Rapid genetic identification of local provenance seed collection zones for ecological restoration and biodiversity conservation

The ecological restoration of native plant communities requires the collection of large amounts of seed. Use of non-local provenance seed can have detrimental consequences for the success of restoration if there is a home-site advantage, and for nature conservation through the erosion of natural patterns of population genetic structuring and/or genetic swamping (and extirpation) of locally significant genotypes. As part of an ongoing project to genetically delineate local provenance seed collection zones for species within a large urban bushland remnant of high conservation value, we assessed population genetic differentiation in two widespread coastal leguminous species, Acacia rostellifera and A. cochlearis (Fabaceae), commonly used in restoration programmes in SW Australia. Using amplified fragment length polymorphism (AFLP), we found very high levels of genetic differentiation among populations, with an analysis of molecular variance (AMOVA) showing more than 50% of the total genetic variance to be partitioned among populations (Φ_ST=0.58 and 0.51 for A. rostellifera and A. cochlearis, respectively), and marked non-overlap of almost all potential seed source populations from the local population in ordinations. Our results suggest extremely restricted natural dispersal among populations, possibly due to a combination of low seed set, seed dispersal by ants, clonality, a linear distribution of naturally fragmented populations and possibly low outcrossing rates. We suggest a narrow seed collection zone should be applied to these species for the conservation of genetic diversity and natural patterns of population genetic structure, and we highlight the value and importance of provenance evaluation to ecological restoration.     

Requirements for plant coexistence through pollination niche partitioning

Plant–pollinator interactions are often thought to have been a decisive factor in the diversification of flowering plants, but to be of little or no importance for the maintenance of existing plant diversity. In a recent opinion paper, Pauw (2013 Trends Ecol. Evol. 28, 30–37. (doi:10.1016/j.tree.2012.07.019)) challenged this view by proposing a mechanism of diversity maintenance based on pollination niche partitioning. In this article, I investigate under which conditions the mechanism suggested by Pauw can promote plant coexistence, using a mathematical model of plant and pollinator population dynamics. Numerical simulations show that this mechanism is most effective when the costs of searching for flowers are low, pollinator populations are strongly limited by resources other than pollen and nectar, and plant–pollinator interactions are sufficiently specialized. I review the empirical literature on these three requirements, discuss additional factors that may be important for diversity maintenance through pollination niche partitioning, and provide recommendations on how to detect this coexistence mechanism in natural plant communities.     

Off-channel temporary pools contribute to native riparian plant species diversity in a regulated river floodplain

Off-channel temporary pools on riverbanks have characteristic seasonal wet–dry cycles resulting from direct inflow of river water or hyporheic flow seepage. This study addressed two questions regarding the role of temporary pools in supporting diversity of riparian vegetation in a regulated river in Japan: (1) do temporary pools maintain high native riparian plant species diversity? And, (2) how do physical environmental factors affect the pattern of plant species distribution? The study was conducted on a 1-km section of the Hayade River alluvial fan in Niigata Prefecture, central Japan. Two to five transect belts consisting of 20 contiguous plots (1 m × 1 m) were laid out in two off-channel temporary pools and six other sites classified by physiognomy. Vascular plant presence, relative elevation, and substratum type were recorded in all plots. Species richness, Simpson’s reciprocal index (1/D), and Shannon–Wiener function (H′) were calculated by life form to estimate plant species diversity. Two conclusions could be drawn from the results. First, the temporary pools maintained high native riparian plant species diversity in this regulated river floodplain. Second, several environmental factors (seasonal wet–dry cycle, low elevation, complex micro-topography, and fine substrata) created spatial and seasonal heterogeneity of moisture conditions in the temporary pools, supporting plant species diversity. For sustainable maintenance of riparian plant species diversity, progressive river-management should restore original riverine dynamics to generate a shifting mosaic of diverse geomorphology.     

