization following habitat conversion. Additionally, our study suggests that extensive cattle grazing over wide native pastures may provide an alternative more compatible with conservation than short‐term crops in subtropical grasslands.Abstract in Portuguese is available with online material.

Long-term droughts may drive drier tropical forests towards increased functional, taxonomic and phylogenetic homogeneity

Tropical ecosystems adapted to high water availability may be highly impacted by climatic changes that increase soil and atmospheric moisture deficits. Many tropical regions are experiencing significant changes in climatic conditions, which may induce strong shifts in taxonomic, functional and phylogenetic diversity of forest communities. However, it remains unclear if and to what extent tropical forests are shifting in these facets of diversity along climatic gradients in response to climate change. Here, we show that changes in climate affected all three facets of diversity in West Africa in recent decades. Taxonomic and functional diversity increased in wetter forests but tended to decrease in forests with drier climate. Phylogenetic diversity showed a large decrease along a wet-dry climatic gradient. Notably, we find that all three facets of diversity tended to be higher in wetter forests. Drier forests showed functional, taxonomic and phylogenetic homogenization. Understanding how different facets of diversity respond to a changing environment across climatic gradients is essential for effective long-term conservation of tropical forest ecosystems.

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.

Contribution of non‐native plants to the phylogenetic homogenization of U.S. yard floras

AbstractCultivation and spread of non‐native plant species may result in either phylogenetic homogenization (increasing similarity) or differentiation (decreasing similarity) of urban floras. However, it is unknown how non‐native species influence homogenization of cultivated versus spontaneously occurring species in cities, and which traits are associated with species that promote homogenization versus differentiation. In this study, we compared homogenization effects of cultivated and spontaneous non‐native species in yard floras across and within seven widely distributed U.S. cities. Additionally, we explored which traits explained their particular contribution to homogenization. We recorded plant presence/absence in 178 private yards distributed among seven metropolitan statistical areas in the United States. We compared phylogenetic homogenization effects of non‐native species within both the cultivated and spontaneous species pools using phylogenetic dissimilarities and the homogenization index. Then, we expressed contributions of non‐native species to the homogenization of each pool as a function of two different sets of plant functional traits using phylogenetic generalized least square (PGLS) models across and within cities. Across cities, spontaneous non‐native species homogenized, and cultivated non‐native species differentiated, yard floras. Within the spontaneous pool, short, small‐seeded non‐native plants and non‐native grasses significantly homogenized yard floras. Within the cultivated pool, species contribution to homogenization was best predicted by plant height, presence of showy flowers, and growth form, with non‐native grasses significantly homogenizing cultivated yard floras. Within cities, non‐native species—whether they were cultivated or spontaneous—consistently homogenized yard floras of the three northern cities and differentiated yard floras of three of the four southern cities, suggesting that homogenization processes are context‐ and scale‐dependent. Likewise, traits explaining homogenization differed substantially among cities. The inconsistent patterns among cities in the plant traits that promoted homogenization of both cultivated and spontaneous species suggest that local environmental and anthropogenic conditions of individual cities imposed strong constraints on trait selection. Linking plant functional traits that promote homogenization with residents’ preferences for vegetation may further enhance understanding of how yard plant communities assemble at regional and local scales.

Do drivers of forestry vehicles also drive herb layer changes (1970–2015) in a temperate forest with contrasting habitat and management conditions?

