Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.     

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.     

Global phylogenetic structure of the hyperdiverse ant genus Pheidole reveals the repeated evolution of macroecological patterns

Adaptive radiations are of particular interest owing to what they reveal about the ecological and evolutionary regulation of biodiversity. This applies to localized island radiations such as Darwin''s finches, and also to rapid radiations occurring on a global scale. Here we analyse the macroevolution and macroecology of Pheidole, a famously hyperdiverse and ecologically dominant ant genus. We generate and analyse four novel datasets: (i) a robust global phylogeny including 285 Pheidole species, (ii) a global database on regional Pheidole richness in 365 political areas summarizing over 97 000 individual records from more than 6500 studies, (iii) a global database of Pheidole richness from 3796 local communities and (iv) a database of Pheidole body sizes across species. Analysis of the potential climate drivers of richness revealed that the patterns are statistically very similar across different biogeographic regions, with both regional and local richness associated with the same coefficients of temperature and precipitation. This similarity occurs even though phylogenetic analysis shows that Pheidole reached dominance in communities through serial localized radiations into different biomes within different continents and islands. Pheidole body size distributions have likewise converged across geographical regions. We propose these cases of convergence indicate that the global radiation of Pheidole is structured by deterministic factors regulating diversification and diversity.     

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.     

生态学的多样性指数:功能与系统发育

生物多样性是生态学的核心问题。传统的多样性指数仅包含物种数和相对多度的信息,这类基于分类学的多样性指数并不能很好地帮助理解群落构建和生态系统功能。不同物种对群落构建和生态系统功能所起到的作用类型和贡献也不完全相同,且物种在生态过程中的作用和贡献往往与性状密切相关,因此功能多样性已经成为反映物种群落构建、干扰以及环境因素对群落影响的重要指标。同时,由于亲缘关系相近的物种往往具有相似的性状,系统发育多样性也可以作为功能多样性的一个替代。功能多样性和系统发育多样性各自具有优缺点,但二者均比分类多样性更能揭示群落和生态系统的构建、维持与功能。     

Temporal patterns of microbial community structure in the Mid-Atlantic Bight

Although open ocean time-series sites have been areas of microbial research for years, relatively little is known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35 m (n=178). Microbial populations were fingerprinted using ribosomal 16S rRNA genes and terminal restriction fragment length polymorphism analysis. Results from cluster analysis revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth. Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.     

A culture-dependent bacterial community structure analysis based on liquid cultivation and its application to a marine environment

A method for analyzing culture-dependent bacterial community structure by liquid cultivation was established using 96-well microplates. Using 96-well microplates, this method can easily provide accurate enumeration of viable microorganisms and simultaneous separation of bacteria, which allowed us to analyze the bacterial community. Bacteria in diluted surface seawater were separated using 96-well microplates and cultivated with 1/5 ZoBell 2216E liquid medium. The 98 cultures obtained were subsequently applied to phylogenetic analysis based on 16S rRNA gene sequences. The bacterial diversity, evaluated by the Shannon–Weaver index, was relatively small but comparable to previously reported bacterial communities of several environments. The most abundant group was the family Rhodobacteraceae , which has been frequently detected in marine environments. Most bacteria were phylogenetically related to bacteria or uncultured clones detected in marine environments, but distant from published species. The analysis of bacterial community structure by liquid cultivation would be useful as an alternative culture-dependent approach.     

The phylogenetic structure of habitat shift and morphological convergence in Asian Clarias (Teleostei, Siluriformes: Clariidae)

