Understanding primate communities: Recent developments and future directions

In 1999, the edited volume Primate Communities presented several studies that examined broad‐scale patterns of primate diversity.¹ Similar studies were being conducted on nonprimate taxa; advances in data availability and statistical approaches were allowing scientists to investigate a variety of new questions and to reexamine classical questions in novel ways. While such studies on nonprimate taxa have continued at a steady pace, they have only crept forward for primate species (Fig. 1 ). In the intervening time, the field of macroecology (Box 1) rapidly developed and has resulted in several books 2 - 4 and the establishment of new research institutes. We suggest that examining primate communities, especially in a macroecological context, is an important line of research for our field to embrace and an area where biological anthropologists can provide major contributions. We review the current state of research, describe new datasets and research tools, and suggest future research directions.     

The impact of urbanization on taxonomic and functional similarity among bird communities

Aim To assess spatial relationships between avian community similarity and level of urbanization. We tested the following hypotheses for taxonomic similarity: Hypothesis A – the decline in taxonomic similarity with distance is stronger for the least urbanized locations compared to the most urbanized locations; Hypothesis B – the converse of Hypothesis A; and Hypothesis C – the decline in taxonomic similarity with distance is stronger for the most and least urbanized locations compared to locations with intermediate levels of urbanization. We also determined if increasing urbanization led to increased functional similarity within bird communities. Location South‐eastern Australia. Methods Bird species occurrence and density were sampled across 18 towns and 72 neighbourhoods occupying a spatial gradient of up to 882 km. We calculated pairwise values in taxonomic similarity among each town and neighbourhood using the Sørenson coefficient and a similarity measure that accounts for differences in species richness among locations. These values were plotted against pairwise distances among towns and neighbourhoods using linear regression to measure similarity–distance relationships. Neighbourhoods were categorized into four levels of urban development based on dwelling density, urban intensity, vegetation cover, or the density of native, nectar‐rich plants. Variation in bird species density across neighbourhoods and frequency of occurrence across broad habitat types (habitat specialization) was used to assess functional similarity of bird communities in each neighbourhood. Results Among the 18 towns, the decline in taxonomic similarity with distance was weak and significantly less than among regional bird communities that occurred within a 1° grid square around each town. Among the 72 neighbourhoods, similarity–distance relationships differed substantially depending on the level of urban development. Generally, the strongest decline in similarity with distance was for neighbourhoods with the highest and lowest dwelling density, urban intensity and vegetation cover, supporting Hypothesis C. The functional similarity of bird communities increased significantly with dwelling density, and decreased significantly with an increasing density of nectar plants. Main conclusions At the town level, urbanization appears to homogenize regional bird communities. Among neighbourhoods, similarity–distance relationships are substantially influenced by the level of urban development, and increasing urbanization leads to greater functional similarity within bird communities.     

Exploring the homogeneity of terrestrial subterranean communities at a local spatial scale

1. Although caves are generally perceived as isolated habitats, at the local scale, they are often interconnected via a network of fissures in the bedrock. Accordingly, caves in close proximity are expected to host the same, or very similar, animal communities. 2. We explored the extent to which subterranean arthropod communities are homogenous at a local spatial scale of less than 1 km², along with which cave-specific environmental features result in a departure from the expected homogeneous pattern. We approached this question by studying richness and turnover in terrestrial invertebrate communities of 27 caves in a small karst massif in the Western Italian Alps. 3. Specialised subterranean species were homogeneously distributed among caves and were not influenced by seasonality. The only factor driving their distribution was the distance from the cave entrance, with deeper caves yielding a greater diversity of species. 4. Significant spatio-temporal turnover in species not specialised to subterranean life was observed. In summer, there was a significant homogenisation of the community and a more even distribution of species among sites; in winter, these species were missing or found exclusively at greater depths, where environmental conditions were more stable. Furthermore, caves at lower elevations yielded, on average, a greater diversity and abundance of these species. 5. This study demonstrated that the theoretical expectation of no turnover in community composition in caves in close proximity is not always met. Turnover can be mostly attributed to seasonal patterns and sampling depth; thus, our findings have implications for planning sampling and monitoring activities in caves.     