The evolution of foliar terpene diversity in Myrtaceae

Plant terpenes play many roles in natural systems, from altering plant–animal interactions, to altering the local abiotic environment. Additionally, many industries depend on terpenes. For example, commercially used essential oils, including tea tree oil and lavender oil, are a mixture of terpenes. Many species of the family Myrtaceae form a key resource for these industries due to the high concentration of terpenes found predominately in their leaves. The frequency of chemotypic differences within many species and populations can lead to costly errors in industry. Terpene diversity in Myrtaceae is driven by variation in the terpene synthase enzymes, which catalyse the conversion a few common substrates into thousands of terpene structures. We review terpene diversity within and between species of Myrtaceae and relate this to variation in the terpene synthase enzymes to reconstruct the evolution of foliar terpene diversity in Myrtaceae. We found that (1) high inter- and intra-species variation exists in terpene profile and that α-pinene the most likely ancestral foliar terpene, and (2) that high concentration of 1,8-cineole (a compound which is regarded as the signature compound of Myrtaceae) is limited to just four Myrtaceae sub-families. We suggest that the terpene synthase enzymes do not limit terpene diversity in this family and variation in these enzymes suggests a mode of enzymatic evolution that could lead to high 1,8-cineole production. Our analysis highlights the need to standardise methods for collecting and reporting foliar terpene data, and we discuss some methods and issues here. Although there are many gaps in the published data, our large scale analysis using the results of many studies, shows the value of a family wide analysis for understanding both the evolution and industrial potential of terpene-producing plants.     

A mathematical approach to the analysis of diversity in antibody gene families

In this article, we develop a mathematical approach for the analysis of diversity in antibody gene families. This approach is arrived at by examining two general questions about protein populations: (1) What is a relative measure of the diversity exhibited by one protein family when compared with a second? (2) What is the probability that two protein populations were derived from a single common population? These quantitative approaches permit a variety of precise evolutionary, genetic, and developmental questions to be asked of antibody gene families. Using this methodology, we demonstrate that the diversity in mouse κ-immunoglobulin chains is considerably greater than in their human κ counterparts. We also show that the variable (V_L) regions of light chains associated with IgG and IgA immunoglobulins in the mouse appear to have been derived from a common population of V_L genes. This approach also can be used to analyse sequence data from other informational multigene families.     

Modification by an invasive ecosystem engineer shifts a wet prairie to a monotypic stand

At the landscape scale, ecosystem engineers are expected to increase species diversity; however, diversity could decline if the ecosystem engineer is over-abundant. Thus, invasive ecosystem engineers are expected to have strong impacts, due to their high abundances and novel disturbances. An invasive ecosystem engineer, the feral swine (Sus scrofa), is a species that creates intense soil disturbances, altering soil and plant communities. In this study, we examine the effects of this invasive ecosystem engineer on experimental plant plots that had been protected for over a decade. Feral swine avoided recently burned plots and preferred plots with N addition. Rooted plots shifted from a bunchgrass dominated wet prairie to a monotypic stand of the native, Lachnanthes caroliana. Feral swine were also attracted to plots with existing patches of L. caroliana suggesting a potential positive feedback between swine activity and L. caroliana patch expansion that could result in an alternative state.     

The relevance,biases, and importance of digitising opportunistic non-standardised collections: A case study in Iberian harvestmen fauna with BOS Arthropod Collection datasets (Arachnida,Opiliones)

In this study, we analyse the relevance of harvestmen distribution data derived from opportunistic, unplanned, and non-standardised collection events in an area in the north of the Iberian Peninsula. Using specimens deposited in the BOS Arthropod Collection at the University of Oviedo, we compared these data with data from planned, standardised, and periodic collections with pitfall traps in several locations in the same area. The Arthropod Collection, begun in 1977, includes specimens derived from both sampling types, and its recent digitisation allows for this type of comparative analysis. Therefore, this is the first data-paper employing a hybrid approach, wherein subset metadata are described alongside a comparative analysis. The full dataset can be accessed through Spanish GBIF IPT at http://www.gbif.es:8080/ipt/archive.do?r=Bos-Opi, and the metadata of the unplanned collection events at http://www.gbif.es:8080/ipt/resource.do?r=bos-opi_unplanned_collection_events. We have mapped the data on the 18 harvestmen species included in the unplanned collections and provided records for some species in six provinces for the first time. We have also provided the locations of Phalangium opilio in eight provinces without published records. These results highlight the importance of digitising data from unplanned biodiversity collections, as well as those derived from planned collections, especially in scarcely studied groups and areas.     

The ecology of seeds. * Fenner M, Thompson K. 2005. Cambridge: Cambridge University Press. {pound}26 (softback) {pound}55 (hardback) 260 pp.

