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.     

Functional and phylogenetic structure of forest and savanna bird assemblages across spatial scales

Ecological and evolutionary mechanisms that drive community assembly vary in space and time. However, little is known about how such mechanisms act in contrasting habitats. Here, we estimated the functional and phylogenetic structure of forest and savanna bird assemblages across different spatial scales to understand: 1) the mechanisms that govern the structure of assemblages in these habitats; 2) the relationship between phylogenetic and functional structure; and 3) the influence of species richness on the functional and phylogenetic structure of assemblages. We used a null model where forest and savanna bird species were allowed to occur in the same null assemblages and other where species were separated based on their habitats. According to the first null model, forest bird assemblages were functionally and phylogenetically clustered at all spatial scales, whereas savanna bird assemblages generally showed random functional and phylogenetic structure. These results can be explained by the low dispersal rate of forest species across of the patchy habitats and the widespread distribution of savanna species. However, in the second null model, both forest and savanna bird assemblages showed random functional and phylogenetic structure at regional and local scales. This suggests that trait‐based assembly might not play an important role in both habitats and across different spatial scales. In addition, the phylogenetic and functional structure of assemblages were not correlated, evidencing that caution is necessary when using phylogenetic relationships as a surrogate to functional distances among species. Finally, the relationships between species richness and functional and phylogenetic structure indicated that an increase in the number of species can promote both clustering and overdispersion, depending on the studied habitat and scale. Our study shows that integrating different types of habitat, spatial scales and biodiversity components in a single framework can shed light on the mechanisms that determine the community assembly.     

Species pool structure determines the level of generalism of island parasitoid faunas

Aim To examine whether island parasitoid faunas are biased towards generalists when compared with the mainland and their species pool, and to evaluate the effects of climate, island characteristics and regional factors on the relative proportions of idiobionts (i.e. generalists) and koinobionts (i.e. specialists) of two parasitic wasp families, Braconidae and Ichneumonidae. Location Seventy‐three archipelagos distributed world‐wide. Methods We used data on the distribution and biology obtained from a digital catalogue and several literature sources. We related level of generalism, measured as the ratio between the number of idiobiont and koinobiont species, to climatic, physiographic and regional factors using generalized linear models. We compared models by means of Akaike weighting, and evaluated the spatial structure of their residuals. We used partial regressions to determine whether the final models account for all latitudinal structure in the level of generalism. Results Islands host comparatively more idiobionts than continental areas. Although there is a latitudinal gradient in the level of generalism of island faunas correlating with both environmental factors and island characteristics, the most important determinant of island community structure is their source pool. This effect is stronger for ichneumonids, where generalism is higher in the Indomalayan region, arguably due to the higher diversity of endophytic hosts in its large rain forests. Main conclusions The level of generalism of island parasitoid faunas is largely constrained by regional factors, namely by the structure of the species pool, which emphasizes the importance of including regional processes in our understanding of the functioning of ecological communities. The fact that generalist species are more predominant in islands with a large cover of rain forests pinpoints the importance of the indirect effects of ecological requirements on community structure, highlighting the complex nature of geographical gradients of diversity.     

Comparison of pome fruit orchard inhabiting spider assemblages at different geographical scales

1 The composition of pome fruit orchard inhabiting spider assemblages was investigated at different geographical scales (Holarctic, European, inter- and intraregional levels within Hungary) using previous faunistic studies and data collected in Hungary between 1995 and 1997. Samples in Hungary were taken from the canopy and herb layer of apple and pear orchards in five markedly different fruit-growing regions by beating and sweep-netting methods. 2 The composition of canopy spider assemblages of apple orchards was analysed for the Holartic region and found to be determined by latitude at family level, and by the main zoogoegraphical regions at genus level. At the European scale, both the genus and species composition changed along a north–south gradient. 3 A comparison among apple and pear orchards located in different regions in Hungary, showed that both foliage- and grass-dwelling spider assemblages varied considerably in species composition and dominance order. 4 Within the same region, both the foliage- and grass-dwelling spider assemblages showed moderate differences in apple and pear orchards submitted to different treatments. Although the assemblages of spiders inhabiting the canopy and the herbaceous layer can be unambiguously distinguished, some overlap still occurs. 5 We conclude that the composition of spider assemblages is basically determined by geographical location. Although both pesticide treatments and available prey densities can influence the population of spiders, such factors are of moderate importance when compared with the effect of regionality, even when considered at smaller scale. However, most members of the family Theridiidae and the large orb-weavers (Araneidae) decreased considerably in treated plots. Scale-specific differences are thus relevant in determining the composition of prey–predator systems in orchards, and should be taken into account when designing integrated pest management (IPM) programs for apple and pear orchards.     

Unravelling the evolutionary origins of biogeographic assemblages

Aim

Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping present‐day diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of present‐day biogeographic assemblages and highlight their conservation value.

Location

Southern Africa.

Methods

We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their present‐day structure emerges. We suggest present‐day assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.

Results

We show the differentiation of most present‐day vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most species‐rich or threatened.

