Phylogeny and co‐occurrence of mammal species on Southeast Asian islands

Aim Islands have often been used as model systems in community ecology. The incorporation of information on phylogenetic relatedness of species in studies of island assemblage structure is still uncommon, but could provide valuable insights into the processes of island community assembly. We propose six models of island community assembly that make different predictions about the associations between co‐occurrences of species pairs on islands, phylogenetic relatedness and ecological similarity. We then test these models using data on mammals of Southeast Asian islands. Location Two hundred and forty islands of the Sundaland region of Southeast Asia. Methods We quantified the co‐occurrence of species pairs on islands, and identified pairs that co‐occur more frequently (positive co‐occurrence) or less frequently (negative co‐occurrence) than expected under null models. We then examined the distributions of these significantly deviating pairs with respect to phylogenetic relatedness and ecological differentiation, and compared these patterns with those predicted by the six community assembly models. We used permutation regression to test whether co‐occurrence patterns are predicted by relatedness, body size difference or difference in diet quality. Separate co‐occurrence matrices were analysed in this way for seven mammal families and four smaller subsets of the islands of Sundaland. Results In many matrices, average numbers of negative co‐occurrences were higher than expected under null models. This is consistent with assemblage structuring by competition, but may also result from low geographic overlap of species pairs, which contributes to negative co‐occurrences at the archipelago‐wide level. Distributions of species pairs within plots of phylogenetic distance × ecological differentiation were consistent with competition, habitat filtering or within‐island speciation models, depending on the taxon. Regressions indicated that co‐occurrence was more likely among closely related species pairs within the Viverridae and Sciuridae, but in most matrices phylogenetic distance was unrelated to co‐occurrence. Main conclusions Simple deterministic models linking co‐occurrence with phylogeny and ecology are a useful framework for interpreting distributions and assemblage structure of island species. However, island assemblages in Sundaland have probably been shaped by a complex idiosyncratic set of interacting ecological and evolutionary processes, limiting the predictive power of such models.     

Are phylogenies derived from family‐level supertrees robust for studies on macroecological patterns along environmental gradients?

Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relationship between phylogenetic properties and environment, by comparing the relationship between phylogenetic metrics and environmental variables derived from a phylogeny reconstructed with a supertree method to that derived from a phylogeny resolved at species level. North America was divided into equal area quadrats of 12 100 km². Nine indices of phylogenetic structure were calculated for angiosperm tree assemblages in each quadrat using two phylogenies resolved at different levels (one resolved at the family level and the other resolved at the species level). Scores of phylogenetic indices were related to two major climatic variables (temperature and precipitation) using correlation and regression analyses. Scores of phylogenetic indices resulting from the two phylogenies are perfectly or nearly perfectly correlated. On average, there is no difference in the variation explained by the two climatic variables between scores of phylogenetic indices derived from the two phylogenies. Our study suggests that a phylogeny derived from a well resolved family-level supertree as backbone with genera and species attached to the backbone as polytomies is robust for studies investigating the relationship between phylogenetic structure and environment in biological assemblages at a broad spatial scale.     

Phylogenetic structure of mammal assemblages at large geographical scales: linking phylogenetic community ecology with macroecology

Phylogenetic community ecology seeks to explain the processes involved in the formation of species assemblages by analysing their phylogenetic structure, and to date has focused primarily on local-scale communities. Macroecology, on the other hand, is concerned with the structure of assemblages at large geographical scales, but has remained largely non-phylogenetic. Analysing the phylogenetic structure of large-scale assemblages provides a link between these two research programmes. In this paper, I ask whether we should expect large-scale assemblages to show significant phylogenetic structure, by outlining some of the ecological and macroevolutionary processes that may play a role in assemblage formation. As a case study, I then explore the phylogenetic structure of carnivore assemblages within the terrestrial ecoregions of Africa. Many assemblages at these scales are indeed phylogenetically non-random (either clustered or overdispersed). One interpretation of the observed patterns of phylogenetic structure is that many clades underwent rapid biome-filling radiations, followed by diversification slowdown and competitive sorting as niche space became saturated.     