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high‐throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon–Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer.     

Environment drives high phylogenetic turnover among oceanic bacterial communities

Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.     

Environmental heterogeneity among lakes promotes hyper β‐diversity across phytoplankton communities

相似文献   

Discriminating ecological processes affecting different dimensions of α‐ and β‐diversity in desert plant communities

Understanding the spatial distribution of plant diversity and its drivers are major challenges in biogeography and conservation biology. Integrating multiple facets of biodiversity (e.g., taxonomic, phylogenetic, and functional biodiversity) may advance our understanding on how community assembly processes drive the distribution of biodiversity. In this study, plant communities in 60 sampling plots in desert ecosystems were investigated. The effects of local environment and spatial factors on the species, functional, and phylogenetic α‐ and β‐diversity (including turnover and nestedness components) of desert plant communities were investigated. The results showed that functional and phylogenetic α‐diversity were negatively correlated with species richness, and were significantly positively correlated with each other. Environmental filtering mainly influenced species richness and Rao quadratic entropy; phylogenetic α‐diversity was mainly influenced by dispersal limitation. Species and phylogenetic β‐diversity were mainly consisted of turnover component. The functional β‐diversity and its turnover component were mainly influenced by environmental factors, while dispersal limitation dominantly effected species and phylogenetic β‐diversity and their turnover component of species and phylogenetic β‐diversity. Soil organic carbon and soil pH significantly influenced different dimensions of α‐diversity, and soil moisture, salinity, organic carbon, and total nitrogen significantly influenced different dimensions of α‐ and β‐diversity and their components. Overall, it appeared that the relative influence of environmental and spatial factors on taxonomic, functional, and phylogenetic diversity differed at the α and β scales. Quantifying α‐ and β‐diversity at different biodiversity dimensions can help researchers to more accurately assess patterns of diversity and community assembly.     

Environmental drivers of species composition and functional diversity of dung beetles along the Atlantic Forest–Pampa transition zone

Human activities are causing a rapid loss of biodiversity, which impairs ecosystem functions and services. Therefore, understanding which processes shape how biodiversity is distributed along spatial and environmental gradients is a first step to guide conservation and management efforts. We aimed to determine the relative explanatory importance of biogeographic, environmental, landscape and spatial variables on assemblage dissimilarities and functional diversity of dung beetles along the Atlantic Forest–Pampa (i.e. forest–grassland) transition zone located in Southeast South America. We described each site according to their biogeographic position, environmental conditions, landscape features and spatial patterns. The compositional dissimilarity was partitioned into turnover and nestedness components of β‐diversity. Mantel tests and generalised dissimilarity models were used to relate β‐diversity and its components to biogeographic, environmental, landscape and spatial variables. Variation partitioning analysis was used to estimate the pure and shared variation in species composition and functional diversity explained by the four categories of predictors. Biome domain was the main factor causing dung beetle compositional dissimilarity, with a high species replacement between Atlantic Forest and Pampa. Biogeographic, environmental, landscape and spatial distances also affected the patterns of dung beetle dissimilarity and β‐diversity components. The shared effects of the four sets of predictors explained most of the variation in dung beetle composition. A similar response pattern was found for dung beetle functional diversity, which excluded biogeographic effects. Only the pure effects of environmental and spatial predictors were significant for species composition and functional diversity. Our results indicate that dung beetle species composition and functional diversity are jointly driven by environmental, landscape and spatial predictors with higher pure environmental and spatial effects. The forest–grassland transition zone promotes a strong species and trait replacement highly influenced both by environmental filtering and dispersal limitation.     

Geographical ecology of dry forest tree communities in the West Indies

Aim

Seasonally dry tropical forest (SDTF) of the Caribbean Islands (primarily West Indies) is floristically distinct from Neotropical SDTF in Central and South America. We evaluate whether tree species composition was associated with climatic gradients or geographical distance. Turnover (dissimilarity) in species composition of different islands or among more distant sites would suggest communities structured by speciation and dispersal limitations. A nested pattern would be consistent with a steep resource gradient. Correlation of species composition with climatic variation would suggest communities structured by broad‐scale environmental filtering.

