Picante: R tools for integrating phylogenies and ecology

Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation.

Neighborhoods have little effect on fungal attack or insect predation of developing seeds in a grassland biodiversity experiment

Numerous observational studies have documented conspecific negative density-dependence that is consistent with the Janzen-Connell Hypothesis (JCH) of diversity maintenance. However, there have been few experimental tests of a central prediction of the JCH: that removing host-specific enemies should lead to greater increases in per capita recruitment in areas of higher host density or lower relative phylogenetic diversity. Using spatially randomized plots of high and low host biomass in a temperate grassland biodiversity experiment, we treated developing seedheads of six prairie perennials to factorial applications of fungicide and insecticide. We measured predispersal seed production, seed viability, and seedling biomass. Results were highly species-specific and idiosyncratic. Effects of insect seed predators and fungal pathogens on predispersal responses varied with neither conspecific biomass nor phylogenetic diversity, suggesting that-at least at the predispersal stage and for the insect and fungal seed predators we were able to exclude-the JCH is not sufficient to contribute to negative conspecific density-dependence for these dominant prairie species.

Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson’s index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPD_θ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.

The saliva microbiome of Pan and Homo

Background

It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors.

Results

To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals.

Conclusions

The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild.

Conservation actions based on red lists do not capture the functional and phylogenetic diversity of birds in Brazil

Red Lists of threatened species play a critical role in conservation science and practice. However, policy-making based on Red Lists ignores ecological and evolutionary consequences of losing biodiversity because these lists focus on species alone. To decide if relying on Red Lists alone can help to conserve communities' functional (FD) and phylogenetic (PD) diversity, it is useful to evaluate whether Red List categories represent species with diverse ecological traits and evolutionary histories. Additionally, local scale analyses using regional Red Lists should represent more realistic pools of co-occurring species and thereby better capture eventual losses of FD and PD. Here, we used 21 life-history traits and a phylogeny for all Brazilian birds to determine whether species assigned under the IUCN global Red List, the Brazilian national, and regional Red Lists capture more FD and PD than expected by chance. We also built local Red Lists and analysed if they capture more FD and PD at the local scale. Further, we investigated whether individual threat categories have species with greater FD and PD than expected by chance. At any given scale, threat categories did not capture greater FD or PD than expected by chance. Indeed, mostly categories captured equal or less FD or PD than expected by chance. These findings would not have great consequences if Red Lists were not often considered as a major decision support tool for policy-making. Our results challenge the practice of investing conservation resources based only on species Red Lists because, from an ecological and evolutionary point of view, this would be the same as protecting similar or random sets of species. Thus, new prioritization methods, such as the EDGE of Existence initiative, should be developed and applied to conserve species' ecological traits and evolutionary histories at different spatial scales.

Phylogenetic structure of host spectra in Palaearctic fleas: stability versus spatial variation in widespread, generalist species

We investigated spatial variation in the phylogenetic structure of host spectra in fleas parasitic on small mammals. Measures of phylogenetic host specificity ((phylogenetic species clustering (PSC) and phylogenetic species variability (PSV)) varied significantly more between than within flea species, but the proportion of variation which accounted for among-species differences was low. In 13 of 18 common flea species, at least one of the indices of the phylogenetic structure of regional host spectra revealed a significantly positive association with the phylogenetic structure of regional host assemblage, while relationships between PSC or PSV of the regional host spectrum and the distance from either the region of a flea's maximal abundance or latitude were not supported. Overall, results of this study demonstrated that although the degree of phylogenetic host specificity in fleas can be considered as a true attribute of a flea species, it is highly spatially variable, with phylogenetic structure of the surrounding host pool being the main reason behind this variation.

