Coexistence of insect species competing for a pulsed resource: toward a unified theory of biodiversity in fluctuating environments

Background

One major challenge in understanding how biodiversity is organized is finding out whether communities of competing species are shaped exclusively by species-level differences in ecological traits (niche theory), exclusively by random processes (neutral theory of biodiversity), or by both processes simultaneously. Communities of species competing for a pulsed resource are a suitable system for testing these theories: due to marked fluctuations in resource availability, the theories yield very different predictions about the timing of resource use and the synchronization of the population dynamics between the competing species. Accordingly, we explored mechanisms that might promote the local coexistence of phytophagous insects (four sister species of the genus Curculio) competing for oak acorns, a pulsed resource.

Methodology/Principal Findings

We analyzed the time partitioning of the exploitation of oak acorns by the four weevil species in two independent communities, and we assessed the level of synchronization in their population dynamics. In accordance with the niche theory, overall these species exhibited marked time partitioning of resource use, both within a given year and between different years owing to different dormancy strategies between species, as well as distinct demographic patterns. Two of the four weevil species, however, consistently exploited the resource during the same period of the year, exhibited a similar dormancy pattern, and did not show any significant difference in their population dynamics.

Conclusions/Significance

The marked time partitioning of the resource use appears as a keystone of the coexistence of these competing insect species, except for two of them which are demographically nearly equivalent. Communities of consumers of pulsed resources thus seem to offer a promising avenue for developing a unifying theory of biodiversity in fluctuating environments which might predict the co-occurrence, within the same community, of species that are ecologically either very similar, or very different.     

Species interactions during diversification and community assembly in an island radiation of shrews

Background

Closely related, ecologically similar species often have adjacent distributions, suggesting competitive exclusion may contribute to the structure of some natural communities. In systems such as island archipelagos, where speciation is often tightly associated with dispersal over oceanic barriers, competitive exclusion may prevent population establishment following inter-island dispersal and subsequent cladogenesis.

Methodology/Principal Findings

Using a combination of tools, we test the hypothesis that the distributions of shrew (Crocidura) species in the Philippines are the result of competitive exclusion preventing secondary invasion of occupied islands. We first compare ecological niche models between two widespread, allopatric species and find statistical support for their ecological similarity, implying that competition for habitat between these species is possible. We then examine dispersion patterns among sympatric species and find some signal for overdispersion of body size, but not for phylogenetic branch length. Finally, we simulate the process of inter-island colonization under a stochastic model of dispersal lacking ecological forces. Results are dependent on the geographic scope and colonization probability employed. However, some combinations suggest that the number of inter-island dispersal events necessary to populate the archipelago may be much higher than the minimum number of colonization events necessary to explain current estimates of species richness and phylogenetic relationships. If our model is appropriate, these results imply that alternative factors, such as competitive exclusion, may have influenced the process of inter-island colonization and subsequent cladogenesis.

Conclusions/Significance

We interpret the combined results as providing tenuous evidence that similarity in body size may prevent co-occurrence in Philippine shrews and that competitive exclusion among ecologically similar species, rather than an inability to disperse among islands, may have limited diversification in this group, and, possibly other clades endemic to island archipelagos.     

Seasonal Dynamics of the Plant Community and Soil Seed Bank along a Successional Gradient in a Subalpine Meadow on the Tibetan Plateau

Background

Knowledge about how change the importance of soil seed bank and relationship between seed mass and abundance during vegetation succession is crucial for understanding vegetation dynamics. Many studies have been conducted, but their ecological mechanisms of community assembly are not fully understood.

Methodology

We examined the seasonal dynamics of the vegetation and soil seed bank as well as seed size distribution along a successional gradient. We also explored the potential role of the soil seed bank in plant community regeneration, the relationship between seed mass and species abundance, and the relative importance of deterministic and stochastic processes along a successional gradient.

Principal Findings

Species richness of seed bank increased (shallow layer and the total) and seed density decreased (each layer and the total) significantly with succession. Species richness and seed density differed significantly between different seasons and among soil depths. Seed mass showed a significant negative relationship with relative abundance in the earliest successional stage, but the relationships were not significant in later stages. Seed mass showed no relationship with relative abundance in the whole successional series in seed bank. Results were similar for both July 2005 and April 2006.