This volume is a timely updateand considerable expansion of the small book Seed Ecology, publishedby the first author twenty years ago, and long out of print. Is it useful to separate a particular branch of study such as‘seed ecology’ from the wider field of plant ecology?Aren't seeds just a particular packaged form of the sporophyte,at a certain stage in its life cycle? While some may ask thosequestions, a major strength of this book is the care that theauthors take throughout to set their review in the context ofcurrent ecological     

Scale- and taxon-dependent patterns of plant diversity in steppes of Khakassia,South Siberia (Russia)

The drivers of plant richness at fine spatial scales in steppe ecosystems are still not sufficiently understood. Our main research questions were: (i) How rich in plant species are the natural steppes of Southern Siberia compared to natural and semi-natural grasslands in other regions of the Palaearctic? (ii) What are the main environmental drivers of the diversity patterns in these steppes? (iii) What are the diversity–environment relationships and do they vary between spatial scales and among different taxonomic groups? We sampled the steppe vegetation (vascular plants, bryophytes and lichens) in Khakassia (Russia) with 39 nested-plot series (0.0001–100-m² plot size) and 54 additional 10-m² quadrats across the regional range of steppe types and measured various environmental variables. We measured β-diversity using z-values of power-law species–area relationships. GLM analyses were performed to assess the importance of environmental variables as predictors of species richness and z-value. Khakassian steppes showed both high α- and β-diversity. We found significant scale dependence for the z-values, which had their highest values at small spatial scales and then decreased exponentially. Total species richness was controlled predominantly by heat load index, mean annual precipitation, humus content and soil skeleton content. The positive role of soil pH was evident only for vascular plant species richness. Similar to other studies, we found that the importance of environmental factors strongly differed among taxonomic groups and across spatial scales, thus highlighting the need to study more than one taxon and more than one plot size to get a reliable picture.     

Location of the extrinsic subunit PsbP in photosystem II studied by pulsed electron-electron double resonance

The binding site of the extrinsic protein PsbP in plant photosystem II was mapped by pulsed electron-electron double resonance, using mutant spinach PsbP (Pro20Cys, Ser82Cys, Ala111Cys, and Ala186Cys) labeled with 4-maleimido-TEMPO (MSL) spin label. The distances between the spin label and the Tyr160 neutral radical (Y_D) in PsbD, the D2 subunit of plant photosystem II, were 50.8?±?3.5?Å, 54.9?±?4.0?Å, 57.8?±?4.9?Å, and 58.4?±?14.1?Å, respectively. The geometry inferred from these distances was fitted to the PsbP crystal structure (PDB: 4RTI) to obtain the coordinates of Y_D relative to PsbP. These coordinates were then fitted under boundary conditions to the structure of cyanobacterial photosystem II (PDB: 4UB6), by rotating on Euler angles centered at fixed Y_D coordinates. The result proposed two models which show possible acidic amino acid residues in CP43, CP47 and D2 that can bind the basic amino acids Arg48, Lys143, and Lys160 in PsbP.     

Responses of mammalian carnivores to land use in arid savanna rangelands

Shrub encroachment due to heavy grazing has led to dramatic changes in arid savanna landscape structure worldwide. It is considered to be one of the most threatening forms of rangeland degradation altering plant diversity. However, possible impacts of shrub encroachment on species diversity at higher trophic levels remain poorly understood. Additionally, indirect effects, such as changes of trophic interactions, are often ignored when trying to understand changes in biodiversity patterns. In this study, conducted in the southern Kalahari, we explored how the diversity of small carnivores and their prey is affected by shrub encroachment. We analysed the relationships between abundance and diversity of small carnivores, the availability of their main prey groups (coleopterans, termites, grasshoppers, rodents) and the structural diversity of the landscape (shrub, grass and herb cover). Eight hundred track surveys were conducted to determine carnivore abundance on 20 rangeland habitats, which represented a gradient of grazing intensity. Prey availability was surveyed for each study site and related to vegetation cover.

Results show a significant impact of shrub cover on abundance and diversity of carnivores and their prey. The diversity of both, carnivores and their prey, showed a hump-shaped response to increasing shrub cover whereas relative carnivore abundance decreased. Availability of prey groups was affected differently by shrub cover increase. Diversity of carnivores was best predicted by shrub cover (R²>0.7, p<0.001) indicating the overriding role of habitat structure as compared to prey availability. We conclude that intermediate shrub cover values enrich structural diversity of savanna landscape and in consequence sustain diversity of small carnivores and their prey in arid and semiarid ecosystems.     

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.     