Evolution of limited seed dispersal ability on gypsum islands

PREMISE OF THE STUDY

Dispersal is a major feature of plant evolution that has many advantages but is not always favored. Wide dispersal, for example, leads to greater seed loss in oceanic-island endemics, and evolution has favored morphologies that limit dispersal. I tested the hypothesis that selection favored limited dispersal on gypsum islands in western North America, where edaphic communities are sparsely vegetated except for a specialized flora that competes poorly with the surrounding flora. •

METHODS

I applied a series of comparative phylogenetic approaches to gypsophilic species of Mentzelia section Bartonia (Loasaceae) to investigate the evolution of limited dispersal function in seed wings, which increase primary dispersal by wind. Through these tests, I determined whether narrowed wings were selected for in gypsophilic species. •

KEY RESULTS

Gypsophily was derived four to seven times. Seed area was not significantly correlated with gypsophily or wing area. Wing area was significantly smaller in the derived gypsum endemics, supporting the hypothesis in favor of limited dispersal function. A model-fitting approach identified two trait optima in wing area, with gypsum endemics having a lower optimum. •

CONCLUSIONS

Evolution into novel ecologies influences morphological evolution. Morphological characters have been selected for limited dispersal following evolution onto gypsum islands. Selection for limited dispersal ability has occurred across animals and plants, both in oceanic and terrestrial systems, which suggests that reduced dispersal ability may be a general process: selection favors limited dispersal if the difference in survival between the habitat of the parent and the surrounding area is great enough.

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus

Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by (15)N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.

Size-dependent changes in wood chemical traits: a comparison of neotropical saplings and large trees

We have a fundamental and applied understanding of how differences in the wood chemistry of trees affects the durability of wood products. By comparison, relatively little is known about the ecological causes and consequences of species differences in wood chemistry; even less is known about how or why wood chemistry differs within species, across trees of different sizes. In this study we find strong and consistent differences in wood chemistry of saplings and canopy trees, in several tropical hardwood species. These differences point to the importance of pathogens and tree biomechanics as evolutionary causes of size-dependent changes in wood chemistry.

Wood anatomical traits are important correlates of life-history strategies among tree species, yet little is known about wood chemical traits. Additionally, size-dependent changes in wood chemical traits have been rarely examined, although these changes may represent an important aspect of tree ontogeny. Owing to selection for pathogen resistance and biomechanical stability, we predicted that saplings would show higher lignin (L) and wood carbon (C_conv), and lower holocellulose (H) concentrations, compared with conspecific large trees. To test these expectations, we quantified H, L and C_conv in co-occurring Panamanian tree species at the large tree vs. sapling size classes. We also examined inter- and intraspecific patterns using multivariate and phylogenetic analyses. In 15 of 16 species, sapling L concentration was higher than that in conspecific large trees, and in all 16 species, sapling H was lower than that in conspecific large trees. In 16 of 24 species, C_conv was higher in saplings than conspecific large trees. All large-tree traits were unrelated to sapling values and were unrelated to four life-history variables. Wood chemical traits did not show a phylogenetic signal in saplings, instead showing similar values across distantly related taxa; in large trees, only H showed a significant phylogenetic signal. Size-dependent changes in wood chemistry show consistent and predictable patterns, suggesting that ontogenetic changes in wood chemical traits are an important aspect of tree functional biology. Our results are consistent with the hypothesis that at early ontogenetic stages, trees are selected for greater L to defend against cellulose-decaying pathogens, or possibly to confer biomechanical stability.

Molecular phylogeny, biogeography, and host plant shifts in the bee genus Melitta (Hymenoptera: Anthophila)

New molecular studies suggested that the family Melittidae is either a paraphyletic group from which all the other bees are derived, or the sister clade to all other existing bees. Studying the historical biogeography and evolution of each major lineage within this group is a key step to understand the origin and early radiation of bees. Melitta is the largest genus of melittid bees, for which a robust molecular phylogeny and a biogeographic analysis are still lacking. Here, we derive a phylogenetic hypothesis from the sequences of seven independent DNA fragments of mitochondrial and nuclear origin. This phylogenetic hypothesis is then used to infer the evolution of the species range and of the host-plant shifts in Melitta. Our results confirmed the monophyly of Melitta, but did not recover all previously defined clades within the genus. We propose new taxa by splitting the genus in three subgenera (including two new subgenera described in the Appendix: Afromelitta subgen. nov., Plesiomelitta subgen. nov.) and describe two new species: Melitta avontuurensis sp. n. and M. richtersveldensis sp. n. Regarding the evolution of host-plant use, our analysis suggests that all species currently specialized on one plant family originated from an ancestor that was specialized on Fabaceae plants. The inferred biogeographic history for the genus supported an African origin. In concordance with previous studies identifying Africa as the geographic origin for many clades of bees, our data bring new evidence for an African origin of melittid bees.