Location

The West Indies (The Bahamas, Cuba, Hispaniola, Jamaica, Puerto Rico, US Virgin Islands, Guadeloupe, Martinique, St. Lucia), Providencia (Colombia), south Florida (USA) and Florida Keys (USA).

Taxon

Seed plants—woody taxa (primarily trees).

Methods

We compiled 572 plots from 23 surveys conducted between 1969 and 2016. Hierarchical clustering of species in plots, and indicator species analysis for the resulting groups of sites, identified geographical patterns of turnover in species composition. Nonparametric analysis of variance, applied to principal components of bioclimatic variables, determined the degree of covariation in climate with location. Nestedness versus turnover in species composition was evaluated using beta diversity partitioning. Generalized dissimilarity modelling partitioned the effect of climate versus geographical distance on species composition.

Results

Despite a set of commonly occurring species, SDTF tree community composition was distinct among islands and was characterized by spatial turnover on climatic gradients that covaried with geographical gradients. Greater Antillean islands were characterized by endemic indicator species. Northern subtropical areas supported distinct, rather than nested, SDTF communities in spite of low levels of endemism.

Main conclusions

The SDTF species composition was correlated with climatic variation. SDTF on large Greater Antillean islands (Hispaniola, Jamaica and Cuba) was characterized by endemic species, consistent with their geological history and the biogeography of plant lineages. These results suggest that both environmental filtering and speciation shape Caribbean SDTF tree communities.     

An alien in an archipelago: Spathodea campanulata and the geographic variability of its moth (Lepidoptera) communities in the New Guinea and Bismarck Islands

Aim This analysis of moth (Lepidoptera) communities colonizing an alien tree invading secondary rain forest vegetation in Melanesia examines the predictability of insect herbivorous communities across distances of tens to thousands of km and the effect of dispersal barriers on community composition in the tropics. Location Six secondary rain forest sites were studied within four equidistant yet distinct geographic areas of the New Guinea mainland and the Bismarck Archipelago, including two watershed areas (Madang and Sepik) on mainland New Guinea and the adjacent large island of New Britain and small island of Unea. Methods The analysis is based on feeding records obtained by quantitative sampling and rearing of caterpillars from the alien host Spathodea campanulata (Bignoniaceae). It examines the variation in Lepidoptera community composition at six study sites distributed on three adjacent islands ranging in size from 30 to 865,000 km². Results Spathodea campanulata was colonized by 54 folivorous species of Lepidoptera. Most of them were generalists, feeding on > 1 native plant family. However, the three most abundant species representing 83% of all individuals (Acherontia lachesis, Hyblaea puera complex and Psilogramma menephron) were relatively host specific, feeding predominantly on a single native family that is not the Bignoniaceae. Most of the 23 species analysed in detail had a wide geographic distribution, including 13 species spanning the entire 1000‐km study transect. While the Lepidoptera in two New Guinea areas 280 km apart were similar to each other, there was a discontinuity in species composition between New Guinea and the smaller islands. However, no negative effect of small islands on species richness was detected. Main conclusions Spathodea campanulata was rapidly colonized by folivorous Lepidoptera communities with species richness and dominance structure indistinguishable from the assemblages feeding on native hosts, despite its phylogenetic isolation from the native vegetation. Although most species were generalists, the highest population densities were reached by relatively specialized species, similar to the communities on native hosts. The species turnover across distances from 10 to 1000 km was relatively low as most of the species had wide geographic ranges.     

Anthropogenic disturbance homogenizes seagrass fish communities

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat‐forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta‐diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance‐ and incidence‐based beta‐diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within‐region comparisons using abundance‐ and incidence‐based measures of beta‐diversity, and in across‐region comparisons using incidence‐based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta‐diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land‐ and seascapes, as well as managing anthropogenic impacts in high activity areas.     