The plant cytoskeleton in cell differentiation and development. Annual Plant Reviews, volume 10. * Hussey PJ, ed. 2004. * Oxford: Blackwell Publishing/Boca Raton: CRC Press. * {pound}99{middle dot}50 (hardback). 325 pp

Over 40 years ago, in what is surelyone of the most famous ‘throw-away lines’ in botany,Ledbetter and Porter (1963) suggested that the similar orientationsof cytoplasmic microtubules and structures considered to becellulose microfibrils in the cell wall was not coincidental.This notion led almost single-handedly to the present and enduringinterest amongst certain plant cell biologists in understandingthe role of microtubules in wall formation. And as a resultof this intense interest in such matters, it has become clearthat microtubules are not only ‘just one’ componentamongst an ever-expanding array of     

Paternal care behaviors of Japanese giant salamander <Emphasis Type="Italic">Andrias japonicus</Emphasis> in natural populations

Parental care among salamanders is typically provided by females. A rare case of parental care by male salamanders appears to occur in Cryptobranchidae. Yet, paternal behaviors have rarely been reported from natural populations of any Cryptobranchid salamanders, and their adaptive significance is poorly understood. The present study aimed to examine paternal care behaviors in a fully aquatic Japanese giant salamander (Andrias japonicus) in situ. At the beginning of the summer breeding season, large males, called den-masters, occupy burrows along stream banks for breeding and nesting. We videotaped post-breeding behaviors of two den-masters that stayed with the eggs, one in a natural and the other in an artificial nest in natural streams. We identified three behaviors, tail fanning, agitating and egg eating, to be parental care. Tail fanning provides oxygenated water for the eggs. We found that the den-master in the artificial nest, where dissolved oxygen level was lower, displayed tail fanning more frequently. Agitating the eggs with its head and body likely prevents yolk adhesions. The den-masters selectively ate whiter eggs that appeared to be dead or infected with water mold. This behavior, which we termed hygienic filial cannibalism, likely prevents water mold from spreading over healthy eggs. Digital video images relating to this article are available at http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj01a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj02a, http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj03a and http://www.momo-p.com/showdetail-e.php?movieid=momo140906aj04a.     

Plant roots. Growth, activity and interaction with soils

It is (or should be) self-evident that life on Earth dependsmainly on life in earth, and in this respect soil–plantinteractions are of key importance. This book brings togetherareas that are still often compartmented into fields such aschemical and physical aspects of soil science (where plantsare still sometimes regarded as a ‘black box’ ofuncertain relevance), plant physiology (now sometimes re-badgedas plant functional biology), and soil microbial ecology. Agriculturalscientists have, of course, rarely been guilty of ignoring soilfactors in relation to plant growth and productivity. Plantecologists sometimes have, and to some of them it's the soilthat is the ‘black box’ when it comes to understandingplant population and community ecology. Models of the     

There is more to autophagy than induction

Considerable attention has been paid to the topic of autophagy induction. In part, this is because of the potential for modulating this process for therapeutic purposes. Of course we know that induced autophagy can also be problematic—for example, when trying to eliminate an established tumor that might be relying on autophagy for its own cytoprotective uses. Accordingly, inhibitory mechanisms have been considered; however, the corresponding studies have tended to focus on the pathways that block autophagy under noninducing conditions, such as when nutrients are available. In contrast, relatively little is known about the mechanisms for inhibiting autophagy under inducing conditions. Yet, this type of regulation must be occurring on a routine basis. We know that dysregulation of autophagy, e.g., due to improper activation of Beclin 1 leading to excessive autophagy activity, can cause cell death.¹ Pattingre S, Tassa A, Qu X, Garuti R, Liang XH, Mizushima N, et al. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 2005; 122:927 - 39; http://dx.doi.org/10.1016/j.cell.2005.07.002; PMID: 16179260 [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Accordingly, we assume that during starvation or other inducing conditions there must be a mechanism to modulate autophagy. That is, once you turn it on, you do not want to let it continue unchecked. But how is autophagy downregulated when the inducing conditions still exist?     