Conclusions

The seed mass and abundance relationship was determined by a complex interaction between small and larger seeded species and environmental factors. Both stochastic processes and deterministic processes were important determinants of the structure of the earliest stage. The importance of seed bank decreased with succession. The restoration of abandoned farmed and grazed meadows to the species-rich subalpine meadow in Tibetan Plateau can be successfully achieved from the soil seed bank. However, at least 20 years are required to fully restore an abandoned agricultural meadow to a natural mature subalpine meadow.     

Departures from neutrality induced by niche and relative fitness differences

Breaking the core assumption of ecological equivalence in Hubbell’s “neutral theory of biodiversity” requires a theory of species differences. In one framework for characterizing differences between competing species, non-neutral interactions are said to involve both niche differences, which promote stable coexistence, and relative fitness differences, which promote competitive exclusion. We include both in a stochastic community model in order to determine if relative fitness differences compensate for changes in community structure and dynamics induced by niche differences, possibly explaining neutral theory’s apparent success. We show that species abundance distributions are sensitive to both niche and relative fitness differences, but that certain combinations of differences result in abundance distributions that are indistinguishable from the neutral case. In contrast, the distribution of species’ lifetimes, or the time between speciation and extinction, differs under all combinations of niche and relative fitness differences. The results from our model experiment are inconsistent with the hypothesis of “emergent neutrality” and support instead a hypothesis that relative fitness differences counteract effects of niche differences on distributions of abundance. However, an even more developed theory of interspecific variation appears necessary to explain the diversity and structure of non-neutral communities.     

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

Background

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.

Methodology/Principal Findings

By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.

Conclusions/Significance

We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.     

Experimental investigation of the origin of fynbos plant community structure after fire

Background and aims

Species in plant communities segregate along fine-scale hydrological gradients. Although this phenomenon is not unique to fynbos, this community regenerates after fire and therefore provides an opportunity to study the ecological genesis of hydrological niche segregation.

Methods

Following wildfires at two field sites where we had previously mapped the vegetation and monitored the hydrology, seeds were moved experimentally in >2500 intact soil cores up and down soil-moisture gradients to test the hypothesis that hydrological niche segregation is established during the seedling phase of the life cycle. Seedling numbers and growth were then monitored and they were identified using DNA bar-coding, the first use of this technology for an experiment of this kind.

Key Results

At the site where niche segregation among Restionaceae had previously been found, the size of seedlings was significantly greater, the wetter the location into which they were moved, regardless of the soil moisture status of their location of origin, or of the species. Seedling weight was also significantly greater in a competition treatment where the roots of other species were excluded. No such effects were detected at the control site where niche segregation among Restionaceae was previously found to be absent.

Conclusions

The finding that seedling growth on hydrological gradients in the field is affected by soil moisture status and by root competition shows that hydrological niche segregation could potentially originate in the seedling stage. The methodology, applied at a larger scale and followed-through for a longer period, could be used to determine whether species are differently affected by soil moisture.     

Impact of Herbivore Identity on Algal Succession and Coral Growth on a Caribbean Reef

Background

Herbivory is an important top-down force on coral reefs that regulates macroalgal abundance, mediates competitive interactions between macroalgae and corals, and provides resilience following disturbances such as hurricanes and coral bleaching. However, reductions in herbivore diversity and abundance via disease or over-fishing may harm corals directly and may indirectly increase coral susceptibility to other disturbances.

Methodology and Principal Findings

In two experiments over two years, we enclosed equivalent densities and masses of either single-species or mixed-species of herbivorous fishes in replicate, 4 m² cages at a depth of 17 m on a reef in the Florida Keys, USA to evaluate the effects of herbivore identity and species richness on colonization and development of macroalgal communities and the cascading effects of algae on coral growth. In Year 1, we used the redband parrotfish (Sparisoma aurofrenatum) and the ocean surgeonfish (Acanthurus bahianus); in Year 2, we used the redband parrotfish and the princess parrotfish (Scarus taeniopterus). On new substrates, rapid grazing by ocean surgeonfish and princess parrotfish kept communities in an early successional stage dominated by short, filamentous algae and crustose coralline algae that did not suppress coral growth. In contrast, feeding by redband parrotfish allowed an accumulation of tall filaments and later successional macroalgae that suppressed coral growth. These patterns contrast with patterns from established communities not undergoing primary succession; on established substrates redband parrotfish significantly reduced upright macroalgal cover while ocean surgeonfish and princess parrotfish allowed significant increases in late successional macroalgae.