Non‐random patterns of invasion and extinction reduce phylogenetic diversity in island bird assemblages

Anthropogenically driven changes in bird communities on oceanic islands exemplify the biotic upheaval experienced by island floras and faunas. While the influence of invasions and extinctions on species richness and beta‐diversity of island bird assemblages has been explored, little is known about the impact of these invasions and extinctions on phylogenetic diversity. Here we quantify phylogenetic diversity of island bird assemblages resulting from extinctions alone, invasions alone, and the combination of extinctions and invasions in the historic time period (1500 CE to the current), and compare it to the expected phylogenetic diversity that would result if these processes involved randomly selected island bird species. We assessed phylogenetic diversity and structure at the scale of the island (n = 152), the archipelago containing the islands (n = 22), and the four oceans containing the archipelagos using three measures. We found that extinction, invasion, and the combination of invasion and extinction generally resulted in lower phylogenetic diversity than expected, regardless of the spatial scale examined. We conclude that extinction and invasion of birds on islands are non‐random with respect to phylogeny and that these processes generally leave bird assemblages with lower phylogenetic diversity than we would expect under random invasion or extinction.     

An updated megaphylogeny of plants,a tool for generating plant phylogenies and an analysis of phylogenetic community structure

Aims The aim of this article is 3-fold. First, we present an updated version of a published megaphylogeny of vascular plants that can be used in studies of plant ecology and biogeography. Second, we develop a tool that can be used by botanists and plant ecologists to generate phylogenetic hypotheses in three scenarios. Third, we use a set of regional assemblages of angiosperm trees in North America as a model system to evaluate the effect of differences in phylogenies generated using the three scenarios on the quantification of phylogenetic properties and the relationship between measures of phylogenetic properties and environment.Methods The taxonomy and nomenclature of plant species in the megaphylogeny were standardized according to The Plant List (version 1.1). A tool for generating phylogenies was created using the R language. The robustness of derived phylogenies was evaluated using correlation and regression analyses.Important findings An updated megaphylogeny of vascular plants (PhytoPhylo) and a tool for reconstructing phylogenies of seed plants (S.PhyloMaker) were generated. Our study shows that phylogenies generated by S.PhyloMaker using the PhytoPhylo megaphylogeny as a backbone are nearly as good as phylogeny resolved at the species level when using derived phylogenies to quantify phylogenetic properties (e.g. phylogenetic diversity and phylogenetic relatedness) of biological assemblages, and that S.PhyloMaker-generated phylogenies are robust for studies of community ecology and biogeography, particularly those seeking for patterns of phylogenetic properties along environmental gradients.     

Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests

Forest fragmentation and defaunation are considered the main drivers of biodiversity loss, yet the synergistic effects of landscape changes and biotic interactions on assemblage structure have been poorly investigated. Here, we use an extensive dataset of 283 assemblages and 105 species of small mammals to understand how defaunation of medium and large mammals and forest fragmentation change the community composition and diversity of rodents and marsupials in tropical forests of South America. We used structured equation models to investigate the relationship between small mammal species, functional and phylogenetic diversity with forest size, forest cover and the occurrence of medium and large mammals. The best‐fit model showed that defaunation reduced functional diversity, and that species diversity of small mammals increased with forest patch size. Forest cover did not affect functional and phylogenetic diversity. Our results indicate that occurrence of medium and large sized mammals (probably acting as predators, or competitors of small mammals) and forest patch size help to retain species and functional diversity in small mammal communities. Further, the number of species in a small mammal community was critical to the maintenance of phylogenetic diversity, and may have a pronounced influence on the ecological functions played by small mammals. Identifying how phylogenetic and functional diversity change in function of human pressures allows us to better understand the contribution of extant lineages to ecosystem functioning in tropical forests.     