Let's Make Gender Diversity in Data Science a Priority Right from the Start

The emergent field of data science is a critical driver for innovation in all sectors, a focus of tremendous workforce development, and an area of increasing importance within science, technology, engineering, and math (STEM). In all of its aspects, data science has the potential to narrow the gender gap and set a new bar for inclusion. To evolve data science in a way that promotes gender diversity, we must address two challenges: (1) how to increase the number of women acquiring skills and working in data science and (2) how to evolve organizations and professional cultures to better retain and advance women in data science. Everyone can contribute.Every March we celebrate both International Women’s Day and Women’s History Month. These annual celebrations remind us that through our current individual and collective behavior, all stakeholders can influence how gender-diverse our future history is likely to be. This is especially important in data science, an emerging science, technology, engineering, and math (STEM) field that is a critical driver for 21st century innovation.Data science focuses on the extraction of knowledge from data. It is a STEM discipline, but requires skills not yet widely taught in STEM disciplines: Skills in managing large datasets, novel analysis and inference approaches, rigorous statistical analysis, new ways to convey outcomes, and more. A recent McKinsey Report [1] indicates that the United States alone will need 1.5 million more data-savvy professionals and 140,000–190,000 more professionals with deep analytic skills by 2020. Helping to create and nurture a broad pool of individuals with data science skills is critical to addressing this growing need and will require intentional action.The emergent field of data science offers the opportunity to narrow the gender gap in STEM (in which only 13% of the engineering workforce and 25% of the computer and mathematical sciences workforce are women [2]) by making diversity a priority early on. In addition to this being the right thing to do, it is the smart thing to do: studies show that companies with employees characterized by diverse inherent traits (traits you were born with) and acquired traits (traits you gain from experience) are 45% more likely to report a growth in market share over the previous year, and 70% more likely to report capture of a new market [3]. Companies with diverse executive boards show higher returns on equity [4]. In short, diversity is a competitive asset in the private sector. In addition, increased diversity in STEM fields, including data science, is a national research and education priority [5].What better time, with increased focus on data science in the public sector, emerging educational curricula and focus within universities, and greater need within the private sector, to foster greater inclusivity and gender diversity? What can we do now to grow data science in a way that reflects the gender diversity and potential for innovation of the greater society?To evolve data science in a way that makes it a rewarding and sustainable career choice for women, we need to address two challenges: how can we increase the number of women acquiring skills and working in data science, and how can we evolve organizations and professional cultures to better retain and advance women in data science?     

It's a long way to the top: Plant species diversity in the transition from managed to old‐growth forests

Questions

Do vascular plant species richness and beta‐diversity differ between managed and structurally complex unmanaged stands? To what extent do species richness and beta‐diversity relate to forest structural attributes and heterogeneity?

Location

Five national parks in central and southern Italy.

Methods

We sampled vascular plant species composition and forest structural attributes in eight unmanaged temperate mesic forest stands dominated or co‐dominated by beech, and in eight comparison stands managed as high forests with similar environmental features. We compared plant species richness, composition and beta‐diversity across pairs of stands (unmanaged vs managed) using GLMM s. Beta‐diversity was quantified both at the scale of each pair of stands using plot‐to‐plot dissimilarity matrices (species turnover), and across the whole data set, considering the distance in the multivariate species space of individual plots from their centroid within the same stand (compositional heterogeneity). We modelled the relationship between species diversity (richness and beta‐diversity) and forest structural heterogeneity and individual structural variables using GLMM s and multiple regression on distance matrices.

Results

Species composition differed significantly between managed and unmanaged stands, but not richness and beta‐diversity. We found weak evidence that plant species richness increased with increasing levels of structural heterogeneity and canopy diversification. At the scale of individual stands, species turnover was explained by different variables in distinct stands, with variables related to deadwood quantity and quality being selected most often. We did not find support for the hypothesis that compositional heterogeneity varies as a function of forest structural characteristics at the scale of the whole data set.

Conclusions

Structurally complex unmanaged stands have a distinct herb layer species composition from that of mature stands in similar environmental conditions. Nevertheless, we did not find significantly higher levels of vascular plant species richness and beta‐diversity in unmanaged stands. Beta‐diversity was related to patterns of deadwood accumulation, while for species richness the evidence that it increases with increasing levels of canopy diversification was weak. These results suggest that emulating natural disturbance, and favouring deadwood accumulation and canopy diversification may benefit some, but not all, facets of plant species diversity in Apennine beech forests.

     

No universal scale-dependent impacts of invasive species on native plant species richness

A growing number of studies seeking generalizations about the impact of plant invasions compare heavily invaded sites to uninvaded sites. But does this approach warrant any generalizations? Using two large datasets from forests, grasslands and desert ecosystems across the conterminous United States, we show that (i) a continuum of invasion impacts exists in many biomes and (ii) many possible species–area relationships may emerge reflecting a wide range of patterns of co-occurrence of native and alien plant species. Our results contradict a smaller recent study by Powell et al. 2013 (Science 339, 316–318. (doi:10.1126/science.1226817)), who compared heavily invaded and uninvaded sites in three biomes and concluded that plant communities invaded by non-native plant species generally have lower local richness (intercepts of log species richness–log area regression lines) but steeper species accumulation with increasing area (slopes of the regression lines) than do uninvaded communities. We conclude that the impacts of plant invasions on plant species richness are not universal.