Significance

This study further highlights the importance of biodiversity in affecting ecosystem function in that different species of herbivorous fishes had very different impacts on reef communities depending on the developmental stage of the community. The species-specific effects of herbivorous fishes suggest that a species-rich herbivore fauna can be critical in providing the resilience that reefs need for recovery from common disturbances such as coral bleaching and storm damage.     

Mating system shifts and transposable element evolution in the plant genus Capsella

Background

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora.

Results

We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species.

Conclusion

Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.     

Size-specific interaction patterns and size matching in a plant�Cpollinator interaction web

Background and Aims

Many recent studies show that plant–pollinator interaction webs exhibit consistent structural features such as long-tailed distributions of the degree of generalization, nestedness of interactions and asymmetric interaction dependencies. Recognition of these shared features has led to a variety of mechanistic attempts at explanation. Here it is hypothesized that beside size thresholds and species abundances, the frequency distribution of sizes (nectar depths and proboscis lengths) will play a key role in determining observed interaction patterns.

Methods

To test the influence of size distributions, a new network parameter is introduced: the degree of size matching between nectar depth and proboscis length. The observed degree of size matching in a Spanish plant–pollinator web was compared with the expected degree based on joint probability distributions, integrating size thresholds and abundance, and taking the sampling method into account.

Key Results

Nectar depths and proboscis lengths both exhibited right-skewed frequency distributions across species and individuals. Species-based size matching was equally close for plants, independent of nectar depth, but differed significantly for pollinators of dissimilar proboscis length. The observed patterns were predicted well by a model considering size distributions across species. Observed size matching was closer when relative abundances of species were included, especially for flowers with openly accessible nectar and pollinators with long proboscises, but was predicted somewhat less successfully by the model that included abundances.

Conclusions

The results suggest that in addition to size thresholds and species abundances, size distributions are important for understanding interaction patterns in plant–pollinator webs. It is likely that the understanding will be improved further by characterizing for entire communities how nectar production of flowers and energetic requirements of pollinators covary with size, and how sampling methods influence the observed interaction patterns.Key words: Plant–pollinator community, flower morphology, generalization, nectar, pollination network, body size, size matching, specialization     

Non-Additive Effects of Genotypic Diversity Increase Floral Abundance and Abundance of Floral Visitors

Background

In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention.

Methodology/Principal Findings

Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot) of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1) plant genotype explained 45% and 92% of the variation in flower visitor abundance in 2007 and 2008, respectively; and 2) plant genotypic diversity had a positive and non-additive effect on floral abundance and the abundance of flower visitors, as plots established with multiple genotypes produced 25% more flowers and received 45% more flower visits than would be expected under an additive model.

Conclusions/Significance

These results provide evidence that declines in genotypic diversity may be an important but little considered factor for understanding plant-pollinator dynamics, with implications for the global decline in pollinators due to reduced plant diversity in both agricultural and natural ecosystems.     

Differential competitive ability between sexes in the dioecious Antennaria dioica (Asteraceae)

Background and Aims

Differences in competitive ability between the sexes of dioecious plants are expected as a result of allocation trade-offs associated with sex-differential reproductive costs. However, the available data on competitive ability in dioecious plants are scarce and contradictory. In this study sexual competition was evaluated using the dioecious plant Antennaria dioica in a common garden transplantation experiment.

Methods

Male and female plants were grown for 3 years either in isolation, or in competition with a plant of the same sex or the opposite sex. Flowering phenology, sexual and asexual reproduction, plant growth, nutrient content and arbuscular mycorrhizal colonization in the roots were assessed.

Key Results

Our results showed little evidence of sexual differences in competitive ability. Both sexes suffered similarly from competition, and competitive effects were manifested in some traits related to fitness but not in others. Survival was unaffected by competition, but competing plants reduced their vegetative growth and reproductive investment compared with non-competing plants. In addition, differences in sexual competitive ability were observed in relation to flowering frequency, an important life history trait not reported in previous studies.

Conclusions

The findings indicate that female and male A. dioica plants possess similar intersexual competitive abilities which may be related to the similar costs of reproduction between sexes in this species. Nevertheless, intrasexual competition is higher in females, giving support for asymmetric niche segregation between the sexes.     