Trait associations across evolutionary time within a drosophila phylogeny: correlated selection or genetic constraint?

Traits do not evolve independently. To understand how trait changes under selection might constrain adaptive changes, phenotypic and genetic correlations are typically considered within species, but these capture constraints across a few generations rather than evolutionary time. For longer-term constraints, comparisons are needed across species but associations may arise because of correlated selection pressures rather than genetic interactions. Implementing a unique approach, we use known patterns of selection to separate likely trait correlations arising due to correlated selection from those reflecting genetic constraints. We examined the evolution of stress resistance in >90 Drosophila species adapted to a range of environments, while controlling for phylogeny. Initially we examined the role of climate and phylogeny in shaping the evolution of starvation and body size, two traits previously not examined in this context. Following correction for phylogeny only a weak relationship between climate and starvation resistance was detected, while all of the variation in the relationship between body size and climate could be attributed to phylogeny. Species were divided into three environmental groups (hot and dry, hot and wet, cold) with the expectation that, if genetic correlations underpin trait correlations, these would persist irrespective of the environment, whereas selection-driven evolution should produce correlations dependent on the environment. We found positive associations between most traits in hot and dry environments coupled with high trait means. In contrast few trait correlations were observed in hot/wet and cold environments. These results suggest trait associations are primarily driven by correlated selection rather than genetic interactions, highlighting that such interactions are unlikely to limit evolution of stress resistance.

Climate drives vein anatomy in Proteaceae

PREMISE OF STUDY

The mechanisms by which plants tolerate water deficit are only just becoming clear. One key factor in drought tolerance is the ability to maintain the capacity to conduct water through the leaves in conditions of water stress. Recent work has shown that a simple feature of the leaf xylem cells, the cube of the thickness of cell walls divided by the lumen width (t/b)(3), is strongly correlated with this ability.

METHODS

Using ecologically, phylogenetically, and anatomically diverse members of Proteaceae, we tested the relationships between (t/b)(3) and climate, leaf mass per unit area, leaf area, and vein density. To test relationships at high phylogenetic levels (mostly genus), we used phylogenetic and nonphylogenetic single and multiple regressions based on data from 50 species. We also used 14 within-genus species pairs to test for relationships at lower phylogenetic levels.

KEY RESULTS

All analyses revealed that climate, especially mean annual precipitation, was the best predictor of (t/b)(3). The variation in (t/b)(3) was driven by variation in both lumen diameter and wall thickness, implying active control of these dimensions. Total vein density was weakly related to (t/b)(3) but unrelated to either leaf area or climate.

CONCLUSIONS

We conclude that xylem reinforcement is a fundamental adaptation for water stress tolerance and, among evergreen woody plants, drives a strong association between rainfall and xylem anatomy. The strong association between (t/b)(3) and climate cannot be explained by autocorrelation with other aspects of leaf form and anatomy that vary along precipitation gradients.

A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

PREMISE OF THE STUDY

Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade.

METHODS

Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus.

KEY RESULTS

We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan-Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous-late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates.

CONCLUSIONS

Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.

Change in phylogenetic community structure during succession of traditionally managed tropical rainforest in southwest China

Tropical rainforests in Southeast Asia are facing increasing and ever more intense human disturbance that often negatively affects biodiversity. The aim of this study was to determine how tree species phylogenetic diversity is affected by traditional forest management types and to understand the change in community phylogenetic structure during succession. Four types of forests with different management histories were selected for this purpose: old growth forests, understorey planted old growth forests, old secondary forests (∼200-years after slash and burn), and young secondary forests (15–50-years after slash and burn). We found that tree phylogenetic community structure changed from clustering to over-dispersion from early to late successional forests and finally became random in old-growth forest. We also found that the phylogenetic structure of the tree overstorey and understorey responded differentially to change in environmental conditions during succession. In addition, we show that slash and burn agriculture (swidden cultivation) can increase landscape level plant community evolutionary information content.