Main conclusions

Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.

     

Global patterns in the phylogenetic structure of island mammal assemblages

Assemblage-level phylogenies carry the signature of ecological and evolutionary processes, which may provide useful information on modes of assemblage formation. We present a global-scale analysis of the emergent phylogenetic properties of mammal assemblages on islands, in which we compared the structure of 595 island assemblages with null models constructed under four alternative definitions of regional source pools. Although most assemblages had a structure indistinguishable from random samples, for some mammal taxa, up to 40% of island assemblages were phylogenetically overdispersed. This suggests that in at least some cases, the processes that shape island faunas are not independent of phylogeny. Furthermore, measures of phylogenetic structure were associated in some cases with island geographical features (size, maximum elevation and habitat diversity). Our results suggest that part of the signal of assemblage formation processes is detectable in the phylogenies of contemporary island mammal faunas, though much is obscured by the complexity of these processes.     

Homogenization of fish assemblages in different lake depth strata at local and regional scales

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Community structure in ichneumonid parasitoids at different spatial scales

The processes underlying parasitoid community structure are little known. Stochastic niche-apportionment models provide one route to underlying assemblage rules in this and other groups. Previous work has applied this approach to parasitoids found on single host species in single populations. However, parasitoid communities are known to extend across multiple hosts and scales. The patterns of relative abundances generated by five niche-apportionment models were compared to those observed in assemblages of two sub-families of the Ichneumonidae, the Diplazontinae and Pimplinae, at landscape and patch scales, Yorkshire, UK. Three of the five models produced patterns that were significantly different to the observed pattern for all taxonomic levels at both spatial scales. The Diplazontinae fit the random fraction (RF) model at the landscape scale in broadleaved woods. This suggests that hierarchical structuring and biotic interactions may play a role in the structuring of Diplazontinae assemblages at this scale. In contrast the Pimplinae fit the RF model only at the patch scale and only at one site. However, the Pimplini tribe (all chiefly parasitoids of Lepidoptera) fit the random assortment (RA) model at both the landscape and the patch scales, whilst the Ephialtini tribe (wide range of hosts) fit no model at either scale. The ecological interpretation of the RA model suggests that the Pimplini tribe is an unsaturated assemblage, where some of the total available resources are unused. Our results show, through the fit of mechanistic niche-apportionment models, that the processes that may structure ichneumonid parasitoid assemblages are not consistent across taxa and spatial scales.     

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 and tectonic history of India

Aim To present an up to date account of the Mesozoic history of India and its relationship to the other Gondwana continents and to Eurasia. Location Continents surrounding the Western Indian Ocean. Methods Utilization of recent evidence of continental relationships based upon research in stratigraphy, palaeomagnetism, palaeontology, and contemporary biotas. Results The physical data revealed a sequence of events as India moved northward: (1) India–Madagascar rifted from east Africa 158–160 Ma (million years ago), (2) India–Madagascar from Antarctica c. 130 Ma, (3) India–Seychelles from Madagascar 84–96 Ma, (4) India from Seychelles 65 Ma, (5) India began collision with Eurasia 55–65 Ma and (6) final suturing took place c. 42–55 Ma. However, data from fossil and contemporary faunas indicate that, throughout the late Cretaceous, India maintained exchanges with adjacent lands. There is an absence in the fossil record of peculiar animals and plants that should have evolved, had India undergone an extended period of isolation just before its contact with Eurasia. Main conclusions The depiction of India in late Cretaceous as an isolated continent is in error. Most global palaeomaps, including the most recent one, show India, as it moves northward, following a track far out in the Indian Ocean. But the evidence now indicates that India's journey into northern latitudes cannot have taken place under such isolated circumstances. Although real breaks among the lands were indicated by the physical data, faunal links were maintained by vagile animals that were able to surmount minor marine barriers. India, during its northward journey, remained close to Africa and Madagascar even as it began to contact Eurasia.     

Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas

Identifying the main determinants of tropical marine biodiversity is essential for devising appropriate conservation measures mitigating the ongoing degradation of coral reef habitats. Based on a gridded distribution database and phylogenetic information, we compared the phylogenetic structure of assemblages for three tropical reef fish families (Labridae: wrasses, Pomacentridae: damselfishes and Chaetodontidae: butterflyfishes) using the net relatedness (NRI) and nearest taxon (NTI) indices. We then related these indices to contemporary and historical environmental conditions of coral reefs using spatial regression analyses. Higher levels of phylogenetic clustering were found for fish assemblages in the Indo‐Australian Archipelago (IAA), and more particularly when considering the NTI index. The phylogenetic structure of the Pomacentridae, and to a lower extent of the Chaeotodontidae and Labridae, was primarily associated with the location of refugia during the Quaternary period. Phylogenetic clustering in the IAA may partly result from vicariance events associated with coral reef fragmentation during the glacial periods of the Quaternary. Variation in the patterns among fish families further suggest that dispersal abilities may have interacted with past habitat availability in shaping the phylogenetic structure of tropical reef fish assemblages.     