Abstract Managing ecosystems effectively for the maintenance of biodiversity and ecosystem functions and services requires to understand how these ecosystems are changing and what are the drivers behind these changes. The resurvey of plant communities sampled some decades ago is increasingly used for this purpose. We used a life‐history trait‐based approach to test a number of hypothesized drivers behind decadal changes (1970–2015) in the herb layer of an ancient broadleaved lowland forest exhibiting contrasted soil and management types, while minimizing potential relocation and observer errors. Process‐based hypotheses were tested using paired comparisons (old vs. new records) of community‐weighted means and conditional inference classification trees for a number of traits across soil and management types. We then investigated how these processes impacted species composition and diversity within stands, among stands and at the entire forest scale, using metrics of taxonomic, functional and phylogenetic diversity. Though they have been continuously managed as regular high forest, managed stands experienced more pronounced vegetation changes than those left unmanaged. This could be directly or indirectly related to modifications in forest harvesting practices since 1970, via light availability at the forest floor, soil disturbance and local N deposition. While forest specialists increased their abundance over the entire forest, managed stands showed the strongest compositional changes, especially on the soil types that were more susceptible to compaction. Increasingly heavy forestry vehicles that drive more frequently across forest stands likely generate microhabitats suitable for ferns, graminoids and N‐demanding forbs and also act as dispersal agents. Species richness of vascular plants increased at both stand (α‐diversity) and forest (γ‐diversity) scales, due to the non‐random, directional colonization by the same suite of species, causing compositional, functional and phylogenetic homogenization among habitats (i.e. decreased β‐diversity). Synthesis. Forest management, via the repeated passing of heavy forestry vehicles, emerged as the key driver of local vegetation changes. By altering canopy structure, it also increased the vulnerability of understories to climate warming and atmospheric deposits. Changes were not only taxonomic, but also functional, suggesting long‐term effects on ecosystem functioning and thus deserve attention from forest managers and conservationists.

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.

Goat grazing reduces diversity and leads to functional, taxonomic, and phylogenetic homogenization in an arid shrubland

AbstractLivestock production is an important activity in drylands. However, lack of adequate regulation of ranching activities can lead to the degradation of plant communities, which in turn can impact ecosystem functioning. In the arid ecosystems of north‐central Chile, unregulated goat grazing is widespread. Because the vegetation has a relatively short evolutionary history of grazing, it is expected to be highly susceptible to this activity. In this study, we evaluated the effects of goat grazing on plant taxonomic, functional, and phylogenetic community structure by comparing 39‐year‐old grazing exclusion plots and unprotected plots in an arid shrubland in north‐central Chile. By integrating analyses of the impact of goat grazing on functional and phylogenetic diversity and dispersion, we studied the mechanisms behind goat impact and the potential consequences. Loss of functional and/or phylogenetic diversity can result in important losses in ecosystem function. As a measure of functional diversity, we recorded plant growth form, life span, and life form. We also reconstructed a phylogeny of all plant species found at the study site and determined the phylogenetic structure of the plant community in ungrazed and grazed areas. We found that goat grazing affected diversity and community composition, leading to taxonomic, functional, and phylogenetic biotic homogenization and causing overall community impoverishment. Goats acted as a habitat filter, increasing functional convergence and promoting the establishment of exotics plants, which can lead to further losses of biodiversity, decreased ecosystem function and overall lower ecosystem stability. Our results indicate that sustainable management strategies are necessary to prevent the further degradation of these ecosystems.

Phylogenetic homogenization of bee communities across ecoregions

AbstractAimLand use change reorganizes local communities, resulting in complex changes in biodiversity at larger scales. The biotic homogenization hypothesis predicts that the replacement of sensitive loser species with widespread winner species will lead to loss of beta diversity and ultimately loss of regional diversity at multiple levels of ecological organization. We ask if land use is associated with biotic homogenization patterns in bee communities at two large spatial scales, using both species and phylogenetic dissimilarity indices.LocationNorth‐eastern USA (New Jersey, New York and Pennsylvania).Time period2013–2015.Major taxa studiedSuperfamily Apoidea (bees).MethodsWe sampled bee communities from replicated sites in forest, agriculture and urban land use types within a large spatial extent spanning four distinct ecoregions. We compared pairwise compositional dissimilarity within and between ecoregions, using both species and phylogenetic dissimilarity indices. We also investigated how compositional difference is related to geographic distance between sites.ResultsForested, agricultural and urban landscapes did not differ detectably in either mean pairwise species dissimilarity or slope of distance‐decay. Dissimilarity among both agricultural and urban bee communities increased with geographic distance. However, urban landscapes had significantly lower phylogenetic pairwise dissimilarity, indicating strong phylogenetic homogenization at within‐ and between‐ecoregion scales.Main conclusionsWe did not detect bee species homogenization in agricultural or urban land use types. However, urban land use was associated with phylogenetic homogenization across a large regional extent. Urban bee communities are dominated by closely related species that maintain beta diversity at the species level, but contribute to low phylogenetic beta diversity relative to forest and agricultural bee communities. We observed similar levels of homogenization at landscape and regional spatial extents, despite inter‐site distances differing by an order of magnitude between these scales. Further urbanization could result in loss of bee biodiversity and evolutionary history at multiple spatial scales.