The evolution of social monogamy in mammals

The evolution of social monogamy has intrigued biologists for over a century. Here, we show that the ancestral condition for all mammalian groups is of solitary individuals and that social monogamy is derived almost exclusively from this social system. The evolution of social monogamy does not appear to have been associated with a high risk of male infanticide, and paternal care is a consequence rather than a cause of social monogamy. Social monogamy has evolved in nonhuman mammals where breeding females are intolerant of each other and female density is low, suggesting that it represents a mating strategy that has developed where males are unable to defend access to multiple females.

Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia

Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha- (plot) and beta- (among plot) diversity (Fisher's alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the elevational gradient. We recorded 902 trees and shrubs among 92 species, and 67 species of ground-cover plants. For understorey, subcanopy and canopy plants, an increase in elevation was associated with a decline in alpha-diversity, whereas data for ground-cover plants suggested a hump-shaped pattern. Elevation was consistently the most important factor in determining alpha-diversity for all components. The alpha-diversity of ground-cover vegetation was also negatively correlated with leaf area index, which suggests low light conditions in the understorey may limit diversity at lower elevations. Beta-diversity increased with elevation for ground-cover plants and declined at higher elevations for other components of the vegetation. However, statistical power was low and we could not resolve the relative importance to beta-diversity of different factors. Multivariate GLMs of variation in community composition among plots explained 67.05%, 27.63%, 18.24%, and 19.80% of the variation (deviance) for ground-cover, understorey, subcanopy and canopy plants, respectively, and demonstrated that elevation was a consistently important factor in determining community composition. Above-ground biomass showed no significant pattern with elevation and was also not significantly associated with alpha-diversity. At lower elevations communities had a random phylogenetic structure, but from 1600 m communities were phylogenetically clustered. This suggests a greater role of environmental filtering at higher elevations, and thus provides a possible explanation for the observed decline in diversity with elevation.

Niche conservatism constrains Australian honeyeater assemblages in stressful environments

The hypothesis of phylogenetic niche conservatism proposes that most extant members of a clade remain in ancestral environments because expansion into new ecological space imposes a selectional load on a population. A prediction that follows is that local assemblages contain increasingly phylogenetically clustered subsets of species with increasing difference from the ancestral environment of a clade. We test this in Australian Meliphagidae, a continental radiation of birds that originated in wet, subtropical environments, but subsequently spread to drier environments as Australia became more arid during the late Cenozoic. We find local assemblages are increasingly phylogenetically clustered along a gradient of decreasing precipitation. The pattern is less clear along a temperature gradient. We develop a novel phyloclimatespace to visualise the expansion of some lineages into drier habitats. Although few species extend into arid regions, those that do occupy larger ranges and thus local species richness does not decline predictably with precipitation.

Complete mitochondrial genome of endangered Maroon-fronted Parrot (Rhynchopsitta terrisi) - conspecific relation of the species with Thick-billed Parrot (Rhynchopsitta pachyrhyncha)

Maroon-fronted Parrot (Rhynchopsitta terrisi) is an endangered parrot endemic to pine-oak forests in north-eastern Mexico. According to all present classifications, R. terrisi as well as Rhynchopsitta pachyrhyncha are treated as a separate species based on some morphological and behavioral discrepancies. Despite this formal separation of the two species, some taxonomists conjecture their conspecific character. However, mutual taxonomic position of both species/subspecies was never verified by molecular research. We sequenced full mitochondrial genome of R. terrisi and constructed phylogenetic tree using sequences of mitochondrial ND2 gene from R. terrisi. R. pahyrchyncha and some other representative species of the tribe Arini. Our results indicated that in contrast to formal classification, both Rhynchopsitta taxa should be treated as subspecies.

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

BACKGROUND

The genetic network involved in the bacterial cell cycle is poorly understood even though it underpins the remarkable ability of bacteria to proliferate. How such network evolves is even less clear. The major aims of this work were to identify and examine the genes and pathways that are differentially expressed during the Caulobacter crescentus cell cycle, and to analyze the evolutionary features of the cell cycle network.