Mediterranean v. continental small mammal communities and the environmental degradation of the Dinaric Alps

In order to test for the existence of distinct, regionally-based small mammal faunas, distributional patterns were examined in thirty one species of small mammals (insectivores and rodents) inhabiting the Dinaric Alps (western Balkans). The small mammal fauna was found to consist of three groups: a group of ‘generalist’ species that occurred throughout the study area, plus distinct coastal and continental small mammal assemblages. The continental small mammal assemblage is considerably more species-rich, whilst that of the coastal zone is largely restricted to generalists and species with geophilic or fossorial life-styles (many of which are also commensal with humans). The two assemblages appear to be associated with different vegetation types, and the transition between them lies on the coastal slopes of the Dinaric Alps at c. 700–900 m of altitude. We discuss possible determinants of assemblage composition and species richness, and particularly the possible role of prehistoric environmental degradation in the context of the reduced species-richness of the coastal zone.     

Fish assemblage convergence along stream environmental gradients: an intercontinental analysis

Species that pass through similar environmental filters, regardless of geographic proximity or evolutionary history, are expected to share many traits, resulting in similar assemblage trait distributions. Convergence of assemblage trait distributions among different biotic regions would indicate that consistent ecological processes produce repeated patterns of adaptive evolution. This study analyzes trait–environment relationships across multiple stream fish assemblages representing evolutionarily divergent faunas. We hypothesized that trait–environment patterns converge across regional faunas in response to a common set of environmental filters acting on functional traits. One hundred and ninety‐seven species and forty streams were sampled from five regions: Belize, Benin, Brazil, Cambodia and USA. By examining trait–environment plots, multiple congruent trait–environment patterns were found across all regions, indicative of a consistent set of environmental filters acting on local community assembly. The consistency of these patterns strongly suggests that water velocity and habitat structural complexity function as universal environmental filters, producing similar assemblage trait distributions in streams across all regions. Bivariate relationships were not universal, and only one of the associations between a single functional trait and single environmental variable was statistically significant across all five regions. Strong phylogenetic signal was found in traits and habitat use, which implies that niche conservatism also influenced assemblage trait distributions. Overall, results support the idea that habitat templates structure trait distributions of stream fish assemblages and do so in a consistent manner.     

A common tendency for phylogenetic overdispersion in mammalian assemblages

Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both.     

Phylogenetic community structure: temporal variation in fish assemblage

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales (grouped at three temporal scales). Phylogenetic distance was measured as the mean pairwise distances (MPD) and as mean nearest‐neighbor distance (MNTD). Both distances were based on counts of nodes. We compared the observed values of MPD and MNTD with values that were generated randomly using null model independent swap. A serial runs test was used to assess the temporal independence of indices over time. The phylogenetic pattern in the whole assemblage and the functional groups varied widely over time. Conclusions about phylogenetic clustering or dispersion depended on the temporal scales. Conclusions about the frequency with which biotic processes and environmental filters affect the local assembly do not depend only on taxonomic grouping and spatial scales. While these analyzes allow the assertion that all proposed patterns apply to the fish assemblages in the floodplain, the assessment of the relative importance of these processes, and how they vary depending on the temporal scale and functional group studied, cannot be determined with the effort commonly used. It appears that, at least in the system that we studied, the assemblages are forming and breaking continuously, resulting in various phylogeny‐related structures that makes summarizing difficult.     

Organization of Squamata (Reptilia) assemblages in Mediterranean archipelagos

Mediterranean islands have complex reptile assemblages, but little is known about the factors that determine their organization. In this study, the structure of assemblages of Squamata was evaluated based on their species richness and two measures of phylogenetic diversity (variability and clustering). I evaluated the composition of the assemblages comparing distinct biogeographic subregions within the Mediterranean: Adriatic, Aegean, Balearic, Corsica–Sardinia, Crete, Gulf of Gabés, Ionian Sea, Ligurian Sea, Malta, Sicily, and Tyrrhenian Sea. The effect of island environments and geographical isolation on the diversity metrics was assessed using generalized linear models. The analyses indicated that species richness was mostly influenced by island area and geographical isolation. Assemblages on smaller islands were poorer in species and phylogenetically dispersed, possibly as an effect of interspecific competition. The species composition of the assemblages was determined by similar environmental drivers within the biogeographic subregions, including island area, island elevation, geographical isolation, and aridity. In several subregions, significant patterns of phylogenetic attraction were found in species co‐occurrences, caused by the limits imposed by the island size on large predatory species.     