Phylogenetic homogenization of amphibian assemblages in human-altered habitats across the globe

Habitat conversion is driving biodiversity loss and restructuring species assemblages across the globe. Responses to habitat conversion vary widely, however, and little is known about the degree to which shared evolutionary history underlies changes in species richness and composition. We analyzed data from 48 studies, comprising 438 species on five continents, to understand how taxonomic and phylogenetic diversity of amphibian assemblages shifts in response to habitat conversion. We found that evolutionary history explains the majority of variation in species' responses to habitat conversion, with specific clades scattered across the amphibian tree of life being favored by human land uses. Habitat conversion led to an average loss of 139 million years of amphibian evolutionary history within assemblages, high species and lineage turnover at landscape scales, and phylogenetic homogenization at the global scale (despite minimal taxonomic homogenization). Lineage turnover across habitats was greatest in lowland tropical regions where large species pools and stable climates have perhaps given rise to many microclimatically specialized species. Together, our results indicate that strong phylogenetic clustering of species' responses to habitat conversion mediates nonrandom structuring of local assemblages and loss of global phylogenetic diversity. In an age of rapid global change, identifying clades that are most sensitive to habitat conversion will help prioritize use of limited conservation resources.

Human legacies differentially organize functional and phylogenetic diversity of urban herbaceous plant communities at multiple spatial scales

AbstractQuestionsPatterns of functional and phylogenetic homogenization of plant diversity at the scale of entire cities are well established. However, fewer studies have investigated how shifts in the composition of urban species pools may alter spatial variation in community assembly across patches within a city. We compared plant diversity both within and between vacant lots in a single urban neighborhood and asked: (1) how do heterogeneous human legacies of land use within vacant lots structure plant community diversity and composition and (2) what is the importance of human legacies for structuring community composition, relative to spatial and environmental variation?LocationUrban residential neighbourhood in Baltimore, MD, US (39°17′ N, 76°38′ W).MethodsWe surveyed herbaceous plant species identity and abundance in 24 unmanaged vacant lots. We constructed functional and phylogenetic diversity metrics from databases and the literature and compared taxonomic, functional and phylogenetic diversity between sections of the lot where a residential building was once located (building footprint), and the area that was originally the garden or backyard (remnant garden). We term these different ‘human legacy’ groups. We partitioned variation in plant community composition between human legacy groups as well as across measured environmental and spatial gradients.ResultsWe report significant plant community compositional divergence between human legacy groups. Beta‐diversity, in particular, was significantly higher in remnant garden sections compared to building footprint sections for all metrics of biodiversity. Plant community compositional variation was primarily explained by differences in human legacies. We found no measurable effects of selected metrics of local environmental variation (abiotic soil characteristics) or environmental context (lot area, proximity to other vacant lots and tree canopy) on compositional variation. Geographic distance between sites, however, did interact with human legacy variation to structure phylogenetic composition.ConclusionsOur findings suggest that human land‐use legacies have complex but measurable effects on both the patterns and the processes by which species co‐existence is maintained across the urban landscape. Within a single habitat type (here, residential vacant lots), variation in legacies of land use may have a stronger plant community structuring effect than contemporary environmental variation.