Relationship between reproductive allocation and relative abundance among 32 species of a Tibetan alpine meadow: effects of fertilization and grazing

Background

Understanding the relationship between species traits and species abundance is an important goal in ecology and biodiversity science. Although theoretical studies predict that traits related to performance (e.g. reproductive allocation) are most directly linked to species abundance within a community, empirical investigations have rarely been done. It also remains unclear how environmental factors such as grazing or fertilizer application affect the predicted relationship.

Methodology

We conducted a 3-year field experiment in a Tibetan alpine meadow to assess the relationship between plant reproductive allocation (RA) and species relative abundance (SRA) on control, grazed and fertilized plots. Overall, the studied plant community contained 32 common species.

Principal Findings

At the treatment level, (i) RA was negatively correlated with SRA on control plots and during the first year on fertilized plots. (ii) No negative RA–SRA correlations were observed on grazed plots and during the second and third year on fertilized plots. (iii) Seed size was positively correlated with SRA on control plots. At the plot level, the correlation between SRA and RA were not affected by treatment, year or species composition.

Conclusions/Significance

Our study shows that the performance-related trait RA can negatively affect SRA within communities, which is possibly due to the tradeoffs between clonal growth (for space occupancy) and sexual reproduction. We propose that if different species occupy different positions along these tradeoffs it will contribute to biodiversity maintenance in local communities or even at lager scale.     

Fire,Fuel Composition and Resilience Threshold in Subalpine Ecosystem

Background

Forecasting the effects of global changes on high altitude ecosystems requires an understanding of the long-term relationships between biota and forcing factors to identify resilience thresholds. Fire is a crucial forcing factor: both fuel build-up from land-abandonment in European mountains, and more droughts linked to global warming are likely to increase fire risks.

Methods

To assess the vegetation response to fire on a millennium time-scale, we analyzed evidence of stand-to-local vegetation dynamics derived from sedimentary plant macroremains from two subalpine lakes. Paleobotanical reconstructions at high temporal resolution, together with a fire frequency reconstruction inferred from sedimentary charcoal, were analyzed by Superposed Epoch Analysis to model plant behavior before, during and after fire events.

Principal Findings

We show that fuel build-up from arolla pine (Pinus cembra) always precedes fires, which is immediately followed by a rapid increase of birch (Betula sp.), then by ericaceous species after 25–75 years, and by herbs after 50–100 years. European larch (Larix decidua), which is the natural co-dominant species of subalpine forests with Pinus cembra, is not sensitive to fire, while the abundance of Pinus cembra is altered within a 150-year period after fires. A long-term trend in vegetation dynamics is apparent, wherein species that abound later in succession are the functional drivers, loading the environment with fuel for fires. This system can only be functional if fires are mainly driven by external factors (e.g. climate), with the mean interval between fires being longer than the minimum time required to reach the late successional stage, here 150 years.

Conclusion

Current global warming conditions which increase drought occurrences, combined with the abandonment of land in European mountain areas, creates ideal ecological conditions for the ignition and the spread of fire. A fire return interval of less than 150 years would threaten the dominant species and might override the resilience of subalpine forests.     

Host lifestyle affects human microbiota on daily timescales

Background

Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities.

Results

Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically similar species. Still, even during periods of overall community stability, the dynamics of select microbial taxa could be associated with specific host behaviors. Most prominently, changes in host fiber intake positively correlated with next-day abundance changes among 15% of gut microbiota members.

Conclusions

Our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.

Electronic supplementary material

The online version of this article (doi:10.1186/gb-2014-15-7-r89) contains supplementary material, which is available to authorized users.     

Experimental evaluation of seed limitation in alpine snowbed plants

Background

The distribution and abundance of plants is controlled by the availability of seeds and of sites suitable for establishment. The relative importance of these two constraints is still contentious and possibly varies among species and ecosystems. In alpine landscapes, the role of seed limitation has traditionally been neglected, and the role of abiotic gradients emphasized.

Methodology/Principal Findings

We evaluated the importance of seed limitation for the incidence of four alpine snowbed species (Achillea atrata L., Achillea clusiana Tausch, Arabis caerulea L., Gnaphalium hoppeanum W. D. J. Koch) in local plant communities by comparing seedling emergence, seedling, juvenile and adult survival, juvenile and adult growth, flowering frequency as well as population growth rates λ of experimental plants transplanted into snowbed patches which were either occupied or unoccupied by the focal species. In addition, we accounted for possible effects of competition or facilitation on these rates by including a measure of neighbourhood biomass into the analysis. We found that only A. caerulea had significantly lower seedling and adult survival as well as a lower population growth rate in unoccupied sites whereas the vital rates of the other three species did not differ among occupied and unoccupied sites. By contrast, all species were sensitive to competitive effects of the surrounding vegetation in terms of at least one of the studied rates.