Phylogenetic diversity of macromycetes and woody plants along an elevational gradient in Eastern Mexico

Phylogenetic information provides insight into the ecological and evolutionary processes that organize species assemblages. We compared patterns of phylogenetic diversity among macromycete and woody plant communities along a steep elevational gradient in eastern Mexico to better understand the evolutionary processes that structure their communities. Macrofungi and trees were counted and identified in eight sites from 100 to 3500 m asl, and sequence data retrieved from GenBank for the same or closely related species were used to reconstruct their phylogenies. Patterns of species richness and phylogenetic diversity were similar for both macrofungi and trees, but macromycete richness and diversity peaked at mid‐elevations, whereas woody plant richness and diversity did not show significant trends with elevation. Phylogenetic similarity among sites was low for both groups and decreased as elevational distance between sites increased. Macromycete communities displayed phylogenetic overdispersion at low elevations and phylogenetic clustering at high elevations; the latter is consistent with environmental filtering at high elevation sites. Woody plants generally exhibited phylogenetic clustering, consistent with the potential importance of environmental filtering throughout the elevational gradient.     

Australian Tropical and Subtropical Rain Forest Community Assembly: Phylogeny,Functional Biogeography,and Environmental Gradients

To compare community assemblage patterns in tropical northeastern and subtropical central eastern Australia across selected gradients and scales, we tested the relationship of species traits with phylogenetic structure, and niche breadth. We considered phylogenetic relationships across current‐day species in assemblages in relation to rain forest species pool sizes, and trait values along gradients including elevation and latitude. Trait values were quantified across scales for seed size, leaf area, wood density and maximum height at maturity for 1137 species and 596 assemblages using trait gradient analysis (TGA). Local assemblages of subtropical species had narrower trait ranges, and higher niche breadth values than corresponding assemblages of tropical species. Leaf size and seed size increased at low latitudes, and community phylogenetic structure was most strongly correlated with seed traits in the subtropics, reflecting dispersal and re‐colonization processes. Elevation accounted for little of the variance in community phylogenetic structure or trait variation across local and regional scales. Stable moist forest areas retained many species from ancestral rain forest lineages across a range of temporally conserved habitats; species within assemblages were less related; and rain forest assemblages had higher functional diversity, but lower niche breadth. This suggests that on average, assemblages of species in stable areas had greater trait variation and narrower distributions. Historic and recent rain forest contraction and re‐expansion can result in recolonized areas that are dominated by species that are more related (phylogenetically) than by chance, have smaller, widely dispersed seeds, and greater niche breadth (broader distributions).     

Seasonal dynamics of waterbird assembly mechanisms revealed by patterns in phylogenetic and functional diversity in a subtropical wetland

Despite growing interest in using phylogenetic and functional methods to understand community assembly, few studies have examined how these methods can be used to assess seasonal variation in assembly mechanisms among migrant species. Migration can rapidly alter the relative influence of stochastic processes, species interactions, or environmental factors in shaping communities across seasons. Here, we describe seasonal dynamics in the phylogenetic and functional diversity of waterbirds in Mai Po Wetland, a subtropical region with significant and predictable temporal variation in climate and migratory bird density. Phylogenetic α diversity varied seasonally, exhibiting a clustered structure (indicative of environmental filtering) in summer, and over‐dispersed structure (indicative of biotic filtering) in winter. Phylogenetic diversity in spring and autumn exhibited a more intermediate, random structure, consistent with stochastic arrivals and departures of migrants. Functional diversity was clustered in spring but showed over‐dispersion in the other three seasons. Phylogenetic β diversity in summer and winter assemblages was characterized by two distinct groups, while spring and autumn assemblages were mixed. Our results suggest that waterbird assemblages were primarily shaped by interspecific competition in winter, while random processes tended to shape assemblages in spring and fall. Environmental factors played a more important role in summer, during periods of high heat stress. In addition, species co‐occurrence patterns were significantly more strongly related to phylogenetic similarity in winter than in summer. Our results suggest that the relative importance of assemblage mechanisms can vary seasonally in response to changing environmental conditions, suggesting that studies attempting to infer a single dominant assembly mechanism may ignore important assembly processes. Temporal shifts in assembly mechanisms may play an important role in maintaining diversity in subtropical and temperate wetlands and perhaps also in other dynamic systems.     