Catfishes of the genus Clarias are an important component of the ichthyofauna in Asia and in Africa. Previous studies demonstrated a high diversity in number of species, morphology and habitat, but little was known on the evolutionary processes underlying this diversity. We analysed an original data set of molecular sequences (cytochrome b and 16S genes), habitat and geographic distributions, as well as 29 morphometric measurements taken on 454 specimens of Asian Clarias . Maximum likelihood phylogeny estimation showed an unexpected cryptic diversity due to strong morphological convergence. The patterns of intra- and interspecific phylogenetic divergence are overall explained by geographic isolation. The analysis of habitat transitions with Markovian models showed that Asian Clarias evolved from an ancestor probably living in clear waters. The most frequent transitions occurred between clear and white waters, whereas transitions towards black waters occurred only from clear waters and were rare events. The morphometric analysis suggests a complex pattern of morphological evolution with repeated convergence towards an elongated form in black waters. The phylogeographic patterns of diversification of Asian Clarias agree with previous studies on other groups and the hypothesis that changes in sea level during the Pleistocene had little influence on shaping biodiversity on the Sunda Shelf.     

The role of seed traits in determining the phylogenetic structure of temperate plant communities

Background and Aims

Phylogenetic clustering of species within plant communities can be expected to result from environmental filtering acting on an evolutionary-conserved plant trait. One such a candidate trait is the embryo to seed-size ratio (E:S). A high E:S may allow faster germination immediately after imbibition, and is therefore assumed to be advantageous in dry habitats. In this study the hypothesis was tested that habitat filtering driven by soil moisture conditions and acting on seed germination and seedling establishment is an important ecological mechanism in structuring temperate plant communities.

Methods

Vegetation samplings were performed in three habitats located within 200 km of each other in western Europe: Ellenberg indicator values showed that the habitats selected differed substantially in terms of soil moisture and light availability. E.S ratio and seed mass data for all genera were obtained from literature. Data were analysed using recently developed phylogenetic methods.

Key Results

Genera with a similar E:S tend to co-occur, as low and high E:S genera dominate in moist and dry habitats, respectively. A phylogenetically clustered pattern of community structure was evident, and dispersion of E:S was positively related to phylogenetic dispersion.

Conclusions

The phenotypically and phylogenetically clustered pattern indicates that E:S-mediated habitat filtering is an important assembly process structuring the plant community of the temperate climate habitats studied.     

Effects of logging and recruitment on community phylogenetic structure in 32 permanent forest plots of Kampong Thom,Cambodia

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.     

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe

Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.     

SEARCHING FOR EVOLUTIONARY PATTERNS IN THE SHAPE OF A PHYLOGENETIC TREE

If all species in a clade are equally likely to speciate or become extinct, then highly symmetric and highly asymmetric phylogenetic trees are unlikely to result. Variation between species in speciation and extinction rates can cause excessive asymmetry. We developed six non-parametric statistical tests that test for nonrandom patterns of branching in any bifurcating tree. The tests are demonstrated by applying them to two published phylogenies for genera of beetles. Comparison of the power of the six statistics under a simple model of biased speciation suggests which of them may be most useful for detecting nonrandom tree shapes.     

Polychaete community structure of the northwestern coast of Mexico: patterns of abundance and distribution

In August 1998, 72 benthic stations were sampled off the northwestern coast of Mexico. A baseline survey of the polychaete macrofauna was carried out for the southernmost portion of the Southern California Bight (SCB) region. Spatial patterns of polychaete assemblages were characterized to determine evidence of environmental impact from point sources of wastewater discharge near the study area, and to define a standard against which to detect future change. A total of 4231 polychaetous annelids representing 38 families and 210 species were identified, which constituted 53% of the total macrofauna. Families with highest species richness were Spionidae (18 spp.), Onuphidae (15 spp.), and Terebellidae (14 spp.). Species with greatest abundances were Spiophanes duplex (490 ind.), Spiophanes fimbriata (330 ind.), Lanassa sp. D (209 ind.), Pectinaria californiensis (138 ind.), and Euclymeninae sp. A (124 ind.). Based on polychaete assemblages, communities for the southernmost SCB were found to be composed primarily of non-opportunistic species, and no numerically dominant species were found. High values of polychaete diversity (H) indicated the majority of the area of study could be considered an undisturbed environment. Principal Components Analysis (PCA) applied to environmental and faunistic parameters indicated depth, organic carbon, and sediment grain size as the main influences determining the polychaete faunal communities.