Response of coccinellids to their aphid prey at different spatial scales

Predators that have an increasing numerical response for aggregation, attack and oviposition to increasing prey density are thought to be ideal for biological control. However density-dependent processes are infrequently detected and explanations include differences in the scales at which observations are made, behavioral differences among species, and habitat features. We examined the aggregation of four species of colonizing adult coccinellids to varying prey densities at two spatial scales in a maize system. Three of the species, Adalia bipunctata, Hippodamia tredecimpunctata, and Hippodamia convergens, responded to aphid abundance at the plant scale, and one species, Coleomegilla maculata, responded to the average aphid density at the plot (10×10 m) scale. In addition, H. convergens responded to individual plants with high aphid abundance in those plots with many plants of high aphid abundance. These results suggests that C. maculata (and possibly H. convergens) may be better able to colonize fields before aphid populations reach high levels, whereas A. bipunctata and H. tredecimpunctata may only be able to respond to high aphid abundance at the plant scale. This study suggests that spatial scale can affect predator–prey dynamics in a species-specific manner. However, the differences among coccinellid species in the community appear to be complementary, potentially contributing to greater aphid suppression.An erratum to this article can be found at     

Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

The extent to which the distribution of soil bacteria is controlled by local environment vs. spatial factors (e.g. dispersal, colonization limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here, we constrained environmental factors (soil chemistry, climate, above‐ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 10² km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilization) was also shown to be highly correlated with community structure, but not to abiotic factors, suggesting nonstochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio‐temporal patterns of microbial diversity, as well as life history of the groups being investigated, much as is the case for macro‐organisms.     

The influence of biogeographic history on the functional and phylogenetic diversity of passerine birds in savannas and forests of the Brazilian Amazon

Passeriformes is the largest and most diverse avian order in the world and comprises the Passeri and Tyranni suborders. These suborders constitute a monophyletic group, but differ in their ecology and history of occupation of South America. We investigated the influence of biogeographic history on functional and phylogenetic diversities of Passeri and Tyranni in forest and savanna habitats in the Brazilian Amazon. We compiled species composition data for 34 Passeriformes assemblages, 12 in savannas and 22 in forests. We calculated the functional (Rao's quadratic entropy, FD_Q) and phylogenetic diversities (mean pairwise distance, MPD, and mean nearest taxon distance, MNTD), and the functional beta diversity to investigate the potential role of biogeographic history in shaping ecological traits and species lineages of both suborders. The functional diversity of Passeri was higher than for Tyranni in both habitats. The MPD for Tyranni was higher than for Passeri in forests; however, there was no difference between the suborders in savannas. In savannas, Passeri presented higher MNTD than Tyranni, while in forest areas, Tyranni assemblages showed higher MNTD than Passeri. We found a high functional turnover (~75%) between Passeri and Tyranni in both habitats. The high functional diversity of Passeri in both habitats is due to the high diversity of ecological traits exhibited by species of this group, which enables the exploitation of a wide variety of resources and foraging strategies. The higher Tyranni MPD and MNTD in forests is likely due to Tyranni being older settlers in this habitat, resulting in the emergence and persistence of more lineages. The higher Passeri MNTD in savannas can be explained by the existence of a larger number of different Passeri lineages adapted to this severe habitat. The high functional turnover between the suborders in both habitats suggests an ecological strategy to avoid niche overlap.     

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.     

Molecular phylogeny of elapid snakes and a consideration of their biogeographic history

Evolutionary relationships among the major elapid clades, particularly the taxonomic position of the partially aquatic sea kraits (Latkauda) and the fully aquatic true sea snakes have been the subject of much debate. To discriminate among existing phylogenetic and biogeographic hypotheses, portions of both the 16S rRNA and cytochrome b mitochondrial DNA genes were sequenced from 16 genera and 17 species representing all major elapid snake clades from throughout the world and two non-elapid outgroups. This sequence data yielded 181 informative sites under parsimony. Parsimony analyses of the separate data sets produced trees of broad agreement although less well supported than the single most parsimonious tree resulting from the combined analyses. These results support the following hypotheses: (1) the Afro-Asian cobra radiation forms one or more sister groups to other elapids, (2) American and Asian coral snakes form a clade, corroborating morphological studies, (3) Bungarus forms a sister group to the hydrophiines comprised of Latkauda, terrestrial Australo-Papuan elapids and true sea snakes, (4) Latkauda and true sea snakes do not form a monophyletic group but instead each group shares an independent history with terrestrial Australo-Papuan elapids, corroborating previous studies, (5) a lineage of Melanesian elapids forms the sister group to Latkauda, terrestrial Australian species and true sea snakes. In agreement with previous morphologically based studies, the sequence data suggests that Bungarus and Latkauda represent transitional clades between the elapine 'palatine erectors' and hydrophiine 'palatine draggers'. Both intra and inter-clade genetic distances are considerable, implying that each of the major radiations have had long independent histories. I suggest an African, Asian, or Afro-Asian origin for elapids as a group, with independent Asian origins for American coral snakes and the hydrophiines.