RESULTS

We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many genes previously unknown for their cell cycle regulation, includes almost half of the genes involved in primary metabolism, suggesting that these "house-keeping" genes are not constitutively transcribed during the cell cycle, as often assumed. Gene and module co-expression clustering reveal co-regulated pathways and suggest functionally coupled genes. In addition, an evolutionary analysis of the cell cycle network shows a high correlation between co-expression and co-evolution. Most co-expression modules have strong phylogenetic signals, with broadly conserved genes and clade-specific genes predominating different substructures of the cell cycle co-expression network. We also found that conserved genes tend to determine the expression profile of their module.

CONCLUSION

We describe the first phylogenetic and single-nucleotide-resolution transcriptomic analysis of a bacterial cell cycle network. In addition, the study suggests how evolution has shaped this network and provides direct biological network support that selective pressure is not on individual genes but rather on the relationship between genes, which highlights the importance of integrating phylogenetic analysis into biological network studies.

The evolution and function of vessel and pit characters with respect to cavitation resistance across 10 Prunus species

Various structure-function relationships regarding drought-induced cavitation resistance of secondary xylem have been postulated. These hypotheses were tested on wood of 10 Prunus species showing a range in P50 (i.e., the pressure corresponding to 50% loss of hydraulic conductivity) from -3.54 to -6.27 MPa. Hydraulically relevant wood characters were quantified using light and electron microscopy. A phylogenetic tree was constructed to investigate evolutionary correlations using a phylogenetically independent contrast (PIC) analysis. Vessel-grouping characters were found to be most informative in explaining interspecific variation in P50, with cavitation-resistant species showing more solitary vessels than less resistant species. Co-evolution between vessel-grouping indices and P50 was reported. P50 was weakly correlated with the shape of the intervessel pit aperture, but not with the total intervessel pit membrane area per vessel. A negative correlation was found between P50 and intervessel pit membrane thickness, but this relationship was not supported by the PIC analysis. Cavitation resistance has co-evolved with vessel grouping within Prunus and was mainly influenced by the spatial distribution of the vessel network.

Temperature-dependent shifts in phenology contribute to the success of exotic species with climate change

PREMISE OF THE STUDY

The study of how phenology may contribute to the assembly of plant communities has a long history in ecology. Climate change has brought renewed interest in this area, with many studies examining how phenology may contribute to the success of exotic species. In particular, there is increasing evidence that exotic species occupy unique phenological niches and track climate change more closely than native species.

METHODS

Here, we use long-term records of species’ first flowering dates from fi ve northern hemisphere temperate sites (Chinnor, UK and in the United States, Concord, Massachusetts; Fargo, North Dakota; Konza Prairie, Kansas; and Washington,D.C.) to examine whether invaders have distinct phenologies. Using a broad phylogenetic framework, we tested for differences between exotic and native species in mean annual flowering time, phenological changes in response to temperature and precipitation,and longer-term shifts in first flowering dates during recent pronounced climate change (“flowering time shifts”).

KEY RESULTS

Across North American sites, exotic species have shifted flowering with climate change while native species, on average, have not. In the three mesic systems, exotic species exhibited higher tracking of interannual variation in temperature,such that flowering advances more with warming, than native species. Across the two grassland systems, however, exotic species differed from native species primarily in responses to precipitation and soil moisture, not temperature.

CONCLUSIONS

Our findings provide cross-site support for the role of phenology and climate change in explaining species’ invasions.Further, they support recent evidence that exotic species may be important drivers of extended growing seasons observed with climate change in North America.

Changes in soil bacterial community structure with increasing disturbance frequency

Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

Phylogenetic influences on leaf trait integration in Pelargonium (Geraniaceae): convergence, divergence, and historical adaptation to a rapidly changing climate

PREMISE OF THE STUDY

Trait integration may improve prediction of species and lineage responses to future climate change more than individual traits alone, particularly when analyses incorporate effects of phylogenetic relationships. The South African genus Pelargonium contains divergent major clades that have radiated along the same seasonal aridity gradient, presenting the opportunity to ask whether patterns of evolution in mean leaf trait values are achieved through the same set of coordinated changes among traits in each clade.

METHODS

Seven leaf traits were measured on field-collected leaves from one-third of the species (98) of the genus. Trait relationships were examined using phylogenetic regression within major clades. Disparity analysis determined whether the course of trait evolution paralleled historical climate change events.