幕阜山森林群落结构与物种多样性研究

幕阜山地处中亚热带-北亚热带过渡地带,物种资源丰富.通过对其典型样地的调查,分别采用Shannon-Wiener指数、Simpson指数和Pielou均匀度指数作为测度指标,研究了幕阜山地区森林群落结构及其物种多样性特征.结果表明,该地区主要有21个森林群落类型.其中常绿阔叶林中,物种丰富度指数与多样性指数在群落梯度上的总体趋势均为灌木层相对高于乔木层,乔木层相对高于草本层;在落叶阔叶林中,其丰富度指数的趋势为灌木层＞草本层和乔木层,而在草本层与乔木层间是波动的,多样性指数的趋势为灌木层＞草本层＞乔木层;在针叶林中,物种丰富度、多样性指数表现的总趋势基本一致,即灌木层的丰富度相对较高,其次为草本层,乔木层的相对较小.在其他群落类型中,多样性指数、均匀度指数在乔木层、灌木层和草本层则表现出多样化的趋势;另外,从总体上看,各种指数在海拔梯度上并未表现出明显的规律性.     

The phylogenetic structure of primate communities: variation within and across continents

Aim Our goals are: (1) to examine the relative degree of phylogenetic overdispersion or clustering of species in communities relative to the entire species pool, (2) to test for across‐continent differences in community phylogenetic structure, and (3) to examine the relationship between species richness and community phylogenetic structure. Location Africa, Madagascar, Asia, and the Neotropics. Methods We collected species composition and phylogenetic data for over 100 primate communities. For each community, we calculated two measures of phylogenetic structure: (1) the net relatedness index (NRI), which provides a measure of the mean pairwise phylogenetic distance among all species in the community; and (2) the nearest taxon index (NTI), which measures the relative phylogenetic distance among the closest related species in a community. Both measures are relative to the phylogeny of the species in the entire species pool. The phylocom package uses a randomization procedure to test whether the NRI and NTI values are higher or lower than expected by chance alone. In addition, we used a Kruskal–Wallis test to examine differences in NRI and NTI across continents, and linear regressions to examine the relationship between species richness and NRI/NTI. Results We found that the majority of individual primate communities in Africa, Asia and the Neotropics consist of member species that are neither more nor less closely related than expected by chance alone. Yet 37% of Malagasy communities contain species that are more distantly related to each other compared with random species assemblages. Also, we found that the average degree of relatedness among species in communities differed significantly across continents, with African and Malagasy communities consisting of more distantly related taxa compared with communities in Asia and the Neotropics. Finally, we found a significant negative relationship between species richness and phylogenetic distance among species in African, Asian and Malagasy communities. The average relatedness among species in communities decreased as community size increased. Main conclusions The majority of individual primate communities exhibit a phylogenetic structure no different from random. Yet there are across‐continent differences in the phylogenetic structure of primate communities that probably result from the unique ecological and evolutionary characteristics exhibited by the endemic species found on each continent. In particular, the recent extinctions of numerous primates on Madagascar are likely responsible for the low levels of evolutionary relatedness among species in Malagasy communities.     

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages

Bacteriophages are the most abundant biological life forms on Earth. However, relatively little is known regarding which bacteriophages infect and exploit which bacteria. A recent meta-analysis showed that empirically measured phage-bacteria infection networks are often significantly nested, on average, and not modular. A perfectly nested network is one in which phages can be ordered from specialist to generalist such that the host range of a given phage is a subset of the host range of the subsequent phage in the ordering. The same meta-analysis hypothesized that modularity, in which groups of phages specialize on distinct groups of hosts, should emerge at larger geographic and/or taxonomic scales. In this paper, we evaluate the largest known phage-bacteria interaction data set, representing the interaction of 215 phage types with 286 host types sampled from geographically separated sites in the Atlantic Ocean. We find that this interaction network is highly modular. In addition, some of the modules identified in this data set are nested or contain submodules, indicating the presence of multi-scale structure, as hypothesized in the earlier meta-analysis. We examine the role of geography in driving these patterns and find evidence that the host range of phages and the phage permissibility of bacteria is driven, in part, by geographic separation. We conclude by discussing approaches to disentangle the roles of ecology and evolution in driving complex patterns of interaction between phages and bacteria.