Conclusions/Significance

We conclude that seed and site limitation jointly determine the species composition of these snowbed plant communities and that constraining site factors include both abiotic conditions and biotic interactions. The traditional focus on abiotic gradients for explaining alpine plant distribution hence appears lopsided. The influence of seed limitation on the current distribution of these plants casts doubt on their ability to readily track shifting habitats under climate change unless seed production is considerably enhanced under a warmer climate.     

The effects of large herbivores on the landscape dynamics of a perennial herb

Background and Aims

Models assessing the prospects of plant species at the landscape level often focus primarily on the relationship between species dynamics and landscape structure. However, the short-term prospects of species with slow responses to landscape changes depend on the factors affecting local population dynamics. In this study it is hypothesized that large herbivores may be a major factor affecting the short-term prospects of slow-responding species in the European landscape, because large herbivores have increased in number in this region in recent decades and can strongly influence local population dynamics.

Methods

The impact of browsing by large herbivores was simulated on the landscape-level dynamics of the dry grassland perennial polycarpic herb Scorzonera hispanica. A dynamic, spatially explicit model was used that incorporated information on the location of patches suitable for S. hispanica, local population dynamics (matrices including the impact of large herbivores), initial population sizes and dispersal rate of the species. Simulations were performed relating to the prospects of S. hispanica over the next 30 years under different rates of herbivory (browsing intensity) and varying frequencies of population destruction (e.g. by human activity).

Key Results

Although a high rate of herbivory was detected in most populations of S. hispanica, current landscape-level dynamics of S. hispanica were approximately in equilibrium. A decline or increase of over 20 % in the herbivory rate promoted rapid expansion or decline of S. hispanica, respectively. This effect was much stronger in the presence of population destruction.

Conclusions

Browsing by large herbivores can have a dramatic effect on the landscape dynamics of plant species. Changes in the density of large herbivores and the probability of population destruction should be incorporated into models predicting species abundance and distribution.     

Ecological effects of cell-level processes: genome size,functional traits and regional abundance of herbaceous plant species

Background and Aims

Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate.

Methods

Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis.

Key Results

Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R² = 0·145) than for perennials (R² = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance.

Conclusions

The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes.     

Longevity of clonal plants: why it matters and how to measure it

Background

Species'' life-history and population dynamics are strongly shaped by the longevity of individuals, but life span is one of the least accessible demographic traits, particularly in clonal plants. Continuous vegetative reproduction of genets enables persistence despite low or no sexual reproduction, affecting genet turnover rates and population stability. Therefore, the longevity of clonal plants is of considerable biological interest, but remains relatively poorly known.

Scope

Here, we critically review the present knowledge on the longevity of clonal plants and discuss its importance for population persistence. Direct life-span measurements such as growth-ring analysis in woody plants are relatively easy to take, although, for many clonal plants, these methods are not adequate due to the variable growth pattern of ramets and difficult genet identification. Recently, indirect methods have been introduced in which genet size and annual shoot increments are used to estimate genet age. These methods, often based on molecular techniques, allow the investigation of genet size and age structure of whole populations, a crucial issue for understanding their viability and persistence. However, indirect estimates of clonal longevity are impeded because the process of ageing in clonal plants is still poorly understood and because their size and age are not always well correlated. Alternative estimators for genet life span such as somatic mutations have recently been suggested.

Conclusions

Empirical knowledge on the longevity of clonal species has increased considerably in the last few years. Maximum age estimates are an indicator of population persistence, but are not sufficient to evaluate turnover rates and the ability of long-lived clonal plants to enhance community stability and ecosystem resilience. In order to understand the dynamics of populations it will be necessary to measure genet size and age structure, not only life spans of single individuals, and to use such data for modelling of genet dynamics.     

Niche Divergence versus Neutral Processes: Combined Environmental and Genetic Analyses Identify Contrasting Patterns of Differentiation in Recently Diverged Pine Species

Background and Aims

Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis.

Methods

Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species.

Key Results and Conclusion

Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.     

Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance

Background

The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of Utricularia gibba to more than 80 % in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants.

Results

Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of Gypsy retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in Gypsy abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner.

Conclusions

We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1830-8) contains supplementary material, which is available to authorized users.