KEY RESULTS

Divergence in mean trait values between sister clades A1 and A2 was consistent with expectations for leaves differing in longevity, despite strong similarity between clades in trait interactions. No traits in either clade exhibited significant relationships with multivariate climate axes, with one exception. Species in clades C and A2 included in this study occupied similar environments. These clades had similar values of individual trait means, except for δ(13)C, but they exhibited distinctive patterns of trait integration.

CONCLUSIONS

Differing present-day patterns of trait integration are consistent with interpretations of adaptive responses to the prevailing climate at the time of each clade's origin. These differing patterns of integration are likely to exert strong effects on clade-level responses to future climate change in the winter rainfall region of South Africa.

Phylogeny-based comparative analysis of venom proteome variation in a clade of rattlesnakes (Sistrurus sp.)

A long-standing question in evolutionary studies of snake venoms is the extent to which phylogenetic divergence and diet can account for between-species differences in venom composition. Here we apply phylogeny-based comparative methods to address this question. We use data on venom variation generated using proteomic techniques for all members of a small clade of rattlesnakes (Sistrurus sp.) and two outgroups for which phylogenetic and diet information is available. We first complete the characterization of venom variation for all members of this clade with a “venomic” analysis of pooled venoms from two members of this genus, S. milarius streckeri and S. m. milarius. These venoms exhibit the same general classes of proteins as those found in other Sistrurus species but differ in their relative abundances of specific protein families. We then test whether there is significant phylogenetic signal in the relative abundances of major venom proteins across species and if diet (measured as percent mammals and lizards among all prey consumed) covaries with venom composition after phylogenetic divergence is accounted for. We found no evidence for significant phylogenetic signal in venom variation: K values for seven snake venom proteins and two composite venom variables [PC 1 and 2]) were all nonsignificant and lower (mean = 0.11+0.06 sd) than mean K values (>0.35) previously reported for a wide range of morphological, life history, physiological and behavioral traits from other species. Finally, analyses based on Phylogenetic Generalized Least Squares (PGLS) methods reveal that variation in abundance of some venom proteins, most strongly CRISP is significantly related to snake diet. Our results demonstrate that venom variation in these snakes is evolutionarily a highly labile trait even among very closely-related taxa and that natural selection acting through diet variation may play a role in molding the relative abundance of specific venom proteins.

A Global Trend towards the Loss of Evolutionarily Unique Species in Mangrove Ecosystems

The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.

Heterospecific aggression and dominance in a guild of coral-feeding fishes: the roles of dietary ecology and phylogeny

Interspecific competition mediates biodiversity maintenance and is an important selective pressure for evolution. Competition is often conceptualized as being exploitative (indirect) or involving direct interference. However, most empirical studies are phenomenological, focusing on quantifying effects of density manipulations, and most competition theory has characterized exploitation competition systems. The effects on resource use of traits associated with direct, interference competition has received far less attention. Here we examine the relationships of dietary ecology and phylogeny to heterospecific aggression in a guild of corallivorous reef fishes. We find that, among chaetodontids (butterflyfishes), heterospecific aggression depends on a synergistic interaction of dietary overlap and specialization: aggression increases with dietary overlap for interactions between specialists but not for interactions involving generalists. Moreover, behavioral dominance is a monotonically increasing function of dietary specialization. The strong, positive relationship of dominance to specialization suggests that heterospecific aggression may contribute to the maintenance of biodiversity where it promotes resource partitioning. Additionally, we find strong phylogenetic signals in dietary overlap and specialization but not behavioral dominance. Our results support the use of phylogeny as a proxy for ecological similarity among butterflyfishes, but we find that direct measures of dietary overlap and specialization predict heterospecific agression much better than phylogeny.