The shapes of phylogenetic trees of clades, faunas, and local assemblages: exploring spatial pattern in differential diversification

Life on Earth is characterized by strong diversity skewness: related lineages typically show pronounced variation in diversification success, and clades contain hyperdiverse and depauperate subclades. Previous studies have documented diversity skewness only for entire (global) clades. We demonstrate methods for measurement and significance testing of diversity skewness of local assemblages and regional biotas; we illustrate this with an analysis of geographic structure in diversity skewness of primate assemblages. For primates, continental faunas differ in diversity skewness from expectations based on the global phylogeny: South American faunas have significantly low skewness and African faunas have significantly high skewness. However, no local assemblage has diversity skewness different from that expected based on sampling the continental fauna. We also document a latitudinal gradient in diversity skewness for the African assemblages and test for (but do not find) associations of skewness with longitude, local species richness, and net primary productivity. Our data suggest that continental-scale biogeographic events rather than local-scale processes have shaped diversity skewness in modern primate faunas.     

The biogeographic history of ruminant faunas determines the phylogenetic structure of their assemblages at different scales

Phylogenetic community structure may help us understand how macroecological and macroevolutionary processes shape assemblages at large geographical scales. In this paper, we test hypotheses linking the formation of large‐scale assemblages, evolutionary processes and macroecology. To provide new insight into ruminant biogeography and evolution, phylogenetic community structure metrics were calculated for faunal assemblages at four hierarchical levels. Phylogenetic relatedness indices (net relatedness index and nearest taxon index) were determined for 59 ruminant assemblages at the landscape scale and scale of their respective climate domains (continuous biome stretches). Species pools at the global and biogeographic realm levels were used to construct null observation models. Significantly, assemblages were selected if they were distributed across biogeographic realms and represented all the world's biomes. Non‐random patterns were also tested for biogeographic realms within the global ruminant species pool. By examining ruminant assemblages at different scales we were able to observe that ruminant faunas show a distribution mainly limited within the boundaries of their biogeographic realms. However, the diversification of some clades was found to be restricted to extremely arid domains in the Sahara and Arabia. The random patterns featured by other extreme climate domains could reflect phylogenetically heterogeneous filling by less biome‐restricted lineages outside Africa.     

Exploring the phylogenetic history of mammal species richness

Aim At broad geographical scales, species richness is a product of three basic processes: speciation, extinction and migration. However, determining which of these processes predominates is a major challenge. Whilst palaeontological studies can provide information on speciation and extinction rates, data are frequently lacking. Here we use a recent dated phylogenetic tree of mammals to explore the relative importance of these three processes in structuring present‐day richness gradients. Location The global terrestrial biosphere. Methods We combine macroecological data with phylogenetic methods more typically used in community ecology to describe the phylogenetic history of regional faunas. Using simulations, we explore two simple phylogenetic metrics, the mean and variance in the pairwise distances between taxa, and describe their relationship to phylogenetic tree topology. We then use these two metrics to characterize the evolutionary relationships among mammal species assemblages across the terrestrial biome. Results We show that the mean and variance in the pairwise distances describe phylogenetic tree topology well, but are less sensitive to phylogenetic uncertainty than more direct measures of tree shape. We find the phylogeny for South American mammals is imbalanced and ‘stemmy’ (long branches towards the root), consistent with recent diversification within evolutionarily disparate lineages. In contrast, the phylogeny for African mammals is balanced and ‘tippy’ (long branches towards the tips), more consistent with the slow accumulation of diversity over long times, reflecting the Old World origin of many mammal clades. Main conclusions We show that phylogeny can accurately capture biogeographical processes operating at broad spatial scales and over long time periods. Our results support inferences from the fossil record – that the New World tropics are a diversity cradle whereas the Old World tropics are a museum of old diversity.     

Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients

Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km(2) plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.