Vanadate and acetate biostimulation of contaminated sediments decreases diversity, selects for specific taxa, and decreases aqueous V5+ concentration

Vanadium is a commercially important metal that is released into the environment by fossil fuel combustion and mining. Despite its prevalence as a contaminant, the potential for vanadium bioremediation has not been widely studied. Injection of acetate (as a carbon source) directly into an aquifer to biostimulate contaminated sediments in Colorado, United States, resulted in prolonged removal of aqueous vanadium for a period of at least two years. To further investigate this process, we simultaneously added acetate and vanadate (V(5+)) to columns that were packed with aquifer sediment and inserted into groundwater wells installed on the Colorado River floodplain. This allowed evaluation of the microbial response to amendments in columns that received an influx of natural groundwater. Our results demonstrate the removal of up to 99% of the added V(5+)(aq) and suggest microbial mediation. Most probable number measurements demonstrate up to a 50-fold increase in numbers of V(5+)-reducing cells in vanadium-amended columns compared to controls. 16S rRNA gene sequencing indicates decreased diversity and selection for specific taxa in columns that received vanadate compared to those that did not. Overall, our results demonstrate that acetate amendment can be an effective strategy for V removal, and that V bioremediation may be a viable technology.

Spatial variation in the phylogenetic structure of flea assemblages across geographic ranges of small mammalian hosts in the Palearctic

We investigated spatial variation in the phylogenetic structure (measured as a degree of phylogenetic clustering) of flea assemblages across the geographic ranges of 11 Palearctic species of small mammalian hosts and asked whether the phylogenetic structure of the flea assemblage of a host in a locality is affected by (i) distance of this locality from the centre of the host's geographic range, (ii) geographic position of the locality (distance to the equator) and (iii) phylogenetic structure of the entire flea assemblage of the locality. Our results demonstrated that the key factor underlying spatial variation of the phylogenetic structure of the flea assemblage of a host was the distance from the centre of the host's geographic range. However, the pattern of this spatial variation differed between host species and might be explained by their species-specific immunogenetic and/or distributional patterns. Local flea assemblages may also, to some extent, be shaped by environmental filtering coupled with historical events. In addition, the phylogenetic structure of a local within-host flea assemblage may mirror the phylogenetic structure of the entire across-host flea assemblage in that locality and, thus, be affected by the availability of certain phylogenetic lineages.

Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents

Genetic variation at the major histocompatibility complex (MHC) is vitally important for wildlife populations to respond to pathogen threats. As natural populations can fluctuate greatly in size, a key issue concerns how population cycles and bottlenecks that could reduce genetic diversity will influence MHC genes. Using 454 sequencing, we characterized genetic diversity at the DRB Class II locus in montane voles (Microtus montanus), a North American rodent that regularly undergoes high-amplitude fluctuations in population size. We tested for evidence of historic balancing selection, recombination, and gene duplication to identify mechanisms maintaining allelic diversity. Counter to our expectations, we found strong evidence of purifying selection acting on the DRB locus in montane voles. We speculate that the interplay between population fluctuations and gene duplication might be responsible for the weak evidence of historic balancing selection and strong evidence of purifying selection detected. To further explore this idea, we conducted a phylogenetically controlled comparative analysis across 16 rodent species with varying demographic histories and MHC duplication events (based on the maximum number of alleles detected per individual). On the basis of phylogenetic generalized linear model-averaging, we found evidence that the estimated number of duplicated loci was positively related to allelic diversity and, surprisingly, to the strength of purifying selection at the DRB locus. Our analyses also revealed that species that had undergone population bottlenecks had lower allelic richness than stable species. This study highlights the need to consider demographic history and genetic structure alongside patterns of natural selection to understand resulting patterns of genetic variation at the MHC.

Congruence and diversity of butterfly-host plant associations at higher taxonomic levels

We aggregated data on butterfly-host plant associations from existing sources in order to address the following questions: (1) is there a general correlation between host diversity and butterfly species richness?, (2) has the evolution of host plant use followed consistent patterns across butterfly lineages?, (3) what is the common ancestral host plant for all butterfly lineages? The compilation included 44,148 records from 5,152 butterfly species (28.6% of worldwide species of Papilionoidea) and 1,193 genera (66.3%). The overwhelming majority of butterflies use angiosperms as host plants. Fabales is used by most species (1,007 spp.) from all seven butterfly families and most subfamilies, Poales is the second most frequently used order, but is mostly restricted to two species-rich subfamilies: Hesperiinae (56.5% of all Hesperiidae), and Satyrinae (42.6% of all Nymphalidae). We found a significant and strong correlation between host plant diversity and butterfly species richness. A global test for congruence (Parafit test) was sensitive to uncertainty in the butterfly cladogram, and suggests a mixed system with congruent associations between Papilionidae and magnoliids, Hesperiidae and monocots, and the remaining subfamilies with the eudicots (fabids and malvids), but also numerous random associations. The congruent associations are also recovered as the most probable ancestral states in each node using maximum likelihood methods. The shift from basal groups to eudicots appears to be more likely than the other way around, with the only exception being a Satyrine-clade within the Nymphalidae that feed on monocots. Our analysis contributes to the visualization of the complex pattern of interactions at superfamily level and provides a context to discuss the timing of changes in host plant utilization that might have promoted diversification in some butterfly lineages.

Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae

Although discordance between taxonomic diversity and morphological disparity is common, little is known about the underlying dynamics that drive this decoupling. Early in the history of the Cambrian trilobite family Pterocephaliidae, there was an increase in taxonomic diversity and morphological diversity. As taxonomic diversity declined in the later history of the clade, range of variation stayed high and disparity continued to increase. However, per-branch rates of morphological evolution estimated from a recent phylogeny decreased with time. Neither within-trait nor within-species variation increased or decreased, suggesting that the declining rates of morphological evolution were more likely related to ecological opportunity or niche partitioning, rather than increasing intrinsic constraints. This is further supported by evidence for increased biofacies associations throughout the time period. Thus, the high disparity seen at low taxonomic diversity late in the history of this clade was due to extinction - either random or targeting mean forms - rather than increased rates of morphological evolution. This pattern also provides a scenario that could account for instances of low taxonomic diversity but high morphological disparity in modern groups.

Ecological differentiation of cryptic species within an asexual protist morphospecies: a case study of filamentous green alga Klebsormidium (Streptophyta)

Taxa of microbial eukaryotes defined on morphological basis display a large degree of genetic diversity, implying the existence of numerous cryptic species. However, it has been postulated that genetic diversity merely mirrors accumulation of neutral mutations. As a case taxon to study cryptic diversity in protists, we used a widely distributed filamentous genus, Klebsormidium, specifically the lineage E (K. flaccidum/K. nitens complex) containing a number of morphologically similar strains. Fourteen clades were recognized in the phylogenetic analysis based on a concatenated ITS rDNA + rbcL data set of more than 70 strains. The results of inferred character evolution indicated the existence of phylogenetic signal in at least two phenotypic characters (production of hydro-repellent filaments and morphology of zoosporangia). Moreover, the lineages recovered exhibited strong ecological preferences to one of the three habitat types: natural subaerial substrata, artificial subaerial substrata, and aquatic habitats. We interpret these results as evidence of existence of a high number of cryptic species within the single morphospecies. We consider that the permanent existence of genetically and ecologically well-defined cryptic species is enabled by the mechanism of selective sweep.

A phylogenetic perspective on the individual species-area relationship in temperate and tropical tree communities

Ecologists have historically used species-area relationships (SARs) as a tool to understand the spatial distribution of species. Recent work has extended SARs to focus on individual-level distributions to generate individual species area relationships (ISARs). The ISAR approach quantifies whether individuals of a species tend have more or less species richness surrounding them than expected by chance. By identifying richness 'accumulators' and 'repellers', respectively, the ISAR approach has been used to infer the relative importance of abiotic and biotic interactions and neutrality. A clear limitation of the SAR and ISAR approaches is that all species are treated as evolutionarily independent and that a large amount of work has now shown that local tree neighborhoods exhibit non-random phylogenetic structure given the species richness. Here, we use nine tropical and temperate forest dynamics plots to ask: (i) do ISARs change predictably across latitude?; (ii) is the phylogenetic diversity in the neighborhood of species accumulators and repellers higher or lower than that expected given the observed species richness?; and (iii) do species accumulators, repellers distributed non-randomly on the community phylogenetic tree? The results indicate no clear trend in ISARs from the temperate zone to the tropics and that the phylogenetic diversity surrounding the individuals of species is generally only non-random on very local scales. Interestingly the distribution of species accumulators and repellers was non-random on the community phylogenies suggesting the presence of phylogenetic signal in the ISAR across latitude.